From: preecej Date: Wed, 26 Oct 2011 21:45:24 +0000 (+0000) Subject: Cleanup... X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=82d8f9ea49d7345d39dc3d89c626691940ca7b53;p=old-jaiswallab-svn%2F.git Cleanup... svn path=/; revision=199 --- diff --git a/Personnel/preecej/.gitignore b/Personnel/preecej/.gitignore deleted file mode 100644 index e69de29..0000000 diff --git a/Personnel/preecej/perl_singletons/aracyc_to_reactome_conversion/ara_rice_exclusive_sets.pl b/Personnel/preecej/perl_singletons/aracyc_to_reactome_conversion/ara_rice_exclusive_sets.pl new file mode 100644 index 0000000..75e6ea0 --- /dev/null +++ b/Personnel/preecej/perl_singletons/aracyc_to_reactome_conversion/ara_rice_exclusive_sets.pl @@ -0,0 +1,68 @@ +#!usr/bin/perl -w +use strict; + +system 'clear'; + +# determine mapped ChEBI molecules listed in arabidopsis but not in rice, +# and vice-versa + +my $dir = "/home/preecej/Documents/projects/reactome/aracyc_to_reactome_conversion/ara_rice_exclusive_sets/"; +my @rice; +my @ara; + +open(IN_FILE, $dir . "Rice_ReferenceNameToChEBIId.txt") or die; +while () { + my $line = $_; + chomp $line; + push(@rice,$line); +} +close IN_FILE; + +open(IN_FILE, $dir . "Ara_ReferenceNameToChEBIId.txt") or die; +while () { + my $line = $_; + chomp $line; + push(@ara,$line); +} +close IN_FILE; + +my %ara_seen; # lookup tbl +my @rice_only; #exclusive to rice + +# build lookup tbl +@ara_seen{@ara} = (); + +foreach my $item (@rice) { + push(@rice_only, $item) unless exists $ara_seen{$item}; +} + +my %rice_seen; # lookup tbl +my @ara_only; #exclusive to rice + +# build lookup tbl +@rice_seen{@rice} = (); + +foreach my $item (@ara) { + push(@ara_only, $item) unless exists $rice_seen{$item}; +} + +my $exc_rice_count = 0; +print "-- [EXCLUSIVE RICE MOLECULES] --\n"; +foreach my $item (@rice_only) { + $exc_rice_count++; + print "$exc_rice_count: $item\n"; +} + +#print "$exc_rice_count\n\n"; + +my $exc_ara_count = 0; +print "-- [EXCLUSIVE ARABIDOPSIS MOLECULES] --\n"; +foreach my $item (@ara_only) { + $exc_ara_count++; + print "$exc_ara_count: $item\n"; +} + +print "$exc_ara_count\n\n"; + +# clean up +exit; diff --git a/Personnel/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_pub_authors_to_years.pl b/Personnel/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_pub_authors_to_years.pl new file mode 100644 index 0000000..8769b10 --- /dev/null +++ b/Personnel/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_pub_authors_to_years.pl @@ -0,0 +1,44 @@ +#!usr/bin/perl -w +use strict; + +system 'clear'; + +# temp script used to fix elements that mistakenly refer to years in +# parentheses. replaces those elements with . + +my $dir = "/home/preecej/Documents/projects/reactome/aracyc_to_reactome_conversion/aracyc_data/"; + +open(in_file, $dir . "aracyc_v8_0_biopax-level2_STOIdouble.owl"); +open(out_file, ">>" . $dir . "aracyc_v8_0_biopax-level2_STOIdouble_AUTHORSYEAR.owl"); + +my $i = 0; # limiter for testing + +while () +{ + $i++; + + # read the next line of the file + my $line = $_; + chomp $line; + + # is it a bad author? + if ($line =~ /\(/) + { + print "$i: $line\n"; + # change the line to a well-formatted year tag + $line =~ s/AUTHORS/YEAR/g; + $line =~ s/\(//; + $line =~ s/\)//; + $line =~ s/string/int/; + print "$i: $line\n"; + } + print out_file "$line\n"; + + #last if $i > 1000; # let's test w/ low numbers for now +} + +close in_file; +close out_file; + +# clean up +exit; diff --git a/Personnel/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_step_interaction_datatypes.pl b/Personnel/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_step_interaction_datatypes.pl new file mode 100644 index 0000000..13d8e83 --- /dev/null +++ b/Personnel/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_step_interaction_datatypes.pl @@ -0,0 +1,45 @@ +#!usr/bin/perl -w +use strict; + +system 'clear'; + +# temp script used to fix elements that mistakenly refer to years in +# parentheses. replaces those elements with . +# Example: +# BEFORE: catalysis42055 +# AFTER: + +my $dir = "/home/preecej/Documents/projects/reactome/aracyc_to_reactome_conversion/aracyc_data/"; + +open(in_file, $dir . "aracyc_v8_0_biopax-level2_STOIdouble_AUTHORSYEAR.owl"); +open(out_file, ">>" . $dir . "aracyc_v8_0_biopax-level2_STOIdouble_AUTHORSYEAR_STEPINT.owl"); + +my $i = 0; # limiter for testing + +while () +{ + $i++; + + # read the next line of the file + my $line = $_; + chomp $line; + + # is it a bad step interaction? + if ($line =~ //) + { + print "$i: $line\n"; + # change the line to a well-formatted STEP-INTERACTION tag + $line =~ s/datatype="http:\/\/www.w3.org\/2001\/XMLSchema#string">/resource="\#/g; + $line =~ s/<\/bp:STEP-INTERACTIONS>/"\/>/; + print "$i: $line\n"; + } + print out_file "$line\n"; + + #last if $i > 1000; # let's test w/ low numbers for now +} + +close in_file; +close out_file; + +# clean up +exit; diff --git a/Personnel/preecej/perl_singletons/pathway_gene_swapper.pl b/Personnel/preecej/perl_singletons/pathway_gene_swapper.pl new file mode 100644 index 0000000..490959f --- /dev/null +++ b/Personnel/preecej/perl_singletons/pathway_gene_swapper.pl @@ -0,0 +1,910 @@ +#!/usr/bin/perl -w + +=head1 NAME + +Pathway Gene Swapper + +=head1 VERSION + +0.2 + +=head1 DESCRIPTION + +Swap out one set of genes (or gene representations) for another in an +existing PathVisio GPML file. Optionally removes literature references. + +If multiple replacement genes map to a single original gene, +multiple PathVisio boxes will be drawn in place of the +original. + +If a group associating multiple gene boxes already existed, +that group will extend to any replacement genes. If no group +existed previously, and multiple replacement gene boxes are required, +a new group will be created. + +If an original gene had multiple instances (homologs) displayed on the pathway +diagram, each instance will be subjected to the replacement process. There +is a "heat-map" option avaliable to help highlight homolog sets. + +There is also an option to read in an extra column of gene symbols, if the +user wishes to provide their own. Otherwise, the application will +continue to use the label prefix and auto-numbering suffix settings. + +The replacement gene symbols can be prefixed to separate them from the +original, and an ordinal suffix ('-#') will be added to a group of +replacement genes. + +Any new gene boxes may be painted with a custom color and border, and +will be stacked and offset for ease of visualization (much like a deck +of cards). + +=head1 FUTURE CHANGES + +Add a legend for the heat map (upper right-hand corner). + +Add a comment containing the NCBI species id of the new homolog (for +the purpose of multi-species pathway comparison or host-pathogen +interaction diagrams). + +=head1 USAGE + +pathway_gene_swapper.pl -i INPUT_FILE -g GENE_MAPPING_FILE -c CONFIG_FILE -o OUTPUT_FILE [-shLvGd] + +=head1 OPTIONS + + -i Name of input GPML file. + -g CSV file containing the genes to swap + -c config file containing color, label, and placement preferences + -o Name of output GPML file. + (NOTE: if no path supplied for input files, + current working directory is assumed) + -s use provided gene symbols instead of config file's LabelPrefix + -h apply a heat-map to any multi-mapped set of homologs + (NOTE: precludes custom box-coloring for homologs) + -L Remove literature references. + -v View verbose information + -G Display GPML input/output documents + -d View debugging information + +=head1 DEPENDENCIES and PREREQUISITES + + - Non-standard Perl modules: Switch, Data::Dumper, XML::DOM + - The input file must be a valid GPML file + - The CSV file must have a single-line column header. + + The first column must have one and only one gene -- the + "original" gene. + + The second column may have one and only one gene variant or + homolog -- the "replacement" gene(s). + + An optional "gene symbol" column may be placed between the + first two columns, if the user would prefer to use a list of + symbols for the new homologous genes. + + - The config file may have any or all of the following entries, + in addition to the required fields (in any order): + + Source= (required) + Database= (required) + Version= (required) + Title= + Author= + Maintainer= + Organism= + CommentPrefix= (will precede back-reference to prior source, + default: "Previously labeled as: ") + LabelPrefix= (precedes current gene label) + BoxBorder= (RRGGBB hex, default: black) + BoxColor= (RRGGBB hex, default: white) + BoxWidth= (integer, in px, default: 60) + X-Offset= (integer, in px, default: 5px) + Y-Offset= (integer, in px, default: 4px) + +=head1 AUTHORS + +Justin Preece and Mamatha Hanumappa + Faculty Research Assistants + Jaiswal Lab, Botany & Plant Pathology + Oregon State University + L + L + +=cut + +# --------------------------------------------------------------------------- +# modules +# --------------------------------------------------------------------------- + +# general +use strict; +use Cwd; +use Switch; +use Getopt::Std; +use Data::Dumper; + +# specific +use Graphics::ColorUtils qw( :gradients ); +use XML::DOM; + +# --------------------------------------------------------------------------- +# declarations +# --------------------------------------------------------------------------- + +# command-line options +my %opts; # arg options +my $input_gpml_file; +my $input_gene_file; +my $input_config_file; +my $output_file; +my $apply_homolog_heat = 0; +my $remove_lit = 0; # flag to remove literature and lit references +my $use_symbols = 0; # flag to indicate use of provided gene symbols +my $verbose = 0; # flag for verbose output +my $doc_mode = 0; # flag for extra GPML doc output +my $debug = 0; # debugging switch + +# global data containers +my %configs; # configuration settings +my %swap_genes; # original and swapped genes +my $gpml_doc; # imported GPML data for manipulation and output +my %unmapped_genes; # original genes not mapped to homologs +my %gradient; # blue-red gradient used for opt. heat map box-coloring +my $max_homolog_count = 0; # count for heat map calibration + +$Data::Dumper::Pad = "... "; + +# --------------------------------------------------------------------------- +=head1 FUNCTIONS + +=over + +=cut +# --------------------------------------------------------------------------- + + +# --------------------------------------------------------------------------- +=item B +Accepts a config file path. +Reads a configuration file and sets config values. +Returns a hash with config values set. +=cut +# --------------------------------------------------------------------------- +sub config($) +{ + + print "Opening configuration file and reading data...\n\n"; + my %local_config_hash; + + open(CONFIG_FILE, $_[0]) or die("Could not open $_[0]"); + + while () + { + my $line = $_; + chomp $line; + my @line_ary = split('=',$line); + my $data_field = $line_ary[0]; + my $data_val = $line_ary[1]; + + if ($data_val) + { + $local_config_hash{$data_field} = $data_val; + } + } + + close(CONFIG_FILE); + + # check for required settings + if (!$local_config_hash{"Source"}) { + die("You are required to provide a Source for your new data.\n" + . "Run \"perldoc pathway_gene_swapper.pl\" for more information.\n\n"); } + if (!$local_config_hash{"Database"}) { + die("You are required to identify a Database for your new data.\n" + . "Run \"perldoc pathway_gene_swapper.pl\" for more information.\n\n"); } + if (!$local_config_hash{"Version"}) { + die("You are required to provide a Version idenifier for your new data.\n" + . "Run \"perldoc pathway_gene_swapper.pl\" for more information.\n\n"); } + + # set defaults, if none declared + if (!$local_config_hash{"CommentPrefix"}) { + $local_config_hash{"CommentPrefix"} = "Previously labeled as: "; + } + if (!$local_config_hash{"BoxWidth"}) { + $local_config_hash{"BoxWidth"} = 60; + } + if (!$local_config_hash{"X-Offset"}) { + $local_config_hash{"X-Offset"} = 4; + } + if (!$local_config_hash{"Y-Offset"}) { + $local_config_hash{"Y-Offset"} = 3; + } + + return %local_config_hash; +} + + +# --------------------------------------------------------------------------- +=item B +Reads in command-line values, calls for config settings, and begins +screen output. +=cut +# --------------------------------------------------------------------------- +sub init +{ + # read and set options + getopts('i:g:c:o:hLsvGd', \%opts); + + foreach my $key (keys %opts) { + my $value = $opts{$key}; + switch ($key) { + case "i" { + if ($value =~ /\//) { # assume path + $input_gpml_file = $value; + } else { + $input_gpml_file = getcwd() . "\/$value"; + } + } + case "g" { + if ($value =~ /\//) { # assume path + $input_gene_file = $value; + } else { + $input_gene_file = getcwd() . "\/$value"; + } + } + case "c" { + if ($value =~ /\//) { # assume path + $input_config_file = $value; + } else { + $input_config_file = getcwd() . "\/$value"; + } + } + case "o" { + if ($value =~ /\//) { # assume path + $output_file = $value; + } else { + $output_file = getcwd() . "\/$value"; + } + } + case "s" { $use_symbols = 1; } + case "h" { $apply_homolog_heat = 1; } + case "L" { $remove_lit = 1; } + case "v" { $verbose = 1; } + case "G" { $doc_mode = 1; } + case "d" { $debug = 1; } + } + } + + system "clear"; + print "\n" + . "------------------------------------------------------------\n" + . "------------------ Pathway Gene Swapper --------------------\n" + . "------------------------------------------------------------\n" + . "\n" + . "Input Files:\n" + . " - PathVisio File (GPML): $input_gpml_file\n" + . " - Gene List (CSV): $input_gene_file\n" + . " - Configuration settings: $input_config_file\n" + . "\n" + . "Output File: $output_file\n" + . "\n" + . "Use provided gene symbols? " . ($use_symbols ? "Yes" : "No") . "\n" + . "Provide homolog heat-map? " . ($apply_homolog_heat ? "Yes" : "No") . "\n" + . "Remove literature references? " . ($remove_lit ? "Yes" : "No") . "\n" + . "Running in verbose mode? " . ($verbose ? "Yes" : "No") . "\n" + . "Running in document mode? " . ($doc_mode ? "Yes" : "No") . "\n" + . "Running in debug mode? " . ($debug ? "Yes" : "No") . "\n" + . "\n" + . "------------------------------------------------------------\n" + . "------------------------------------------------------------\n" + . "------------------------------------------------------------\n" + . "\n"; + + %configs = config($input_config_file); +} + + +# --------------------------------------------------------------------------- +=item B +Accepts: The maximum number of homologs for one gene in this data set +Creates a blue-red gradient and stores it in a hash. +Returns: A hash of RRGGBB color values, keyed to the number set of +possible homologs (1..n). +=cut +# --------------------------------------------------------------------------- +sub set_gradient($) +{ + my @blue_red_array; + + for (my $i=0; $i<256; $i++) { + push @blue_red_array, [$i, 0, (255-$i)]; + } + + register_gradient("blue_red",\@blue_red_array); + + my %blue_red_gradient; + my $max_grad = $_[0]; + my $inc = sprintf("%.2f", 1/$max_grad); + my $count = 1; + + for (my $i=$inc; $i<=0.99; $i=$i+$inc) { + my $tmp_hex = grad2rgb("blue_red",$i); + $tmp_hex =~ s/\#//; + $blue_red_gradient{$count} = $tmp_hex; + $count++; + } + + return %blue_red_gradient; +} + + +# --------------------------------------------------------------------------- +=item B +Reads, parses, and stores gene mapping file and source GPML. +=cut +# --------------------------------------------------------------------------- +sub import_data +{ + print "Opening gene mapping file and reading data...\n\n"; + + open(GENE_FILE, $input_gene_file) or die("Could not open $input_gene_file"); + + # used to generate total counts of each species' gene list; sanity check + my $original_gene_count = 0; + my $replacement_homolog_count = 0; + + my $orig_data_item; + my $new_symbol = ""; + my $new_data_item; + + # ignore header + my $line = ; + + while () + { + $line = $_; + chomp $line; + my @line_ary = split(',',$line); + my $orig_data_item = $line_ary[0]; + + if ($use_symbols) { + if (scalar(@line_ary) != 3) { + die("If you specify that your gene-mapping file includes " + . "symbols, then your CSV input file must have three " + . "columns of data (in this order): " + . "old gene, new symbol, new gene\n"); + } + $new_symbol = $line_ary[1]; + $new_data_item = $line_ary[2]; + } + else + { + $new_data_item = $line_ary[1]; + } + + #Does ath_gene exist? + if (!exists $swap_genes{$orig_data_item}) + { + $original_gene_count++; + } + $replacement_homolog_count++; # count this every time + + # add new gene to hash value (array) for old gene hash key + push @{$swap_genes{$orig_data_item}}, + { "symbol"=>$new_symbol, "new_item"=>$new_data_item }; + + $new_symbol = ""; # reset for next iter. + } + + # determine the original gene(s) with the highest # of homologs in the new + # gene set + my @most_popular_genes; # identity of the gene(s) with the highest number of homologs + foreach my $orig_gene_key (keys %swap_genes) + { + if ($max_homolog_count < scalar(@{$swap_genes{$orig_gene_key}})) + { + $max_homolog_count = scalar(@{$swap_genes{$orig_gene_key}}); + @most_popular_genes = (); # new max; refresh + push @most_popular_genes, $orig_gene_key; + } + else + { + if ($max_homolog_count == scalar(@{$swap_genes{$orig_gene_key}})) + { + push @most_popular_genes, $orig_gene_key; + } + } + } + + if ($verbose) # give add'l stats on gene and homolog counts + { + print "[Total number of original genes and homologs]\n" + . "Original gene count: " . $original_gene_count . "\n" + . "Replacement homolog count: $replacement_homolog_count\n\n"; + + print "[Highest number of homologs per gene]\n"; + print "Number of homologs: $max_homolog_count\n"; + print "Gene(s): @most_popular_genes\n\n"; + + print "[Number of homologs per original gene]\n"; + foreach my $orig_gene_key (keys %swap_genes) + { + print "$orig_gene_key: " . scalar(@{$swap_genes{$orig_gene_key}}) . "\n"; + } + print "\n"; + } + + close(GENE_FILE); + + # initialize the blue-red gradient for heat mapping + if ($apply_homolog_heat) + { + %gradient = set_gradient($max_homolog_count); + } + + print "Opening GPML pathway file and reading data...\n\n"; + + my $parser = new XML::DOM::Parser; + $gpml_doc = $parser->parsefile($input_gpml_file); +} + + +# --------------------------------------------------------------------------- +=item B +Spits out the data to make sure you've read in the files correctly. +Verbose only. +=cut +# --------------------------------------------------------------------------- +sub show_input +{ + if ($verbose) + { + print "[Configuration Settings]\n"; + print Dumper(\%configs) . "\n\n"; + print "\n"; + + print "[Gene Mappings]\n"; + print Dumper(\%swap_genes) . "\n\n"; + print "\n"; + } + if ($doc_mode) + { + print "[Source GPML]\n"; + print $gpml_doc->toString; + print "\n"; + } +} + +# --------------------------------------------------------------------------- +=item B +Accepts a reference to a hash of existing hex ids and a string as +the "type" of ID (e.g. "Group.GraphId"). The latter is currently for +documentary purposes only. +Generates a "random" 5-digit hexadecimal id, checks to see if it +already exists in the hex list, and if not, adds it to the list +of hex ids already present in the GPML doc. Otherwise, generates +another "random" id and repeats the process until a new unique id +is identified. +Returns a string containing the new hex id. +=cut +# --------------------------------------------------------------------------- +sub create_unique_hex_id($$) +{ + # NOTE: This algorithm breaks down at VERY large scale (100K genes+). The + # larger the number of original genes, groups, and new homologs you need to + # create, the more inefficient it becomes to make sure your "random" 5-digit + # hex number is not already present in your "existing ids" list via + # recursion. However, for a few hundred or thousand genes, it should be ok. + + my $first_digit; # limited to a..f + my $last_four_digits; # 0..f + + $first_digit = (('a'..'f')[rand(6)]); + $last_four_digits .= ((0..9,'a'..'f')[rand(16)]) for 1..4; + + my $candidate_id = $first_digit . $last_four_digits; + + # recurse if you haven't generated a unique id yet + if (exists ${$_[0]}{$candidate_id}) + { + # print "not unique...\n"; # TEST + # the '&' suppresses prototype checking and avoids a runtime warning + # since this is a recursive call + $candidate_id = &create_unique_hex_id($_[0],$_[1]); + } + else + { + # print "unique!\n"; # TEST + ${$_[0]}{$candidate_id} = $_[1]; + } + + return $candidate_id; +} + +# --------------------------------------------------------------------------- +=item B +Substitutes gene data. +=cut +# --------------------------------------------------------------------------- +sub swap_genes +{ + print "Swapping gene data and making other document modifications...\n\n"; + + my $pathway_node = ($gpml_doc->getElementsByTagName("Pathway"))[0]; + + # change Pathway header info to config settings + if ($configs{"Title"}) { + $pathway_node->setAttribute("Name",$configs{"Title"}); } + if ($configs{"Author"}) { + $pathway_node->setAttribute("Author",$configs{"Author"}); } + if ($configs{"Maintainer"}) { + $pathway_node->setAttribute("Maintainer",$configs{"Maintainer"}); } + if ($configs{"Version"}) { + $pathway_node->setAttribute("Version",$configs{"Version"}); } + if ($configs{"Organism"}) { + $pathway_node->setAttribute("Organism",$configs{"Organism"}); } + + # get all "gene box" data nodes + my $data_nodes = $pathway_node->getElementsByTagName("DataNode"); + # print $data_nodes->getLength . "\n"; # TEST + + # remove all and elements and children + if ($remove_lit) + { + print "Removing literature references...\n\n"; + my $biopax_node = ($pathway_node->getElementsByTagName("Biopax"))[0]; + $pathway_node->removeChild($biopax_node); + + for (@$data_nodes) + { + my $curr_datanode = $_; + my $biopaxref_nodes = $curr_datanode->getElementsByTagName("BiopaxRef"); + for (@$biopaxref_nodes) + { + # print $_->getTagName . "\n"; # TEST + $curr_datanode->removeChild($_); + } + } + } + + # will hold a convenient nested hash of data node references in the gpml doc, + # indexed by the id of the gene located in the element for each + # node, and sub-indexed by the GraphId of each corresponding node + my %data_nodes_by_gene_id; + + if ($verbose) { + print "[Original genes]\n"; + } + + # create a hash of all 5-digit hex ids in the gpml doc (this is the black list) + # one list of DataNode.GraphId, Group.GroupId, and Group.GraphId + my %existing_hex_ids; + for (@$data_nodes) + { + # print $_ . "\n"; # TEST + + if ($_->getAttributeNode("GraphId")) + { + $existing_hex_ids{$_->getAttributeNode("GraphId")->getValue} + = $_->getTagName . ".GraphId"; + } + + # also build a data node hash to make lookup easier in the next section + my $curr_xref_id = ($_->getElementsByTagName("Xref"))[0] + ->getAttributeNode("ID")->getValue; + my $curr_graph_id = $_->getAttributeNode("GraphId")->getValue; + + $curr_xref_id =~ s/\s+$//; # rtrim whitespace + $curr_xref_id =~ s/^\s+//; # ltrim whitespace + + if ($verbose) { + my $curr_text_label = $_->getAttributeNode('TextLabel')->getValue; + $curr_text_label =~ s/^\s+|\s+$//; # trim whitespace + print "$curr_text_label\t$curr_xref_id\n"; + } + + if (length($curr_xref_id) > 0) + { + #if ($curr_xref_id eq "AT3G12810") { print "** hit on AT3G12810\n"; } # TEST + $data_nodes_by_gene_id{$curr_xref_id}{$curr_graph_id} = $_; + } + else + { + if ($verbose) { + print "WARNING: Found DataNode (TextLabel: " + . $_->getAttributeNode('TextLabel')->getValue . ") " + . "with missing Xref ID.\n" + } + } + } + print "\n"; + + if ($debug) { + print "...\n"; + foreach my $tmp_gene (keys %data_nodes_by_gene_id) { + foreach my $tmp_node (keys %{$data_nodes_by_gene_id{$tmp_gene}}) { + print "... $tmp_gene => $tmp_node => $data_nodes_by_gene_id{$tmp_gene}{$tmp_node}\n"; + #if ($tmp_gene eq "AT3G12810") { print "** hit on AT3G12810 node\n"; } # TEST + } + } + print "\n"; + } + + my $group_nodes = $pathway_node->getElementsByTagName("Group"); + for (@$group_nodes) + { + if ($_->getAttributeNode("GroupId")) + { + $existing_hex_ids{$_->getAttributeNode("GroupId")->getValue} + = $_->getTagName . ".GroupId"; + } + if ($_->getAttributeNode("GraphId")) + { + $existing_hex_ids{$_->getAttributeNode("GraphId")->getValue} + = $_->getTagName . ".GraphId"; + } + } + + if ($debug) { print "...\n" + . Dumper(\%existing_hex_ids) . "\n\n"; } + + # iterate through gene mappings from csv file + foreach my $old_gene (keys %swap_genes) + { + # print $old_gene . "\n"; # TEST + + # find curr old gene nodes in doc + if (exists $data_nodes_by_gene_id{$old_gene}) + { + # iterate through each node by its GraphId + foreach my $curr_old_genes_by_hex_id (keys %{$data_nodes_by_gene_id{$old_gene}}) + { + my $curr_old_gene_node = $data_nodes_by_gene_id{$old_gene}{$curr_old_genes_by_hex_id}; + # print $curr_old_gene_node . "\n"; # TEST + + # holds list of newly-created nodes, used to replace old node + my @new_nodes_map; + + # iterate through new gene replacements + for (@{$swap_genes{$old_gene}}) + { + # copy the curr old gene node + my $new_node = $curr_old_gene_node->cloneNode("deep"); + + # print "[$_]\n$new_node->toString\n\n"; # TEST + + # add to new nodes ary + push @new_nodes_map, [$new_node, $_]; + } + # print "@new_nodes_map\n"; # TEST + + # if more than one new homolog exists, and the old gene doesn't + # already belong to a group, you'll need a new Group for multiple + # gene boxes + my $new_GroupId; + + if (scalar(@new_nodes_map) > 1) + { + # if curr old gene does not belong to a group + + # print $curr_old_gene_node->toString . "\n"; # TEST + # print $curr_old_gene_node->getAttribute("GroupRef"); # TEST + + if (!$curr_old_gene_node->getAttribute("GroupRef")) + { + #print "no existing group ref\n"; # TEST + + # generate a new GroupId and Group.GraphId hex ids not + # already in use + $new_GroupId = create_unique_hex_id(\%existing_hex_ids,"Group.GroupId"); + # my $new_Group_GraphId = create_unique_hex_id(\%existing_hex_ids,"Group.GraphId"); + #print "new group id: $new_GroupId\n"; # TEST + # print "$new_GroupId, $new_Group_GraphId\n"; # TEST + + # create a new group node + my $new_group = $gpml_doc->createElement("Group"); + $new_group->setAttribute("GroupId",$new_GroupId); + #$new_group->setAttribute("GraphId",$new_Group_GraphId); + $new_group->setAttribute("Style","Group"); + + # add to beginning of group nodes + $pathway_node->insertBefore($new_group,${$group_nodes}[0]); + } + } + + # flag for determining if there are one or many replacement homologs + my $is_first_homolog = 1; + + # makes sure each box is increasingly offset from the original + # (in all three dimensions) + my $offset_multiplier = 0; + my $gene_suffix_counter = 0; # used to affix numbers to multiple new gene symbols + + # for new nodes ary + for (@new_nodes_map) + { + if (scalar(@new_nodes_map) > 1) + { + $gene_suffix_counter++; + } + + my $curr_new_node = $$_[0]; + my $curr_symbol = ${$$_[1]}{"symbol"}; + my $curr_homolog = ${$$_[1]}{"new_item"}; + + #print "$_: $curr_new_node, $curr_symbol, $curr_homolog\n"; # TEST + #print "[Curr New Node before editing...]\n" . $curr_new_node->toString . "\n\n"; # TEST + + # update all new nodes w/ attributes... + + # grab original text label + my $old_label = $curr_new_node->getAttributeNode("TextLabel")->getValue; + + # rename TextLabel... + if ($use_symbols && length($curr_symbol) > 0) # apply the provided gene symbol + { + $curr_new_node->setAttribute("TextLabel", $curr_symbol); + } + else # prefix (from config), suffix: new '-#' for multiple homologs + { + $curr_new_node->setAttribute("TextLabel", + (($configs{"LabelPrefix"}) ? $configs{"LabelPrefix"} : "") + . $curr_new_node->getAttributeNode("TextLabel")->getValue + . (($gene_suffix_counter > 0) ? "-$gene_suffix_counter" : "")); + } + + # add new GroupRef if necessary + if ($new_GroupId) + { + $curr_new_node->setAttribute("GroupRef",$new_GroupId); + } + + # add Comment back-referencing TAIR locus id (use "source" attribute) + # NOTE: order is important in GPML; the tags are first + my $new_comment = $gpml_doc->createElement("Comment"); + $new_comment->setAttribute("Source",$configs{"Source"}); + $new_comment->addText($configs{"CommentPrefix"} . " $old_gene ($old_label)."); + $curr_new_node->insertBefore($new_comment,$curr_new_node->getFirstChild); # assumes other child nodes + + # edit + my $curr_xref = ($curr_new_node->getElementsByTagName("Xref"))[0]; + $curr_xref->setAttribute("Database",$configs{"Database"}); + $curr_xref->setAttribute("ID",$curr_homolog); + + # change box width and colors () + my $curr_graphics = ($curr_new_node->getElementsByTagName("Graphics"))[0]; + $curr_graphics->setAttribute("Width",$configs{"BoxWidth"}); + + # add "heat" to genes with multiple homologs + if ($apply_homolog_heat && ($gene_suffix_counter > 0)) + { + $curr_graphics->setAttribute("FillColor", $gradient{scalar(@new_nodes_map)}); + $curr_graphics->setAttribute("Color","8888ff"); + } + else + { + if ($configs{"BoxColor"}) { + $curr_graphics->setAttribute("FillColor",$configs{"BoxColor"}); } + if ($configs{"BoxBorder"}) { + $curr_graphics->setAttribute("Color",$configs{"BoxBorder"}); } + } + + if ($is_first_homolog) + { + # print "that was the first homolog...\n"; # TEST + $is_first_homolog = 0; # first homolog complete + } + else # add'l homologs required + { + $offset_multiplier++; + + # print "that was an add'l homolog, change more attrs...\n"; # TEST + # update add'l nodes w/ special attributes... + + # generate a new DataNode GraphId not already in use + my $new_GraphId = + create_unique_hex_id(\%existing_hex_ids,"DataNode.GraphId"); + # print $new_GraphId . "\n"; # TEST + $curr_new_node->setAttribute("GraphId",$new_GraphId); + + # decrement the Z-order + $curr_graphics->setAttribute("ZOrder", + $curr_graphics->getAttributeNode("ZOrder")->getValue + - $offset_multiplier); + # stagger the extra boxes by decrementing the coords + $curr_graphics->setAttribute("CenterX", + $curr_graphics->getAttributeNode("CenterX")->getValue + - ($configs{"X-Offset"} * $offset_multiplier)); + $curr_graphics->setAttribute("CenterY", + $curr_graphics->getAttributeNode("CenterY")->getValue + - ($configs{"Y-Offset"} * $offset_multiplier)); + } + } + undef $new_GroupId; # clear this out so we can test against its existence next time + + # replace old node w/ new node(s) + for (@new_nodes_map) { + # add all the new nodes... + $pathway_node->insertBefore($$_[0],$curr_old_gene_node); + } + # ...and remove the original node + $pathway_node->removeChild($curr_old_gene_node); + } + # once mapped, remove the old gene so we are left with a list of + # unmapped original genes (for show_ouput()) + delete($data_nodes_by_gene_id{$old_gene}); + } + else + { + print "ALERT: Gene identifier $old_gene is not present in this " + . "PathVisio GPML document.\n"; + } + } + %unmapped_genes = %data_nodes_by_gene_id; # whatever is left over +} + +# --------------------------------------------------------------------------- +=item B +Displays the transformed data. Verbose only. +=cut +# --------------------------------------------------------------------------- +sub show_output +{ + if ($verbose) { + print "[Unmapped original genes]\n"; + my $count = 0; + foreach my $tmp_gene (keys %unmapped_genes) + { + foreach my $tmp_node (keys %{$unmapped_genes{$tmp_gene}}) + { + $count++; + print $unmapped_genes{$tmp_gene}{$tmp_node} + ->getAttributeNode("TextLabel")->getValue + . "\t($tmp_gene)\n"; + } + } + print "\nTotal unmapped genes: $count\n"; + } + if ($doc_mode) + { + print "\n[Modified GPML Output]\n"; + print $gpml_doc->toString; + print "\n"; + } +} + +# --------------------------------------------------------------------------- +=item B +Writes the transformed GPML doc out to the specified output file. +=cut +# --------------------------------------------------------------------------- +sub export_data +{ + print "\nWriting GPML to output file...\n\n"; + + # ensures utf-8 encoding (for accent marks, etc.) + open my $out_file_handle, ">:utf8", "$output_file" or die $!; + + $gpml_doc->print($out_file_handle); +} + +=back +=cut + +# --------------------------------------------------------------------------- +# main +# --------------------------------------------------------------------------- + +init; +import_data; +show_input; +swap_genes(); +show_output; +export_data; + +$gpml_doc->dispose; # cleanup +exit; + +# --------------------------------------------------------------------------- +# end +# --------------------------------------------------------------------------- + diff --git a/Personnel/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl b/Personnel/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl new file mode 100755 index 0000000..cf6f4c9 --- /dev/null +++ b/Personnel/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl @@ -0,0 +1,428 @@ +#!/usr/bin/perl -w +use strict; + +# --------------------------------------------------------------------------- +# Reactome - CHEBI Ontology Mapping Script +# +# Justin Preece, 10/06/10 +# v1.0: 10/13/10 (svn rev. 66) +# v1.1: 10/20/10 (svn rev. 70) +# v1.2: 02/07/11 (svn rev. 86) +# +# Purpose: Map CHEBI ontology terms onto the Reactome database. +# +# Inputs: +# +# CHEBI OBO file (preset) +# +# Reactome file (preset, provided by Guanming Wu) +# (Header) [ReactomeID] [Compound_Name] [CAS] [LIGAND] [Cyc] +# (Row) 923893 S-adenosyl-L-methionine 29908-03-0 C00019 S-ADENOSYLMETHIONINE ** the '-' (dash) symbol will be applied to any empty columns +# +# Outputs: tab-del mapping file (reactome_chebi_mapping_complete_sorted.txt) +# +# [ReactomeID] [CHEBI] [XREF_Type] [XREF_ID] +# 923893 15414 CAS 29908-03-0 +# 923893 15414 LIGAND C00019 +# 923893 15414 CompoundTerm S-ADENOSYLMETHIONINE +# 923893 15414 CompoundSynonym s-AdenosylMethionine +# 923893 15414 CycTerm S-ADENOSYLMETHIONINE ** optional +# 923893 15414 CycSynonym s-adenosylmethionine ** optional +# --------------------------------------------------------------------------- + + +# --------------------------------------------------------------------------- +# modules +# --------------------------------------------------------------------------- + +use GO::Parser; + +# --------------------------------------------------------------------------- +# declarations +# --------------------------------------------------------------------------- + +# set paths to data files +my $data_path = "/home/preecej/Documents/projects/reactome/reactome_to_chebi_mapping/AraCyc/gk_central_041811/no_synonyms/"; +my $chebi_obo_file = "../../chebi_v78.obo"; +my $reactome_file = "AraReferenceMolecules.txt"; +my $mapped_output_file = "1.2_reactome_chebi_mapping_complete.txt"; +my $sorted_output_file = "1.2_reactome_chebi_mapping_complete_sorted.txt"; +my $unique_mappings = "1.2_reactome_unique_mappings.txt"; +my $sorted_no_match_file = "1.2_reactome_entries_with_no_chebi_match.txt"; + +# options +my $allow_obsolete_terms = 1; +my $allow_cyc = 0; +my $allow_synonyms = 0; + +my $ont; # chebi ontology + +my %reactome_CompoundName; # reactome Compound Name hash +my %reactome_CAS; # reactome CAS hash +my %reactome_LIGAND; # reactome LIGAND hash +my %reactome_Cyc; # reactome Cyc hash + +my @map_results = (); # successful mappings between chebi and reactome + + +# --------------------------------------------------------------------------- +# functions +# --------------------------------------------------------------------------- + + +# setup chebi parser and reactome data +# --------------------------------------------------------------------------- +sub init +{ + # init ontology parser and ontology + my $parser = GO::Parser->new({handler=>'obj'}); + $parser->parse($data_path . $chebi_obo_file); + $ont = $parser->handler->graph; + + # read reactome file into 3 separate hashes + open(REACTOME_FILE,$data_path . $reactome_file); + + my $line = ; # skip the header + my $reactome_count = 0; + + while () + { + $line = $_; + chomp $line; + $reactome_count++; + my @reactome_entry = split(/\t/, $line); # break up our tab-del line + + # load up this reactome entry's Compound_Name, ID, CAS, LIGAND, and Cyc values + my $reactome_id = $reactome_entry[0]; + my $compound_name = uc $reactome_entry[1]; # for case-insensitivity + + # strips off "AN " and "A " indefinite articles + $compound_name =~ s/^ //; + $compound_name =~ s/^AN //; + $compound_name =~ s/^A //; + + my $CAS_id = $reactome_entry[2]; + my $LIGAND_id = $reactome_entry[3]; + my $Cyc_term = uc $reactome_entry[4]; # for case-insensitivity + + # There is a possibility that a single CAS, LIGAND, or Cyc + # identifier may appear in more than one reactome entry. This + # temp array allows each matched hash value to hold more than + # one ReactomeID, if necessary. + + # --CAS Hash Load-- + if ($CAS_id ne "-") { # keep those "-" placeholders out + # build the CAS hash; each value may hold 1...n reactome + # ids (as an array) + push @{$reactome_CAS{$CAS_id}}, $reactome_id; + } + + # similarly... + + # --LIGAND Hash Load-- + if ($LIGAND_id ne "-") { + push @{$reactome_LIGAND{$LIGAND_id}}, $reactome_id; + } + + # --CompoundName Hash Load-- + if ($compound_name ne "-") { + push @{$reactome_CompoundName{"$compound_name"}}, $reactome_id; + } + + # --Cyc Hash Load-- + if ($allow_cyc) + { + if ($Cyc_term ne "-") { + push @{$reactome_Cyc{"$Cyc_term"}}, $reactome_id; + } + + } + } + close REACTOME_FILE; + + print "\n[Reactome Stats]", + "\nTotal Reactome Entries: $reactome_count\n"; + +} + + +# spit out some data to make sure you've read in the files correctly +# --------------------------------------------------------------------------- +sub test_inputs +{ + # basic ontology info + print "[Node Count]: " . $ont->node_count . "\n"; + + # get all chebi terms in the ontology + my $terms = $ont->get_all_nodes; + + # output contents of parsed ontology + foreach my $term (@$terms) + { + print "\n" . $term->acc . " " . $term->name . "\n[SYNONYMS]\n"; + + my $synonyms = $term->synonym_list; + foreach my $synonym (@$synonyms) { + print $synonym . "\n"; + } + + print "[XREFS]\n"; + my $xrefs = $term->dbxref_list; + foreach my $xref (@$xrefs) { + print $xref->xref_key . ",", + $xref->xref_keytype . ",", + $xref->xref_dbname . ",", + $xref->xref_desc . "\n"; + } + print "\n"; + } + + # show dupes in reactome hashes - give data to Pankaj; + # this is important b/c the duplicates may represent erroneous data in + # the Reactome dataset + my $k; my @v; + print "\n[Reactome Hashes - Dupes]\n"; + print "\n--CAS Hash--\n"; + for $k (keys %reactome_CAS) { + if (@{$reactome_CAS{$k}} > 1) { + print "$k: @{$reactome_CAS{$k}}\n"; + } + } + print "\n--LIGAND Hash--\n"; + for $k (keys %reactome_LIGAND) { + if (@{$reactome_LIGAND{$k}} > 1) { + print "$k: @{$reactome_LIGAND{$k}}\n"; + } + } + print "\n--CompoundName Hash--\n"; + for $k (keys %reactome_CompoundName) { + if (@{$reactome_CompoundName{$k}} > 1) { + print "$k: @{$reactome_CompoundName{$k}}\n"; + } + } + if ($allow_cyc) + { + print "\n--Cyc Hash--\n"; + for $k (keys %reactome_Cyc) { + if (@{$reactome_Cyc{$k}} > 1) { + print "$k: @{$reactome_Cyc{$k}}\n"; + } + } + } +} + + +# map the chebi terms to the reactome entries +# --------------------------------------------------------------------------- +sub perform_map +{ + my $chebi_obo_terms = $ont->get_all_nodes; + + # vars for mapping stats + my $attempted_mappings = 0; + my $successful_mappings = 0; + my $attempted_CAS_mappings = 0; + my $successful_CAS_mappings = 0; + my $attempted_LIGAND_mappings = 0; + my $successful_LIGAND_mappings = 0; + my $attempted_name_mappings = 0; + my $successful_name_mappings = 0; + my $attempted_synonym_mappings = 0; + my $successful_synonym_mappings = 0; + + # loop through each chebi term + foreach my $term (@$chebi_obo_terms) + { + # eliminate "typedef" nodes (non-CHEBI terms), also check for obsolete + # terms and whether to allow them + if (($term->acc =~ m/^CHEBI:/) + && (!$term->is_obsolete || ($term->is_obsolete && $allow_obsolete_terms))) + { + # attempt CHEBI match on CAS and LIGAND ID's + $attempted_mappings++; + my $xrefs = $term->dbxref_list; + foreach my $xref (@$xrefs) + { + $attempted_CAS_mappings++; + $attempted_LIGAND_mappings++; + + # temp-foo to skirt an interpolation problem + my $tmp_key = $xref->xref_key; + + if (defined($reactome_CAS{"$tmp_key"})) + { + foreach my $tmp_reactome_id (@{$reactome_CAS{$tmp_key}}) + { + $successful_CAS_mappings++; + push (@map_results, "$tmp_reactome_id\t" . + $term->acc . "\t" . + "CAS\t" . + $tmp_key); + } + } + + if (defined($reactome_LIGAND{"$tmp_key"})) + { + foreach my $tmp_reactome_id (@{$reactome_LIGAND{$tmp_key}}) + { + $successful_LIGAND_mappings++; + push (@map_results, "$tmp_reactome_id\t" . + $term->acc . "\t" . + "LIGAND\t" . + $tmp_key); + } + } + } + + # attempt CHEBI match on Reactome Compound Names (and optional Cyc names/synonyms)... + $attempted_name_mappings++; + + # more temp-foo to skirt said interpolation problem + my $tmp_name = uc $term->name; + + # reactome compound names... + if (defined($reactome_CompoundName{"$tmp_name"})) + { + foreach my $tmp_reactome_id (@{$reactome_CompoundName{$tmp_name}}) + { + $successful_name_mappings++; + push (@map_results, "$tmp_reactome_id\t" . + $term->acc . "\t" . + "CompoundTerm\t" . + $term->name); + } + } + # ...and synonyms (optional) + if ($allow_synonyms) + { + my $synonyms = $term->synonym_list; + foreach my $synonym (@$synonyms) + { + $attempted_synonym_mappings++; + + # yet more temp-foo to skirt interpolation problem + my $tmp_syn = "\U$synonym"; + + if (defined($reactome_CompoundName{$tmp_syn})) + { + foreach my $tmp_reactome_id (@{$reactome_CompoundName{$tmp_syn}}) + { + $successful_synonym_mappings++; + push (@map_results, "$tmp_reactome_id\t" . + $term->acc . "\t" . + "CompoundSynonym\t" . + $synonym); + } + } + } + } + + # Cyc names... + if ($allow_cyc) + { + if (defined($reactome_Cyc{"$tmp_name"})) + { + foreach my $tmp_reactome_id (@{$reactome_Cyc{$tmp_name}}) + { + $successful_name_mappings++; + push (@map_results, "$tmp_reactome_id\t" . + $term->acc . "\t" . + "CycTerm\t" . + $term->name); + } + } + # ...and synonyms (optional) + if ($allow_synonyms) + { + my $synonyms = $term->synonym_list; + foreach my $synonym (@$synonyms) + { + $attempted_synonym_mappings++; + + # yet more temp-foo to skirt interpolation problem + my $tmp_syn = "\U$synonym"; + + if (defined($reactome_Cyc{$tmp_syn})) + { + foreach my $tmp_reactome_id (@{$reactome_Cyc{$tmp_syn}}) + { + $successful_synonym_mappings++; + push (@map_results, "$tmp_reactome_id\t" . + $term->acc . "\t" . + "CycSynonym\t" . + $synonym); + } + } + } + } + } + } + } + # send up some stats on the mapping process + $successful_mappings = + + $successful_CAS_mappings + + $successful_LIGAND_mappings + + $successful_name_mappings + + $successful_synonym_mappings; + + print "\n[ChEBI Stats]", + "\nNodes in File: " . $ont->node_count, + "\nTotal Attempted Mappings (with usable ChEBI terms): " . $attempted_mappings, + "\nTotal Successful Mappings: " . $successful_mappings . "\n"; + + print "\n[Mapping Breakdown by Type]", + "\nCAS (matches/attempts): ", + "$successful_CAS_mappings/$attempted_CAS_mappings ", + "(note: can include ChemIDplus and KEGG COMPUND db duplicates)", + "\nLIGAND: ", + "$successful_LIGAND_mappings/$attempted_LIGAND_mappings", + "\nTerm Names " . ($allow_cyc ? "includes Cyc terms and synonyms" : "") . ": ", + "$successful_name_mappings/$attempted_name_mappings"; + if ($allow_synonyms) + { + print "\nTerm Synonyms: ", + "$successful_synonym_mappings/$attempted_synonym_mappings"; + } + print "\n\n"; +} + + +# put the results in the mapped output file +# --------------------------------------------------------------------------- +sub create_mapfile +{ + if (@map_results > 0) + { + # add a header to the results array + unshift (@map_results, "ReactomeID\tCHEBI\tXREF_Type\tXREF_ID"); + + # setup output file + open(OUTPUT_FILE,">" . $data_path . $mapped_output_file); + + #format results for file output + print OUTPUT_FILE "$_\n" foreach @map_results; + + close OUTPUT_FILE; + + # sort on all cols (keep the header at the top), remove exact dupes + system "awk 'NR == 1; NR > 1 {print \$0 | \"sort\"}' $data_path$mapped_output_file | uniq > $data_path$sorted_output_file"; + + # also produce files listing unique Reactome entries having a match...and those without a match + system "awk 'NR == 1; NR > 1 {print \$1}' $data_path$sorted_output_file | uniq > $data_path$unique_mappings"; + system "cat $data_path$reactome_file | grep -vf $data_path$unique_mappings | sort > $data_path$sorted_no_match_file"; + } else { + print "\n\nSorry, there are no mapped results.\n\n"; + } +} + + +# --------------------------------------------------------------------------- +# main +# --------------------------------------------------------------------------- + +init; +#test_inputs; +perform_map; +create_mapfile; + +exit; diff --git a/Personnel/preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl b/Personnel/preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl new file mode 100644 index 0000000..5dda3e7 --- /dev/null +++ b/Personnel/preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl @@ -0,0 +1,74 @@ +#!/usr/bin/perl -w +use strict; +use Data::Dumper; + +my $CoGe_genes_file_name = $ARGV[0]; +my $assoc_file_name = $ARGV[1]; + +# read in CoGe file (arg 0), build hash of gene model ids to symbols/gene names + +open(IN_FILE, $CoGe_genes_file_name); + +my %classical_genes_by_gene_model; + +my $line = ; + +while () +{ + $line = $_; + chomp $line; + + my @curr_line = split(',',$line); + + my $gene_symbol = $curr_line[0]; + $gene_symbol =~ tr/"//d; + my $gene_name = $curr_line[2]; + $gene_name =~ tr/"//d; + my $gene_model_id = $curr_line[8]; + $gene_model_id =~ tr/"//d; + + #print $gene_symbol . "\|" . $gene_name . "\|" . $gene_model_id . "\n"; + + my $gene_model_expr = "^(GRMZM)"; + if ($gene_model_id =~ $gene_model_expr) { + $classical_genes_by_gene_model{$gene_model_id} = [ $gene_symbol, $gene_name ]; + } +} + +close (IN_FILE); + +#print Dumper(\%classical_genes_by_gene_model) . "\n\n"; + +# read in assoc file (arg 1) + +open(ASSOC_IN_FILE, $ARGV[1]); + +open(OUT_FILE,">" . (split('\.',$assoc_file_name))[0] . "_named.assoc"); + +while () +{ + $line = $_; + chomp $line; + + if (length($line) > 0) { + + #print $line. "\n"; + + my @curr_line = split('\t',$line); + + # look for each annotation's hashed gene model id + if (defined $classical_genes_by_gene_model{$curr_line[1]}) { + # add/replace the appropriate cols + $curr_line[2] = ${$classical_genes_by_gene_model{$curr_line[1]}}[0]; + $curr_line[9] = ${$classical_genes_by_gene_model{$curr_line[1]}}[1]; + + } + # output to new assoc file with appended name + #print join("\t", @curr_line) . "\n"; + print OUT_FILE join("\t", @curr_line) . "\n"; + } +} + +close (ASSOC_IN_FILE); +close (OUT_FILE); +exit; diff --git a/Personnel/preecej/php_singletons/PO_web_service.php b/Personnel/preecej/php_singletons/PO_web_service.php new file mode 100644 index 0000000..9ba7afe --- /dev/null +++ b/Personnel/preecej/php_singletons/PO_web_service.php @@ -0,0 +1,106 @@ + 50) { $number_of_terms = 50; } + + $qval = $_GET['qval']; + + $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0 + ? strtolower($_GET['qval']) + : die('Please provide a searchable value'); + + $format = strtolower($_GET['format']) != 'json' + ? strtolower($_GET['format']) + : 'json'; //json is the default + + /* connect to the db */ + $link = mysql_connect($_SERVER['mysql_host'], $_SERVER['mysql_user'], $_SERVER['mysql_pw']) or die('Cannot connect to the DB'); + mysql_select_db($_SERVER['mysql_db'],$link) or die('Cannot select the DB'); + + switch ($type) { + case 'autocomplete': + /* grab the terms from the db */ + $query = "SELECT t.$field FROM term t" + . " LEFT JOIN term_definition d ON d.term_id = t.id" + . " WHERE t.$field LIKE '%$qval%'" + . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')" + . " AND t.is_obsolete = 0" + . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" + . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" + . " ORDER BY name LIMIT $number_of_terms"; + $result = mysql_query($query,$link) or die('Errant query: '.$query); + + /* create one master array of the records */ + $terms = array(); + if(mysql_num_rows($result)) { + while($term = mysql_fetch_assoc($result)) { + $terms[] = array('term'=>$term[$field]); + } + } + + /* output in necessary format */ + if($format == 'json') { + header('Content-type: application/json'); + echo json_encode(array('PO_term_lookup_response'=>$terms)); + } + else { + die('Sorry, this request cannot be fulfilled in '.$format.' format.'); + } + break; + + case 'term_detail': + /* grab the ontology data from the db */ + $query = "SELECT DISTINCT t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'" + . " FROM term t" + . " LEFT JOIN term_definition d ON d.term_id = t.id" + . " WHERE t.name = '$qval'" + . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')" + . " AND t.is_obsolete = 0" + . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" + . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" + . " ORDER BY t.name LIMIT 1"; + $result = mysql_query($query,$link) or die('Errant query: '.$query); + + /* create one master array of the records */ + $terms = array(); + if(mysql_num_rows($result)) { + while($term = mysql_fetch_assoc($result)) { + $terms[] = array( + 'accession_id'=>$term['acc'], + 'aspect'=>$term['type'] == "plant_anatomy" ? "Plant Anatomy" : "Plant Growth and Development Stage", + 'definition'=>$term['definition'], + 'comment'=>$term['comment']); + } + } + /* output in necessary format */ + if($format == 'json') { + header('Content-type: application/json'); + echo json_encode(array('PO_term_detail_response'=>$terms)); + } + else { + die('Sorry, this request cannot be fulfilled in '.$format.' format.'); + } + break; + default: + die('Sorry, this web service method is not available.'); + } + /* disconnect from the db */ + @mysql_close($link); +} +else { die('Not authorized.'); } +?> + diff --git a/Personnel/preecej/php_singletons/cmd_line_test.php b/Personnel/preecej/php_singletons/cmd_line_test.php new file mode 100644 index 0000000..0a58b4e --- /dev/null +++ b/Personnel/preecej/php_singletons/cmd_line_test.php @@ -0,0 +1,14 @@ +load('/home/preecej/Documents/projects/pathvisio/Ath_scratch.gpml'); + +$entry = $doc->getElementsByTagName("Pathway"); +$author = $entry->item(0)->getAttribute("Author"); +print "Author:$author\n"; + +print "test over\n"; + +?> diff --git a/Personnel/preecej/sql_scripts/Reactome_EC_number_reaction_name_mapping.sql b/Personnel/preecej/sql_scripts/Reactome_EC_number_reaction_name_mapping.sql new file mode 100644 index 0000000..6f60c73 --- /dev/null +++ b/Personnel/preecej/sql_scripts/Reactome_EC_number_reaction_name_mapping.sql @@ -0,0 +1,32 @@ +use gk_central_042211; +/* query to id fully-qualified EC numbers in poorly-named A.th. reactions */ +select e2n.name, d.identifier from ReactionlikeEvent r +join Event_2_crossReference e2c on e2c.DB_ID = r.DB_ID +join Event_2_name e2n on e2n.DB_ID = r.DB_ID +join DatabaseIdentifier d on d.DB_ID = e2c.crossReference +join Event_2_species e on e.DB_ID = r.DB_ID +join Species s on s.DB_ID = e.species +join Taxon_2_name t on t.DB_ID = s.DB_ID +where t.name like 'Arabidopsis%' +and d.referenceDatabase = 4 +and e2n.name like '%->%' +and d.identifier not like '%-%' +order by e2n.name; + +use test; +/* load in PJ's EC nums and names file */ +/* mysqlimport -u root -p -v --local --ignore-lines=12 test ./EC_reaction_names.txt */ + +/* scratch queries */ +select * from Taxon_2_name +where name like '%Ara%'; + +select * from Species s +join Taxon_2_name t on t.DB_ID = s.DB_ID +where t.name like '%Arabi%'; + +select * from Event_2_crossReference; + +select * from DatabaseIdentifier; + +select * from ReferenceDatabase; \ No newline at end of file diff --git a/planteome/.gitignore b/planteome/.gitignore deleted file mode 100644 index e69de29..0000000 diff --git a/planteome/paw/content_pages/Main_Page.wiki b/planteome/paw/content_pages/Main_Page.wiki new file mode 100644 index 0000000..7e31afe --- /dev/null +++ b/planteome/paw/content_pages/Main_Page.wiki @@ -0,0 +1,37 @@ +__NOTOC__ +=== Welcome to the Planteome Annotation Wiki, a resource for annotated plant genotypes and phenotypes on the semantic web! === + +We host annotations from a variety of published data sources. You are free to browse these annotations and search for specific genes, synonyms, EC numbers, cross-references, and references to publications, as well as many other types of data. + +You may also add information of your own. If you would like to create your own annotations or add more data to existing annotations, please click [[special:UserLogin|here]] to establish a new curator account. + +If you already have a curator account, just [[Special:UserLogin|log in]] and begin annotating! + +Search for existing annotations (or data therein): (search box) + +[[Special:FormEdit/Annotation|Add a new gene annotation.]] + +=== What is semantic data, and how can it enhance my research? === + +examples... + +=== Our Collaborators === + +* Gramene... +* The Plant Ontology... + +=== Credits and Thanks === + +* Jaiswal Lab (and the Planteome portal)... +* OSU... +* POC +* NSF... +* etc... + + + diff --git a/planteome/paw/content_pages/Reference:Plant_Taxa.wiki b/planteome/paw/content_pages/Reference:Plant_Taxa.wiki new file mode 100644 index 0000000..7555bed --- /dev/null +++ b/planteome/paw/content_pages/Reference:Plant_Taxa.wiki @@ -0,0 +1,34 @@ +=== A list of reference species for use on this wiki === +{{#show:{{PAGENAME}} + | format=table + | mainlabel=- + | ?Has Reference Taxon +}} + +{{#set:Has Reference Taxon=Aquilegia coerulea}} +{{#set:Has Reference Taxon=Arabidopsis lyrata}} +{{#set:Has Reference Taxon=Arabidopsis thaliana}} +{{#set:Has Reference Taxon=Brachypodium dystachyon}} +{{#set:Has Reference Taxon=Carica papaya}} +{{#set:Has Reference Taxon=Chlamydomonas reinhardtii}} +{{#set:Has Reference Taxon=Citrus clementina}} +{{#set:Has Reference Taxon=Citrus cinensis}} +{{#set:Has Reference Taxon=Cucumis sativus}} +{{#set:Has Reference Taxon=Eucalyptus grandis}} +{{#set:Has Reference Taxon=Fragaria vesca}} +{{#set:Has Reference Taxon=Glycine max}} +{{#set:Has Reference Taxon=Manihot esculenta}} +{{#set:Has Reference Taxon=Medicago trunculata}} +{{#set:Has Reference Taxon=Mimulus guttatus}} +{{#set:Has Reference Taxon=Oryza sativa}} +{{#set:Has Reference Taxon=Physcomitrella patens}} +{{#set:Has Reference Taxon=Populus trichocarpa}} +{{#set:Has Reference Taxon=Prunus persica}} +{{#set:Has Reference Taxon=Ricinus communis}} +{{#set:Has Reference Taxon=Selaginella moellendorffii}} +{{#set:Has Reference Taxon=Setaria italica}} +{{#set:Has Reference Taxon=Sorghum bicolor}} +{{#set:Has Reference Taxon=Vitis vinifera}} +{{#set:Has Reference Taxon=Volvox carteri}} +{{#set:Has Reference Taxon=Zea mays}} + diff --git a/planteome/paw/extensions/DataTransfer_PS/COPYING b/planteome/paw/extensions/DataTransfer_PS/COPYING new file mode 100644 index 0000000..a865928 --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/COPYING @@ -0,0 +1,348 @@ +The license text below "----" applies to all files within this distribution, other +than those that are in a directory which contains files named "LICENSE" or +"COPYING", or a subdirectory thereof. For those files, the license text contained in +said file overrides any license information contained in directories of smaller depth. +Alternative licenses are typically used for software that is provided by external +parties, and merely packaged with the Data Transfer release for convenience. +---- + + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Library General Public License instead.) You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +this service if you wish), that you receive source code or can get it +if you want it, that you can change the software or use pieces of it +in new free programs; and that you know you can do these things. + + To protect your rights, we need to make restrictions that forbid +anyone to deny you these rights or to ask you to surrender the rights. +These restrictions translate to certain responsibilities for you if you +distribute copies of the software, or if you modify it. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must give the recipients all the rights that +you have. You must make sure that they, too, receive or can get the +source code. And you must show them these terms so they know their +rights. + + We protect your rights with two steps: (1) copyright the software, and +(2) offer you this license which gives you legal permission to copy, +distribute and/or modify the software. + + Also, for each author's protection and ours, we want to make certain +that everyone understands that there is no warranty for this free +software. If the software is modified by someone else and passed on, we +want its recipients to know that what they have is not the original, so +that any problems introduced by others will not reflect on the original +authors' reputations. + + Finally, any free program is threatened constantly by software +patents. We wish to avoid the danger that redistributors of a free +program will individually obtain patent licenses, in effect making the +program proprietary. To prevent this, we have made it clear that any +patent must be licensed for everyone's free use or not licensed at all. + + The precise terms and conditions for copying, distribution and +modification follow. + + GNU GENERAL PUBLIC LICENSE + TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION + + 0. This License applies to any program or other work which contains +a notice placed by the copyright holder saying it may be distributed +under the terms of this General Public License. The "Program", below, +refers to any such program or work, and a "work based on the Program" +means either the Program or any derivative work under copyright law: +that is to say, a work containing the Program or a portion of it, +either verbatim or with modifications and/or translated into another +language. (Hereinafter, translation is included without limitation in +the term "modification".) Each licensee is addressed as "you". + +Activities other than copying, distribution and modification are not +covered by this License; they are outside its scope. The act of +running the Program is not restricted, and the output from the Program +is covered only if its contents constitute a work based on the +Program (independent of having been made by running the Program). +Whether that is true depends on what the Program does. + + 1. You may copy and distribute verbatim copies of the Program's +source code as you receive it, in any medium, provided that you +conspicuously and appropriately publish on each copy an appropriate +copyright notice and disclaimer of warranty; keep intact all the +notices that refer to this License and to the absence of any warranty; +and give any other recipients of the Program a copy of this License +along with the Program. + +You may charge a fee for the physical act of transferring a copy, and +you may at your option offer warranty protection in exchange for a fee. + + 2. You may modify your copy or copies of the Program or any portion +of it, thus forming a work based on the Program, and copy and +distribute such modifications or work under the terms of Section 1 +above, provided that you also meet all of these conditions: + + a) You must cause the modified files to carry prominent notices + stating that you changed the files and the date of any change. + + b) You must cause any work that you distribute or publish, that in + whole or in part contains or is derived from the Program or any + part thereof, to be licensed as a whole at no charge to all third + parties under the terms of this License. + + c) If the modified program normally reads commands interactively + when run, you must cause it, when started running for such + interactive use in the most ordinary way, to print or display an + announcement including an appropriate copyright notice and a + notice that there is no warranty (or else, saying that you provide + a warranty) and that users may redistribute the program under + these conditions, and telling the user how to view a copy of this + License. (Exception: if the Program itself is interactive but + does not normally print such an announcement, your work based on + the Program is not required to print an announcement.) + +These requirements apply to the modified work as a whole. If +identifiable sections of that work are not derived from the Program, +and can be reasonably considered independent and separate works in +themselves, then this License, and its terms, do not apply to those +sections when you distribute them as separate works. But when you +distribute the same sections as part of a whole which is a work based +on the Program, the distribution of the whole must be on the terms of +this License, whose permissions for other licensees extend to the +entire whole, and thus to each and every part regardless of who wrote it. + +Thus, it is not the intent of this section to claim rights or contest +your rights to work written entirely by you; rather, the intent is to +exercise the right to control the distribution of derivative or +collective works based on the Program. + +In addition, mere aggregation of another work not based on the Program +with the Program (or with a work based on the Program) on a volume of +a storage or distribution medium does not bring the other work under +the scope of this License. + + 3. You may copy and distribute the Program (or a work based on it, +under Section 2) in object code or executable form under the terms of +Sections 1 and 2 above provided that you also do one of the following: + + a) Accompany it with the complete corresponding machine-readable + source code, which must be distributed under the terms of Sections + 1 and 2 above on a medium customarily used for software interchange; or, + + b) Accompany it with a written offer, valid for at least three + years, to give any third party, for a charge no more than your + cost of physically performing source distribution, a complete + machine-readable copy of the corresponding source code, to be + distributed under the terms of Sections 1 and 2 above on a medium + customarily used for software interchange; or, + + c) Accompany it with the information you received as to the offer + to distribute corresponding source code. (This alternative is + allowed only for noncommercial distribution and only if you + received the program in object code or executable form with such + an offer, in accord with Subsection b above.) + +The source code for a work means the preferred form of the work for +making modifications to it. For an executable work, complete source +code means all the source code for all modules it contains, plus any +associated interface definition files, plus the scripts used to +control compilation and installation of the executable. However, as a +special exception, the source code distributed need not include +anything that is normally distributed (in either source or binary +form) with the major components (compiler, kernel, and so on) of the +operating system on which the executable runs, unless that component +itself accompanies the executable. + +If distribution of executable or object code is made by offering +access to copy from a designated place, then offering equivalent +access to copy the source code from the same place counts as +distribution of the source code, even though third parties are not +compelled to copy the source along with the object code. + + 4. You may not copy, modify, sublicense, or distribute the Program +except as expressly provided under this License. Any attempt +otherwise to copy, modify, sublicense or distribute the Program is +void, and will automatically terminate your rights under this License. +However, parties who have received copies, or rights, from you under +this License will not have their licenses terminated so long as such +parties remain in full compliance. + + 5. You are not required to accept this License, since you have not +signed it. However, nothing else grants you permission to modify or +distribute the Program or its derivative works. These actions are +prohibited by law if you do not accept this License. Therefore, by +modifying or distributing the Program (or any work based on the +Program), you indicate your acceptance of this License to do so, and +all its terms and conditions for copying, distributing or modifying +the Program or works based on it. + + 6. Each time you redistribute the Program (or any work based on the +Program), the recipient automatically receives a license from the +original licensor to copy, distribute or modify the Program subject to +these terms and conditions. You may not impose any further +restrictions on the recipients' exercise of the rights granted herein. +You are not responsible for enforcing compliance by third parties to +this License. + + 7. If, as a consequence of a court judgment or allegation of patent +infringement or for any other reason (not limited to patent issues), +conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot +distribute so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you +may not distribute the Program at all. For example, if a patent +license would not permit royalty-free redistribution of the Program by +all those who receive copies directly or indirectly through you, then +the only way you could satisfy both it and this License would be to +refrain entirely from distribution of the Program. + +If any portion of this section is held invalid or unenforceable under +any particular circumstance, the balance of the section is intended to +apply and the section as a whole is intended to apply in other +circumstances. + +It is not the purpose of this section to induce you to infringe any +patents or other property right claims or to contest validity of any +such claims; this section has the sole purpose of protecting the +integrity of the free software distribution system, which is +implemented by public license practices. Many people have made +generous contributions to the wide range of software distributed +through that system in reliance on consistent application of that +system; it is up to the author/donor to decide if he or she is willing +to distribute software through any other system and a licensee cannot +impose that choice. + +This section is intended to make thoroughly clear what is believed to +be a consequence of the rest of this License. + + 8. If the distribution and/or use of the Program is restricted in +certain countries either by patents or by copyrighted interfaces, the +original copyright holder who places the Program under this License +may add an explicit geographical distribution limitation excluding +those countries, so that distribution is permitted only in or among +countries not thus excluded. In such case, this License incorporates +the limitation as if written in the body of this License. + + 9. The Free Software Foundation may publish revised and/or new versions +of the General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies a version number of this License which applies to it and "any +later version", you have the option of following the terms and conditions +either of that version or of any later version published by the Free +Software Foundation. If the Program does not specify a version number of +this License, you may choose any version ever published by the Free Software +Foundation. + + 10. If you wish to incorporate parts of the Program into other free +programs whose distribution conditions are different, write to the author +to ask for permission. For software which is copyrighted by the Free +Software Foundation, write to the Free Software Foundation; we sometimes +make exceptions for this. Our decision will be guided by the two goals +of preserving the free status of all derivatives of our free software and +of promoting the sharing and reuse of software generally. + + NO WARRANTY + + 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY +FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN +OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED +OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS +TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE +PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, +REPAIR OR CORRECTION. + + 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR +REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED +TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Library General +Public License instead of this License. diff --git a/planteome/paw/extensions/DataTransfer_PS/DataTransfer.php b/planteome/paw/extensions/DataTransfer_PS/DataTransfer.php new file mode 100644 index 0000000..a5fbcfd --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/DataTransfer.php @@ -0,0 +1,149 @@ + __FILE__, + 'name' => 'Data Transfer', + 'version' => DATA_TRANSFER_VERSION, + 'author' => 'Yaron Koren', + 'url' => 'http://www.mediawiki.org/wiki/Extension:Data_Transfer', + 'descriptionmsg' => 'datatransfer-desc', +); + +### +# This is the path to your installation of Semantic Forms as +# seen on your local filesystem. Used against some PHP file path +# issues. +## +$dtgIP = dirname( __FILE__ ); +## + +// register all special pages and other classes +$wgAutoloadClasses['DTUtils'] = $dtgIP . '/includes/DT_Utils.php'; +$wgSpecialPages['ViewXML'] = 'DTViewXML'; +$wgAutoloadClasses['DTViewXML'] = $dtgIP . '/specials/DT_ViewXML.php'; +$wgSpecialPages['ImportXML'] = 'DTImportXML'; +$wgAutoloadClasses['DTImportXML'] = $dtgIP . '/specials/DT_ImportXML.php'; +$wgSpecialPages['ImportCSV'] = 'DTImportCSV'; +$wgAutoloadClasses['DTImportCSV'] = $dtgIP . '/specials/DT_ImportCSV.php'; +$wgJobClasses['dtImport'] = 'DTImportJob'; +$wgAutoloadClasses['DTImportJob'] = $dtgIP . '/includes/DT_ImportJob.php'; +$wgAutoloadClasses['DTXMLParser'] = $dtgIP . '/includes/DT_XMLParser.php'; +$wgHooks['AdminLinks'][] = 'dtfAddToAdminLinks'; +$wgHooks['smwInitProperties'][] = 'dtfInitProperties'; + +### +# This is the path to your installation of the Data Transfer extension as +# seen from the web. Change it if required ($wgScriptPath is the +# path to the base directory of your wiki). No final slash. +## +$dtgScriptPath = $wgScriptPath . '/extensions/DataTransfer_PS'; +## + +### +# Permission to import files +### +$wgGroupPermissions['sysop']['datatransferimport'] = true; +$wgAvailableRights[] = 'datatransferimport'; + +// initialize content language +require_once($dtgIP . '/languages/DT_Language.php'); +global $wgLanguageCode; +dtfInitContentLanguage($wgLanguageCode); + +$wgExtensionMessagesFiles['DataTransfer'] = $dtgIP . '/languages/DT_Messages.php'; +$wgExtensionAliasesFiles['DataTransfer'] = $dtgIP . '/languages/DT_Aliases.php'; + +/**********************************************/ +/***** language settings *****/ +/**********************************************/ + +/** + * Initialise a global language object for content language. This + * must happen early on, even before user language is known, to + * determine labels for additional namespaces. In contrast, messages + * can be initialised much later when they are actually needed. + */ +function dtfInitContentLanguage( $langcode ) { + global $dtgIP, $dtgContLang; + + if ( !empty( $dtgContLang ) ) { return; } + + $dtContLangClass = 'DT_Language' . str_replace( '-', '_', ucfirst( $langcode ) ); + + if ( file_exists( $dtgIP . '/languages/' . $dtContLangClass . '.php' ) ) { + include_once( $dtgIP . '/languages/' . $dtContLangClass . '.php' ); + } + + // fallback if language not supported + if ( !class_exists( $dtContLangClass ) ) { + include_once( $dtgIP . '/languages/DT_LanguageEn.php' ); + $dtContLangClass = 'DT_LanguageEn'; + } + + $dtgContLang = new $dtContLangClass(); +} + +/** + * Initialise the global language object for user language. This + * must happen after the content language was initialised, since + * this language is used as a fallback. + */ +function dtfInitUserLanguage( $langcode ) { + global $dtgIP, $dtgLang; + + if ( !empty( $dtgLang ) ) { return; } + + $dtLangClass = 'DT_Language' . str_replace( '-', '_', ucfirst( $langcode ) ); + + if ( file_exists( $dtgIP . '/languages/' . $dtLangClass . '.php' ) ) { + include_once( $dtgIP . '/languages/' . $dtLangClass . '.php' ); + } + + // fallback if language not supported + if ( !class_exists( $dtLangClass ) ) { + global $dtgContLang; + $dtgLang = $dtgContLang; + } else { + $dtgLang = new $dtLangClass(); + } +} + +/**********************************************/ +/***** other global helpers *****/ +/**********************************************/ + +function dtfInitProperties() { + global $dtgContLang; + $dt_props = $dtgContLang->getPropertyLabels(); + SMWPropertyValue::registerProperty( '_DT_XG', '_str', $dt_props[DT_HAS_XML_GROUPING], true ); + // TODO - this should set a "backup" English value as well, + // so that the phrase "Has XML grouping" works in all languages + return true; +} + +/** + * Add links to the 'AdminLinks' special page, defined by the Admin Links + * extension + */ +function dtfAddToAdminLinks( $admin_links_tree ) { + $import_export_section = $admin_links_tree->getSection( wfMsg( 'adminlinks_importexport' ) ); + $main_row = $import_export_section->getRow( 'main' ); + $main_row->addItem( ALItem::newFromSpecialPage( 'ViewXML' ) ); + $main_row->addItem( ALItem::newFromSpecialPage( 'ImportXML' ) ); + $main_row->addItem( ALItem::newFromSpecialPage( 'ImportCSV' ) ); + return true; +} diff --git a/planteome/paw/extensions/DataTransfer_PS/INSTALL b/planteome/paw/extensions/DataTransfer_PS/INSTALL new file mode 100644 index 0000000..16462b6 --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/INSTALL @@ -0,0 +1,31 @@ +[[Data Transfer 0.3.8]] + +Contents: +* Disclaimer +* Requirements +* Installation +* Contact + +== Disclaimer == + +For a proper legal disclaimer, see the file "COPYING". + +== Requirements == + +The extension can make use of, but does not require, an install of +Semantic MediaWiki. If Semantic MediaWiki is used, it must be of +version 1.0 or greater. For more details, see Semantic MediaWiki's +own installation requirements. + +== Installation == + +(1) Extract the archive to obtain the directory "DataTransfer" + that contains all relevant files. Copy this directory (or + extract/download it) to "[wikipath]/extensions/". +(2) Insert the following line into the file "[wikipath]/LocalSettings.php": + include_once('extensions/DataTransfer/DataTransfer.php'); + +== Contact == + +If you have any issues or questions, please send them to +yaron57@gmail.com. diff --git a/planteome/paw/extensions/DataTransfer_PS/README b/planteome/paw/extensions/DataTransfer_PS/README new file mode 100644 index 0000000..66652b3 --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/README @@ -0,0 +1,24 @@ +== About == + +Data Transfer is an extension to MediaWiki that both exports XML +based on the current contents of pages in a wiki, and imports pages +in both XML format (using the same structure as the XML export) and +CSV format. Both the XML and CSV formats use template calls, and +the fields within them, to define the data structure. Any text that +is not within a template calls gets placed into one or more "free +text" fields. + +For more information on Data Transfer, see the extension +homepage at +http://www.mediawiki.org/wiki/Extension:Data_Transfer + +Notes on installing Data Transfer can be found in the file INSTALL. + +== Credits == + +Data Transfer was written by Yaron Koren. + +== Contact == + +Comments, questions, suggestions and bug reports should be +sent to Yaron at yaron57@gmail.com. diff --git a/planteome/paw/extensions/DataTransfer_PS/data_transfer_0.3.8.tar.gz b/planteome/paw/extensions/DataTransfer_PS/data_transfer_0.3.8.tar.gz new file mode 100644 index 0000000..8c58be9 Binary files /dev/null and b/planteome/paw/extensions/DataTransfer_PS/data_transfer_0.3.8.tar.gz differ diff --git a/planteome/paw/extensions/DataTransfer_PS/includes/DT_ImportJob.php b/planteome/paw/extensions/DataTransfer_PS/includes/DT_ImportJob.php new file mode 100644 index 0000000..3a5e76f --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/includes/DT_ImportJob.php @@ -0,0 +1,53 @@ +title ) ) { + $this->error = "dtImport: Invalid title"; + wfProfileOut( __METHOD__ ); + return false; + } + + $article = new Article( $this->title ); + if ( !$article ) { + $this->error = 'dtImport: Article not found "' . $this->title->getPrefixedDBkey() . '"'; + wfProfileOut( __METHOD__ ); + return false; + } + $for_pages_that_exist = $this->params['for_pages_that_exist']; + if ( $for_pages_that_exist == 'skip' && $this->title->exists() ) { + return true; + } + + // change global $wgUser variable to the one specified by + // the job only for the extent of this import + global $wgUser; + $actual_user = $wgUser; + $wgUser = User::newFromId( $this->params['user_id'] ); + $text = $this->params['text']; + if ( $for_pages_that_exist == 'append' && $this->title->exists() ) { + $text = $article->getContent() . "\n" . $text; + } + $edit_summary = $this->params['edit_summary']; + $article->doEdit( $text, $edit_summary ); + $wgUser = $actual_user; + wfProfileOut( __METHOD__ ); + return true; + } +} diff --git a/planteome/paw/extensions/DataTransfer_PS/includes/DT_Utils.php b/planteome/paw/extensions/DataTransfer_PS/includes/DT_Utils.php new file mode 100644 index 0000000..30736b1 --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/includes/DT_Utils.php @@ -0,0 +1,89 @@ +

+ +END; + $text .= "\t" . '
' . "\n"; + return $text; + } + + static function printExistingPagesHandling() { + $text = "\t" . Xml::element( 'p', null, wfMsg( 'dt_import_forexisting' ) ) . "\n"; + $existingPagesText = "\n\t" . + Xml::element( 'input', + array( + 'type' => 'radio', + 'name' => 'pagesThatExist', + 'value' => 'overwrite', + 'checked' => 'checked' + ) ) . "\n" . + "\t" . wfMsg( 'dt_import_overwriteexisting' ) . "
" . "\n" . + "\t" . Xml::element( 'input', + array( + 'type' => 'radio', + 'name' => 'pagesThatExist', + 'value' => 'skip', + ) ) . "\n" . + "\t" . wfMsg( 'dt_import_skipexisting' ) . "
" . "\n" . + "\t" . Xml::element( 'input', + array( + 'type' => 'radio', + 'name' => 'pagesThatExist', + 'value' => 'append', + ) ) . "\n" . + "\t" . wfMsg( 'dt_import_appendtoexisting' ) . "
" . "\n\t"; + $text .= "\t" . Xml::tags( 'p', null, $existingPagesText ) . "\n"; + $text .= "\t" . '
' . "\n"; + return $text; + } + + static function printImportSummaryInput( $fileType ) { + $importSummaryText = "\t" . Xml::element( 'input', + array( + 'type' => 'text', + 'id' => 'wpSummary', // ID is necessary for CSS formatting + 'class' => 'mw-summary', + 'name' => 'import_summary', + 'value' => wfMsgForContent( 'dt_import_editsummary', $fileType ) + ) + ) . "\n"; + return "\t" . Xml::tags( 'p', null, + wfMsg( 'dt_import_summarydesc' ) . "\n" . + $importSummaryText ) . "\n"; + } + + static function printSubmitButton() { + $formSubmitText = Xml::element( 'input', + array( + 'type' => 'submit', + 'name' => 'import_file', + 'value' => wfMsg( 'import-interwiki-submit' ) + ) + ); + return "\t" . Xml::tags( 'p', null, $formSubmitText ) . "\n"; + } +} diff --git a/planteome/paw/extensions/DataTransfer_PS/includes/DT_XMLParser.php b/planteome/paw/extensions/DataTransfer_PS/includes/DT_XMLParser.php new file mode 100644 index 0000000..c8c48e0 --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/includes/DT_XMLParser.php @@ -0,0 +1,273 @@ +mName = $name; + } + + function addField( $name, $value ) { + $this->mFields[$name] = $value; + } + + function createText() { + $multi_line_template = false; + $text = '{{' . $this->mName; + foreach ( $this->mFields as $field_name => $field_val ) { + if ( is_numeric( $field_name ) ) { + $text .= "|$field_val"; + } else { + $text .= "\n|$field_name=$field_val"; + $multi_line_template = true; + } + } + if ( $multi_line_template ) + $text .= "\n"; + $text .= '}}' . "\n"; + return $text; + } +} + +class DTWikiPage { + private $mPageName = null; + private $mElements = array(); + + public function DTWikiPage( $name ) { + $this->mPageName = $name; + } + + function getName() { + return $this->mPageName; + } + + function addTemplate( $template ) { + $this->mElements[] = $template; + } + + function addFreeText( $free_text ) { + $this->mElements[] = $free_text; + } + + function createText() { + $text = ""; + foreach ( $this->mElements as $elem ) { + if ( $elem instanceof DTWikiTemplate ) { + $text .= $elem->createText(); + } else { + $text .= $elem; + } + } + return $text; + } +} + +class DTXMLParser { + var $mDebug = false; + var $mSource = null; + var $mCurFieldName = null; + var $mCurFieldValue = ''; + var $mCurTemplate = null; + var $mCurPage = null; // new DTWikiPage(); + var $mPages = array(); + + function __construct( $source ) { + $this->mSource = $source; + } + + function debug( $text ) { + // print "$text. "; + } + + function throwXMLerror( $text ) { + print htmlspecialchars( $text ); + } + + function doParse() { + $parser = xml_parser_create( "UTF-8" ); + + # case folding violates XML standard, turn it off + xml_parser_set_option( $parser, XML_OPTION_CASE_FOLDING, false ); + + xml_set_object( $parser, $this ); + xml_set_element_handler( $parser, "in_start", "" ); + + $offset = 0; // for context extraction on error reporting + do { + $chunk = $this->mSource->readChunk(); + if ( !xml_parse( $parser, $chunk, $this->mSource->atEnd() ) ) { + wfDebug( "WikiImporter::doImport encountered XML parsing error\n" ); + // return new WikiXmlError( $parser, wfMsgHtml( 'import-parse-failure' ), $chunk, $offset ); + } + $offset += strlen( $chunk ); + } while ( $chunk !== false && !$this->mSource->atEnd() ); + xml_parser_free( $parser ); + } + + function donothing( $parser, $x, $y = "" ) { + # $this->debug( "donothing" ); + } + + + function in_start( $parser, $name, $attribs ) { + // $this->debug( "in_start $name" ); + $pages_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_pages' ) ); + if ( $name != $pages_str ) { + print( "Expected '$pages_str', got '$name'" ); + } + xml_set_element_handler( $parser, "in_pages", "out_pages" ); + } + + function in_pages( $parser, $name, $attribs ) { + $this->debug( "in_pages $name" ); + $page_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_page' ) ); + if ( $name == $page_str ) { + $title_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_title' ) ); + if ( array_key_exists( $title_str, $attribs ) ) { + $this->mCurPage = new DTWikiPage( $attribs[$title_str] ); + xml_set_element_handler( $parser, "in_page", "out_page" ); + } else { + return $this->throwXMLerror( "'$title_str' attribute missing for page" ); + } + } else { + return $this->throwXMLerror( "Expected <$page_str>, got <$name>" ); + } + } + + function out_pages( $parser, $name ) { + $this->debug( "out_pages $name" ); + $pages_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_pages' ) ); +/* + if( $name != $pages_str ) { + return $this->throwXMLerror( "Expected , got " ); + } +*/ + xml_set_element_handler( $parser, "donothing", "donothing" ); + } + + function in_category( $parser, $name, $attribs ) { + $this->debug( "in_category $name" ); + $page_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_page' ) ); + if ( $name == $page_str ) { + if ( array_key_exists( $title_str, $attribs ) ) { + $this->mCurPage = new DTWikiPage( $attribs[$title_str] ); + xml_set_element_handler( $parser, "in_page", "out_page" ); + } else { + return $this->throwXMLerror( "'$title_str' attribute missing for page" ); + } + } else { + return $this->throwXMLerror( "Expected <$page_str>, got <$name>" ); + } + } + + function out_category( $parser, $name ) { + $this->debug( "out_category $name" ); + if ( $name != "category" ) { + return $this->throwXMLerror( "Expected , got " ); + } + xml_set_element_handler( $parser, "donothing", "donothing" ); + } + + function in_page( $parser, $name, $attribs ) { + $this->debug( "in_page $name" ); + $template_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_template' ) ); + $name_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_name' ) ); + $free_text_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_freetext' ) ); + if ( $name == $template_str ) { + if ( array_key_exists( $name_str, $attribs ) ) { + $this->mCurTemplate = new DTWikiTemplate( $attribs[$name_str] ); + xml_set_element_handler( $parser, "in_template", "out_template" ); + } else { + return $this->throwXMLerror( "'$name_str' attribute missing for template" ); + } + } elseif ( $name == $free_text_str ) { + xml_set_element_handler( $parser, "in_freetext", "out_freetext" ); + xml_set_character_data_handler( $parser, "freetext_value" ); + } else { + return $this->throwXMLerror( "Expected <$template_str>, got <$name>" ); + } + } + + function out_page( $parser, $name ) { + $this->debug( "out_page $name" ); + $page_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_page' ) ); + if ( $name != $page_str ) { + return $this->throwXMLerror( "Expected , got " ); + } + $this->mPages[] = $this->mCurPage; + xml_set_element_handler( $parser, "in_pages", "out_pages" ); + } + + function in_template( $parser, $name, $attribs ) { + $this->debug( "in_template $name" ); + $field_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_field' ) ); + if ( $name == $field_str ) { + $name_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_name' ) ); + if ( array_key_exists( $name_str, $attribs ) ) { + $this->mCurFieldName = $attribs[$name_str]; + // $this->push( $name ); + $this->workRevisionCount = 0; + $this->workSuccessCount = 0; + $this->uploadCount = 0; + $this->uploadSuccessCount = 0; + xml_set_element_handler( $parser, "in_field", "out_field" ); + xml_set_character_data_handler( $parser, "field_value" ); + } else { + return $this->throwXMLerror( "'$name_str' attribute missing for field" ); + } + } else { + return $this->throwXMLerror( "Expected <$field_str>, got <$name>" ); + } + } + + function out_template( $parser, $name ) { + $this->debug( "out_template $name" ); + $template_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_template' ) ); + if ( $name != $template_str ) { + return $this->throwXMLerror( "Expected , got " ); + } + $this->mCurPage->addTemplate( $this->mCurTemplate ); + xml_set_element_handler( $parser, "in_page", "out_page" ); + } + + function in_field( $parser, $name, $attribs ) { + // xml_set_element_handler( $parser, "donothing", "donothing" ); + } + + function out_field( $parser, $name ) { + $this->debug( "out_field $name" ); + $field_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_field' ) ); + if ( $name == $field_str ) { + $this->mCurTemplate->addField( $this->mCurFieldName, $this->mCurFieldValue ); + $this->mCurFieldValue = ''; + } else { + return $this->throwXMLerror( "Expected , got " ); + } + xml_set_element_handler( $parser, "in_template", "out_template" ); + } + + function field_value( $parser, $data ) { + $this->mCurFieldValue .= $data; + } + + function in_freetext( $parser, $name, $attribs ) { + // xml_set_element_handler( $parser, "donothing", "donothing" ); + } + + function out_freetext( $parser, $name ) { + xml_set_element_handler( $parser, "in_page", "out_page" ); + } + + function freetext_value( $parser, $data ) { + $this->mCurPage->addFreeText( $data ); + } + +} diff --git a/planteome/paw/extensions/DataTransfer_PS/languages/DT_Aliases.php b/planteome/paw/extensions/DataTransfer_PS/languages/DT_Aliases.php new file mode 100644 index 0000000..96a1809 --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/languages/DT_Aliases.php @@ -0,0 +1,274 @@ + array( 'ImportCSV' ), + 'ImportXML' => array( 'ImportXML' ), + 'ViewXML' => array( 'ViewXML' ), +); + +/** Afrikaans (Afrikaans) */ +$specialPageAliases['af'] = array( + 'ViewXML' => array( 'WysXML' ), +); + +/** Arabic (العربية) */ +$specialPageAliases['ar'] = array( + 'ViewXML' => array( 'عرض_إكس_إم_إل' ), +); + +/** Egyptian Spoken Arabic (مصرى) */ +$specialPageAliases['arz'] = array( + 'ViewXML' => array( 'عرض_XML' ), +); + +/** Breton (Brezhoneg) */ +$specialPageAliases['br'] = array( + 'ViewXML' => array( 'GweletXML' ), +); + +/** Bosnian (Bosanski) */ +$specialPageAliases['bs'] = array( + 'ViewXML' => array( 'VidiXML' ), +); + +/** German (Deutsch) */ +$specialPageAliases['de'] = array( + 'ImportCSV' => array( 'CSV_importieren' ), + 'ImportXML' => array( 'XML_importieren' ), + 'ViewXML' => array( 'XML_anzeigen' ), +); + +/** Esperanto (Esperanto) */ +$specialPageAliases['eo'] = array( + 'ViewXML' => array( 'Montri_XML' ), +); + +/** Spanish (Español) */ +$specialPageAliases['es'] = array( + 'ViewXML' => array( 'Ver_XML', 'VerXML' ), +); + +/** Basque (Euskara) */ +$specialPageAliases['eu'] = array( + 'ViewXML' => array( 'XMLIkusi' ), +); + +/** Persian (فارسی) */ +$specialPageAliases['fa'] = array( + 'ImportCSV' => array( 'درون‌ریزی_سی‌اس‌وی' ), + 'ImportXML' => array( 'درون‌ریزی_اکس‌ام‌ال' ), + 'ViewXML' => array( 'مشاهده_اکس‌ام‌ال' ), +); + +/** Finnish (Suomi) */ +$specialPageAliases['fi'] = array( + 'ImportCSV' => array( 'Tuo_CSV' ), + 'ImportXML' => array( 'Tuo_XML' ), + 'ViewXML' => array( 'Näytä_XML' ), +); + +/** French (Français) */ +$specialPageAliases['fr'] = array( + 'ImportCSV' => array( 'Importer_CVS', 'ImporterCVS' ), + 'ImportXML' => array( 'Importer_XML', 'ImporterXML' ), + 'ViewXML' => array( 'Voir_le_XML', 'Voir_XML', 'VoirXML' ), +); + +/** Franco-Provençal (Arpetan) */ +$specialPageAliases['frp'] = array( + 'ViewXML' => array( 'Vêre_lo_XML', 'VêreLoXML' ), +); + +/** Galician (Galego) */ +$specialPageAliases['gl'] = array( + 'ViewXML' => array( 'Ver XML' ), +); + +/** Swiss German (Alemannisch) */ +$specialPageAliases['gsw'] = array( + 'ViewXML' => array( 'Lueg XML' ), +); + +/** Gujarati (ગુજરાતી) */ +$specialPageAliases['gu'] = array( + 'ViewXML' => array( 'XMLજુઓ' ), +); + +/** Hungarian (Magyar) */ +$specialPageAliases['hu'] = array( + 'ViewXML' => array( 'XML_megtekintése' ), +); + +/** Interlingua (Interlingua) */ +$specialPageAliases['ia'] = array( + 'ImportCSV' => array( 'Importar_CSV' ), + 'ImportXML' => array( 'Importar_XML' ), + 'ViewXML' => array( 'Visualisar_XML' ), +); + +/** Indonesian (Bahasa Indonesia) */ +$specialPageAliases['id'] = array( + 'ViewXML' => array( 'Lihat_XML', 'LihatXML' ), +); + +/** Italian (Italiano) */ +$specialPageAliases['it'] = array( + 'ImportCSV' => array( 'ImportaCSV' ), + 'ImportXML' => array( 'ImportaXML' ), + 'ViewXML' => array( 'VediXML' ), +); + +/** Japanese (日本語) */ +$specialPageAliases['ja'] = array( + 'ImportCSV' => array( 'CSVインポート' ), + 'ImportXML' => array( 'XMLインポート' ), + 'ViewXML' => array( 'XML表示', 'ＸＭＬ表示' ), +); + +/** Khmer (ភាសាខ្មែរ) */ +$specialPageAliases['km'] = array( + 'ViewXML' => array( 'មើលXML' ), +); + +/** Colognian (Ripoarisch) */ +$specialPageAliases['ksh'] = array( + 'ImportCSV' => array( 'CSV_Empotteere' ), + 'ImportXML' => array( 'XML_Empoteere' ), + 'ViewXML' => array( 'XML_beloore' ), +); + +/** Ladino (Ladino) */ +$specialPageAliases['lad'] = array( + 'ImportCSV' => array( 'Aktarear_CSV_Ariento' ), + 'ImportXML' => array( 'Aktarear_XML_Ariento' ), + 'ViewXML' => array( 'Ver_XML' ), +); + +/** Luxembourgish (Lëtzebuergesch) */ +$specialPageAliases['lb'] = array( + 'ImportCSV' => array( 'CSV_importéieren' ), + 'ImportXML' => array( 'XML_importéieren' ), + 'ViewXML' => array( 'XML_weisen' ), +); + +/** Macedonian (Македонски) */ +$specialPageAliases['mk'] = array( + 'ViewXML' => array( 'ВидиXML' ), +); + +/** Malayalam (മലയാളം) */ +$specialPageAliases['ml'] = array( + 'ImportCSV' => array( 'സി.എസ്.വി.ഇറക്കുമതി' ), + 'ImportXML' => array( 'എക്സ്.എം.എൽ.ഇറക്കുമതി' ), + 'ViewXML' => array( 'എക്സ്.എം.എൽ.കാണുക' ), +); + +/** Marathi (मराठी) */ +$specialPageAliases['mr'] = array( + 'ViewXML' => array( 'XMLपहा' ), +); + +/** Maltese (Malti) */ +$specialPageAliases['mt'] = array( + 'ViewXML' => array( 'UriXML' ), +); + +/** Nedersaksisch (Nedersaksisch) */ +$specialPageAliases['nds-nl'] = array( + 'ViewXML' => array( 'XML_bekieken' ), +); + +/** Dutch (Nederlands) */ +$specialPageAliases['nl'] = array( + 'ImportCSV' => array( 'CSVImporteren' ), + 'ImportXML' => array( 'XMLImporteren' ), + 'ViewXML' => array( 'XMLBekijken' ), +); + +/** Norwegian (bokmål)‬ (‪Norsk (bokmål)‬) */ +$specialPageAliases['no'] = array( + 'ViewXML' => array( 'Vis_XML' ), +); + +/** Occitan (Occitan) */ +$specialPageAliases['oc'] = array( + 'ViewXML' => array( 'Veire_XML', 'VeireXML' ), +); + +/** Polish (Polski) */ +$specialPageAliases['pl'] = array( + 'ViewXML' => array( 'XML' ), +); + +/** Portuguese (Português) */ +$specialPageAliases['pt'] = array( + 'ViewXML' => array( 'Ver_XML' ), +); + +/** Romanian (Română) */ +$specialPageAliases['ro'] = array( + 'ImportCSV' => array( 'Import_CSV', 'ImportCSV' ), + 'ImportXML' => array( 'Import_XML', 'ImportXML' ), + 'ViewXML' => array( 'Vizualizare_XML' ), +); + +/** Sanskrit (संस्कृत) */ +$specialPageAliases['sa'] = array( + 'ViewXML' => array( 'XMLपश्यति' ), +); + +/** Slovak (Slovenčina) */ +$specialPageAliases['sk'] = array( + 'ViewXML' => array( 'ZobraziťXML' ), +); + +/** Albanian (Shqip) */ +$specialPageAliases['sq'] = array( + 'ViewXML' => array( 'ShihXML' ), +); + +/** Swedish (Svenska) */ +$specialPageAliases['sv'] = array( + 'ViewXML' => array( 'Visa_XML' ), +); + +/** Swahili (Kiswahili) */ +$specialPageAliases['sw'] = array( + 'ViewXML' => array( 'OnyeshaXML' ), +); + +/** Tagalog (Tagalog) */ +$specialPageAliases['tl'] = array( + 'ViewXML' => array( 'Tingnan ang XML' ), +); + +/** Turkish (Türkçe) */ +$specialPageAliases['tr'] = array( + 'ViewXML' => array( 'XMLGör' ), +); + +/** Татарча (Татарча) */ +$specialPageAliases['tt-cyrl'] = array( + 'ImportCSV' => array( 'CSV_импорт' ), + 'ImportXML' => array( 'XML_импорт' ), + 'ViewXML' => array( 'XML_иттереп_ачу' ), +); + +/** Vèneto (Vèneto) */ +$specialPageAliases['vec'] = array( + 'ViewXML' => array( 'VardaXML' ), +); + +/** + * For backwards compatibility with MediaWiki 1.15 and earlier. + */ +$aliases =& $specialPageAliases; \ No newline at end of file diff --git a/planteome/paw/extensions/DataTransfer_PS/languages/DT_Language.php b/planteome/paw/extensions/DataTransfer_PS/languages/DT_Language.php new file mode 100644 index 0000000..00e7b5c --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/languages/DT_Language.php @@ -0,0 +1,34 @@ + DT_SP_HAS_XML_GROUPING, + 'Excluded from XML' => DT_SP_IS_EXCLUDED_FROM_XML, + ); + + /** + * Function that returns the labels for the special properties. + */ + function getPropertyLabels() { + return $this->m_SpecialProperties; + } + + /** + * Aliases for special properties, if any. + */ + function getPropertyAliases() { + return $this->m_SpecialPropertyAliases; + } +} diff --git a/planteome/paw/extensions/DataTransfer_PS/languages/DT_LanguageEn.php b/planteome/paw/extensions/DataTransfer_PS/languages/DT_LanguageEn.php new file mode 100644 index 0000000..49bb88d --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/languages/DT_LanguageEn.php @@ -0,0 +1,13 @@ + 'Has XML grouping', + DT_SP_IS_EXCLUDED_FROM_XML => 'Excluded from XML' +); + +} diff --git a/planteome/paw/extensions/DataTransfer_PS/languages/DT_Messages.php b/planteome/paw/extensions/DataTransfer_PS/languages/DT_Messages.php new file mode 100644 index 0000000..2032380 --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/languages/DT_Messages.php @@ -0,0 +1,2503 @@ + 'Allows for importing and exporting data contained in template calls', + 'viewxml' => 'View XML', + 'dt_viewxml_docu' => 'Please select among the following categories and namespaces to view in XML format.', + 'dt_viewxml_categories' => 'Categories', + 'dt_viewxml_namespaces' => 'Namespaces', + 'dt_viewxml_simplifiedformat' => 'Simplified format', + 'dt_xml_namespace' => 'Namespace', + 'dt_xml_pages' => 'Pages', + 'dt_xml_page' => 'Page', + 'dt_xml_template' => 'Template', + 'dt_xml_field' => 'Field', + 'dt_xml_name' => 'Name', + 'dt_xml_title' => 'Title', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Free Text', + 'importxml' => 'Import XML', + 'dt_import_selectfile' => 'Please select the $1 file to import:', + 'dt_import_encodingtype' => 'Encoding type:', + 'dt_import_forexisting' => 'For pages that already exist:', + 'dt_import_overwriteexisting' => 'Overwrite existing content', + 'dt_import_skipexisting' => 'Skip', + 'dt_import_appendtoexisting' => 'Append to existing content', + 'dt_import_summarydesc' => 'Summary of import:', + 'dt_import_editsummary' => '$1 import', + 'dt_import_importing' => 'Importing...', + 'dt_import_success' => '$1 {{PLURAL:$1|page|pages}} will be created from the $2 file.', + 'importcsv' => 'Import CSV', + 'dt_importcsv_badheader' => "Error: the column $1 header, '$2', must be either '$3', '$4' or of the form 'template_name[field_name]'", + 'right-datatransferimport' => 'Import data', +); + +/** Message documentation (Message documentation) + * @author EugeneZelenko + * @author Fryed-peach + * @author Jon Harald Søby + * @author Purodha + * @author Raymond + * @author Siebrand + */ +$messages['qqq'] = array( + 'datatransfer-desc' => 'Extension description displayed on [[Special:Version]].', + 'dt_viewxml_categories' => '{{Identical|Categories}}', + 'dt_viewxml_namespaces' => '{{Identical|Namespaces}}', + 'dt_xml_namespace' => '{{Identical|Namespace}} +Used as XML tag name.', + 'dt_xml_pages' => '{{Identical|Pages}} + +Used as XML tag name.', + 'dt_xml_page' => '{{Identical|Page}} +Used as XML tag name.', + 'dt_xml_template' => '{{Identical|Template}} +Used as XML tag name.', + 'dt_xml_field' => '{{Identical|Field}} +Used as XML tag name.', + 'dt_xml_name' => '{{Identical|Name}} + +Used as XML tag name.', + 'dt_xml_title' => '{{Identical|Title}} +Used as XML tag name.', + 'dt_xml_id' => '{{Identical|ID}} + +Used as XML tag name.', + 'dt_xml_freetext' => '{{Identical|Free text}} +Used as XML tag name.', + 'dt_import_selectfile' => '$1 is the file format: either CSV or XML', + 'dt_import_encodingtype' => 'The type of encoding for the file: either UTF-8 or UTF-16', + 'dt_import_skipexisting' => '{{Identical|Skip}}', + 'dt_import_editsummary' => '$1 is the file format: either CSV or XML', + 'dt_import_success' => 'Parameters: +* $1 is the number of pages +* $2 is the file format: either CSV or XML', + 'dt_importcsv_badheader' => 'The text "template_name[field_name]" can be translated. +*$1 is a column number in the first row of the CVS file +*$2 is the value found for the $1th colomn in the first line of the CSV file +*$3 is the title label +*$4 is a free text label', + 'right-datatransferimport' => '{{doc-right}}', +); + +/** Faeag Rotuma (Faeag Rotuma) + * @author Jose77 + */ +$messages['rtm'] = array( + 'dt_viewxml_categories' => 'Katekori', +); + +/** Afrikaans (Afrikaans) + * @author Arnobarnard + * @author Naudefj + */ +$messages['af'] = array( + 'datatransfer-desc' => 'Maak die laai en ontlaai van gestruktureerde gegewens in sjabloonaanroepe moontlik', + 'viewxml' => 'Sien XML', + 'dt_viewxml_docu' => 'Kies een van die volgende kategorieë en naamruimtes om in XML-formaat te sien.', + 'dt_viewxml_categories' => 'Ketagorieë', + 'dt_viewxml_namespaces' => 'Naamruimtes', + 'dt_viewxml_simplifiedformat' => 'Vereenvoudigde formaat', + 'dt_xml_namespace' => 'Naamruimte', + 'dt_xml_pages' => 'Bladsye', + 'dt_xml_page' => 'Bladsy', + 'dt_xml_template' => 'Sjabloon', + 'dt_xml_field' => 'Veld', + 'dt_xml_name' => 'Naam', + 'dt_xml_title' => 'Titel', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Vrye teks', + 'importxml' => 'Laai XML', + 'dt_import_selectfile' => 'Kies die $1 lêer om te laai:', + 'dt_import_encodingtype' => 'Enkoderingstipe:', + 'dt_import_skipexisting' => 'Slaan oor', + 'dt_import_editsummary' => '$1-laai', + 'dt_import_importing' => 'Besig om te laai...', + 'dt_import_success' => '$1 {{PLURAL:$1|bladsy|bladsye}} sal geskep word vanaf die lêer $2.', + 'importcsv' => 'Laai CSV', + 'dt_importcsv_badheader' => 'Fout: Die opskrif van kolom $1, "$2", moet "$3" of "$4" wees, of in die vorm "sjabloonnaam[veldnaam]" genoteer word.', + 'right-datatransferimport' => 'Laai data', +); + +/** Gheg Albanian (Gegë) + * @author Mdupont + */ +$messages['aln'] = array( + 'datatransfer-desc' => 'Lejon për import dhe eksport të dhënave të përmbajtura në modelin e quan', + 'viewxml' => 'Shiko XML', + 'dt_viewxml_docu' => 'Ju lutem zgjidhni midis kategorive të mëposhtme dhe hapësira për të parë në formatin XML.', + 'dt_viewxml_categories' => 'Kategoritë', + 'dt_viewxml_namespaces' => 'Hapësira', + 'dt_viewxml_simplifiedformat' => 'Formati i thjeshtuar', + 'dt_xml_namespace' => 'Hapësira', + 'dt_xml_pages' => 'Faqet', + 'dt_xml_page' => 'Faqe', + 'dt_xml_template' => 'Shabllon', + 'dt_xml_field' => 'Fushë', + 'dt_xml_name' => 'Emër', + 'dt_xml_title' => 'Titull', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Free Tekst', + 'importxml' => 'Importi XML', + 'dt_import_selectfile' => 'Ju lutem përzgjidhni kartelën $1 për të importuar:', + 'dt_import_encodingtype' => 'Encoding lloj:', + 'dt_import_editsummary' => '$1 importit', + 'dt_import_importing' => 'Importimi ...', + 'dt_import_success' => '$1 {{PLURAL:$1|faqe|faqe}} do të krijohet nga file $2.', + 'importcsv' => 'Importi CSV', + 'dt_importcsv_badheader' => "Gabim: $1 column header, '$2', duhet të jenë ose '$3', '$4' ose të formës 'template_name [field_name]'", + 'right-datatransferimport' => 'Të dhënat e importit', +); + +/** Amharic (አማርኛ) + * @author Codex Sinaiticus + */ +$messages['am'] = array( + 'dt_viewxml_categories' => 'መደቦች', + 'dt_viewxml_namespaces' => 'ክፍለ-ዊኪዎች', + 'dt_xml_namespace' => 'ክፍለ-ዊኪ', + 'dt_xml_name' => 'ስም', + 'dt_xml_title' => 'አርዕስት', +); + +/** Aragonese (Aragonés) + * @author Juanpabl + * @author Remember the dot + */ +$messages['an'] = array( + 'dt_viewxml_namespaces' => 'Espacios de nombres', + 'dt_xml_namespace' => 'Espacio de nombres', + 'dt_xml_page' => 'Pachina', + 'dt_xml_template' => 'Plantilla', + 'dt_xml_name' => 'Nombre', +); + +/** Arabic (العربية) + * @author Meno25 + * @author OsamaK + */ +$messages['ar'] = array( + 'datatransfer-desc' => 'يسمح باستيراد وتصدير بيانات محتواة في استدعاءات قالب', + 'viewxml' => 'عرض XML', + 'dt_viewxml_docu' => 'من فضلك اختر من بين التصنيفات والنطاقات التالية للعرض في صيغة XML.', + 'dt_viewxml_categories' => 'تصنيفات', + 'dt_viewxml_namespaces' => 'نطاقات', + 'dt_viewxml_simplifiedformat' => 'صيغة مبسطة', + 'dt_xml_namespace' => 'نطاق', + 'dt_xml_pages' => 'صفحات', + 'dt_xml_page' => 'صفحة', + 'dt_xml_template' => 'قالب', + 'dt_xml_field' => 'حقل', + 'dt_xml_name' => 'اسم', + 'dt_xml_title' => 'عنوان', + 'dt_xml_id' => 'رقم', + 'dt_xml_freetext' => 'نص حر', + 'importxml' => 'استيراد XML', + 'dt_import_selectfile' => 'من فضلك اختر ملف $1 للاستيراد:', + 'dt_import_encodingtype' => 'نوع الترميز:', + 'dt_import_editsummary' => 'استيراد $1', + 'dt_import_importing' => 'جاري الاستيراد...', + 'dt_import_success' => 'سوف تُنشأ {{PLURAL:$1||صفحة واحدة|صفحتين|$1 صفحات|$1 صفحة}} من ملف $2.', + 'importcsv' => 'استورد CSV', + 'dt_importcsv_badheader' => "خطأ: عنوان العامود $1، '$2'، يجب أن يكون إما '$3'، '$4' أو من الصيغة 'template_name[field_name]'", + 'right-datatransferimport' => 'استورد بيانات', +); + +/** Aramaic (ܐܪܡܝܐ) + * @author Basharh + */ +$messages['arc'] = array( + 'dt_viewxml_categories' => 'ܣܕܪ̈ܐ', + 'dt_viewxml_namespaces' => 'ܚܩܠܬ̈ܐ', + 'dt_xml_namespace' => 'ܚܩܠܐ', + 'dt_xml_pages' => 'ܕ̈ܦܐ', + 'dt_xml_page' => 'ܕܦܐ', + 'dt_xml_template' => 'ܩܠܒܐ', + 'dt_xml_name' => 'ܫܡܐ', + 'dt_xml_title' => 'ܟܘܢܝܐ', + 'dt_xml_id' => 'ܗܝܝܘܬܐ', + 'dt_import_summarydesc' => 'ܦܣܝܩܬ̈ܐ ܕܡܥܠܢܘܬܐ:', + 'right-datatransferimport' => 'ܡܥܠܢܘܬܐ ܕܓܠܝܬ̈ܐ', +); + +/** Araucanian (Mapudungun) + * @author Remember the dot + */ +$messages['arn'] = array( + 'dt_xml_page' => 'Pakina', +); + +/** Egyptian Spoken Arabic (مصرى) + * @author Dudi + * @author Ghaly + * @author Meno25 + */ +$messages['arz'] = array( + 'datatransfer-desc' => 'بيسمح بـ import و export للداتا اللى جوّا القالب', + 'viewxml' => 'شوف XML', + 'dt_viewxml_docu' => 'لو سمحت اختار من التصانيف و اسامى المساحات الجايه علشان العرض فى XML format.', + 'dt_viewxml_categories' => 'تصانيف', + 'dt_viewxml_namespaces' => 'مساحات اسامى', + 'dt_viewxml_simplifiedformat' => 'format متبسطه', + 'dt_xml_namespace' => 'اسم مساحه', + 'dt_xml_pages' => 'صفح', + 'dt_xml_page' => 'صفحه', + 'dt_xml_template' => 'قالب', + 'dt_xml_field' => 'حقل', + 'dt_xml_name' => 'اسم', + 'dt_xml_title' => 'عنوان', + 'dt_xml_id' => 'رقم', + 'dt_xml_freetext' => 'نص حر', + 'dt_import_selectfile' => 'لو سمحت اختار فايل $1 علشان تعمل import:', + 'dt_import_editsummary' => 'استوراد $1', + 'dt_import_success' => '$1 {{PLURAL:$1|صفحه|صفحه}} ح يتعملو من الفايل $2.', +); + +/** Belarusian (Беларуская) + * @author Тест + */ +$messages['be'] = array( + 'dt_viewxml_categories' => 'Катэгорыі', + 'dt_xml_template' => 'Шаблон', +); + +/** Belarusian (Taraškievica orthography) (‪Беларуская (тарашкевіца)‬) + * @author EugeneZelenko + * @author Jim-by + * @author Wizardist + */ +$messages['be-tarask'] = array( + 'datatransfer-desc' => 'Дазваляе імпартаваць і экспартаваць зьвесткі, якія ўтрымліваюцца ў выкліках шаблёнах', + 'viewxml' => 'Паказаць XML', + 'dt_viewxml_docu' => 'Калі ласка, выберыце што праглядаць у фармаце XML сярод наступных катэгорыяў і прастораў назваў.', + 'dt_viewxml_categories' => 'Катэгорыі', + 'dt_viewxml_namespaces' => 'Прасторы назваў', + 'dt_viewxml_simplifiedformat' => 'Спрошчаны фармат', + 'dt_xml_namespace' => 'Прастора назваў', + 'dt_xml_pages' => 'Старонкі', + 'dt_xml_page' => 'Старонка', + 'dt_xml_template' => 'Шаблён', + 'dt_xml_field' => 'Поле', + 'dt_xml_name' => 'Назва', + 'dt_xml_title' => 'Назва', + 'dt_xml_id' => 'Ідэнтыфікатар', + 'dt_xml_freetext' => 'Вольны тэкст', + 'importxml' => 'Імпарт XML', + 'dt_import_selectfile' => 'Калі ласка, выберыце файл у фармаце $1 для імпарту:', + 'dt_import_encodingtype' => 'Тып кадыроўкі:', + 'dt_import_forexisting' => 'Для старонак якія ўжо існуюць:', + 'dt_import_overwriteexisting' => 'Перазапісваць існуючы зьмест', + 'dt_import_skipexisting' => 'Прапускаць', + 'dt_import_appendtoexisting' => 'Далучаць да існуючага зьместу', + 'dt_import_summarydesc' => 'Кароткае апісаньне імпарту:', + 'dt_import_editsummary' => 'імпарт $1', + 'dt_import_importing' => 'Імпартаваньне...', + 'dt_import_success' => '$1 {{PLURAL:$1|старонка будзе|старонкі будуць|старонак будзе}} створана з файла ў фармаце $2.', + 'importcsv' => 'Імпарт CSV', + 'dt_importcsv_badheader' => "Памылка: загаловак слупка $1, '$2', павінен быць адным з '$3', '$4' альбо у форме 'назва_шаблёну[назва_поля]'", + 'right-datatransferimport' => 'імпарт зьвестак', +); + +/** Bulgarian (Български) + * @author DCLXVI + */ +$messages['bg'] = array( + 'viewxml' => 'Преглед на XML', + 'dt_viewxml_categories' => 'Категории', + 'dt_viewxml_namespaces' => 'Именни пространства', + 'dt_viewxml_simplifiedformat' => 'Опростен формат', + 'dt_xml_namespace' => 'Именно пространство', + 'dt_xml_pages' => 'Страници', + 'dt_xml_page' => 'Страница', + 'dt_xml_template' => 'Шаблон', + 'dt_xml_field' => 'Поле', + 'dt_xml_name' => 'Име', + 'dt_xml_title' => 'Заглавие', + 'dt_xml_id' => 'Номер', + 'dt_xml_freetext' => 'Свободен текст', + 'importxml' => 'Внасяне на XML', + 'dt_import_importing' => 'Внасяне...', + 'importcsv' => 'Внасяне на CSV', + 'right-datatransferimport' => 'Внасяне на данни', +); + +/** Breton (Brezhoneg) + * @author Fohanno + * @author Fulup + * @author Gwendal + * @author Y-M D + */ +$messages['br'] = array( + 'datatransfer-desc' => 'Aotreañ a ra da enporzhiañ hag ezporzhiañ roadennoù eus galvoù patromoù', + 'viewxml' => 'Gwelet XML', + 'dt_viewxml_docu' => 'Dibabit e-touez ar rummadoù hag an esaouennoù anv da heul evit gwelet er furmad XML.', + 'dt_viewxml_categories' => 'Rummadoù', + 'dt_viewxml_namespaces' => 'Esaouennoù anv', + 'dt_viewxml_simplifiedformat' => 'Furmad eeunaet', + 'dt_xml_namespace' => 'Esaouenn anv', + 'dt_xml_pages' => 'Pajennoù', + 'dt_xml_page' => 'Pajenn', + 'dt_xml_template' => 'Patrom', + 'dt_xml_field' => 'Maezienn', + 'dt_xml_name' => 'Anv', + 'dt_xml_title' => 'Titl', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Testenn dieub', + 'importxml' => 'Enporzhiañ XML', + 'dt_import_selectfile' => 'Dibabit ar restr $1 da enporzhiañ :', + 'dt_import_encodingtype' => 'Seurt enkodadur :', + 'dt_import_forexisting' => 'Evit pajennoù zo anezho dija :', + 'dt_import_overwriteexisting' => "erlec'hiañ an endalc'had zo anezhañ dija", + 'dt_import_skipexisting' => 'Lezel a-gostez', + 'dt_import_appendtoexisting' => "Ouzhpennañ d'an endalc'had zo anezhañ dija", + 'dt_import_summarydesc' => 'Diverradenn an enporzh :', + 'dt_import_editsummary' => 'Enporzhiadur $1', + 'dt_import_importing' => "Oc'h enporzhiañ...", + 'dt_import_success' => '$1 {{PLURAL:$1|bajenn|pajenn}} a vo krouet diwar ar restr $2.', + 'importcsv' => 'Enporzh CSV', + 'dt_importcsv_badheader' => 'Fazi : titl ar bann $1, "$2", a rank bezañ "$3", "$4" pe gant ar stumm "anv_ar_patrom[anv_ar_vaezienn]"', + 'right-datatransferimport' => 'Enporzhiañ roadennoù', +); + +/** Bosnian (Bosanski) + * @author CERminator + */ +$messages['bs'] = array( + 'datatransfer-desc' => 'Omogućuje uvoz i izvoz podataka koji su sadržani u pozivima šablona', + 'viewxml' => 'Pregledaj XML', + 'dt_viewxml_docu' => 'Molimo Vas odaberite unutar slijedećih kategorija i imenskih prostora za pregled u XML formatu.', + 'dt_viewxml_categories' => 'Kategorije', + 'dt_viewxml_namespaces' => 'Imenski prostori', + 'dt_viewxml_simplifiedformat' => 'Pojednostavljeni format', + 'dt_xml_namespace' => 'Imenski prostor', + 'dt_xml_pages' => 'Stranice', + 'dt_xml_page' => 'Stranica', + 'dt_xml_template' => 'Šablon', + 'dt_xml_field' => 'Polje', + 'dt_xml_name' => 'Naziv', + 'dt_xml_title' => 'Naslov', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Slobodni tekst', + 'importxml' => 'Uvezi XML', + 'dt_import_selectfile' => 'Molimo odaberite $1 datoteku za uvoz:', + 'dt_import_encodingtype' => 'Tip šifriranja:', + 'dt_import_forexisting' => 'Za stranice koje već postoje:', + 'dt_import_overwriteexisting' => 'Piši preko postojećeg sadržaja', + 'dt_import_skipexisting' => 'Preskoči', + 'dt_import_appendtoexisting' => 'Dodaj na postojeći sadržaj', + 'dt_import_summarydesc' => 'Sažetak uvoza:', + 'dt_import_editsummary' => '$1 uvoz', + 'dt_import_importing' => 'Uvoz...', + 'dt_import_success' => '$1 {{PLURAL:$1|stranica|stranice|stranica}} će biti napravljeno iz $2 datoteke.', + 'importcsv' => 'Uvoz CSV', + 'dt_importcsv_badheader' => "Greška: zaglavlje $1 kolone, '$2', mora biti ili '$3', '$4' ili od obrasca 'template_name[field_name]'", + 'right-datatransferimport' => 'Uvoz podataka', +); + +/** Catalan (Català) + * @author Jordi Roqué + * @author SMP + * @author Solde + * @author Toniher + */ +$messages['ca'] = array( + 'datatransfer-desc' => 'Permet importar i exportar les dades que contenen les crides de les plantilles', + 'viewxml' => "Visualitza l'XML", + 'dt_viewxml_docu' => "Seleccioneu d'entre les següents categories i espais de noms per a veure'l en format XML.", + 'dt_viewxml_categories' => 'Categories', + 'dt_viewxml_namespaces' => 'Espais de noms', + 'dt_viewxml_simplifiedformat' => 'Format simplificat', + 'dt_xml_namespace' => 'Espai de noms', + 'dt_xml_pages' => 'Pàgines', + 'dt_xml_page' => 'Pàgina', + 'dt_xml_template' => 'Plantilla', + 'dt_xml_field' => 'Camp', + 'dt_xml_name' => 'Nom', + 'dt_xml_title' => 'Títol', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Text lliure', + 'importxml' => 'Importa un XML', + 'dt_import_selectfile' => 'Seleccioneu el fitxer $1 per importar:', + 'dt_import_encodingtype' => 'Joc de caràcters:', + 'dt_import_summarydesc' => 'Resum de la importació:', + 'dt_import_editsummary' => 'Importació $1', + 'dt_import_importing' => "S'està important...", + 'dt_import_success' => '$1 {{PLURAL:$1|pàgina|pàgines}} es crearan des del fitxer $2.', + 'importcsv' => 'Importa un CSV', + 'dt_importcsv_badheader' => "Error: la capçalera de la columna $1, '$2', ha de ser o bé '$3', '$4' o bé de la forma 'template_name[field_name]'", + 'right-datatransferimport' => 'Importa les dades', +); + +/** Chechen (Нохчийн) + * @author Sasan700 + */ +$messages['ce'] = array( + 'dt_xml_template' => 'Куцкеп', +); + +/** Czech (Česky) + * @author Jkjk + * @author Matěj Grabovský + */ +$messages['cs'] = array( + 'datatransfer-desc' => 'Umožňuje import a export strukturovaných údajů v buňkách šablon.', + 'viewxml' => 'Zobrazit XML', + 'dt_viewxml_categories' => 'Kategorie', + 'dt_viewxml_namespaces' => 'Jmenné prostory', + 'dt_viewxml_simplifiedformat' => 'Zjednodušený formát', + 'dt_xml_namespace' => 'Jmenný prostor', + 'dt_xml_pages' => 'Stránky', + 'dt_xml_page' => 'Stránka', + 'dt_xml_template' => 'Šablona', + 'dt_xml_field' => 'Pole', + 'dt_xml_name' => 'Název', + 'dt_xml_title' => 'Název', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Libovolný text', + 'importxml' => 'Importovat XML', + 'dt_import_selectfile' => 'Prosím vyberte $1 soubor k importu:', + 'dt_import_encodingtype' => 'Typ kódování:', + 'dt_import_summarydesc' => 'Shrnutí importu:', + 'dt_import_editsummary' => 'import $1', + 'dt_import_importing' => 'Probíhá import...', + 'dt_import_success' => ' $1 {{PLURAL:$1|stránky|stránky|stránek}} bude vytvořeno z $2 souboru.', + 'importcsv' => 'Import CSV', + 'right-datatransferimport' => 'Importovat data', +); + +/** Danish (Dansk) + * @author Jon Harald Søby + */ +$messages['da'] = array( + 'dt_viewxml_categories' => 'Kategorier', + 'dt_xml_namespace' => 'Navnerum', + 'dt_xml_page' => 'Side', + 'dt_xml_name' => 'Navn', + 'dt_xml_title' => 'Titel', + 'dt_xml_id' => 'ID', +); + +/** German (Deutsch) + * @author Als-Holder + * @author Kghbln + * @author Krabina + * @author Revolus + * @author Umherirrender + */ +$messages['de'] = array( + 'datatransfer-desc' => 'Ermöglicht den Export von Daten im XML-Format sowie den Import von Daten im XML- und CSV-Format', + 'viewxml' => 'XML ansehen', + 'dt_viewxml_docu' => 'Bitte auswählen, welche Kategorien und Namensräume im XML-Format angezeigt werden sollen:', + 'dt_viewxml_categories' => 'Kategorien', + 'dt_viewxml_namespaces' => 'Namensräume', + 'dt_viewxml_simplifiedformat' => 'Vereinfachtes Format', + 'dt_xml_namespace' => 'Namensraum', + 'dt_xml_pages' => 'Seiten', + 'dt_xml_page' => 'Seite', + 'dt_xml_template' => 'Vorlage', + 'dt_xml_field' => 'Feld', + 'dt_xml_name' => 'Name', + 'dt_xml_title' => 'Titel', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Freitext', + 'importxml' => 'XML-Datei importieren', + 'dt_import_selectfile' => 'Bitte die zu importierende $1-Datei auswählen:', + 'dt_import_encodingtype' => 'Zeichenkodierung:', + 'dt_import_forexisting' => 'Im Fall von Seiten, die bereits vorhanden sind:', + 'dt_import_overwriteexisting' => 'Vorhandenen Inhalt überschreiben', + 'dt_import_skipexisting' => 'Seite nicht importieren', + 'dt_import_appendtoexisting' => 'Vorhandenen Inhalt ergänzen', + 'dt_import_summarydesc' => 'Zusammenfassung zum Import:', + 'dt_import_editsummary' => '$1-Import', + 'dt_import_importing' => 'Importiere …', + 'dt_import_success' => '$1 {{PLURAL:$1|Seite|Seiten}} werden aus der $2-Datei importiert.', + 'importcsv' => 'CSV-Datei importieren', + 'dt_importcsv_badheader' => "'''Fehler:''' Der Kopf der Spalte $1, „$2“, muss entweder „$3“, „$4“ oder im Format „Vorlagenname[Feldname]“ sein", + 'right-datatransferimport' => 'Daten importieren', +); + +/** Lower Sorbian (Dolnoserbski) + * @author Michawiki + */ +$messages['dsb'] = array( + 'datatransfer-desc' => 'Zmóžnja importěrowanje a eksportěrowanje datow w zawołanjach pśedłogow', + 'viewxml' => 'XML se woglědaś', + 'dt_viewxml_docu' => 'Pšosym wubjeŕ, kótare slědujucych kategorijow a mjenjowych rumow maju se pokazaś w formaśe XML.', + 'dt_viewxml_categories' => 'Kategorije', + 'dt_viewxml_namespaces' => 'Mjenjowe rumy', + 'dt_viewxml_simplifiedformat' => 'Zjadnorjony format', + 'dt_xml_namespace' => 'Mjenjowy rum', + 'dt_xml_pages' => 'Boki', + 'dt_xml_page' => 'Bok', + 'dt_xml_template' => 'Pśedłoga', + 'dt_xml_field' => 'Pólo', + 'dt_xml_name' => 'Mě', + 'dt_xml_title' => 'Titel', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Lichy tekst', + 'importxml' => 'XML importěrowaś', + 'dt_import_selectfile' => 'Pšosym wubjeŕ dataju $1 za importěrowanje:', + 'dt_import_encodingtype' => 'Typ znamuškowego koda:', + 'dt_import_forexisting' => 'Za boki, kótarež južo ekistěruju:', + 'dt_import_overwriteexisting' => 'Eksistěrujuce wopśimjeśe pśepisaś', + 'dt_import_skipexisting' => 'Pśeskócyś', + 'dt_import_appendtoexisting' => 'K eksistěrujucemu wopśimjeśoju pśipowjesyś', + 'dt_import_summarydesc' => 'Zespominanje importa:', + 'dt_import_editsummary' => 'Importěrowanje $1', + 'dt_import_importing' => 'Importěrujo se...', + 'dt_import_success' => '$1 {{PLURAL:$1|bok twóri|boka twóritej|boki twórje|bokow twóri}} se z dataje $2.', + 'importcsv' => 'Importěrowanje CSV', + 'dt_importcsv_badheader' => "Zmólka: głowa słupa $1, '$2', musy pak '$3', '$4' byś pak formu 'mě_pśedłogi[mě_póla]' měś", + 'right-datatransferimport' => 'Daty importěrowaś', +); + +/** Ewe (Eʋegbe) */ +$messages['ee'] = array( + 'dt_xml_page' => 'Axa', +); + +/** Greek (Ελληνικά) + * @author Consta + * @author Crazymadlover + * @author Omnipaedista + */ +$messages['el'] = array( + 'viewxml' => 'Προβολή XML', + 'dt_viewxml_categories' => 'Κατηγορίες', + 'dt_viewxml_namespaces' => 'Περιοχές ονομάτων', + 'dt_xml_namespace' => 'Περιοχή ονομάτων', + 'dt_xml_pages' => 'Σελίδες', + 'dt_xml_page' => 'Σελίδα', + 'dt_xml_template' => 'Πρότυπο', + 'dt_xml_field' => 'Πεδίο', + 'dt_xml_name' => 'Όνομα', + 'dt_xml_title' => 'Τίτλος', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Ελεύθερο Κείμενο', + 'importxml' => 'Εισαγωγή σε XML', + 'dt_import_encodingtype' => 'Τύπος κωδικοποίησης', + 'dt_import_editsummary' => 'Εισαγωγή $1', + 'dt_import_importing' => 'Εισάγεται...', + 'importcsv' => 'Εισαγωγή CSV', + 'right-datatransferimport' => 'Εισαγωγή δεδομένων', +); + +/** Esperanto (Esperanto) + * @author Michawiki + * @author Yekrats + */ +$messages['eo'] = array( + 'datatransfer-desc' => 'Permesas importadon kaj eksportadon de datumoj enhave en ŝablonaj vokoj', + 'viewxml' => 'Rigardu XML-on', + 'dt_viewxml_docu' => 'Bonvolu elekti inter la subaj kategorioj kaj nomspacoj por rigardi en XML-formato.', + 'dt_viewxml_categories' => 'Kategorioj', + 'dt_viewxml_namespaces' => 'Nomspacoj', + 'dt_viewxml_simplifiedformat' => 'Simpligita formato', + 'dt_xml_namespace' => 'Nomspaco', + 'dt_xml_pages' => 'Paĝoj', + 'dt_xml_page' => 'Paĝo', + 'dt_xml_template' => 'Ŝablono', + 'dt_xml_field' => 'Kampo', + 'dt_xml_name' => 'Nomo', + 'dt_xml_title' => 'Titolo', + 'dt_xml_id' => 'identigo', + 'dt_xml_freetext' => 'Libera Teksto', + 'importxml' => 'Importi XML', + 'dt_import_editsummary' => '$1 importo', + 'dt_import_importing' => 'Importante...', + 'importcsv' => 'Importi CSV', + 'right-datatransferimport' => 'Importi datenojn', +); + +/** Spanish (Español) + * @author Crazymadlover + * @author Imre + * @author Locos epraix + * @author Peter17 + * @author Sanbec + * @author Translationista + */ +$messages['es'] = array( + 'datatransfer-desc' => 'Permite importar y exportar datos contenidos en llamadas de plantilla', + 'viewxml' => 'Ver XML', + 'dt_viewxml_docu' => 'Por favor seleccionar entre las siguientes categorías y nombres de espacio para ver en formato XML.', + 'dt_viewxml_categories' => 'Categorías', + 'dt_viewxml_namespaces' => 'Espacios de nombres', + 'dt_viewxml_simplifiedformat' => 'Formato simplificado', + 'dt_xml_namespace' => 'Espacio de nombres', + 'dt_xml_pages' => 'Páginas', + 'dt_xml_page' => 'Página', + 'dt_xml_template' => 'Plantilla', + 'dt_xml_field' => 'Campo', + 'dt_xml_name' => 'Nombre', + 'dt_xml_title' => 'Título', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Texto libre', + 'importxml' => 'Importar XML', + 'dt_import_selectfile' => 'Por favor seleccione el archivo $1 a importar:', + 'dt_import_encodingtype' => 'Tipo de codificación:', + 'dt_import_summarydesc' => 'Resumen de importación:', + 'dt_import_editsummary' => '$1 importación', + 'dt_import_importing' => 'Importando...', + 'dt_import_success' => '$1 {{PLURAL:$1|página|páginas}} serán creadas del archivo $2.', + 'importcsv' => 'Importar CSV', + 'dt_importcsv_badheader' => 'Error : el título de columna $1, "$2", tiene que ser "$3", "$4" o de la forma \'nombre_de_plantilla[nombre_del_campo]\'', + 'right-datatransferimport' => 'Importar datos', +); + +/** Estonian (Eesti) + * @author Avjoska + * @author Pikne + */ +$messages['et'] = array( + 'dt_viewxml_categories' => 'Kategooriad', + 'dt_viewxml_namespaces' => 'Nimeruumid', + 'dt_viewxml_simplifiedformat' => 'Lihtsustatud vorming', + 'dt_xml_namespace' => 'Nimeruum', + 'dt_xml_pages' => 'Leheküljed', + 'dt_xml_page' => 'Lehekülg', + 'dt_xml_template' => 'Mall', + 'dt_xml_name' => 'Nimi', +); + +/** Basque (Euskara) + * @author Kobazulo + */ +$messages['eu'] = array( + 'viewxml' => 'XML ikusi', + 'dt_viewxml_categories' => 'Kategoriak', + 'dt_xml_pages' => 'Orrialdeak', + 'dt_xml_page' => 'Orrialdea', + 'dt_xml_template' => 'Txantiloia', + 'dt_xml_field' => 'Eremua', + 'dt_xml_name' => 'Izena', + 'dt_xml_title' => 'Izenburua', + 'importxml' => 'XML inportatu', + 'dt_import_selectfile' => 'Mesedez, aukera ezazu inportatzeko $1 fitxategia:', + 'dt_import_editsummary' => '$1 inportatu', + 'dt_import_importing' => 'Inportatzen...', + 'importcsv' => 'CSV inportatu', + 'right-datatransferimport' => 'Datuak inportatu', +); + +/** Persian (فارسی) + * @author Mjbmr + */ +$messages['fa'] = array( + 'dt_xml_template' => 'الگو', + 'dt_xml_name' => 'نام', + 'dt_xml_title' => 'عنوان', +); + +/** Finnish (Suomi) + * @author Centerlink + * @author Crt + * @author Nike + * @author Str4nd + * @author Vililikku + */ +$messages['fi'] = array( + 'datatransfer-desc' => 'Mahdollistaa tuoda ja viedä dataa, joka on mallinekutsuissa.', + 'viewxml' => 'Näytä XML', + 'dt_viewxml_docu' => 'Valitse yksi seuraavista luokista ja nimiavaruuksista tarkasteltavaksi XML-muodossa.', + 'dt_viewxml_categories' => 'Luokat', + 'dt_viewxml_namespaces' => 'Nimiavaruudet', + 'dt_viewxml_simplifiedformat' => 'Yksinkertaistettu muoto', + 'dt_xml_namespace' => 'Nimiavaruus', + 'dt_xml_pages' => 'Sivut', + 'dt_xml_page' => 'Sivu', + 'dt_xml_template' => 'Malline', + 'dt_xml_field' => 'Kenttä', + 'dt_xml_name' => 'Nimi', + 'dt_xml_title' => 'Otsikko', + 'dt_xml_id' => 'Tunnus', + 'dt_xml_freetext' => 'Vapaa teksti', + 'importxml' => 'XML-tuonti', + 'dt_import_selectfile' => 'Valitse $1-tiedosto tuotavaksi:', + 'dt_import_encodingtype' => 'Merkistötyyppi:', + 'dt_import_skipexisting' => 'Ohita', + 'dt_import_summarydesc' => 'Tuonnin yhteenveto', + 'dt_import_editsummary' => '$1-tuonti', + 'dt_import_importing' => 'Tuodaan...', + 'dt_import_success' => '$1 {{PLURAL:$1|sivu|sivua}} luodaan $2-tiedostosta.', + 'importcsv' => 'CSV-tuonti', + 'dt_importcsv_badheader' => "Virhe: sarake $1 otsake, '$2', on oltava joko '$3', '$4' tai muotoa 'mallinne_nimi[kenttä_nimi]'", + 'right-datatransferimport' => 'Tuoda tiedot', +); + +/** French (Français) + * @author Crochet.david + * @author Grondin + * @author IAlex + * @author Peter17 + * @author PieRRoMaN + * @author Zetud + */ +$messages['fr'] = array( + 'datatransfer-desc' => 'Permet l’import et l’export de données contenues dans des appels de modèles', + 'viewxml' => 'Voir XML', + 'dt_viewxml_docu' => 'Veuillez sélectionner parmi les catégories et les espaces de noms suivants afin de visionner au format XML.', + 'dt_viewxml_categories' => 'Catégories', + 'dt_viewxml_namespaces' => 'Espaces de noms', + 'dt_viewxml_simplifiedformat' => 'Format simplifié', + 'dt_xml_namespace' => 'Espace de noms', + 'dt_xml_pages' => 'Pages', + 'dt_xml_page' => 'Page', + 'dt_xml_template' => 'Modèle', + 'dt_xml_field' => 'Champ', + 'dt_xml_name' => 'Nom', + 'dt_xml_title' => 'Titre', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Texte libre', + 'importxml' => 'Import en XML', + 'dt_import_selectfile' => 'Veuillez sélectionner le fichier $1 à importer :', + 'dt_import_encodingtype' => 'Type d’encodage:', + 'dt_import_forexisting' => 'Pour les pages qui existent déjà :', + 'dt_import_overwriteexisting' => 'Remplacer le contenu existant', + 'dt_import_skipexisting' => 'Passer', + 'dt_import_appendtoexisting' => 'Ajouter au contenu existant', + 'dt_import_summarydesc' => 'Résumé de l’import :', + 'dt_import_editsummary' => 'Import de $1', + 'dt_import_importing' => 'Import en cours...', + 'dt_import_success' => '$1 {{PLURAL:$1|page sera créée|pages seront créées}} depuis le fichier $2.', + 'importcsv' => 'Import CSV', + 'dt_importcsv_badheader' => 'Erreur : le titre de colonne $1, « $2 », doit être soit « $3 », « $4 » ou de la forme « nom_du_modèle[nom_du_champ] »', + 'right-datatransferimport' => 'Importer des données', +); + +/** Franco-Provençal (Arpetan) + * @author Cedric31 + */ +$messages['frp'] = array( + 'dt_viewxml_categories' => 'Catègories', + 'dt_viewxml_namespaces' => 'Èspâços de noms', + 'dt_xml_namespace' => 'Èspâço de noms', + 'dt_xml_pages' => 'Pâges', + 'dt_xml_page' => 'Pâge', + 'dt_xml_template' => 'Modèlo', +); + +/** Western Frisian (Frysk) + * @author Snakesteuben + */ +$messages['fy'] = array( + 'dt_viewxml_namespaces' => 'Nammeromten', + 'dt_xml_page' => 'Side', + 'dt_xml_name' => 'Namme', +); + +/** Irish (Gaeilge) + * @author Alison + */ +$messages['ga'] = array( + 'dt_xml_namespace' => 'Ainmspás', +); + +/** Galician (Galego) + * @author Alma + * @author Toliño + */ +$messages['gl'] = array( + 'datatransfer-desc' => 'Permite importar e exportar datos contidos en chamadas de modelos', + 'viewxml' => 'Ver XML', + 'dt_viewxml_docu' => 'Por favor seleccione entre as seguintes categorías e espazos de nomes para ver en formato XML.', + 'dt_viewxml_categories' => 'Categorías', + 'dt_viewxml_namespaces' => 'Espazos de nomes', + 'dt_viewxml_simplifiedformat' => 'Formato simplificado', + 'dt_xml_namespace' => 'Espazo de nomes', + 'dt_xml_pages' => 'Páxinas', + 'dt_xml_page' => 'Páxina', + 'dt_xml_template' => 'Modelo', + 'dt_xml_field' => 'Campo', + 'dt_xml_name' => 'Nome', + 'dt_xml_title' => 'Título', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Texto Libre', + 'importxml' => 'Importar XML', + 'dt_import_selectfile' => 'Por favor, seleccione o ficheiro $1 a importar:', + 'dt_import_encodingtype' => 'Tipo de codificación:', + 'dt_import_forexisting' => 'Para páxinas que xa existen:', + 'dt_import_overwriteexisting' => 'Sobrescribir o contido existente', + 'dt_import_skipexisting' => 'Saltar', + 'dt_import_appendtoexisting' => 'Engadir ao contido existente', + 'dt_import_summarydesc' => 'Resumo da importación:', + 'dt_import_editsummary' => 'Importación en $1', + 'dt_import_importing' => 'Importando...', + 'dt_import_success' => '{{PLURAL:$1|Unha páxina será creada|$1 páxinas serán creadas}} a partir do ficheiro $2.', + 'importcsv' => 'Importación en CSV', + 'dt_importcsv_badheader' => 'Erro: a cabeceira da columna $1, "$2", debe ser un "$3", "$4" ou do formulario "template_name[field_name]"', + 'right-datatransferimport' => 'Importar datos', +); + +/** Gothic (Gothic) + * @author Jocke Pirat + */ +$messages['got'] = array( + 'dt_xml_namespace' => 'Seidofera', +); + +/** Ancient Greek (Ἀρχαία ἑλληνικὴ) + * @author Crazymadlover + * @author Omnipaedista + */ +$messages['grc'] = array( + 'dt_viewxml_categories' => 'Κατηγορίαι', + 'dt_viewxml_namespaces' => 'Ὀνοματεῖα', + 'dt_xml_namespace' => 'Ὀνοματεῖον', + 'dt_xml_pages' => 'Δέλτοι', + 'dt_xml_page' => 'Δέλτος', + 'dt_xml_template' => 'Πρότυπον', + 'dt_xml_field' => 'Πεδίον', + 'dt_xml_name' => 'Ὄνομα', + 'dt_xml_title' => 'Ἐπιγραφή', + 'dt_xml_freetext' => 'Ἐλεύθερον κείμενον', +); + +/** Swiss German (Alemannisch) + * @author Als-Holder + * @author J. 'mach' wust + */ +$messages['gsw'] = array( + 'datatransfer-desc' => 'Macht dr Import un dr Export vu strukturierte Date megli, wu in Ufrief vu Vorlage bruucht wäre.', + 'viewxml' => 'XML aaluege', + 'dt_viewxml_docu' => 'Bitte wehl uus, weli Kategorien un Namensryym im XML-Format solle aazeigt wäre.', + 'dt_viewxml_categories' => 'Kategorie', + 'dt_viewxml_namespaces' => 'Namensryym', + 'dt_viewxml_simplifiedformat' => 'Vereifacht Format', + 'dt_xml_namespace' => 'Namensruum', + 'dt_xml_pages' => 'Syte', + 'dt_xml_page' => 'Syte', + 'dt_xml_template' => 'Vorlag', + 'dt_xml_field' => 'Fäld', + 'dt_xml_name' => 'Name', + 'dt_xml_title' => 'Titel', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Freje Täxt', + 'importxml' => 'XML importiere', + 'dt_import_selectfile' => 'Bitte wehl d $1-Datei zum importiere uus:', + 'dt_import_encodingtype' => 'Verschlisseligstyp:', + 'dt_import_forexisting' => 'Im Fall vu Syte, wu s scho git:', + 'dt_import_overwriteexisting' => 'Vorhandene Inhalt iberschryybe', + 'dt_import_skipexisting' => 'Ibergumpe', + 'dt_import_appendtoexisting' => 'Vorhandene Inhalt ergänze', + 'dt_import_summarydesc' => 'Zämmefassig vum Import:', + 'dt_import_editsummary' => '$1-Import', + 'dt_import_importing' => 'Am Importiere ...', + 'dt_import_success' => '$1 {{PLURAL:$1|Syte|Syte}} wäre us dr $2-Datei aagleit.', + 'importcsv' => 'CSV-Datei importiere', + 'dt_importcsv_badheader' => "Fähler: d Spalte $1 Iberschrift, '$2', muess entwäder '$3', '$4' syy oder us em Format 'template_name[field_name]'", + 'right-datatransferimport' => 'Date importiere', +); + +/** Manx (Gaelg) + * @author MacTire02 + */ +$messages['gv'] = array( + 'viewxml' => 'Jeeagh er XML', + 'dt_viewxml_categories' => 'Ronnaghyn', + 'dt_xml_page' => 'Duillag', + 'dt_xml_name' => 'Ennym', + 'dt_xml_title' => 'Ard-ennym', + 'dt_xml_freetext' => 'Teks seyr', +); + +/** Hausa (هَوُسَ) */ +$messages['ha'] = array( + 'dt_xml_namespace' => 'Sararin suna', + 'dt_xml_page' => 'Shafi', +); + +/** Hawaiian (Hawai`i) + * @author Singularity + */ +$messages['haw'] = array( + 'dt_xml_page' => '‘Ao‘ao', + 'dt_xml_name' => 'Inoa', +); + +/** Hebrew (עברית) + * @author Amire80 + * @author Rotemliss + * @author YaronSh + */ +$messages['he'] = array( + 'datatransfer-desc' => 'אפשרות לייבא ולייצא נתונים בתבניות', + 'viewxml' => 'הצגת XML', + 'dt_viewxml_docu' => 'אנא בחרו את מרחבי השם והקטגוריות אותם תרצו להציג בפורמט XML.', + 'dt_viewxml_categories' => 'קטגוריות', + 'dt_viewxml_namespaces' => 'מרחבי שם', + 'dt_viewxml_simplifiedformat' => 'מבנה מפושט', + 'dt_xml_namespace' => 'מרחב שם', + 'dt_xml_pages' => 'דפים', + 'dt_xml_page' => 'דף', + 'dt_xml_template' => 'תבנית', + 'dt_xml_field' => 'שדה', + 'dt_xml_name' => 'שם', + 'dt_xml_title' => 'כותרת', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'טקסט חופשי', + 'importxml' => 'יבוא XML', + 'dt_import_selectfile' => 'אנא בחרו את קובץ ה־$1 ליבוא:', + 'dt_import_encodingtype' => 'סוג הקידוד:', + 'dt_import_forexisting' => 'עבור הדפים שכבר קיימים:', + 'dt_import_overwriteexisting' => 'לדרוס את התוכן הקיים', + 'dt_import_skipexisting' => 'לדלג', + 'dt_import_appendtoexisting' => 'לצרף את התוכן הקיים', + 'dt_import_summarydesc' => 'תקציר היבוא:', + 'dt_import_editsummary' => 'יבוא $1', + 'dt_import_importing' => 'מתבצע יבוא...', + 'dt_import_success' => '{{PLURAL:$1|דף אחד ייוצר|$1 דפים ייוצרו}} מקובץ ה־$2.', + 'importcsv' => 'יבוא CSV', + 'dt_importcsv_badheader' => "שגיאה: כותרת העמודה $1, '$2', חייבת להיות או '$3', '$4' או מהצורה 'שם_התבנית[שם_השדה]'", + 'right-datatransferimport' => 'יבוא נתונים', +); + +/** Hindi (हिन्दी) + * @author Kaustubh + */ +$messages['hi'] = array( + 'datatransfer-desc' => 'टेम्प्लेट कॉल में उपलब्ध डाटाकी आयात-निर्यात करने की अनुमति देता हैं', + 'viewxml' => 'XML देखें', + 'dt_viewxml_docu' => 'कॄपया XML में देखने के लिये श्रेणीयाँ और नामस्थान चुनें।', + 'dt_viewxml_categories' => 'श्रेणीयाँ', + 'dt_viewxml_namespaces' => 'नामस्थान', + 'dt_viewxml_simplifiedformat' => 'आसान फॉरमैट', + 'dt_xml_namespace' => 'नामस्थान', + 'dt_xml_page' => 'पन्ना', + 'dt_xml_field' => 'फिल्ड़', + 'dt_xml_name' => 'नाम', + 'dt_xml_title' => 'शीर्षक', + 'dt_xml_id' => 'आईडी', + 'dt_xml_freetext' => 'मुक्त पाठ', +); + +/** Croatian (Hrvatski) + * @author Dalibor Bosits + */ +$messages['hr'] = array( + 'dt_viewxml_categories' => 'Kategorije', + 'dt_xml_namespace' => 'Imenski prostor', + 'dt_xml_page' => 'Stranica', +); + +/** Upper Sorbian (Hornjoserbsce) + * @author Michawiki + */ +$messages['hsb'] = array( + 'datatransfer-desc' => 'Dowola importowanje a eksportowanje datow, kotrež su we wołanjach předłohow wobsahowane', + 'viewxml' => 'XML wobhladać', + 'dt_viewxml_docu' => 'Prošu wubjer ze slědowacych kategorijow a mjenowych rumow, zo by w XML-formaće wobhladał.', + 'dt_viewxml_categories' => 'Kategorije', + 'dt_viewxml_namespaces' => 'Mjenowe rumy', + 'dt_viewxml_simplifiedformat' => 'Zjednorjeny format', + 'dt_xml_namespace' => 'Mjenowy rum', + 'dt_xml_pages' => 'Strony', + 'dt_xml_page' => 'Strona', + 'dt_xml_template' => 'Předłoha', + 'dt_xml_field' => 'Polo', + 'dt_xml_name' => 'Mjeno', + 'dt_xml_title' => 'Titul', + 'dt_xml_id' => 'Id', + 'dt_xml_freetext' => 'Swobodny tekst', + 'importxml' => 'XML importować', + 'dt_import_selectfile' => 'Prošu wubjer dataju $1 za importowanje:', + 'dt_import_encodingtype' => 'Typ znamješkoweho koda:', + 'dt_import_forexisting' => 'Za strony, kotrež hižo eksistuja:', + 'dt_import_overwriteexisting' => 'Eksistowacy wobsah přepisać', + 'dt_import_skipexisting' => 'Přeskočić', + 'dt_import_appendtoexisting' => 'K eksistowacemu wobsahej připowěsnyć', + 'dt_import_summarydesc' => 'Zjeće importa:', + 'dt_import_editsummary' => 'Importowanje $1', + 'dt_import_importing' => 'Importuje so...', + 'dt_import_success' => '$1 {{PLURAL:$1|strona so z dataje $2 twori|stronje so z dataje $2 tworitej|strony so z dataje $2 tworja|stronow so z dataje $2 twori}}.', + 'importcsv' => 'Importowanje CSV', + 'dt_importcsv_badheader' => "Zmylk: hłowa špalty $1, '$2', dyrbi pak '$3', '$4' być pak formu 'mjeno_předłohi[mjeno_pola]' měć", + 'right-datatransferimport' => 'Daty importować', +); + +/** Hungarian (Magyar) + * @author Dani + * @author Glanthor Reviol + */ +$messages['hu'] = array( + 'datatransfer-desc' => 'Lehetővé teszi a sablonhívásokban található adatok importálását és exportálását', + 'viewxml' => 'XML megtekintése', + 'dt_viewxml_docu' => 'Válaszd ki a kategóriák és a névterek közül azt, amelyiket meg akarod tekinteni XML formátumban.', + 'dt_viewxml_categories' => 'Kategóriák', + 'dt_viewxml_namespaces' => 'Névterek', + 'dt_viewxml_simplifiedformat' => 'Egyszerűsített formátum', + 'dt_xml_namespace' => 'Névtér', + 'dt_xml_pages' => 'Lapok', + 'dt_xml_page' => 'Lap', + 'dt_xml_template' => 'Sablon', + 'dt_xml_field' => 'Mező', + 'dt_xml_name' => 'Név', + 'dt_xml_title' => 'Cím', + 'dt_xml_id' => 'Azonosító', + 'dt_xml_freetext' => 'Szabad szöveg', + 'importxml' => 'XML importálás', + 'dt_import_selectfile' => 'Kérlek válaszd ki az importálandó $1 fájlt:', + 'dt_import_encodingtype' => 'Kódolás típusa:', + 'dt_import_summarydesc' => 'Az importálás összefoglalója:', + 'dt_import_editsummary' => '$1 importálás', + 'dt_import_importing' => 'Importálás…', + 'dt_import_success' => '{{PLURAL:$1|egy|$1}} lap fog készülni a(z) $2 fájlból.', + 'importcsv' => 'CSV importálása', + 'dt_importcsv_badheader' => 'Hiba: a(z) $1 oszlop fejlécének („$2”) vagy „$3”, „$4”, vagy pedig „sablonnév[mezőnév]” formátumúnak kell lennie', + 'right-datatransferimport' => 'Adatok importálása', +); + +/** Interlingua (Interlingua) + * @author McDutchie + */ +$messages['ia'] = array( + 'datatransfer-desc' => 'Permitte importar e exportar datos continite in appellos a patronos', + 'viewxml' => 'Vider XML', + 'dt_viewxml_docu' => 'Per favor selige inter le sequente categorias e spatios de nomines pro vider in formato XML.', + 'dt_viewxml_categories' => 'Categorias', + 'dt_viewxml_namespaces' => 'Spatios de nomines', + 'dt_viewxml_simplifiedformat' => 'Formato simplificate', + 'dt_xml_namespace' => 'Spatio de nomines', + 'dt_xml_pages' => 'Paginas', + 'dt_xml_page' => 'Pagina', + 'dt_xml_template' => 'Patrono', + 'dt_xml_field' => 'Campo', + 'dt_xml_name' => 'Nomine', + 'dt_xml_title' => 'Titulo', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Texto libere', + 'importxml' => 'Importar XML', + 'dt_import_selectfile' => 'Per favor selige le file $1 a importar:', + 'dt_import_encodingtype' => 'Typo de codification:', + 'dt_import_forexisting' => 'Pro paginas que ja existe:', + 'dt_import_overwriteexisting' => 'Superscriber le contento existente', + 'dt_import_skipexisting' => 'Saltar', + 'dt_import_appendtoexisting' => 'Adjunger al contento existente', + 'dt_import_summarydesc' => 'Summario de importation:', + 'dt_import_editsummary' => 'Importation de $1', + 'dt_import_importing' => 'Importation in curso…', + 'dt_import_success' => '$1 {{PLURAL:$1|pagina|paginas}} essera create ex le file $2.', + 'importcsv' => 'Importar CSV', + 'dt_importcsv_badheader' => "Error: le capite del columna $1, '$2', debe esser '$3', '$4' o in le forma 'nomine_de_patrono[nomine_de_campo]'", + 'right-datatransferimport' => 'Importar datos', +); + +/** Indonesian (Bahasa Indonesia) + * @author Bennylin + * @author Farras + * @author Irwangatot + * @author IvanLanin + * @author Rex + */ +$messages['id'] = array( + 'datatransfer-desc' => 'Membolehkan untuk impor dan ekspor data diisikan pada pemangilan templat', + 'viewxml' => 'Tilik XML', + 'dt_viewxml_docu' => 'Silakan pilih di antara kategori dan ruang nama berikut untuk melihat dalam format XML', + 'dt_viewxml_categories' => 'Kategori', + 'dt_viewxml_namespaces' => 'Ruang nama', + 'dt_viewxml_simplifiedformat' => 'Penyederhanaan format', + 'dt_xml_namespace' => 'Ruang nama', + 'dt_xml_pages' => 'Halaman', + 'dt_xml_page' => 'Halaman', + 'dt_xml_template' => 'Templat', + 'dt_xml_field' => 'Ruas', + 'dt_xml_name' => 'Nama', + 'dt_xml_title' => 'Judul', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Teks Gratis', + 'importxml' => 'Impor XML', + 'dt_import_selectfile' => 'Pilih berkas $1 untuk di impor:', + 'dt_import_encodingtype' => 'Tipe penyandian:', + 'dt_import_forexisting' => 'Untuk halaman yang sudah ada:', + 'dt_import_overwriteexisting' => 'Menimpa konten yang ada', + 'dt_import_skipexisting' => 'Lewati', + 'dt_import_appendtoexisting' => 'Tambahkan kepada konten yang ada', + 'dt_import_summarydesc' => 'Ringkasan impor:', + 'dt_import_editsummary' => '$1 impor', + 'dt_import_importing' => 'Mengimpor...', + 'dt_import_success' => '$1 {{PLURAL:$1|halaman|halaman}} akan di buat dari berkas $2.', + 'importcsv' => 'Impor CSV', + 'dt_importcsv_badheader' => "Kesalahan: kepala kolom $1, '$2', harus berupa '$3', '$4' atau bentuk 'template_name [field_name]'", + 'right-datatransferimport' => 'Impor data', +); + +/** Igbo (Igbo) + * @author Ukabia + */ +$messages['ig'] = array( + 'dt_viewxml_categories' => 'Ébéanọr', + 'dt_xml_template' => 'Àtụ', +); + +/** Ido (Ido) + * @author Malafaya + */ +$messages['io'] = array( + 'dt_xml_template' => 'Shablono', + 'dt_xml_name' => 'Nomo', + 'dt_xml_title' => 'Titulo', +); + +/** Icelandic (Íslenska) + * @author S.Örvarr.S + */ +$messages['is'] = array( + 'dt_viewxml_namespaces' => 'Nafnrými', + 'dt_xml_page' => 'Síða', +); + +/** Italian (Italiano) + * @author Beta16 + * @author BrokenArrow + * @author Darth Kule + */ +$messages['it'] = array( + 'datatransfer-desc' => "Permette l'importazione e l'esportazione di dati strutturati contenuti in chiamate a template", + 'viewxml' => 'Vedi XML', + 'dt_viewxml_docu' => 'Selezionare tra le categorie e namespace indicati di seguito quelli da visualizzare in formato XML.', + 'dt_viewxml_categories' => 'Categorie', + 'dt_viewxml_namespaces' => 'Namespace', + 'dt_viewxml_simplifiedformat' => 'Formato semplificato', + 'dt_xml_namespace' => 'Namespace', + 'dt_xml_pages' => 'Pagine', + 'dt_xml_page' => 'Pagina', + 'dt_xml_template' => 'Template', + 'dt_xml_field' => 'Campo', + 'dt_xml_name' => 'Nome', + 'dt_xml_title' => 'Titolo', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Testo libero', + 'dt_import_encodingtype' => 'Tipo di codifica', + 'right-datatransferimport' => 'Importa dati', +); + +/** Japanese (日本語) + * @author Aotake + * @author Fryed-peach + * @author JtFuruhata + * @author Ohgi + * @author 青子守歌 + */ +$messages['ja'] = array( + 'datatransfer-desc' => 'テンプレート呼び出しに関わるデータのインポートおよびエクスポートを可能にする', + 'viewxml' => 'XML表示', + 'dt_viewxml_docu' => 'XML形式で表示するカテゴリや名前空間を以下から選択してください。', + 'dt_viewxml_categories' => 'カテゴリ', + 'dt_viewxml_namespaces' => '名前空間', + 'dt_viewxml_simplifiedformat' => '簡易形式', + 'dt_xml_namespace' => '名前空間', + 'dt_xml_pages' => 'ページ群', + 'dt_xml_page' => 'ページ', + 'dt_xml_template' => 'テンプレート', + 'dt_xml_field' => 'フィールド', + 'dt_xml_name' => '名前', + 'dt_xml_title' => 'タイトル', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => '自由形式テキスト', + 'importxml' => 'XMLインポート', + 'dt_import_selectfile' => 'インポートする $1 ファイルを選択してください:', + 'dt_import_encodingtype' => 'エンコーディング方式:', + 'dt_import_forexisting' => 'すでに存在するページの場合：', + 'dt_import_overwriteexisting' => '既存の内容に上書き', + 'dt_import_skipexisting' => 'スキップ', + 'dt_import_appendtoexisting' => '既存の内容に追加', + 'dt_import_summarydesc' => '移入の概要：', + 'dt_import_editsummary' => '$1 のインポート', + 'dt_import_importing' => 'インポート中…', + 'dt_import_success' => '$2ファイルから$1{{PLURAL:$1|ページ}}がインポートされます。', + 'importcsv' => 'CSVのインポート', + 'dt_importcsv_badheader' => 'エラー: 列 $1 のヘッダ「$2」は、「$3」もしくは「$4」であるか、または「テンプレート名[フィールド名]」という形式になっていなければなりません。', + 'right-datatransferimport' => 'データをインポートする', +); + +/** Javanese (Basa Jawa) + * @author Meursault2004 + */ +$messages['jv'] = array( + 'viewxml' => 'Ndeleng XML', + 'dt_viewxml_categories' => 'Kategori-kategori', + 'dt_viewxml_simplifiedformat' => 'Format prasaja', + 'dt_xml_namespace' => 'Bilik nama', + 'dt_xml_page' => 'Kaca', + 'dt_xml_name' => 'Jeneng', + 'dt_xml_title' => 'Irah-irahan (judhul)', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Tèks Bébas', +); + +/** Khmer (ភាសាខ្មែរ) + * @author Chhorran + * @author Lovekhmer + * @author Thearith + * @author គីមស៊្រុន + * @author វ័ណថារិទ្ធ + */ +$messages['km'] = array( + 'viewxml' => 'មើល XML', + 'dt_viewxml_docu' => 'ជ្រើសយកក្នុងចំណោមចំណាត់ថ្នាក់ក្រុមនិងលំហឈ្មោះដើម្បីមើលជាទម្រង់ XML ។', + 'dt_viewxml_categories' => 'ចំណាត់ថ្នាក់ក្រុម', + 'dt_viewxml_namespaces' => 'ប្រភេទ', + 'dt_viewxml_simplifiedformat' => 'ទម្រង់សាមញ្ញ', + 'dt_xml_namespace' => 'ប្រភេទ', + 'dt_xml_pages' => 'ទំព័រ', + 'dt_xml_page' => 'ទំព័រ', + 'dt_xml_template' => 'ទំព័រគំរូ', + 'dt_xml_field' => 'ផ្នែក', + 'dt_xml_name' => 'ឈ្មោះ', + 'dt_xml_title' => 'ចំណងជើង', + 'dt_xml_id' => 'អត្តសញ្ញាណ', + 'dt_xml_freetext' => 'អត្ថបទសេរី', + 'importxml' => 'នាំចូល XML', + 'dt_import_selectfile' => 'សូម​ជ្រើស​រើស​ឯកសារ $1 ដើម្បី​នាំ​ចូល​៖', + 'dt_import_encodingtype' => 'ប្រភេទនៃការធ្វើកូដ៖', + 'dt_import_forexisting' => 'សំរាប់ទំព័រដែលមានរួចហើយ៖', + 'dt_import_overwriteexisting' => 'សរសេរជាន់ពីលើខ្លឹមសារដែលមានហើយ', + 'dt_import_skipexisting' => 'រំលង', + 'dt_import_appendtoexisting' => 'សរសេរបន្ថែមទៅលើខ្លឹមសារដែលមានហើយ', + 'dt_import_summarydesc' => 'ចំណារពន្យល់ស្ដីពីការនាំចូល៖', + 'dt_import_editsummary' => '$1 នាំចូល​', + 'dt_import_importing' => 'កំពុងនាំចូល​...', + 'dt_import_success' => 'ទំព័រចំនួន $1 នឹងត្រូវបានបង្កើតពីឯកសារ $2 នេះ។', + 'importcsv' => 'នាំចូល CSV', + 'right-datatransferimport' => 'នាំចូល​ទិន្នន័យ​', +); + +/** Kannada (ಕನ್ನಡ) + * @author Nayvik + */ +$messages['kn'] = array( + 'dt_viewxml_categories' => 'ವರ್ಗಗಳು', + 'dt_xml_namespace' => 'ನಾಮವರ್ಗ', + 'dt_xml_pages' => 'ಪುಟಗಳು', + 'dt_xml_page' => 'ಪುಟ', + 'dt_xml_template' => 'ಟೆಂಪ್ಲೇಟು', + 'dt_xml_name' => 'ಹೆಸರು', + 'dt_xml_title' => 'ಶೀರ್ಷಿಕೆ', +); + +/** Kinaray-a (Kinaray-a) + * @author Jose77 + */ +$messages['krj'] = array( + 'dt_viewxml_categories' => 'Manga Kategorya', + 'dt_xml_page' => 'Pahina', +); + +/** Colognian (Ripoarisch) + * @author Purodha + */ +$messages['ksh'] = array( + 'datatransfer-desc' => 'Määt et müjjelesch, Date uß Schabloone ier Oproofe ze emporteere un ze exporteere.', + 'viewxml' => 'XML beloore', + 'dt_viewxml_docu' => 'Don ußsöke, wat fö_n Saachjruppe un Appachtemangs De em XML Fommaat aanloore wells.', + 'dt_viewxml_categories' => 'Saachjroppe', + 'dt_viewxml_namespaces' => 'Appachtemangs', + 'dt_viewxml_simplifiedformat' => 'Em eijfachere Fommaat', + 'dt_xml_namespace' => 'Appachtemang', + 'dt_xml_pages' => 'Sigge', + 'dt_xml_page' => 'Sigg', + 'dt_xml_template' => 'Schablohn', + 'dt_xml_field' => 'Felldt', + 'dt_xml_name' => 'Name', + 'dt_xml_title' => 'Tėttel', + 'dt_xml_id' => 'Kännong', + 'dt_xml_freetext' => 'Freije Täx', + 'importxml' => 'XML Empotteere', + 'dt_import_selectfile' => 'Söhk de $1-Dattei för zem Empotteere uß:', + 'dt_import_encodingtype' => 'Zoot Kodeerung för de Bohchshtahbe un Zeishe:', + 'dt_import_forexisting' => 'För Sigge, di et ald jitt:', + 'dt_import_overwriteexisting' => 'Övverschrieve, wat ald doh es', + 'dt_import_skipexisting' => 'Övverjonn', + 'dt_import_appendtoexisting' => 'An dat aanhange, wat ald doh es', + 'dt_import_summarydesc' => 'Zesammefassung vun däm Empoot:', + 'dt_import_editsummary' => 'uss ene $1-Datei empotteet', + 'dt_import_importing' => 'Ben aam Empotteere{{int:Ellipsis}}', + 'dt_import_success' => '{{PLURAL:$1|Ein Sigg weed_uß|$1 Sigge weede uß|Kein einzelne Sigg weed_uß}} dä $2-Dattei empotteet.', + 'importcsv' => 'CSV-Dattei empoteere', + 'dt_importcsv_badheader' => 'Fähler: De Shpallde-Övverschreff för $1 es „$2“, mööt ävver „$3“ udder „$4“ sin, udder dat Fommaat „Name_vun_ene_Schablohn[Name_vun_enem_Felldt]“ han.', + 'right-datatransferimport' => 'Daate empoteere', +); + +/** Kurdish (Latin) (Kurdî (Latin)) + * @author George Animal + */ +$messages['ku-latn'] = array( + 'dt_xml_page' => 'Rûpel', + 'dt_xml_name' => 'Nav', + 'dt_xml_title' => 'Sernav', + 'dt_import_summarydesc' => 'Kurteya împortê:', +); + +/** Cornish (Kernowek) + * @author Kernoweger + * @author Kw-Moon + */ +$messages['kw'] = array( + 'dt_viewxml_categories' => 'Classys', + 'dt_xml_page' => 'Folen', +); + +/** Luxembourgish (Lëtzebuergesch) + * @author Robby + */ +$messages['lb'] = array( + 'datatransfer-desc' => "Erlaabt et Daten déi an Opruffer vu schabloune benotzt ginn z'importéieren an z'exportéieren", + 'viewxml' => 'XML weisen', + 'dt_viewxml_docu' => 'Wielt w.e.g. ënnert dëse Kategorien an Nimmraim fir am XML-Format unzeweisen.', + 'dt_viewxml_categories' => 'Kategorien', + 'dt_viewxml_namespaces' => 'Nummraim', + 'dt_viewxml_simplifiedformat' => 'Vereinfachte Format', + 'dt_xml_namespace' => 'Nummraum', + 'dt_xml_pages' => 'Säiten', + 'dt_xml_page' => 'Säit', + 'dt_xml_template' => 'Schabloun', + 'dt_xml_field' => 'Feld', + 'dt_xml_name' => 'Numm', + 'dt_xml_title' => 'Titel', + 'dt_xml_id' => 'Nummer', + 'dt_xml_freetext' => 'Fräien Text', + 'importxml' => 'XML importéieren', + 'dt_import_selectfile' => "Sicht de(n) $1-Fichier eraus fir z'importéieren:", + 'dt_import_encodingtype' => 'Encoding-Typ:', + 'dt_import_forexisting' => 'Fir Säiten déi et scho gëtt:', + 'dt_import_overwriteexisting' => 'Den Inhalt den et gëtt iwwerschreiwen', + 'dt_import_skipexisting' => 'Iwwersprangen', + 'dt_import_appendtoexisting' => 'Bäi den Inhalt deen et gëtt derbäisetzen', + 'dt_import_summarydesc' => 'Resumé vum Import:', + 'dt_import_editsummary' => '$1 importéieren', + 'dt_import_importing' => 'Import am gaang ...', + 'dt_import_success' => '$1 {{PLURAL:$1|Säit gëtt|Säite ginn}} aus dem $2-Fichier ugeluecht.', + 'importcsv' => 'CSV importéieren', + 'dt_importcsv_badheader' => "Feeler: D'Iwwerschrëft vun der Kolonn $1, '$2', muss entweder '$3', '$4' oder am Format 'Numm_vun_der_Schabloun(Numm_vum_Feld)' sinn", + 'right-datatransferimport' => 'Donnéeën importéieren', +); + +/** Limburgish (Limburgs) + * @author Aelske + * @author Remember the dot + */ +$messages['li'] = array( + 'dt_xml_page' => 'Pagina', +); + +/** Lithuanian (Lietuvių) + * @author Tomasdd + */ +$messages['lt'] = array( + 'dt_viewxml_categories' => 'Kategorijos', +); + +/** Latgalian (Latgaļu) + * @author Dark Eagle + */ +$messages['ltg'] = array( + 'dt_viewxml_namespaces' => 'Vuordu pluoti', + 'dt_xml_namespace' => 'Vuordu pluots', + 'dt_xml_pages' => 'Puslopys', +); + +/** Latvian (Latviešu) + * @author GreenZeb + */ +$messages['lv'] = array( + 'dt_viewxml_categories' => 'Kategorijas', + 'dt_viewxml_namespaces' => 'Vārdtelpas', + 'dt_viewxml_simplifiedformat' => 'Vienkāršots formāts', + 'dt_xml_namespace' => 'Vārdtelpa', + 'dt_xml_pages' => 'Lapas', + 'dt_xml_page' => 'Lapa', + 'dt_xml_template' => 'Veidne', + 'dt_xml_field' => 'Lauks', + 'dt_xml_name' => 'Vārds', + 'dt_xml_title' => 'Nosaukums', + 'dt_xml_id' => 'ID', +); + +/** Eastern Mari (Олык Марий) + * @author Сай + */ +$messages['mhr'] = array( + 'dt_xml_namespace' => 'Лӱм-влакын кумдыкышт', + 'dt_xml_page' => 'Лаштык', +); + +/** Macedonian (Македонски) + * @author Bjankuloski06 + */ +$messages['mk'] = array( + 'datatransfer-desc' => 'Овозможува увоз и извоз на податоци содржани во повикувањата на шаблоните', + 'viewxml' => 'Преглед на XML', + 'dt_viewxml_docu' => 'Одберете од следиве категории и именски простори за преглед во XML формат.', + 'dt_viewxml_categories' => 'Категории', + 'dt_viewxml_namespaces' => 'Именски простори', + 'dt_viewxml_simplifiedformat' => 'Упростен формат', + 'dt_xml_namespace' => 'Именски простор', + 'dt_xml_pages' => 'Страници', + 'dt_xml_page' => 'Страница', + 'dt_xml_template' => 'Шаблон', + 'dt_xml_field' => 'Поле', + 'dt_xml_name' => 'Име', + 'dt_xml_title' => 'Наслов', + 'dt_xml_id' => 'ид. бр.', + 'dt_xml_freetext' => 'Слободен текст', + 'importxml' => 'Увоз на XML', + 'dt_import_selectfile' => 'Одберете ја $1 податотеката за увоз:', + 'dt_import_encodingtype' => 'Тип на кодирање:', + 'dt_import_forexisting' => 'За страници што веќе постојат:', + 'dt_import_overwriteexisting' => 'Презапиши врз постоечките содржини', + 'dt_import_skipexisting' => 'Прескокни', + 'dt_import_appendtoexisting' => 'Додај во постоечката содржина', + 'dt_import_summarydesc' => 'Опис на увозот:', + 'dt_import_editsummary' => 'Увоз на $1', + 'dt_import_importing' => 'Увезувам...', + 'dt_import_success' => '$1 {{PLURAL:$1|страница ќе биде создадена|страници ќе бидат создадени}} од $2 податотеката.', + 'importcsv' => 'Увоз на CSV', + 'dt_importcsv_badheader' => 'Грешка: насловот на колона $1, „$2“, мора да биде или „$3“, или „$4“, или пак од обликот „template_name[field_name]“', + 'right-datatransferimport' => 'Увезување податоци', +); + +/** Malayalam (മലയാളം) + * @author Junaidpv + * @author Praveenp + * @author Shijualex + */ +$messages['ml'] = array( + 'viewxml' => 'XML കാണുക', + 'dt_viewxml_categories' => 'വർഗ്ഗങ്ങൾ', + 'dt_viewxml_namespaces' => 'നാമമേഖലകൾ', + 'dt_viewxml_simplifiedformat' => 'ലളിതവത്ക്കരിക്കപ്പെട്ട ഫോർമാറ്റ്', + 'dt_xml_namespace' => 'നാമമേഖല', + 'dt_xml_pages' => 'താളുകൾ', + 'dt_xml_page' => 'താൾ', + 'dt_xml_template' => 'ഫലകം', + 'dt_xml_field' => 'ഫീൽഡ്', + 'dt_xml_name' => 'പേര്‌', + 'dt_xml_title' => 'ശീർഷകം', + 'dt_xml_id' => 'ഐ.ഡി.', + 'dt_xml_freetext' => 'സ്വതന്ത്ര എഴുത്ത്', + 'importxml' => 'എക്സ്.എം.എൽ. ഇറക്കുമതി', + 'dt_import_selectfile' => 'ദയവായി ഇറക്കുമതിക്കായി $1 പ്രമാണം തിരഞ്ഞെടുക്കുക:', + 'dt_import_encodingtype' => 'എൻ‌കോഡിങ് തരം:', + 'dt_import_forexisting' => 'നിലവിലുള്ള താളുകൾക്ക് വേണ്ടി:', + 'dt_import_appendtoexisting' => 'നിലവിലുള്ള ഉള്ളടക്കത്തോട് കൂട്ടിച്ചേർക്കുക', + 'dt_import_summarydesc' => 'ഇറക്കുമതിയുടെ സംഗ്രഹം:', + 'dt_import_editsummary' => '$1 ഇറക്കുമതി', + 'dt_import_importing' => 'ഇറക്കുമതി ചെയ്യുന്നു...', + 'importcsv' => 'സി.എസ്.വി. ഇറക്കുമതി', +); + +/** Mongolian (Монгол) + * @author Chinneeb + */ +$messages['mn'] = array( + 'dt_viewxml_categories' => 'Ангиллууд', + 'dt_viewxml_namespaces' => 'Нэрний зайнууд', + 'dt_xml_namespace' => 'Нэрний зай', + 'dt_xml_page' => 'Хуудас', +); + +/** Marathi (मराठी) + * @author Kaustubh + * @author V.narsikar + */ +$messages['mr'] = array( + 'datatransfer-desc' => 'साचा कॉल मध्ये असणार्‍या डाटाची आयात निर्यात करण्याची परवानगी देतो', + 'viewxml' => 'XML पहा', + 'dt_viewxml_docu' => 'कॄपया XML मध्ये पाहण्यासाठी खालीलपैकी वर्ग व नामविश्वे निवडा.', + 'dt_viewxml_categories' => 'वर्ग', + 'dt_viewxml_namespaces' => 'नामविश्वे', + 'dt_viewxml_simplifiedformat' => 'सोप्या प्रकारे', + 'dt_xml_namespace' => 'नामविश्व', + 'dt_xml_page' => 'पान', + 'dt_xml_field' => 'रकाना', + 'dt_xml_name' => 'नाव', + 'dt_xml_title' => 'शीर्षक', + 'dt_xml_id' => 'क्रमांक (आयडी)', + 'dt_xml_freetext' => 'मुक्त मजकूर', + 'importxml' => 'एक्सएमएल आयात करा', +); + +/** Mirandese (Mirandés) + * @author Malafaya + */ +$messages['mwl'] = array( + 'dt_xml_page' => 'Páigina', +); + +/** Erzya (Эрзянь) + * @author Botuzhaleny-sodamo + */ +$messages['myv'] = array( + 'dt_viewxml_categories' => 'Категорият', + 'dt_viewxml_namespaces' => 'Лем потмот', + 'dt_xml_page' => 'Лопа', + 'dt_xml_template' => 'Лопа парцун', + 'dt_xml_field' => 'Пакся', + 'dt_xml_name' => 'Лемезэ', + 'dt_xml_title' => 'Конякс', +); + +/** Mazanderani (مازِرونی) + * @author محک + */ +$messages['mzn'] = array( + 'dt_viewxml_categories' => 'رج‌ئون', +); + +/** Nahuatl (Nāhuatl) + * @author Fluence + */ +$messages['nah'] = array( + 'dt_viewxml_categories' => 'Neneuhcāyōtl', + 'dt_viewxml_namespaces' => 'Tōcātzin', + 'dt_xml_namespace' => 'Tōcātzin', + 'dt_xml_page' => 'Zāzanilli', + 'dt_xml_name' => 'Tōcāitl', + 'dt_xml_title' => 'Tōcāitl', + 'dt_xml_id' => 'ID', +); + +/** Low German (Plattdüütsch) + * @author Slomox + */ +$messages['nds'] = array( + 'dt_xml_name' => 'Naam', +); + +/** Dutch (Nederlands) + * @author Siebrand + * @author Tvdm + */ +$messages['nl'] = array( + 'datatransfer-desc' => 'Maakt het importeren en exporteren van gestructureerde gegevens in sjabloonaanroepen mogelijk', + 'viewxml' => 'XML bekijken', + 'dt_viewxml_docu' => 'Selecteer uit de volgende categorieën en naamruimten om in XML-formaat te bekijken.', + 'dt_viewxml_categories' => 'Categorieën', + 'dt_viewxml_namespaces' => 'Naamruimten', + 'dt_viewxml_simplifiedformat' => 'Vereenvoudigd formaat', + 'dt_xml_namespace' => 'Naamruimte', + 'dt_xml_pages' => "Pagina's", + 'dt_xml_page' => 'Pagina', + 'dt_xml_template' => 'Sjabloon', + 'dt_xml_field' => 'Veld', + 'dt_xml_name' => 'Naam', + 'dt_xml_title' => 'Titel', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Vrije tekst', + 'importxml' => 'XML importeren', + 'dt_import_selectfile' => 'Selecteer het te importeren bestand van het type $1:', + 'dt_import_encodingtype' => 'Coderingstype:', + 'dt_import_forexisting' => "Voor pagina's die al bestaan:", + 'dt_import_overwriteexisting' => 'Bestaande inhoud overschrijven', + 'dt_import_skipexisting' => 'Overslaan', + 'dt_import_appendtoexisting' => 'Toevoegen aan bestaande inhoud', + 'dt_import_summarydesc' => 'Samenvatting van de import:', + 'dt_import_editsummary' => '$1-import', + 'dt_import_importing' => 'Bezig met importeren…', + 'dt_import_success' => "Uit het $2-bestand {{PLURAL:$1|wordt één pagina|worden $1 pagina's}} geïmporteerd.", + 'importcsv' => 'CSV importeren', + 'dt_importcsv_badheader' => 'Fout: De kop van kolom $1, "$2", moet "$3" of "$4" zijn, of in de vorm "sjabloonnaam[veldnaam]" genoteerd worden.', + 'right-datatransferimport' => 'Gegevens importeren', +); + +/** Norwegian Nynorsk (‪Norsk (nynorsk)‬) + * @author Gunnernett + * @author Harald Khan + * @author Jon Harald Søby + */ +$messages['nn'] = array( + 'datatransfer-desc' => 'Gjer det mogleg å importera og eksportera data i maloppkallingar', + 'viewxml' => 'Syn XML', + 'dt_viewxml_docu' => 'Vel mellom følgjande kategoriar og namnerom for å syna dei i XML-format.', + 'dt_viewxml_categories' => 'Kategoriar', + 'dt_viewxml_namespaces' => 'Namnerom', + 'dt_viewxml_simplifiedformat' => 'Forenkla format', + 'dt_xml_namespace' => 'Namnerom', + 'dt_xml_pages' => 'Sider', + 'dt_xml_page' => 'Side', + 'dt_xml_template' => 'Mal', + 'dt_xml_field' => 'Felt', + 'dt_xml_name' => 'Namn', + 'dt_xml_title' => 'Tittel', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Fritekst', + 'importxml' => 'Importer XML', + 'dt_import_selectfile' => 'Ver venleg og vel $1-fila som skal verta importert:', + 'dt_import_encodingtype' => 'Teiknkodingstype:', + 'dt_import_editsummary' => '$1-importering', + 'dt_import_importing' => 'Importerer...', + 'dt_import_success' => '$1 {{PLURAL:$1|Éi side vil verta importert|$1 sider vil verta importerte}} frå $2-fila.', + 'importcsv' => 'Importer CSV', + 'dt_importcsv_badheader' => "Feil: kolonneoverskrifta $1, '$2', må vera anten '$3', '$4' eller på forma 'malnamn[feltnamn]'", + 'right-datatransferimport' => 'Importer data', +); + +/** Norwegian (bokmål)‬ (‪Norsk (bokmål)‬) + * @author Jon Harald Søby + * @author Nghtwlkr + */ +$messages['no'] = array( + 'datatransfer-desc' => 'Gjør det mulig å importere og eksportere data som finnes i maloppkallinger', + 'viewxml' => 'Se XML', + 'dt_viewxml_docu' => 'Velg blant følgende kategorier og navnerom for å se dem i XML-format', + 'dt_viewxml_categories' => 'Kategorier', + 'dt_viewxml_namespaces' => 'Navnerom', + 'dt_viewxml_simplifiedformat' => 'Forenklet format', + 'dt_xml_namespace' => 'Navnerom', + 'dt_xml_pages' => 'Sider', + 'dt_xml_page' => 'Side', + 'dt_xml_template' => 'Mal', + 'dt_xml_field' => 'Felt', + 'dt_xml_name' => 'Navn', + 'dt_xml_title' => 'Tittel', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Fritekst', + 'importxml' => 'Importer XML', + 'dt_import_selectfile' => 'Vennligst velg $1-filen som skal importeres:', + 'dt_import_encodingtype' => 'Tegnkodingstype:', + 'dt_import_forexisting' => 'For sider som allerede finnes:', + 'dt_import_overwriteexisting' => 'Skriv over eksisterende innhold', + 'dt_import_skipexisting' => 'Hopp over', + 'dt_import_appendtoexisting' => 'Tilføy til eksisterende innhold', + 'dt_import_summarydesc' => 'Importsammendrag:', + 'dt_import_editsummary' => '$1-importering', + 'dt_import_importing' => 'Importerer...', + 'dt_import_success' => '{{PLURAL:$1|Én side|$1 sider}} vil bli importert fra $2-filen.', + 'importcsv' => 'Importer CSV', + 'dt_importcsv_badheader' => "Feil: kolonneoverskriften $1, '$2', må være enten '$3', '$4' eller på formen 'malnavn[feltnavn]'", + 'right-datatransferimport' => 'Importer data', +); + +/** Occitan (Occitan) + * @author Cedric31 + */ +$messages['oc'] = array( + 'datatransfer-desc' => "Permet l’impòrt e l’expòrt de donadas contengudas dins d'apèls de modèls", + 'viewxml' => 'Veire XML', + 'dt_viewxml_docu' => 'Seleccionatz demest las categorias e los espacis de nomenatges per visionar en format XML.', + 'dt_viewxml_categories' => 'Categorias', + 'dt_viewxml_namespaces' => 'Espacis de nomenatge', + 'dt_viewxml_simplifiedformat' => 'Format simplificat', + 'dt_xml_namespace' => 'Espaci de nom', + 'dt_xml_pages' => 'Paginas', + 'dt_xml_page' => 'Pagina', + 'dt_xml_template' => 'Modèl', + 'dt_xml_field' => 'Camp', + 'dt_xml_name' => 'Nom', + 'dt_xml_title' => 'Títol', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Tèxte Liure', + 'importxml' => 'Impòrt en XML', + 'dt_import_selectfile' => "Seleccionatz lo fichièr $1 d'importar :", + 'dt_import_encodingtype' => 'Tipe d’encodatge:', + 'dt_import_editsummary' => 'Importacion $1', + 'dt_import_importing' => 'Impòrt en cors...', + 'dt_import_success' => '$1 {{PLURAL:$1|pagina serà creada|paginas seràn creadas}} dempuèi lo fichièr $2.', + 'importcsv' => 'Impòrt CSV', + 'dt_importcsv_badheader' => 'Error : lo títol de colomna $1, « $2 », deu èsser siá « $3 », « $4 » o de la forma « nom_del_modèl[nom_del_camp] »', + 'right-datatransferimport' => 'Importar de donadas', +); + +/** Ossetic (Иронау) + * @author Amikeco + */ +$messages['os'] = array( + 'dt_xml_page' => 'Фарс', + 'dt_xml_template' => 'Шаблон', + 'dt_xml_title' => 'Сæргонд', +); + +/** Deitsch (Deitsch) + * @author Xqt + */ +$messages['pdc'] = array( + 'dt_viewxml_categories' => 'Abdeelinge', + 'dt_viewxml_namespaces' => 'Blatznaame', + 'dt_xml_namespace' => 'Blatznaame', + 'dt_xml_pages' => 'Bledder', + 'dt_xml_page' => 'Blatt', + 'dt_xml_template' => 'Moddel', + 'dt_xml_name' => 'Naame', + 'dt_xml_title' => 'Titel', +); + +/** Polish (Polski) + * @author McMonster + * @author Sp5uhe + * @author Wpedzich + */ +$messages['pl'] = array( + 'datatransfer-desc' => 'Pozwala na importowanie i eksportowanie danych zawartych w wywołaniach szablonu', + 'viewxml' => 'Podgląd XML', + 'dt_viewxml_docu' => 'Wybierz, które spośród następujących kategorii i przestrzeni nazw chcesz podejrzeć w formacie XML.', + 'dt_viewxml_categories' => 'Kategorie', + 'dt_viewxml_namespaces' => 'Przestrzenie nazw', + 'dt_viewxml_simplifiedformat' => 'Format uproszczony', + 'dt_xml_namespace' => 'Przestrzeń nazw', + 'dt_xml_pages' => 'Strony', + 'dt_xml_page' => 'Strona', + 'dt_xml_template' => 'Szablon', + 'dt_xml_field' => 'Pole', + 'dt_xml_name' => 'Nazwa', + 'dt_xml_title' => 'Tytuł', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Dowolny tekst', + 'importxml' => 'Import XML', + 'dt_import_selectfile' => 'Wybierz plik $1 do zaimportowania', + 'dt_import_encodingtype' => 'Typ kodowania', + 'dt_import_forexisting' => 'Dla stron, które już istnieją:', + 'dt_import_overwriteexisting' => 'Zastąp istniejącą zawartość', + 'dt_import_skipexisting' => 'Pomiń', + 'dt_import_appendtoexisting' => 'Dołącz do istniejącej zawartości', + 'dt_import_summarydesc' => 'Podsumowanie importu', + 'dt_import_editsummary' => 'Import $1', + 'dt_import_importing' => 'Importowanie...', + 'dt_import_success' => '$1 {{PLURAL:$1|strona zostanie utworzona|strony zostaną utworzone|stron zostanie utworzonych}} z pliku $2.', + 'importcsv' => 'Import CSV', + 'dt_importcsv_badheader' => 'Błąd – w kolumnie $1 nagłówka jest „$2”, a powinno być: „$3”, „$4” lub „nazwa_szablonu[nazwa_pola]”', + 'right-datatransferimport' => 'Importowanie danych', +); + +/** Piedmontese (Piemontèis) + * @author Borichèt + * @author Dragonòt + */ +$messages['pms'] = array( + 'datatransfer-desc' => "A përmëtt d'amporté e esporté ij dat contnù ant le ciamà a stamp", + 'viewxml' => 'Varda XML', + 'dt_viewxml_docu' => 'Për piasì selession-a an tra le categorìe sota e jë spassi nominaj për vëdde an formà XLM.', + 'dt_viewxml_categories' => 'Categorìe', + 'dt_viewxml_namespaces' => 'Spassi nominaj', + 'dt_viewxml_simplifiedformat' => 'Formà semplificà', + 'dt_xml_namespace' => 'Spassi nominal', + 'dt_xml_pages' => 'Pàgine', + 'dt_xml_page' => 'Pàgina', + 'dt_xml_template' => 'Stamp', + 'dt_xml_field' => 'Camp', + 'dt_xml_name' => 'Nòm', + 'dt_xml_title' => 'Tìtol', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Test lìber', + 'importxml' => 'Ampòrta XML', + 'dt_import_selectfile' => 'Për piasì selession-a ël file $1 da amporté:', + 'dt_import_encodingtype' => 'Tipo ëd codìfica:', + 'dt_import_forexisting' => "Për pàgine ch'a esisto già:", + 'dt_import_overwriteexisting' => 'Coaté ël contnù esistent', + 'dt_import_skipexisting' => 'Saoté', + 'dt_import_appendtoexisting' => 'Gionté al contnù esistent', + 'dt_import_summarydesc' => "Somari dj'amportassion:", + 'dt_import_editsummary' => '$1 ampòrta', + 'dt_import_importing' => "An camin ch'as ampòrta...", + 'dt_import_success' => "$1 {{PLURAL:$1|pàgina|pàgine}} a saran creà da l'archivi $2.", + 'importcsv' => 'Ampòrta CSV', + 'dt_importcsv_badheader' => "Eror: l'antestassion ëd la colòna $1, '$2', a deuv esse '$3', '$4' o ëd la forma 'template_name[field_name]'", + 'right-datatransferimport' => 'Ampòrta dat', +); + +/** Pashto (پښتو) + * @author Ahmed-Najib-Biabani-Ibrahimkhel + */ +$messages['ps'] = array( + 'dt_viewxml_categories' => 'وېشنيزې', + 'dt_viewxml_namespaces' => 'نوم-تشيالونه', + 'dt_xml_namespace' => 'نوم-تشيال', + 'dt_xml_pages' => 'مخونه', + 'dt_xml_page' => 'مخ', + 'dt_xml_template' => 'کينډۍ', + 'dt_xml_name' => 'نوم', + 'dt_xml_title' => 'سرليک', + 'dt_xml_freetext' => 'خپلواکه متن', +); + +/** Portuguese (Português) + * @author Hamilton Abreu + * @author Lijealso + * @author Malafaya + */ +$messages['pt'] = array( + 'datatransfer-desc' => 'Permite importação e exportação de dados contidos em chamadas de predefinições', + 'viewxml' => 'Ver XML', + 'dt_viewxml_docu' => 'Por favor, seleccione de entre as categorias e espaços nominais seguintes para ver em formato XML.', + 'dt_viewxml_categories' => 'Categorias', + 'dt_viewxml_namespaces' => 'Espaços nominais', + 'dt_viewxml_simplifiedformat' => 'Formato simplificado', + 'dt_xml_namespace' => 'Espaço nominal', + 'dt_xml_pages' => 'Páginas', + 'dt_xml_page' => 'Página', + 'dt_xml_template' => 'Predefinição', + 'dt_xml_field' => 'Campo', + 'dt_xml_name' => 'Nome', + 'dt_xml_title' => 'Título', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Texto Livre', + 'importxml' => 'Importar XML', + 'dt_import_selectfile' => 'Por favor, selecione o ficheiro $1 a importar:', + 'dt_import_encodingtype' => 'Tipo de codificação:', + 'dt_import_forexisting' => 'Para páginas que já existem:', + 'dt_import_overwriteexisting' => 'Sobrescrever o conteúdo existente', + 'dt_import_skipexisting' => 'Saltar', + 'dt_import_appendtoexisting' => 'Acrescentar ao conteúdo existente', + 'dt_import_summarydesc' => 'Resumo da importação:', + 'dt_import_editsummary' => 'Importação de $1', + 'dt_import_importing' => 'Importando...', + 'dt_import_success' => '{{PLURAL:$1|A página será importada|As páginas serão importadas}} a partir do ficheiro $2.', + 'importcsv' => 'Importar CSV', + 'dt_importcsv_badheader' => "Erro: o cabeçalho da coluna $1, '$2', deve ser '$3', '$4' ou ter a forma 'nome_da_predefinição[nome_do_campo]'", + 'right-datatransferimport' => 'Importar dados', +); + +/** Brazilian Portuguese (Português do Brasil) + * @author Eduardo.mps + * @author Giro720 + */ +$messages['pt-br'] = array( + 'datatransfer-desc' => 'Permite a importação e exportação de dados contidos em chamadas de predefinições', + 'viewxml' => 'Ver XML', + 'dt_viewxml_docu' => 'Por favor, selecione dentre as categorias e espaços nominais seguintes para ver em formato XML.', + 'dt_viewxml_categories' => 'Categorias', + 'dt_viewxml_namespaces' => 'Espaços nominais', + 'dt_viewxml_simplifiedformat' => 'Formato simplificado', + 'dt_xml_namespace' => 'Espaço nominal', + 'dt_xml_pages' => 'Páginas', + 'dt_xml_page' => 'Página', + 'dt_xml_template' => 'Predefinição', + 'dt_xml_field' => 'Campo', + 'dt_xml_name' => 'Nome', + 'dt_xml_title' => 'Título', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Texto Livre', + 'importxml' => 'Importar XML', + 'dt_import_selectfile' => 'Por favor selecione o arquivo $1 para importar:', + 'dt_import_encodingtype' => 'Codificação:', + 'dt_import_forexisting' => 'Para páginas que já existem:', + 'dt_import_overwriteexisting' => 'Sobrescrever o conteúdo existente', + 'dt_import_skipexisting' => 'Pular', + 'dt_import_appendtoexisting' => 'Adicionar ao conteúdo existente', + 'dt_import_summarydesc' => 'Resumo da importação:', + 'dt_import_editsummary' => 'Importação de $1', + 'dt_import_importing' => 'Importando...', + 'dt_import_success' => '$1 {{PLURAL:$1|página será importada|páginas serão importadas}} do arquivo $2.', + 'importcsv' => 'Importar CSV', + 'dt_importcsv_badheader' => "Erro: o cabeçalho da coluna $1, '$2', deve ser '$3', ou '$4' ou da forma 'nome_modelo[nome_campo]'", + 'right-datatransferimport' => 'Importar dados', +); + +/** Romanian (Română) + * @author KlaudiuMihaila + * @author Stelistcristi + */ +$messages['ro'] = array( + 'viewxml' => 'Vizualizează XML', + 'dt_viewxml_categories' => 'Categorii', + 'dt_viewxml_namespaces' => 'Spații de nume', + 'dt_viewxml_simplifiedformat' => 'Format simplificat', + 'dt_xml_namespace' => 'Spațiu de nume', + 'dt_xml_pages' => 'Pagini', + 'dt_xml_page' => 'Pagină', + 'dt_xml_template' => 'Format', + 'dt_xml_field' => 'Câmp', + 'dt_xml_name' => 'Nume', + 'dt_xml_title' => 'Titlu', + 'dt_xml_id' => 'ID', + 'importxml' => 'Importă XML', + 'dt_import_summarydesc' => 'Descrierea importului:', + 'dt_import_importing' => 'Importare...', + 'importcsv' => 'Importă CSV', + 'right-datatransferimport' => 'Importă date', +); + +/** Tarandíne (Tarandíne) + * @author Joetaras + */ +$messages['roa-tara'] = array( + 'datatransfer-desc' => "Permètte de 'mbortà e esportà date strutturate ca stonne jndr'à le chiamate a le template", + 'viewxml' => "Vide l'XML", + 'dt_viewxml_docu' => "Pe piacere scacchie ìmbrà le categorije seguende e le namespace seguende pe vedè 'u formate XML.", + 'dt_viewxml_categories' => 'Categorije', + 'dt_viewxml_namespaces' => 'Namespace', + 'dt_viewxml_simplifiedformat' => 'Formate semblifichete', + 'dt_xml_namespace' => 'Namespace', + 'dt_xml_pages' => 'Pàggene', + 'dt_xml_page' => 'Pàgene', + 'dt_xml_template' => 'Template', + 'dt_xml_field' => 'Cambe', + 'dt_xml_name' => 'Nome', + 'dt_xml_title' => 'Titele', + 'dt_xml_id' => 'Codece (ID)', + 'dt_xml_freetext' => 'Teste libbere', + 'importxml' => "'Mborte XML", +); + +/** Russian (Русский) + * @author Ferrer + * @author Innv + * @author Александр Сигачёв + */ +$messages['ru'] = array( + 'datatransfer-desc' => 'Позволяет импортировать и экспортировать данные, содержащиеся в вызовах шаблонов', + 'viewxml' => 'Просмотр XML', + 'dt_viewxml_docu' => 'Пожалуйста, выберите категории и пространства имён для просмотра в формате XML.', + 'dt_viewxml_categories' => 'Категории', + 'dt_viewxml_namespaces' => 'Пространства имён', + 'dt_viewxml_simplifiedformat' => 'Упрощённый формат', + 'dt_xml_namespace' => 'Пространство имён', + 'dt_xml_pages' => 'Страницы', + 'dt_xml_page' => 'Страница', + 'dt_xml_template' => 'Шаблон', + 'dt_xml_field' => 'Поле', + 'dt_xml_name' => 'Имя', + 'dt_xml_title' => 'Заголовок', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Свободный текст', + 'importxml' => 'Импорт XML', + 'dt_import_selectfile' => 'Пожалуйста, выберите файл $1 для импорта:', + 'dt_import_encodingtype' => 'Тип кодировки:', + 'dt_import_forexisting' => 'Для страниц, которые уже существуют:', + 'dt_import_overwriteexisting' => 'Переписать существующие данные', + 'dt_import_skipexisting' => 'Пропустить', + 'dt_import_appendtoexisting' => 'Добавить к существующим данным', + 'dt_import_summarydesc' => 'Описание импорта:', + 'dt_import_editsummary' => 'импорт $1', + 'dt_import_importing' => 'Импортирование...', + 'dt_import_success' => '$1 {{PLURAL:$1|страница была|страницы были|страниц были}} созданы из файла $2.', + 'importcsv' => 'Импорт CSV', + 'dt_importcsv_badheader' => 'Ошибка. Заголовок колонки №$1 «$2» должен быть или «$3», или «$4», или в форме «template_name[field_name]»', + 'right-datatransferimport' => 'импорт информации', +); + +/** Rusyn (Русиньскый) + * @author Gazeb + */ +$messages['rue'] = array( + 'dt_viewxml_categories' => 'Катеґорії', + 'dt_viewxml_namespaces' => 'Просторы назв', + 'dt_viewxml_simplifiedformat' => 'Простый формат', + 'dt_xml_namespace' => 'Простор назв', + 'dt_xml_pages' => 'Сторінкы', + 'dt_xml_page' => 'Сторінка', + 'dt_xml_template' => 'Шаблона', + 'dt_xml_field' => 'Поле', + 'dt_xml_name' => 'Назва', + 'dt_xml_title' => 'Надпис', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Вольный текст', + 'importxml' => 'Імпортовати XML', +); + +/** Sicilian (Sicilianu) + * @author Aushulz + */ +$messages['scn'] = array( + 'dt_xml_name' => 'Nomu', + 'dt_xml_id' => 'ID', +); + +/** Slovak (Slovenčina) + * @author Helix84 + */ +$messages['sk'] = array( + 'datatransfer-desc' => 'Umožňuje import a export údajov obsiahnutých v bunkách šablón', + 'viewxml' => 'Zobraziť XML', + 'dt_viewxml_docu' => 'Prosím, vyberte ktorý spomedzi nasledovných kategórií a menných priestorov zobraziť vo formáte XML.', + 'dt_viewxml_categories' => 'Kategórie', + 'dt_viewxml_namespaces' => 'Menné priestory', + 'dt_viewxml_simplifiedformat' => 'Zjednodušený formát', + 'dt_xml_namespace' => 'Menný priestor', + 'dt_xml_pages' => 'Stránky', + 'dt_xml_page' => 'Stránka', + 'dt_xml_template' => 'Šablóna', + 'dt_xml_field' => 'Pole', + 'dt_xml_name' => 'Názov', + 'dt_xml_title' => 'Nadpis', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Voľný text', + 'importxml' => 'Importovať XML', + 'dt_import_selectfile' => 'Prosím, vyberte $1 súbor, ktorý chcete importovať:', + 'dt_import_encodingtype' => 'Typ kódovania:', + 'dt_import_editsummary' => 'Import $1', + 'dt_import_importing' => 'Prebieha import...', + 'dt_import_success' => 'Z $2 súboru sa {{PLURAL:$1|importuje $1 stránka|importujú $1 stránky|importuje $1 stránok}}.', + 'importcsv' => 'Import CSV', + 'dt_importcsv_badheader' => 'Chyba: stĺpec $1 hlavičky, „$2“ musí mať hodnotu buď „$3“, „$4“ alebo byť v tvare „názov_šablóny[názov_poľa]“', + 'right-datatransferimport' => 'Importovať údaje', +); + +/** Slovenian (Slovenščina) + * @author Dbc334 + */ +$messages['sl'] = array( + 'dt_xml_pages' => 'Strani', + 'dt_xml_page' => 'Stran', +); + +/** Serbian Cyrillic ekavian (‪Српски (ћирилица)‬) + * @author Rancher + * @author Sasa Stefanovic + * @author Жељко Тодоровић + * @author Михајло Анђелковић + */ +$messages['sr-ec'] = array( + 'viewxml' => 'Види XML', + 'dt_viewxml_categories' => 'Категорије', + 'dt_viewxml_namespaces' => 'Именски простори', + 'dt_viewxml_simplifiedformat' => 'Поједностављени формат', + 'dt_xml_namespace' => 'Именски простор', + 'dt_xml_pages' => 'Чланци', + 'dt_xml_page' => 'Страница', + 'dt_xml_template' => 'Шаблон', + 'dt_xml_field' => 'Поље', + 'dt_xml_name' => 'Име', + 'dt_xml_title' => 'Наслов', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Слободан текст', + 'importxml' => 'Увези XML', + 'dt_import_editsummary' => '$1 увоз', + 'dt_import_importing' => 'Увоз у току...', + 'importcsv' => 'Увези CSV', + 'right-datatransferimport' => 'Увези податке', +); + +/** Serbian Latin ekavian (‪Srpski (latinica)‬) + * @author Michaello + * @author Жељко Тодоровић + */ +$messages['sr-el'] = array( + 'viewxml' => 'Vidi XML', + 'dt_viewxml_categories' => 'Kategorije', + 'dt_viewxml_namespaces' => 'Imenski prostori', + 'dt_viewxml_simplifiedformat' => 'Pojednostavljeni format', + 'dt_xml_namespace' => 'Imenski prostor', + 'dt_xml_pages' => 'Članci', + 'dt_xml_page' => 'Stranica', + 'dt_xml_template' => 'Šablon', + 'dt_xml_field' => 'Polje', + 'dt_xml_name' => 'Ime', + 'dt_xml_title' => 'Naslov', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Slobodan tekst', + 'importxml' => 'Uvezi XML', + 'dt_import_editsummary' => '$1 uvoz', + 'dt_import_importing' => 'Uvoz u toku...', + 'importcsv' => 'Uvezi CSV', + 'right-datatransferimport' => 'Uvezi podatke', +); + +/** Seeltersk (Seeltersk) + * @author Pyt + */ +$messages['stq'] = array( + 'datatransfer-desc' => 'Ferlööwet dän Import un Export fon strukturierde Doaten, do der in Aproupen un Foarloagen ferwoand wäide.', + 'viewxml' => 'XML ankiekje', + 'dt_viewxml_docu' => 'Wääl uut, wäkke Kategorien in dät XML-Formoat anwiesd wäide schällen.', + 'dt_viewxml_categories' => 'Kategorien', + 'dt_viewxml_namespaces' => 'Noomensruume', + 'dt_viewxml_simplifiedformat' => 'Fereenfacht Formoat', + 'dt_xml_namespace' => 'Noomensruum', + 'dt_xml_page' => 'Siede', + 'dt_xml_field' => 'Fäild', + 'dt_xml_name' => 'Noome', + 'dt_xml_title' => 'Tittel', +); + +/** Sundanese (Basa Sunda) + * @author Irwangatot + */ +$messages['su'] = array( + 'dt_viewxml_namespaces' => 'Ngaranspasi', +); + +/** Swedish (Svenska) + * @author Fluff + * @author Gabbe.g + * @author Lejonel + * @author M.M.S. + * @author Per + */ +$messages['sv'] = array( + 'datatransfer-desc' => 'Tillåter import och export av data som finns i mallanrop', + 'viewxml' => 'Visa XML', + 'dt_viewxml_docu' => 'Välj vilka av följande kategorier och namnrymder som ska visas i XML-format.', + 'dt_viewxml_categories' => 'Kategorier', + 'dt_viewxml_namespaces' => 'Namnrymder', + 'dt_viewxml_simplifiedformat' => 'Förenklat format', + 'dt_xml_namespace' => 'Namnrymd', + 'dt_xml_pages' => 'Sidor', + 'dt_xml_page' => 'Sida', + 'dt_xml_template' => 'Mall', + 'dt_xml_field' => 'Fält', + 'dt_xml_name' => 'Namn', + 'dt_xml_title' => 'Titel', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Fritext', + 'importxml' => 'Importera XML', + 'dt_import_selectfile' => 'Vänligen välj $1-filen som skall importeras:', + 'dt_import_encodingtype' => 'Teckenkodningstyp:', + 'dt_import_editsummary' => '$1-importering', + 'dt_import_importing' => 'Importerar...', + 'dt_import_success' => '$1 {{PLURAL:$1|sida|sidor}} kommer skapas från $2-filen.', + 'importcsv' => 'Importera CSV', + 'dt_importcsv_badheader' => "Fel: Titeln $2 för kolumnen $1 måste vara antingen $3, $4 eller på formen 'mallnamn[fältnamn]'", + 'right-datatransferimport' => 'Importera data', +); + +/** Silesian (Ślůnski) + * @author Herr Kriss + */ +$messages['szl'] = array( + 'dt_xml_page' => 'Zajta', + 'dt_xml_name' => 'Mjano', +); + +/** Tamil (தமிழ்) + * @author TRYPPN + * @author Trengarasu + * @author Ulmo + */ +$messages['ta'] = array( + 'dt_viewxml_categories' => 'பகுப்புகள்', + 'dt_viewxml_namespaces' => 'பெயர்வெளிகள்', + 'dt_viewxml_simplifiedformat' => 'எளிதாக்கப்பட்ட வடிவம்', + 'dt_xml_namespace' => 'பெயர்வெளி', + 'dt_xml_pages' => 'பக்கங்கள்', + 'dt_xml_page' => 'பக்கம்', + 'dt_xml_template' => 'வார்ப்புரு', + 'dt_xml_name' => 'பெயர்', + 'dt_xml_title' => 'தலைப்பு', + 'dt_xml_id' => 'அடையாளம்', + 'dt_xml_freetext' => 'எந்த கட்டுப்பாடும் இல்லா சொற்றொடர்', + 'dt_import_importing' => 'இறக்குமதியாகிறது...', +); + +/** Telugu (తెలుగు) + * @author Veeven + */ +$messages['te'] = array( + 'viewxml' => 'XMLని చూడండి', + 'dt_viewxml_categories' => 'వర్గాలు', + 'dt_viewxml_namespaces' => 'పేరుబరులు', + 'dt_xml_namespace' => 'పేరుబరి', + 'dt_xml_pages' => 'పేజీలు', + 'dt_xml_page' => 'పేజీ', + 'dt_xml_template' => 'మూస', + 'dt_xml_name' => 'పేరు', + 'dt_xml_title' => 'శీర్షిక', + 'dt_xml_id' => 'ఐడీ', + 'dt_xml_freetext' => 'స్వేచ్ఛా పాఠ్యం', +); + +/** Tetum (Tetun) + * @author MF-Warburg + */ +$messages['tet'] = array( + 'dt_viewxml_categories' => 'Kategoria sira', + 'dt_xml_namespace' => 'Espasu pájina nian', + 'dt_xml_page' => 'Pájina', + 'dt_xml_name' => 'Naran', + 'dt_xml_title' => 'Títulu:', + 'dt_xml_id' => 'ID', +); + +/** Tajik (Cyrillic) (Тоҷикӣ (Cyrillic)) + * @author Ibrahim + */ +$messages['tg-cyrl'] = array( + 'dt_viewxml_categories' => 'Гурӯҳҳо', + 'dt_viewxml_namespaces' => 'Фазоҳои ном', + 'dt_xml_namespace' => 'Фазоином', + 'dt_xml_page' => 'Саҳифа', + 'dt_xml_name' => 'Ном', + 'dt_xml_title' => 'Унвон', + 'dt_xml_freetext' => 'Матни дилхоҳ', +); + +/** Tajik (Latin) (Тоҷикӣ (Latin)) + * @author Liangent + */ +$messages['tg-latn'] = array( + 'dt_viewxml_categories' => 'Gurūhho', + 'dt_viewxml_namespaces' => 'Fazohoi nom', + 'dt_xml_namespace' => 'Fazoinom', + 'dt_xml_page' => 'Sahifa', + 'dt_xml_name' => 'Nom', + 'dt_xml_title' => 'Unvon', + 'dt_xml_freetext' => 'Matni dilxoh', +); + +/** Thai (ไทย) + * @author Octahedron80 + */ +$messages['th'] = array( + 'dt_viewxml_categories' => 'หมวดหมู่', + 'dt_viewxml_namespaces' => 'เนมสเปซ', + 'dt_xml_namespace' => 'เนมสเปซ', +); + +/** Turkmen (Türkmençe) + * @author Hanberke + */ +$messages['tk'] = array( + 'dt_xml_page' => 'Sahypa', + 'dt_xml_name' => 'At', +); + +/** Tagalog (Tagalog) + * @author AnakngAraw + */ +$messages['tl'] = array( + 'datatransfer-desc' => 'Nagpapahintulot sa pag-aangkat at pagluluwas ng mga datong nasa loob ng mga pagtawag sa suleras', + 'viewxml' => 'Tingnan ang XML', + 'dt_viewxml_docu' => 'Pumili po lamang mula sa sumusunod na mga kaurian at mga espasyo ng pangalan upang makita ang anyong XML.', + 'dt_viewxml_categories' => 'Mga kaurian', + 'dt_viewxml_namespaces' => 'Mga espasyo ng pangalan', + 'dt_viewxml_simplifiedformat' => 'Pinapayak na anyo', + 'dt_xml_namespace' => 'Espasyo ng pangalan', + 'dt_xml_pages' => 'Mga pahina', + 'dt_xml_page' => 'Pahina', + 'dt_xml_template' => 'Suleras', + 'dt_xml_field' => 'Hanay', + 'dt_xml_name' => 'Pangalan', + 'dt_xml_title' => 'Pamagat', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Malayang Teksto', + 'importxml' => 'Angkatin ang XML', + 'dt_import_selectfile' => 'Pakipili ang talaksang $1 na aangkatin:', + 'dt_import_encodingtype' => 'Uri ng pagkokodigo:', + 'dt_import_forexisting' => 'Para sa mga pahinang umiiral na:', + 'dt_import_overwriteexisting' => 'Patungan ang umiiral na nilalaman', + 'dt_import_skipexisting' => 'Laktawan', + 'dt_import_appendtoexisting' => 'Isugpong sa umiiral na nilalaman', + 'dt_import_summarydesc' => 'Buod ng pag-angkat:', + 'dt_import_editsummary' => 'Pag-angkat ng $1', + 'dt_import_importing' => 'Inaangkat...', + 'dt_import_success' => '$1 {{PLURAL:$1|pahina|mga pahina}} ang lilikhain mula sa talaksang $2.', + 'importcsv' => 'Angkatin ang CSV', + 'dt_importcsv_badheader' => "Kamalian: ang patayong hanay ng paulong $1, '$2', ay dapat na '$3', '$4' o nasa pormang 'template_name[field_name]'", + 'right-datatransferimport' => 'Angkatin ang dato', +); + +/** Turkish (Türkçe) + * @author Joseph + * @author Karduelis + * @author Mach + * @author Manco Capac + * @author Srhat + * @author Vito Genovese + */ +$messages['tr'] = array( + 'datatransfer-desc' => 'Şablon çağrılarında içerilen verilerin içe ve dışa aktarımına izin verir', + 'viewxml' => "XML'i gör", + 'dt_viewxml_docu' => 'Lütfen, XML formatında görüntülemek için aşağıdaki kategori ve ad alanları arasından seçin.', + 'dt_viewxml_categories' => 'Kategoriler', + 'dt_viewxml_namespaces' => 'İsim alanları', + 'dt_viewxml_simplifiedformat' => 'Basitleştirilmiş format', + 'dt_xml_namespace' => 'Ad alanı', + 'dt_xml_pages' => 'Sayfalar', + 'dt_xml_page' => 'Sayfa', + 'dt_xml_template' => 'Şablon', + 'dt_xml_field' => 'Alan', + 'dt_xml_name' => 'İsim', + 'dt_xml_title' => 'Başlık', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Özgür Metin', + 'importxml' => 'XML içe aktar', + 'dt_import_selectfile' => 'Lütfen içe aktarmak için $1 dosyasını seçin:', + 'dt_import_encodingtype' => 'Kodlama türü:', + 'dt_import_summarydesc' => 'İçe aktarma özeti:', + 'dt_import_editsummary' => '$1 içe aktarımı', + 'dt_import_importing' => 'İçe aktarıyor...', + 'dt_import_success' => '$2 dosyasından $1 {{PLURAL:$1|sayfa|sayfa}} oluşturulacak.', + 'importcsv' => "CSV'yi içe aktar", + 'dt_importcsv_badheader' => "Hata: $1 kolonunun başlığı olan '$2', '$3', '$4' ya da 'şablon_adı[alan_adı]' şeklinde olmalıdır", + 'right-datatransferimport' => 'Verileri içe aktarır', +); + +/** Uighur (Latin) (ئۇيغۇرچە / Uyghurche‎ (Latin)) + * @author Jose77 + */ +$messages['ug-latn'] = array( + 'dt_xml_page' => 'Bet', +); + +/** Ukrainian (Українська) + * @author AS + * @author Arturyatsko + * @author Prima klasy4na + * @author Тест + */ +$messages['uk'] = array( + 'datatransfer-desc' => 'Дозволяє імпортувати та експортувати дані, які містяться в викликах шаблонів', + 'viewxml' => 'Перегляд XML', + 'dt_viewxml_docu' => 'Будь ласка, виберіть одну з наступних категорій та імен для перегляду в форматі XML.', + 'dt_viewxml_categories' => 'Категорії', + 'dt_viewxml_namespaces' => 'Простори назв', + 'dt_viewxml_simplifiedformat' => 'Спрощений формат', + 'dt_xml_namespace' => 'Простір назв', + 'dt_xml_pages' => 'Сторінки', + 'dt_xml_page' => 'Сторінка', + 'dt_xml_template' => 'Шаблон', + 'dt_xml_field' => 'Поле', + 'dt_xml_name' => 'Назва', + 'dt_xml_title' => 'Заголовок', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Вільний текст', + 'importxml' => 'Імпорт XML', + 'dt_import_selectfile' => 'Будь ласка, виберіть файл $1 для імпорту:', + 'dt_import_encodingtype' => 'Тип кодування:', + 'dt_import_forexisting' => 'Для сторінок, які вже існують:', + 'dt_import_overwriteexisting' => 'Перезаписати існуючий вміст', + 'dt_import_skipexisting' => 'Пропустити', + 'dt_import_appendtoexisting' => 'Додати до існуючого вмісту', + 'dt_import_summarydesc' => 'Опис імпорту:', + 'dt_import_editsummary' => 'імпорт $1', + 'dt_import_importing' => 'Імпорт ...', + 'dt_import_success' => '$1 {{PLURAL:$1|сторінка була|сторінки було|сторінок було}} створено з файлу $2.', + 'importcsv' => 'Імпорт CSV', + 'dt_importcsv_badheader' => 'Помилка. Заголовок колонки №$1 «$2» повинен бути або «$3», або «$4», або у формі «template_name[field_name]»', + 'right-datatransferimport' => 'Імпорт даних', +); + +/** Vietnamese (Tiếng Việt) + * @author Minh Nguyen + * @author Vinhtantran + */ +$messages['vi'] = array( + 'datatransfer-desc' => 'Cho phép nhập xuất dữ liệu có cấu trúc được chứa trong lời gọi bản mẫu', + 'viewxml' => 'Xem XML', + 'dt_viewxml_docu' => 'Xin hãy chọn trong những thể loại và không gian tên dưới đây để xem ở dạng XML.', + 'dt_viewxml_categories' => 'Thể loại', + 'dt_viewxml_namespaces' => 'Không gian tên', + 'dt_viewxml_simplifiedformat' => 'Định dạng đơn giản hóa', + 'dt_xml_namespace' => 'Không gian tên', + 'dt_xml_pages' => 'Trang', + 'dt_xml_page' => 'Trang', + 'dt_xml_template' => 'Bản mẫu', + 'dt_xml_field' => 'Trường', + 'dt_xml_name' => 'Tên', + 'dt_xml_title' => 'Tựa đề', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => 'Văn bản Tự do', + 'importxml' => 'Nhập XML', + 'dt_import_selectfile' => 'Xin hãy chọn tập tin $1 để nhập:', + 'dt_import_encodingtype' => 'Bảng mã:', + 'dt_import_editsummary' => 'Nhập $1', + 'dt_import_importing' => 'Đang nhập…', + 'dt_import_success' => '{{PLURAL:$1|Trang|$1 trang}} sẽ được nhập từ tập tin $2.', + 'importcsv' => 'Nhập CSV', + 'dt_importcsv_badheader' => 'Lỗi: tên của cột $1, “$2”, phải là “$3” hay “$4”, hoặc phải theo hình dạng “tên_tiêu_bản[tên_trường]”', + 'right-datatransferimport' => 'Nhập dữ liệu', +); + +/** Volapük (Volapük) + * @author Malafaya + * @author Smeira + */ +$messages['vo'] = array( + 'datatransfer-desc' => 'Dälon nüveigi e seveigi nünodas peleodüköl in samafomotilüvoks paninädöls', + 'viewxml' => 'Logön eli XML', + 'dt_viewxml_docu' => 'Välolös bevü klads e nemaspads foviks utosi, kelosi vilol logön fomätü XML.', + 'dt_viewxml_categories' => 'Klads', + 'dt_viewxml_namespaces' => 'Nemaspads', + 'dt_viewxml_simplifiedformat' => 'Fomät pebalugüköl', + 'dt_xml_namespace' => 'Nemaspad', + 'dt_xml_page' => 'Pad', + 'dt_xml_field' => 'Fel', + 'dt_xml_name' => 'Nem', + 'dt_xml_title' => 'Tiäd', + 'dt_xml_id' => 'Dientifanüm', + 'dt_xml_freetext' => 'Vödem libik', +); + +/** Yiddish (ייִדיש) + * @author פוילישער + */ +$messages['yi'] = array( + 'dt_xml_name' => 'נאָמען', + 'dt_xml_title' => 'טיטל', +); + +/** Simplified Chinese (‪中文(简体)‬) + * @author Gaoxuewei + */ +$messages['zh-hans'] = array( + 'datatransfer-desc' => '允许根据模板的要求导入导出结构化的数据', + 'viewxml' => '查看XML', + 'dt_viewxml_docu' => '请在下列分类、名称空间中选择，以使用XML格式查看。', + 'dt_viewxml_categories' => '分类', + 'dt_viewxml_namespaces' => '名称空间', + 'dt_viewxml_simplifiedformat' => '简化格式', + 'dt_xml_namespace' => '名称空间', + 'dt_xml_pages' => '页面', + 'dt_xml_page' => '页面', + 'dt_xml_template' => '模板', + 'dt_xml_field' => '事件', + 'dt_xml_name' => '名称', + 'dt_xml_title' => '标题', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => '自由文本', +); + +/** Traditional Chinese (‪中文(繁體)‬) + * @author Liangent + * @author Mark85296341 + */ +$messages['zh-hant'] = array( + 'datatransfer-desc' => '允許根據模板的要求導入導出結構化的數據', + 'viewxml' => '檢視XML', + 'dt_viewxml_docu' => '請在下列分類、名稱空間中選擇，以使用XML格式查看。', + 'dt_viewxml_categories' => '分類', + 'dt_viewxml_namespaces' => '名稱空間', + 'dt_viewxml_simplifiedformat' => '簡化格式', + 'dt_xml_namespace' => '名稱空間', + 'dt_xml_pages' => '頁面', + 'dt_xml_page' => '頁面', + 'dt_xml_template' => '模板', + 'dt_xml_name' => '名稱', + 'dt_xml_title' => '標題', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => '自由文字', +); + +/** Chinese (Taiwan) (‪中文(台灣)‬) + * @author Pbdragonwang + * @author Roc michael + */ +$messages['zh-tw'] = array( + 'datatransfer-desc' => '允許匯入及匯出引用樣板(template calls)的結構性資料', + 'viewxml' => '查看 XML', + 'dt_viewxml_docu' => '請選取以下的分類及名字空間以查看其XML格式的資料', + 'dt_viewxml_categories' => '分類', + 'dt_viewxml_namespaces' => '名字空間', + 'dt_viewxml_simplifiedformat' => '簡化的格式', + 'dt_xml_namespace' => '名字空間', + 'dt_xml_pages' => '頁面', + 'dt_xml_page' => '頁面', + 'dt_xml_template' => '模板', + 'dt_xml_field' => '欄位', + 'dt_xml_name' => '名稱', + 'dt_xml_title' => '標題(Title)', + 'dt_xml_id' => 'ID', + 'dt_xml_freetext' => '隨意文字', + 'importxml' => '匯入XML', + 'dt_import_selectfile' => '請選取$1檔以供匯入', + 'dt_import_encodingtype' => '編碼類型', + 'dt_import_summarydesc' => '輸入的摘要', + 'dt_import_editsummary' => '匯入$1', + 'dt_import_importing' => '匯入中...', + 'dt_import_success' => '將從該$2檔匯入$1{{PLURAL:$1|頁面頁面}}。', + 'importcsv' => '匯入CSV檔', + 'dt_importcsv_badheader' => "錯誤：$1欄位的標題「$2」或必須為「$3」，「$4」或表單「模板名稱[欄位名稱]」
+Error: the column $1 header, '$2', must be either '$3', '$4' or of the form 'template_name[field_name]'", + 'right-datatransferimport' => '輸入資料', +); + diff --git a/planteome/paw/extensions/DataTransfer_PS/specials/DT_ImportCSV.php b/planteome/paw/extensions/DataTransfer_PS/specials/DT_ImportCSV.php new file mode 100644 index 0000000..30b833f --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/specials/DT_ImportCSV.php @@ -0,0 +1,231 @@ +mTemplates = array(); + } + + function setName( $name ) { + $this->mName = $name; + } + + function getName() { + return $this->mName; + } + + function addTemplateField( $template_name, $field_name, $value ) { + if ( ! array_key_exists( $template_name, $this->mTemplates ) ) { + $this->mTemplates[$template_name] = array(); + } + $this->mTemplates[$template_name][$field_name] = $value; + } + + function setFreeText( $free_text ) { + $this->mFreeText = $free_text; + } + + function createText() { + $text = ""; + foreach ( $this->mTemplates as $template_name => $fields ) { + $text .= '{{' . $template_name . "\n"; + foreach ( $fields as $field_name => $val ) { + $text .= "|$field_name=$val\n"; + } + $text .= '}}' . "\n"; + } + $text .= $this->mFreeText; + return $text; + } +} + +class DTImportCSV extends SpecialPage { + + /** + * Constructor + */ + public function DTImportCSV() { + global $wgLanguageCode; + parent::__construct( 'ImportCSV' ); + DTUtils::loadMessages(); + } + + function execute( $query ) { + global $wgUser, $wgOut, $wgRequest; + $this->setHeaders(); + + if ( ! $wgUser->isAllowed( 'datatransferimport' ) ) { + global $wgOut; + $wgOut->permissionRequired( 'datatransferimport' ); + return; + } + + if ( $wgRequest->getCheck( 'import_file' ) ) { + $text = DTUtils::printImportingMessage(); + $uploadResult = ImportStreamSource::newFromUpload( "file_name" ); + // handling changed in MW 1.17 + $uploadError = null; + if ( $uploadResult instanceof Status ) { + if ( $uploadResult->isOK() ) { + $source = $uploadResult->value; + } else { + $uploadError = $wgOut->parse( $uploadResult->getWikiText() ); + } + } elseif ( $uploadResult instanceof WikiErrorMsg ) { + $uploadError = $uploadResult->getMessage(); + } else { + $source = $uploadResult; + } + + if ( !is_null( $uploadError ) ) { + $text .= $uploadError; + $wgOut->addHTML( $text ); + return; + } + + $encoding = $wgRequest->getVal( 'encoding' ); + $pages = array(); + $error_msg = self::getCSVData( $source->mHandle, $encoding, $pages ); + if ( ! is_null( $error_msg ) ) { + $text .= $error_msg; + $wgOut->addHTML( $text ); + return; + } + + $importSummary = $wgRequest->getVal( 'import_summary' ); + $forPagesThatExist = $wgRequest->getVal( 'pagesThatExist' ); + $text .= self::modifyPages( $pages, $importSummary, $forPagesThatExist ); + } else { + $formText = DTUtils::printFileSelector( 'CSV' ); + $utf8OptionText = "\t" . Xml::element( 'option', + array( + 'selected' => 'selected', + 'value' => 'utf8' + ), 'UTF-8' ) . "\n"; + $utf16OptionText = "\t" . Xml::element( 'option', + array( + 'value' => 'utf16' + ), 'UTF-16' ) . "\n"; + $encodingSelectText = Xml::tags( 'select', + array( 'name' => 'encoding' ), + "\n" . $utf8OptionText . $utf16OptionText. "\t" ) . "\n\t"; + $formText .= "\t" . Xml::tags( 'p', null, wfMsg( 'dt_import_encodingtype', 'CSV' ) . " " . $encodingSelectText ) . "\n"; + $formText .= "\t" . '
' . "\n"; + $formText .= DTUtils::printExistingPagesHandling(); + $formText .= DTUtils::printImportSummaryInput( 'CSV' ); + $formText .= DTUtils::printSubmitButton(); + $text = "\t" . Xml::tags( 'form', + array( + 'enctype' => 'multipart/form-data', + 'action' => '', + 'method' => 'post' + ), $formText ) . "\n"; + } + + $wgOut->addHTML( $text ); + } + + + static function getCSVData( $csv_file, $encoding, &$pages ) { + if ( is_null( $csv_file ) ) + return wfMsg( 'emptyfile' ); + $table = array(); + if ( $encoding == 'utf16' ) { + // change encoding to UTF-8 + // Starting with PHP 5.3 we could use str_getcsv(), + // which would save the tempfile hassle + $tempfile = tmpfile(); + $csv_string = ''; + while ( !feof( $csv_file ) ) { + $csv_string .= fgets( $csv_file, 65535 ); + } + fwrite( $tempfile, iconv( 'UTF-16', 'UTF-8', $csv_string ) ); + fseek( $tempfile, 0 ); + while ( $line = fgetcsv( $tempfile ) ) { + array_push( $table, $line ); + } + fclose( $tempfile ); + } else { + while ( $line = fgetcsv( $csv_file ) ) { + array_push( $table, $line ); + } + } + fclose( $csv_file ); + + // Get rid of the "byte order mark", if it's there - this is + // a three-character string sometimes put at the beginning + // of files to indicate its encoding. + // Code copied from: + // http://www.dotvoid.com/2010/04/detecting-utf-bom-byte-order-mark/ + $byteOrderMark = pack( "CCC", 0xef, 0xbb, 0xbf ); + if ( 0 == strncmp( $table[0][0], $byteOrderMark, 3 ) ) { + $table[0][0] = substr( $table[0][0], 3 ); + // If there were quotation marks around this value, + // they didn't get removed, so remove them now. + $table[0][0] = trim( $table[0][0], '"' ); + } + + // check header line to make sure every term is in the + // correct format + $title_label = wfMsgForContent( 'dt_xml_title' ); + $free_text_label = wfMsgForContent( 'dt_xml_freetext' ); + foreach ( $table[0] as $i => $header_val ) { + if ( $header_val !== $title_label && $header_val !== $free_text_label && + ! preg_match( '/^[^\[\]]+\[[^\[\]]+]$/', $header_val ) ) { + $error_msg = wfMsg( 'dt_importcsv_badheader', $i, $header_val, $title_label, $free_text_label ); + return $error_msg; + } + } + foreach ( $table as $i => $line ) { + if ( $i == 0 ) continue; + $page = new DTPage(); + foreach ( $line as $j => $val ) { + if ( $val == '' ) continue; + if ( $table[0][$j] == $title_label ) { + $page->setName( $val ); + } elseif ( $table[0][$j] == $free_text_label ) { + $page->setFreeText( $val ); + } else { + list( $template_name, $field_name ) = explode( '[', str_replace( ']', '', $table[0][$j] ) ); + $page->addTemplateField( $template_name, $field_name, $val ); + } + } + $pages[] = $page; + } + } + + function modifyPages( $pages, $editSummary, $forPagesThatExist ) { + global $wgUser, $wgLang; + + $text = ""; + $jobs = array(); + $jobParams = array(); + $jobParams['user_id'] = $wgUser->getId(); + $jobParams['edit_summary'] = $editSummary; + $jobParams['for_pages_that_exist'] = $forPagesThatExist; + foreach ( $pages as $page ) { + $title = Title::newFromText( $page->getName() ); + if ( is_null( $title ) ) { + $text .= '

' . wfMsg( 'img-auth-badtitle', $page->getName() ) . "

\n"; + continue; + } + $jobParams['text'] = $page->createText(); + $jobs[] = new DTImportJob( $title, $jobParams ); + } + Job::batchInsert( $jobs ); + $text .= wfMsgExt( 'dt_import_success', array( 'parse' ), $wgLang->formatNum( count( $jobs ) ), 'CSV' ); + + return $text; + } + +} diff --git a/planteome/paw/extensions/DataTransfer_PS/specials/DT_ImportXML.php b/planteome/paw/extensions/DataTransfer_PS/specials/DT_ImportXML.php new file mode 100644 index 0000000..ffb4398 --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/specials/DT_ImportXML.php @@ -0,0 +1,82 @@ +setHeaders(); + + if ( ! $wgUser->isAllowed( 'datatransferimport' ) ) { + global $wgOut; + $wgOut->permissionRequired( 'datatransferimport' ); + return; + } + + if ( $wgRequest->getCheck( 'import_file' ) ) { + $text = DTUtils::printImportingMessage(); + $uploadResult = ImportStreamSource::newFromUpload( "file_name" ); + // handling changed in MW 1.17 + if ( $uploadResult instanceof Status ) { + $source = $uploadResult->value; + } else { + $source = $uploadResult; + } + $importSummary = $wgRequest->getVal( 'import_summary' ); + $forPagesThatExist = $wgRequest->getVal( 'pagesThatExist' ); + $text .= self::modifyPages( $source, $importSummary, $forPagesThatExist ); + } else { + $formText = DTUtils::printFileSelector( 'XML' ); + $formText .= DTUtils::printExistingPagesHandling(); + $formText .= DTUtils::printImportSummaryInput( 'XML' ); + $formText .= DTUtils::printSubmitButton(); + $text = "\t" . Xml::tags( 'form', + array( + 'enctype' => 'multipart/form-data', + 'action' => '', + 'method' => 'post' + ), $formText ) . "\n"; + + } + + $wgOut->addHTML( $text ); + } + + function modifyPages( $source, $editSummary, $forPagesThatExist ) { + $text = ""; + $xml_parser = new DTXMLParser( $source ); + $xml_parser->doParse(); + $jobs = array(); + $job_params = array(); + global $wgUser; + $job_params['user_id'] = $wgUser->getId(); + $job_params['edit_summary'] = $editSummary; + $job_params['for_pages_that_exist'] = $forPagesThatExist; + + foreach ( $xml_parser->mPages as $page ) { + $title = Title::newFromText( $page->getName() ); + $job_params['text'] = $page->createText(); + $jobs[] = new DTImportJob( $title, $job_params ); + } + Job::batchInsert( $jobs ); + global $wgLang; + $text .= wfMsgExt( 'dt_import_success', array( 'parse' ), $wgLang->formatNum( count( $jobs ) ), 'XML' ); + return $text; + } +} diff --git a/planteome/paw/extensions/DataTransfer_PS/specials/DT_ViewXML.php b/planteome/paw/extensions/DataTransfer_PS/specials/DT_ViewXML.php new file mode 100644 index 0000000..cb2497f --- /dev/null +++ b/planteome/paw/extensions/DataTransfer_PS/specials/DT_ViewXML.php @@ -0,0 +1,511 @@ +setHeaders(); + doSpecialViewXML( $query ); + } +} + +function getCategoriesList() { + global $wgContLang, $dtgContLang; + $dt_props = $dtgContLang->getPropertyLabels(); + $exclusion_cat_name = str_replace( ' ', '_', $dt_props[DT_SP_IS_EXCLUDED_FROM_XML] ); + $exclusion_cat_full_name = $wgContLang->getNSText( NS_CATEGORY ) . ':' . $exclusion_cat_name; + $dbr = wfGetDB( DB_SLAVE ); + $categorylinks = $dbr->tableName( 'categorylinks' ); + $res = $dbr->query( "SELECT DISTINCT cl_to FROM $categorylinks" ); + $categories = array(); + while ( $row = $dbr->fetchRow( $res ) ) { + $cat_name = $row[0]; + // add this category to the list, if it's not the + // "Excluded from XML" category, and it's not a child of that + // category + if ( $cat_name != $exclusion_cat_name ) { + $title = Title::newFromText( $cat_name, NS_CATEGORY ); + $parent_categories = $title->getParentCategoryTree( array() ); + if ( ! treeContainsElement( $parent_categories, $exclusion_cat_full_name ) ) + $categories[] = $cat_name; + } + } + $dbr->freeResult( $res ); + sort( $categories ); + return $categories; +} + +function getNamespacesList() { + $dbr = wfGetDB( DB_SLAVE ); + $page = $dbr->tableName( 'page' ); + $res = $dbr->query( "SELECT DISTINCT page_namespace FROM $page" ); + $namespaces = array(); + while ( $row = $dbr->fetchRow( $res ) ) { + $namespaces[] = $row[0]; + } + $dbr->freeResult( $res ); + return $namespaces; +} + +function getGroupings() { + global $dtgContLang; + + global $smwgIP; + if ( ! isset( $smwgIP ) ) { + return array(); + } else { + $groupings = array(); + $store = smwfGetStore(); + $grouping_prop = SMWPropertyValue::makeProperty( '_DT_XG' ); + $grouped_props = $store->getAllPropertySubjects( $grouping_prop ); + foreach ( $grouped_props as $grouped_prop ) { + $res = $store->getPropertyValues( $grouped_prop, $grouping_prop ); + $num = count( $res ); + if ( $num > 0 ) { + $grouping_label = $res[0]->getShortWikiText(); + $groupings[] = array( $grouped_prop, $grouping_label ); + } + } + return $groupings; + } +} + +function getSubpagesForPageGrouping( $page_name, $relation_name ) { + $dbr = wfGetDB( DB_SLAVE ); + $smw_relations = $dbr->tableName( 'smw_relations' ); + $smw_attributes = $dbr->tableName( 'smw_attributes' ); + $res = $dbr->query( "SELECT subject_title FROM $smw_relations WHERE object_title = '$page_name' AND relation_title = '$relation_name'" ); + $subpages = array(); + while ( $row = $dbr->fetchRow( $res ) ) { + $subpage_name = $row[0]; + $query_subpage_name = str_replace( "'", "\'", $subpage_name ); + // get the display order + $res2 = $dbr->query( "SELECT value_num FROM $smw_attributes WHERE subject_title = '$query_subpage_name' AND attribute_title = 'Display_order'" ); + if ( $row2 = $dbr->fetchRow( $res2 ) ) { + $display_order = $row2[0]; + } else { + $display_order = - 1; + } + $dbr->freeResult( $res2 ); + // HACK - page name is the key, display order is the value + $subpages[$subpage_name] = $display_order; + } + $dbr->freeResult( $res ); + uasort( $subpages, "cmp" ); + return array_keys( $subpages ); +} + + +/* + * Get all the pages that belong to a category and all its subcategories, + * down a certain number of levels - heavily based on SMW's + * SMWInlineQuery::includeSubcategories() + */ + function getPagesForCategory( $top_category, $num_levels ) { + if ( 0 == $num_levels ) return $top_category; + + $db = wfGetDB( DB_SLAVE ); + $fname = "getPagesForCategory"; + $categories = array( $top_category ); + $checkcategories = array( $top_category ); + $titles = array(); + for ( $level = $num_levels; $level > 0; $level-- ) { + $newcategories = array(); + foreach ( $checkcategories as $category ) { + $res = $db->select( // make the query + array( 'categorylinks', 'page' ), + array( 'page_id', 'page_title', 'page_namespace' ), + array( 'cl_from = page_id', + 'cl_to = ' . $db->addQuotes( $category ) ), + $fname ); + if ( $res ) { + while ( $res && $row = $db->fetchRow( $res ) ) { + if ( array_key_exists( 'page_title', $row ) ) { + $page_namespace = $row['page_namespace']; + if ( $page_namespace == NS_CATEGORY ) { + $new_category = $row[ 'page_title' ]; + if ( !in_array( $new_category, $categories ) ) { + $newcategories[] = $new_category; + } + } else { + $titles[] = Title::newFromID( $row['page_id'] ); + } + } + } + $db->freeResult( $res ); + } + } + if ( count( $newcategories ) == 0 ) { + return $titles; + } else { + $categories = array_merge( $categories, $newcategories ); + } + $checkcategories = array_diff( $newcategories, array() ); + } + return $titles; + } + +/* +function getPagesForCategory($category) { + $dbr = wfGetDB( DB_SLAVE ); + $categorylinks = $dbr->tableName( 'categorylinks' ); + $res = $dbr->query("SELECT cl_from FROM $categorylinks WHERE cl_to = '$category'"); + $titles = array(); + while ($row = $dbr->fetchRow($res)) { + $titles[] = Title::newFromID($row[0]); + } + $dbr->freeResult($res); + return $titles; +} +*/ + +function getPagesForNamespace( $namespace ) { + $dbr = wfGetDB( DB_SLAVE ); + $page = $dbr->tableName( 'page' ); + $res = $dbr->query( "SELECT page_id FROM $page WHERE page_namespace = '$namespace'" ); + $titles = array(); + while ( $row = $dbr->fetchRow( $res ) ) { + $titles[] = Title::newFromID( $row[0] ); + } + $dbr->freeResult( $res ); + return $titles; +} + +/** + * Helper function for getXMLForPage() + */ +function treeContainsElement( $tree, $element ) { + // escape out if there's no tree (i.e., category) + if ( $tree == null ) + return false; + + foreach ( $tree as $node => $child_tree ) { + if ( $node === $element ) { + return true; + } elseif ( count( $child_tree ) > 0 ) { + if ( treeContainsElement( $child_tree, $element ) ) { + return true; + } + } + } + // no match found + return false; +} + +function getXMLForPage( $title, $simplified_format, $groupings, $depth = 0 ) { + if ( $depth > 5 ) { return ""; } + + global $wgContLang, $dtgContLang; + + $namespace_labels = $wgContLang->getNamespaces(); + $template_label = $namespace_labels[NS_TEMPLATE]; + $namespace_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_namespace' ) ); + $page_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_page' ) ); + $field_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_field' ) ); + $name_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_name' ) ); + $title_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_title' ) ); + $id_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_id' ) ); + $free_text_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_freetext' ) ); + + // if this page belongs to the exclusion category, exit + $parent_categories = $title->getParentCategoryTree( array() ); + $dt_props = $dtgContLang->getPropertyLabels(); + // $exclusion_category = $title->newFromText($dt_props[DT_SP_IS_EXCLUDED_FROM_XML], NS_CATEGORY); + $exclusion_category = $wgContLang->getNSText( NS_CATEGORY ) . ':' . str_replace( ' ', '_', $dt_props[DT_SP_IS_EXCLUDED_FROM_XML] ); + if ( treeContainsElement( $parent_categories, $exclusion_category ) ) + return ""; + $article = new Article( $title ); + $page_title = str_replace( '"', '"', $title->getText() ); + $page_title = str_replace( '&', '&', $page_title ); + if ( $simplified_format ) + $text = "<$page_str><$id_str>{$article->getID()}<$title_str>$page_title\n"; + else + $text = "<$page_str $id_str=\"" . $article->getID() . "\" $title_str=\"" . $page_title . '" >'; + + // traverse the page contents, one character at a time + $uncompleted_curly_brackets = 0; + $page_contents = $article->getContent(); + // escape out variables like "{{PAGENAME}}" + $page_contents = str_replace( '{{PAGENAME}}', '{{PAGENAME}}', $page_contents ); + // escape out parser functions + $page_contents = preg_replace( '/{{(#.+)}}/', '{{$1}}', $page_contents ); + // escape out transclusions + $page_contents = preg_replace( '/{{(:.+)}}/', '{{$1}}', $page_contents ); + // escape out variable names + $page_contents = str_replace( '{{{', '{{{', $page_contents ); + $page_contents = str_replace( '}}}', '}}}', $page_contents ); + // escape out tables + $page_contents = str_replace( '{|', '{|', $page_contents ); + $page_contents = str_replace( '|}', '|}', $page_contents ); + $free_text = ""; + $free_text_id = 1; + $template_name = ""; + $field_name = ""; + $field_value = ""; + $field_has_name = false; + for ( $i = 0; $i < strlen( $page_contents ); $i++ ) { + $c = $page_contents[$i]; + if ( $uncompleted_curly_brackets == 0 ) { + if ( $c == "{" || $i == strlen( $page_contents ) - 1 ) { + if ( $i == strlen( $page_contents ) - 1 ) + $free_text .= $c; + $uncompleted_curly_brackets++; + $free_text = trim( $free_text ); + $free_text = str_replace( '&', '&', $free_text ); + $free_text = str_replace( '[', '[', $free_text ); + $free_text = str_replace( ']', ']', $free_text ); + $free_text = str_replace( '<', '<', $free_text ); + $free_text = str_replace( '>', '>', $free_text ); + if ( $free_text != "" ) { + $text .= "<$free_text_str id=\"$free_text_id\">$free_text"; + $free_text = ""; + $free_text_id++; + } + } elseif ( $c == "{" ) { + // do nothing + } else { + $free_text .= $c; + } + } elseif ( $uncompleted_curly_brackets == 1 ) { + if ( $c == "{" ) { + $uncompleted_curly_brackets++; + $creating_template_name = true; + } elseif ( $c == "}" ) { + $uncompleted_curly_brackets--; + // is this needed? + // if ($field_name != "") { + // $field_name = ""; + // } + if ( $page_contents[$i - 1] == '}' ) { + if ( $simplified_format ) + $text .= ""; + else + $text .= ""; + } + $template_name = ""; + } + } else { // 2 or greater - probably 2 + if ( $c == "}" ) { + $uncompleted_curly_brackets--; + } + if ( $c == "{" ) { + $uncompleted_curly_brackets++; + } else { + if ( $creating_template_name ) { + if ( $c == "|" || $c == "}" ) { + $template_name = str_replace( ' ', '_', trim( $template_name ) ); + $template_name = str_replace( '&', '&', $template_name ); + if ( $simplified_format ) { + $text .= "<" . $template_name . ">"; + } else + $text .= "<$template_label $name_str=\"$template_name\">"; + $creating_template_name = false; + $creating_field_name = true; + $field_id = 1; + } else { + $template_name .= $c; + } + } else { + if ( $c == "|" || $c == "}" ) { + if ( $field_has_name ) { + $field_value = str_replace( '&', '&', $field_value ); + if ( $simplified_format ) { + $field_name = str_replace( ' ', '_', trim( $field_name ) ); + $text .= "<" . $field_name . ">"; + $text .= trim( $field_value ); + $text .= ""; + } else { + $text .= "<$field_str $name_str=\"" . trim( $field_name ) . "\">"; + $text .= trim( $field_value ); + $text .= ""; + } + $field_value = ""; + $field_has_name = false; + } else { + // "field_name" is actually the value + if ( $simplified_format ) { + $field_name = str_replace( ' ', '_', $field_name ); + // add "Field" to the beginning of the file name, since + // XML tags that are simply numbers aren't allowed + $text .= "<" . $field_str . '_' . $field_id . ">"; + $text .= trim( $field_name ); + $text .= ""; + } else { + $text .= "<$field_str $name_str=\"$field_id\">"; + $text .= trim( $field_name ); + $text .= ""; + } + $field_id++; + } + $creating_field_name = true; + $field_name = ""; + } elseif ( $c == "=" ) { + // handle case of = in value + if ( ! $creating_field_name ) { + $field_value .= $c; + } else { + $creating_field_name = false; + $field_has_name = true; + } + } elseif ( $creating_field_name ) { + $field_name .= $c; + } else { + $field_value .= $c; + } + } + } + } + } + + // handle groupings, if any apply here; first check if SMW is installed + global $smwgIP; + if ( isset( $smwgIP ) ) { + $store = smwfGetStore(); + foreach ( $groupings as $pair ) { + list( $property_page, $grouping_label ) = $pair; + $wiki_page = SMWDataValueFactory::newTypeIDValue( '_wpg', $page_title ); + $options = new SMWRequestOptions(); + $options->sort = "subject_title"; + // get actual property from the wiki-page of the property + $property = SMWPropertyValue::makeProperty( $property_page->getTitle()->getText() ); + $res = $store->getPropertySubjects( $property, $wiki_page, $options ); + $num = count( $res ); + if ( $num > 0 ) { + $grouping_label = str_replace( ' ', '_', $grouping_label ); + $text .= "<$grouping_label>\n"; + foreach ( $res as $subject ) { + $subject_title = $subject->getTitle(); + $text .= getXMLForPage( $subject_title, $simplified_format, $groupings, $depth + 1 ); + } + $text .= "\n"; + } + } + } + + $text .= "\n"; + // escape back the curly brackets that were escaped out at the beginning + $text = str_replace( '&#123;', '{', $text ); + $text = str_replace( '&#125;', '}', $text ); + return $text; +} + +function doSpecialViewXML() { + global $wgOut, $wgRequest, $wgUser, $wgContLang; + $skin = $wgUser->getSkin(); + $namespace_labels = $wgContLang->getNamespaces(); + $category_label = $namespace_labels[NS_CATEGORY]; + $template_label = $namespace_labels[NS_TEMPLATE]; + $name_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_name' ) ); + $namespace_str = str_replace( ' ', '_', wfMsg( 'dt_xml_namespace' ) ); + $pages_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_pages' ) ); + + $form_submitted = false; + $page_titles = array(); + $cats = $wgRequest->getArray( 'categories' ); + $nses = $wgRequest->getArray( 'namespaces' ); + if ( count( $cats ) > 0 || count( $nses ) > 0 ) { + $form_submitted = true; + } + + if ( $form_submitted ) { + $wgOut->disable(); + + // Cancel output buffering and gzipping if set + // This should provide safer streaming for pages with history + wfResetOutputBuffers(); + header( "Content-type: application/xml; charset=utf-8" ); + + $groupings = getGroupings(); + $simplified_format = $wgRequest->getVal( 'simplified_format' ); + $text = "<$pages_str>"; + if ( $cats ) { + foreach ( $cats as $cat => $val ) { + if ( $simplified_format ) + $text .= '<' . str_replace( ' ', '_', $cat ) . ">\n"; + else + $text .= "<$category_label $name_str=\"$cat\">\n"; + $titles = getPagesForCategory( $cat, 10 ); + foreach ( $titles as $title ) { + $text .= getXMLForPage( $title, $simplified_format, $groupings ); + } + if ( $simplified_format ) + $text .= '\n"; + else + $text .= "\n"; + } + } + + if ( $nses ) { + foreach ( $nses as $ns => $val ) { + if ( $ns == 0 ) { + $ns_name = "Main"; + } else { + $ns_name = MWNamespace::getCanonicalName( $ns ); + } + if ( $simplified_format ) + $text .= '<' . str_replace( ' ', '_', $ns_name ) . ">\n"; + else + $text .= "<$namespace_str $name_str=\"$ns_name\">\n"; + $titles = getPagesForNamespace( $ns ); + foreach ( $titles as $title ) { + $text .= getXMLForPage( $title, $simplified_format, $groupings ); + } + if ( $simplified_format ) + $text .= '\n"; + else + $text .= "\n"; + } + } + $text .= ""; + print $text; + } else { + // set 'title' as hidden field, in case there's no URL niceness + global $wgContLang; + $mw_namespace_labels = $wgContLang->getNamespaces(); + $special_namespace = $mw_namespace_labels[NS_SPECIAL]; + $text = << + + +END; + $text .= "

" . wfMsg( 'dt_viewxml_docu' ) . "

\n"; + $text .= "

" . wfMsg( 'dt_viewxml_categories' ) . "

\n"; + $categories = getCategoriesList(); + foreach ( $categories as $category ) { + $title = Title::makeTitle( NS_CATEGORY, $category ); + $link = $skin->makeLinkObj( $title, $title->getText() ); + $text .= " $link
\n"; + } + $text .= "

" . wfMsg( 'dt_viewxml_namespaces' ) . "

\n"; + $namespaces = getNamespacesList(); + foreach ( $namespaces as $namespace ) { + if ( $namespace == 0 ) { + $ns_name = wfMsgHtml( 'blanknamespace' ); + } else { + $ns_name = htmlspecialchars( $wgContLang->getFormattedNsText( $namespace ) ); + } + $ns_name = str_replace( '_', ' ', $ns_name ); + $text .= " $ns_name
\n"; + } + $text .= "

" . wfMsg( 'dt_viewxml_simplifiedformat' ) . "

\n"; + $text .= "\n"; + $text .= "\n"; + + $wgOut->addHTML( $text ); + } +} diff --git a/planteome/paw/forms/Annotation.wiki b/planteome/paw/forms/Annotation.wiki new file mode 100644 index 0000000..b9c677d --- /dev/null +++ b/planteome/paw/forms/Annotation.wiki @@ -0,0 +1,206 @@ + +This is the "Annotation" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. +{{#forminput:form=Annotation}} + + +{{{info|page name=Annotation:}}} +__NOTOC__ +{{#ifexist: {{PAGENAME}} + |'''{{#show:{{PAGENAME}}|?has_Gene_Symbol}} (''{{#show:{{PAGENAME}}|?has_Species_Name}}'')''' + | +}} + + += Annotation = + +{{{for template|Annotation}}} + +{| class="formtable" +! Species Name: +| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] + [[Is Associated With Field Or Object::Species Name]] + [[Is Associated With Category::Annotations]] + |?is_Provenance + }} + | {{{field|Species Name|autocomplete on property=Has Reference Taxon|restricted}}} + | {{{field|Species Name|autocomplete on property=Has Reference Taxon}}} + }} +|- +! Gene Symbol: +| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] + [[Is Associated With Field Or Object::Gene Symbol]] + [[Is Associated With Category::Annotations]] + |?is_Provenance + }} + |{{{field|Gene Symbol|restricted}}} + |{{{field|Gene Symbol}}} + }} +|- +! Gene Name: +| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] + [[Is Associated With Field Or Object::Gene Name]] + [[Is Associated With Category::Annotations]] + |?is_Provenance + }} + | {{{field|Gene Name|restricted}}} + | {{{field|Gene Name}}} + }} +|- +! Gene Synonyms: +| {{#ifexist: {{PAGENAME}} + | {{#if: {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]] + | ?is_Gene_Synonym + | headers=hide + | mainlabel=- + | format=list + }} {{#formlink:form=Gene_Synonyms|link text=Edit|link type=button|target={{PAGENAME}}/Gene_Synonyms }} + | {{#formlink:form=Gene_Synonyms|link text=Add Synonyms|link type=button|query string=Gene_Synonyms[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} + }} + | To add gene synonyms, first save your basic annotation information on this "Annotation" tab. +}} +|- +! Gene Locus: +| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] + [[Is Associated With Field Or Object::Gene Locus]] + [[Is Associated With Category::Annotations]] + |?is_Provenance + }} + | {{{field|Gene Locus|restricted}}} + | {{{field|Gene Locus}}} + }} +|- +! Gene Type: +| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] + [[Is Associated With Field Or Object::Gene Type]] + [[Is Associated With Category::Annotations]] + |?is_Provenance + }} + | {{{field|Gene Type|restricted}}} + | {{{field|Gene Type}}} + }} +|- +! EC Number(s): +| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] + [[Is Associated With Field Or Object::EC Numbers]] + [[Is Associated With Category::Annotations]] + |?is_Provenance + }} + | {{{field|EC Numbers|restricted|list|delimiter=,}}} + | {{{field|EC Numbers|list|delimiter=,}}} + }} +|- +! Chromosome: +| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] + [[Is Associated With Field Or Object::Chromosome]] + [[Is Associated With Category::Annotations]] + |?is_Provenance + }} + |{{{field|Chromosome|restricted}}} + |{{{field|Chromosome}}} + }} +|- +! Has Phenotype: +| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] + [[Is Associated With Field Or Object::Has Phenotype]] + [[Is Associated With Category::Annotations]] + |?is_Provenance + }} + | {{{field|Has Phenotype|restricted}}} + | {{{field|Has Phenotype}}} + }} +|- +! Description: +| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] + [[Is Associated With Field Or Object::Annotation Description]] + [[Is Associated With Category::Annotations]] + |?is_Provenance + }} + | {{{field|Annotation Description|restricted}}} + | {{{field|Annotation Description}}} + }} +|} + +{{{end template}}} + += External References = + +{{#ifexist: {{PAGENAME}} + | {{#if: {{#ask:[[Category:External_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | Add, edit, or remove external reference data {{#formlink:form=External_References|link text=here|target={{PAGENAME}}/External_References }}. + {{#ask:[[Is External Reference::~{{PAGENAME}}/External_References* ]] + | mainlabel=- + |? from_External_Source + |? has_External_Accession_ID + }} + | Add external references for this annotation.
{{#formlink:form=External_References|link text=Add|link type=button|query string=External_References[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} + }} + | To add external references, first save your basic annotation information on the "Annotation" tab. +}} + += Ontologies = + +{{#ifexist: {{PAGENAME}} + | {{#if: {{#ask:[[Category:Ontological_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | Add, edit, or remove ontology references {{#formlink:form=Ontological_References|link text=here|target={{PAGENAME}}/Ontologies }}. + {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies*]] + | mainlabel=- + |? from_Ontology + |? has_Term_ID + |? has_Term_Name + |? has_Aspect + |? has_Evidence_Code + |? has_Evidence + }} + | Add ontological associations for this annotation.
{{#formlink:form=Ontological_References|link text=Add|link type=button|query string=Ontological_References[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} + }} + | To add ontological references, first save your basic annotation information on the "Annotation" tab. +}} + += Sequences = + +{{#ifexist: {{PAGENAME}} + | {{#if: {{#ask:[[Category:Sequences]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | Add, edit, or remove sequence references {{#formlink:form=Sequences|link text=here|target={{PAGENAME}}/Sequences }}. + {{#ask:[[Is Sequence Reference::~{{PAGENAME}}/Sequences*]] + | mainlabel=- + |? has_Sequence_Type + |? has_Sequence_Source + |? has_External_Accession_ID + }} + | Add sequence references for this annotation.
{{#formlink:form=Sequences|link text=Add|link type=button|query string=Sequences[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} + }} + | To add sequence references, first save your basic annotation information on the "Annotation" tab. +}} + += Literature = + +{{#ifexist: {{PAGENAME}} + | Add a reference to a publication listed with PubMed or the DOI registry {{#formlink:form=Reference_Publication|link text=here|link type=|query string=Reference_Publication[New Annotation Reference]={{PAGENAME}} }}.
+ +Need to add a reference to a publication without a PubMed ID or DOI (Digital Object Identifier)?
+{{#formlink:form=Publication|link text=Add a new publication reference|link type=|query string=Publication[New Annotation Reference]={{PAGENAME}} }} + + {{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] }} + | {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] + |? has First Author + |? has Publication Title + |? has Journal Name + |? has Publication ID + }} + | + }} + | To add publication references, first save your basic annotation information on the "Annotation" tab. +}} + + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + + diff --git a/planteome/paw/forms/External_References.wiki b/planteome/paw/forms/External_References.wiki new file mode 100644 index 0000000..4796ba6 --- /dev/null +++ b/planteome/paw/forms/External_References.wiki @@ -0,0 +1,31 @@ + +This is the "External References" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. + + +{{#forminput:form=External References}} + + + +{{{info|page name=External_References}}} + +{{{for template|External References}}} +{| class="formtable" +! Annotation Page: +| {{{field|Annotation Page}}} +|} +{{{end template}}} + +{{{for template|External Reference Repeater|multiple}}} +'''Source:''' {{{field|External Source}}} +'''Accession ID:''' {{{field|External Accession ID}}} +{{{end template}}} + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + diff --git a/planteome/paw/forms/Gene_Synonyms.wiki b/planteome/paw/forms/Gene_Synonyms.wiki new file mode 100644 index 0000000..16add14 --- /dev/null +++ b/planteome/paw/forms/Gene_Synonyms.wiki @@ -0,0 +1,70 @@ + +This is the "Gene Synonyms" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. + +{{#forminput:form=Gene Synonyms}} + + + +{{{info|page name=Gene_Synonyms}}} + +{{{for template|Gene Synonyms}}} +{| class="formtable" +! Annotation Page: +| {{{field|Annotation Page}}} +|} +{{{end template}}} + +{{{for template|Gene Synonym Repeater|multiple}}} + + + +'''Gene Synonym:''' {{{field|Gene Synonym}}} + + + +{{{end template}}} + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + diff --git a/planteome/paw/forms/Ontological_References.wiki b/planteome/paw/forms/Ontological_References.wiki new file mode 100644 index 0000000..eef09a0 --- /dev/null +++ b/planteome/paw/forms/Ontological_References.wiki @@ -0,0 +1,54 @@ + +This is the "Ontological References" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. + + +{{#forminput:form=Ontological References}} + + + +{{{info|page name=Ontologies}}} +__NOTOC__ + +{{{for template|Ontological References}}} +{| class="formtable" +! Annotation Page: +| {{{field|Annotation Page}}} +|} +{{{end template}}} + +=== Plant Ontology === +{{{for template|Plant Ontology Reference Repeater|multiple}}} +'''Term Name:''' {{{field|Term Name|autocomplete from url=remote_PO_terms}}} '''or''' '''Term ID:''' {{{field|Term ID|autocomplete from url=remote_PO_ids}}} +

'''Evidence Code:'''
+{{{field|Evidence Code|list}}} +

'''Evidence:''' {{{field|Evidence|}}} +{{{end template}}} + +=== Gene Ontology === +{{{for template|Gene Ontology Reference Repeater|multiple}}} +'''Term Name:''' {{{field|Term Name|autocomplete from url=remote_GO_terms}}} '''or''' '''Term ID:''' {{{field|Term ID|autocomplete from url=remote_GO_ids}}} +

'''Evidence Code:'''
+{{{field|Evidence Code|list}}} +

'''Evidence:''' {{{field|Evidence|}}} +{{{end template}}} + +=== Other Ontologies === +{{{for template|Ontological Reference Repeater|multiple}}} +'''Ontology:''' {{{field|Ontology|}}} +'''Term Name:''' {{{field|Term Name|}}} +'''Term ID:''' {{{field|Term ID|}}} +'''Branch:''' {{{field|Aspect|}}} +

'''Evidence Code:'''
+{{{field|Evidence Code|list}}} +

'''Evidence:''' {{{field|Evidence|}}} +{{{end template}}} + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + diff --git a/planteome/paw/forms/Provenance.wiki b/planteome/paw/forms/Provenance.wiki new file mode 100644 index 0000000..6baec4b --- /dev/null +++ b/planteome/paw/forms/Provenance.wiki @@ -0,0 +1,32 @@ + +This is the "Provenance" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. + +{{#forminput:form=Provenance}} + + + +{{{info|page name=Provenance}}} + +{{{for template|Provenance}}} +{| class="formtable" +! Annotation Page: +| {{{field|Annotation Page}}} +|} +{{{end template}}} + +{{{for template|Provenance Repeater|multiple}}} +'''Field or Object:''' {{{field|Source Field or Object}}} +'''Category:''' {{{field|Source Category}}} +'''Accession ID:''' {{{field|Source Accession ID}}} +'''Source:''' {{{field|Source}}} +{{{end template}}} + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + diff --git a/planteome/paw/forms/Publication.wiki b/planteome/paw/forms/Publication.wiki new file mode 100644 index 0000000..b86c6e8 --- /dev/null +++ b/planteome/paw/forms/Publication.wiki @@ -0,0 +1,55 @@ + +This is the "Publication" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. + + +{{#forminput:form=Publication}} + + + +{{{info|page name=Publication:}}} +{{{for template|Publication}}} + +{{#set:Annotation References={{{Annotation References|}}}, {{{New Annotation Reference|}}} }} + +{| class="formtable" +! Publication: +| {{{field|Publication}}} +|- +! Publication ID: +| {{{field|Publication ID}}} +|- +! Publication Title: +| {{{field|Publication Title}}} +|- +! First Author: +| {{{field|First Author}}} +|- +! Journal Name: +| {{{field|Journal Name}}} +|- +! Volume: +| {{{field|Volume}}} +|- +! Year: +| {{{field|Year}}} +|- +! Pages: +| {{{field|Pages}}} +|- +! Annotation References: +| {{{field|Annotation References}}} +|- +! New Annotation Reference (to be hidden): +| {{{field|New Annotation Reference}}} +|} +{{{end template}}} + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + diff --git a/planteome/paw/forms/Reference_Publication.wiki b/planteome/paw/forms/Reference_Publication.wiki new file mode 100644 index 0000000..f358e5f --- /dev/null +++ b/planteome/paw/forms/Reference_Publication.wiki @@ -0,0 +1,52 @@ + +This is the "Reference Publication" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. + + +{{#forminput:form=Reference Publication}} + + + +{{{info|page name=Publication:}}} +{{{for template|Reference Publication}}} +{| class="formtable" +! Publication: +| {{{field|Publication}}} +|- +! Publication ID: +| {{{field|Publication ID}}} +|- +! Publication Title: +| {{{field|Publication Title|hidden}}} +|- +! First Author: +| {{{field|First Author|hidden}}} +|- +! Journal Name: +| {{{field|Journal Name|hidden}}} +|- +! Volume: +| {{{field|Volume|hidden}}} +|- +! Year: +| {{{field|Year|hidden}}} +|- +! Pages: +| {{{field|Pages|hidden}}} +|- +! Annotation References: +| {{{field|Annotation References}}} +|- +! New Annotation Reference (to be hidden): +| {{{field|New Annotation Reference}}} +|} +{{{end template}}} + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + diff --git a/planteome/paw/forms/Sequences.wiki b/planteome/paw/forms/Sequences.wiki new file mode 100644 index 0000000..e2127df --- /dev/null +++ b/planteome/paw/forms/Sequences.wiki @@ -0,0 +1,32 @@ + +This is the "Sequences" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. + + +{{#forminput:form=Sequences}} + + + +{{{info|page name=Sequences}}} + +{{{for template|Sequences}}} +{| class="formtable" +! Annotation Page: +| {{{field|Annotation Page}}} +|} +{{{end template}}} + +{{{for template|Sequence Repeater|multiple}}} +'''Sequence Type:''' {{{field|Sequence Type}}} +'''Sequence Source:''' {{{field|Sequence Source}}} +'''Accession ID:''' {{{field|External Accession ID}}} +{{{end template}}} + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + diff --git a/planteome/paw/forms/Source.wiki b/planteome/paw/forms/Source.wiki new file mode 100644 index 0000000..62f26d6 --- /dev/null +++ b/planteome/paw/forms/Source.wiki @@ -0,0 +1,38 @@ + +This is the "Source" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. + + +{{#forminput:form=Source}} + + + +{{{info|page name=Source:}}} + +{{{for template|Source}}} +{| class="formtable" +! Source Date Stamp: +| {{{field|Source Date Stamp}}} +|- +! Source Database: +| {{{field|Source Database}}} +|- +! Source Version: +| {{{field|Source Version}}} +|- +! Source URI: +| {{{field|Source URI}}} +|- +! Source File: +| {{{field|Source File}}} +|} +{{{end template}}} + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + diff --git a/planteome/paw/local_settings/dev.LocalSettings.php b/planteome/paw/local_settings/dev.LocalSettings.php new file mode 100644 index 0000000..3b264e1 --- /dev/null +++ b/planteome/paw/local_settings/dev.LocalSettings.php @@ -0,0 +1,173 @@ +&format=json&max=20'; +$sfgAutocompletionURLs['remote_PO_ids'] = 'http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=acc&ontology=po&qval=&format=json&max=20'; + +# GO web service calls +$sfgAutocompletionURLs['remote_GO_terms'] = 'http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&ontology=go&qval=&format=json&max=25'; +$sfgAutocompletionURLs['remote_GO_ids'] = 'http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=acc&ontology=go&qval=&format=json&max=25'; + +$sfgAutocompleteOnAllChars = false; + +# END: Justin Preece - Semantic Bundle (SMW and other extensions) + +/** Allow client-side caching of pages */ +$wgCachePages = false; + +/** + * * Set this to current time to invalidate all prior cached pages. Affects both + * * client- and server-side caching. + * * You can get the current date on your server by using the command: + * * date +%Y%m%d%H%M%S + * */ +$wgCacheEpoch = 'date +%Y%m%d%H%M%S'; + + +# When you make changes to this configuration file, this will make +# sure that cached pages are cleared. +$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) ); diff --git a/planteome/paw/local_settings/proto.LocalSettings.php b/planteome/paw/local_settings/proto.LocalSettings.php new file mode 100644 index 0000000..15b7902 --- /dev/null +++ b/planteome/paw/local_settings/proto.LocalSettings.php @@ -0,0 +1,175 @@ +&format=json&max=20'; +$sfgAutocompleteOnAllChars = false; + +# END 02/22/11: Justin Preece - Semantic Bundle (SMW and other extensions) + +/** Allow client-side caching of pages */ +$wgCachePages = false; + +/** + * * Set this to current time to invalidate all prior cached pages. Affects both + * * client- and server-side caching. + * * You can get the current date on your server by using the command: + * * date +%Y%m%d%H%M%S + * */ +$wgCacheEpoch = 'date +%Y%m%d%H%M%S'; + + +# When you make changes to this configuration file, this will make +# sure that cached pages are cleared. +$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) ); diff --git a/planteome/paw/local_settings/test.LocalSettings.php b/planteome/paw/local_settings/test.LocalSettings.php new file mode 100644 index 0000000..5bf519d --- /dev/null +++ b/planteome/paw/local_settings/test.LocalSettings.php @@ -0,0 +1,170 @@ +&format=json&max=20'; +$sfgAutocompletionURLs['remote_PO_ids'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=acc&ontology=po&qval=&format=json&max=20'; + +# GO web service calls +$sfgAutocompletionURLs['remote_GO_terms'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&ontology=go&qval=&format=json&max=25'; +$sfgAutocompletionURLs['remote_GO_ids'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=acc&ontology=go&qval=&format=json&max=25'; + +$sfgAutocompleteOnAllChars = false; + +# END: Justin Preece - Semantic Bundle (SMW and other extensions) + +/** Allow client-side caching of pages */ +$wgCachePages = false; + +/** + * * Set this to current time to invalidate all prior cached pages. Affects both + * * client- and server-side caching. + * * You can get the current date on your server by using the command: + * * date +%Y%m%d%H%M%S + * */ +$wgCacheEpoch = 'date +%Y%m%d%H%M%S'; + +# When you make changes to this configuration file, this will make +# sure that cached pages are cleared. +$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) ); diff --git a/planteome/paw/local_settings/test.SemanticBundleSettings.php b/planteome/paw/local_settings/test.SemanticBundleSettings.php new file mode 100644 index 0000000..966e4d2 --- /dev/null +++ b/planteome/paw/local_settings/test.SemanticBundleSettings.php @@ -0,0 +1,93 @@ + + +=cut + +# TODO: file size check and clip +# TODO: file numbering + +# --------------------------------------------------------------------------- +# modules +# --------------------------------------------------------------------------- + +# general +use strict; +use Cwd; +use Switch; +use Getopt::Std; +use Data::Dumper; + +# specific +use XML::Smart; +use XML::Writer; +use IO::File; +use Encode; + +# --------------------------------------------------------------------------- +# declarations +# --------------------------------------------------------------------------- + +my %opts; # arg options +my $file_type; # tab, csv, gaf +my $file_del; # data delimeter +my $input_file; +my $output_file; +my $verbose = 0; # flag for verbose output +my $debug = 0; # debugging switch + +# global data storage ---------- + +# universal +my %source; +my $output_data; + +# tab, csv +my $template_name; +my @field_names; +my @field_data; +my $xml; # represents the xml doc + +# gaf +my %ontology_info; # holds ontology names and aspects, keyed by abbreviation +my $curr_ontology_type; # flag to track the proper ontology to reference, line by line +my %annotation_universals; # holds values assumed not to vary across the file +my %annotations; # keyed on Gene Symbol + +# other config constants (including temporary arrangements) + +# default page id seeds, until I can figure out how to auto-increment w/in the +# an import/update script +my $SOURCE_TITLE_SEED = 1; +my $ANNOT_TITLE_SEED = 1; +my $PUB_TITLE_SEED = 1; + +$Data::Dumper::Pad = "... "; + +# --------------------------------------------------------------------------- +# functions +# --------------------------------------------------------------------------- + + +# --------------------------------------------------------------------------- +sub init +{ + # read and set options + getopts('i:t:o:s:vd', \%opts); + + foreach my $key (keys %opts) { + my $value = $opts{$key}; + switch ($key) { + case "i" { + if ($value =~ /\//) { # assume path + $input_file = $value; + } else { + $input_file = getcwd() . "\/$value"; + } + } + case "t" { $file_type = $value; } + + case "o" { + if ($value =~ /\//) { # assume path + $output_file = $value; + } else { + $output_file = getcwd() . "\/$value"; + } + } + case "s" { + my @seeds = split(',',$value); + if (scalar @seeds == 3) { + $SOURCE_TITLE_SEED = $seeds[0]; + $ANNOT_TITLE_SEED = $seeds[1]; + $PUB_TITLE_SEED = $seeds[2]; + } else { + die("Please supply three consecutive, comma-delimited seed" + . "values for the 's' option."); + } + } + case "v" { $verbose = 1; } + + case "d" { $debug = 1; } + } + } + + # split data on either commas or tabs + switch ($file_type) { + case "csv" { $file_del = ','; } + case "tab" { $file_del = '\t'; } + case "gaf" { $file_del = '\t'; } + else { + die(uc($file_type) . " is not a valid file type. Please supply " + . "a tab, csv, or gaf file.\n"); + } + } + + system "clear"; + print "\n" + . "------------------------------------------------------------\n" + . "-- Planteome Annotation Wiki Import Transformation Script --\n" + . "------------------------------------------------------------\n" + . "\n" + . "Input File: $input_file\n" + . "Designated input file type: $file_type\n" + . "Output File (Template): $output_file\n" + . "Source ID Seed: $SOURCE_TITLE_SEED\n" + . "Annotations ID Seed: $ANNOT_TITLE_SEED\n" + . "Publications ID Seed: $PUB_TITLE_SEED\n" + . "Running in verbose mode? " . ($verbose ? "Yes" : "No") . "\n" + . "Running in debug mode? " . ($debug ? "Yes" : "No") . "\n" + . "\n" + . "------------------------------------------------------------\n" + . "------------------------------------------------------------\n" + . "------------------------------------------------------------\n" + . "\n"; +} + + +# read, parse, and store generic CSV and tab templates and annotations +# --------------------------------------------------------------------------- +sub import_generic +{ + # read in "[Format] section... + my $line; + my $count = 0; + + while () + { + $count++; + $line = $_; + chomp $line; + my $data_val = (split('=',$line))[1]; + switch ($count) { + case 2 { $template_name = $data_val; } + case 3 { @field_names = split($file_del,$data_val); } + else {;} + } + if ($count == 3) { last; } + } + + # loop through data rows and add all data fields to an array of hashes + while () + { + $line = $_; + chomp $line; + + my @tmp_data_ary = split($file_del, $line); + my %tmp_hash; + + if ($debug) { print join(',',@tmp_data_ary) . "\n"; } + + for (my $i=0; $i { + name => "Gene Ontology", + aspects => { + P => "Biological Process", + C => "Cellular Component", + F => "Molecular Function" + } + }, + PO => { + name => "Plant Ontology", + aspects => { + A => "Plant Anatomy", + G => "Plant Growth and Development Stage" + } + } + ); + + if ($debug) { print "...\n" + . Dumper(\%ontology_info) . "\n\n"; } +} + +# read, parse, and store GAF annotations +# --------------------------------------------------------------------------- +sub import_gaf +{ + #[GAF implied data structure] + # singletons: db/Source (not really, but OK for now), taxon/Species ID, + # assigned_by, gene_type/Gene Type (later: proteins, too) + # lower priority: db_object_id, date + # not needed: qualifier + # unvaried fields (gene-level): db_object_symbol/Gene Symbol, + # db_object_name/Gene Name, + # db_object_synonym/Gene Locus|Source Accession ID|Chromosome|Gene Synonyms (see below), + # varied fields (gene synonyms): db_object_synonym/Gene Synonym + # varied fields (ontology-level): term_id/Term ID, evidence_code/Evidence Code, + # aspect/Aspect, db_reference (multi-, get PMID from here), with_or_from (multi-) + + # [Annotation Object Structure] + # %annotation_universals + # "Source" + # "Species ID" + # "Gene Type" + # %annotations + # "$Gene Symbol" => %annotation_properties + # "Gene Name" => string + # "Gene Locus"/"Source Accession ID" (first uc("AT.G")) => string + # "Chromosome" (AT#G in "Gene Locus") => string + # "Gene Synonyms" => % strings + # "Ontological References" => % "$Term ID" => %annotation_ontology_ref + # "Aspect" => string (assumes only one) + # "Evidence Codes" => % strings + # "Evidence" => % strings ("with_or_from" ) + # "Publications" => % PMID's from "db:reference", used to create separate Pub pages + + # set up a hash of ontology types and aspects to be referenced during data import + initialize_ontology(); + + # loop through data rows and build hashed annotation data structure + my $count = 0; + + # regex for locating a useable accession id from a locus (species-specific) + my $locus_finder_expr; + + while () + { + $count++; + my $line = $_; + chomp $line; + + my @curr_line_ary = split("\t", $line); + if ($debug) { print "...\n" + . Dumper(\@curr_line_ary) . "\n\n"; } + + my %curr_line_hash = ( + "db" => $curr_line_ary[0], # Source + "db_object_symbol" => $curr_line_ary[2], # Gene Symbol + "term_id" => $curr_line_ary[4], # Term ID + "db_reference" => $curr_line_ary[5], # inc. Publication info (PMID) + "evidence_code" => $curr_line_ary[6], # Evidence Code + "with_or_from" => $curr_line_ary[7], # Evidence (data) + "aspect" => $curr_line_ary[8], # Aspect + "db_object_name" => $curr_line_ary[9], # Gene Name + + # Gene Locus, Source Accession ID, Chromosome, Gene Synonyms + "db_object_synonym" => $curr_line_ary[10], + "db_object_type" => $curr_line_ary[11], # Gene Type + "taxon" => $curr_line_ary[12] # Species ID + ); + + if ($debug) { print "...\n" + . Dumper(\%curr_line_hash) . "\n\n"; } + + # grab the unvaried values from the first line + if ($count == 1) { + %annotation_universals = ( + "Source" => $curr_line_hash{"db"}, # currently not in use + "Gene Type" => $curr_line_hash{"db_object_type"}, + "Species ID" => "NCBI:" . (split(':',$curr_line_hash{"taxon"}))[1]#, + #"Species Name" => $species_name # TODO: get this from NCBI + ); + + # set species-specific values + switch ($annotation_universals{"Species ID"}) { + case "NCBI:3702" { + $locus_finder_expr = "^([Aa][Tt].[Gg])"; + $annotation_universals{"Species Name"} = "Arabidopsis thaliana"; # temp; need an NCBI lookup + } + case "NCBI:4530" { + $locus_finder_expr = "^(LOC_|[Oo][Ss]|osa-)"; + $annotation_universals{"Species Name"} = "Oryza sativa"; # temp; need an NCBI lookup + } + else { + die($annotation_universals{"Species ID"} + . " is not a valid NCBI taxon ID.\n"); + } + } + + if ($debug) { print "...\n" + . Dumper(\%annotation_universals) . "\n\n"; } + + } + + # set the ontology for the current line + $curr_ontology_type = uc((split(':',$curr_line_hash{"term_id"}))[0]); + + # check to see if Gene Symbol hash key exists (for grouping) + # if not, add the new Gene Symbol and its associated props + if (!exists $annotations{$curr_line_hash{"db_object_symbol"}}) + { + + # print "\n*** NEW SYMBOL: $curr_line_hash{'db_object_symbol'} ***\n"; # TEST + + # prepare Gene Locus, Source Accession ID, Chromosome, Gene Synonyms + my @loci; + my $locus = ""; + + if (exists $curr_line_hash{"db_object_synonym"}) + { + my @synonyms = split('\|',$curr_line_hash{"db_object_synonym"}); + + if ($debug) { print "...\n" + . Dumper(\@synonyms) . "\n\n"; } + + # find the gene locus, if it is listed + @loci = grep /$locus_finder_expr/, @synonyms; + + if ($debug) { print "...\n" + . Dumper(\@loci) . "\n\n"; } + } + + if (scalar(@loci) > 0) # we have at least one match; use the first one + { + $locus = $loci[0]; + } + else # no match; attempt to use the Gene Symbol instead + { + if ($curr_line_hash{"db_object_symbol"} =~ $locus_finder_expr) + { + # the split drops the variant/allele signifier, if present + if (!(split('.',$curr_line_hash{"db_object_symbol"}))[0]) + { + $locus = $curr_line_hash{"db_object_symbol"}; + } + else + { + $locus = (split('.',$curr_line_hash{"db_object_symbol"}))[0]; + } + } + else # no match; attempt to use the Gene Name instead + { + if ($curr_line_hash{"db_object_name"} =~ $locus_finder_expr) + { + $locus = (split('.',$curr_line_hash{"db_object_name"}))[0]; + } + } + } + + my $chromosome = ""; + if ($locus) { + if ($annotation_universals{"Species ID"} eq "NCBI:3702") { + # for Ath, third char in locus, if it exists + $chromosome = ($locus ne "" ? (split('',$locus))[2] : ""); + } + } + + # set some sort of pseudo-unique value as the accession id, + # in order of succession: locus, then symbol + # (NOTE: this is dangerous; a stable identifier is preferred) + my $accession_id = + $locus ? $locus : $curr_line_hash{"db_object_symbol"}; + + # set up props + my $annotation_properties = { + "Accession ID" => $accession_id, + "Gene Name" => $curr_line_hash{"db_object_name"}, + "Gene Locus" => $locus, + "Chromosome" => $chromosome + }; + + # add synonyms + for (split('\|', $curr_line_hash{"db_object_synonym"})) { + $$annotation_properties{"Gene Synonyms"}{$_} = ""; } + + if ($debug) { print "...\n" + . Dumper($annotation_properties) . "\n\n"; } + + # add new gene annotation and assign props + $annotations{$curr_line_hash{"db_object_symbol"}} = $annotation_properties; + + add_ontology_ref_data(\%curr_line_hash, $curr_ontology_type); # add the first ontology reference (every time) + } + # that Gene Symbol does exist, so we just need to roll-up multi-line + # annotation information, like gene synonyms and ontology refs + else + { + #print "\n*** EXISTING SYMBOL: $curr_line_hash{'db_object_symbol'} ***\n"; # TEST + + # add any add'l synonyms + for (split('\|', $curr_line_hash{"db_object_synonym"})) { + $annotations{$curr_line_hash{"db_object_symbol"}} + {"Gene Synonyms"}{$_} = ""; } + + add_ontology_ref_data(\%curr_line_hash, $curr_ontology_type); # add add'l ontology reference data + } + } + if ($debug) { print "...\n" + . Dumper(\%annotations) . "\n\n"; } +} + + +# read, parse, and store source +# --------------------------------------------------------------------------- +sub import_data +{ + print "Opening input file and reading header info...\n\n"; + + # open file + open(INPUT_FILE,$input_file) or die("Could not open input file."); + + # read in the source data + my $count = 0; + my $line; + while () + { + $count++; + $line = $_; + chomp $line; + my $data_val = (split('=',$line))[1]; + switch ($count) { + case 2 { $source{'SourceDateStamp'} = $data_val; } + case 3 { $source{'SourceDatabase'} = $data_val; } + case 4 { $source{'SourceVersion'} = $data_val; } + case 5 { $source{'SourceURI'} = $data_val; } + case 6 { $source{'SourceFile'} = $data_val; } + else {;} + } + if ($count == 6) { last; } + } + + print "Reading data...\n\n"; + $line = ; # skip "[Data]" + + switch ($file_type) { + case ('csv' || 'tab') { import_generic(); } + case 'gaf' { import_gaf(); } + } + + close INPUT_FILE; +} + + +# spit out the data to make sure you've read in the files correctly +# --------------------------------------------------------------------------- +sub show_input +{ + print "\n[Source]\n"; + foreach my $key (keys %source) { + print "$key: $source{$key}\n"; + } + print "\n"; + + switch ($file_type) { + case ('csv' || 'tab') { + print "[Template]\n$template_name\n\n"; + print "[Fields]\n" . join(', ',@field_names) . "\n\n"; + + print "[Data]\n"; + foreach my $row (@field_data) { + foreach my $key (keys %$row) { + print "$key => " . $row->{$key} . "\n"; + } + print "\n"; + } + } + case 'gaf' { + print "[Data]\n"; + + for my $key (keys %annotation_universals) { + print "$key: " . $annotation_universals{$key} . "\n"; + } + print "\n"; + + print "[Annotations]\n" . Dumper(\%annotations) . "\n\n"; + } + } + print "\n"; +} + +# xml transformation for generic tab or CSV-templated data +# (currently uses XML::Smart) +# --------------------------------------------------------------------------- +sub transform_generic +{ + my $curr_node; # placeholder for general node cursor + my $curr_prov_node; # placeholder for node cursor in provenance pages + my $curr_annot_node; # placeholder for node cursor in annotation pages + my $curr_accession_id; # holds each rows accession id for provenance marking + + + $xml = new XML::Smart($output_data, 'XML::Smart::Parser'); + + # set root element, source page and elements + # (temp set of page title until moved to import extension) + $xml->{Pages}{Page} = {Title => "Source:$SOURCE_TITLE_SEED"}; + + $curr_node = $xml->{Pages}{Page}; + $curr_node->{Template} = {Name => 'Source'}; + $curr_node = $curr_node->{Template}; + + $curr_node->{Field}[0] = {Name => 'Source Date Stamp'}; + $curr_node->{Field}[0]->content(0,$source{'SourceDateStamp'}); + $curr_node->{Field}[1] = {Name => 'Source Database'}; + $curr_node->{Field}[1]->content(0,$source{'SourceDatabase'}); + $curr_node->{Field}[2] = {Name => 'Source Version'}; + $curr_node->{Field}[2]->content(0,$source{'SourceVersion'}); + $curr_node->{Field}[3] = {Name => 'Source URI'}; + $curr_node->{Field}[3]->content(0,$source{'SourceURI'}); + $curr_node->{Field}[4] = {Name => 'Source File'}; + $curr_node->{Field}[4]->content(0,$source{'SourceFile'}); + + $curr_node = $curr_node->back->back; # return to node + + if ($debug) { print "Current node: " . $curr_node->path . "\n"; } + + my $next_page_title_id = $ANNOT_TITLE_SEED; + + # iterate through the data + foreach my $row (@field_data) { + + # set up next annotation page + my $next_page = { Title => "Annotation:$next_page_title_id" }; + push(@{$curr_node->{Page}}, $next_page); + + $curr_annot_node = $curr_node->{Page}( + "Title","eq","Annotation:$next_page_title_id"); + + if ($debug) { print "Curr annot node: ".$curr_annot_node->path."\n";} + + $curr_annot_node->{Template} = {Name => "$template_name"}; + $curr_annot_node = $curr_annot_node->{Template}; + + # set up next provenance page + $next_page = { Title => "Annotation:$next_page_title_id/Provenance" }; + push(@{$curr_node->{Page}}, $next_page); + + $curr_prov_node = $curr_node->{Page}( + "Title","eq","Annotation:$next_page_title_id/Provenance"); + + if ($debug) {print "Curr prov node: " . $curr_prov_node->path . "\n"; } + + $curr_prov_node->{Template} = {Name => 'Provenance'}; + $curr_prov_node = $curr_prov_node->{Template}; + $curr_prov_node->{Field} = {Name => 'Annotation Page'}; + $curr_prov_node->{Field}->content(0,"Annotation:$next_page_title_id"); + $curr_prov_node = $curr_prov_node->back; + + my $field_ct = 0; # counter for field position in pages + + # grab the Accession ID for the current row of data + foreach my $key (keys %$row) { + if ($key eq "Accession ID") { + $curr_accession_id = $row->{$key}; + if ($debug) { + print "* Found Accession ID: $curr_accession_id *\n"; + } + } + } + if (!(defined $curr_accession_id)) { + die "Error: No Accession ID available. Ending program.\n"; + } + + # iterate through the annotation data and assign to elements + foreach my $key (keys %$row) { + if ($debug) { print "$key => " . $row->{$key} . "\n"; } + + # build the annotation page + $curr_annot_node->{Field}[$field_ct] = {Name => $key}; + $curr_annot_node->{Field}[$field_ct]->content(0,$row->{$key}); + $field_ct++; + + # add a corresponding template to the annotation provenance page + my $next_prov_node = {Name => 'Provenance_Repeater'}; + push(@{$curr_prov_node->{Template}}, $next_prov_node); + + # grab the last template you added + $curr_prov_node = @{$curr_prov_node->{Template}}[-1]; + + # assign the relevant provenance field data + $curr_prov_node->{Field}[0] = {Name => 'Source'}; + $curr_prov_node->{Field}[0]->content(0,"Source:$SOURCE_TITLE_SEED"); + $curr_prov_node->{Field}[1] = {Name => 'Source Accession ID'}; + $curr_prov_node->{Field}[1]->content(0,$curr_accession_id); + $curr_prov_node->{Field}[2] = {Name => 'Source Template'}; + $curr_prov_node->{Field}[2]->content(0,$template_name); + $curr_prov_node->{Field}[3] = {Name => 'Source Field'}; + $curr_prov_node->{Field}[3]->content(0,$key); + + $curr_prov_node = $curr_prov_node->back; + } + $next_page_title_id++; + } + + # write out xml doc to a single ImportXML file + print "Writing data to output file...\n\n"; + $xml->save($output_file); + $output_data = $xml->data; +} + +# xml transformation for GAF data +# (currently uses XML::DOM) +# --------------------------------------------------------------------------- +sub transform_gaf +{ + # define templates and their fields for Provenance-generation + my $template_field_map = { + Annotation => [ + 'Species Name', + 'Species ID', + 'Gene Symbol', + 'Gene Name', + 'Gene Locus', + 'Gene Type', + 'Chromosome', + 'Has Phenotype' + ] + }; + + my %ref_pubs; # list of non-duplicate publication references + + # create new xml doc, write to string + my $writer = new XML::Writer( + OUTPUT => \$output_data, + DATA_MODE => 1, + DATA_INDENT => 4, + ENCODING => 'utf-8' + ); + + # create root elements + $writer->xmlDecl; + $writer->startTag("Pages"); + + # create source page + $writer->startTag("Page",Title=>"Source:$SOURCE_TITLE_SEED"); + $writer->startTag("Template",Name=>"Source"); + + # iterate the source hash for element name attribs and vals + my @pretty_elements; + foreach my $element (keys %source) + { + # split on CamelCase (saves a few lines and was fun to write) + for ($element) { + @pretty_elements = /[A-Z](?:[A-Z]+|[a-z]*)(?=$|[A-Z])/g; + } + $writer->dataElement("Field", $source{$element}, Name=>"@pretty_elements"); + } + + $writer->endTag("Template"); + $writer->endTag("Page"); + + # iterate %annotations + my $annot_title_count = $ANNOT_TITLE_SEED; + + foreach my $annotation (keys %annotations) + { + # create annotation page + $writer->startTag("Page",Title=>"Annotation:$annot_title_count"); + $writer->startTag("Template",Name=>"Annotation"); + $writer->dataElement("Field", $annotation_universals{"Species Name"}, Name=>"Species Name"); + $writer->dataElement("Field", $annotation_universals{"Species ID"}, Name=>"Species ID"); + $writer->dataElement("Field", $annotation, Name=>"Gene Symbol"); + $writer->dataElement("Field", $annotations{$annotation}{"Gene Name"}, Name=>"Gene Name"); + $writer->dataElement("Field", $annotations{$annotation}{"Gene Locus"}, Name=>"Gene Locus"); + $writer->dataElement("Field", ucfirst($annotation_universals{"Gene Type"}), Name=>"Gene Type"); + $writer->dataElement("Field", $annotations{$annotation}{"Chromosome"}, Name=>"Chromosome"); + $writer->dataElement("Field", "No", Name=>"Has Phenotype"); + $writer->endTag("Template"); + $writer->endTag("Page"); + + # create gene synonyms page + if (scalar keys (%{$annotations{$annotation}{'Gene Synonyms'}}) > 0) + { + $writer->startTag("Page",Title=>"Annotation:$annot_title_count/Gene Synonyms"); + $writer->startTag("Template",Name=>"Gene_Synonyms"); + $writer->dataElement("Field", "Annotation:$annot_title_count", Name=>"Annotation Page"); + $writer->endTag("Template"); + + foreach my $synonym (keys %{$annotations{$annotation}{'Gene Synonyms'}}) + { + $writer->startTag("Template",Name=>"Gene_Synonym_Repeater"); + $writer->dataElement("Field", $synonym, Name=>"Gene Synonym"); + $writer->endTag("Template"); + } + $writer->endTag("Page"); + } + + # create ont refs page + if (scalar keys (%{$annotations{$annotation}{"Ontological References"}}) > 0) + { + $writer->startTag("Page",Title=>"Annotation:$annot_title_count/Ontologies"); + $writer->startTag("Template",Name=>"Ontological_References"); + $writer->dataElement("Field", "Annotation:$annot_title_count", Name=>"Annotation Page"); + $writer->endTag("Template"); + + foreach my $ont_term (keys %{$annotations{$annotation}{"Ontological References"}}) + { + # gather PMID's for separate Ref Publication page creation (avoid dupes) + if (scalar keys (%{$annotations{$annotation}{"Ontological References"}{$ont_term}{"Publications"}}) > 0) { + foreach my $pub_term (keys %{$annotations{$annotation}{"Ontological References"}{$ont_term}{"Publications"}}) + { + if (!exists $ref_pubs{$pub_term}) { + $ref_pubs{$pub_term} = { "Annotation:$annot_title_count" => "" }; + } + else + { + $ref_pubs{$pub_term}{"Annotation:$annot_title_count"} = ""; + } + } + } + + $writer->startTag("Template",Name=>"$ontology_info{$curr_ontology_type}{name} Reference Repeater"); + $writer->dataElement("Field", $ontology_info{$curr_ontology_type}{"name"}, Name=>"Ontology"); + $writer->dataElement("Field", $ont_term, Name=>"Term ID"); + $writer->dataElement("Field", $annotations{$annotation}{"Ontological References"}{$ont_term}{"Aspect"}, Name=>"Aspect"); + + my @evidence_codes; + foreach my $evidence_code (keys %{$annotations{$annotation}{"Ontological References"}{$ont_term}{"Evidence Codes"}}) { + push @evidence_codes, $evidence_code; + } + $writer->dataElement("Field", join(', ',@evidence_codes), Name=>"Evidence Code"); + + my @ary_evidence; + foreach my $evidence (keys %{$annotations{$annotation}{"Ontological References"}{$ont_term}{"Evidence"}}) { + push @ary_evidence, $evidence; + } + $writer->dataElement("Field", join(', ',@ary_evidence), Name=>"Evidence"); + + $writer->endTag("Template"); + } + $writer->endTag("Page"); + } + + # create provenance page + $writer->startTag("Page",Title=>"Annotation:$annot_title_count/Provenance"); + $writer->startTag("Template",Name=>"Provenance"); + $writer->dataElement("Field", "Annotation:$annot_title_count", Name=>"Annotation Page"); + $writer->endTag("Template"); + + # items on the Annotation page + foreach (@{@$template_field_map{"Annotation"}}) + { + $writer->startTag("Template",Name=>"Provenance_Repeater"); + $writer->dataElement("Field", $_, Name=>"Source Field or Object"); + $writer->dataElement("Field", "Annotations", Name=>"Source Category"); + $writer->dataElement("Field", $annotations{$annotation}{"Accession ID"}, Name=>"Source Accession ID"); + $writer->dataElement("Field", "Source:$SOURCE_TITLE_SEED", Name=>"Source"); + $writer->endTag("Template"); + } + + # items on the Gene Synonyms subpage + if (scalar keys (%{$annotations{$annotation}{'Gene Synonyms'}}) > 0) + { + foreach my $synonym (keys %{$annotations{$annotation}{'Gene Synonyms'}}) + { + $writer->startTag("Template",Name=>"Provenance_Repeater"); + $writer->dataElement("Field", $synonym, Name=>"Source Field or Object"); + $writer->dataElement("Field", "Gene Synonyms", Name=>"Source Category"); + $writer->dataElement("Field", $annotations{$annotation}{"Accession ID"}, Name=>"Source Accession ID"); + $writer->dataElement("Field", "Source:$SOURCE_TITLE_SEED", Name=>"Source"); + $writer->endTag("Template"); + } + } + + # items on the Ontologies subpage + if (scalar keys (%{$annotations{$annotation}{"Ontological References"}}) > 0) + { + foreach my $ont_term (keys %{$annotations{$annotation}{"Ontological References"}}) + { + $writer->startTag("Template",Name=>"Provenance_Repeater"); + $writer->dataElement("Field", $ont_term, Name=>"Source Field or Object"); + $writer->dataElement("Field", "Ontological References", Name=>"Source Category"); + $writer->dataElement("Field", $annotations{$annotation}{"Accession ID"}, Name=>"Source Accession ID"); + $writer->dataElement("Field", "Source:$SOURCE_TITLE_SEED", Name=>"Source"); + $writer->endTag("Template"); + } + } + + + $writer->endTag("Page"); + + $annot_title_count++; + } + + if ($debug) { print "...\n" + . Dumper(\%ref_pubs) . "\n\n"; } + + # create Reference Publication pages + my $pub_title_count = $PUB_TITLE_SEED; + + if (scalar keys (%ref_pubs) > 0) { + + foreach my $ref_pub (keys %ref_pubs) + { + $writer->startTag("Page",Title=>"Publication:$pub_title_count"); + $writer->startTag("Template",Name=>"Reference_Publication"); + $writer->dataElement("Field", "PubMed", Name=>"Publication"); # TODO: replace hard-coded pub type w/ something dynamic + $writer->dataElement("Field", $ref_pub, Name=>"Publication ID"); + my @annot_refs; # holds com-del string of annotation page references + foreach my $annot_ref (keys %{$ref_pubs{$ref_pub}}) + { + push @annot_refs, $annot_ref; + } + $writer->dataElement("Field", join(',',@annot_refs), Name=>"Annotation References"); + $writer->endTag("Template"); + $writer->endTag("Page"); + + $pub_title_count++; + } + } + + # close doc + $writer->endTag("Pages"); + $writer->end(); + + # write out the file + open(OUTPUT_FILE,">$output_file"); + print OUTPUT_FILE $output_data; + close OUTPUT_FILE; +} + + +# loop through the hash and build annotation data and source xml doc +# --------------------------------------------------------------------------- +sub write_xml +{ + print "Transforming " . uc($file_type) . " data to SMW/SF XML...\n\n"; + + switch ($file_type) { + case ('csv' || 'tab') { transform_generic(); } + case 'gaf' { transform_gaf(); } + } +} + + +# print the transformed data (as xml) +# --------------------------------------------------------------------------- +sub show_output +{ + print "[XML]\n"; + print $output_data; + print "\n"; +} + +# --------------------------------------------------------------------------- +# main +# --------------------------------------------------------------------------- + +init; +import_data; +if ($verbose) { show_input; } +write_xml(); +if ($verbose) { show_output; } + +exit; + diff --git a/planteome/paw/prototyping/NCBI_eDocSummary.php b/planteome/paw/prototyping/NCBI_eDocSummary.php new file mode 100644 index 0000000..7e38a66 --- /dev/null +++ b/planteome/paw/prototyping/NCBI_eDocSummary.php @@ -0,0 +1,49 @@ +"); // inst. new xml doc for output + +// build xml doc with NCBI data +$DocSum = $xml_out->addChild("DocSum"); +$DocSum->addChild("Id",$NCBI_doc->DocSum->Id); + +foreach ($NCBI_doc->xpath("//Item") as $item) { + switch((string) $item["Name"]) { // Get attributes as element indices + case "PubDate": + $DocSum->addChild("PubDate",$item); + break; + case "Author": + $authorList[] = $item; + break; + case "LastAuthor": + $DocSum->addChild("LastAuthor",$item); + break; + case "Title": + $DocSum->addChild("Title",$item); + break; + case "Volume": + $DocSum->addChild("Volume",$item); + break; + case "Pages": + $DocSum->addChild("Pages",$item); + break; + case "FullJournalName": + $DocSum->addChild("FullJournalName",$item); + break; + } +} + +$author_list = ""; +foreach ($authorList as $author) { + $author_list = $author_list . $author . ", "; +} +$DocSum->addChild("AuthorList",rtrim($author_list,", ")); + + +header('Content-Type: text/xml'); // output xml doctype in your response +echo $xml_out->asXML(); +?> + diff --git a/planteome/paw/prototyping/TermSearch_JSON.php b/planteome/paw/prototyping/TermSearch_JSON.php new file mode 100644 index 0000000..89c1033 --- /dev/null +++ b/planteome/paw/prototyping/TermSearch_JSON.php @@ -0,0 +1,106 @@ + 50) { $number_of_terms = 50; } + + $qval = $_GET['qval']; + + $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0 + ? strtolower($_GET['qval']) + : die('Please provide a searchable value'); + + $format = strtolower($_GET['format']) != 'json' + ? strtolower($_GET['format']) + : 'json'; //json is the default + + /* connect to the db */ + $link = mysql_connect($_SERVER['mysql_host'], $_SERVER['mysql_user'], $_SERVER['mysql_pw']) or die('Cannot connect to the DB'); + mysql_select_db($_SERVER['mysql_db'],$link) or die('Cannot select the DB'); + + switch ($type) { + case 'autocomplete': + /* grab the terms from the db */ + $query = "SELECT t.$field FROM term t" + . " LEFT JOIN term_definition d ON d.term_id = t.id" + . " WHERE t.$field LIKE '%$qval%'" + . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')" + . " AND t.is_obsolete = 0" + . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" + . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" + . " ORDER BY name LIMIT $number_of_terms"; + $result = mysql_query($query,$link) or die('Errant query: '.$query); + + /* create one master array of the records */ + $terms = array(); + if(mysql_num_rows($result)) { + while($term = mysql_fetch_assoc($result)) { + $terms[] = array('title'=>$term[$field]); + } + } + + /* output in necessary format */ + if($format == 'json') { + header('Content-type: application/json'); + echo json_encode(array('sfautocomplete'=>$terms)); + } + else { + die('Sorry, this request cannot be fulfilled in '.$format.' format.'); + } + break; + + case 'term_detail': + /* grab the ontology data from the db */ + $query = "SELECT DISTINCT t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'" + . " FROM term t" + . " LEFT JOIN term_definition d ON d.term_id = t.id" + . " WHERE t.name = '$qval'" + . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')" + . " AND t.is_obsolete = 0" + . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" + . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" + . " ORDER BY t.name LIMIT 1"; + $result = mysql_query($query,$link) or die('Errant query: '.$query); + + /* create one master array of the records */ + $terms = array(); + if(mysql_num_rows($result)) { + while($term = mysql_fetch_assoc($result)) { + $terms[] = array( + 'id'=>$term['acc'], + 'aspect'=>$term['type'] == "plant_anatomy" ? "Plant Anatomy" : "Plant Growth and Development Stage", + 'definition'=>$term['definition'], + 'comment'=>$term['comment']); + } + } + /* output in necessary format */ + if($format == 'json') { + header('Content-type: application/json'); + echo json_encode(array('PO_result'=>$terms)); + } + else { + die('Sorry, this request cannot be fulfilled in '.$format.' format.'); + } + break; + default: + die('Sorry, this web service method is not available.'); + } + /* disconnect from the db */ + @mysql_close($link); +} +else { die('Not authorized.'); } +?> + diff --git a/planteome/paw/prototyping/remote_autocomplete.php b/planteome/paw/prototyping/remote_autocomplete.php new file mode 100755 index 0000000..a0f1f3e --- /dev/null +++ b/planteome/paw/prototyping/remote_autocomplete.php @@ -0,0 +1,7 @@ + + diff --git a/planteome/paw/prototyping/sample_species.xml b/planteome/paw/prototyping/sample_species.xml new file mode 100644 index 0000000..62badaa --- /dev/null +++ b/planteome/paw/prototyping/sample_species.xml @@ -0,0 +1,7 @@ + + + + + + + diff --git a/planteome/paw/prototyping/simple_forms_ajax.php b/planteome/paw/prototyping/simple_forms_ajax.php new file mode 100644 index 0000000..3c8fcd3 --- /dev/null +++ b/planteome/paw/prototyping/simple_forms_ajax.php @@ -0,0 +1 @@ + diff --git a/planteome/paw/services/NCBI_eDocSummary.php b/planteome/paw/services/NCBI_eDocSummary.php new file mode 100644 index 0000000..7e38a66 --- /dev/null +++ b/planteome/paw/services/NCBI_eDocSummary.php @@ -0,0 +1,49 @@ +"); // inst. new xml doc for output + +// build xml doc with NCBI data +$DocSum = $xml_out->addChild("DocSum"); +$DocSum->addChild("Id",$NCBI_doc->DocSum->Id); + +foreach ($NCBI_doc->xpath("//Item") as $item) { + switch((string) $item["Name"]) { // Get attributes as element indices + case "PubDate": + $DocSum->addChild("PubDate",$item); + break; + case "Author": + $authorList[] = $item; + break; + case "LastAuthor": + $DocSum->addChild("LastAuthor",$item); + break; + case "Title": + $DocSum->addChild("Title",$item); + break; + case "Volume": + $DocSum->addChild("Volume",$item); + break; + case "Pages": + $DocSum->addChild("Pages",$item); + break; + case "FullJournalName": + $DocSum->addChild("FullJournalName",$item); + break; + } +} + +$author_list = ""; +foreach ($authorList as $author) { + $author_list = $author_list . $author . ", "; +} +$DocSum->addChild("AuthorList",rtrim($author_list,", ")); + + +header('Content-Type: text/xml'); // output xml doctype in your response +echo $xml_out->asXML(); +?> + diff --git a/planteome/paw/services/dev.TermSearch_JSON.php b/planteome/paw/services/dev.TermSearch_JSON.php new file mode 100644 index 0000000..cffbdaf --- /dev/null +++ b/planteome/paw/services/dev.TermSearch_JSON.php @@ -0,0 +1,140 @@ + 50) { $number_of_terms = 50; } + + $ont = isset($_GET['ontology']) && in_array(strtolower($_GET['ontology']),$arr_ontologies) + ? strtolower($_GET['ontology']) + : die('"ontology" is a required parameter and must match an available data field.'); + + $qval = $_GET['qval']; + + $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0 + ? strtolower($_GET['qval']) + : die('Please provide a searchable value'); + + $format = strtolower($_GET['format']) != 'json' + ? strtolower($_GET['format']) + : 'json'; //json is the default + + /* connect to the appropriate db */ + switch ($ont) { + case 'po': + $link = mysql_connect($_SERVER['dev_po_host'], $_SERVER['dev_po_user'], $_SERVER['dev_po_pw']) or die('Cannot connect to the DB'); + mysql_select_db($_SERVER['dev_po_db'],$link) or die('Cannot select the DB'); + + $term_types = "'plant_anatomy','plant_growth_and_development_stage'"; + break; + + case 'go': + $link = mysql_connect($_SERVER['dev_go_host'], $_SERVER['dev_go_user'], $_SERVER['dev_go_pw']) or die('Cannot connect to the DB'); + mysql_select_db($_SERVER['dev_go_db'],$link) or die('Cannot select the DB'); + + $term_types = "'biological_process','cellular_component','molecular_function'"; + break; + + default: + die('Sorry, this ontology type is not available.'); + } + + switch ($type) { + case 'autocomplete': + /* grab the terms from the db */ + $query = "SELECT t.$field FROM term t" + . " LEFT JOIN term_definition d ON d.term_id = t.id" + . " WHERE t.$field LIKE '%$qval%'" + . " AND t.term_type in ($term_types)" + . " AND t.is_obsolete = 0" + . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" + . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" + . " ORDER BY name LIMIT $number_of_terms"; + $result = mysql_query($query,$link) or die('Errant query: '.$query); + + /* create one master array of the records */ + $terms = array(); + if(mysql_num_rows($result)) { + while($term = mysql_fetch_assoc($result)) { + $terms[] = array('title'=>$term[$field]); + } + } + + /* output in necessary format */ + if($format == 'json') { + header('Content-type: application/json'); + echo json_encode(array('sfautocomplete'=>$terms)); + } + else { + die('Sorry, this request cannot be fulfilled in '.$format.' format.'); + } + break; + + case 'term_detail': + /* grab the ontology data from the db */ + $query = "SELECT DISTINCT t.name as 'name', t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'" + . " FROM term t" + . " LEFT JOIN term_definition d ON d.term_id = t.id" + . " WHERE t.$field = '$qval'" + . " AND t.term_type in ($term_types)" + . " AND t.is_obsolete = 0" + . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" + . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" + . " ORDER BY t.name LIMIT 1"; + $result = mysql_query($query,$link) or die('Errant query: '.$query); + + /* create one master array of the records */ + $terms = array(); + if(mysql_num_rows($result)) { + while($term = mysql_fetch_assoc($result)) { + switch($term['type']) { + case 'plant_anatomy': + $term_type_formal = "Plant Anatomy"; break; + case 'plant_growth_and_development_stage': + $term_type_formal = "Plant Growth and Development Stage"; break; + case 'biological_process': + $term_type_formal = "Biological Process"; break; + case 'cellular_component': + $term_type_formal = "Cellular Component"; break; + case 'molecular_function': + $term_type_formal = "Molecular Function"; break; + } + $terms[] = array( + 'name'=>$term['name'], + 'id'=>$term['acc'], + 'aspect'=>$term_type_formal, + 'definition'=>$term['definition'], + 'comment'=>$term['comment']); + } + } + /* output in necessary format */ + if($format == 'json') { + header('Content-type: application/json'); + echo json_encode(array('term_detail_result'=>$terms)); + } + else { + die('Sorry, this request cannot be fulfilled in '.$format.' format.'); + } + break; + default: + die('Sorry, this web service method is not available.'); + } + /* disconnect from the db */ + @mysql_close($link); +} +else { die('Not authorized.'); } +?> + diff --git a/planteome/paw/services/test.TermSearch_JSON.php b/planteome/paw/services/test.TermSearch_JSON.php new file mode 100644 index 0000000..f60dcc5 --- /dev/null +++ b/planteome/paw/services/test.TermSearch_JSON.php @@ -0,0 +1,140 @@ + 50) { $number_of_terms = 50; } + + $ont = isset($_GET['ontology']) && in_array(strtolower($_GET['ontology']),$arr_ontologies) + ? strtolower($_GET['ontology']) + : die('"ontology" is a required parameter and must match an available data field.'); + + $qval = $_GET['qval']; + + $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0 + ? strtolower($_GET['qval']) + : die('Please provide a searchable value'); + + $format = strtolower($_GET['format']) != 'json' + ? strtolower($_GET['format']) + : 'json'; //json is the default + + /* connect to the appropriate db */ + switch ($ont) { + case 'po': + $link = mysql_connect($_SERVER['test_po_host'], $_SERVER['test_po_user'], $_SERVER['test_po_pw']) or die('Cannot connect to the DB'); + mysql_select_db($_SERVER['test_po_db'],$link) or die('Cannot select the DB'); + + $term_types = "'plant_anatomy','plant_growth_and_development_stage'"; + break; + + case 'go': + $link = mysql_connect($_SERVER['test_go_host'], $_SERVER['test_go_user'], $_SERVER['test_go_pw']) or die('Cannot connect to the DB'); + mysql_select_db($_SERVER['test_go_db'],$link) or die('Cannot select the DB'); + + $term_types = "'biological_process','cellular_component','molecular_function'"; + break; + + default: + die('Sorry, this ontology type is not available.'); + } + + switch ($type) { + case 'autocomplete': + /* grab the terms from the db */ + $query = "SELECT t.$field FROM term t" + . " LEFT JOIN term_definition d ON d.term_id = t.id" + . " WHERE t.$field LIKE '%$qval%'" + . " AND t.term_type in ($term_types)" + . " AND t.is_obsolete = 0" + . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" + . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" + . " ORDER BY name LIMIT $number_of_terms"; + $result = mysql_query($query,$link) or die('Errant query: '.$query); + + /* create one master array of the records */ + $terms = array(); + if(mysql_num_rows($result)) { + while($term = mysql_fetch_assoc($result)) { + $terms[] = array('title'=>$term[$field]); + } + } + + /* output in necessary format */ + if($format == 'json') { + header('Content-type: application/json'); + echo json_encode(array('sfautocomplete'=>$terms)); + } + else { + die('Sorry, this request cannot be fulfilled in '.$format.' format.'); + } + break; + + case 'term_detail': + /* grab the ontology data from the db */ + $query = "SELECT DISTINCT t.name as 'name', t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'" + . " FROM term t" + . " LEFT JOIN term_definition d ON d.term_id = t.id" + . " WHERE t.$field = '$qval'" + . " AND t.term_type in ($term_types)" + . " AND t.is_obsolete = 0" + . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" + . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" + . " ORDER BY t.name LIMIT 1"; + $result = mysql_query($query,$link) or die('Errant query: '.$query); + + /* create one master array of the records */ + $terms = array(); + if(mysql_num_rows($result)) { + while($term = mysql_fetch_assoc($result)) { + switch($term['type']) { + case 'plant_anatomy': + $term_type_formal = "Plant Anatomy"; break; + case 'plant_growth_and_development_stage': + $term_type_formal = "Plant Growth and Development Stage"; break; + case 'biological_process': + $term_type_formal = "Biological Process"; break; + case 'cellular_component': + $term_type_formal = "Cellular Component"; break; + case 'molecular_function': + $term_type_formal = "Molecular Function"; break; + } + $terms[] = array( + 'name'=>$term['name'], + 'id'=>$term['acc'], + 'aspect'=>$term_type_formal, + 'definition'=>$term['definition'], + 'comment'=>$term['comment']); + } + } + /* output in necessary format */ + if($format == 'json') { + header('Content-type: application/json'); + echo json_encode(array('term_detail_result'=>$terms)); + } + else { + die('Sorry, this request cannot be fulfilled in '.$format.' format.'); + } + break; + default: + die('Sorry, this web service method is not available.'); + } + /* disconnect from the db */ + @mysql_close($link); +} +else { die('Not authorized.'); } +?> + diff --git a/planteome/paw/skins/Planteome.deps.php b/planteome/paw/skins/Planteome.deps.php new file mode 100644 index 0000000..7a8c288 --- /dev/null +++ b/planteome/paw/skins/Planteome.deps.php @@ -0,0 +1,11 @@ +addStyle( 'planteome/main-rtl.css', 'screen', '', 'rtl' ); + $out->addStyle( 'planteome/main-ltr.css', 'screen', '', 'ltr' ); + // Append CSS which includes IE only behavior fixes for hover support - + // this is better than including this in a CSS fille since it doesn't + // wait for the CSS file to load before fetching the HTC file. + $out->addScript( + '' + ); + // Add extra stylesheets + // THIS IS ONLY USEFUL FOR EXPERIMENTING WITH DIFFERNT STYLE OPTIONS! THIS WILL BE REMOVED IN THE NEAR FUTURE. + if ( is_array( $wgPlanteomeExtraStyles ) ) { + foreach ( $wgPlanteomeExtraStyles as $style ) { + $out->addStyle( 'planteome/' . $style, 'screen' ); + } + } + } + /** + * Builds a structured array of links used for tabs and menus + * @return array + * @private + */ + function buildNavigationUrls() { + global $wgContLang, $wgLang, $wgOut, $wgUser, $wgRequest, $wgArticle, $wgStylePath; + global $wgDisableLangConversion, $wgPlanteomeUseIconWatch; + + wfProfileIn( __METHOD__ ); + + $links = array( + 'namespaces' => array(), + 'views' => array(), + 'actions' => array(), + 'variants' => array() + ); + + // Detects parameters + $action = $wgRequest->getVal( 'action', 'view' ); + $section = $wgRequest->getVal( 'section' ); + + // Checks if page is some kind of content + if( $this->iscontent ) { + + // Gets page objects for the related namespaces + $subjectPage = $this->mTitle->getSubjectPage(); + $talkPage = $this->mTitle->getTalkPage(); + + // Determines if this is a talk page + $isTalk = $this->mTitle->isTalkPage(); + + // Generates XML IDs from namespace names + $subjectId = $this->mTitle->getNamespaceKey( '' ); + + if ( $subjectId == 'main' ) { + $talkId = 'talk'; + } else { + $talkId = "{$subjectId}_talk"; + } + $currentId = $isTalk ? $talkId : $subjectId; + + // Adds namespace links + $links['namespaces'][$subjectId] = $this->tabAction( + $subjectPage, 'vector-namespace-' . $subjectId, !$isTalk, '', true + ); + $links['namespaces'][$subjectId]['context'] = 'subject'; + $links['namespaces'][$talkId] = $this->tabAction( + $talkPage, 'vector-namespace-talk', $isTalk, '', true + ); + $links['namespaces'][$talkId]['context'] = 'talk'; + + // Adds view view link + if ( $this->mTitle->exists() ) { + $links['views']['view'] = $this->tabAction( + $isTalk ? $talkPage : $subjectPage, + 'vector-view-view', ( $action == 'view' ), '', true + ); + } + + wfProfileIn( __METHOD__ . '-edit' ); + + // Checks if user can... + if ( + // edit the current page + $this->mTitle->quickUserCan( 'edit' ) && + ( + // if it exists + $this->mTitle->exists() || + // or they can create one here + $this->mTitle->quickUserCan( 'create' ) + ) + ) { + // Builds CSS class for talk page links + $isTalkClass = $isTalk ? ' istalk' : ''; + + // Determines if we're in edit mode + $selected = ( + ( $action == 'edit' || $action == 'submit' ) && + ( $section != 'new' ) + ); + $links['views']['edit'] = array( + 'class' => ( $selected ? 'selected' : '' ) . $isTalkClass, + 'text' => $this->mTitle->exists() + ? wfMsg( 'vector-view-edit' ) + : wfMsg( 'vector-view-create' ), + 'href' => + $this->mTitle->getLocalUrl( $this->editUrlOptions() ) + ); + // Checks if this is a current rev of talk page and we should show a new + // section link + if ( ( $isTalk && $wgArticle->isCurrent() ) || ( $wgOut->showNewSectionLink() ) ) { + // Checks if we should ever show a new section link + if ( !$wgOut->forceHideNewSectionLink() ) { + // Adds new section link + //$links['actions']['addsection'] + $links['views']['addsection'] = array( + 'class' => 'collapsible ' . ( $section == 'new' ? 'selected' : false ), + 'text' => wfMsg( 'vector-action-addsection' ), + 'href' => $this->mTitle->getLocalUrl( + 'action=edit§ion=new' + ) + ); + } + } + // Checks if the page is known (some kind of viewable content) + } elseif ( $this->mTitle->isKnown() ) { + // Adds view source view link + $links['views']['viewsource'] = array( + 'class' => ( $action == 'edit' ) ? 'selected' : false, + 'text' => wfMsg( 'vector-view-viewsource' ), + 'href' => + $this->mTitle->getLocalUrl( $this->editUrlOptions() ) + ); + } + wfProfileOut( __METHOD__ . '-edit' ); + + wfProfileIn( __METHOD__ . '-live' ); + + // Checks if the page exists + if ( $this->mTitle->exists() ) { + // Adds history view link + $links['views']['history'] = array( + 'class' => 'collapsible ' . ( ($action == 'history') ? 'selected' : false ), + 'text' => wfMsg( 'vector-view-history' ), + 'href' => $this->mTitle->getLocalUrl( 'action=history' ), + 'rel' => 'archives', + ); + + if( $wgUser->isAllowed( 'delete' ) ) { + $links['actions']['delete'] = array( + 'class' => ($action == 'delete') ? 'selected' : false, + 'text' => wfMsg( 'vector-action-delete' ), + 'href' => $this->mTitle->getLocalUrl( 'action=delete' ) + ); + } + if ( $this->mTitle->quickUserCan( 'move' ) ) { + $moveTitle = SpecialPage::getTitleFor( + 'Movepage', $this->thispage + ); + $links['actions']['move'] = array( + 'class' => $this->mTitle->isSpecial( 'Movepage' ) ? + 'selected' : false, + 'text' => wfMsg( 'vector-action-move' ), + 'href' => $moveTitle->getLocalUrl() + ); + } + + if ( + $this->mTitle->getNamespace() !== NS_MEDIAWIKI && + $wgUser->isAllowed( 'protect' ) + ) { + if ( !$this->mTitle->isProtected() ){ + $links['actions']['protect'] = array( + 'class' => ($action == 'protect') ? + 'selected' : false, + 'text' => wfMsg( 'vector-action-protect' ), + 'href' => + $this->mTitle->getLocalUrl( 'action=protect' ) + ); + + } else { + $links['actions']['unprotect'] = array( + 'class' => ($action == 'unprotect') ? + 'selected' : false, + 'text' => wfMsg( 'vector-action-unprotect' ), + 'href' => + $this->mTitle->getLocalUrl( 'action=unprotect' ) + ); + } + } + } else { + // article doesn't exist or is deleted + if ( + $wgUser->isAllowed( 'deletedhistory' ) && + $wgUser->isAllowed( 'undelete' ) + ) { + if( $n = $this->mTitle->isDeleted() ) { + $undelTitle = SpecialPage::getTitleFor( 'Undelete' ); + $links['actions']['undelete'] = array( + 'class' => false, + 'text' => wfMsgExt( + 'vector-action-undelete', + array( 'parsemag' ), + $wgLang->formatNum( $n ) + ), + 'href' => $undelTitle->getLocalUrl( + 'target=' . urlencode( $this->thispage ) + ) + ); + } + } + + if ( + $this->mTitle->getNamespace() !== NS_MEDIAWIKI && + $wgUser->isAllowed( 'protect' ) + ) { + if ( !$this->mTitle->getRestrictions( 'create' ) ) { + $links['actions']['protect'] = array( + 'class' => ($action == 'protect') ? + 'selected' : false, + 'text' => wfMsg( 'vector-action-protect' ), + 'href' => + $this->mTitle->getLocalUrl( 'action=protect' ) + ); + + } else { + $links['actions']['unprotect'] = array( + 'class' => ($action == 'unprotect') ? + 'selected' : false, + 'text' => wfMsg( 'vector-action-unprotect' ), + 'href' => + $this->mTitle->getLocalUrl( 'action=unprotect' ) + ); + } + } + } + wfProfileOut( __METHOD__ . '-live' ); + /** + * The following actions use messages which, if made particular to + * the Planteome skin, would break the Ajax code which makes this + * action happen entirely inline. Skin::makeGlobalVariablesScript + * defines a set of messages in a javascript object - and these + * messages are assumed to be global for all skins. Without making + * a change to that procedure these messages will have to remain as + * the global versions. + */ + // Checks if the user is logged in + if ( $this->loggedin ) { + if ( $wgPlanteomeUseIconWatch ) { + $class = 'icon '; + $place = 'views'; + } else { + $class = ''; + $place = 'actions'; + } + $mode = $this->mTitle->userIsWatching() ? 'unwatch' : 'watch'; + $links[$place][$mode] = array( + 'class' => $class . ( ( $action == 'watch' || $action == 'unwatch' ) ? ' selected' : false ), + 'text' => wfMsg( $mode ), // uses 'watch' or 'unwatch' message + 'href' => $this->mTitle->getLocalUrl( 'action=' . $mode ) + ); + } + // This is instead of SkinTemplateTabs - which uses a flat array + wfRunHooks( 'SkinTemplateNavigation', array( &$this, &$links ) ); + + // If it's not content, it's got to be a special page + } else { + $links['namespaces']['special'] = array( + 'class' => 'selected', + 'text' => wfMsg( 'vector-namespace-special' ), + 'href' => $wgRequest->getRequestURL() + ); + } + + // Gets list of language variants + $variants = $wgContLang->getVariants(); + // Checks that language conversion is enabled and variants exist + if( !$wgDisableLangConversion && count( $variants ) > 1 ) { + // Gets preferred variant + $preferred = $wgContLang->getPreferredVariant(); + // Loops over each variant + foreach( $variants as $code ) { + // Gets variant name from language code + $varname = $wgContLang->getVariantname( $code ); + // Checks if the variant is marked as disabled + if( $varname == 'disable' ) { + // Skips this variant + continue; + } + // Appends variant link + $links['variants'][] = array( + 'class' => ( $code == $preferred ) ? 'selected' : false, + 'text' => $varname, + 'href' => $this->mTitle->getLocalURL( '', $code ) + ); + } + } + + wfProfileOut( __METHOD__ ); + + return $links; + } +} + +/** + * QuickTemplate class for Planteome skin + * @ingroup Skins + */ +class PlanteomeTemplate extends QuickTemplate { + + /* Members */ + + /** + * @var Cached skin object + */ + var $skin; + + /* Functions */ + + /** + * Outputs the entire contents of the XHTML page + */ + public function execute() { + global $wgRequest, $wgOut, $wgContLang; + + $this->skin = $this->data['skin']; + $action = $wgRequest->getText( 'action' ); + + // Build additional attributes for navigation urls + $nav = $this->skin->buildNavigationUrls(); + foreach ( $nav as $section => $links ) { + foreach ( $links as $key => $link ) { + $xmlID = $key; + if ( isset( $link['context'] ) && $link['context'] == 'subject' ) { + $xmlID = 'ca-nstab-' . $xmlID; + } else if ( isset( $link['context'] ) && $link['context'] == 'talk' ) { + $xmlID = 'ca-talk'; + } else { + $xmlID = 'ca-' . $xmlID; + } + $nav[$section][$key]['attributes'] = + ' id="' . Sanitizer::escapeId( $xmlID ) . '"'; + if ( $nav[$section][$key]['class'] ) { + $nav[$section][$key]['attributes'] .= + ' class="' . htmlspecialchars( $link['class'] ) . '"'; + unset( $nav[$section][$key]['class'] ); + } + // We don't want to give the watch tab an accesskey if the page + // is being edited, because that conflicts with the accesskey on + // the watch checkbox. We also don't want to give the edit tab + // an accesskey, because that's fairly superfluous and conflicts + // with an accesskey (Ctrl-E) often used for editing in Safari. + if ( + in_array( $action, array( 'edit', 'submit' ) ) && + in_array( $key, array( 'edit', 'watch', 'unwatch' ) ) + ) { + $nav[$section][$key]['key'] = + $this->skin->tooltip( $xmlID ); + } else { + $nav[$section][$key]['key'] = + $this->skin->tooltipAndAccesskey( $xmlID ); + } + } + } + $this->data['namespace_urls'] = $nav['namespaces']; + $this->data['view_urls'] = $nav['views']; + $this->data['action_urls'] = $nav['actions']; + $this->data['variant_urls'] = $nav['variants']; + // Build additional attributes for personal_urls + foreach ( $this->data['personal_urls'] as $key => $item) { + $this->data['personal_urls'][$key]['attributes'] = + ' id="' . Sanitizer::escapeId( "pt-$key" ) . '"'; + if ( isset( $item['active'] ) && $item['active'] ) { + $this->data['personal_urls'][$key]['attributes'] .= + ' class="active"'; + } + $this->data['personal_urls'][$key]['key'] = + $this->skin->tooltipAndAccesskey('pt-'.$key); + } + + // Generate additional footer links + $footerlinks = array( + 'info' => array( + 'lastmod', + 'viewcount', + 'numberofwatchingusers', + 'credits', + 'copyright', + 'tagline', + ), + 'places' => array( + 'privacy', + 'about', + 'disclaimer', + ), + ); + // Reduce footer links down to only those which are being used + $validFooterLinks = array(); + foreach( $footerlinks as $category => $links ) { + $validFooterLinks[$category] = array(); + foreach( $links as $link ) { + if( isset( $this->data[$link] ) && $this->data[$link] ) { + $validFooterLinks[$category][] = $link; + } + } + } + // Reverse horizontally rendered navigation elements + if ( $wgContLang->isRTL() ) { + $this->data['view_urls'] = + array_reverse( $this->data['view_urls'] ); + $this->data['namespace_urls'] = + array_reverse( $this->data['namespace_urls'] ); + $this->data['personal_urls'] = + array_reverse( $this->data['personal_urls'] ); + } + // Output HTML Page + $this->html( 'headelement' ); +?> +
+
+ +
html('specialpageattributes') ?>> + + + data['sitenotice'] ): ?> + +
html( 'sitenotice' ) ?>
+ + + +

html( 'title' ) ?>

+ + +
+ +

msg( 'tagline' ) ?>

+ + +
html('userlangattributes') ?>>html( 'subtitle' ) ?>
+ + data['undelete'] ): ?> + +
html( 'undelete' ) ?>
+ + + data['newtalk'] ): ?> + +
html( 'newtalk' ) ?>
+ + + data['showjumplinks'] ): ?> + + + + + + html( 'bodytext' ) ?> + + data['catlinks'] ): ?> + + html( 'catlinks' ); ?> + + + data['dataAfterContent'] ): ?> + + html( 'dataAfterContent' ); ?> + + +
+
+ +
+ + +
+ renderNavigation( 'PERSONAL' ); ?> +
+ renderNavigation( array( 'NAMESPACES', 'VARIANTS' ) ); ?> +
+
+ renderNavigation( array( 'VIEWS', 'ACTIONS', 'SEARCH' ) ); ?> +
+
+ + +
+ + + + renderPortals( $this->data['sidebar'] ); ?> +
+ + + + + + + + html( 'bottomscripts' ); /* JS call to runBodyOnloadHook */ ?> + html( 'reporttime' ) ?> + data['debug'] ): ?> + + + + + $content ) { + echo "\n\n"; + switch( $name ) { + case 'SEARCH': + break; + case 'TOOLBOX': +?> +
+ html('userlangattributes') ?>>msg( 'toolbox' ) ?> +
+ +
+
+data['language_urls'] ) { +?> +
+ html('userlangattributes') ?>>msg( 'otherlanguages' ) ?> +
+
    + data['language_urls'] as $langlink ): ?> +
    • + +
+
+
+ +
skin->tooltip( 'p-' . $name ) ?>> + html('userlangattributes') ?>> +
+ + + + + +
+
+\n"; + } + } + + /** + * Render one or more navigations elements by name, automatically reveresed + * when UI is in RTL mode + */ + private function renderNavigation( $elements ) { + global $wgContLang, $wgPlanteomeUseSimpleSearch, $wgStylePath; + + // If only one element was given, wrap it in an array, allowing more + // flexible arguments + if ( !is_array( $elements ) ) { + $elements = array( $elements ); + // If there's a series of elements, reverse them when in RTL mode + } else if ( $wgContLang->isRTL() ) { + $elements = array_reverse( $elements ); + } + // Render elements + foreach ( $elements as $name => $element ) { + echo "\n\n"; + switch ( $element ) { + case 'NAMESPACES': +?> +
+
msg('namespaces') ?>
+ html('userlangattributes') ?>> + data['namespace_urls'] as $key => $link ): ?> +
  • >>
    • + + +
    + +
    +
    msg('variants') ?>
    +
    + html('userlangattributes') ?>> + data['variant_urls'] as $key => $link ): ?> + >> + + +
    +
    + +
    +
    msg('views') ?>
    + html('userlangattributes') ?>> + data['view_urls'] as $key => $link ): ?> + >>' : ''.htmlspecialchars( $link['text'] ).'') ?> + + +
    + +
    +
    msg('actions') ?>
    +
    + html('userlangattributes') ?>> + data['action_urls'] as $key => $link ): ?> + >> + + +
    +
    + +
    +
    msg('personaltools') ?>
    + html('userlangattributes') ?>> + data['personal_urls'] as $key => $item): ?> +
  • > class="">
    • + + +
    + + +\n"; + } + } +} diff --git a/planteome/paw/skins/planteome/Makefile b/planteome/paw/skins/planteome/Makefile new file mode 100644 index 0000000..74e36c4 --- /dev/null +++ b/planteome/paw/skins/planteome/Makefile @@ -0,0 +1,18 @@ +# +# Handy makefile to build the RTL variant with cssjanus +# + +all: main-rtl.css + +main-rtl.css: main-ltr.css cssjanus/cssjanus.py + python cssjanus/cssjanus.py --swap_ltr_rtl_in_url < main-ltr.css > main-rtl.css + +# SVN version is broken; checking in our own. +#cssjanus/cssjanus.py: +# svn co http://cssjanus.googlecode.com/svn/trunk cssjanus + +#distclean: clean +# rm -rf cssjanus + +clean: + rm -f main-rtl.css diff --git a/planteome/paw/skins/planteome/csshover.htc b/planteome/paw/skins/planteome/csshover.htc new file mode 100644 index 0000000..a88fa08 --- /dev/null +++ b/planteome/paw/skins/planteome/csshover.htc @@ -0,0 +1,262 @@ + + \ No newline at end of file diff --git a/planteome/paw/skins/planteome/cssjanus/COPYING b/planteome/paw/skins/planteome/cssjanus/COPYING new file mode 100644 index 0000000..3f2c895 --- /dev/null +++ b/planteome/paw/skins/planteome/cssjanus/COPYING @@ -0,0 +1,13 @@ + Copyright 2008 Google Inc. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/planteome/paw/skins/planteome/cssjanus/LICENSE b/planteome/paw/skins/planteome/cssjanus/LICENSE new file mode 100644 index 0000000..d645695 --- /dev/null +++ b/planteome/paw/skins/planteome/cssjanus/LICENSE @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/planteome/paw/skins/planteome/cssjanus/README b/planteome/paw/skins/planteome/cssjanus/README new file mode 100644 index 0000000..9b92215 --- /dev/null +++ b/planteome/paw/skins/planteome/cssjanus/README @@ -0,0 +1,91 @@ +=CSSJanus= + +_Flips CSS from LTR to an RTL orienation and vice-versa_ + +Author: `Lindsey Simon ` + +==Introduction== + +CSSJanus is CSS parser utility designed to aid the conversion of a website's +layout from left-to-right(LTR) to right-to-left(RTL). The script was born out of +a need to convert CSS for RTL languages when tables are not being used for layout (since tables will automatically reorder TD's in RTL). +CSSJanus will change most of the obvious CSS property names and their values as +well as some not-so-obvious ones (cursor, background-position %, etc...). +The script is designed to offer flexibility to account for cases when you do +not want to change certain rules which exist to account for bidirectional text +display bugs, as well as situations where you may or may not want to flip annotations inside of the background url string. +Note that you can disable CSSJanus from running on an entire class or any +rule within a class by prepending a /* @noflip */ comment before the rule(s) +you want CSSJanus to ignore. + +CSSJanus itself is not always enough to make a website that works in a LTR +language context work in a RTL language all the way, but it is a start. + +==Getting the code== + +View the trunk at: + + http://cssjanus.googlecode.com/svn/trunk/ + +Check out the latest development version anonymously with: + +{{{ + $ svn checkout http://cssjanus.googlecode.com/svn/trunk/ cssjanus +}}} + +==Using== + +Usage: + ./cssjanus.py < file.css > file-rtl.css +Flags: + --swap_left_right_in_url: Fixes "left"/"right" string within urls. + Ex: ./cssjanus.py --swap_left_right_in_url < file.css > file_rtl.css + --swap_ltr_rtl_in_url: Fixes "ltr"/"rtl" string within urls. + Ex: ./cssjanus.py --swap_ltr_rtl_in_url < file.css > file_rtl.css + +If you'd like to make use of the webapp version of cssjanus, you'll need to +download the Google App Engine SDK + http://code.google.com/appengine/downloads.html +and also drop a "django" directory into this directory, with the latest svn +from django. You should be good to go with that setup. Please let me know +otherwise. + +==Bugs, Patches== + +Patches and bug reports are welcome, just please keep the style +consistent with the original source. If you find a bug, please include a diff +of cssjanus_test.py with the bug included as a new unit test which fails. It +will make understanding and fixing the bug easier. + +==Todo== + +* Include some helpers for some typical bidi text solutions? +* Aural CSS (azimuth) swapping? + +==Contributors== + +Additional thanks to Mike Samuel for his work on csslex.py, Andy Perelson for +his help coding and reviewing, Stephen Zabel for his help with i18n and my sanity, +and to Eric Meyer for his thoughtful input. +Thanks to Junyu Wang for the Chinese translation. +Thanks to Masashi Kawashima for the Japanese translation. +Thanks to Taaryk Taar and Tariq Al-Omaireeni for an updated Arabic translation. +Thanks to Jens Meiert for the German translation. + +==License== + +{{{ + Copyright 2008 Google Inc. All Rights Reserved. + + Licensed under the Apache License, Version 2.0 (the 'License'); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an 'AS IS' BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. +}}} diff --git a/planteome/paw/skins/planteome/cssjanus/cssjanus.py b/planteome/paw/skins/planteome/cssjanus/cssjanus.py new file mode 100755 index 0000000..dd14bd5 --- /dev/null +++ b/planteome/paw/skins/planteome/cssjanus/cssjanus.py @@ -0,0 +1,574 @@ +#!/usr/bin/python +# +# Copyright 2008 Google Inc. All Rights Reserved. + +"""Converts a LeftToRight Cascading Style Sheet into a RightToLeft one. + + This is a utility script for replacing "left" oriented things in a CSS file + like float, padding, margin with "right" oriented values. + It also does the opposite. + The goal is to be able to conditionally serve one large, cat'd, compiled CSS + file appropriate for LeftToRight oriented languages and RightToLeft ones. + This utility will hopefully help your structural layout done in CSS in + terms of its RTL compatibility. It will not help with some of the more + complicated bidirectional text issues. +""" + +__author__ = 'elsigh@google.com (Lindsey Simon)' +__version__ = '0.1' + +import logging +import re +import sys +import getopt +import os + +import csslex + +logging.getLogger().setLevel(logging.INFO) + +# Global for the command line flags. +SWAP_LTR_RTL_IN_URL_DEFAULT = False +SWAP_LEFT_RIGHT_IN_URL_DEFAULT = False +FLAGS = {'swap_ltr_rtl_in_url': SWAP_LTR_RTL_IN_URL_DEFAULT, + 'swap_left_right_in_url': SWAP_LEFT_RIGHT_IN_URL_DEFAULT} + +# Generic token delimiter character. +TOKEN_DELIMITER = '~' + +# This is a temporary match token we use when swapping strings. +TMP_TOKEN = '%sTMP%s' % (TOKEN_DELIMITER, TOKEN_DELIMITER) + +# Token to be used for joining lines. +TOKEN_LINES = '%sJ%s' % (TOKEN_DELIMITER, TOKEN_DELIMITER) + +# Global constant text strings for CSS value matches. +LTR = 'ltr' +RTL = 'rtl' +LEFT = 'left' +RIGHT = 'right' + +# This is a lookbehind match to ensure that we don't replace instances +# of our string token (left, rtl, etc...) if there's a letter in front of it. +# Specifically, this prevents replacements like 'background: url(bright.png)'. +LOOKBEHIND_NOT_LETTER = r'(?)*?{)' % + (csslex.NMCHAR, TOKEN_LINES, csslex.SPACE)) + + +# These two lookaheads are to test whether or not we are within a +# background: url(HERE) situation. +# Ref: http://www.w3.org/TR/CSS21/syndata.html#uri +VALID_AFTER_URI_CHARS = r'[\'\"]?%s' % csslex.WHITESPACE +LOOKAHEAD_NOT_CLOSING_PAREN = r'(?!%s?%s\))' % (csslex.URL_CHARS, + VALID_AFTER_URI_CHARS) +LOOKAHEAD_FOR_CLOSING_PAREN = r'(?=%s?%s\))' % (csslex.URL_CHARS, + VALID_AFTER_URI_CHARS) + +# Compile a regex to swap left and right values in 4 part notations. +# We need to match negatives and decimal numeric values. +# ex. 'margin: .25em -2px 3px 0' becomes 'margin: .25em 0 3px -2px'. +POSSIBLY_NEGATIVE_QUANTITY = r'((?:-?%s)|(?:inherit|auto))' % csslex.QUANTITY +POSSIBLY_NEGATIVE_QUANTITY_SPACE = r'%s%s%s' % (POSSIBLY_NEGATIVE_QUANTITY, + csslex.SPACE, + csslex.WHITESPACE) +FOUR_NOTATION_QUANTITY_RE = re.compile(r'%s%s%s%s' % + (POSSIBLY_NEGATIVE_QUANTITY_SPACE, + POSSIBLY_NEGATIVE_QUANTITY_SPACE, + POSSIBLY_NEGATIVE_QUANTITY_SPACE, + POSSIBLY_NEGATIVE_QUANTITY), + re.I) +COLOR = r'(%s|%s)' % (csslex.NAME, csslex.HASH) +COLOR_SPACE = r'%s%s' % (COLOR, csslex.SPACE) +FOUR_NOTATION_COLOR_RE = re.compile(r'(-color%s:%s)%s%s%s(%s)' % + (csslex.WHITESPACE, + csslex.WHITESPACE, + COLOR_SPACE, + COLOR_SPACE, + COLOR_SPACE, + COLOR), + re.I) + +# Compile the cursor resize regexes +CURSOR_EAST_RE = re.compile(LOOKBEHIND_NOT_LETTER + '([ns]?)e-resize') +CURSOR_WEST_RE = re.compile(LOOKBEHIND_NOT_LETTER + '([ns]?)w-resize') + +# Matches the condition where we need to replace the horizontal component +# of a background-position value when expressed in horizontal percentage. +# Had to make two regexes because in the case of position-x there is only +# one quantity, and otherwise we don't want to match and change cases with only +# one quantity. +BG_HORIZONTAL_PERCENTAGE_RE = re.compile(r'background(-position)?(%s:%s)' + '([^%%]*?)(%s)%%' + '(%s(?:%s|%s))' % (csslex.WHITESPACE, + csslex.WHITESPACE, + csslex.NUM, + csslex.WHITESPACE, + csslex.QUANTITY, + csslex.IDENT)) + +BG_HORIZONTAL_PERCENTAGE_X_RE = re.compile(r'background-position-x(%s:%s)' + '(%s)%%' % (csslex.WHITESPACE, + csslex.WHITESPACE, + csslex.NUM)) + +# Matches the opening of a body selector. +BODY_SELECTOR = r'body%s{%s' % (csslex.WHITESPACE, csslex.WHITESPACE) + +# Matches anything up until the closing of a selector. +CHARS_WITHIN_SELECTOR = r'[^\}]*?' + +# Matches the direction property in a selector. +DIRECTION_RE = r'direction%s:%s' % (csslex.WHITESPACE, csslex.WHITESPACE) + +# These allow us to swap "ltr" with "rtl" and vice versa ONLY within the +# body selector and on the same line. +BODY_DIRECTION_LTR_RE = re.compile(r'(%s)(%s)(%s)(ltr)' % + (BODY_SELECTOR, CHARS_WITHIN_SELECTOR, + DIRECTION_RE), + re.I) +BODY_DIRECTION_RTL_RE = re.compile(r'(%s)(%s)(%s)(rtl)' % + (BODY_SELECTOR, CHARS_WITHIN_SELECTOR, + DIRECTION_RE), + re.I) + + +# Allows us to swap "direction:ltr" with "direction:rtl" and +# vice versa anywhere in a line. +DIRECTION_LTR_RE = re.compile(r'%s(ltr)' % DIRECTION_RE) +DIRECTION_RTL_RE = re.compile(r'%s(rtl)' % DIRECTION_RE) + +# We want to be able to switch left with right and vice versa anywhere +# we encounter left/right strings, EXCEPT inside the background:url(). The next +# two regexes are for that purpose. We have alternate IN_URL versions of the +# regexes compiled in case the user passes the flag that they do +# actually want to have left and right swapped inside of background:urls. +LEFT_RE = re.compile('%s(%s)%s%s' % (LOOKBEHIND_NOT_LETTER, + LEFT, + LOOKAHEAD_NOT_CLOSING_PAREN, + LOOKAHEAD_NOT_OPEN_BRACE), + re.I) +RIGHT_RE = re.compile('%s(%s)%s%s' % (LOOKBEHIND_NOT_LETTER, + RIGHT, + LOOKAHEAD_NOT_CLOSING_PAREN, + LOOKAHEAD_NOT_OPEN_BRACE), + re.I) +LEFT_IN_URL_RE = re.compile('%s(%s)%s' % (LOOKBEHIND_NOT_LETTER, + LEFT, + LOOKAHEAD_FOR_CLOSING_PAREN), + re.I) +RIGHT_IN_URL_RE = re.compile('%s(%s)%s' % (LOOKBEHIND_NOT_LETTER, + RIGHT, + LOOKAHEAD_FOR_CLOSING_PAREN), + re.I) +LTR_IN_URL_RE = re.compile('%s(%s)%s' % (LOOKBEHIND_NOT_LETTER, + LTR, + LOOKAHEAD_FOR_CLOSING_PAREN), + re.I) +RTL_IN_URL_RE = re.compile('%s(%s)%s' % (LOOKBEHIND_NOT_LETTER, + RTL, + LOOKAHEAD_FOR_CLOSING_PAREN), + re.I) + +COMMENT_RE = re.compile('(%s)' % csslex.COMMENT, re.I) + +NOFLIP_TOKEN = r'\@noflip' +# The NOFLIP_TOKEN inside of a comment. For now, this requires that comments +# be in the input, which means users of a css compiler would have to run +# this script first if they want this functionality. +NOFLIP_ANNOTATION = r'/\*%s%s%s\*/' % (csslex.WHITESPACE, + NOFLIP_TOKEN, + csslex. WHITESPACE) + +# After a NOFLIP_ANNOTATION, and within a class selector, we want to be able +# to set aside a single rule not to be flipped. We can do this by matching +# our NOFLIP annotation and then using a lookahead to make sure there is not +# an opening brace before the match. +NOFLIP_SINGLE_RE = re.compile(r'(%s%s[^;}]+;?)' % (NOFLIP_ANNOTATION, + LOOKAHEAD_NOT_OPEN_BRACE), + re.I) + +# After a NOFLIP_ANNOTATION, we want to grab anything up until the next } which +# means the entire following class block. This will prevent all of its +# declarations from being flipped. +NOFLIP_CLASS_RE = re.compile(r'(%s%s})' % (NOFLIP_ANNOTATION, + CHARS_WITHIN_SELECTOR), + re.I) + + +class Tokenizer: + """Replaces any CSS comments with string tokens and vice versa.""" + + def __init__(self, token_re, token_string): + """Constructor for the Tokenizer. + + Args: + token_re: A regex for the string to be replace by a token. + token_string: The string to put between token delimiters when tokenizing. + """ + logging.debug('Tokenizer::init token_string=%s' % token_string) + self.token_re = token_re + self.token_string = token_string + self.originals = [] + + def Tokenize(self, line): + """Replaces any string matching token_re in line with string tokens. + + By passing a function as an argument to the re.sub line below, we bypass + the usual rule where re.sub will only replace the left-most occurrence of + a match by calling the passed in function for each occurrence. + + Args: + line: A line to replace token_re matches in. + + Returns: + line: A line with token_re matches tokenized. + """ + line = self.token_re.sub(self.TokenizeMatches, line) + logging.debug('Tokenizer::Tokenize returns: %s' % line) + return line + + def DeTokenize(self, line): + """Replaces tokens with the original string. + + Args: + line: A line with tokens. + + Returns: + line with any tokens replaced by the original string. + """ + + # Put all of the comments back in by their comment token. + for i, original in enumerate(self.originals): + token = '%s%s_%s%s' % (TOKEN_DELIMITER, self.token_string, i + 1, + TOKEN_DELIMITER) + line = line.replace(token, original) + logging.debug('Tokenizer::DeTokenize i:%s w/%s' % (i, token)) + logging.debug('Tokenizer::DeTokenize returns: %s' % line) + return line + + def TokenizeMatches(self, m): + """Replaces matches with tokens and stores the originals. + + Args: + m: A match object. + + Returns: + A string token which replaces the CSS comment. + """ + logging.debug('Tokenizer::TokenizeMatches %s' % m.group(1)) + self.originals.append(m.group(1)) + return '%s%s_%s%s' % (TOKEN_DELIMITER, + self.token_string, + len(self.originals), + TOKEN_DELIMITER) + + +def FixBodyDirectionLtrAndRtl(line): + """Replaces ltr with rtl and vice versa ONLY in the body direction. + + Args: + line: A string to replace instances of ltr with rtl. + Returns: + line with direction: ltr and direction: rtl swapped only in body selector. + line = FixBodyDirectionLtrAndRtl('body { direction:ltr }') + line will now be 'body { direction:rtl }'. + """ + + line = BODY_DIRECTION_LTR_RE.sub('\\1\\2\\3%s' % TMP_TOKEN, line) + line = BODY_DIRECTION_RTL_RE.sub('\\1\\2\\3%s' % LTR, line) + line = line.replace(TMP_TOKEN, RTL) + logging.debug('FixBodyDirectionLtrAndRtl returns: %s' % line) + return line + + +def FixLeftAndRight(line): + """Replaces left with right and vice versa in line. + + Args: + line: A string in which to perform the replacement. + + Returns: + line with left and right swapped. For example: + line = FixLeftAndRight('padding-left: 2px; margin-right: 1px;') + line will now be 'padding-right: 2px; margin-left: 1px;'. + """ + + line = LEFT_RE.sub(TMP_TOKEN, line) + line = RIGHT_RE.sub(LEFT, line) + line = line.replace(TMP_TOKEN, RIGHT) + logging.debug('FixLeftAndRight returns: %s' % line) + return line + + +def FixLeftAndRightInUrl(line): + """Replaces left with right and vice versa ONLY within background urls. + + Args: + line: A string in which to replace left with right and vice versa. + + Returns: + line with left and right swapped in the url string. For example: + line = FixLeftAndRightInUrl('background:url(right.png)') + line will now be 'background:url(left.png)'. + """ + + line = LEFT_IN_URL_RE.sub(TMP_TOKEN, line) + line = RIGHT_IN_URL_RE.sub(LEFT, line) + line = line.replace(TMP_TOKEN, RIGHT) + logging.debug('FixLeftAndRightInUrl returns: %s' % line) + return line + + +def FixLtrAndRtlInUrl(line): + """Replaces ltr with rtl and vice versa ONLY within background urls. + + Args: + line: A string in which to replace ltr with rtl and vice versa. + + Returns: + line with left and right swapped. For example: + line = FixLtrAndRtlInUrl('background:url(rtl.png)') + line will now be 'background:url(ltr.png)'. + """ + + line = LTR_IN_URL_RE.sub(TMP_TOKEN, line) + line = RTL_IN_URL_RE.sub(LTR, line) + line = line.replace(TMP_TOKEN, RTL) + logging.debug('FixLtrAndRtlInUrl returns: %s' % line) + return line + + +def FixCursorProperties(line): + """Fixes directional CSS cursor properties. + + Args: + line: A string to fix CSS cursor properties in. + + Returns: + line reformatted with the cursor properties substituted. For example: + line = FixCursorProperties('cursor: ne-resize') + line will now be 'cursor: nw-resize'. + """ + + line = CURSOR_EAST_RE.sub('\\1' + TMP_TOKEN, line) + line = CURSOR_WEST_RE.sub('\\1e-resize', line) + line = line.replace(TMP_TOKEN, 'w-resize') + logging.debug('FixCursorProperties returns: %s' % line) + return line + + +def FixFourPartNotation(line): + """Fixes the second and fourth positions in 4 part CSS notation. + + Args: + line: A string to fix 4 part CSS notation in. + + Returns: + line reformatted with the 4 part notations swapped. For example: + line = FixFourPartNotation('padding: 1px 2px 3px 4px') + line will now be 'padding: 1px 4px 3px 2px'. + """ + line = FOUR_NOTATION_QUANTITY_RE.sub('\\1 \\4 \\3 \\2', line) + line = FOUR_NOTATION_COLOR_RE.sub('\\1\\2 \\5 \\4 \\3', line) + logging.debug('FixFourPartNotation returns: %s' % line) + return line + + +def FixBackgroundPosition(line): + """Fixes horizontal background percentage values in line. + + Args: + line: A string to fix horizontal background position values in. + + Returns: + line reformatted with the 4 part notations swapped. + """ + line = BG_HORIZONTAL_PERCENTAGE_RE.sub(CalculateNewBackgroundPosition, line) + line = BG_HORIZONTAL_PERCENTAGE_X_RE.sub(CalculateNewBackgroundPositionX, + line) + logging.debug('FixBackgroundPosition returns: %s' % line) + return line + + +def CalculateNewBackgroundPosition(m): + """Fixes horizontal background-position percentages. + + This function should be used as an argument to re.sub since it needs to + perform replacement specific calculations. + + Args: + m: A match object. + + Returns: + A string with the horizontal background position percentage fixed. + BG_HORIZONTAL_PERCENTAGE_RE.sub(FixBackgroundPosition, + 'background-position: 75% 50%') + will return 'background-position: 25% 50%'. + """ + + # The flipped value is the offset from 100% + new_x = str(100-int(m.group(4))) + + # Since m.group(1) may very well be None type and we need a string.. + if m.group(1): + position_string = m.group(1) + else: + position_string = '' + + return 'background%s%s%s%s%%%s' % (position_string, m.group(2), m.group(3), + new_x, m.group(5)) + + +def CalculateNewBackgroundPositionX(m): + """Fixes percent based background-position-x. + + This function should be used as an argument to re.sub since it needs to + perform replacement specific calculations. + + Args: + m: A match object. + + Returns: + A string with the background-position-x percentage fixed. + BG_HORIZONTAL_PERCENTAGE_X_RE.sub(CalculateNewBackgroundPosition, + 'background-position-x: 75%') + will return 'background-position-x: 25%'. + """ + + # The flipped value is the offset from 100% + new_x = str(100-int(m.group(2))) + + return 'background-position-x%s%s%%' % (m.group(1), new_x) + + +def ChangeLeftToRightToLeft(lines, + swap_ltr_rtl_in_url=None, + swap_left_right_in_url=None): + """Turns lines into a stream and runs the fixing functions against it. + + Args: + lines: An list of CSS lines. + swap_ltr_rtl_in_url: Overrides this flag if param is set. + swap_left_right_in_url: Overrides this flag if param is set. + + Returns: + The same lines, but with left and right fixes. + """ + + global FLAGS + + # Possibly override flags with params. + logging.debug('ChangeLeftToRightToLeft swap_ltr_rtl_in_url=%s, ' + 'swap_left_right_in_url=%s' % (swap_ltr_rtl_in_url, + swap_left_right_in_url)) + if swap_ltr_rtl_in_url is None: + swap_ltr_rtl_in_url = FLAGS['swap_ltr_rtl_in_url'] + if swap_left_right_in_url is None: + swap_left_right_in_url = FLAGS['swap_left_right_in_url'] + + # Turns the array of lines into a single line stream. + logging.debug('LINES COUNT: %s' % len(lines)) + line = TOKEN_LINES.join(lines) + + # Tokenize any single line rules with the /* noflip */ annotation. + noflip_single_tokenizer = Tokenizer(NOFLIP_SINGLE_RE, 'NOFLIP_SINGLE') + line = noflip_single_tokenizer.Tokenize(line) + + # Tokenize any class rules with the /* noflip */ annotation. + noflip_class_tokenizer = Tokenizer(NOFLIP_CLASS_RE, 'NOFLIP_CLASS') + line = noflip_class_tokenizer.Tokenize(line) + + # Tokenize the comments so we can preserve them through the changes. + comment_tokenizer = Tokenizer(COMMENT_RE, 'C') + line = comment_tokenizer.Tokenize(line) + + # Here starteth the various left/right orientation fixes. + line = FixBodyDirectionLtrAndRtl(line) + + if swap_left_right_in_url: + line = FixLeftAndRightInUrl(line) + + if swap_ltr_rtl_in_url: + line = FixLtrAndRtlInUrl(line) + + line = FixLeftAndRight(line) + line = FixCursorProperties(line) + line = FixFourPartNotation(line) + line = FixBackgroundPosition(line) + + # DeTokenize the single line noflips. + line = noflip_single_tokenizer.DeTokenize(line) + + # DeTokenize the class-level noflips. + line = noflip_class_tokenizer.DeTokenize(line) + + # DeTokenize the comments. + line = comment_tokenizer.DeTokenize(line) + + # Rejoin the lines back together. + lines = line.split(TOKEN_LINES) + + return lines + +def usage(): + """Prints out usage information.""" + + print 'Usage:' + print ' ./cssjanus.py < file.css > file-rtl.css' + print 'Flags:' + print ' --swap_left_right_in_url: Fixes "left"/"right" string within urls.' + print ' Ex: ./cssjanus.py --swap_left_right_in_url < file.css > file_rtl.css' + print ' --swap_ltr_rtl_in_url: Fixes "ltr"/"rtl" string within urls.' + print ' Ex: ./cssjanus --swap_ltr_rtl_in_url < file.css > file_rtl.css' + +def setflags(opts): + """Parse the passed in command line arguments and set the FLAGS global. + + Args: + opts: getopt iterable intercepted from argv. + """ + + global FLAGS + + # Parse the arguments. + for opt, arg in opts: + logging.debug('opt: %s, arg: %s' % (opt, arg)) + if opt in ("-h", "--help"): + usage() + sys.exit() + elif opt in ("-d", "--debug"): + logging.getLogger().setLevel(logging.DEBUG) + elif opt == '--swap_ltr_rtl_in_url': + FLAGS['swap_ltr_rtl_in_url'] = True + elif opt == '--swap_left_right_in_url': + FLAGS['swap_left_right_in_url'] = True + + +def main(argv): + """Sends stdin lines to ChangeLeftToRightToLeft and writes to stdout.""" + + # Define the flags. + try: + opts, args = getopt.getopt(argv, 'hd', ['help', 'debug', + 'swap_left_right_in_url', + 'swap_ltr_rtl_in_url']) + except getopt.GetoptError: + usage() + sys.exit(2) + + # Parse and set the flags. + setflags(opts) + + # Call the main routine with all our functionality. + fixed_lines = ChangeLeftToRightToLeft(sys.stdin.readlines()) + sys.stdout.write(''.join(fixed_lines)) + +if __name__ == '__main__': + main(sys.argv[1:]) diff --git a/planteome/paw/skins/planteome/cssjanus/csslex.py b/planteome/paw/skins/planteome/cssjanus/csslex.py new file mode 100755 index 0000000..1fc7304 --- /dev/null +++ b/planteome/paw/skins/planteome/cssjanus/csslex.py @@ -0,0 +1,114 @@ +#!/usr/bin/python +# +# Copyright 2007 Google Inc. All Rights Reserved. + +"""CSS Lexical Grammar rules. + +CSS lexical grammar from http://www.w3.org/TR/CSS21/grammar.html +""" + +__author__ = ['elsigh@google.com (Lindsey Simon)', + 'msamuel@google.com (Mike Samuel)'] + +# public symbols +__all__ = [ "NEWLINE", "HEX", "NON_ASCII", "UNICODE", "ESCAPE", "NMSTART", "NMCHAR", "STRING1", "STRING2", "IDENT", "NAME", "HASH", "NUM", "STRING", "URL", "SPACE", "WHITESPACE", "COMMENT", "QUANTITY", "PUNC" ] + +# The comments below are mostly copied verbatim from the grammar. + +# "@import" {return IMPORT_SYM;} +# "@page" {return PAGE_SYM;} +# "@media" {return MEDIA_SYM;} +# "@charset" {return CHARSET_SYM;} +KEYWORD = r'(?:\@(?:import|page|media|charset))' + +# nl \n|\r\n|\r|\f ; a newline +NEWLINE = r'\n|\r\n|\r|\f' + +# h [0-9a-f] ; a hexadecimal digit +HEX = r'[0-9a-f]' + +# nonascii [\200-\377] +NON_ASCII = r'[\200-\377]' + +# unicode \\{h}{1,6}(\r\n|[ \t\r\n\f])? +UNICODE = r'(?:(?:\\' + HEX + r'{1,6})(?:\r\n|[ \t\r\n\f])?)' + +# escape {unicode}|\\[^\r\n\f0-9a-f] +ESCAPE = r'(?:' + UNICODE + r'|\\[^\r\n\f0-9a-f])' + +# nmstart [_a-z]|{nonascii}|{escape} +NMSTART = r'(?:[_a-z]|' + NON_ASCII + r'|' + ESCAPE + r')' + +# nmchar [_a-z0-9-]|{nonascii}|{escape} +NMCHAR = r'(?:[_a-z0-9-]|' + NON_ASCII + r'|' + ESCAPE + r')' + +# ident -?{nmstart}{nmchar}* +IDENT = r'-?' + NMSTART + NMCHAR + '*' + +# name {nmchar}+ +NAME = NMCHAR + r'+' + +# hash +HASH = r'#' + NAME + +# string1 \"([^\n\r\f\\"]|\\{nl}|{escape})*\" ; "string" +STRING1 = r'"(?:[^\"\\]|\\.)*"' + +# string2 \'([^\n\r\f\\']|\\{nl}|{escape})*\' ; 'string' +STRING2 = r"'(?:[^\'\\]|\\.)*'" + +# string {string1}|{string2} +STRING = '(?:' + STRING1 + r'|' + STRING2 + ')' + +# num [0-9]+|[0-9]*"."[0-9]+ +NUM = r'(?:[0-9]*\.[0-9]+|[0-9]+)' + +# s [ \t\r\n\f] +SPACE = r'[ \t\r\n\f]' + +# w {s}* +WHITESPACE = '(?:' + SPACE + r'*)' + +# url special chars +URL_SPECIAL_CHARS = r'[!#$%&*-~]' + +# url chars ({url_special_chars}|{nonascii}|{escape})* +URL_CHARS = r'(?:%s|%s|%s)*' % (URL_SPECIAL_CHARS, NON_ASCII, ESCAPE) + +# url +URL = r'url\(%s(%s|%s)%s\)' % (WHITESPACE, STRING, URL_CHARS, WHITESPACE) + +# comments +# see http://www.w3.org/TR/CSS21/grammar.html +COMMENT = r'/\*[^*]*\*+([^/*][^*]*\*+)*/' + +# {E}{M} {return EMS;} +# {E}{X} {return EXS;} +# {P}{X} {return LENGTH;} +# {C}{M} {return LENGTH;} +# {M}{M} {return LENGTH;} +# {I}{N} {return LENGTH;} +# {P}{T} {return LENGTH;} +# {P}{C} {return LENGTH;} +# {D}{E}{G} {return ANGLE;} +# {R}{A}{D} {return ANGLE;} +# {G}{R}{A}{D} {return ANGLE;} +# {M}{S} {return TIME;} +# {S} {return TIME;} +# {H}{Z} {return FREQ;} +# {K}{H}{Z} {return FREQ;} +# % {return PERCENTAGE;} +UNIT = r'(?:em|ex|px|cm|mm|in|pt|pc|deg|rad|grad|ms|s|hz|khz|%)' + +# {num}{UNIT|IDENT} {return NUMBER;} +QUANTITY = '%s(?:%s%s|%s)?' % (NUM, WHITESPACE, UNIT, IDENT) + +# "" {return CDC;} +# "~=" {return INCLUDES;} +# "|=" {return DASHMATCH;} +# {w}"{" {return LBRACE;} +# {w}"+" {return PLUS;} +# {w}">" {return GREATER;} +# {w}"," {return COMMA;} +PUNC = r'|~=|\|=|[\{\+>,:;]' diff --git a/planteome/paw/skins/planteome/experiments/babaco-colors-a.css b/planteome/paw/skins/planteome/experiments/babaco-colors-a.css new file mode 100644 index 0000000..ce6f67d --- /dev/null +++ b/planteome/paw/skins/planteome/experiments/babaco-colors-a.css @@ -0,0 +1,109 @@ +/* Babaco Color Scheme A */ + + +a:visited, +a:visited div.vectorTabs li.selected a:visited span { + color: #260e9c; +} + +html .thumbimage, +#toc, .toc, .mw-warning, div.thumbinner { + border-color: #cccccc; + background-color: #f7f7f7; +} + +/* Framework */ +#mw-page-base { + background-color: inherit !important; + background-image: none !important; +} +body { + background-color: #f9f9f9 !important; + background-image:url(images/page-base-updated.png); +} + +/* Links */ +a { + color: #0066cc; +} +a:visited { + color: #004d99; +} +a:active { + color: #ff6600; +} +a.stub { + color: #56228b; +} +a.new, #p-personal a.new { + color: #a31205 !important; +} +a.new:visited, #p-personal a.new:visited { + color: #a31205; +} + +h1, +h2, +h3, +h4, +h5, +h6 { + border-color:#999999; + font-family:georgia, times, serif; + font-weight:bold; +} +#firstHeading { + font-size:1.5em; +} +h2 .editsection, +.portal h5{ + font-family:sans-serif; + font-weight:normal; + +} +#toc h2, .toc h2 { + font-family:sans-serif; + font-weight:normal; +} +body #mw-panel div.portal div.body { + background-image:url(images/new-portal-break-ltr.png); +} +body.rtl #mw-panel div.portal div.body { + background-image:url(images/new-portal-break-rtl.png); +} +body div.vectorTabs li a, div.vectorTabs li a span{ + color:#4d4d4d; +} +body div.vectorTabs li.selected a, +body div.vectorTabs li.selected a span, +body div.vectorTabs li.selected a:visited +body div.vectorTabs li.selected a:visited span { + color: #ff9900 !important; + font-weight:bold; +} +div.vectorTabs li.new a, +div.vectorTabs li.new a span, +div.vectorTabs li.new a:visited, +div.vectorTabs li.new a:visited span { + color:#a31205; +} +#toc, +.toc, +.mw-warning, +div.gallerybox div.thumb, +table.gallery, +#preferences fieldset.prefsection fieldset, +#preferences, +html .thumbimage, +.usermessage, +img.thumbborder, +div.thumbinner{ + border: 1px solid #cccccc; + background-color: #f7f7f7; +} +#mw-panel div.portal h5 { + font-weight:bold; + margin-bottom:0; + padding-bottom:0.05em; + color:#000000; +} diff --git a/planteome/paw/skins/planteome/experiments/babaco-colors-b.css b/planteome/paw/skins/planteome/experiments/babaco-colors-b.css new file mode 100644 index 0000000..227e197 --- /dev/null +++ b/planteome/paw/skins/planteome/experiments/babaco-colors-b.css @@ -0,0 +1,67 @@ +/* Babaco Color Scheme A */ + + +html .thumbimage, +#toc, .toc, .mw-warning, div.thumbinner { + border-color: #cccccc; + background-color: #f7f7f7; +} + +/* Framework */ +#mw-page-base { + background-color: inherit !important; + background-image: none !important; +} +body { + background-color: #f9f9f9 !important; + background-image:url(images/page-base-updated.png); +} +/* Links */ +a { + color: #003cb3; +} +a.stub { + color: #772233; +} +a.new, #p-personal a.new { + color: #a31205 !important; +} +{ + color: #260e9c; +} +a:visited, +a:visited div.vectorTabs li.selected a:visited span, +a.new:visited, +#p-personal a.new:visited { + color: #260e9c; +} +h1, +h2, +h3, +h4, +h5, +h6 { + border-color:#999999; +} + +div.vectorTabs li.new a, +div.vectorTabs li.new a span, +div.vectorTabs li.new a:visited, +div.vectorTabs li.new a:visited span { + color:#a31205; +} + +#toc, +.toc, +.mw-warning, +div.gallerybox div.thumb, +table.gallery, +#preferences fieldset.prefsection fieldset, +#preferences, +html .thumbimage, +.usermessage, +img.thumbborder, +div.thumbinner{ + border: 1px solid #cccccc; + background-color: #f7f7f7; +} diff --git a/planteome/paw/skins/planteome/experiments/babaco-colors-c.css b/planteome/paw/skins/planteome/experiments/babaco-colors-c.css new file mode 100644 index 0000000..d2dabf7 --- /dev/null +++ b/planteome/paw/skins/planteome/experiments/babaco-colors-c.css @@ -0,0 +1,91 @@ +/* Babaco Color Scheme C */ + +/* ridding ourselves of the gradient */ +#mw-page-base { + background-color: inherit !important; + background-image: none !important; +} + +a:visited, +a:visited div.vectorTabs li.selected a:visited span { + color: #260e9c; +} + +html .thumbimage, +#toc, .toc, .mw-warning, div.thumbinner { + border-color: #cccccc; + background-color: #f7f7f7; +} + +/* Framework */ +body { + background-color: #f9f9f9 !important; + background-image:url(images/page-base-updated.png); +} + +/* Links */ +a { + color: #0066cc; +} +a:visited { + color: #004d99; +} +a:active { + color: #ff6600; +} +a.stub { + color: #56228b; +} +a.new, #p-personal a.new { + color: #a31205 !important; +} +a.new:visited, #p-personal a.new:visited { + color: #a31205; +} + +#firstHeading { + font-size:1.5em; +} +h2 .editsection, +.portal h5 { + font-weight:normal; +} +#toc h2, .toc h2 { + font-weight:normal; +} +body #mw-panel div.portal div.body { + background-image:url(images/new-portal-break-ltr.png); +} + +div.vectorTabs li.new a, +div.vectorTabs li.new a span, +div.vectorTabs li.new a:visited, +div.vectorTabs li.new a:visited span { + color:#a31205; +} +#toc, +.toc, +.mw-warning, +div.gallerybox div.thumb, +table.gallery, +#preferences fieldset.prefsection fieldset, +#preferences, +html .thumbimage, +.usermessage, +img.thumbborder, +div.thumbinner { + border: 1px solid #cccccc; + background-color: #f7f7f7; +} +#mw-panel div.portal h5 { + font-weight:bold; + margin-bottom:0; + padding-bottom:0.05em; + color:#000000; +} +div.vectorTabs li.selected a, +div.vectorTabs li.selected a span, +div.vectorTabs li.selected a:visited +div.vectorTabs li.selected a:visited span { + color: #333333 !important; +} \ No newline at end of file diff --git a/planteome/paw/skins/planteome/experiments/images/new-border.png b/planteome/paw/skins/planteome/experiments/images/new-border.png 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mode 100644 index 0000000..4492550 Binary files /dev/null and b/planteome/paw/skins/planteome/experiments/images/tab-new-fade.png differ diff --git a/planteome/paw/skins/planteome/experiments/new-tabs.css b/planteome/paw/skins/planteome/experiments/new-tabs.css new file mode 100644 index 0000000..e3850e8 --- /dev/null +++ b/planteome/paw/skins/planteome/experiments/new-tabs.css @@ -0,0 +1,322 @@ +/* new border color */ +#content { + background-image: url(images/new-border.png); +} + +#footer { + background-image: url(images/new-border.png); +} + body div#left-navigation, + body div#right-navigation { + top:3.2em; + } + body div#right-navigation { + margin-top:3.2em; + } + body #p-search form, + body #p-search input, + body #simpleSearch { + margin-top:0; + } + body div#p-cactions { + margin-top:0; + } + /* Namespaces and Views */ + /* @noflip */ + div.vectorTabs { + float: left; + } + body div.vectorTabs { + background-image: none; + padding-left: 0; + } + /* @noflip */ + div.vectorTabs ul { + float: left; + } + div.vectorTabs ul { + height: 100%; + list-style: none; + background-image:none; + margin: 0; + padding: 0; + } + /* @noflip */ + div.vectorTabs ul li { + float: left; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + body div.vectorTabs ul li { + line-height: 1em; + display: inline-block; + height: 2em; + margin: 0 1px 0 0; + padding: 0; + background:none; + overflow:hidden; + white-space:nowrap; + } + /* IGNORED BY IE6 */ + div.vectorTabs ul > li { + display: block; + } + body div.vectorTabs li.selected { + background-image: none; + border:none; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + body div.vectorTabs li a { + border-top:1px solid #cccccc; + border-left:1px solid #cccccc; + border-right:1px solid #cccccc; + display: inline-block; + height: 1.7em; + padding-left: 0.6em; + padding-right: 0.6em; + background-image:url(images/tab-fade.png); + background-position:bottom left; + background-repeat:repeat-x; + background-color:#ffffff; + } + body div.vectorTabs li.new a{ + background-image:url(images/tab-new-fade.png); + + } + div.vectorTabs li a, + div.vectorTabs li a span { + cursor: pointer; + } + div.vectorTabs li a span { + font-size: 0.8em; + } + /* IGNORED BY IE6 */ + div.vectorTabs li > a { + display: block; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + body div.vectorTabs a span { + display: inline-block; + padding-top: 0.5em; + } + /* IGNORED BY IE6 */ + /* @noflip */ + div.vectorTabs a > span { + float: left; + display: block; + } + body div.vectorTabs li.last { + background-image: url(images/tab-last.png); + background-repeat:no-repeat; + background-position:top right; + border:none; + } + body div.vectorTabs li.last a { + margin-right:7px; + padding-left:0.4em; + padding-right:0; + border-left:1px solid #cccccc; + border-top:1px solid #cccccc; + border-right:none; + background-image:url(images/tab-fade.png); + background-position:top left; + background-repeat:repeat-x; + } + body div.vectorTabs li.first { + background-image: url(images/tab-first.png); + background-repeat:no-repeat; + background-position:top left; + border:none; + } + body div.vectorTabs li.first a { + margin-left:7px; + padding-left:0em; + padding-right:0.4em; + border-right:1px solid #cccccc; + border-top:1px solid #cccccc; + background-image:url(images/tab-fade.png); + background-position:top left; + background-repeat:repeat-x; + } + + div.vectorTabs li.selected a, + div.vectorTabs li.selected a span, + div.vectorTabs li.selected a:visited + div.vectorTabs li.selected a:visited span { + color: #be5900 !important; + text-decoration: none; + } + + body div.vectorTabs li.selected a { + border-top:1px solid #6cc8f3; + border-right:1px solid #6cc8f3; + border-left:1px solid #6cc8f3; + background-color:#fff; + height:1.75em; + background-image:none; + } + body div.vectorTabs li.selected.first { + background-image: url(images/tab-active-first.png); + background-repeat:no-repeat; + background-position:top left; + } + body div.vectorTabs li.selected.first a { + margin-left:7px; + padding-right:0.6em; + padding-left:0.4em; + border-left:none; + } + body div.vectorTabs li.selected.last { + background-image: url(images/tab-active-last.png); + background-repeat:no-repeat; + background-position:top right; + } + body div.vectorTabs li.selected.last a { + margin-right:7px; + padding-left:0.6em; + padding-right:0.4em; + border-right:none; + } + + /* Variants and Actions */ + /* @noflip */ + div.vectorMenu { + background-image:url(images/tab-fade.png); + background-position:bottom left; + background-repeat:repeat-x; + border-top:1px solid #cccccc; + border-left:1px solid #cccccc; + border-right:1px solid #cccccc; + } + body.rtl div.vectorMenu { + direction: rtl; + } + /* @noflip */ + body #mw-head div.vectorMenu h5 { + background-image: url(../images/arrow-down-icon.png); + background-position: center center; + background-repeat: no-repeat; + padding-left: 0; + margin-left: 0px; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + body div.vectorMenu h5 a { + display: inline-block; + width: 24px; + height:1.5em; + background-image: none !important; + + } + /* IGNORED BY IE6 */ + div.vectorMenu h5 > a { + display: block; + } + div.vectorMenu div.menu { + position: relative; + left:1px; + display: none; + clear: both; + text-align: left; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + body.rtl div.vectorMenu div.menu { + margin-right: 24px; + } + /* IGNORED BY IE6 */ + body.rtl div.vectorMenu > div.menu { + margin-right: auto; + } + /* Fixes old versions of FireFox */ + body.rtl div.vectorMenu > div.menu, + x:-moz-any-link { + margin-right: 24px; + } + div.vectorMenu:hover div.menu { + display: block; + } + div.vectorMenu ul { + position: absolute; + background-color: white; + border: solid 1px silver; + border-top-width: 0; + list-style: none; + list-style-image: none; + list-style-type: none; + padding: 0; + margin: 0; + margin-left: -1px; + text-align: left; + } + /* Fixes old versions of FireFox */ + div.vectorMenu ul, + x:-moz-any-link { + min-width: 5em; + } + /* Returns things back to normal in modern versions of FireFox */ + div.vectorMenu ul, + x:-moz-any-link, + x:default { + min-width: 0; + } + div.vectorMenu li { + padding: 0; + margin: 0; + text-align: left; + line-height: 1em; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + div.vectorMenu li a { + display: inline-block; + padding: 0.5em; + white-space: nowrap; + } + /* IGNORED BY IE6 */ + div.vectorMenu li > a { + display: block; + } + div.vectorMenu li a { + color: #0645ad; + cursor: pointer; + font-size: 0.8em; + } + div.vectorMenu li.selected a, + div.vectorMenu li.selected a:visited { + color: #333333; + text-decoration: none; + } +#ca-unwatch.icon, +#ca-watch.icon { + background-color:#ffffff; + height:1.75em !important; + background-image:url(images/tab-fade.png); + background-position:bottom left; + background-repeat:repeat-x; +} +#ca-unwatch.icon a, +#ca-watch.icon a { + height: 1.7em !important; + border-bottom:none; + background-color:transparent; +} +#ca-watch.icon a, +#ca-unwatch.icon a { + background-repeat:no-repeat; +} +.wikiEditor-ui-tabs { + border: none; + height: 2.15em; +} +.wikiEditor-ui-buttons { + height: 2.15em; +} +.wikiEditor-ui-tabs div { + border: 1px solid silver; + margin-right: 1px; + height: 2.15em; +} +.wikiEditor-ui-tabs div a { + line-height: 2.15em; + background: #FFFFFF url(images/tab-fade.png) repeat-x 0 100%; +} +.wikiEditor-ui-tabs div.current a { + background: #FFFFFF; +} diff --git a/planteome/paw/skins/planteome/images/arrow-down-icon.png b/planteome/paw/skins/planteome/images/arrow-down-icon.png new file mode 100644 index 0000000..bf2d4fb Binary files /dev/null and b/planteome/paw/skins/planteome/images/arrow-down-icon.png differ diff --git a/planteome/paw/skins/planteome/images/audio-icon.png b/planteome/paw/skins/planteome/images/audio-icon.png new file mode 100644 index 0000000..0f59a2b Binary files /dev/null and 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a/planteome/paw/skins/planteome/images/watch-icon-loading.gif b/planteome/paw/skins/planteome/images/watch-icon-loading.gif new file mode 100644 index 0000000..618c308 Binary files /dev/null and b/planteome/paw/skins/planteome/images/watch-icon-loading.gif differ diff --git a/planteome/paw/skins/planteome/images/watch-icons.png b/planteome/paw/skins/planteome/images/watch-icons.png new file mode 100644 index 0000000..54b2c79 Binary files /dev/null and b/planteome/paw/skins/planteome/images/watch-icons.png differ diff --git a/planteome/paw/skins/planteome/main-ltr.css b/planteome/paw/skins/planteome/main-ltr.css new file mode 100644 index 0000000..0b0f46d --- /dev/null +++ b/planteome/paw/skins/planteome/main-ltr.css @@ -0,0 +1,1200 @@ +/* + * main-rtl.css is automatically generated using CSSJanus, a python script for + * creating RTL versions of otherwise LTR stylesheets. + * + * You may download the tool to rebuild this stylesheet + * http://code.google.com/p/cssjanus/ + * + * An online version of this tool can be used at: + * http://cssjanus.commoner.com/ + * + * The following command is used to generate the RTL version of this file + * ./cssjanus.py --swap_ltr_rtl_in_url < main-ltr.css > main-rtl.css + * + * Any rules which should not be flipped should be prepended with @noflip in + * a comment block. + */ +/* Framework */ +html, +body { + height: 100%; + margin: 0; + padding: 0; + font-family: sans-serif; + font-size: 1em; +} +body { + /*background-color: #f3f3f3;*/ + /*background-color: #b7c8b7;*/ + /*background-image: url(images/page-base.png);*/ + + /* thanks to http://blog.fakedarren.com/2010/01/cross-browser-css-gradients/ */ + /* and http://www.puremango.co.uk/2010/04/css-gradient/ */ + /* fallback (Opera) */ + background: #b7c8b7; + /* Mozilla: */ + background: -moz-linear-gradient(top, #b7c8b7, #e7f8e7); + /* Chrome, Safari:*/ + background: -webkit-gradient(linear, + left top, left bottom, from(#b7c8b7), to(#e7f8e7)); + /* MSIE */ + filter: progid:DXImageTransform.Microsoft.Gradient( + StartColorStr='#b7c8b7', EndColorStr='#e7f8e7', GradientType=0); +} + +/* Content */ +#content { + margin-left: 10em; + padding: 1em; + background-image: url(images/border.png); + background-position: top left; + background-repeat: repeat-y; + /* fallback (Opera) */ + background: white; + /* Mozilla: */ + background: -moz-linear-gradient(top, white, #c7b3cc); + /* Chrome, Safari:*/ + background: -webkit-gradient(linear, + left top, left bottom, from(white), to(#c7b3cc)); + /* MSIE */ + filter: progid:DXImageTransform.Microsoft.Gradient( + StartColorStr='white', EndColorStr='#c7b3cc', GradientType=0); + /*background-color: white;*/ +} +/* Head */ +#mw-page-base { + height: 5em; + /*background-color: grey;*/ + background-image: url(images/page-fade.png); + opacity: 0.0; + background-position: bottom left; + background-repeat: repeat-x; +} +#mw-head-base { + margin-top: -5em; + margin-left: 10em; + height: 5em; + background-image: url(images/border.png); + background-position: bottom left; + background-repeat: repeat-x; +} +#mw-head { + position: absolute; + top: 0; + right: 0; + width: 100%; +} +#mw-head h5 { + margin: 0; + padding: 0; +} + /* Hide empty portlets */ + div.emptyPortlet { + display: none; + } + /* Personal */ + #p-personal { + position: absolute; + top: 0; + margin-left: 10em; + right: 0.75em; + } + #p-personal h5 { + display: none; + } + #p-personal ul { + list-style: none; + margin: 0; + padding: 0; + } + /* @noflip */ + #p-personal li { + line-height: 1.125em; + float: left; + } + #p-personal li { + margin-left: 0.75em; + margin-top: 0.5em; + font-size: 0.75em; + } + /* Navigation Containers */ + #left-navigation { + position: absolute; + left: 10em; + top: 2.5em; + } + #right-navigation { + float: right; + margin-top: 2.5em; + } + /* Navigation Labels */ + div.vectorTabs h5, + div.vectorMenu h5 span { + display: none; + } + /* Namespaces and Views */ + /* @noflip */ + div.vectorTabs { + float: left; + } + div.vectorTabs { + background-image: url(images/tab-break.png); + background-position: bottom left; + background-repeat: no-repeat; + padding-left: 1px; + } + /* @noflip */ + div.vectorTabs ul { + float: left; + } + div.vectorTabs ul { + height: 100%; + list-style: none; + margin: 0; + padding: 0; + } + /* @noflip */ + div.vectorTabs ul li { + float: left; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + div.vectorTabs ul li { + line-height: 1.125em; + display: inline-block; + height: 100%; + margin: 0; + padding: 0; + + /* thanks to http://blog.fakedarren.com/2010/01/cross-browser-css-gradients/ */ + /* and http://www.puremango.co.uk/2010/04/css-gradient/ */ + /* fallback (Opera) */ + background: #b7c8b7; + /* Mozilla: */ + background: -moz-linear-gradient(top, #b7c8b7, #aaaaaa); + /* Chrome, Safari:*/ + background: -webkit-gradient(linear, + left top, left bottom, from(#b7c8b7), to(#aaaaaa)); + /* MSIE */ + filter: progid:DXImageTransform.Microsoft.Gradient( + StartColorStr='#b7c8b7', EndColorStr='#aaaaaa', GradientType=0); + + /*background-color: #f3f3f3;*/ + /*background-color: #b7c8b7;*/ + /*background-image: url(images/tab-normal-fade.png);*/ + background-position: bottom left; + background-repeat: repeat-x; + white-space:nowrap; + } + /* IGNORED BY IE6 */ + div.vectorTabs ul > li { + display: block; + } + div.vectorTabs li.selected { + + /* thanks to http://blog.fakedarren.com/2010/01/cross-browser-css-gradients/ */ + /* and http://www.puremango.co.uk/2010/04/css-gradient/ */ + /* fallback (Opera) */ + background: #b7c8b7; + /* Mozilla: */ + background: -moz-linear-gradient(top, #b7c8b7, white); + /* Chrome, Safari:*/ + background: -webkit-gradient(linear, + left top, left bottom, from(#b7c8b7), to(white)); + /* MSIE */ + filter: progid:DXImageTransform.Microsoft.Gradient( + StartColorStr='#b7c8b7', EndColorStr='white', GradientType=0); + + /*background-image: url(images/tab-current-fade.png);*/ + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + div.vectorTabs li a { + display: inline-block; + height: 2.5em; + padding-left: 0.4em; + padding-right: 0.4em; + background-image: url(images/tab-break.png); + background-position: bottom right; + background-repeat: no-repeat; + } + div.vectorTabs li a, + div.vectorTabs li a span { + /*color: #0645ad;*/ + color: #67536c; + cursor: pointer; + } + div.vectorTabs li a span { + font-size: 0.8em; + } + /* IGNORED BY IE6 */ + div.vectorTabs li > a { + display: block; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + div.vectorTabs a span { + display: inline-block; + padding-top: 1.25em; + } + /* IGNORED BY IE6 */ + /* @noflip */ + div.vectorTabs a > span { + float: left; + display: block; + } + div.vectorTabs li.selected a, + div.vectorTabs li.selected a span, + div.vectorTabs li.selected a:visited + div.vectorTabs li.selected a:visited span { + color: #333333; + text-decoration: none; + } + div.vectorTabs li.new a, + div.vectorTabs li.new a span, + div.vectorTabs li.new a:visited, + div.vectorTabs li.new a:visited span { + color: #a55858; + } + /* Variants and Actions */ + /* @noflip */ + div.vectorMenu { + direction: ltr; + float: left; + background-image: url(images/arrow-down-icon.png); + background-position: center center; + background-repeat: no-repeat; + } + /* @noflip */ + body.rtl div.vectorMenu { + direction: rtl; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + /* @noflip */ + #mw-head div.vectorMenu h5 { + float: left; + background-image: url(images/tab-break.png); + background-repeat: no-repeat; + } + /* IGNORED BY IE6 */ + #mw-head div.vectorMenu > h5 { + background-image: none; + } + #mw-head div.vectorMenu h5 { + background-position: bottom left; + margin-left: -1px; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + /* @noflip */ + div.vectorMenu h5 a { + display: inline-block; + width: 24px; + height: 2.5em; + text-decoration: none; + background-image: url(images/tab-break.png); + background-repeat: no-repeat; + } + div.vectorMenu h5 a{ + background-position: bottom right; + } + /* IGNORED BY IE6 */ + div.vectorMenu h5 > a { + display: block; + } + div.vectorMenu div.menu { + position: relative; + display: none; + clear: both; + text-align: left; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + /* @noflip */ + body.rtl div.vectorMenu div.menu { + margin-left: 24px; + } + /* IGNORED BY IE6 */ + /* @noflip */ + body.rtl div.vectorMenu > div.menu { + margin-left: auto; + } + /* Fixes old versions of FireFox */ + /* @noflip */ + body.rtl div.vectorMenu > div.menu, + x:-moz-any-link { + margin-left: 23px; + } + div.vectorMenu:hover div.menu { + display: block; + } + div.vectorMenu ul { + position: absolute; + + /* thanks to http://blog.fakedarren.com/2010/01/cross-browser-css-gradients/ */ + /* and http://www.puremango.co.uk/2010/04/css-gradient/ */ + /* fallback (Opera) */ + background: white; + /* Mozilla: */ + background: -moz-linear-gradient(top, white, #b7c8b7); + /* Chrome, Safari:*/ + background: -webkit-gradient(linear, + left top, left bottom, from(white), to(#b7c8b7)); + /* MSIE */ + filter: progid:DXImageTransform.Microsoft.Gradient( + StartColorStr='white', EndColorStr='#b7c8b7', GradientType=0); + + /*background-color: white;*/ + border: solid 1px silver; + border-top-width: 0; + list-style: none; + list-style-image: none; + list-style-type: none; + padding: 0; + margin: 0; + margin-left: -1px; + text-align: left; + } + /* Fixes old versions of FireFox */ + div.vectorMenu ul, + x:-moz-any-link { + min-width: 5em; + } + /* Returns things back to normal in modern versions of FireFox */ + div.vectorMenu ul, + x:-moz-any-link, + x:default { + min-width: 0; + } + div.vectorMenu li { + padding: 0; + margin: 0; + text-align: left; + line-height: 1em; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + div.vectorMenu li a { + display: inline-block; + padding: 0.5em; + white-space: nowrap; + } + /* IGNORED BY IE6 */ + div.vectorMenu li > a { + display: block; + } + div.vectorMenu li a { + color: #0645ad; + cursor: pointer; + font-size: 0.8em; + } + div.vectorMenu li.selected a, + div.vectorMenu li.selected a:visited { + color: #333333; + text-decoration: none; + } + /* Search */ + #p-search h5 { + display: none; + } + /* @noflip */ + #p-search { + float: left; + } + #p-search { + margin-right: 0.5em; + margin-left: 0.5em; + } + #p-search form, + #p-search input { + margin: 0; + margin-top: 0.4em; + } + #simpleSearch { + margin-top: 0.5em; + position: relative; + border: solid 1px #AAAAAA; + background-color: white; + background-image: url(images/search-fade.png); + background-position: top left; + background-repeat: repeat-x; + } + #simpleSearch label { + font-size: 0.8em; + top: 0.25em; + } + #simpleSearch input#searchInput { + margin: 0; + border-width: 0; + padding: 0.25em; + line-height: 1em; + font-size: 0.8em; + width: 9em; + background-color: transparent; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + #simpleSearch button#searchButton { + margin: 0; + padding: 0; + width: 1.75em; + height: 1.5em; + border: none; + cursor: pointer; + background-color: transparent; + background-image: url(images/search-ltr.png); + background-position: center center; + background-repeat: no-repeat; + } + /* IGNORED BY IE6 */ + #simpleSearch > button#searchButton { + height: 100%; + } + .suggestions-special .special-label { + font-size: 0.8em; + color: gray; + } + .suggestions-special .special-query { + color: black; + font-style: italic; + } + .suggestions-special .special-hover { + background-color: silver; + } +/* Panel */ +#mw-panel { + position: absolute; + top: 160px; + padding-top: 1em; + width: 10em; + left: 0; +} + #mw-panel div.portal { + padding-bottom: 1.5em; + } + #mw-panel div.portal h5 { + font-weight: normal; + color: #444444; + padding: 0.25em; + padding-top: 0; + padding-left: 1.75em; + cursor: default; + border: none; + font-size: 0.75em; + } + #mw-panel div.portal div.body { + margin: 0; + padding-top: 0.5em; + margin-left: 1.25em; + background-image: url(images/portal-break.png); + background-repeat: no-repeat; + background-position: top left; + } + #mw-panel div.portal div.body ul { + list-style: none; + list-style-image: none; + list-style-type: none; + padding: 0; + margin: 0; + } + #mw-panel div.portal div.body ul li { + line-height: 1.125em; + padding: 0; + padding-bottom: 0.5em; + margin: 0; + overflow: hidden; + font-size: 0.75em; + } + #mw-panel div.portal div.body ul li a { + color: #0645ad; + } + #mw-panel div.portal div.body ul li a:visited { + color: #0b0080; + } +/* Footer */ +#footer { + margin-left: 10em; + margin-top: 0; + padding: 0.75em; + background-image: url(images/border.png); + background-position: top left; + background-repeat: repeat-x; +} +#footer ul { + list-style: none; + list-style-image: none; + list-style-type: none; + margin: 0; + padding: 0; +} +#footer ul li { + margin: 0; + padding: 0; + padding-top: 0.5em; + padding-bottom: 0.5em; + color: #333333; + font-size: 0.7em; +} +#footer #footer-icons { + float: right; +} +/* @noflip */ +body.ltr #footer #footer-places { + float: left; +} +#footer #footer-info li { + line-height: 1.4em; +} +#footer #footer-icons li { + float: left; + margin-left: 0.5em; + line-height: 2em; +} +#footer #footer-places li { + float: left; + margin-right: 1em; + line-height: 2em; +} +/* Logo */ +#p-logo { + position: absolute; + top: -160px; + left: 0; + width: 10em; + height: 160px; +} +#p-logo a { + display: block; + width: 10em; + height: 160px; + background-repeat: no-repeat; + background-position: center center; + text-decoration: none; +} + +/* + * + * The following code is highly modified from monobook. It would be nice if the + * preftoc id was more human readable like preferences-toc for instance, + * howerver this would require backporting the other skins. + */ + +/* Preferences */ +#preftoc { + /* Tabs */ + width: 100%; + float: left; + clear: both; + margin: 0 !important; + padding: 0 !important; + background-image: url(images/preferences-break.png); + background-position: bottom left; + background-repeat: no-repeat; +} + #preftoc li { + /* Tab */ + float: left; + margin: 0; + padding: 0; + padding-right: 1px; + height: 2.25em; + white-space: nowrap; + list-style-type: none; + list-style-image: none; + background-image: url(images/preferences-break.png); + background-position: bottom right; + background-repeat: no-repeat; + } + /* IGNORED BY IE6 */ + #preftoc li:first-child { + margin-left: 1px; + } + #preftoc a, + #preftoc a:active { + display: inline-block; + position: relative; + color: #0645ad; + padding: 0.5em; + text-decoration: none; + background-image: none; + font-size: 0.9em; + } + #preftoc a:hover { + text-decoration: underline; + } + #preftoc li.selected a { + background-image: url(images/preferences-fade.png); + background-position: bottom; + background-repeat: repeat-x; + color: #333333; + text-decoration: none; + } +#preferences { + float: left; + width: 100%; + margin: 0; + margin-top: -2px; + clear: both; + border: solid 1px #cccccc; + background-color: #f9f9f9; + background-image: url(images/preferences-base.png); +} +#preferences fieldset.prefsection { + border: none; + padding: 0; + margin: 1em; +} +#preferences fieldset.prefsection fieldset { + border: none; + border-top: solid 1px #cccccc; +} +#preferences legend { + color: #666666; +} +#preferences fieldset.prefsection legend.mainLegend { + display: none; +} +#preferences td { + padding-left: 0.5em; + padding-right: 0.5em; +} +#preferences td.htmlform-tip { + font-size: x-small; + padding: .2em 2em; + color: #666666; +} +#preferences div.mw-prefs-buttons { + padding: 1em; +} +#preferences div.mw-prefs-buttons input { + margin-right: 0.25em; +} + +/* + * Styles for the user login and create account forms + */ +#userlogin, #userloginForm { + border: solid 1px #cccccc; + padding: 1.2em; + margin: .5em; + float: left; +} + +#userlogin { + min-width: 20em; + max-width: 90%; + width: 40em; +} + +/* + * + * The following code is slightly modified from monobook + * + */ +#content { + line-height: 1.5em; +} +#bodyContent { + font-size: 0.8em; +} +/* Links */ +a { + text-decoration: none; + color: #0645ad; + /*color: #67536c;*/ + background: none; +} +a:visited { + color: #0b0080; +} +a:active { + color: #faa700; +} +a:hover { + text-decoration: underline; +} +a.stub { + color: #772233; +} +a.new, #p-personal a.new { + color: #ba0000; +} +a.new:visited, #p-personal a.new:visited { + color: #a55858; +} + +/* Inline Elements */ +img { + border: none; + vertical-align: middle; +} +hr { + height: 1px; + color: #aaa; + background-color: #aaa; + border: 0; + margin: .2em 0 .2em 0; +} + +/* Structural Elements */ +h1, +h2, +h3, +h4, +h5, +h6 { + /*color: black;*/ + color: #67536c; + background: none; + font-weight: normal; + margin: 0; + padding-top: .5em; + padding-bottom: .17em; + border-bottom: 1px solid #aaa; + width: auto; +} +h1 { font-size: 188%; } +h1 .editsection { font-size: 53%; } +h2 { font-size: 150%; } +h2 .editsection { font-size: 67%; } +h3, +h4, +h5, +h6 { + border-bottom: none; + font-weight: bold; +} +h3 { font-size: 132%; } +h3 .editsection { font-size: 76%; font-weight: normal; } +h4 { font-size: 116%; } +h4 .editsection { font-size: 86%; font-weight: normal; } +h5 { font-size: 100%; } +h5 .editsection { font-weight: normal; } +h6 { font-size: 80%; } +h6 .editsection { font-size: 125%; font-weight: normal; } +p { + margin: .4em 0 .5em 0; + line-height: 1.5em; +} + p img { + margin: 0; + } +abbr, +acronym, +.explain { + border-bottom: 1px dotted black; + color: black; + background: none; + cursor: help; +} +q { + font-family: Times, "Times New Roman", serif; + font-style: italic; +} +/* Disabled for now +blockquote { + font-family: Times, "Times New Roman", serif; + font-style: italic; +}*/ +code { + background-color: #f9f9f9; +} +pre { + padding: 1em; + border: 1px dashed #2f6fab; + color: black; + background-color: #f9f9f9; + line-height: 1.1em; +} +ul { + line-height: 1.5em; + list-style-type: square; + margin: .3em 0 0 1.5em; + padding: 0; + list-style-image: url(images/bullet-icon.png); +} +ol { + line-height: 1.5em; + margin: .3em 0 0 3.2em; + padding: 0; + list-style-image: none; +} +li { + margin-bottom: .1em; +} +dt { + font-weight: bold; + margin-bottom: .1em; +} +dl { + margin-top: .2em; + margin-bottom: .5em; +} +dd { + line-height: 1.5em; + margin-left: 2em; + margin-bottom: .1em; +} +/* Tables */ +table { + font-size: 100%; + color: black; + /* we don't want the bottom borders of

    s to be visible through + * floated tables */ + background-color: white; +} +fieldset table { + /* but keep table layouts in forms clean... */ + background: none; +} +/* Forms */ +fieldset { + border: 1px solid #2f6fab; + margin: 1em 0 1em 0; + padding: 0 1em 1em; + line-height: 1.5em; +} + fieldset.nested { + margin: 0 0 0.5em 0; + padding: 0 0.5em 0.5em; + } +legend { + padding: .5em; + font-size: 95%; +} +form { + border: none; + margin: 0; +} +textarea { + width: 100%; + padding: .1em; +} +select { + vertical-align: top; +} +/* Table of Contents */ +#toc, +.toc, +.mw-warning { + border: 1px solid #aaa; + background-color: #f9f9f9; + padding: 5px; + font-size: 95%; +} +#toc h2, +.toc h2 { + display: inline; + border: none; + padding: 0; + font-size: 100%; + font-weight: bold; +} +#toc #toctitle, +.toc #toctitle, +#toc .toctitle, +.toc .toctitle { + text-align: center; +} +#toc ul, +.toc ul { + list-style-type: none; + list-style-image: none; + margin-left: 0; + padding-left: 0; + text-align: left; +} +#toc ul ul, +.toc ul ul { + margin: 0 0 0 2em; +} +#toc .toctoggle, +.toc .toctoggle { + font-size: 94%; +} +/* Images */ +div.floatright, table.floatright { + clear: right; + float: right; + position: relative; + margin: 0 0 .5em .5em; + border: 0; +} +div.floatright p { font-style: italic; } +div.floatleft, table.floatleft { + float: left; + clear: left; + position: relative; + margin: 0 .5em .5em 0; + border: 0; +} +div.floatleft p { font-style: italic; } +/* Thumbnails */ +div.thumb { + margin-bottom: .5em; + border-style: solid; + border-color: white; + width: auto; + background-color: transparent; +} +div.thumbinner { + border: 1px solid #cccccc; + padding: 3px !important; + background-color: #f9f9f9; + font-size: 94%; + text-align: center; + overflow: hidden; +} +html .thumbimage { + border: 1px solid #ccc; +} +html .thumbcaption { + border: none; + text-align: left; + line-height: 1.4em; + padding: 3px !important; + font-size: 94%; +} +div.magnify { + float: right; + border: none !important; + background: none !important; +} +div.magnify a, div.magnify img { + display: block; + border: none !important; + background: none !important; +} +div.tright { + clear: right; + float: right; + border-width: .5em 0 .8em 1.4em; +} +div.tleft { + float: left; + clear: left; + margin-right: .5em; + border-width: .5em 1.4em .8em 0; +} +img.thumbborder { + border: 1px solid #dddddd; +} +.hiddenStructure { + display: none; +} +/* Warning */ +.mw-warning { + margin-left: 50px; + margin-right: 50px; + text-align: center; +} +/* User Message */ +.usermessage { + background-color: #ffce7b; + border: 1px solid #ffa500; + color: black; + font-weight: bold; + margin: 2em 0 1em; + padding: .5em 1em; + vertical-align: middle; +} +/* Site Notice */ +#siteNotice { + text-align: center; + font-size: 0.8em; + margin: 0; +} + #siteNotice div, + #siteNotice p { + margin: 0; + padding: 0; + margin-bottom: 0.9em; + } +/* Categories */ +.catlinks { + border: 1px solid #888; + background-color: #cccccc; + padding: 5px; + margin-top: 1em; + clear: both; +} +/* Sub-navigation */ +#siteSub { + display: none; +} +#jump-to-nav { + display: none; +} +#contentSub, #contentSub2 { + font-size: 84%; + line-height: 1.2em; + margin: 0 0 1.4em 1em; + color: #7d7d7d; + width: auto; +} +span.subpages { + display: block; +} +/* Emulate Center */ +.center { + width: 100%; + text-align: center; +} +*.center * { + margin-left: auto; + margin-right: auto; +} +/* Small for tables and similar */ +.small, .small * { + font-size: 94%; +} +table.small { + font-size: 100%; +} +/* Edge Cases for Content */ +h1, h2 { + margin-bottom: .6em; +} +h3, h4, h5 { + margin-bottom: .3em; +} +#firstHeading { + padding-top: 0; + margin-top: 0; + padding-top: 0; + margin-bottom: 0.1em; + line-height: 1.2em; + font-size: 1.6em; + padding-bottom: 0; +} +#content a.external, +#content a[href ^="gopher://"] { + background: url(images/external-link-ltr-icon.png) center right no-repeat; + padding: 0 13px 0 0; +} +#content a[href ^="https://"], +.link-https { + background: url(images/lock-icon.png) center right no-repeat; + padding: 0 18px 0 0; +} +#content a[href ^="mailto:"], +.link-mailto { + background: url(images/mail-icon.png) center right no-repeat; + padding: 0 18px 0 0; +} +#content a[href ^="news://"] { + background: url(images/news-icon.png) center right no-repeat; + padding: 0 18px 0 0; +} +#content a[href ^="ftp://"], +.link-ftp { + background: url(images/file-icon.png) center right no-repeat; + padding: 0 18px 0 0; +} +#content a[href ^="irc://"], +#content a.extiw[href ^="irc://"], +.link-irc { + background: url(images/talk-icon.png) center right no-repeat; + padding: 0 18px 0 0; +} +#content a.external[href $=".ogg"], #content a.external[href $=".OGG"], +#content a.external[href $=".mid"], #content a.external[href $=".MID"], +#content a.external[href $=".midi"], #content a.external[href $=".MIDI"], +#content a.external[href $=".mp3"], #content a.external[href $=".MP3"], +#content a.external[href $=".wav"], #content a.external[href $=".WAV"], +#content a.external[href $=".wma"], #content a.external[href $=".WMA"], +.link-audio { + background: url("images/audio-icon.png") center right no-repeat; + padding: 0 18px 0 0; +} +#content a.external[href $=".ogm"], #content a.external[href $=".OGM"], +#content a.external[href $=".avi"], #content a.external[href $=".AVI"], +#content a.external[href $=".mpeg"], #content a.external[href $=".MPEG"], +#content a.external[href $=".mpg"], #content a.external[href $=".MPG"], +.link-video { + background: url("images/video-icon.png") center right no-repeat; + padding: 0 18px 0 0; +} +#content a.external[href $=".pdf"], #content a.external[href $=".PDF"], +#content a.external[href *=".pdf#"], #content a.external[href *=".PDF#"], +#content a.external[href *=".pdf?"], #content a.external[href *=".PDF?"], +.link-document { + background: url("images/document-icon.png") center right no-repeat; + padding: 0 18px 0 0; +} +/* Interwiki Styling (Disabled) */ +#content a.extiw, +#content a.extiw:active { + color: #36b; + background: none; + padding: 0; +} +#content a.external { + color: #36b; +} +#content .printfooter { + display: none; +} +/* Icon for Usernames */ +#pt-userpage, +#pt-anonuserpage, +#pt-login { + background: url(images/user-icon.png) left top no-repeat; + padding-left: 15px !important; + text-transform: none; +} + +.toccolours { + border: 1px solid #aaa; + background-color: #f9f9f9; + padding: 5px; + font-size: 95%; +} +#bodyContent { + position: relative; + width: 100%; +} +#mw-js-message { + font-size: 0.8em; +} +div#bodyContent { + line-height: 1.5em; +} + +/* Watch/Unwatch Icon Styling */ +#ca-unwatch.icon, +#ca-watch.icon { + margin-right:1px; +} +#ca-unwatch.icon a, +#ca-watch.icon a { + margin: 0; + padding: 0; + outline: none; + display: block; + width: 26px; + height: 2.5em; +} +#ca-unwatch.icon a { + background-image: url(images/watch-icons.png); + background-position: -43px 60%; +} +#ca-watch.icon a { + background-image: url(images/watch-icons.png); + background-position: 5px 60%; +} +#ca-unwatch.icon a:hover { + background-image: url(images/watch-icons.png); + background-position: -67px 60%; +} +#ca-watch.icon a:hover { + background-image: url(images/watch-icons.png); + background-position: -19px 60%; +} +#ca-unwatch.icon a.loading, +#ca-watch.icon a.loading { + background-image: url(images/watch-icon-loading.gif); + background-position: center 60%; +} +#ca-unwatch.icon a span, +#ca-watch.icon a span { + display: none; +} +div.vectorTabs ul { + background-image:url(images/tab-break.png); + background-position:right bottom; + background-repeat:no-repeat; +} diff --git a/planteome/paw/skins/planteome/main-rtl.css b/planteome/paw/skins/planteome/main-rtl.css new file mode 100644 index 0000000..5387289 --- /dev/null +++ b/planteome/paw/skins/planteome/main-rtl.css @@ -0,0 +1,1128 @@ +/* + * main-rtl.css is automatically generated using CSSJanus, a python script for + * creating RTL versions of otherwise LTR stylesheets. + * + * You may download the tool to rebuild this stylesheet + * http://code.google.com/p/cssjanus/ + * + * An online version of this tool can be used at: + * http://cssjanus.commoner.com/ + * + * The following command is used to generate the RTL version of this file + * ./cssjanus.py --swap_ltr_rtl_in_url < main-ltr.css > main-rtl.css + * + * Any rules which should not be flipped should be prepended with @noflip in + * a comment block. + */ +/* Framework */ +html, +body { + height: 100%; + margin: 0; + padding: 0; + font-family: sans-serif; + font-size: 1em; +} +body { + background-color: #f3f3f3; + background-image: url(images/page-base.png); +} +/* Content */ +#content { + margin-right: 10em; + padding: 1em; + background-image: url(images/border.png); + background-position: top right; + background-repeat: repeat-y; + background-color: white; +} +/* Head */ +#mw-page-base { + height: 5em; + background-color: white; + background-image: url(images/page-fade.png); + background-position: bottom right; + background-repeat: repeat-x; +} +#mw-head-base { + margin-top: -5em; + margin-right: 10em; + height: 5em; + background-image: url(images/border.png); + background-position: bottom right; + background-repeat: repeat-x; +} +#mw-head { + position: absolute; + top: 0; + left: 0; + width: 100%; +} +#mw-head h5 { + margin: 0; + padding: 0; +} + /* Hide empty portlets */ + div.emptyPortlet { + display: none; + } + /* Personal */ + #p-personal { + position: absolute; + top: 0; + margin-right: 10em; + left: 0.75em; + } + #p-personal h5 { + display: none; + } + #p-personal ul { + list-style: none; + margin: 0; + padding: 0; + } + /* @noflip */ + #p-personal li { + line-height: 1.125em; + float: left; + } + #p-personal li { + margin-right: 0.75em; + margin-top: 0.5em; + font-size: 0.75em; + } + /* Navigation Containers */ + #left-navigation { + position: absolute; + right: 10em; + top: 2.5em; + } + #right-navigation { + float: left; + margin-top: 2.5em; + } + /* Navigation Labels */ + div.vectorTabs h5, + div.vectorMenu h5 span { + display: none; + } + /* Namespaces and Views */ + /* @noflip */ + div.vectorTabs { + float: left; + } + div.vectorTabs { + background-image: url(images/tab-break.png); + background-position: bottom right; + background-repeat: no-repeat; + padding-right: 1px; + } + /* @noflip */ + div.vectorTabs ul { + float: left; + } + div.vectorTabs ul { + height: 100%; + list-style: none; + margin: 0; + padding: 0; + } + /* @noflip */ + div.vectorTabs ul li { + float: left; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + div.vectorTabs ul li { + line-height: 1.125em; + display: inline-block; + height: 100%; + margin: 0; + padding: 0; + background-color: #f3f3f3; + background-image: url(images/tab-normal-fade.png); + background-position: bottom right; + background-repeat: repeat-x; + white-space:nowrap; + } + /* IGNORED BY IE6 */ + div.vectorTabs ul > li { + display: block; + } + div.vectorTabs li.selected { + background-image: url(images/tab-current-fade.png); + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + div.vectorTabs li a { + display: inline-block; + height: 2.5em; + padding-right: 0.4em; + padding-left: 0.4em; + background-image: url(images/tab-break.png); + background-position: bottom left; + background-repeat: no-repeat; + } + div.vectorTabs li a, + div.vectorTabs li a span { + color: #0645ad; + cursor: pointer; + } + div.vectorTabs li a span { + font-size: 0.8em; + } + /* IGNORED BY IE6 */ + div.vectorTabs li > a { + display: block; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + div.vectorTabs a span { + display: inline-block; + padding-top: 1.25em; + } + /* IGNORED BY IE6 */ + /* @noflip */ + div.vectorTabs a > span { + float: left; + display: block; + } + div.vectorTabs li.selected a, + div.vectorTabs li.selected a span, + div.vectorTabs li.selected a:visited + div.vectorTabs li.selected a:visited span { + color: #333333; + text-decoration: none; + } + div.vectorTabs li.new a, + div.vectorTabs li.new a span, + div.vectorTabs li.new a:visited, + div.vectorTabs li.new a:visited span { + color: #a55858; + } + /* Variants and Actions */ + /* @noflip */ + div.vectorMenu { + direction: ltr; + float: left; + background-image: url(images/arrow-down-icon.png); + background-position: center center; + background-repeat: no-repeat; + } + /* @noflip */ + body.rtl div.vectorMenu { + direction: rtl; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + /* @noflip */ + #mw-head div.vectorMenu h5 { + float: left; + background-image: url(images/tab-break.png); + background-repeat: no-repeat; + } + /* IGNORED BY IE6 */ + #mw-head div.vectorMenu > h5 { + background-image: none; + } + #mw-head div.vectorMenu h5 { + background-position: bottom right; + margin-right: -1px; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + /* @noflip */ + div.vectorMenu h5 a { + display: inline-block; + width: 24px; + height: 2.5em; + text-decoration: none; + background-image: url(images/tab-break.png); + background-repeat: no-repeat; + } + div.vectorMenu h5 a{ + background-position: bottom left; + } + /* IGNORED BY IE6 */ + div.vectorMenu h5 > a { + display: block; + } + div.vectorMenu div.menu { + position: relative; + display: none; + clear: both; + text-align: right; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + /* @noflip */ + body.rtl div.vectorMenu div.menu { + margin-left: 24px; + } + /* IGNORED BY IE6 */ + /* @noflip */ + body.rtl div.vectorMenu > div.menu { + margin-left: auto; + } + /* Fixes old versions of FireFox */ + /* @noflip */ + body.rtl div.vectorMenu > div.menu, + x:-moz-any-link { + margin-left: 23px; + } + div.vectorMenu:hover div.menu { + display: block; + } + div.vectorMenu ul { + position: absolute; + background-color: white; + border: solid 1px silver; + border-top-width: 0; + list-style: none; + list-style-image: none; + list-style-type: none; + padding: 0; + margin: 0; + margin-right: -1px; + text-align: right; + } + /* Fixes old versions of FireFox */ + div.vectorMenu ul, + x:-moz-any-link { + min-width: 5em; + } + /* Returns things back to normal in modern versions of FireFox */ + div.vectorMenu ul, + x:-moz-any-link, + x:default { + min-width: 0; + } + div.vectorMenu li { + padding: 0; + margin: 0; + text-align: right; + line-height: 1em; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + div.vectorMenu li a { + display: inline-block; + padding: 0.5em; + white-space: nowrap; + } + /* IGNORED BY IE6 */ + div.vectorMenu li > a { + display: block; + } + div.vectorMenu li a { + color: #0645ad; + cursor: pointer; + font-size: 0.8em; + } + div.vectorMenu li.selected a, + div.vectorMenu li.selected a:visited { + color: #333333; + text-decoration: none; + } + /* Search */ + #p-search h5 { + display: none; + } + /* @noflip */ + #p-search { + float: left; + } + #p-search { + margin-left: 0.5em; + margin-right: 0.5em; + } + #p-search form, + #p-search input { + margin: 0; + margin-top: 0.4em; + } + #simpleSearch { + margin-top: 0.5em; + position: relative; + border: solid 1px #AAAAAA; + background-color: white; + background-image: url(images/search-fade.png); + background-position: top right; + background-repeat: repeat-x; + } + #simpleSearch label { + font-size: 0.8em; + top: 0.25em; + } + #simpleSearch input#searchInput { + margin: 0; + border-width: 0; + padding: 0.25em; + line-height: 1em; + font-size: 0.8em; + width: 9em; + background-color: transparent; + } + /* OVERRIDDEN BY COMPLIANT BROWSERS */ + #simpleSearch button#searchButton { + margin: 0; + padding: 0; + width: 1.75em; + height: 1.5em; + border: none; + cursor: pointer; + background-color: transparent; + background-image: url(images/search-rtl.png); + background-position: center center; + background-repeat: no-repeat; + } + /* IGNORED BY IE6 */ + #simpleSearch > button#searchButton { + height: 100%; + } + .suggestions-special .special-label { + font-size: 0.8em; + color: gray; + } + .suggestions-special .special-query { + color: black; + font-style: italic; + } + .suggestions-special .special-hover { + background-color: silver; + } +/* Panel */ +#mw-panel { + position: absolute; + top: 160px; + padding-top: 1em; + width: 10em; + right: 0; +} + #mw-panel div.portal { + padding-bottom: 1.5em; + } + #mw-panel div.portal h5 { + font-weight: normal; + color: #444444; + padding: 0.25em; + padding-top: 0; + padding-right: 1.75em; + cursor: default; + border: none; + font-size: 0.75em; + } + #mw-panel div.portal div.body { + margin: 0; + padding-top: 0.5em; + margin-right: 1.25em; + background-image: url(images/portal-break.png); + background-repeat: no-repeat; + background-position: top right; + } + #mw-panel div.portal div.body ul { + list-style: none; + list-style-image: none; + list-style-type: none; + padding: 0; + margin: 0; + } + #mw-panel div.portal div.body ul li { + line-height: 1.125em; + padding: 0; + padding-bottom: 0.5em; + margin: 0; + overflow: hidden; + font-size: 0.75em; + } + #mw-panel div.portal div.body ul li a { + color: #0645ad; + } + #mw-panel div.portal div.body ul li a:visited { + color: #0b0080; + } +/* Footer */ +#footer { + margin-right: 10em; + margin-top: 0; + padding: 0.75em; + background-image: url(images/border.png); + background-position: top right; + background-repeat: repeat-x; +} +#footer ul { + list-style: none; + list-style-image: none; + list-style-type: none; + margin: 0; + padding: 0; +} +#footer ul li { + margin: 0; + padding: 0; + padding-top: 0.5em; + padding-bottom: 0.5em; + color: #333333; + font-size: 0.7em; +} +#footer #footer-icons { + float: left; +} +/* @noflip */ +body.ltr #footer #footer-places { + float: left; +} +#footer #footer-info li { + line-height: 1.4em; +} +#footer #footer-icons li { + float: right; + margin-right: 0.5em; + line-height: 2em; +} +#footer #footer-places li { + float: right; + margin-left: 1em; + line-height: 2em; +} +/* Logo */ +#p-logo { + position: absolute; + top: -160px; + right: 0; + width: 10em; + height: 160px; +} +#p-logo a { + display: block; + width: 10em; + height: 160px; + background-repeat: no-repeat; + background-position: center center; + text-decoration: none; +} + +/* + * + * The following code is highly modified from monobook. It would be nice if the + * preftoc id was more human readable like preferences-toc for instance, + * howerver this would require backporting the other skins. + */ + +/* Preferences */ +#preftoc { + /* Tabs */ + width: 100%; + float: right; + clear: both; + margin: 0 !important; + padding: 0 !important; + background-image: url(images/preferences-break.png); + background-position: bottom right; + background-repeat: no-repeat; +} + #preftoc li { + /* Tab */ + float: right; + margin: 0; + padding: 0; + padding-left: 1px; + height: 2.25em; + white-space: nowrap; + list-style-type: none; + list-style-image: none; + background-image: url(images/preferences-break.png); + background-position: bottom left; + background-repeat: no-repeat; + } + /* IGNORED BY IE6 */ + #preftoc li:first-child { + margin-right: 1px; + } + #preftoc a, + #preftoc a:active { + display: inline-block; + position: relative; + color: #0645ad; + padding: 0.5em; + text-decoration: none; + background-image: none; + font-size: 0.9em; + } + #preftoc a:hover { + text-decoration: underline; + } + #preftoc li.selected a { + background-image: url(images/preferences-fade.png); + background-position: bottom; + background-repeat: repeat-x; + color: #333333; + text-decoration: none; + } +#preferences { + float: right; + width: 100%; + margin: 0; + margin-top: -2px; + clear: both; + border: solid 1px #cccccc; + background-color: #f9f9f9; + background-image: url(images/preferences-base.png); +} +#preferences fieldset.prefsection { + border: none; + padding: 0; + margin: 1em; +} +#preferences fieldset.prefsection fieldset { + border: none; + border-top: solid 1px #cccccc; +} +#preferences legend { + color: #666666; +} +#preferences fieldset.prefsection legend.mainLegend { + display: none; +} +#preferences td { + padding-right: 0.5em; + padding-left: 0.5em; +} +#preferences td.htmlform-tip { + font-size: x-small; + padding: .2em 2em; + color: #666666; +} +#preferences div.mw-prefs-buttons { + padding: 1em; +} +#preferences div.mw-prefs-buttons input { + margin-left: 0.25em; +} + +/* + * Styles for the user login and create account forms + */ +#userlogin, #userloginForm { + border: solid 1px #cccccc; + padding: 1.2em; + margin: .5em; + float: right; +} + +#userlogin { + min-width: 20em; + max-width: 90%; + width: 40em; +} + +/* + * + * The following code is slightly modified from monobook + * + */ +#content { + line-height: 1.5em; +} +#bodyContent { + font-size: 0.8em; +} +/* Links */ +a { + text-decoration: none; + color: #0645ad; + background: none; +} +a:visited { + color: #0b0080; +} +a:active { + color: #faa700; +} +a:hover { + text-decoration: underline; +} +a.stub { + color: #772233; +} +a.new, #p-personal a.new { + color: #ba0000; +} +a.new:visited, #p-personal a.new:visited { + color: #a55858; +} + +/* Inline Elements */ +img { + border: none; + vertical-align: middle; +} +hr { + height: 1px; + color: #aaa; + background-color: #aaa; + border: 0; + margin: .2em 0 .2em 0; +} + +/* Structural Elements */ +h1, +h2, +h3, +h4, +h5, +h6 { + color: black; + background: none; + font-weight: normal; + margin: 0; + padding-top: .5em; + padding-bottom: .17em; + border-bottom: 1px solid #aaa; + width: auto; +} +h1 { font-size: 188%; } +h1 .editsection { font-size: 53%; } +h2 { font-size: 150%; } +h2 .editsection { font-size: 67%; } +h3, +h4, +h5, +h6 { + border-bottom: none; + font-weight: bold; +} +h3 { font-size: 132%; } +h3 .editsection { font-size: 76%; font-weight: normal; } +h4 { font-size: 116%; } +h4 .editsection { font-size: 86%; font-weight: normal; } +h5 { font-size: 100%; } +h5 .editsection { font-weight: normal; } +h6 { font-size: 80%; } +h6 .editsection { font-size: 125%; font-weight: normal; } +p { + margin: .4em 0 .5em 0; + line-height: 1.5em; +} + p img { + margin: 0; + } +abbr, +acronym, +.explain { + border-bottom: 1px dotted black; + color: black; + background: none; + cursor: help; +} +q { + font-family: Times, "Times New Roman", serif; + font-style: italic; +} +/* Disabled for now +blockquote { + font-family: Times, "Times New Roman", serif; + font-style: italic; +}*/ +code { + background-color: #f9f9f9; +} +pre { + padding: 1em; + border: 1px dashed #2f6fab; + color: black; + background-color: #f9f9f9; + line-height: 1.1em; +} +ul { + line-height: 1.5em; + list-style-type: square; + margin: .3em 1.5em 0 0; + padding: 0; + list-style-image: url(images/bullet-icon.png); +} +ol { + line-height: 1.5em; + margin: .3em 3.2em 0 0; + padding: 0; + list-style-image: none; +} +li { + margin-bottom: .1em; +} +dt { + font-weight: bold; + margin-bottom: .1em; +} +dl { + margin-top: .2em; + margin-bottom: .5em; +} +dd { + line-height: 1.5em; + margin-right: 2em; + margin-bottom: .1em; +} +/* Tables */ +table { + font-size: 100%; + color: black; + /* we don't want the bottom borders of

    s to be visible through + * floated tables */ + background-color: white; +} +fieldset table { + /* but keep table layouts in forms clean... */ + background: none; +} +/* Forms */ +fieldset { + border: 1px solid #2f6fab; + margin: 1em 0 1em 0; + padding: 0 1em 1em; + line-height: 1.5em; +} + fieldset.nested { + margin: 0 0 0.5em 0; + padding: 0 0.5em 0.5em; + } +legend { + padding: .5em; + font-size: 95%; +} +form { + border: none; + margin: 0; +} +textarea { + width: 100%; + padding: .1em; +} +select { + vertical-align: top; +} +/* Table of Contents */ +#toc, +.toc, +.mw-warning { + border: 1px solid #aaa; + background-color: #f9f9f9; + padding: 5px; + font-size: 95%; +} +#toc h2, +.toc h2 { + display: inline; + border: none; + padding: 0; + font-size: 100%; + font-weight: bold; +} +#toc #toctitle, +.toc #toctitle, +#toc .toctitle, +.toc .toctitle { + text-align: center; +} +#toc ul, +.toc ul { + list-style-type: none; + list-style-image: none; + margin-right: 0; + padding-right: 0; + text-align: right; +} +#toc ul ul, +.toc ul ul { + margin: 0 2em 0 0; +} +#toc .toctoggle, +.toc .toctoggle { + font-size: 94%; +} +/* Images */ +div.floatright, table.floatright { + clear: left; + float: left; + position: relative; + margin: 0 .5em .5em 0; + border: 0; +} +div.floatright p { font-style: italic; } +div.floatleft, table.floatleft { + float: right; + clear: right; + position: relative; + margin: 0 0 .5em .5em; + border: 0; +} +div.floatleft p { font-style: italic; } +/* Thumbnails */ +div.thumb { + margin-bottom: .5em; + border-style: solid; + border-color: white; + width: auto; + background-color: transparent; +} +div.thumbinner { + border: 1px solid #ccc; + padding: 3px !important; + background-color: #f9f9f9; + font-size: 94%; + text-align: center; + overflow: hidden; +} +html .thumbimage { + border: 1px solid #ccc; +} +html .thumbcaption { + border: none; + text-align: right; + line-height: 1.4em; + padding: 3px !important; + font-size: 94%; +} +div.magnify { + float: left; + border: none !important; + background: none !important; +} +div.magnify a, div.magnify img { + display: block; + border: none !important; + background: none !important; +} +div.tright { + clear: left; + float: left; + border-width: .5em 1.4em .8em 0; +} +div.tleft { + float: right; + clear: right; + margin-left: .5em; + border-width: .5em 0 .8em 1.4em; +} +img.thumbborder { + border: 1px solid #dddddd; +} +.hiddenStructure { + display: none; +} +/* Warning */ +.mw-warning { + margin-right: 50px; + margin-left: 50px; + text-align: center; +} +/* User Message */ +.usermessage { + background-color: #ffce7b; + border: 1px solid #ffa500; + color: black; + font-weight: bold; + margin: 2em 0 1em; + padding: .5em 1em; + vertical-align: middle; +} +/* Site Notice */ +#siteNotice { + text-align: center; + font-size: 0.8em; + margin: 0; +} + #siteNotice div, + #siteNotice p { + margin: 0; + padding: 0; + margin-bottom: 0.9em; + } +/* Categories */ +.catlinks { + border: 1px solid #aaa; + background-color: #f9f9f9; + padding: 5px; + margin-top: 1em; + clear: both; +} +/* Sub-navigation */ +#siteSub { + display: none; +} +#jump-to-nav { + display: none; +} +#contentSub, #contentSub2 { + font-size: 84%; + line-height: 1.2em; + margin: 0 1em 1.4em 0; + color: #7d7d7d; + width: auto; +} +span.subpages { + display: block; +} +/* Emulate Center */ +.center { + width: 100%; + text-align: center; +} +*.center * { + margin-right: auto; + margin-left: auto; +} +/* Small for tables and similar */ +.small, .small * { + font-size: 94%; +} +table.small { + font-size: 100%; +} +/* Edge Cases for Content */ +h1, h2 { + margin-bottom: .6em; +} +h3, h4, h5 { + margin-bottom: .3em; +} +#firstHeading { + padding-top: 0; + margin-top: 0; + padding-top: 0; + margin-bottom: 0.1em; + line-height: 1.2em; + font-size: 1.6em; + padding-bottom: 0; +} +#content a.external, +#content a[href ^="gopher://"] { + background: url(images/external-link-rtl-icon.png) center left no-repeat; + padding: 0 0 0 13px; +} +#content a[href ^="https://"], +.link-https { + background: url(images/lock-icon.png) center left no-repeat; + padding: 0 0 0 18px; +} +#content a[href ^="mailto:"], +.link-mailto { + background: url(images/mail-icon.png) center left no-repeat; + padding: 0 0 0 18px; +} +#content a[href ^="news://"] { + background: url(images/news-icon.png) center left no-repeat; + padding: 0 0 0 18px; +} +#content a[href ^="ftp://"], +.link-ftp { + background: url(images/file-icon.png) center left no-repeat; + padding: 0 0 0 18px; +} +#content a[href ^="irc://"], +#content a.extiw[href ^="irc://"], +.link-irc { + background: url(images/talk-icon.png) center left no-repeat; + padding: 0 0 0 18px; +} +#content a.external[href $=".ogg"], #content a.external[href $=".OGG"], +#content a.external[href $=".mid"], #content a.external[href $=".MID"], +#content a.external[href $=".midi"], #content a.external[href $=".MIDI"], +#content a.external[href $=".mp3"], #content a.external[href $=".MP3"], +#content a.external[href $=".wav"], #content a.external[href $=".WAV"], +#content a.external[href $=".wma"], #content a.external[href $=".WMA"], +.link-audio { + background: url("images/audio-icon.png") center left no-repeat; + padding: 0 0 0 18px; +} +#content a.external[href $=".ogm"], #content a.external[href $=".OGM"], +#content a.external[href $=".avi"], #content a.external[href $=".AVI"], +#content a.external[href $=".mpeg"], #content a.external[href $=".MPEG"], +#content a.external[href $=".mpg"], #content a.external[href $=".MPG"], +.link-video { + background: url("images/video-icon.png") center left no-repeat; + padding: 0 0 0 18px; +} +#content a.external[href $=".pdf"], #content a.external[href $=".PDF"], +#content a.external[href *=".pdf#"], #content a.external[href *=".PDF#"], +#content a.external[href *=".pdf?"], #content a.external[href *=".PDF?"], +.link-document { + background: url("images/document-icon.png") center left no-repeat; + padding: 0 0 0 18px; +} +/* Interwiki Styling (Disabled) */ +#content a.extiw, +#content a.extiw:active { + color: #36b; + background: none; + padding: 0; +} +#content a.external { + color: #36b; +} +#content .printfooter { + display: none; +} +/* Icon for Usernames */ +#pt-userpage, +#pt-anonuserpage, +#pt-login { + background: url(images/user-icon.png) right top no-repeat; + padding-right: 15px !important; + text-transform: none; +} + +.toccolours { + border: 1px solid #aaa; + background-color: #f9f9f9; + padding: 5px; + font-size: 95%; +} +#bodyContent { + position: relative; + width: 100%; +} +#mw-js-message { + font-size: 0.8em; +} +div#bodyContent { + line-height: 1.5em; +} + +/* Watch/Unwatch Icon Styling */ +#ca-unwatch.icon, +#ca-watch.icon { + margin-left:1px; +} +#ca-unwatch.icon a, +#ca-watch.icon a { + margin: 0; + padding: 0; + outline: none; + display: block; + width: 26px; + height: 2.5em; +} +#ca-unwatch.icon a { + background-image: url(images/watch-icons.png); + background-position: -43px 60%; +} +#ca-watch.icon a { + background-image: url(images/watch-icons.png); + background-position: 5px 60%; +} +#ca-unwatch.icon a:hover { + background-image: url(images/watch-icons.png); + background-position: -67px 60%; +} +#ca-watch.icon a:hover { + background-image: url(images/watch-icons.png); + background-position: -19px 60%; +} +#ca-unwatch.icon a.loading, +#ca-watch.icon a.loading { + background-image: url(images/watch-icon-loading.gif); + background-position: center 60%; +} +#ca-unwatch.icon a span, +#ca-watch.icon a span { + display: none; +} +div.vectorTabs ul { + background-image:url(images/tab-break.png); + background-position:left bottom; + background-repeat:no-repeat; +} diff --git a/planteome/paw/skins/planteome/wiki-indexed.png b/planteome/paw/skins/planteome/wiki-indexed.png new file mode 100644 index 0000000..189a2ae Binary files /dev/null and b/planteome/paw/skins/planteome/wiki-indexed.png differ diff --git a/planteome/paw/skins/planteome/wiki.png b/planteome/paw/skins/planteome/wiki.png new file mode 100644 index 0000000..2463b52 Binary files /dev/null and b/planteome/paw/skins/planteome/wiki.png differ diff --git a/planteome/paw/templates/Annotation.wiki b/planteome/paw/templates/Annotation.wiki new file mode 100644 index 0000000..f6d4f54 --- /dev/null +++ b/planteome/paw/templates/Annotation.wiki @@ -0,0 +1,133 @@ + +This is the "Annotation" template. +It should be called in the following format: +
    +{{Annotation
+|Species Name=
+|Species ID=
+|Gene Symbol=
+|Gene Name=
+|Gene Locus=
+|Gene Type=
+|EC Number(s)=
+|Chromosome=
+|Has Phenotype=
+|Annotation Description=
+}}
+
    +Edit the page to see the template text. +    __NOTOC__ +'''[[Has Gene Symbol::{{{Gene Symbol|}}}]] (''[[Has Species Name::{{{Species Name|}}}]]'')''' + +{{#get_web_data: + |url=http://eutils.ncbi.nlm.nih.gov/entrez/eutils//esearch.fcgi?db=taxonomy&term={{{Species Name|}}} + |format=XML + |data=species_id=id +}} +{{#set:Has Species ID={{#external_value:species_id}} }} + += Annotation = + +{| class="wikitable" +! Species Name +| [[Has Species Name::{{{Species Name|}}}]] +|- +! Species ID +| NCBI:[[Has Species ID::{{#external_value:species_id}}]] +|- +! Gene Symbol +| [[Has Gene Symbol::{{{Gene Symbol|}}}]] +|- +! Gene Name +| [[Has Gene Name::{{{Gene Name|}}}]] +|- +! Gene Synonyms +| {{#if: {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}}]] + | ?is_Gene_Synonym + | headers=hide + | mainlabel=- + | format=list + }} + | None available +}} +|- +! Gene Locus +| [[Has Gene Locus::{{{Gene Locus|}}}]] +|- +! Gene Type +| [[Has Gene Type::{{{Gene Type|}}}]] +|- +! EC number(s) +| {{#arraymap:{{{EC Numbers|}}}|,|x|[[Has EC Numbers::x]]}} +|- +! Chromosome +| [[Exists On Chromosome Number::{{{Chromosome|}}}]] +|- +! Has Phenotype? +| [[Has Phenotype::{{{Has Phenotype|}}}]] +|} + +{| class="wikitable" +! Description +| [[Has Annotation Description::{{{Annotation Description|}}}]] +|} + +{{#ifexist: {{PAGENAME}}/Provenance + | To review the provenance of this data, click [[{{PAGENAME}}/Provenance|here]]. + | +}} + += External References = + +{{#if: {{#ask:[[Category:External_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | {{#ask:[[Is External Reference::~{{PAGENAME}}/External_References]] + | mainlabel=- + |? from_External_Source + |? has_External_Accession_ID + }} + | There are no external references available for this annotation. +}} + += Ontologies = + +{{#if: {{#ask:[[Category:Ontological_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies]] + | mainlabel=- + |? from_Ontology + |? has_Term_ID + |? has_Term_Name + |? has_Aspect + |? has_Evidence_Code + |? has_Evidence + }} + | There are no ontological associations available for this gene annotation. +}} + += Sequences = + +{{#if: {{#ask:[[Category:Sequences]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | {{#ask:[[Is Sequence Reference::~{{PAGENAME}}/Sequences]] + | mainlabel=- + |? has_Sequence_Type + |? has_Sequence_Source + |? has_External_Accession_ID + }} + | There is no sequence data available for this gene annotation. +}} + += Literature = + +{{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] }} + | {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] + |? has First Author + |? has Publication Title + |? has Journal Name + |? has Publication ID + }} + | There are no publications associated with this annotation. +}} + +[[Category:Annotations]] + + diff --git a/planteome/paw/templates/External_Reference_Repeater.wiki b/planteome/paw/templates/External_Reference_Repeater.wiki new file mode 100644 index 0000000..1772131 --- /dev/null +++ b/planteome/paw/templates/External_Reference_Repeater.wiki @@ -0,0 +1,24 @@ + +This is the "External Reference Repeater" template. +It should be called in the following format: +
    +{{External Reference Repeater
+|External Source=
+|External Accession ID=
+}}
+
    +Edit the page to see the template text. +    {{#set_internal:is_External_Reference +|from_External_Source={{{External Source|}}} +|has_External_Accession_ID={{{External Accession ID|}}} +}} + +{| class="wikitable" +! Source +| [[From External Source::{{{External Source|}}}]] +|- +! Accession ID +| [[Has External Accession ID::{{{External Accession ID|}}}]] +|} + + diff --git a/planteome/paw/templates/External_References.wiki b/planteome/paw/templates/External_References.wiki new file mode 100644 index 0000000..a965393 --- /dev/null +++ b/planteome/paw/templates/External_References.wiki @@ -0,0 +1,18 @@ + +This is the "External References" template. +It should be called in the following format: +
    +{{External References
+|Annotation Page=
+}}
+
    +Edit the page to see the template text. +     +{| class="wikitable" +! Annotation Page +| [[Is Associated With Annotation::{{{Annotation Page|}}}]] +|} + +[[Category:External References]] + + diff --git a/planteome/paw/templates/Gene_Ontology_Reference_Repeater.wiki b/planteome/paw/templates/Gene_Ontology_Reference_Repeater.wiki new file mode 100644 index 0000000..019da7a --- /dev/null +++ b/planteome/paw/templates/Gene_Ontology_Reference_Repeater.wiki @@ -0,0 +1,56 @@ + +This is the "Gene Ontology Reference Repeater" template. +It should be called in the following format: +
    +{{Gene Ontology Reference Repeater
+|Term ID=
+|Term Name=
+|Aspect=
+|Evidence Code=
+|Evidence=
+}}
+
    +Edit the page to see the template text. +    {{#get_web_data: + |url=http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&field={{#if:{{{Term Name|}}}|name|acc}}&type=term_detail&ontology=go&qval={{#if:{{{Term Name|}}}|{{{Term Name|}}}|{{{Term ID|}}}}}&format=json + |format=JSON + |data=term_name=name,term_id=id,term_aspect=aspect,term_definition=definition,term_comment=comment +}} +{{#set_internal:is_Ontological_Reference +|from_Ontology=Gene Ontology +|has_Term_ID={{#external_value:term_id}} +|has_Term_Name={{#external_value:term_name}} +|has_Aspect={{#external_value:term_aspect}} +|has_Evidence_Code#list={{{Evidence Code|}}} +|has_Evidence#list={{{Evidence|}}} +}} +{| class="wikitable" +! Ontology +| Gene Ontology +|- +! Term Name +| [[Has Term Name::{{#external_value:term_name}}]] +|- +! Term ID +| [[Has Term ID::{{#external_value:term_id}}]] +|- +! Branch +| {{#external_value:term_aspect}} +|- +! Definition +| {{#external_value:term_definition}} +{{#if: {{#external_value:term_comment}} + | {{!}}- +! Comment +{{!}} {{#external_value:term_comment}} + | +}} +|- +! Evidence Code +| {{#arraymap:{{{Evidence Code|}}}|,|x|[[Has Evidence Code::x]]}} +|- +! Evidence +| {{#arraymap:{{{Evidence|}}}|,|x|[[Has Evidence::x]]}} +|} + + diff --git a/planteome/paw/templates/Gene_Synonym_Repeater.wiki b/planteome/paw/templates/Gene_Synonym_Repeater.wiki new file mode 100644 index 0000000..20681d1 --- /dev/null +++ b/planteome/paw/templates/Gene_Synonym_Repeater.wiki @@ -0,0 +1,14 @@ + +This is the "Gene Synonym Repeater" template. +It should be called in the following format: +
    +{{Gene Synonym Repeater
+|Gene Synonym=
+}}
+
    +Edit the page to see the template text. +    {| class="wikitable" +! Gene Synonym +| [[Is Gene Synonym::{{{Gene Synonym|}}}]] +|} + diff --git a/planteome/paw/templates/Gene_Synonyms.wiki b/planteome/paw/templates/Gene_Synonyms.wiki new file mode 100644 index 0000000..8ed271d --- /dev/null +++ b/planteome/paw/templates/Gene_Synonyms.wiki @@ -0,0 +1,21 @@ + +This is the "Gene Synonyms" template. +It should be called in the following format: +
    +{{Gene Synonyms
+|Annotation Page=
+}}
+
    +Edit the page to see the template text. +     +{| class="wikitable" +! Annotation Page +| [[Is Associated With Annotation::{{{Annotation Page|}}}]] +|- +! Gene Name +| {{#show: {{{Annotation Page|}}}|?has_Gene_Name}} +|} + +[[Category:Gene Synonyms]] + + diff --git a/planteome/paw/templates/Ontological_Reference_Repeater.wiki b/planteome/paw/templates/Ontological_Reference_Repeater.wiki new file mode 100644 index 0000000..44672e9 --- /dev/null +++ b/planteome/paw/templates/Ontological_Reference_Repeater.wiki @@ -0,0 +1,43 @@ + +This is the "Ontological Reference Repeater" template. +It should be called in the following format: +
    +{{Ontological Reference Repeater
+|Ontology=
+|Term ID=
+|Term Name=
+|Aspect=
+|Evidence Code=
+|Evidence=
+}}
+
    +Edit the page to see the template text. +    {{#set_internal:is_Ontological_Reference +|from_Ontology={{{Ontology|}}} +|has_Term_ID={{{Term ID|}}} +|has_Term_Name={{{Term Name|}}} +|has_Aspect={{{Aspect|}}} +|has_Evidence_Code#list={{{Evidence Code|}}} +|has_Evidence#list={{{Evidence|}}} +}} +{| class="wikitable" +! Ontology +| [[From Ontology::{{{Ontology|}}}]] +|- +! Term Name +| [[Has Term Name::{{{Term Name|}}}]] +|- +! Term ID +| [[Has Term ID::{{{Term ID|}}}]] +|- +! Branch +| [[Has Aspect::{{{Aspect|}}}]] +|- +! Evidence Code +| {{#arraymap:{{{Evidence Code|}}}|,|x|[[Has Evidence Code::x]]}} +|- +! Evidence +| {{#arraymap:{{{Evidence|}}}|,|x|[[Has Evidence::x]]}} +|} + + diff --git a/planteome/paw/templates/Ontological_References.wiki b/planteome/paw/templates/Ontological_References.wiki new file mode 100644 index 0000000..4e88f08 --- /dev/null +++ b/planteome/paw/templates/Ontological_References.wiki @@ -0,0 +1,18 @@ + +This is the "Ontological References" template. +It should be called in the following format: +
    +{{Ontological References
+|Annotation Page=
+}}
+
    +Edit the page to see the template text. +     +{| class="wikitable" +! Annotation Page +| [[Is Associated With Annotation::{{{Annotation Page|}}}]] +|} + +[[Category:Ontological References]] + + diff --git a/planteome/paw/templates/Plant_Ontology_Reference_Repeater.wiki b/planteome/paw/templates/Plant_Ontology_Reference_Repeater.wiki new file mode 100644 index 0000000..ecfda58 --- /dev/null +++ b/planteome/paw/templates/Plant_Ontology_Reference_Repeater.wiki @@ -0,0 +1,57 @@ + +This is the "Plant Ontology Reference Repeater" template. +It should be called in the following format: +
    +{{Plant Ontology Reference Repeater
+|Term ID=
+|Term Name=
+|Aspect=
+|Evidence Code=
+|Evidence=
+}}
+
    +Edit the page to see the template text. +    {{#get_web_data: + |url=http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&field={{#if:{{{Term Name|}}}|name|acc}}&type=term_detail&ontology=po&qval={{#if:{{{Term Name|}}}|{{{Term Name|}}}|{{{Term ID|}}}}}&format=json + |format=JSON + |data=term_name=name,term_id=id,term_aspect=aspect,term_definition=definition,term_comment=comment +}} +{{#set_internal:is_Ontological_Reference +|from_Ontology=Plant Ontology +|has_Term_ID={{#external_value:term_id}} +|has_Term_Name={{#external_value:term_name}} +|has_Aspect={{#external_value:term_aspect}} +|has_Evidence_Code#list={{{Evidence Code|}}} +|has_Evidence#list={{{Evidence|}}} +}} +[[Has Term Search Type::{{{Term Search Type|}}}]] +{| class="wikitable" +! Ontology +| Plant Ontology +|- +! Term Name +| [[Has Term Name::{{#external_value:term_name}}]] +|- +! Term ID +| [[Has Term ID::{{#external_value:term_id}}]] +|- +! Branch +| [[Has Aspect::{{#external_value:term_aspect}}]] +|- +! Definition +| {{#external_value:term_definition}} +{{#if: {{#external_value:term_comment}} + | {{!}}- +! Comment +{{!}} {{#external_value:term_comment}} + | +}} +|- +! Evidence Code +| {{#arraymap:{{{Evidence Code|}}}|,|x|[[Has Evidence Code::x]]}} +|- +! Evidence +| {{#arraymap:{{{Evidence|}}}|,|x|[[Has Evidence::x]]}} +|} + + diff --git a/planteome/paw/templates/Provenance.wiki b/planteome/paw/templates/Provenance.wiki new file mode 100644 index 0000000..2e1764f --- /dev/null +++ b/planteome/paw/templates/Provenance.wiki @@ -0,0 +1,18 @@ + +This is the "Provenance" template. +It should be called in the following format: +
    +{{Provenance
+|Annotation Page=
+}}
+
    +Edit the page to see the template text. +     +{| class="wikitable" +! Annotation +| [[Is Associated With Annotation::{{{Annotation Page|}}}]] +|} + +[[Category:Provenance]] + + diff --git a/planteome/paw/templates/Provenance_Repeater.wiki b/planteome/paw/templates/Provenance_Repeater.wiki new file mode 100644 index 0000000..f46fa2f --- /dev/null +++ b/planteome/paw/templates/Provenance_Repeater.wiki @@ -0,0 +1,29 @@ + +This is the "Provenance Repeater" template. +It should be called in the following format: +
    +{{Provenance Repeater
+|Source=
+|Source Accession ID=
+|Source Category=
+|Source Field or Object=
+}}
+
    +Edit the page to see the template text. +    {{#set_internal:is_Provenance +|has_Source={{{Source|}}} +|has_Source_Accession_ID={{{Source Accession ID|}}} +|is_Associated_With_Field_Or_Object={{{Source Field or Object|}}} +|is_Associated_With_Category={{{Source Category|}}} }} + +{| class="wikitable" +! Source +| [[Has Source::{{{Source|}}}]] +|- +! Accession ID +| [[Has Source Accession ID::{{{Source Accession ID|}}}]] +|- +! Field +| [[Is Associated With Field Or Object::{{{Source Field or Object|}}}]] (''Category'': {{{Source Category|}}}) +|} + diff --git a/planteome/paw/templates/Publication.wiki b/planteome/paw/templates/Publication.wiki new file mode 100644 index 0000000..e447cd8 --- /dev/null +++ b/planteome/paw/templates/Publication.wiki @@ -0,0 +1,54 @@ + +This is the "Publication" template. +It should be called in the following format: +
    +{{Publication
+|Publication=
+|Publication ID=
+|Publication Title=
+|First Author=
+|Journal Name=
+|Volume=
+|Year=
+|Pages=
+|Annotation References=
+|New Annotation Reference=
+}}
+
    +Edit the page to see the template text. +     +{| class="wikitable" +! Publication +| [[Has Publication Type::{{{Publication|}}}]] +|- +! Publication Identifier +| [[Has Publication ID::{{{Publication ID|}}}]] +|- +! Publication Title +| [[Has Publication Title::{{{Publication Title|}}}]] +|- +! First Author +| [[Has First Author::{{{First Author|}}}]] +|- +! Journal Name +| [[Has Journal Name::{{{Journal Name|}}}]] +|- +! Volume +| [[Has Publication Volume::{{{Volume|}}}]] +|- +! Year +| [[Has Publication Year::{{{Year|}}}]] +|- +! Pages +| [[Has Publication Pages::{{{Pages|}}}]] +|- +! Annotation References +| {{#arraymap:{{{Annotation References|}}}|,|x|[[Is Associated With Annotations::x]]}} +|- +! New Annotation Reference (to be hidden) +| [[Has New Annotation Association::{{{New Annotation Reference|}}}]] +|} + +[[Category:Publications]] + + diff --git a/planteome/paw/templates/Reference_Publication.wiki b/planteome/paw/templates/Reference_Publication.wiki new file mode 100644 index 0000000..1d22e3a --- /dev/null +++ b/planteome/paw/templates/Reference_Publication.wiki @@ -0,0 +1,60 @@ + +This is the "Reference Publication" template. +It should be called in the following format: +
    +{{Reference Publication
+|Publication=
+|Publication ID=
+|Publication Title=
+|First Author=
+|Journal Name=
+|Volume=
+|Year=
+|Pages=
+|Annotation References=
+|New Annotation Reference=
+}}
+
    +Edit the page to see the template text. +     + +{{#get_web_data: +url=http://dev.planteome.org/w/services/NCBI_eDocSummary.php?pub_id={{{Publication ID|}}} +|format=XML +|data=pub_id=Id,year=PubDate,first_author=LastAuthor,journal_name=FullJournalName,title=Title,volume=Volume,pages=Pages +}} + +{| class="wikitable" +! Publication Catalogue +| [[Has Publication Type::{{{Publication|}}}]] +|- +! Publication Identifier +| [[Has Publication ID::{{{Publication ID|}}}]] +|- +! Publication Title +| [[Has Publication Title::{{#for_external_table:{{{title}}} }}]] +|- +! First Author +| [[Has First Author::{{#for_external_table:{{{first_author}}} }}]] +|- +! Journal Name +| [[Has Journal Name::{{#for_external_table:{{{journal_name}}} }}]] +|- +! Volume +| [[Has Publication Volume::{{#for_external_table:{{{volume}}} }}]] +|- +! Year +| [[Has Publication Year::{{#for_external_table:{{{year}}} }}]] +|- +! Pages +| [[Has Publication Pages::{{#for_external_table:{{{pages}}} }}]] +|- +! Annotation References +| {{#arraymap:{{{Annotation References|}}}|,|x|[[Is Associated With Annotations::x]]}} +|} + + + +[[Category:Reference Publications]] + + diff --git a/planteome/paw/templates/Sequence_Repeater.wiki b/planteome/paw/templates/Sequence_Repeater.wiki new file mode 100644 index 0000000..e9c84b6 --- /dev/null +++ b/planteome/paw/templates/Sequence_Repeater.wiki @@ -0,0 +1,28 @@ + +This is the "Sequence Repeater" template. +It should be called in the following format: +
    +{{Sequence Repeater
+|Sequence Type=
+|Sequence Source=
+|External Accession ID=
+}}
+
    +Edit the page to see the template text. +    {{#set_internal:is_Sequence_Reference +|has_Sequence_Type={{{Sequence Type}}} +|has_Sequence_Source={{{Sequence Source|}}} +|has_External_Accession_ID={{{External Accession ID|}}} +}} +{| class="wikitable" +! Sequence Type +| [[Has Sequence Type::{{{Sequence Type|}}}]] +|- +! Sequence Source +| [[Has Sequence Source::{{{Sequence Source|}}}]] +|- +! Accession ID +| [[Has External Accession ID::{{{External Accession ID|}}}]] +|} + + diff --git a/planteome/paw/templates/Sequences.wiki b/planteome/paw/templates/Sequences.wiki new file mode 100644 index 0000000..2a98b35 --- /dev/null +++ b/planteome/paw/templates/Sequences.wiki @@ -0,0 +1,18 @@ + +This is the "Sequences" template. +It should be called in the following format: +
    +{{Sequences
+|Annotation Page=
+}}
+
    +Edit the page to see the template text. +     +{| class="wikitable" +! Annotation Page +| [[Is Associated With Annotation::{{{Annotation Page|}}}]] +|} + +[[Category:Sequences]] + + diff --git a/planteome/paw/templates/Source.wiki b/planteome/paw/templates/Source.wiki new file mode 100644 index 0000000..3cb52f7 --- /dev/null +++ b/planteome/paw/templates/Source.wiki @@ -0,0 +1,34 @@ + +This is the "Source" template. +It should be called in the following format: +
    +{{Source
+|Source Date Stamp=
+|Source Database=
+|Source Version=
+|Source URI=
+|Source File=
+}}
+
    +Edit the page to see the template text. +     +{| class="wikitable" +! Release Date +| [[Has Date Stamp::{{{Source Date Stamp|}}}]] +|- +! Data Source +| [[Has Source Database::{{{Source Database|}}}]] +|- +! Version +| [[Has Source Version::{{{Source Version|}}}]] +|- +! Web Address +| [[From Source URI::{{{Source URI|}}}]] +|- +! File +| [[From Source File::{{{Source File|}}}]] +|} + +[[Category:Sources]] + + diff --git a/preecej/.gitignore b/preecej/.gitignore new file mode 100644 index 0000000..e69de29 diff --git a/preecej/perl_singletons/aracyc_to_reactome_conversion/ara_rice_exclusive_sets.pl b/preecej/perl_singletons/aracyc_to_reactome_conversion/ara_rice_exclusive_sets.pl deleted file mode 100644 index 75e6ea0..0000000 --- a/preecej/perl_singletons/aracyc_to_reactome_conversion/ara_rice_exclusive_sets.pl +++ /dev/null @@ -1,68 +0,0 @@ -#!usr/bin/perl -w -use strict; - -system 'clear'; - -# determine mapped ChEBI molecules listed in arabidopsis but not in rice, -# and vice-versa - -my $dir = "/home/preecej/Documents/projects/reactome/aracyc_to_reactome_conversion/ara_rice_exclusive_sets/"; -my @rice; -my @ara; - -open(IN_FILE, $dir . "Rice_ReferenceNameToChEBIId.txt") or die; -while () { - my $line = $_; - chomp $line; - push(@rice,$line); -} -close IN_FILE; - -open(IN_FILE, $dir . "Ara_ReferenceNameToChEBIId.txt") or die; -while () { - my $line = $_; - chomp $line; - push(@ara,$line); -} -close IN_FILE; - -my %ara_seen; # lookup tbl -my @rice_only; #exclusive to rice - -# build lookup tbl -@ara_seen{@ara} = (); - -foreach my $item (@rice) { - push(@rice_only, $item) unless exists $ara_seen{$item}; -} - -my %rice_seen; # lookup tbl -my @ara_only; #exclusive to rice - -# build lookup tbl -@rice_seen{@rice} = (); - -foreach my $item (@ara) { - push(@ara_only, $item) unless exists $rice_seen{$item}; -} - -my $exc_rice_count = 0; -print "-- [EXCLUSIVE RICE MOLECULES] --\n"; -foreach my $item (@rice_only) { - $exc_rice_count++; - print "$exc_rice_count: $item\n"; -} - -#print "$exc_rice_count\n\n"; - -my $exc_ara_count = 0; -print "-- [EXCLUSIVE ARABIDOPSIS MOLECULES] --\n"; -foreach my $item (@ara_only) { - $exc_ara_count++; - print "$exc_ara_count: $item\n"; -} - -print "$exc_ara_count\n\n"; - -# clean up -exit; diff --git a/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_pub_authors_to_years.pl b/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_pub_authors_to_years.pl deleted file mode 100644 index 8769b10..0000000 --- a/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_pub_authors_to_years.pl +++ /dev/null @@ -1,44 +0,0 @@ -#!usr/bin/perl -w -use strict; - -system 'clear'; - -# temp script used to fix elements that mistakenly refer to years in -# parentheses. replaces those elements with . - -my $dir = "/home/preecej/Documents/projects/reactome/aracyc_to_reactome_conversion/aracyc_data/"; - -open(in_file, $dir . "aracyc_v8_0_biopax-level2_STOIdouble.owl"); -open(out_file, ">>" . $dir . "aracyc_v8_0_biopax-level2_STOIdouble_AUTHORSYEAR.owl"); - -my $i = 0; # limiter for testing - -while () -{ - $i++; - - # read the next line of the file - my $line = $_; - chomp $line; - - # is it a bad author? - if ($line =~ /\(/) - { - print "$i: $line\n"; - # change the line to a well-formatted year tag - $line =~ s/AUTHORS/YEAR/g; - $line =~ s/\(//; - $line =~ s/\)//; - $line =~ s/string/int/; - print "$i: $line\n"; - } - print out_file "$line\n"; - - #last if $i > 1000; # let's test w/ low numbers for now -} - -close in_file; -close out_file; - -# clean up -exit; diff --git a/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_step_interaction_datatypes.pl b/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_step_interaction_datatypes.pl deleted file mode 100644 index 13d8e83..0000000 --- a/preecej/perl_singletons/aracyc_to_reactome_conversion/convert_bad_step_interaction_datatypes.pl +++ /dev/null @@ -1,45 +0,0 @@ -#!usr/bin/perl -w -use strict; - -system 'clear'; - -# temp script used to fix elements that mistakenly refer to years in -# parentheses. replaces those elements with . -# Example: -# BEFORE: catalysis42055 -# AFTER: - -my $dir = "/home/preecej/Documents/projects/reactome/aracyc_to_reactome_conversion/aracyc_data/"; - -open(in_file, $dir . "aracyc_v8_0_biopax-level2_STOIdouble_AUTHORSYEAR.owl"); -open(out_file, ">>" . $dir . "aracyc_v8_0_biopax-level2_STOIdouble_AUTHORSYEAR_STEPINT.owl"); - -my $i = 0; # limiter for testing - -while () -{ - $i++; - - # read the next line of the file - my $line = $_; - chomp $line; - - # is it a bad step interaction? - if ($line =~ //) - { - print "$i: $line\n"; - # change the line to a well-formatted STEP-INTERACTION tag - $line =~ s/datatype="http:\/\/www.w3.org\/2001\/XMLSchema#string">/resource="\#/g; - $line =~ s/<\/bp:STEP-INTERACTIONS>/"\/>/; - print "$i: $line\n"; - } - print out_file "$line\n"; - - #last if $i > 1000; # let's test w/ low numbers for now -} - -close in_file; -close out_file; - -# clean up -exit; diff --git a/preecej/perl_singletons/pathway_gene_swapper.pl b/preecej/perl_singletons/pathway_gene_swapper.pl deleted file mode 100644 index 490959f..0000000 --- a/preecej/perl_singletons/pathway_gene_swapper.pl +++ /dev/null @@ -1,910 +0,0 @@ -#!/usr/bin/perl -w - -=head1 NAME - -Pathway Gene Swapper - -=head1 VERSION - -0.2 - -=head1 DESCRIPTION - -Swap out one set of genes (or gene representations) for another in an -existing PathVisio GPML file. Optionally removes literature references. - -If multiple replacement genes map to a single original gene, -multiple PathVisio boxes will be drawn in place of the -original. - -If a group associating multiple gene boxes already existed, -that group will extend to any replacement genes. If no group -existed previously, and multiple replacement gene boxes are required, -a new group will be created. - -If an original gene had multiple instances (homologs) displayed on the pathway -diagram, each instance will be subjected to the replacement process. There -is a "heat-map" option avaliable to help highlight homolog sets. - -There is also an option to read in an extra column of gene symbols, if the -user wishes to provide their own. Otherwise, the application will -continue to use the label prefix and auto-numbering suffix settings. - -The replacement gene symbols can be prefixed to separate them from the -original, and an ordinal suffix ('-#') will be added to a group of -replacement genes. - -Any new gene boxes may be painted with a custom color and border, and -will be stacked and offset for ease of visualization (much like a deck -of cards). - -=head1 FUTURE CHANGES - -Add a legend for the heat map (upper right-hand corner). - -Add a comment containing the NCBI species id of the new homolog (for -the purpose of multi-species pathway comparison or host-pathogen -interaction diagrams). - -=head1 USAGE - -pathway_gene_swapper.pl -i INPUT_FILE -g GENE_MAPPING_FILE -c CONFIG_FILE -o OUTPUT_FILE [-shLvGd] - -=head1 OPTIONS - - -i Name of input GPML file. - -g CSV file containing the genes to swap - -c config file containing color, label, and placement preferences - -o Name of output GPML file. - (NOTE: if no path supplied for input files, - current working directory is assumed) - -s use provided gene symbols instead of config file's LabelPrefix - -h apply a heat-map to any multi-mapped set of homologs - (NOTE: precludes custom box-coloring for homologs) - -L Remove literature references. - -v View verbose information - -G Display GPML input/output documents - -d View debugging information - -=head1 DEPENDENCIES and PREREQUISITES - - - Non-standard Perl modules: Switch, Data::Dumper, XML::DOM - - The input file must be a valid GPML file - - The CSV file must have a single-line column header. - - The first column must have one and only one gene -- the - "original" gene. - - The second column may have one and only one gene variant or - homolog -- the "replacement" gene(s). - - An optional "gene symbol" column may be placed between the - first two columns, if the user would prefer to use a list of - symbols for the new homologous genes. - - - The config file may have any or all of the following entries, - in addition to the required fields (in any order): - - Source= (required) - Database= (required) - Version= (required) - Title= - Author= - Maintainer= - Organism= - CommentPrefix= (will precede back-reference to prior source, - default: "Previously labeled as: ") - LabelPrefix= (precedes current gene label) - BoxBorder= (RRGGBB hex, default: black) - BoxColor= (RRGGBB hex, default: white) - BoxWidth= (integer, in px, default: 60) - X-Offset= (integer, in px, default: 5px) - Y-Offset= (integer, in px, default: 4px) - -=head1 AUTHORS - -Justin Preece and Mamatha Hanumappa - Faculty Research Assistants - Jaiswal Lab, Botany & Plant Pathology - Oregon State University - L - L - -=cut - -# --------------------------------------------------------------------------- -# modules -# --------------------------------------------------------------------------- - -# general -use strict; -use Cwd; -use Switch; -use Getopt::Std; -use Data::Dumper; - -# specific -use Graphics::ColorUtils qw( :gradients ); -use XML::DOM; - -# --------------------------------------------------------------------------- -# declarations -# --------------------------------------------------------------------------- - -# command-line options -my %opts; # arg options -my $input_gpml_file; -my $input_gene_file; -my $input_config_file; -my $output_file; -my $apply_homolog_heat = 0; -my $remove_lit = 0; # flag to remove literature and lit references -my $use_symbols = 0; # flag to indicate use of provided gene symbols -my $verbose = 0; # flag for verbose output -my $doc_mode = 0; # flag for extra GPML doc output -my $debug = 0; # debugging switch - -# global data containers -my %configs; # configuration settings -my %swap_genes; # original and swapped genes -my $gpml_doc; # imported GPML data for manipulation and output -my %unmapped_genes; # original genes not mapped to homologs -my %gradient; # blue-red gradient used for opt. heat map box-coloring -my $max_homolog_count = 0; # count for heat map calibration - -$Data::Dumper::Pad = "... "; - -# --------------------------------------------------------------------------- -=head1 FUNCTIONS - -=over - -=cut -# --------------------------------------------------------------------------- - - -# --------------------------------------------------------------------------- -=item B -Accepts a config file path. -Reads a configuration file and sets config values. -Returns a hash with config values set. -=cut -# --------------------------------------------------------------------------- -sub config($) -{ - - print "Opening configuration file and reading data...\n\n"; - my %local_config_hash; - - open(CONFIG_FILE, $_[0]) or die("Could not open $_[0]"); - - while () - { - my $line = $_; - chomp $line; - my @line_ary = split('=',$line); - my $data_field = $line_ary[0]; - my $data_val = $line_ary[1]; - - if ($data_val) - { - $local_config_hash{$data_field} = $data_val; - } - } - - close(CONFIG_FILE); - - # check for required settings - if (!$local_config_hash{"Source"}) { - die("You are required to provide a Source for your new data.\n" - . "Run \"perldoc pathway_gene_swapper.pl\" for more information.\n\n"); } - if (!$local_config_hash{"Database"}) { - die("You are required to identify a Database for your new data.\n" - . "Run \"perldoc pathway_gene_swapper.pl\" for more information.\n\n"); } - if (!$local_config_hash{"Version"}) { - die("You are required to provide a Version idenifier for your new data.\n" - . "Run \"perldoc pathway_gene_swapper.pl\" for more information.\n\n"); } - - # set defaults, if none declared - if (!$local_config_hash{"CommentPrefix"}) { - $local_config_hash{"CommentPrefix"} = "Previously labeled as: "; - } - if (!$local_config_hash{"BoxWidth"}) { - $local_config_hash{"BoxWidth"} = 60; - } - if (!$local_config_hash{"X-Offset"}) { - $local_config_hash{"X-Offset"} = 4; - } - if (!$local_config_hash{"Y-Offset"}) { - $local_config_hash{"Y-Offset"} = 3; - } - - return %local_config_hash; -} - - -# --------------------------------------------------------------------------- -=item B -Reads in command-line values, calls for config settings, and begins -screen output. -=cut -# --------------------------------------------------------------------------- -sub init -{ - # read and set options - getopts('i:g:c:o:hLsvGd', \%opts); - - foreach my $key (keys %opts) { - my $value = $opts{$key}; - switch ($key) { - case "i" { - if ($value =~ /\//) { # assume path - $input_gpml_file = $value; - } else { - $input_gpml_file = getcwd() . "\/$value"; - } - } - case "g" { - if ($value =~ /\//) { # assume path - $input_gene_file = $value; - } else { - $input_gene_file = getcwd() . "\/$value"; - } - } - case "c" { - if ($value =~ /\//) { # assume path - $input_config_file = $value; - } else { - $input_config_file = getcwd() . "\/$value"; - } - } - case "o" { - if ($value =~ /\//) { # assume path - $output_file = $value; - } else { - $output_file = getcwd() . "\/$value"; - } - } - case "s" { $use_symbols = 1; } - case "h" { $apply_homolog_heat = 1; } - case "L" { $remove_lit = 1; } - case "v" { $verbose = 1; } - case "G" { $doc_mode = 1; } - case "d" { $debug = 1; } - } - } - - system "clear"; - print "\n" - . "------------------------------------------------------------\n" - . "------------------ Pathway Gene Swapper --------------------\n" - . "------------------------------------------------------------\n" - . "\n" - . "Input Files:\n" - . " - PathVisio File (GPML): $input_gpml_file\n" - . " - Gene List (CSV): $input_gene_file\n" - . " - Configuration settings: $input_config_file\n" - . "\n" - . "Output File: $output_file\n" - . "\n" - . "Use provided gene symbols? " . ($use_symbols ? "Yes" : "No") . "\n" - . "Provide homolog heat-map? " . ($apply_homolog_heat ? "Yes" : "No") . "\n" - . "Remove literature references? " . ($remove_lit ? "Yes" : "No") . "\n" - . "Running in verbose mode? " . ($verbose ? "Yes" : "No") . "\n" - . "Running in document mode? " . ($doc_mode ? "Yes" : "No") . "\n" - . "Running in debug mode? " . ($debug ? "Yes" : "No") . "\n" - . "\n" - . "------------------------------------------------------------\n" - . "------------------------------------------------------------\n" - . "------------------------------------------------------------\n" - . "\n"; - - %configs = config($input_config_file); -} - - -# --------------------------------------------------------------------------- -=item B -Accepts: The maximum number of homologs for one gene in this data set -Creates a blue-red gradient and stores it in a hash. -Returns: A hash of RRGGBB color values, keyed to the number set of -possible homologs (1..n). -=cut -# --------------------------------------------------------------------------- -sub set_gradient($) -{ - my @blue_red_array; - - for (my $i=0; $i<256; $i++) { - push @blue_red_array, [$i, 0, (255-$i)]; - } - - register_gradient("blue_red",\@blue_red_array); - - my %blue_red_gradient; - my $max_grad = $_[0]; - my $inc = sprintf("%.2f", 1/$max_grad); - my $count = 1; - - for (my $i=$inc; $i<=0.99; $i=$i+$inc) { - my $tmp_hex = grad2rgb("blue_red",$i); - $tmp_hex =~ s/\#//; - $blue_red_gradient{$count} = $tmp_hex; - $count++; - } - - return %blue_red_gradient; -} - - -# --------------------------------------------------------------------------- -=item B -Reads, parses, and stores gene mapping file and source GPML. -=cut -# --------------------------------------------------------------------------- -sub import_data -{ - print "Opening gene mapping file and reading data...\n\n"; - - open(GENE_FILE, $input_gene_file) or die("Could not open $input_gene_file"); - - # used to generate total counts of each species' gene list; sanity check - my $original_gene_count = 0; - my $replacement_homolog_count = 0; - - my $orig_data_item; - my $new_symbol = ""; - my $new_data_item; - - # ignore header - my $line = ; - - while () - { - $line = $_; - chomp $line; - my @line_ary = split(',',$line); - my $orig_data_item = $line_ary[0]; - - if ($use_symbols) { - if (scalar(@line_ary) != 3) { - die("If you specify that your gene-mapping file includes " - . "symbols, then your CSV input file must have three " - . "columns of data (in this order): " - . "old gene, new symbol, new gene\n"); - } - $new_symbol = $line_ary[1]; - $new_data_item = $line_ary[2]; - } - else - { - $new_data_item = $line_ary[1]; - } - - #Does ath_gene exist? - if (!exists $swap_genes{$orig_data_item}) - { - $original_gene_count++; - } - $replacement_homolog_count++; # count this every time - - # add new gene to hash value (array) for old gene hash key - push @{$swap_genes{$orig_data_item}}, - { "symbol"=>$new_symbol, "new_item"=>$new_data_item }; - - $new_symbol = ""; # reset for next iter. - } - - # determine the original gene(s) with the highest # of homologs in the new - # gene set - my @most_popular_genes; # identity of the gene(s) with the highest number of homologs - foreach my $orig_gene_key (keys %swap_genes) - { - if ($max_homolog_count < scalar(@{$swap_genes{$orig_gene_key}})) - { - $max_homolog_count = scalar(@{$swap_genes{$orig_gene_key}}); - @most_popular_genes = (); # new max; refresh - push @most_popular_genes, $orig_gene_key; - } - else - { - if ($max_homolog_count == scalar(@{$swap_genes{$orig_gene_key}})) - { - push @most_popular_genes, $orig_gene_key; - } - } - } - - if ($verbose) # give add'l stats on gene and homolog counts - { - print "[Total number of original genes and homologs]\n" - . "Original gene count: " . $original_gene_count . "\n" - . "Replacement homolog count: $replacement_homolog_count\n\n"; - - print "[Highest number of homologs per gene]\n"; - print "Number of homologs: $max_homolog_count\n"; - print "Gene(s): @most_popular_genes\n\n"; - - print "[Number of homologs per original gene]\n"; - foreach my $orig_gene_key (keys %swap_genes) - { - print "$orig_gene_key: " . scalar(@{$swap_genes{$orig_gene_key}}) . "\n"; - } - print "\n"; - } - - close(GENE_FILE); - - # initialize the blue-red gradient for heat mapping - if ($apply_homolog_heat) - { - %gradient = set_gradient($max_homolog_count); - } - - print "Opening GPML pathway file and reading data...\n\n"; - - my $parser = new XML::DOM::Parser; - $gpml_doc = $parser->parsefile($input_gpml_file); -} - - -# --------------------------------------------------------------------------- -=item B -Spits out the data to make sure you've read in the files correctly. -Verbose only. -=cut -# --------------------------------------------------------------------------- -sub show_input -{ - if ($verbose) - { - print "[Configuration Settings]\n"; - print Dumper(\%configs) . "\n\n"; - print "\n"; - - print "[Gene Mappings]\n"; - print Dumper(\%swap_genes) . "\n\n"; - print "\n"; - } - if ($doc_mode) - { - print "[Source GPML]\n"; - print $gpml_doc->toString; - print "\n"; - } -} - -# --------------------------------------------------------------------------- -=item B -Accepts a reference to a hash of existing hex ids and a string as -the "type" of ID (e.g. "Group.GraphId"). The latter is currently for -documentary purposes only. -Generates a "random" 5-digit hexadecimal id, checks to see if it -already exists in the hex list, and if not, adds it to the list -of hex ids already present in the GPML doc. Otherwise, generates -another "random" id and repeats the process until a new unique id -is identified. -Returns a string containing the new hex id. -=cut -# --------------------------------------------------------------------------- -sub create_unique_hex_id($$) -{ - # NOTE: This algorithm breaks down at VERY large scale (100K genes+). The - # larger the number of original genes, groups, and new homologs you need to - # create, the more inefficient it becomes to make sure your "random" 5-digit - # hex number is not already present in your "existing ids" list via - # recursion. However, for a few hundred or thousand genes, it should be ok. - - my $first_digit; # limited to a..f - my $last_four_digits; # 0..f - - $first_digit = (('a'..'f')[rand(6)]); - $last_four_digits .= ((0..9,'a'..'f')[rand(16)]) for 1..4; - - my $candidate_id = $first_digit . $last_four_digits; - - # recurse if you haven't generated a unique id yet - if (exists ${$_[0]}{$candidate_id}) - { - # print "not unique...\n"; # TEST - # the '&' suppresses prototype checking and avoids a runtime warning - # since this is a recursive call - $candidate_id = &create_unique_hex_id($_[0],$_[1]); - } - else - { - # print "unique!\n"; # TEST - ${$_[0]}{$candidate_id} = $_[1]; - } - - return $candidate_id; -} - -# --------------------------------------------------------------------------- -=item B -Substitutes gene data. -=cut -# --------------------------------------------------------------------------- -sub swap_genes -{ - print "Swapping gene data and making other document modifications...\n\n"; - - my $pathway_node = ($gpml_doc->getElementsByTagName("Pathway"))[0]; - - # change Pathway header info to config settings - if ($configs{"Title"}) { - $pathway_node->setAttribute("Name",$configs{"Title"}); } - if ($configs{"Author"}) { - $pathway_node->setAttribute("Author",$configs{"Author"}); } - if ($configs{"Maintainer"}) { - $pathway_node->setAttribute("Maintainer",$configs{"Maintainer"}); } - if ($configs{"Version"}) { - $pathway_node->setAttribute("Version",$configs{"Version"}); } - if ($configs{"Organism"}) { - $pathway_node->setAttribute("Organism",$configs{"Organism"}); } - - # get all "gene box" data nodes - my $data_nodes = $pathway_node->getElementsByTagName("DataNode"); - # print $data_nodes->getLength . "\n"; # TEST - - # remove all and elements and children - if ($remove_lit) - { - print "Removing literature references...\n\n"; - my $biopax_node = ($pathway_node->getElementsByTagName("Biopax"))[0]; - $pathway_node->removeChild($biopax_node); - - for (@$data_nodes) - { - my $curr_datanode = $_; - my $biopaxref_nodes = $curr_datanode->getElementsByTagName("BiopaxRef"); - for (@$biopaxref_nodes) - { - # print $_->getTagName . "\n"; # TEST - $curr_datanode->removeChild($_); - } - } - } - - # will hold a convenient nested hash of data node references in the gpml doc, - # indexed by the id of the gene located in the element for each - # node, and sub-indexed by the GraphId of each corresponding node - my %data_nodes_by_gene_id; - - if ($verbose) { - print "[Original genes]\n"; - } - - # create a hash of all 5-digit hex ids in the gpml doc (this is the black list) - # one list of DataNode.GraphId, Group.GroupId, and Group.GraphId - my %existing_hex_ids; - for (@$data_nodes) - { - # print $_ . "\n"; # TEST - - if ($_->getAttributeNode("GraphId")) - { - $existing_hex_ids{$_->getAttributeNode("GraphId")->getValue} - = $_->getTagName . ".GraphId"; - } - - # also build a data node hash to make lookup easier in the next section - my $curr_xref_id = ($_->getElementsByTagName("Xref"))[0] - ->getAttributeNode("ID")->getValue; - my $curr_graph_id = $_->getAttributeNode("GraphId")->getValue; - - $curr_xref_id =~ s/\s+$//; # rtrim whitespace - $curr_xref_id =~ s/^\s+//; # ltrim whitespace - - if ($verbose) { - my $curr_text_label = $_->getAttributeNode('TextLabel')->getValue; - $curr_text_label =~ s/^\s+|\s+$//; # trim whitespace - print "$curr_text_label\t$curr_xref_id\n"; - } - - if (length($curr_xref_id) > 0) - { - #if ($curr_xref_id eq "AT3G12810") { print "** hit on AT3G12810\n"; } # TEST - $data_nodes_by_gene_id{$curr_xref_id}{$curr_graph_id} = $_; - } - else - { - if ($verbose) { - print "WARNING: Found DataNode (TextLabel: " - . $_->getAttributeNode('TextLabel')->getValue . ") " - . "with missing Xref ID.\n" - } - } - } - print "\n"; - - if ($debug) { - print "...\n"; - foreach my $tmp_gene (keys %data_nodes_by_gene_id) { - foreach my $tmp_node (keys %{$data_nodes_by_gene_id{$tmp_gene}}) { - print "... $tmp_gene => $tmp_node => $data_nodes_by_gene_id{$tmp_gene}{$tmp_node}\n"; - #if ($tmp_gene eq "AT3G12810") { print "** hit on AT3G12810 node\n"; } # TEST - } - } - print "\n"; - } - - my $group_nodes = $pathway_node->getElementsByTagName("Group"); - for (@$group_nodes) - { - if ($_->getAttributeNode("GroupId")) - { - $existing_hex_ids{$_->getAttributeNode("GroupId")->getValue} - = $_->getTagName . ".GroupId"; - } - if ($_->getAttributeNode("GraphId")) - { - $existing_hex_ids{$_->getAttributeNode("GraphId")->getValue} - = $_->getTagName . ".GraphId"; - } - } - - if ($debug) { print "...\n" - . Dumper(\%existing_hex_ids) . "\n\n"; } - - # iterate through gene mappings from csv file - foreach my $old_gene (keys %swap_genes) - { - # print $old_gene . "\n"; # TEST - - # find curr old gene nodes in doc - if (exists $data_nodes_by_gene_id{$old_gene}) - { - # iterate through each node by its GraphId - foreach my $curr_old_genes_by_hex_id (keys %{$data_nodes_by_gene_id{$old_gene}}) - { - my $curr_old_gene_node = $data_nodes_by_gene_id{$old_gene}{$curr_old_genes_by_hex_id}; - # print $curr_old_gene_node . "\n"; # TEST - - # holds list of newly-created nodes, used to replace old node - my @new_nodes_map; - - # iterate through new gene replacements - for (@{$swap_genes{$old_gene}}) - { - # copy the curr old gene node - my $new_node = $curr_old_gene_node->cloneNode("deep"); - - # print "[$_]\n$new_node->toString\n\n"; # TEST - - # add to new nodes ary - push @new_nodes_map, [$new_node, $_]; - } - # print "@new_nodes_map\n"; # TEST - - # if more than one new homolog exists, and the old gene doesn't - # already belong to a group, you'll need a new Group for multiple - # gene boxes - my $new_GroupId; - - if (scalar(@new_nodes_map) > 1) - { - # if curr old gene does not belong to a group - - # print $curr_old_gene_node->toString . "\n"; # TEST - # print $curr_old_gene_node->getAttribute("GroupRef"); # TEST - - if (!$curr_old_gene_node->getAttribute("GroupRef")) - { - #print "no existing group ref\n"; # TEST - - # generate a new GroupId and Group.GraphId hex ids not - # already in use - $new_GroupId = create_unique_hex_id(\%existing_hex_ids,"Group.GroupId"); - # my $new_Group_GraphId = create_unique_hex_id(\%existing_hex_ids,"Group.GraphId"); - #print "new group id: $new_GroupId\n"; # TEST - # print "$new_GroupId, $new_Group_GraphId\n"; # TEST - - # create a new group node - my $new_group = $gpml_doc->createElement("Group"); - $new_group->setAttribute("GroupId",$new_GroupId); - #$new_group->setAttribute("GraphId",$new_Group_GraphId); - $new_group->setAttribute("Style","Group"); - - # add to beginning of group nodes - $pathway_node->insertBefore($new_group,${$group_nodes}[0]); - } - } - - # flag for determining if there are one or many replacement homologs - my $is_first_homolog = 1; - - # makes sure each box is increasingly offset from the original - # (in all three dimensions) - my $offset_multiplier = 0; - my $gene_suffix_counter = 0; # used to affix numbers to multiple new gene symbols - - # for new nodes ary - for (@new_nodes_map) - { - if (scalar(@new_nodes_map) > 1) - { - $gene_suffix_counter++; - } - - my $curr_new_node = $$_[0]; - my $curr_symbol = ${$$_[1]}{"symbol"}; - my $curr_homolog = ${$$_[1]}{"new_item"}; - - #print "$_: $curr_new_node, $curr_symbol, $curr_homolog\n"; # TEST - #print "[Curr New Node before editing...]\n" . $curr_new_node->toString . "\n\n"; # TEST - - # update all new nodes w/ attributes... - - # grab original text label - my $old_label = $curr_new_node->getAttributeNode("TextLabel")->getValue; - - # rename TextLabel... - if ($use_symbols && length($curr_symbol) > 0) # apply the provided gene symbol - { - $curr_new_node->setAttribute("TextLabel", $curr_symbol); - } - else # prefix (from config), suffix: new '-#' for multiple homologs - { - $curr_new_node->setAttribute("TextLabel", - (($configs{"LabelPrefix"}) ? $configs{"LabelPrefix"} : "") - . $curr_new_node->getAttributeNode("TextLabel")->getValue - . (($gene_suffix_counter > 0) ? "-$gene_suffix_counter" : "")); - } - - # add new GroupRef if necessary - if ($new_GroupId) - { - $curr_new_node->setAttribute("GroupRef",$new_GroupId); - } - - # add Comment back-referencing TAIR locus id (use "source" attribute) - # NOTE: order is important in GPML; the tags are first - my $new_comment = $gpml_doc->createElement("Comment"); - $new_comment->setAttribute("Source",$configs{"Source"}); - $new_comment->addText($configs{"CommentPrefix"} . " $old_gene ($old_label)."); - $curr_new_node->insertBefore($new_comment,$curr_new_node->getFirstChild); # assumes other child nodes - - # edit - my $curr_xref = ($curr_new_node->getElementsByTagName("Xref"))[0]; - $curr_xref->setAttribute("Database",$configs{"Database"}); - $curr_xref->setAttribute("ID",$curr_homolog); - - # change box width and colors () - my $curr_graphics = ($curr_new_node->getElementsByTagName("Graphics"))[0]; - $curr_graphics->setAttribute("Width",$configs{"BoxWidth"}); - - # add "heat" to genes with multiple homologs - if ($apply_homolog_heat && ($gene_suffix_counter > 0)) - { - $curr_graphics->setAttribute("FillColor", $gradient{scalar(@new_nodes_map)}); - $curr_graphics->setAttribute("Color","8888ff"); - } - else - { - if ($configs{"BoxColor"}) { - $curr_graphics->setAttribute("FillColor",$configs{"BoxColor"}); } - if ($configs{"BoxBorder"}) { - $curr_graphics->setAttribute("Color",$configs{"BoxBorder"}); } - } - - if ($is_first_homolog) - { - # print "that was the first homolog...\n"; # TEST - $is_first_homolog = 0; # first homolog complete - } - else # add'l homologs required - { - $offset_multiplier++; - - # print "that was an add'l homolog, change more attrs...\n"; # TEST - # update add'l nodes w/ special attributes... - - # generate a new DataNode GraphId not already in use - my $new_GraphId = - create_unique_hex_id(\%existing_hex_ids,"DataNode.GraphId"); - # print $new_GraphId . "\n"; # TEST - $curr_new_node->setAttribute("GraphId",$new_GraphId); - - # decrement the Z-order - $curr_graphics->setAttribute("ZOrder", - $curr_graphics->getAttributeNode("ZOrder")->getValue - - $offset_multiplier); - # stagger the extra boxes by decrementing the coords - $curr_graphics->setAttribute("CenterX", - $curr_graphics->getAttributeNode("CenterX")->getValue - - ($configs{"X-Offset"} * $offset_multiplier)); - $curr_graphics->setAttribute("CenterY", - $curr_graphics->getAttributeNode("CenterY")->getValue - - ($configs{"Y-Offset"} * $offset_multiplier)); - } - } - undef $new_GroupId; # clear this out so we can test against its existence next time - - # replace old node w/ new node(s) - for (@new_nodes_map) { - # add all the new nodes... - $pathway_node->insertBefore($$_[0],$curr_old_gene_node); - } - # ...and remove the original node - $pathway_node->removeChild($curr_old_gene_node); - } - # once mapped, remove the old gene so we are left with a list of - # unmapped original genes (for show_ouput()) - delete($data_nodes_by_gene_id{$old_gene}); - } - else - { - print "ALERT: Gene identifier $old_gene is not present in this " - . "PathVisio GPML document.\n"; - } - } - %unmapped_genes = %data_nodes_by_gene_id; # whatever is left over -} - -# --------------------------------------------------------------------------- -=item B -Displays the transformed data. Verbose only. -=cut -# --------------------------------------------------------------------------- -sub show_output -{ - if ($verbose) { - print "[Unmapped original genes]\n"; - my $count = 0; - foreach my $tmp_gene (keys %unmapped_genes) - { - foreach my $tmp_node (keys %{$unmapped_genes{$tmp_gene}}) - { - $count++; - print $unmapped_genes{$tmp_gene}{$tmp_node} - ->getAttributeNode("TextLabel")->getValue - . "\t($tmp_gene)\n"; - } - } - print "\nTotal unmapped genes: $count\n"; - } - if ($doc_mode) - { - print "\n[Modified GPML Output]\n"; - print $gpml_doc->toString; - print "\n"; - } -} - -# --------------------------------------------------------------------------- -=item B -Writes the transformed GPML doc out to the specified output file. -=cut -# --------------------------------------------------------------------------- -sub export_data -{ - print "\nWriting GPML to output file...\n\n"; - - # ensures utf-8 encoding (for accent marks, etc.) - open my $out_file_handle, ">:utf8", "$output_file" or die $!; - - $gpml_doc->print($out_file_handle); -} - -=back -=cut - -# --------------------------------------------------------------------------- -# main -# --------------------------------------------------------------------------- - -init; -import_data; -show_input; -swap_genes(); -show_output; -export_data; - -$gpml_doc->dispose; # cleanup -exit; - -# --------------------------------------------------------------------------- -# end -# --------------------------------------------------------------------------- - diff --git a/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl b/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl deleted file mode 100755 index cf6f4c9..0000000 --- a/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl +++ /dev/null @@ -1,428 +0,0 @@ -#!/usr/bin/perl -w -use strict; - -# --------------------------------------------------------------------------- -# Reactome - CHEBI Ontology Mapping Script -# -# Justin Preece, 10/06/10 -# v1.0: 10/13/10 (svn rev. 66) -# v1.1: 10/20/10 (svn rev. 70) -# v1.2: 02/07/11 (svn rev. 86) -# -# Purpose: Map CHEBI ontology terms onto the Reactome database. -# -# Inputs: -# -# CHEBI OBO file (preset) -# -# Reactome file (preset, provided by Guanming Wu) -# (Header) [ReactomeID] [Compound_Name] [CAS] [LIGAND] [Cyc] -# (Row) 923893 S-adenosyl-L-methionine 29908-03-0 C00019 S-ADENOSYLMETHIONINE ** the '-' (dash) symbol will be applied to any empty columns -# -# Outputs: tab-del mapping file (reactome_chebi_mapping_complete_sorted.txt) -# -# [ReactomeID] [CHEBI] [XREF_Type] [XREF_ID] -# 923893 15414 CAS 29908-03-0 -# 923893 15414 LIGAND C00019 -# 923893 15414 CompoundTerm S-ADENOSYLMETHIONINE -# 923893 15414 CompoundSynonym s-AdenosylMethionine -# 923893 15414 CycTerm S-ADENOSYLMETHIONINE ** optional -# 923893 15414 CycSynonym s-adenosylmethionine ** optional -# --------------------------------------------------------------------------- - - -# --------------------------------------------------------------------------- -# modules -# --------------------------------------------------------------------------- - -use GO::Parser; - -# --------------------------------------------------------------------------- -# declarations -# --------------------------------------------------------------------------- - -# set paths to data files -my $data_path = "/home/preecej/Documents/projects/reactome/reactome_to_chebi_mapping/AraCyc/gk_central_041811/no_synonyms/"; -my $chebi_obo_file = "../../chebi_v78.obo"; -my $reactome_file = "AraReferenceMolecules.txt"; -my $mapped_output_file = "1.2_reactome_chebi_mapping_complete.txt"; -my $sorted_output_file = "1.2_reactome_chebi_mapping_complete_sorted.txt"; -my $unique_mappings = "1.2_reactome_unique_mappings.txt"; -my $sorted_no_match_file = "1.2_reactome_entries_with_no_chebi_match.txt"; - -# options -my $allow_obsolete_terms = 1; -my $allow_cyc = 0; -my $allow_synonyms = 0; - -my $ont; # chebi ontology - -my %reactome_CompoundName; # reactome Compound Name hash -my %reactome_CAS; # reactome CAS hash -my %reactome_LIGAND; # reactome LIGAND hash -my %reactome_Cyc; # reactome Cyc hash - -my @map_results = (); # successful mappings between chebi and reactome - - -# --------------------------------------------------------------------------- -# functions -# --------------------------------------------------------------------------- - - -# setup chebi parser and reactome data -# --------------------------------------------------------------------------- -sub init -{ - # init ontology parser and ontology - my $parser = GO::Parser->new({handler=>'obj'}); - $parser->parse($data_path . $chebi_obo_file); - $ont = $parser->handler->graph; - - # read reactome file into 3 separate hashes - open(REACTOME_FILE,$data_path . $reactome_file); - - my $line = ; # skip the header - my $reactome_count = 0; - - while () - { - $line = $_; - chomp $line; - $reactome_count++; - my @reactome_entry = split(/\t/, $line); # break up our tab-del line - - # load up this reactome entry's Compound_Name, ID, CAS, LIGAND, and Cyc values - my $reactome_id = $reactome_entry[0]; - my $compound_name = uc $reactome_entry[1]; # for case-insensitivity - - # strips off "AN " and "A " indefinite articles - $compound_name =~ s/^ //; - $compound_name =~ s/^AN //; - $compound_name =~ s/^A //; - - my $CAS_id = $reactome_entry[2]; - my $LIGAND_id = $reactome_entry[3]; - my $Cyc_term = uc $reactome_entry[4]; # for case-insensitivity - - # There is a possibility that a single CAS, LIGAND, or Cyc - # identifier may appear in more than one reactome entry. This - # temp array allows each matched hash value to hold more than - # one ReactomeID, if necessary. - - # --CAS Hash Load-- - if ($CAS_id ne "-") { # keep those "-" placeholders out - # build the CAS hash; each value may hold 1...n reactome - # ids (as an array) - push @{$reactome_CAS{$CAS_id}}, $reactome_id; - } - - # similarly... - - # --LIGAND Hash Load-- - if ($LIGAND_id ne "-") { - push @{$reactome_LIGAND{$LIGAND_id}}, $reactome_id; - } - - # --CompoundName Hash Load-- - if ($compound_name ne "-") { - push @{$reactome_CompoundName{"$compound_name"}}, $reactome_id; - } - - # --Cyc Hash Load-- - if ($allow_cyc) - { - if ($Cyc_term ne "-") { - push @{$reactome_Cyc{"$Cyc_term"}}, $reactome_id; - } - - } - } - close REACTOME_FILE; - - print "\n[Reactome Stats]", - "\nTotal Reactome Entries: $reactome_count\n"; - -} - - -# spit out some data to make sure you've read in the files correctly -# --------------------------------------------------------------------------- -sub test_inputs -{ - # basic ontology info - print "[Node Count]: " . $ont->node_count . "\n"; - - # get all chebi terms in the ontology - my $terms = $ont->get_all_nodes; - - # output contents of parsed ontology - foreach my $term (@$terms) - { - print "\n" . $term->acc . " " . $term->name . "\n[SYNONYMS]\n"; - - my $synonyms = $term->synonym_list; - foreach my $synonym (@$synonyms) { - print $synonym . "\n"; - } - - print "[XREFS]\n"; - my $xrefs = $term->dbxref_list; - foreach my $xref (@$xrefs) { - print $xref->xref_key . ",", - $xref->xref_keytype . ",", - $xref->xref_dbname . ",", - $xref->xref_desc . "\n"; - } - print "\n"; - } - - # show dupes in reactome hashes - give data to Pankaj; - # this is important b/c the duplicates may represent erroneous data in - # the Reactome dataset - my $k; my @v; - print "\n[Reactome Hashes - Dupes]\n"; - print "\n--CAS Hash--\n"; - for $k (keys %reactome_CAS) { - if (@{$reactome_CAS{$k}} > 1) { - print "$k: @{$reactome_CAS{$k}}\n"; - } - } - print "\n--LIGAND Hash--\n"; - for $k (keys %reactome_LIGAND) { - if (@{$reactome_LIGAND{$k}} > 1) { - print "$k: @{$reactome_LIGAND{$k}}\n"; - } - } - print "\n--CompoundName Hash--\n"; - for $k (keys %reactome_CompoundName) { - if (@{$reactome_CompoundName{$k}} > 1) { - print "$k: @{$reactome_CompoundName{$k}}\n"; - } - } - if ($allow_cyc) - { - print "\n--Cyc Hash--\n"; - for $k (keys %reactome_Cyc) { - if (@{$reactome_Cyc{$k}} > 1) { - print "$k: @{$reactome_Cyc{$k}}\n"; - } - } - } -} - - -# map the chebi terms to the reactome entries -# --------------------------------------------------------------------------- -sub perform_map -{ - my $chebi_obo_terms = $ont->get_all_nodes; - - # vars for mapping stats - my $attempted_mappings = 0; - my $successful_mappings = 0; - my $attempted_CAS_mappings = 0; - my $successful_CAS_mappings = 0; - my $attempted_LIGAND_mappings = 0; - my $successful_LIGAND_mappings = 0; - my $attempted_name_mappings = 0; - my $successful_name_mappings = 0; - my $attempted_synonym_mappings = 0; - my $successful_synonym_mappings = 0; - - # loop through each chebi term - foreach my $term (@$chebi_obo_terms) - { - # eliminate "typedef" nodes (non-CHEBI terms), also check for obsolete - # terms and whether to allow them - if (($term->acc =~ m/^CHEBI:/) - && (!$term->is_obsolete || ($term->is_obsolete && $allow_obsolete_terms))) - { - # attempt CHEBI match on CAS and LIGAND ID's - $attempted_mappings++; - my $xrefs = $term->dbxref_list; - foreach my $xref (@$xrefs) - { - $attempted_CAS_mappings++; - $attempted_LIGAND_mappings++; - - # temp-foo to skirt an interpolation problem - my $tmp_key = $xref->xref_key; - - if (defined($reactome_CAS{"$tmp_key"})) - { - foreach my $tmp_reactome_id (@{$reactome_CAS{$tmp_key}}) - { - $successful_CAS_mappings++; - push (@map_results, "$tmp_reactome_id\t" . - $term->acc . "\t" . - "CAS\t" . - $tmp_key); - } - } - - if (defined($reactome_LIGAND{"$tmp_key"})) - { - foreach my $tmp_reactome_id (@{$reactome_LIGAND{$tmp_key}}) - { - $successful_LIGAND_mappings++; - push (@map_results, "$tmp_reactome_id\t" . - $term->acc . "\t" . - "LIGAND\t" . - $tmp_key); - } - } - } - - # attempt CHEBI match on Reactome Compound Names (and optional Cyc names/synonyms)... - $attempted_name_mappings++; - - # more temp-foo to skirt said interpolation problem - my $tmp_name = uc $term->name; - - # reactome compound names... - if (defined($reactome_CompoundName{"$tmp_name"})) - { - foreach my $tmp_reactome_id (@{$reactome_CompoundName{$tmp_name}}) - { - $successful_name_mappings++; - push (@map_results, "$tmp_reactome_id\t" . - $term->acc . "\t" . - "CompoundTerm\t" . - $term->name); - } - } - # ...and synonyms (optional) - if ($allow_synonyms) - { - my $synonyms = $term->synonym_list; - foreach my $synonym (@$synonyms) - { - $attempted_synonym_mappings++; - - # yet more temp-foo to skirt interpolation problem - my $tmp_syn = "\U$synonym"; - - if (defined($reactome_CompoundName{$tmp_syn})) - { - foreach my $tmp_reactome_id (@{$reactome_CompoundName{$tmp_syn}}) - { - $successful_synonym_mappings++; - push (@map_results, "$tmp_reactome_id\t" . - $term->acc . "\t" . - "CompoundSynonym\t" . - $synonym); - } - } - } - } - - # Cyc names... - if ($allow_cyc) - { - if (defined($reactome_Cyc{"$tmp_name"})) - { - foreach my $tmp_reactome_id (@{$reactome_Cyc{$tmp_name}}) - { - $successful_name_mappings++; - push (@map_results, "$tmp_reactome_id\t" . - $term->acc . "\t" . - "CycTerm\t" . - $term->name); - } - } - # ...and synonyms (optional) - if ($allow_synonyms) - { - my $synonyms = $term->synonym_list; - foreach my $synonym (@$synonyms) - { - $attempted_synonym_mappings++; - - # yet more temp-foo to skirt interpolation problem - my $tmp_syn = "\U$synonym"; - - if (defined($reactome_Cyc{$tmp_syn})) - { - foreach my $tmp_reactome_id (@{$reactome_Cyc{$tmp_syn}}) - { - $successful_synonym_mappings++; - push (@map_results, "$tmp_reactome_id\t" . - $term->acc . "\t" . - "CycSynonym\t" . - $synonym); - } - } - } - } - } - } - } - # send up some stats on the mapping process - $successful_mappings = - + $successful_CAS_mappings - + $successful_LIGAND_mappings - + $successful_name_mappings - + $successful_synonym_mappings; - - print "\n[ChEBI Stats]", - "\nNodes in File: " . $ont->node_count, - "\nTotal Attempted Mappings (with usable ChEBI terms): " . $attempted_mappings, - "\nTotal Successful Mappings: " . $successful_mappings . "\n"; - - print "\n[Mapping Breakdown by Type]", - "\nCAS (matches/attempts): ", - "$successful_CAS_mappings/$attempted_CAS_mappings ", - "(note: can include ChemIDplus and KEGG COMPUND db duplicates)", - "\nLIGAND: ", - "$successful_LIGAND_mappings/$attempted_LIGAND_mappings", - "\nTerm Names " . ($allow_cyc ? "includes Cyc terms and synonyms" : "") . ": ", - "$successful_name_mappings/$attempted_name_mappings"; - if ($allow_synonyms) - { - print "\nTerm Synonyms: ", - "$successful_synonym_mappings/$attempted_synonym_mappings"; - } - print "\n\n"; -} - - -# put the results in the mapped output file -# --------------------------------------------------------------------------- -sub create_mapfile -{ - if (@map_results > 0) - { - # add a header to the results array - unshift (@map_results, "ReactomeID\tCHEBI\tXREF_Type\tXREF_ID"); - - # setup output file - open(OUTPUT_FILE,">" . $data_path . $mapped_output_file); - - #format results for file output - print OUTPUT_FILE "$_\n" foreach @map_results; - - close OUTPUT_FILE; - - # sort on all cols (keep the header at the top), remove exact dupes - system "awk 'NR == 1; NR > 1 {print \$0 | \"sort\"}' $data_path$mapped_output_file | uniq > $data_path$sorted_output_file"; - - # also produce files listing unique Reactome entries having a match...and those without a match - system "awk 'NR == 1; NR > 1 {print \$1}' $data_path$sorted_output_file | uniq > $data_path$unique_mappings"; - system "cat $data_path$reactome_file | grep -vf $data_path$unique_mappings | sort > $data_path$sorted_no_match_file"; - } else { - print "\n\nSorry, there are no mapped results.\n\n"; - } -} - - -# --------------------------------------------------------------------------- -# main -# --------------------------------------------------------------------------- - -init; -#test_inputs; -perform_map; -create_mapfile; - -exit; diff --git a/preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl b/preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl deleted file mode 100644 index 5dda3e7..0000000 --- a/preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl +++ /dev/null @@ -1,74 +0,0 @@ -#!/usr/bin/perl -w -use strict; -use Data::Dumper; - -my $CoGe_genes_file_name = $ARGV[0]; -my $assoc_file_name = $ARGV[1]; - -# read in CoGe file (arg 0), build hash of gene model ids to symbols/gene names - -open(IN_FILE, $CoGe_genes_file_name); - -my %classical_genes_by_gene_model; - -my $line = ; - -while () -{ - $line = $_; - chomp $line; - - my @curr_line = split(',',$line); - - my $gene_symbol = $curr_line[0]; - $gene_symbol =~ tr/"//d; - my $gene_name = $curr_line[2]; - $gene_name =~ tr/"//d; - my $gene_model_id = $curr_line[8]; - $gene_model_id =~ tr/"//d; - - #print $gene_symbol . "\|" . $gene_name . "\|" . $gene_model_id . "\n"; - - my $gene_model_expr = "^(GRMZM)"; - if ($gene_model_id =~ $gene_model_expr) { - $classical_genes_by_gene_model{$gene_model_id} = [ $gene_symbol, $gene_name ]; - } -} - -close (IN_FILE); - -#print Dumper(\%classical_genes_by_gene_model) . "\n\n"; - -# read in assoc file (arg 1) - -open(ASSOC_IN_FILE, $ARGV[1]); - -open(OUT_FILE,">" . (split('\.',$assoc_file_name))[0] . "_named.assoc"); - -while () -{ - $line = $_; - chomp $line; - - if (length($line) > 0) { - - #print $line. "\n"; - - my @curr_line = split('\t',$line); - - # look for each annotation's hashed gene model id - if (defined $classical_genes_by_gene_model{$curr_line[1]}) { - # add/replace the appropriate cols - $curr_line[2] = ${$classical_genes_by_gene_model{$curr_line[1]}}[0]; - $curr_line[9] = ${$classical_genes_by_gene_model{$curr_line[1]}}[1]; - - } - # output to new assoc file with appended name - #print join("\t", @curr_line) . "\n"; - print OUT_FILE join("\t", @curr_line) . "\n"; - } -} - -close (ASSOC_IN_FILE); -close (OUT_FILE); -exit; diff --git a/preecej/php_singletons/PO_web_service.php b/preecej/php_singletons/PO_web_service.php deleted file mode 100644 index 9ba7afe..0000000 --- a/preecej/php_singletons/PO_web_service.php +++ /dev/null @@ -1,106 +0,0 @@ - 50) { $number_of_terms = 50; } - - $qval = $_GET['qval']; - - $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0 - ? strtolower($_GET['qval']) - : die('Please provide a searchable value'); - - $format = strtolower($_GET['format']) != 'json' - ? strtolower($_GET['format']) - : 'json'; //json is the default - - /* connect to the db */ - $link = mysql_connect($_SERVER['mysql_host'], $_SERVER['mysql_user'], $_SERVER['mysql_pw']) or die('Cannot connect to the DB'); - mysql_select_db($_SERVER['mysql_db'],$link) or die('Cannot select the DB'); - - switch ($type) { - case 'autocomplete': - /* grab the terms from the db */ - $query = "SELECT t.$field FROM term t" - . " LEFT JOIN term_definition d ON d.term_id = t.id" - . " WHERE t.$field LIKE '%$qval%'" - . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')" - . " AND t.is_obsolete = 0" - . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" - . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" - . " ORDER BY name LIMIT $number_of_terms"; - $result = mysql_query($query,$link) or die('Errant query: '.$query); - - /* create one master array of the records */ - $terms = array(); - if(mysql_num_rows($result)) { - while($term = mysql_fetch_assoc($result)) { - $terms[] = array('term'=>$term[$field]); - } - } - - /* output in necessary format */ - if($format == 'json') { - header('Content-type: application/json'); - echo json_encode(array('PO_term_lookup_response'=>$terms)); - } - else { - die('Sorry, this request cannot be fulfilled in '.$format.' format.'); - } - break; - - case 'term_detail': - /* grab the ontology data from the db */ - $query = "SELECT DISTINCT t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'" - . " FROM term t" - . " LEFT JOIN term_definition d ON d.term_id = t.id" - . " WHERE t.name = '$qval'" - . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')" - . " AND t.is_obsolete = 0" - . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" - . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" - . " ORDER BY t.name LIMIT 1"; - $result = mysql_query($query,$link) or die('Errant query: '.$query); - - /* create one master array of the records */ - $terms = array(); - if(mysql_num_rows($result)) { - while($term = mysql_fetch_assoc($result)) { - $terms[] = array( - 'accession_id'=>$term['acc'], - 'aspect'=>$term['type'] == "plant_anatomy" ? "Plant Anatomy" : "Plant Growth and Development Stage", - 'definition'=>$term['definition'], - 'comment'=>$term['comment']); - } - } - /* output in necessary format */ - if($format == 'json') { - header('Content-type: application/json'); - echo json_encode(array('PO_term_detail_response'=>$terms)); - } - else { - die('Sorry, this request cannot be fulfilled in '.$format.' format.'); - } - break; - default: - die('Sorry, this web service method is not available.'); - } - /* disconnect from the db */ - @mysql_close($link); -} -else { die('Not authorized.'); } -?> - diff --git a/preecej/php_singletons/cmd_line_test.php b/preecej/php_singletons/cmd_line_test.php deleted file mode 100644 index 0a58b4e..0000000 --- a/preecej/php_singletons/cmd_line_test.php +++ /dev/null @@ -1,14 +0,0 @@ -load('/home/preecej/Documents/projects/pathvisio/Ath_scratch.gpml'); - -$entry = $doc->getElementsByTagName("Pathway"); -$author = $entry->item(0)->getAttribute("Author"); -print "Author:$author\n"; - -print "test over\n"; - -?> diff --git a/preecej/semantic_wiki/content_pages/Main_Page.wiki b/preecej/semantic_wiki/content_pages/Main_Page.wiki deleted file mode 100644 index 7e31afe..0000000 --- a/preecej/semantic_wiki/content_pages/Main_Page.wiki +++ /dev/null @@ -1,37 +0,0 @@ -__NOTOC__ -=== Welcome to the Planteome Annotation Wiki, a resource for annotated plant genotypes and phenotypes on the semantic web! === - -We host annotations from a variety of published data sources. You are free to browse these annotations and search for specific genes, synonyms, EC numbers, cross-references, and references to publications, as well as many other types of data. - -You may also add information of your own. If you would like to create your own annotations or add more data to existing annotations, please click [[special:UserLogin|here]] to establish a new curator account. - -If you already have a curator account, just [[Special:UserLogin|log in]] and begin annotating! - -Search for existing annotations (or data therein): (search box) - -[[Special:FormEdit/Annotation|Add a new gene annotation.]] - -=== What is semantic data, and how can it enhance my research? === - -examples... - -=== Our Collaborators === - -* Gramene... -* The Plant Ontology... - -=== Credits and Thanks === - -* Jaiswal Lab (and the Planteome portal)... -* OSU... -* POC -* NSF... -* etc... - - - diff --git a/preecej/semantic_wiki/content_pages/Reference:Plant_Taxa.wiki b/preecej/semantic_wiki/content_pages/Reference:Plant_Taxa.wiki deleted file mode 100644 index 7555bed..0000000 --- a/preecej/semantic_wiki/content_pages/Reference:Plant_Taxa.wiki +++ /dev/null @@ -1,34 +0,0 @@ -=== A list of reference species for use on this wiki === -{{#show:{{PAGENAME}} - | format=table - | mainlabel=- - | ?Has Reference Taxon -}} - -{{#set:Has Reference Taxon=Aquilegia coerulea}} -{{#set:Has Reference Taxon=Arabidopsis lyrata}} -{{#set:Has Reference Taxon=Arabidopsis thaliana}} -{{#set:Has Reference Taxon=Brachypodium dystachyon}} -{{#set:Has Reference Taxon=Carica papaya}} -{{#set:Has Reference Taxon=Chlamydomonas reinhardtii}} -{{#set:Has Reference Taxon=Citrus clementina}} -{{#set:Has Reference Taxon=Citrus cinensis}} -{{#set:Has Reference Taxon=Cucumis sativus}} -{{#set:Has Reference Taxon=Eucalyptus grandis}} -{{#set:Has Reference Taxon=Fragaria vesca}} -{{#set:Has Reference Taxon=Glycine max}} -{{#set:Has Reference Taxon=Manihot esculenta}} -{{#set:Has Reference Taxon=Medicago trunculata}} -{{#set:Has Reference Taxon=Mimulus guttatus}} -{{#set:Has Reference Taxon=Oryza sativa}} -{{#set:Has Reference Taxon=Physcomitrella patens}} -{{#set:Has Reference Taxon=Populus trichocarpa}} -{{#set:Has Reference Taxon=Prunus persica}} -{{#set:Has Reference Taxon=Ricinus communis}} -{{#set:Has Reference Taxon=Selaginella moellendorffii}} -{{#set:Has Reference Taxon=Setaria italica}} -{{#set:Has Reference Taxon=Sorghum bicolor}} -{{#set:Has Reference Taxon=Vitis vinifera}} -{{#set:Has Reference Taxon=Volvox carteri}} -{{#set:Has Reference Taxon=Zea mays}} - diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/COPYING b/preecej/semantic_wiki/extensions/DataTransfer_PS/COPYING deleted file mode 100644 index a865928..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/COPYING +++ /dev/null @@ -1,348 +0,0 @@ -The license text below "----" applies to all files within this distribution, other -than those that are in a directory which contains files named "LICENSE" or -"COPYING", or a subdirectory thereof. For those files, the license text contained in -said file overrides any license information contained in directories of smaller depth. -Alternative licenses are typically used for software that is provided by external -parties, and merely packaged with the Data Transfer release for convenience. ----- - - GNU GENERAL PUBLIC LICENSE - Version 2, June 1991 - - Copyright (C) 1989, 1991 Free Software Foundation, Inc. - 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. By contrast, the GNU General Public -License is intended to guarantee your freedom to share and change free -software--to make sure the software is free for all its users. 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See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program; if not, write to the Free Software - Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - - -Also add information on how to contact you by electronic and paper mail. - -If the program is interactive, make it output a short notice like this -when it starts in an interactive mode: - - Gnomovision version 69, Copyright (C) year name of author - Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, the commands you use may -be called something other than `show w' and `show c'; they could even be -mouse-clicks or menu items--whatever suits your program. - -You should also get your employer (if you work as a programmer) or your -school, if any, to sign a "copyright disclaimer" for the program, if -necessary. Here is a sample; alter the names: - - Yoyodyne, Inc., hereby disclaims all copyright interest in the program - `Gnomovision' (which makes passes at compilers) written by James Hacker. - - , 1 April 1989 - Ty Coon, President of Vice - -This General Public License does not permit incorporating your program into -proprietary programs. If your program is a subroutine library, you may -consider it more useful to permit linking proprietary applications with the -library. If this is what you want to do, use the GNU Library General -Public License instead of this License. diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/DataTransfer.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/DataTransfer.php deleted file mode 100644 index a5fbcfd..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/DataTransfer.php +++ /dev/null @@ -1,149 +0,0 @@ - __FILE__, - 'name' => 'Data Transfer', - 'version' => DATA_TRANSFER_VERSION, - 'author' => 'Yaron Koren', - 'url' => 'http://www.mediawiki.org/wiki/Extension:Data_Transfer', - 'descriptionmsg' => 'datatransfer-desc', -); - -### -# This is the path to your installation of Semantic Forms as -# seen on your local filesystem. Used against some PHP file path -# issues. -## -$dtgIP = dirname( __FILE__ ); -## - -// register all special pages and other classes -$wgAutoloadClasses['DTUtils'] = $dtgIP . '/includes/DT_Utils.php'; -$wgSpecialPages['ViewXML'] = 'DTViewXML'; -$wgAutoloadClasses['DTViewXML'] = $dtgIP . '/specials/DT_ViewXML.php'; -$wgSpecialPages['ImportXML'] = 'DTImportXML'; -$wgAutoloadClasses['DTImportXML'] = $dtgIP . '/specials/DT_ImportXML.php'; -$wgSpecialPages['ImportCSV'] = 'DTImportCSV'; -$wgAutoloadClasses['DTImportCSV'] = $dtgIP . '/specials/DT_ImportCSV.php'; -$wgJobClasses['dtImport'] = 'DTImportJob'; -$wgAutoloadClasses['DTImportJob'] = $dtgIP . '/includes/DT_ImportJob.php'; -$wgAutoloadClasses['DTXMLParser'] = $dtgIP . '/includes/DT_XMLParser.php'; -$wgHooks['AdminLinks'][] = 'dtfAddToAdminLinks'; -$wgHooks['smwInitProperties'][] = 'dtfInitProperties'; - -### -# This is the path to your installation of the Data Transfer extension as -# seen from the web. Change it if required ($wgScriptPath is the -# path to the base directory of your wiki). No final slash. -## -$dtgScriptPath = $wgScriptPath . '/extensions/DataTransfer_PS'; -## - -### -# Permission to import files -### -$wgGroupPermissions['sysop']['datatransferimport'] = true; -$wgAvailableRights[] = 'datatransferimport'; - -// initialize content language -require_once($dtgIP . '/languages/DT_Language.php'); -global $wgLanguageCode; -dtfInitContentLanguage($wgLanguageCode); - -$wgExtensionMessagesFiles['DataTransfer'] = $dtgIP . '/languages/DT_Messages.php'; -$wgExtensionAliasesFiles['DataTransfer'] = $dtgIP . '/languages/DT_Aliases.php'; - -/**********************************************/ -/***** language settings *****/ -/**********************************************/ - -/** - * Initialise a global language object for content language. This - * must happen early on, even before user language is known, to - * determine labels for additional namespaces. In contrast, messages - * can be initialised much later when they are actually needed. - */ -function dtfInitContentLanguage( $langcode ) { - global $dtgIP, $dtgContLang; - - if ( !empty( $dtgContLang ) ) { return; } - - $dtContLangClass = 'DT_Language' . str_replace( '-', '_', ucfirst( $langcode ) ); - - if ( file_exists( $dtgIP . '/languages/' . $dtContLangClass . '.php' ) ) { - include_once( $dtgIP . '/languages/' . $dtContLangClass . '.php' ); - } - - // fallback if language not supported - if ( !class_exists( $dtContLangClass ) ) { - include_once( $dtgIP . '/languages/DT_LanguageEn.php' ); - $dtContLangClass = 'DT_LanguageEn'; - } - - $dtgContLang = new $dtContLangClass(); -} - -/** - * Initialise the global language object for user language. This - * must happen after the content language was initialised, since - * this language is used as a fallback. - */ -function dtfInitUserLanguage( $langcode ) { - global $dtgIP, $dtgLang; - - if ( !empty( $dtgLang ) ) { return; } - - $dtLangClass = 'DT_Language' . str_replace( '-', '_', ucfirst( $langcode ) ); - - if ( file_exists( $dtgIP . '/languages/' . $dtLangClass . '.php' ) ) { - include_once( $dtgIP . '/languages/' . $dtLangClass . '.php' ); - } - - // fallback if language not supported - if ( !class_exists( $dtLangClass ) ) { - global $dtgContLang; - $dtgLang = $dtgContLang; - } else { - $dtgLang = new $dtLangClass(); - } -} - -/**********************************************/ -/***** other global helpers *****/ -/**********************************************/ - -function dtfInitProperties() { - global $dtgContLang; - $dt_props = $dtgContLang->getPropertyLabels(); - SMWPropertyValue::registerProperty( '_DT_XG', '_str', $dt_props[DT_HAS_XML_GROUPING], true ); - // TODO - this should set a "backup" English value as well, - // so that the phrase "Has XML grouping" works in all languages - return true; -} - -/** - * Add links to the 'AdminLinks' special page, defined by the Admin Links - * extension - */ -function dtfAddToAdminLinks( $admin_links_tree ) { - $import_export_section = $admin_links_tree->getSection( wfMsg( 'adminlinks_importexport' ) ); - $main_row = $import_export_section->getRow( 'main' ); - $main_row->addItem( ALItem::newFromSpecialPage( 'ViewXML' ) ); - $main_row->addItem( ALItem::newFromSpecialPage( 'ImportXML' ) ); - $main_row->addItem( ALItem::newFromSpecialPage( 'ImportCSV' ) ); - return true; -} diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/INSTALL b/preecej/semantic_wiki/extensions/DataTransfer_PS/INSTALL deleted file mode 100644 index 16462b6..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/INSTALL +++ /dev/null @@ -1,31 +0,0 @@ -[[Data Transfer 0.3.8]] - -Contents: -* Disclaimer -* Requirements -* Installation -* Contact - -== Disclaimer == - -For a proper legal disclaimer, see the file "COPYING". - -== Requirements == - -The extension can make use of, but does not require, an install of -Semantic MediaWiki. If Semantic MediaWiki is used, it must be of -version 1.0 or greater. For more details, see Semantic MediaWiki's -own installation requirements. - -== Installation == - -(1) Extract the archive to obtain the directory "DataTransfer" - that contains all relevant files. Copy this directory (or - extract/download it) to "[wikipath]/extensions/". -(2) Insert the following line into the file "[wikipath]/LocalSettings.php": - include_once('extensions/DataTransfer/DataTransfer.php'); - -== Contact == - -If you have any issues or questions, please send them to -yaron57@gmail.com. diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/README b/preecej/semantic_wiki/extensions/DataTransfer_PS/README deleted file mode 100644 index 66652b3..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/README +++ /dev/null @@ -1,24 +0,0 @@ -== About == - -Data Transfer is an extension to MediaWiki that both exports XML -based on the current contents of pages in a wiki, and imports pages -in both XML format (using the same structure as the XML export) and -CSV format. Both the XML and CSV formats use template calls, and -the fields within them, to define the data structure. Any text that -is not within a template calls gets placed into one or more "free -text" fields. - -For more information on Data Transfer, see the extension -homepage at -http://www.mediawiki.org/wiki/Extension:Data_Transfer - -Notes on installing Data Transfer can be found in the file INSTALL. - -== Credits == - -Data Transfer was written by Yaron Koren. - -== Contact == - -Comments, questions, suggestions and bug reports should be -sent to Yaron at yaron57@gmail.com. diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/data_transfer_0.3.8.tar.gz b/preecej/semantic_wiki/extensions/DataTransfer_PS/data_transfer_0.3.8.tar.gz deleted file mode 100644 index 8c58be9..0000000 Binary files a/preecej/semantic_wiki/extensions/DataTransfer_PS/data_transfer_0.3.8.tar.gz and /dev/null differ diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/includes/DT_ImportJob.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/includes/DT_ImportJob.php deleted file mode 100644 index 3a5e76f..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/includes/DT_ImportJob.php +++ /dev/null @@ -1,53 +0,0 @@ -title ) ) { - $this->error = "dtImport: Invalid title"; - wfProfileOut( __METHOD__ ); - return false; - } - - $article = new Article( $this->title ); - if ( !$article ) { - $this->error = 'dtImport: Article not found "' . $this->title->getPrefixedDBkey() . '"'; - wfProfileOut( __METHOD__ ); - return false; - } - $for_pages_that_exist = $this->params['for_pages_that_exist']; - if ( $for_pages_that_exist == 'skip' && $this->title->exists() ) { - return true; - } - - // change global $wgUser variable to the one specified by - // the job only for the extent of this import - global $wgUser; - $actual_user = $wgUser; - $wgUser = User::newFromId( $this->params['user_id'] ); - $text = $this->params['text']; - if ( $for_pages_that_exist == 'append' && $this->title->exists() ) { - $text = $article->getContent() . "\n" . $text; - } - $edit_summary = $this->params['edit_summary']; - $article->doEdit( $text, $edit_summary ); - $wgUser = $actual_user; - wfProfileOut( __METHOD__ ); - return true; - } -} diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/includes/DT_Utils.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/includes/DT_Utils.php deleted file mode 100644 index 30736b1..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/includes/DT_Utils.php +++ /dev/null @@ -1,89 +0,0 @@ -

    - -END; - $text .= "\t" . '
    ' . "\n"; - return $text; - } - - static function printExistingPagesHandling() { - $text = "\t" . Xml::element( 'p', null, wfMsg( 'dt_import_forexisting' ) ) . "\n"; - $existingPagesText = "\n\t" . - Xml::element( 'input', - array( - 'type' => 'radio', - 'name' => 'pagesThatExist', - 'value' => 'overwrite', - 'checked' => 'checked' - ) ) . "\n" . - "\t" . wfMsg( 'dt_import_overwriteexisting' ) . "
    " . "\n" . - "\t" . Xml::element( 'input', - array( - 'type' => 'radio', - 'name' => 'pagesThatExist', - 'value' => 'skip', - ) ) . "\n" . - "\t" . wfMsg( 'dt_import_skipexisting' ) . "
    " . "\n" . - "\t" . Xml::element( 'input', - array( - 'type' => 'radio', - 'name' => 'pagesThatExist', - 'value' => 'append', - ) ) . "\n" . - "\t" . wfMsg( 'dt_import_appendtoexisting' ) . "
    " . "\n\t"; - $text .= "\t" . Xml::tags( 'p', null, $existingPagesText ) . "\n"; - $text .= "\t" . '
    ' . "\n"; - return $text; - } - - static function printImportSummaryInput( $fileType ) { - $importSummaryText = "\t" . Xml::element( 'input', - array( - 'type' => 'text', - 'id' => 'wpSummary', // ID is necessary for CSS formatting - 'class' => 'mw-summary', - 'name' => 'import_summary', - 'value' => wfMsgForContent( 'dt_import_editsummary', $fileType ) - ) - ) . "\n"; - return "\t" . Xml::tags( 'p', null, - wfMsg( 'dt_import_summarydesc' ) . "\n" . - $importSummaryText ) . "\n"; - } - - static function printSubmitButton() { - $formSubmitText = Xml::element( 'input', - array( - 'type' => 'submit', - 'name' => 'import_file', - 'value' => wfMsg( 'import-interwiki-submit' ) - ) - ); - return "\t" . Xml::tags( 'p', null, $formSubmitText ) . "\n"; - } -} diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/includes/DT_XMLParser.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/includes/DT_XMLParser.php deleted file mode 100644 index c8c48e0..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/includes/DT_XMLParser.php +++ /dev/null @@ -1,273 +0,0 @@ -mName = $name; - } - - function addField( $name, $value ) { - $this->mFields[$name] = $value; - } - - function createText() { - $multi_line_template = false; - $text = '{{' . $this->mName; - foreach ( $this->mFields as $field_name => $field_val ) { - if ( is_numeric( $field_name ) ) { - $text .= "|$field_val"; - } else { - $text .= "\n|$field_name=$field_val"; - $multi_line_template = true; - } - } - if ( $multi_line_template ) - $text .= "\n"; - $text .= '}}' . "\n"; - return $text; - } -} - -class DTWikiPage { - private $mPageName = null; - private $mElements = array(); - - public function DTWikiPage( $name ) { - $this->mPageName = $name; - } - - function getName() { - return $this->mPageName; - } - - function addTemplate( $template ) { - $this->mElements[] = $template; - } - - function addFreeText( $free_text ) { - $this->mElements[] = $free_text; - } - - function createText() { - $text = ""; - foreach ( $this->mElements as $elem ) { - if ( $elem instanceof DTWikiTemplate ) { - $text .= $elem->createText(); - } else { - $text .= $elem; - } - } - return $text; - } -} - -class DTXMLParser { - var $mDebug = false; - var $mSource = null; - var $mCurFieldName = null; - var $mCurFieldValue = ''; - var $mCurTemplate = null; - var $mCurPage = null; // new DTWikiPage(); - var $mPages = array(); - - function __construct( $source ) { - $this->mSource = $source; - } - - function debug( $text ) { - // print "$text. "; - } - - function throwXMLerror( $text ) { - print htmlspecialchars( $text ); - } - - function doParse() { - $parser = xml_parser_create( "UTF-8" ); - - # case folding violates XML standard, turn it off - xml_parser_set_option( $parser, XML_OPTION_CASE_FOLDING, false ); - - xml_set_object( $parser, $this ); - xml_set_element_handler( $parser, "in_start", "" ); - - $offset = 0; // for context extraction on error reporting - do { - $chunk = $this->mSource->readChunk(); - if ( !xml_parse( $parser, $chunk, $this->mSource->atEnd() ) ) { - wfDebug( "WikiImporter::doImport encountered XML parsing error\n" ); - // return new WikiXmlError( $parser, wfMsgHtml( 'import-parse-failure' ), $chunk, $offset ); - } - $offset += strlen( $chunk ); - } while ( $chunk !== false && !$this->mSource->atEnd() ); - xml_parser_free( $parser ); - } - - function donothing( $parser, $x, $y = "" ) { - # $this->debug( "donothing" ); - } - - - function in_start( $parser, $name, $attribs ) { - // $this->debug( "in_start $name" ); - $pages_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_pages' ) ); - if ( $name != $pages_str ) { - print( "Expected '$pages_str', got '$name'" ); - } - xml_set_element_handler( $parser, "in_pages", "out_pages" ); - } - - function in_pages( $parser, $name, $attribs ) { - $this->debug( "in_pages $name" ); - $page_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_page' ) ); - if ( $name == $page_str ) { - $title_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_title' ) ); - if ( array_key_exists( $title_str, $attribs ) ) { - $this->mCurPage = new DTWikiPage( $attribs[$title_str] ); - xml_set_element_handler( $parser, "in_page", "out_page" ); - } else { - return $this->throwXMLerror( "'$title_str' attribute missing for page" ); - } - } else { - return $this->throwXMLerror( "Expected <$page_str>, got <$name>" ); - } - } - - function out_pages( $parser, $name ) { - $this->debug( "out_pages $name" ); - $pages_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_pages' ) ); -/* - if( $name != $pages_str ) { - return $this->throwXMLerror( "Expected , got " ); - } -*/ - xml_set_element_handler( $parser, "donothing", "donothing" ); - } - - function in_category( $parser, $name, $attribs ) { - $this->debug( "in_category $name" ); - $page_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_page' ) ); - if ( $name == $page_str ) { - if ( array_key_exists( $title_str, $attribs ) ) { - $this->mCurPage = new DTWikiPage( $attribs[$title_str] ); - xml_set_element_handler( $parser, "in_page", "out_page" ); - } else { - return $this->throwXMLerror( "'$title_str' attribute missing for page" ); - } - } else { - return $this->throwXMLerror( "Expected <$page_str>, got <$name>" ); - } - } - - function out_category( $parser, $name ) { - $this->debug( "out_category $name" ); - if ( $name != "category" ) { - return $this->throwXMLerror( "Expected , got " ); - } - xml_set_element_handler( $parser, "donothing", "donothing" ); - } - - function in_page( $parser, $name, $attribs ) { - $this->debug( "in_page $name" ); - $template_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_template' ) ); - $name_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_name' ) ); - $free_text_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_freetext' ) ); - if ( $name == $template_str ) { - if ( array_key_exists( $name_str, $attribs ) ) { - $this->mCurTemplate = new DTWikiTemplate( $attribs[$name_str] ); - xml_set_element_handler( $parser, "in_template", "out_template" ); - } else { - return $this->throwXMLerror( "'$name_str' attribute missing for template" ); - } - } elseif ( $name == $free_text_str ) { - xml_set_element_handler( $parser, "in_freetext", "out_freetext" ); - xml_set_character_data_handler( $parser, "freetext_value" ); - } else { - return $this->throwXMLerror( "Expected <$template_str>, got <$name>" ); - } - } - - function out_page( $parser, $name ) { - $this->debug( "out_page $name" ); - $page_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_page' ) ); - if ( $name != $page_str ) { - return $this->throwXMLerror( "Expected , got " ); - } - $this->mPages[] = $this->mCurPage; - xml_set_element_handler( $parser, "in_pages", "out_pages" ); - } - - function in_template( $parser, $name, $attribs ) { - $this->debug( "in_template $name" ); - $field_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_field' ) ); - if ( $name == $field_str ) { - $name_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_name' ) ); - if ( array_key_exists( $name_str, $attribs ) ) { - $this->mCurFieldName = $attribs[$name_str]; - // $this->push( $name ); - $this->workRevisionCount = 0; - $this->workSuccessCount = 0; - $this->uploadCount = 0; - $this->uploadSuccessCount = 0; - xml_set_element_handler( $parser, "in_field", "out_field" ); - xml_set_character_data_handler( $parser, "field_value" ); - } else { - return $this->throwXMLerror( "'$name_str' attribute missing for field" ); - } - } else { - return $this->throwXMLerror( "Expected <$field_str>, got <$name>" ); - } - } - - function out_template( $parser, $name ) { - $this->debug( "out_template $name" ); - $template_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_template' ) ); - if ( $name != $template_str ) { - return $this->throwXMLerror( "Expected , got " ); - } - $this->mCurPage->addTemplate( $this->mCurTemplate ); - xml_set_element_handler( $parser, "in_page", "out_page" ); - } - - function in_field( $parser, $name, $attribs ) { - // xml_set_element_handler( $parser, "donothing", "donothing" ); - } - - function out_field( $parser, $name ) { - $this->debug( "out_field $name" ); - $field_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_field' ) ); - if ( $name == $field_str ) { - $this->mCurTemplate->addField( $this->mCurFieldName, $this->mCurFieldValue ); - $this->mCurFieldValue = ''; - } else { - return $this->throwXMLerror( "Expected , got " ); - } - xml_set_element_handler( $parser, "in_template", "out_template" ); - } - - function field_value( $parser, $data ) { - $this->mCurFieldValue .= $data; - } - - function in_freetext( $parser, $name, $attribs ) { - // xml_set_element_handler( $parser, "donothing", "donothing" ); - } - - function out_freetext( $parser, $name ) { - xml_set_element_handler( $parser, "in_page", "out_page" ); - } - - function freetext_value( $parser, $data ) { - $this->mCurPage->addFreeText( $data ); - } - -} diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_Aliases.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_Aliases.php deleted file mode 100644 index 96a1809..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_Aliases.php +++ /dev/null @@ -1,274 +0,0 @@ - array( 'ImportCSV' ), - 'ImportXML' => array( 'ImportXML' ), - 'ViewXML' => array( 'ViewXML' ), -); - -/** Afrikaans (Afrikaans) */ -$specialPageAliases['af'] = array( - 'ViewXML' => array( 'WysXML' ), -); - -/** Arabic (العربية) */ -$specialPageAliases['ar'] = array( - 'ViewXML' => array( 'عرض_إكس_إم_إل' ), -); - -/** Egyptian Spoken Arabic (مصرى) */ -$specialPageAliases['arz'] = array( - 'ViewXML' => array( 'عرض_XML' ), -); - -/** Breton (Brezhoneg) */ -$specialPageAliases['br'] = array( - 'ViewXML' => array( 'GweletXML' ), -); - -/** Bosnian (Bosanski) */ -$specialPageAliases['bs'] = array( - 'ViewXML' => array( 'VidiXML' ), -); - -/** German (Deutsch) */ -$specialPageAliases['de'] = array( - 'ImportCSV' => array( 'CSV_importieren' ), - 'ImportXML' => array( 'XML_importieren' ), - 'ViewXML' => array( 'XML_anzeigen' ), -); - -/** Esperanto (Esperanto) */ -$specialPageAliases['eo'] = array( - 'ViewXML' => array( 'Montri_XML' ), -); - -/** Spanish (Español) */ -$specialPageAliases['es'] = array( - 'ViewXML' => array( 'Ver_XML', 'VerXML' ), -); - -/** Basque (Euskara) */ -$specialPageAliases['eu'] = array( - 'ViewXML' => array( 'XMLIkusi' ), -); - -/** Persian (فارسی) */ -$specialPageAliases['fa'] = array( - 'ImportCSV' => array( 'درون‌ریزی_سی‌اس‌وی' ), - 'ImportXML' => array( 'درون‌ریزی_اکس‌ام‌ال' ), - 'ViewXML' => array( 'مشاهده_اکس‌ام‌ال' ), -); - -/** Finnish (Suomi) */ -$specialPageAliases['fi'] = array( - 'ImportCSV' => array( 'Tuo_CSV' ), - 'ImportXML' => array( 'Tuo_XML' ), - 'ViewXML' => array( 'Näytä_XML' ), -); - -/** French (Français) */ -$specialPageAliases['fr'] = array( - 'ImportCSV' => array( 'Importer_CVS', 'ImporterCVS' ), - 'ImportXML' => array( 'Importer_XML', 'ImporterXML' ), - 'ViewXML' => array( 'Voir_le_XML', 'Voir_XML', 'VoirXML' ), -); - -/** Franco-Provençal (Arpetan) */ -$specialPageAliases['frp'] = array( - 'ViewXML' => array( 'Vêre_lo_XML', 'VêreLoXML' ), -); - -/** Galician (Galego) */ -$specialPageAliases['gl'] = array( - 'ViewXML' => array( 'Ver XML' ), -); - -/** Swiss German (Alemannisch) */ -$specialPageAliases['gsw'] = array( - 'ViewXML' => array( 'Lueg XML' ), -); - -/** Gujarati (ગુજરાતી) */ -$specialPageAliases['gu'] = array( - 'ViewXML' => array( 'XMLજુઓ' ), -); - -/** Hungarian (Magyar) */ -$specialPageAliases['hu'] = array( - 'ViewXML' => array( 'XML_megtekintése' ), -); - -/** Interlingua (Interlingua) */ -$specialPageAliases['ia'] = array( - 'ImportCSV' => array( 'Importar_CSV' ), - 'ImportXML' => array( 'Importar_XML' ), - 'ViewXML' => array( 'Visualisar_XML' ), -); - -/** Indonesian (Bahasa Indonesia) */ -$specialPageAliases['id'] = array( - 'ViewXML' => array( 'Lihat_XML', 'LihatXML' ), -); - -/** Italian (Italiano) */ -$specialPageAliases['it'] = array( - 'ImportCSV' => array( 'ImportaCSV' ), - 'ImportXML' => array( 'ImportaXML' ), - 'ViewXML' => array( 'VediXML' ), -); - -/** Japanese (日本語) */ -$specialPageAliases['ja'] = array( - 'ImportCSV' => array( 'CSVインポート' ), - 'ImportXML' => array( 'XMLインポート' ), - 'ViewXML' => array( 'XML表示', 'ＸＭＬ表示' ), -); - -/** Khmer (ភាសាខ្មែរ) */ -$specialPageAliases['km'] = array( - 'ViewXML' => array( 'មើលXML' ), -); - -/** Colognian (Ripoarisch) */ -$specialPageAliases['ksh'] = array( - 'ImportCSV' => array( 'CSV_Empotteere' ), - 'ImportXML' => array( 'XML_Empoteere' ), - 'ViewXML' => array( 'XML_beloore' ), -); - -/** Ladino (Ladino) */ -$specialPageAliases['lad'] = array( - 'ImportCSV' => array( 'Aktarear_CSV_Ariento' ), - 'ImportXML' => array( 'Aktarear_XML_Ariento' ), - 'ViewXML' => array( 'Ver_XML' ), -); - -/** Luxembourgish (Lëtzebuergesch) */ -$specialPageAliases['lb'] = array( - 'ImportCSV' => array( 'CSV_importéieren' ), - 'ImportXML' => array( 'XML_importéieren' ), - 'ViewXML' => array( 'XML_weisen' ), -); - -/** Macedonian (Македонски) */ -$specialPageAliases['mk'] = array( - 'ViewXML' => array( 'ВидиXML' ), -); - -/** Malayalam (മലയാളം) */ -$specialPageAliases['ml'] = array( - 'ImportCSV' => array( 'സി.എസ്.വി.ഇറക്കുമതി' ), - 'ImportXML' => array( 'എക്സ്.എം.എൽ.ഇറക്കുമതി' ), - 'ViewXML' => array( 'എക്സ്.എം.എൽ.കാണുക' ), -); - -/** Marathi (मराठी) */ -$specialPageAliases['mr'] = array( - 'ViewXML' => array( 'XMLपहा' ), -); - -/** Maltese (Malti) */ -$specialPageAliases['mt'] = array( - 'ViewXML' => array( 'UriXML' ), -); - -/** Nedersaksisch (Nedersaksisch) */ -$specialPageAliases['nds-nl'] = array( - 'ViewXML' => array( 'XML_bekieken' ), -); - -/** Dutch (Nederlands) */ -$specialPageAliases['nl'] = array( - 'ImportCSV' => array( 'CSVImporteren' ), - 'ImportXML' => array( 'XMLImporteren' ), - 'ViewXML' => array( 'XMLBekijken' ), -); - -/** Norwegian (bokmål)‬ (‪Norsk (bokmål)‬) */ -$specialPageAliases['no'] = array( - 'ViewXML' => array( 'Vis_XML' ), -); - -/** Occitan (Occitan) */ -$specialPageAliases['oc'] = array( - 'ViewXML' => array( 'Veire_XML', 'VeireXML' ), -); - -/** Polish (Polski) */ -$specialPageAliases['pl'] = array( - 'ViewXML' => array( 'XML' ), -); - -/** Portuguese (Português) */ -$specialPageAliases['pt'] = array( - 'ViewXML' => array( 'Ver_XML' ), -); - -/** Romanian (Română) */ -$specialPageAliases['ro'] = array( - 'ImportCSV' => array( 'Import_CSV', 'ImportCSV' ), - 'ImportXML' => array( 'Import_XML', 'ImportXML' ), - 'ViewXML' => array( 'Vizualizare_XML' ), -); - -/** Sanskrit (संस्कृत) */ -$specialPageAliases['sa'] = array( - 'ViewXML' => array( 'XMLपश्यति' ), -); - -/** Slovak (Slovenčina) */ -$specialPageAliases['sk'] = array( - 'ViewXML' => array( 'ZobraziťXML' ), -); - -/** Albanian (Shqip) */ -$specialPageAliases['sq'] = array( - 'ViewXML' => array( 'ShihXML' ), -); - -/** Swedish (Svenska) */ -$specialPageAliases['sv'] = array( - 'ViewXML' => array( 'Visa_XML' ), -); - -/** Swahili (Kiswahili) */ -$specialPageAliases['sw'] = array( - 'ViewXML' => array( 'OnyeshaXML' ), -); - -/** Tagalog (Tagalog) */ -$specialPageAliases['tl'] = array( - 'ViewXML' => array( 'Tingnan ang XML' ), -); - -/** Turkish (Türkçe) */ -$specialPageAliases['tr'] = array( - 'ViewXML' => array( 'XMLGör' ), -); - -/** Татарча (Татарча) */ -$specialPageAliases['tt-cyrl'] = array( - 'ImportCSV' => array( 'CSV_импорт' ), - 'ImportXML' => array( 'XML_импорт' ), - 'ViewXML' => array( 'XML_иттереп_ачу' ), -); - -/** Vèneto (Vèneto) */ -$specialPageAliases['vec'] = array( - 'ViewXML' => array( 'VardaXML' ), -); - -/** - * For backwards compatibility with MediaWiki 1.15 and earlier. - */ -$aliases =& $specialPageAliases; \ No newline at end of file diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_Language.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_Language.php deleted file mode 100644 index 00e7b5c..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_Language.php +++ /dev/null @@ -1,34 +0,0 @@ - DT_SP_HAS_XML_GROUPING, - 'Excluded from XML' => DT_SP_IS_EXCLUDED_FROM_XML, - ); - - /** - * Function that returns the labels for the special properties. - */ - function getPropertyLabels() { - return $this->m_SpecialProperties; - } - - /** - * Aliases for special properties, if any. - */ - function getPropertyAliases() { - return $this->m_SpecialPropertyAliases; - } -} diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_LanguageEn.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_LanguageEn.php deleted file mode 100644 index 49bb88d..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_LanguageEn.php +++ /dev/null @@ -1,13 +0,0 @@ - 'Has XML grouping', - DT_SP_IS_EXCLUDED_FROM_XML => 'Excluded from XML' -); - -} diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_Messages.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_Messages.php deleted file mode 100644 index 2032380..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/languages/DT_Messages.php +++ /dev/null @@ -1,2503 +0,0 @@ - 'Allows for importing and exporting data contained in template calls', - 'viewxml' => 'View XML', - 'dt_viewxml_docu' => 'Please select among the following categories and namespaces to view in XML format.', - 'dt_viewxml_categories' => 'Categories', - 'dt_viewxml_namespaces' => 'Namespaces', - 'dt_viewxml_simplifiedformat' => 'Simplified format', - 'dt_xml_namespace' => 'Namespace', - 'dt_xml_pages' => 'Pages', - 'dt_xml_page' => 'Page', - 'dt_xml_template' => 'Template', - 'dt_xml_field' => 'Field', - 'dt_xml_name' => 'Name', - 'dt_xml_title' => 'Title', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Free Text', - 'importxml' => 'Import XML', - 'dt_import_selectfile' => 'Please select the $1 file to import:', - 'dt_import_encodingtype' => 'Encoding type:', - 'dt_import_forexisting' => 'For pages that already exist:', - 'dt_import_overwriteexisting' => 'Overwrite existing content', - 'dt_import_skipexisting' => 'Skip', - 'dt_import_appendtoexisting' => 'Append to existing content', - 'dt_import_summarydesc' => 'Summary of import:', - 'dt_import_editsummary' => '$1 import', - 'dt_import_importing' => 'Importing...', - 'dt_import_success' => '$1 {{PLURAL:$1|page|pages}} will be created from the $2 file.', - 'importcsv' => 'Import CSV', - 'dt_importcsv_badheader' => "Error: the column $1 header, '$2', must be either '$3', '$4' or of the form 'template_name[field_name]'", - 'right-datatransferimport' => 'Import data', -); - -/** Message documentation (Message documentation) - * @author EugeneZelenko - * @author Fryed-peach - * @author Jon Harald Søby - * @author Purodha - * @author Raymond - * @author Siebrand - */ -$messages['qqq'] = array( - 'datatransfer-desc' => 'Extension description displayed on [[Special:Version]].', - 'dt_viewxml_categories' => '{{Identical|Categories}}', - 'dt_viewxml_namespaces' => '{{Identical|Namespaces}}', - 'dt_xml_namespace' => '{{Identical|Namespace}} -Used as XML tag name.', - 'dt_xml_pages' => '{{Identical|Pages}} - -Used as XML tag name.', - 'dt_xml_page' => '{{Identical|Page}} -Used as XML tag name.', - 'dt_xml_template' => '{{Identical|Template}} -Used as XML tag name.', - 'dt_xml_field' => '{{Identical|Field}} -Used as XML tag name.', - 'dt_xml_name' => '{{Identical|Name}} - -Used as XML tag name.', - 'dt_xml_title' => '{{Identical|Title}} -Used as XML tag name.', - 'dt_xml_id' => '{{Identical|ID}} - -Used as XML tag name.', - 'dt_xml_freetext' => '{{Identical|Free text}} -Used as XML tag name.', - 'dt_import_selectfile' => '$1 is the file format: either CSV or XML', - 'dt_import_encodingtype' => 'The type of encoding for the file: either UTF-8 or UTF-16', - 'dt_import_skipexisting' => '{{Identical|Skip}}', - 'dt_import_editsummary' => '$1 is the file format: either CSV or XML', - 'dt_import_success' => 'Parameters: -* $1 is the number of pages -* $2 is the file format: either CSV or XML', - 'dt_importcsv_badheader' => 'The text "template_name[field_name]" can be translated. -*$1 is a column number in the first row of the CVS file -*$2 is the value found for the $1th colomn in the first line of the CSV file -*$3 is the title label -*$4 is a free text label', - 'right-datatransferimport' => '{{doc-right}}', -); - -/** Faeag Rotuma (Faeag Rotuma) - * @author Jose77 - */ -$messages['rtm'] = array( - 'dt_viewxml_categories' => 'Katekori', -); - -/** Afrikaans (Afrikaans) - * @author Arnobarnard - * @author Naudefj - */ -$messages['af'] = array( - 'datatransfer-desc' => 'Maak die laai en ontlaai van gestruktureerde gegewens in sjabloonaanroepe moontlik', - 'viewxml' => 'Sien XML', - 'dt_viewxml_docu' => 'Kies een van die volgende kategorieë en naamruimtes om in XML-formaat te sien.', - 'dt_viewxml_categories' => 'Ketagorieë', - 'dt_viewxml_namespaces' => 'Naamruimtes', - 'dt_viewxml_simplifiedformat' => 'Vereenvoudigde formaat', - 'dt_xml_namespace' => 'Naamruimte', - 'dt_xml_pages' => 'Bladsye', - 'dt_xml_page' => 'Bladsy', - 'dt_xml_template' => 'Sjabloon', - 'dt_xml_field' => 'Veld', - 'dt_xml_name' => 'Naam', - 'dt_xml_title' => 'Titel', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Vrye teks', - 'importxml' => 'Laai XML', - 'dt_import_selectfile' => 'Kies die $1 lêer om te laai:', - 'dt_import_encodingtype' => 'Enkoderingstipe:', - 'dt_import_skipexisting' => 'Slaan oor', - 'dt_import_editsummary' => '$1-laai', - 'dt_import_importing' => 'Besig om te laai...', - 'dt_import_success' => '$1 {{PLURAL:$1|bladsy|bladsye}} sal geskep word vanaf die lêer $2.', - 'importcsv' => 'Laai CSV', - 'dt_importcsv_badheader' => 'Fout: Die opskrif van kolom $1, "$2", moet "$3" of "$4" wees, of in die vorm "sjabloonnaam[veldnaam]" genoteer word.', - 'right-datatransferimport' => 'Laai data', -); - -/** Gheg Albanian (Gegë) - * @author Mdupont - */ -$messages['aln'] = array( - 'datatransfer-desc' => 'Lejon për import dhe eksport të dhënave të përmbajtura në modelin e quan', - 'viewxml' => 'Shiko XML', - 'dt_viewxml_docu' => 'Ju lutem zgjidhni midis kategorive të mëposhtme dhe hapësira për të parë në formatin XML.', - 'dt_viewxml_categories' => 'Kategoritë', - 'dt_viewxml_namespaces' => 'Hapësira', - 'dt_viewxml_simplifiedformat' => 'Formati i thjeshtuar', - 'dt_xml_namespace' => 'Hapësira', - 'dt_xml_pages' => 'Faqet', - 'dt_xml_page' => 'Faqe', - 'dt_xml_template' => 'Shabllon', - 'dt_xml_field' => 'Fushë', - 'dt_xml_name' => 'Emër', - 'dt_xml_title' => 'Titull', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Free Tekst', - 'importxml' => 'Importi XML', - 'dt_import_selectfile' => 'Ju lutem përzgjidhni kartelën $1 për të importuar:', - 'dt_import_encodingtype' => 'Encoding lloj:', - 'dt_import_editsummary' => '$1 importit', - 'dt_import_importing' => 'Importimi ...', - 'dt_import_success' => '$1 {{PLURAL:$1|faqe|faqe}} do të krijohet nga file $2.', - 'importcsv' => 'Importi CSV', - 'dt_importcsv_badheader' => "Gabim: $1 column header, '$2', duhet të jenë ose '$3', '$4' ose të formës 'template_name [field_name]'", - 'right-datatransferimport' => 'Të dhënat e importit', -); - -/** Amharic (አማርኛ) - * @author Codex Sinaiticus - */ -$messages['am'] = array( - 'dt_viewxml_categories' => 'መደቦች', - 'dt_viewxml_namespaces' => 'ክፍለ-ዊኪዎች', - 'dt_xml_namespace' => 'ክፍለ-ዊኪ', - 'dt_xml_name' => 'ስም', - 'dt_xml_title' => 'አርዕስት', -); - -/** Aragonese (Aragonés) - * @author Juanpabl - * @author Remember the dot - */ -$messages['an'] = array( - 'dt_viewxml_namespaces' => 'Espacios de nombres', - 'dt_xml_namespace' => 'Espacio de nombres', - 'dt_xml_page' => 'Pachina', - 'dt_xml_template' => 'Plantilla', - 'dt_xml_name' => 'Nombre', -); - -/** Arabic (العربية) - * @author Meno25 - * @author OsamaK - */ -$messages['ar'] = array( - 'datatransfer-desc' => 'يسمح باستيراد وتصدير بيانات محتواة في استدعاءات قالب', - 'viewxml' => 'عرض XML', - 'dt_viewxml_docu' => 'من فضلك اختر من بين التصنيفات والنطاقات التالية للعرض في صيغة XML.', - 'dt_viewxml_categories' => 'تصنيفات', - 'dt_viewxml_namespaces' => 'نطاقات', - 'dt_viewxml_simplifiedformat' => 'صيغة مبسطة', - 'dt_xml_namespace' => 'نطاق', - 'dt_xml_pages' => 'صفحات', - 'dt_xml_page' => 'صفحة', - 'dt_xml_template' => 'قالب', - 'dt_xml_field' => 'حقل', - 'dt_xml_name' => 'اسم', - 'dt_xml_title' => 'عنوان', - 'dt_xml_id' => 'رقم', - 'dt_xml_freetext' => 'نص حر', - 'importxml' => 'استيراد XML', - 'dt_import_selectfile' => 'من فضلك اختر ملف $1 للاستيراد:', - 'dt_import_encodingtype' => 'نوع الترميز:', - 'dt_import_editsummary' => 'استيراد $1', - 'dt_import_importing' => 'جاري الاستيراد...', - 'dt_import_success' => 'سوف تُنشأ {{PLURAL:$1||صفحة واحدة|صفحتين|$1 صفحات|$1 صفحة}} من ملف $2.', - 'importcsv' => 'استورد CSV', - 'dt_importcsv_badheader' => "خطأ: عنوان العامود $1، '$2'، يجب أن يكون إما '$3'، '$4' أو من الصيغة 'template_name[field_name]'", - 'right-datatransferimport' => 'استورد بيانات', -); - -/** Aramaic (ܐܪܡܝܐ) - * @author Basharh - */ -$messages['arc'] = array( - 'dt_viewxml_categories' => 'ܣܕܪ̈ܐ', - 'dt_viewxml_namespaces' => 'ܚܩܠܬ̈ܐ', - 'dt_xml_namespace' => 'ܚܩܠܐ', - 'dt_xml_pages' => 'ܕ̈ܦܐ', - 'dt_xml_page' => 'ܕܦܐ', - 'dt_xml_template' => 'ܩܠܒܐ', - 'dt_xml_name' => 'ܫܡܐ', - 'dt_xml_title' => 'ܟܘܢܝܐ', - 'dt_xml_id' => 'ܗܝܝܘܬܐ', - 'dt_import_summarydesc' => 'ܦܣܝܩܬ̈ܐ ܕܡܥܠܢܘܬܐ:', - 'right-datatransferimport' => 'ܡܥܠܢܘܬܐ ܕܓܠܝܬ̈ܐ', -); - -/** Araucanian (Mapudungun) - * @author Remember the dot - */ -$messages['arn'] = array( - 'dt_xml_page' => 'Pakina', -); - -/** Egyptian Spoken Arabic (مصرى) - * @author Dudi - * @author Ghaly - * @author Meno25 - */ -$messages['arz'] = array( - 'datatransfer-desc' => 'بيسمح بـ import و export للداتا اللى جوّا القالب', - 'viewxml' => 'شوف XML', - 'dt_viewxml_docu' => 'لو سمحت اختار من التصانيف و اسامى المساحات الجايه علشان العرض فى XML format.', - 'dt_viewxml_categories' => 'تصانيف', - 'dt_viewxml_namespaces' => 'مساحات اسامى', - 'dt_viewxml_simplifiedformat' => 'format متبسطه', - 'dt_xml_namespace' => 'اسم مساحه', - 'dt_xml_pages' => 'صفح', - 'dt_xml_page' => 'صفحه', - 'dt_xml_template' => 'قالب', - 'dt_xml_field' => 'حقل', - 'dt_xml_name' => 'اسم', - 'dt_xml_title' => 'عنوان', - 'dt_xml_id' => 'رقم', - 'dt_xml_freetext' => 'نص حر', - 'dt_import_selectfile' => 'لو سمحت اختار فايل $1 علشان تعمل import:', - 'dt_import_editsummary' => 'استوراد $1', - 'dt_import_success' => '$1 {{PLURAL:$1|صفحه|صفحه}} ح يتعملو من الفايل $2.', -); - -/** Belarusian (Беларуская) - * @author Тест - */ -$messages['be'] = array( - 'dt_viewxml_categories' => 'Катэгорыі', - 'dt_xml_template' => 'Шаблон', -); - -/** Belarusian (Taraškievica orthography) (‪Беларуская (тарашкевіца)‬) - * @author EugeneZelenko - * @author Jim-by - * @author Wizardist - */ -$messages['be-tarask'] = array( - 'datatransfer-desc' => 'Дазваляе імпартаваць і экспартаваць зьвесткі, якія ўтрымліваюцца ў выкліках шаблёнах', - 'viewxml' => 'Паказаць XML', - 'dt_viewxml_docu' => 'Калі ласка, выберыце што праглядаць у фармаце XML сярод наступных катэгорыяў і прастораў назваў.', - 'dt_viewxml_categories' => 'Катэгорыі', - 'dt_viewxml_namespaces' => 'Прасторы назваў', - 'dt_viewxml_simplifiedformat' => 'Спрошчаны фармат', - 'dt_xml_namespace' => 'Прастора назваў', - 'dt_xml_pages' => 'Старонкі', - 'dt_xml_page' => 'Старонка', - 'dt_xml_template' => 'Шаблён', - 'dt_xml_field' => 'Поле', - 'dt_xml_name' => 'Назва', - 'dt_xml_title' => 'Назва', - 'dt_xml_id' => 'Ідэнтыфікатар', - 'dt_xml_freetext' => 'Вольны тэкст', - 'importxml' => 'Імпарт XML', - 'dt_import_selectfile' => 'Калі ласка, выберыце файл у фармаце $1 для імпарту:', - 'dt_import_encodingtype' => 'Тып кадыроўкі:', - 'dt_import_forexisting' => 'Для старонак якія ўжо існуюць:', - 'dt_import_overwriteexisting' => 'Перазапісваць існуючы зьмест', - 'dt_import_skipexisting' => 'Прапускаць', - 'dt_import_appendtoexisting' => 'Далучаць да існуючага зьместу', - 'dt_import_summarydesc' => 'Кароткае апісаньне імпарту:', - 'dt_import_editsummary' => 'імпарт $1', - 'dt_import_importing' => 'Імпартаваньне...', - 'dt_import_success' => '$1 {{PLURAL:$1|старонка будзе|старонкі будуць|старонак будзе}} створана з файла ў фармаце $2.', - 'importcsv' => 'Імпарт CSV', - 'dt_importcsv_badheader' => "Памылка: загаловак слупка $1, '$2', павінен быць адным з '$3', '$4' альбо у форме 'назва_шаблёну[назва_поля]'", - 'right-datatransferimport' => 'імпарт зьвестак', -); - -/** Bulgarian (Български) - * @author DCLXVI - */ -$messages['bg'] = array( - 'viewxml' => 'Преглед на XML', - 'dt_viewxml_categories' => 'Категории', - 'dt_viewxml_namespaces' => 'Именни пространства', - 'dt_viewxml_simplifiedformat' => 'Опростен формат', - 'dt_xml_namespace' => 'Именно пространство', - 'dt_xml_pages' => 'Страници', - 'dt_xml_page' => 'Страница', - 'dt_xml_template' => 'Шаблон', - 'dt_xml_field' => 'Поле', - 'dt_xml_name' => 'Име', - 'dt_xml_title' => 'Заглавие', - 'dt_xml_id' => 'Номер', - 'dt_xml_freetext' => 'Свободен текст', - 'importxml' => 'Внасяне на XML', - 'dt_import_importing' => 'Внасяне...', - 'importcsv' => 'Внасяне на CSV', - 'right-datatransferimport' => 'Внасяне на данни', -); - -/** Breton (Brezhoneg) - * @author Fohanno - * @author Fulup - * @author Gwendal - * @author Y-M D - */ -$messages['br'] = array( - 'datatransfer-desc' => 'Aotreañ a ra da enporzhiañ hag ezporzhiañ roadennoù eus galvoù patromoù', - 'viewxml' => 'Gwelet XML', - 'dt_viewxml_docu' => 'Dibabit e-touez ar rummadoù hag an esaouennoù anv da heul evit gwelet er furmad XML.', - 'dt_viewxml_categories' => 'Rummadoù', - 'dt_viewxml_namespaces' => 'Esaouennoù anv', - 'dt_viewxml_simplifiedformat' => 'Furmad eeunaet', - 'dt_xml_namespace' => 'Esaouenn anv', - 'dt_xml_pages' => 'Pajennoù', - 'dt_xml_page' => 'Pajenn', - 'dt_xml_template' => 'Patrom', - 'dt_xml_field' => 'Maezienn', - 'dt_xml_name' => 'Anv', - 'dt_xml_title' => 'Titl', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Testenn dieub', - 'importxml' => 'Enporzhiañ XML', - 'dt_import_selectfile' => 'Dibabit ar restr $1 da enporzhiañ :', - 'dt_import_encodingtype' => 'Seurt enkodadur :', - 'dt_import_forexisting' => 'Evit pajennoù zo anezho dija :', - 'dt_import_overwriteexisting' => "erlec'hiañ an endalc'had zo anezhañ dija", - 'dt_import_skipexisting' => 'Lezel a-gostez', - 'dt_import_appendtoexisting' => "Ouzhpennañ d'an endalc'had zo anezhañ dija", - 'dt_import_summarydesc' => 'Diverradenn an enporzh :', - 'dt_import_editsummary' => 'Enporzhiadur $1', - 'dt_import_importing' => "Oc'h enporzhiañ...", - 'dt_import_success' => '$1 {{PLURAL:$1|bajenn|pajenn}} a vo krouet diwar ar restr $2.', - 'importcsv' => 'Enporzh CSV', - 'dt_importcsv_badheader' => 'Fazi : titl ar bann $1, "$2", a rank bezañ "$3", "$4" pe gant ar stumm "anv_ar_patrom[anv_ar_vaezienn]"', - 'right-datatransferimport' => 'Enporzhiañ roadennoù', -); - -/** Bosnian (Bosanski) - * @author CERminator - */ -$messages['bs'] = array( - 'datatransfer-desc' => 'Omogućuje uvoz i izvoz podataka koji su sadržani u pozivima šablona', - 'viewxml' => 'Pregledaj XML', - 'dt_viewxml_docu' => 'Molimo Vas odaberite unutar slijedećih kategorija i imenskih prostora za pregled u XML formatu.', - 'dt_viewxml_categories' => 'Kategorije', - 'dt_viewxml_namespaces' => 'Imenski prostori', - 'dt_viewxml_simplifiedformat' => 'Pojednostavljeni format', - 'dt_xml_namespace' => 'Imenski prostor', - 'dt_xml_pages' => 'Stranice', - 'dt_xml_page' => 'Stranica', - 'dt_xml_template' => 'Šablon', - 'dt_xml_field' => 'Polje', - 'dt_xml_name' => 'Naziv', - 'dt_xml_title' => 'Naslov', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Slobodni tekst', - 'importxml' => 'Uvezi XML', - 'dt_import_selectfile' => 'Molimo odaberite $1 datoteku za uvoz:', - 'dt_import_encodingtype' => 'Tip šifriranja:', - 'dt_import_forexisting' => 'Za stranice koje već postoje:', - 'dt_import_overwriteexisting' => 'Piši preko postojećeg sadržaja', - 'dt_import_skipexisting' => 'Preskoči', - 'dt_import_appendtoexisting' => 'Dodaj na postojeći sadržaj', - 'dt_import_summarydesc' => 'Sažetak uvoza:', - 'dt_import_editsummary' => '$1 uvoz', - 'dt_import_importing' => 'Uvoz...', - 'dt_import_success' => '$1 {{PLURAL:$1|stranica|stranice|stranica}} će biti napravljeno iz $2 datoteke.', - 'importcsv' => 'Uvoz CSV', - 'dt_importcsv_badheader' => "Greška: zaglavlje $1 kolone, '$2', mora biti ili '$3', '$4' ili od obrasca 'template_name[field_name]'", - 'right-datatransferimport' => 'Uvoz podataka', -); - -/** Catalan (Català) - * @author Jordi Roqué - * @author SMP - * @author Solde - * @author Toniher - */ -$messages['ca'] = array( - 'datatransfer-desc' => 'Permet importar i exportar les dades que contenen les crides de les plantilles', - 'viewxml' => "Visualitza l'XML", - 'dt_viewxml_docu' => "Seleccioneu d'entre les següents categories i espais de noms per a veure'l en format XML.", - 'dt_viewxml_categories' => 'Categories', - 'dt_viewxml_namespaces' => 'Espais de noms', - 'dt_viewxml_simplifiedformat' => 'Format simplificat', - 'dt_xml_namespace' => 'Espai de noms', - 'dt_xml_pages' => 'Pàgines', - 'dt_xml_page' => 'Pàgina', - 'dt_xml_template' => 'Plantilla', - 'dt_xml_field' => 'Camp', - 'dt_xml_name' => 'Nom', - 'dt_xml_title' => 'Títol', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Text lliure', - 'importxml' => 'Importa un XML', - 'dt_import_selectfile' => 'Seleccioneu el fitxer $1 per importar:', - 'dt_import_encodingtype' => 'Joc de caràcters:', - 'dt_import_summarydesc' => 'Resum de la importació:', - 'dt_import_editsummary' => 'Importació $1', - 'dt_import_importing' => "S'està important...", - 'dt_import_success' => '$1 {{PLURAL:$1|pàgina|pàgines}} es crearan des del fitxer $2.', - 'importcsv' => 'Importa un CSV', - 'dt_importcsv_badheader' => "Error: la capçalera de la columna $1, '$2', ha de ser o bé '$3', '$4' o bé de la forma 'template_name[field_name]'", - 'right-datatransferimport' => 'Importa les dades', -); - -/** Chechen (Нохчийн) - * @author Sasan700 - */ -$messages['ce'] = array( - 'dt_xml_template' => 'Куцкеп', -); - -/** Czech (Česky) - * @author Jkjk - * @author Matěj Grabovský - */ -$messages['cs'] = array( - 'datatransfer-desc' => 'Umožňuje import a export strukturovaných údajů v buňkách šablon.', - 'viewxml' => 'Zobrazit XML', - 'dt_viewxml_categories' => 'Kategorie', - 'dt_viewxml_namespaces' => 'Jmenné prostory', - 'dt_viewxml_simplifiedformat' => 'Zjednodušený formát', - 'dt_xml_namespace' => 'Jmenný prostor', - 'dt_xml_pages' => 'Stránky', - 'dt_xml_page' => 'Stránka', - 'dt_xml_template' => 'Šablona', - 'dt_xml_field' => 'Pole', - 'dt_xml_name' => 'Název', - 'dt_xml_title' => 'Název', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Libovolný text', - 'importxml' => 'Importovat XML', - 'dt_import_selectfile' => 'Prosím vyberte $1 soubor k importu:', - 'dt_import_encodingtype' => 'Typ kódování:', - 'dt_import_summarydesc' => 'Shrnutí importu:', - 'dt_import_editsummary' => 'import $1', - 'dt_import_importing' => 'Probíhá import...', - 'dt_import_success' => ' $1 {{PLURAL:$1|stránky|stránky|stránek}} bude vytvořeno z $2 souboru.', - 'importcsv' => 'Import CSV', - 'right-datatransferimport' => 'Importovat data', -); - -/** Danish (Dansk) - * @author Jon Harald Søby - */ -$messages['da'] = array( - 'dt_viewxml_categories' => 'Kategorier', - 'dt_xml_namespace' => 'Navnerum', - 'dt_xml_page' => 'Side', - 'dt_xml_name' => 'Navn', - 'dt_xml_title' => 'Titel', - 'dt_xml_id' => 'ID', -); - -/** German (Deutsch) - * @author Als-Holder - * @author Kghbln - * @author Krabina - * @author Revolus - * @author Umherirrender - */ -$messages['de'] = array( - 'datatransfer-desc' => 'Ermöglicht den Export von Daten im XML-Format sowie den Import von Daten im XML- und CSV-Format', - 'viewxml' => 'XML ansehen', - 'dt_viewxml_docu' => 'Bitte auswählen, welche Kategorien und Namensräume im XML-Format angezeigt werden sollen:', - 'dt_viewxml_categories' => 'Kategorien', - 'dt_viewxml_namespaces' => 'Namensräume', - 'dt_viewxml_simplifiedformat' => 'Vereinfachtes Format', - 'dt_xml_namespace' => 'Namensraum', - 'dt_xml_pages' => 'Seiten', - 'dt_xml_page' => 'Seite', - 'dt_xml_template' => 'Vorlage', - 'dt_xml_field' => 'Feld', - 'dt_xml_name' => 'Name', - 'dt_xml_title' => 'Titel', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Freitext', - 'importxml' => 'XML-Datei importieren', - 'dt_import_selectfile' => 'Bitte die zu importierende $1-Datei auswählen:', - 'dt_import_encodingtype' => 'Zeichenkodierung:', - 'dt_import_forexisting' => 'Im Fall von Seiten, die bereits vorhanden sind:', - 'dt_import_overwriteexisting' => 'Vorhandenen Inhalt überschreiben', - 'dt_import_skipexisting' => 'Seite nicht importieren', - 'dt_import_appendtoexisting' => 'Vorhandenen Inhalt ergänzen', - 'dt_import_summarydesc' => 'Zusammenfassung zum Import:', - 'dt_import_editsummary' => '$1-Import', - 'dt_import_importing' => 'Importiere …', - 'dt_import_success' => '$1 {{PLURAL:$1|Seite|Seiten}} werden aus der $2-Datei importiert.', - 'importcsv' => 'CSV-Datei importieren', - 'dt_importcsv_badheader' => "'''Fehler:''' Der Kopf der Spalte $1, „$2“, muss entweder „$3“, „$4“ oder im Format „Vorlagenname[Feldname]“ sein", - 'right-datatransferimport' => 'Daten importieren', -); - -/** Lower Sorbian (Dolnoserbski) - * @author Michawiki - */ -$messages['dsb'] = array( - 'datatransfer-desc' => 'Zmóžnja importěrowanje a eksportěrowanje datow w zawołanjach pśedłogow', - 'viewxml' => 'XML se woglědaś', - 'dt_viewxml_docu' => 'Pšosym wubjeŕ, kótare slědujucych kategorijow a mjenjowych rumow maju se pokazaś w formaśe XML.', - 'dt_viewxml_categories' => 'Kategorije', - 'dt_viewxml_namespaces' => 'Mjenjowe rumy', - 'dt_viewxml_simplifiedformat' => 'Zjadnorjony format', - 'dt_xml_namespace' => 'Mjenjowy rum', - 'dt_xml_pages' => 'Boki', - 'dt_xml_page' => 'Bok', - 'dt_xml_template' => 'Pśedłoga', - 'dt_xml_field' => 'Pólo', - 'dt_xml_name' => 'Mě', - 'dt_xml_title' => 'Titel', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Lichy tekst', - 'importxml' => 'XML importěrowaś', - 'dt_import_selectfile' => 'Pšosym wubjeŕ dataju $1 za importěrowanje:', - 'dt_import_encodingtype' => 'Typ znamuškowego koda:', - 'dt_import_forexisting' => 'Za boki, kótarež južo ekistěruju:', - 'dt_import_overwriteexisting' => 'Eksistěrujuce wopśimjeśe pśepisaś', - 'dt_import_skipexisting' => 'Pśeskócyś', - 'dt_import_appendtoexisting' => 'K eksistěrujucemu wopśimjeśoju pśipowjesyś', - 'dt_import_summarydesc' => 'Zespominanje importa:', - 'dt_import_editsummary' => 'Importěrowanje $1', - 'dt_import_importing' => 'Importěrujo se...', - 'dt_import_success' => '$1 {{PLURAL:$1|bok twóri|boka twóritej|boki twórje|bokow twóri}} se z dataje $2.', - 'importcsv' => 'Importěrowanje CSV', - 'dt_importcsv_badheader' => "Zmólka: głowa słupa $1, '$2', musy pak '$3', '$4' byś pak formu 'mě_pśedłogi[mě_póla]' měś", - 'right-datatransferimport' => 'Daty importěrowaś', -); - -/** Ewe (Eʋegbe) */ -$messages['ee'] = array( - 'dt_xml_page' => 'Axa', -); - -/** Greek (Ελληνικά) - * @author Consta - * @author Crazymadlover - * @author Omnipaedista - */ -$messages['el'] = array( - 'viewxml' => 'Προβολή XML', - 'dt_viewxml_categories' => 'Κατηγορίες', - 'dt_viewxml_namespaces' => 'Περιοχές ονομάτων', - 'dt_xml_namespace' => 'Περιοχή ονομάτων', - 'dt_xml_pages' => 'Σελίδες', - 'dt_xml_page' => 'Σελίδα', - 'dt_xml_template' => 'Πρότυπο', - 'dt_xml_field' => 'Πεδίο', - 'dt_xml_name' => 'Όνομα', - 'dt_xml_title' => 'Τίτλος', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Ελεύθερο Κείμενο', - 'importxml' => 'Εισαγωγή σε XML', - 'dt_import_encodingtype' => 'Τύπος κωδικοποίησης', - 'dt_import_editsummary' => 'Εισαγωγή $1', - 'dt_import_importing' => 'Εισάγεται...', - 'importcsv' => 'Εισαγωγή CSV', - 'right-datatransferimport' => 'Εισαγωγή δεδομένων', -); - -/** Esperanto (Esperanto) - * @author Michawiki - * @author Yekrats - */ -$messages['eo'] = array( - 'datatransfer-desc' => 'Permesas importadon kaj eksportadon de datumoj enhave en ŝablonaj vokoj', - 'viewxml' => 'Rigardu XML-on', - 'dt_viewxml_docu' => 'Bonvolu elekti inter la subaj kategorioj kaj nomspacoj por rigardi en XML-formato.', - 'dt_viewxml_categories' => 'Kategorioj', - 'dt_viewxml_namespaces' => 'Nomspacoj', - 'dt_viewxml_simplifiedformat' => 'Simpligita formato', - 'dt_xml_namespace' => 'Nomspaco', - 'dt_xml_pages' => 'Paĝoj', - 'dt_xml_page' => 'Paĝo', - 'dt_xml_template' => 'Ŝablono', - 'dt_xml_field' => 'Kampo', - 'dt_xml_name' => 'Nomo', - 'dt_xml_title' => 'Titolo', - 'dt_xml_id' => 'identigo', - 'dt_xml_freetext' => 'Libera Teksto', - 'importxml' => 'Importi XML', - 'dt_import_editsummary' => '$1 importo', - 'dt_import_importing' => 'Importante...', - 'importcsv' => 'Importi CSV', - 'right-datatransferimport' => 'Importi datenojn', -); - -/** Spanish (Español) - * @author Crazymadlover - * @author Imre - * @author Locos epraix - * @author Peter17 - * @author Sanbec - * @author Translationista - */ -$messages['es'] = array( - 'datatransfer-desc' => 'Permite importar y exportar datos contenidos en llamadas de plantilla', - 'viewxml' => 'Ver XML', - 'dt_viewxml_docu' => 'Por favor seleccionar entre las siguientes categorías y nombres de espacio para ver en formato XML.', - 'dt_viewxml_categories' => 'Categorías', - 'dt_viewxml_namespaces' => 'Espacios de nombres', - 'dt_viewxml_simplifiedformat' => 'Formato simplificado', - 'dt_xml_namespace' => 'Espacio de nombres', - 'dt_xml_pages' => 'Páginas', - 'dt_xml_page' => 'Página', - 'dt_xml_template' => 'Plantilla', - 'dt_xml_field' => 'Campo', - 'dt_xml_name' => 'Nombre', - 'dt_xml_title' => 'Título', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Texto libre', - 'importxml' => 'Importar XML', - 'dt_import_selectfile' => 'Por favor seleccione el archivo $1 a importar:', - 'dt_import_encodingtype' => 'Tipo de codificación:', - 'dt_import_summarydesc' => 'Resumen de importación:', - 'dt_import_editsummary' => '$1 importación', - 'dt_import_importing' => 'Importando...', - 'dt_import_success' => '$1 {{PLURAL:$1|página|páginas}} serán creadas del archivo $2.', - 'importcsv' => 'Importar CSV', - 'dt_importcsv_badheader' => 'Error : el título de columna $1, "$2", tiene que ser "$3", "$4" o de la forma \'nombre_de_plantilla[nombre_del_campo]\'', - 'right-datatransferimport' => 'Importar datos', -); - -/** Estonian (Eesti) - * @author Avjoska - * @author Pikne - */ -$messages['et'] = array( - 'dt_viewxml_categories' => 'Kategooriad', - 'dt_viewxml_namespaces' => 'Nimeruumid', - 'dt_viewxml_simplifiedformat' => 'Lihtsustatud vorming', - 'dt_xml_namespace' => 'Nimeruum', - 'dt_xml_pages' => 'Leheküljed', - 'dt_xml_page' => 'Lehekülg', - 'dt_xml_template' => 'Mall', - 'dt_xml_name' => 'Nimi', -); - -/** Basque (Euskara) - * @author Kobazulo - */ -$messages['eu'] = array( - 'viewxml' => 'XML ikusi', - 'dt_viewxml_categories' => 'Kategoriak', - 'dt_xml_pages' => 'Orrialdeak', - 'dt_xml_page' => 'Orrialdea', - 'dt_xml_template' => 'Txantiloia', - 'dt_xml_field' => 'Eremua', - 'dt_xml_name' => 'Izena', - 'dt_xml_title' => 'Izenburua', - 'importxml' => 'XML inportatu', - 'dt_import_selectfile' => 'Mesedez, aukera ezazu inportatzeko $1 fitxategia:', - 'dt_import_editsummary' => '$1 inportatu', - 'dt_import_importing' => 'Inportatzen...', - 'importcsv' => 'CSV inportatu', - 'right-datatransferimport' => 'Datuak inportatu', -); - -/** Persian (فارسی) - * @author Mjbmr - */ -$messages['fa'] = array( - 'dt_xml_template' => 'الگو', - 'dt_xml_name' => 'نام', - 'dt_xml_title' => 'عنوان', -); - -/** Finnish (Suomi) - * @author Centerlink - * @author Crt - * @author Nike - * @author Str4nd - * @author Vililikku - */ -$messages['fi'] = array( - 'datatransfer-desc' => 'Mahdollistaa tuoda ja viedä dataa, joka on mallinekutsuissa.', - 'viewxml' => 'Näytä XML', - 'dt_viewxml_docu' => 'Valitse yksi seuraavista luokista ja nimiavaruuksista tarkasteltavaksi XML-muodossa.', - 'dt_viewxml_categories' => 'Luokat', - 'dt_viewxml_namespaces' => 'Nimiavaruudet', - 'dt_viewxml_simplifiedformat' => 'Yksinkertaistettu muoto', - 'dt_xml_namespace' => 'Nimiavaruus', - 'dt_xml_pages' => 'Sivut', - 'dt_xml_page' => 'Sivu', - 'dt_xml_template' => 'Malline', - 'dt_xml_field' => 'Kenttä', - 'dt_xml_name' => 'Nimi', - 'dt_xml_title' => 'Otsikko', - 'dt_xml_id' => 'Tunnus', - 'dt_xml_freetext' => 'Vapaa teksti', - 'importxml' => 'XML-tuonti', - 'dt_import_selectfile' => 'Valitse $1-tiedosto tuotavaksi:', - 'dt_import_encodingtype' => 'Merkistötyyppi:', - 'dt_import_skipexisting' => 'Ohita', - 'dt_import_summarydesc' => 'Tuonnin yhteenveto', - 'dt_import_editsummary' => '$1-tuonti', - 'dt_import_importing' => 'Tuodaan...', - 'dt_import_success' => '$1 {{PLURAL:$1|sivu|sivua}} luodaan $2-tiedostosta.', - 'importcsv' => 'CSV-tuonti', - 'dt_importcsv_badheader' => "Virhe: sarake $1 otsake, '$2', on oltava joko '$3', '$4' tai muotoa 'mallinne_nimi[kenttä_nimi]'", - 'right-datatransferimport' => 'Tuoda tiedot', -); - -/** French (Français) - * @author Crochet.david - * @author Grondin - * @author IAlex - * @author Peter17 - * @author PieRRoMaN - * @author Zetud - */ -$messages['fr'] = array( - 'datatransfer-desc' => 'Permet l’import et l’export de données contenues dans des appels de modèles', - 'viewxml' => 'Voir XML', - 'dt_viewxml_docu' => 'Veuillez sélectionner parmi les catégories et les espaces de noms suivants afin de visionner au format XML.', - 'dt_viewxml_categories' => 'Catégories', - 'dt_viewxml_namespaces' => 'Espaces de noms', - 'dt_viewxml_simplifiedformat' => 'Format simplifié', - 'dt_xml_namespace' => 'Espace de noms', - 'dt_xml_pages' => 'Pages', - 'dt_xml_page' => 'Page', - 'dt_xml_template' => 'Modèle', - 'dt_xml_field' => 'Champ', - 'dt_xml_name' => 'Nom', - 'dt_xml_title' => 'Titre', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Texte libre', - 'importxml' => 'Import en XML', - 'dt_import_selectfile' => 'Veuillez sélectionner le fichier $1 à importer :', - 'dt_import_encodingtype' => 'Type d’encodage:', - 'dt_import_forexisting' => 'Pour les pages qui existent déjà :', - 'dt_import_overwriteexisting' => 'Remplacer le contenu existant', - 'dt_import_skipexisting' => 'Passer', - 'dt_import_appendtoexisting' => 'Ajouter au contenu existant', - 'dt_import_summarydesc' => 'Résumé de l’import :', - 'dt_import_editsummary' => 'Import de $1', - 'dt_import_importing' => 'Import en cours...', - 'dt_import_success' => '$1 {{PLURAL:$1|page sera créée|pages seront créées}} depuis le fichier $2.', - 'importcsv' => 'Import CSV', - 'dt_importcsv_badheader' => 'Erreur : le titre de colonne $1, « $2 », doit être soit « $3 », « $4 » ou de la forme « nom_du_modèle[nom_du_champ] »', - 'right-datatransferimport' => 'Importer des données', -); - -/** Franco-Provençal (Arpetan) - * @author Cedric31 - */ -$messages['frp'] = array( - 'dt_viewxml_categories' => 'Catègories', - 'dt_viewxml_namespaces' => 'Èspâços de noms', - 'dt_xml_namespace' => 'Èspâço de noms', - 'dt_xml_pages' => 'Pâges', - 'dt_xml_page' => 'Pâge', - 'dt_xml_template' => 'Modèlo', -); - -/** Western Frisian (Frysk) - * @author Snakesteuben - */ -$messages['fy'] = array( - 'dt_viewxml_namespaces' => 'Nammeromten', - 'dt_xml_page' => 'Side', - 'dt_xml_name' => 'Namme', -); - -/** Irish (Gaeilge) - * @author Alison - */ -$messages['ga'] = array( - 'dt_xml_namespace' => 'Ainmspás', -); - -/** Galician (Galego) - * @author Alma - * @author Toliño - */ -$messages['gl'] = array( - 'datatransfer-desc' => 'Permite importar e exportar datos contidos en chamadas de modelos', - 'viewxml' => 'Ver XML', - 'dt_viewxml_docu' => 'Por favor seleccione entre as seguintes categorías e espazos de nomes para ver en formato XML.', - 'dt_viewxml_categories' => 'Categorías', - 'dt_viewxml_namespaces' => 'Espazos de nomes', - 'dt_viewxml_simplifiedformat' => 'Formato simplificado', - 'dt_xml_namespace' => 'Espazo de nomes', - 'dt_xml_pages' => 'Páxinas', - 'dt_xml_page' => 'Páxina', - 'dt_xml_template' => 'Modelo', - 'dt_xml_field' => 'Campo', - 'dt_xml_name' => 'Nome', - 'dt_xml_title' => 'Título', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Texto Libre', - 'importxml' => 'Importar XML', - 'dt_import_selectfile' => 'Por favor, seleccione o ficheiro $1 a importar:', - 'dt_import_encodingtype' => 'Tipo de codificación:', - 'dt_import_forexisting' => 'Para páxinas que xa existen:', - 'dt_import_overwriteexisting' => 'Sobrescribir o contido existente', - 'dt_import_skipexisting' => 'Saltar', - 'dt_import_appendtoexisting' => 'Engadir ao contido existente', - 'dt_import_summarydesc' => 'Resumo da importación:', - 'dt_import_editsummary' => 'Importación en $1', - 'dt_import_importing' => 'Importando...', - 'dt_import_success' => '{{PLURAL:$1|Unha páxina será creada|$1 páxinas serán creadas}} a partir do ficheiro $2.', - 'importcsv' => 'Importación en CSV', - 'dt_importcsv_badheader' => 'Erro: a cabeceira da columna $1, "$2", debe ser un "$3", "$4" ou do formulario "template_name[field_name]"', - 'right-datatransferimport' => 'Importar datos', -); - -/** Gothic (Gothic) - * @author Jocke Pirat - */ -$messages['got'] = array( - 'dt_xml_namespace' => 'Seidofera', -); - -/** Ancient Greek (Ἀρχαία ἑλληνικὴ) - * @author Crazymadlover - * @author Omnipaedista - */ -$messages['grc'] = array( - 'dt_viewxml_categories' => 'Κατηγορίαι', - 'dt_viewxml_namespaces' => 'Ὀνοματεῖα', - 'dt_xml_namespace' => 'Ὀνοματεῖον', - 'dt_xml_pages' => 'Δέλτοι', - 'dt_xml_page' => 'Δέλτος', - 'dt_xml_template' => 'Πρότυπον', - 'dt_xml_field' => 'Πεδίον', - 'dt_xml_name' => 'Ὄνομα', - 'dt_xml_title' => 'Ἐπιγραφή', - 'dt_xml_freetext' => 'Ἐλεύθερον κείμενον', -); - -/** Swiss German (Alemannisch) - * @author Als-Holder - * @author J. 'mach' wust - */ -$messages['gsw'] = array( - 'datatransfer-desc' => 'Macht dr Import un dr Export vu strukturierte Date megli, wu in Ufrief vu Vorlage bruucht wäre.', - 'viewxml' => 'XML aaluege', - 'dt_viewxml_docu' => 'Bitte wehl uus, weli Kategorien un Namensryym im XML-Format solle aazeigt wäre.', - 'dt_viewxml_categories' => 'Kategorie', - 'dt_viewxml_namespaces' => 'Namensryym', - 'dt_viewxml_simplifiedformat' => 'Vereifacht Format', - 'dt_xml_namespace' => 'Namensruum', - 'dt_xml_pages' => 'Syte', - 'dt_xml_page' => 'Syte', - 'dt_xml_template' => 'Vorlag', - 'dt_xml_field' => 'Fäld', - 'dt_xml_name' => 'Name', - 'dt_xml_title' => 'Titel', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Freje Täxt', - 'importxml' => 'XML importiere', - 'dt_import_selectfile' => 'Bitte wehl d $1-Datei zum importiere uus:', - 'dt_import_encodingtype' => 'Verschlisseligstyp:', - 'dt_import_forexisting' => 'Im Fall vu Syte, wu s scho git:', - 'dt_import_overwriteexisting' => 'Vorhandene Inhalt iberschryybe', - 'dt_import_skipexisting' => 'Ibergumpe', - 'dt_import_appendtoexisting' => 'Vorhandene Inhalt ergänze', - 'dt_import_summarydesc' => 'Zämmefassig vum Import:', - 'dt_import_editsummary' => '$1-Import', - 'dt_import_importing' => 'Am Importiere ...', - 'dt_import_success' => '$1 {{PLURAL:$1|Syte|Syte}} wäre us dr $2-Datei aagleit.', - 'importcsv' => 'CSV-Datei importiere', - 'dt_importcsv_badheader' => "Fähler: d Spalte $1 Iberschrift, '$2', muess entwäder '$3', '$4' syy oder us em Format 'template_name[field_name]'", - 'right-datatransferimport' => 'Date importiere', -); - -/** Manx (Gaelg) - * @author MacTire02 - */ -$messages['gv'] = array( - 'viewxml' => 'Jeeagh er XML', - 'dt_viewxml_categories' => 'Ronnaghyn', - 'dt_xml_page' => 'Duillag', - 'dt_xml_name' => 'Ennym', - 'dt_xml_title' => 'Ard-ennym', - 'dt_xml_freetext' => 'Teks seyr', -); - -/** Hausa (هَوُسَ) */ -$messages['ha'] = array( - 'dt_xml_namespace' => 'Sararin suna', - 'dt_xml_page' => 'Shafi', -); - -/** Hawaiian (Hawai`i) - * @author Singularity - */ -$messages['haw'] = array( - 'dt_xml_page' => '‘Ao‘ao', - 'dt_xml_name' => 'Inoa', -); - -/** Hebrew (עברית) - * @author Amire80 - * @author Rotemliss - * @author YaronSh - */ -$messages['he'] = array( - 'datatransfer-desc' => 'אפשרות לייבא ולייצא נתונים בתבניות', - 'viewxml' => 'הצגת XML', - 'dt_viewxml_docu' => 'אנא בחרו את מרחבי השם והקטגוריות אותם תרצו להציג בפורמט XML.', - 'dt_viewxml_categories' => 'קטגוריות', - 'dt_viewxml_namespaces' => 'מרחבי שם', - 'dt_viewxml_simplifiedformat' => 'מבנה מפושט', - 'dt_xml_namespace' => 'מרחב שם', - 'dt_xml_pages' => 'דפים', - 'dt_xml_page' => 'דף', - 'dt_xml_template' => 'תבנית', - 'dt_xml_field' => 'שדה', - 'dt_xml_name' => 'שם', - 'dt_xml_title' => 'כותרת', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'טקסט חופשי', - 'importxml' => 'יבוא XML', - 'dt_import_selectfile' => 'אנא בחרו את קובץ ה־$1 ליבוא:', - 'dt_import_encodingtype' => 'סוג הקידוד:', - 'dt_import_forexisting' => 'עבור הדפים שכבר קיימים:', - 'dt_import_overwriteexisting' => 'לדרוס את התוכן הקיים', - 'dt_import_skipexisting' => 'לדלג', - 'dt_import_appendtoexisting' => 'לצרף את התוכן הקיים', - 'dt_import_summarydesc' => 'תקציר היבוא:', - 'dt_import_editsummary' => 'יבוא $1', - 'dt_import_importing' => 'מתבצע יבוא...', - 'dt_import_success' => '{{PLURAL:$1|דף אחד ייוצר|$1 דפים ייוצרו}} מקובץ ה־$2.', - 'importcsv' => 'יבוא CSV', - 'dt_importcsv_badheader' => "שגיאה: כותרת העמודה $1, '$2', חייבת להיות או '$3', '$4' או מהצורה 'שם_התבנית[שם_השדה]'", - 'right-datatransferimport' => 'יבוא נתונים', -); - -/** Hindi (हिन्दी) - * @author Kaustubh - */ -$messages['hi'] = array( - 'datatransfer-desc' => 'टेम्प्लेट कॉल में उपलब्ध डाटाकी आयात-निर्यात करने की अनुमति देता हैं', - 'viewxml' => 'XML देखें', - 'dt_viewxml_docu' => 'कॄपया XML में देखने के लिये श्रेणीयाँ और नामस्थान चुनें।', - 'dt_viewxml_categories' => 'श्रेणीयाँ', - 'dt_viewxml_namespaces' => 'नामस्थान', - 'dt_viewxml_simplifiedformat' => 'आसान फॉरमैट', - 'dt_xml_namespace' => 'नामस्थान', - 'dt_xml_page' => 'पन्ना', - 'dt_xml_field' => 'फिल्ड़', - 'dt_xml_name' => 'नाम', - 'dt_xml_title' => 'शीर्षक', - 'dt_xml_id' => 'आईडी', - 'dt_xml_freetext' => 'मुक्त पाठ', -); - -/** Croatian (Hrvatski) - * @author Dalibor Bosits - */ -$messages['hr'] = array( - 'dt_viewxml_categories' => 'Kategorije', - 'dt_xml_namespace' => 'Imenski prostor', - 'dt_xml_page' => 'Stranica', -); - -/** Upper Sorbian (Hornjoserbsce) - * @author Michawiki - */ -$messages['hsb'] = array( - 'datatransfer-desc' => 'Dowola importowanje a eksportowanje datow, kotrež su we wołanjach předłohow wobsahowane', - 'viewxml' => 'XML wobhladać', - 'dt_viewxml_docu' => 'Prošu wubjer ze slědowacych kategorijow a mjenowych rumow, zo by w XML-formaće wobhladał.', - 'dt_viewxml_categories' => 'Kategorije', - 'dt_viewxml_namespaces' => 'Mjenowe rumy', - 'dt_viewxml_simplifiedformat' => 'Zjednorjeny format', - 'dt_xml_namespace' => 'Mjenowy rum', - 'dt_xml_pages' => 'Strony', - 'dt_xml_page' => 'Strona', - 'dt_xml_template' => 'Předłoha', - 'dt_xml_field' => 'Polo', - 'dt_xml_name' => 'Mjeno', - 'dt_xml_title' => 'Titul', - 'dt_xml_id' => 'Id', - 'dt_xml_freetext' => 'Swobodny tekst', - 'importxml' => 'XML importować', - 'dt_import_selectfile' => 'Prošu wubjer dataju $1 za importowanje:', - 'dt_import_encodingtype' => 'Typ znamješkoweho koda:', - 'dt_import_forexisting' => 'Za strony, kotrež hižo eksistuja:', - 'dt_import_overwriteexisting' => 'Eksistowacy wobsah přepisać', - 'dt_import_skipexisting' => 'Přeskočić', - 'dt_import_appendtoexisting' => 'K eksistowacemu wobsahej připowěsnyć', - 'dt_import_summarydesc' => 'Zjeće importa:', - 'dt_import_editsummary' => 'Importowanje $1', - 'dt_import_importing' => 'Importuje so...', - 'dt_import_success' => '$1 {{PLURAL:$1|strona so z dataje $2 twori|stronje so z dataje $2 tworitej|strony so z dataje $2 tworja|stronow so z dataje $2 twori}}.', - 'importcsv' => 'Importowanje CSV', - 'dt_importcsv_badheader' => "Zmylk: hłowa špalty $1, '$2', dyrbi pak '$3', '$4' być pak formu 'mjeno_předłohi[mjeno_pola]' měć", - 'right-datatransferimport' => 'Daty importować', -); - -/** Hungarian (Magyar) - * @author Dani - * @author Glanthor Reviol - */ -$messages['hu'] = array( - 'datatransfer-desc' => 'Lehetővé teszi a sablonhívásokban található adatok importálását és exportálását', - 'viewxml' => 'XML megtekintése', - 'dt_viewxml_docu' => 'Válaszd ki a kategóriák és a névterek közül azt, amelyiket meg akarod tekinteni XML formátumban.', - 'dt_viewxml_categories' => 'Kategóriák', - 'dt_viewxml_namespaces' => 'Névterek', - 'dt_viewxml_simplifiedformat' => 'Egyszerűsített formátum', - 'dt_xml_namespace' => 'Névtér', - 'dt_xml_pages' => 'Lapok', - 'dt_xml_page' => 'Lap', - 'dt_xml_template' => 'Sablon', - 'dt_xml_field' => 'Mező', - 'dt_xml_name' => 'Név', - 'dt_xml_title' => 'Cím', - 'dt_xml_id' => 'Azonosító', - 'dt_xml_freetext' => 'Szabad szöveg', - 'importxml' => 'XML importálás', - 'dt_import_selectfile' => 'Kérlek válaszd ki az importálandó $1 fájlt:', - 'dt_import_encodingtype' => 'Kódolás típusa:', - 'dt_import_summarydesc' => 'Az importálás összefoglalója:', - 'dt_import_editsummary' => '$1 importálás', - 'dt_import_importing' => 'Importálás…', - 'dt_import_success' => '{{PLURAL:$1|egy|$1}} lap fog készülni a(z) $2 fájlból.', - 'importcsv' => 'CSV importálása', - 'dt_importcsv_badheader' => 'Hiba: a(z) $1 oszlop fejlécének („$2”) vagy „$3”, „$4”, vagy pedig „sablonnév[mezőnév]” formátumúnak kell lennie', - 'right-datatransferimport' => 'Adatok importálása', -); - -/** Interlingua (Interlingua) - * @author McDutchie - */ -$messages['ia'] = array( - 'datatransfer-desc' => 'Permitte importar e exportar datos continite in appellos a patronos', - 'viewxml' => 'Vider XML', - 'dt_viewxml_docu' => 'Per favor selige inter le sequente categorias e spatios de nomines pro vider in formato XML.', - 'dt_viewxml_categories' => 'Categorias', - 'dt_viewxml_namespaces' => 'Spatios de nomines', - 'dt_viewxml_simplifiedformat' => 'Formato simplificate', - 'dt_xml_namespace' => 'Spatio de nomines', - 'dt_xml_pages' => 'Paginas', - 'dt_xml_page' => 'Pagina', - 'dt_xml_template' => 'Patrono', - 'dt_xml_field' => 'Campo', - 'dt_xml_name' => 'Nomine', - 'dt_xml_title' => 'Titulo', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Texto libere', - 'importxml' => 'Importar XML', - 'dt_import_selectfile' => 'Per favor selige le file $1 a importar:', - 'dt_import_encodingtype' => 'Typo de codification:', - 'dt_import_forexisting' => 'Pro paginas que ja existe:', - 'dt_import_overwriteexisting' => 'Superscriber le contento existente', - 'dt_import_skipexisting' => 'Saltar', - 'dt_import_appendtoexisting' => 'Adjunger al contento existente', - 'dt_import_summarydesc' => 'Summario de importation:', - 'dt_import_editsummary' => 'Importation de $1', - 'dt_import_importing' => 'Importation in curso…', - 'dt_import_success' => '$1 {{PLURAL:$1|pagina|paginas}} essera create ex le file $2.', - 'importcsv' => 'Importar CSV', - 'dt_importcsv_badheader' => "Error: le capite del columna $1, '$2', debe esser '$3', '$4' o in le forma 'nomine_de_patrono[nomine_de_campo]'", - 'right-datatransferimport' => 'Importar datos', -); - -/** Indonesian (Bahasa Indonesia) - * @author Bennylin - * @author Farras - * @author Irwangatot - * @author IvanLanin - * @author Rex - */ -$messages['id'] = array( - 'datatransfer-desc' => 'Membolehkan untuk impor dan ekspor data diisikan pada pemangilan templat', - 'viewxml' => 'Tilik XML', - 'dt_viewxml_docu' => 'Silakan pilih di antara kategori dan ruang nama berikut untuk melihat dalam format XML', - 'dt_viewxml_categories' => 'Kategori', - 'dt_viewxml_namespaces' => 'Ruang nama', - 'dt_viewxml_simplifiedformat' => 'Penyederhanaan format', - 'dt_xml_namespace' => 'Ruang nama', - 'dt_xml_pages' => 'Halaman', - 'dt_xml_page' => 'Halaman', - 'dt_xml_template' => 'Templat', - 'dt_xml_field' => 'Ruas', - 'dt_xml_name' => 'Nama', - 'dt_xml_title' => 'Judul', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Teks Gratis', - 'importxml' => 'Impor XML', - 'dt_import_selectfile' => 'Pilih berkas $1 untuk di impor:', - 'dt_import_encodingtype' => 'Tipe penyandian:', - 'dt_import_forexisting' => 'Untuk halaman yang sudah ada:', - 'dt_import_overwriteexisting' => 'Menimpa konten yang ada', - 'dt_import_skipexisting' => 'Lewati', - 'dt_import_appendtoexisting' => 'Tambahkan kepada konten yang ada', - 'dt_import_summarydesc' => 'Ringkasan impor:', - 'dt_import_editsummary' => '$1 impor', - 'dt_import_importing' => 'Mengimpor...', - 'dt_import_success' => '$1 {{PLURAL:$1|halaman|halaman}} akan di buat dari berkas $2.', - 'importcsv' => 'Impor CSV', - 'dt_importcsv_badheader' => "Kesalahan: kepala kolom $1, '$2', harus berupa '$3', '$4' atau bentuk 'template_name [field_name]'", - 'right-datatransferimport' => 'Impor data', -); - -/** Igbo (Igbo) - * @author Ukabia - */ -$messages['ig'] = array( - 'dt_viewxml_categories' => 'Ébéanọr', - 'dt_xml_template' => 'Àtụ', -); - -/** Ido (Ido) - * @author Malafaya - */ -$messages['io'] = array( - 'dt_xml_template' => 'Shablono', - 'dt_xml_name' => 'Nomo', - 'dt_xml_title' => 'Titulo', -); - -/** Icelandic (Íslenska) - * @author S.Örvarr.S - */ -$messages['is'] = array( - 'dt_viewxml_namespaces' => 'Nafnrými', - 'dt_xml_page' => 'Síða', -); - -/** Italian (Italiano) - * @author Beta16 - * @author BrokenArrow - * @author Darth Kule - */ -$messages['it'] = array( - 'datatransfer-desc' => "Permette l'importazione e l'esportazione di dati strutturati contenuti in chiamate a template", - 'viewxml' => 'Vedi XML', - 'dt_viewxml_docu' => 'Selezionare tra le categorie e namespace indicati di seguito quelli da visualizzare in formato XML.', - 'dt_viewxml_categories' => 'Categorie', - 'dt_viewxml_namespaces' => 'Namespace', - 'dt_viewxml_simplifiedformat' => 'Formato semplificato', - 'dt_xml_namespace' => 'Namespace', - 'dt_xml_pages' => 'Pagine', - 'dt_xml_page' => 'Pagina', - 'dt_xml_template' => 'Template', - 'dt_xml_field' => 'Campo', - 'dt_xml_name' => 'Nome', - 'dt_xml_title' => 'Titolo', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Testo libero', - 'dt_import_encodingtype' => 'Tipo di codifica', - 'right-datatransferimport' => 'Importa dati', -); - -/** Japanese (日本語) - * @author Aotake - * @author Fryed-peach - * @author JtFuruhata - * @author Ohgi - * @author 青子守歌 - */ -$messages['ja'] = array( - 'datatransfer-desc' => 'テンプレート呼び出しに関わるデータのインポートおよびエクスポートを可能にする', - 'viewxml' => 'XML表示', - 'dt_viewxml_docu' => 'XML形式で表示するカテゴリや名前空間を以下から選択してください。', - 'dt_viewxml_categories' => 'カテゴリ', - 'dt_viewxml_namespaces' => '名前空間', - 'dt_viewxml_simplifiedformat' => '簡易形式', - 'dt_xml_namespace' => '名前空間', - 'dt_xml_pages' => 'ページ群', - 'dt_xml_page' => 'ページ', - 'dt_xml_template' => 'テンプレート', - 'dt_xml_field' => 'フィールド', - 'dt_xml_name' => '名前', - 'dt_xml_title' => 'タイトル', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => '自由形式テキスト', - 'importxml' => 'XMLインポート', - 'dt_import_selectfile' => 'インポートする $1 ファイルを選択してください:', - 'dt_import_encodingtype' => 'エンコーディング方式:', - 'dt_import_forexisting' => 'すでに存在するページの場合：', - 'dt_import_overwriteexisting' => '既存の内容に上書き', - 'dt_import_skipexisting' => 'スキップ', - 'dt_import_appendtoexisting' => '既存の内容に追加', - 'dt_import_summarydesc' => '移入の概要：', - 'dt_import_editsummary' => '$1 のインポート', - 'dt_import_importing' => 'インポート中…', - 'dt_import_success' => '$2ファイルから$1{{PLURAL:$1|ページ}}がインポートされます。', - 'importcsv' => 'CSVのインポート', - 'dt_importcsv_badheader' => 'エラー: 列 $1 のヘッダ「$2」は、「$3」もしくは「$4」であるか、または「テンプレート名[フィールド名]」という形式になっていなければなりません。', - 'right-datatransferimport' => 'データをインポートする', -); - -/** Javanese (Basa Jawa) - * @author Meursault2004 - */ -$messages['jv'] = array( - 'viewxml' => 'Ndeleng XML', - 'dt_viewxml_categories' => 'Kategori-kategori', - 'dt_viewxml_simplifiedformat' => 'Format prasaja', - 'dt_xml_namespace' => 'Bilik nama', - 'dt_xml_page' => 'Kaca', - 'dt_xml_name' => 'Jeneng', - 'dt_xml_title' => 'Irah-irahan (judhul)', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Tèks Bébas', -); - -/** Khmer (ភាសាខ្មែរ) - * @author Chhorran - * @author Lovekhmer - * @author Thearith - * @author គីមស៊្រុន - * @author វ័ណថារិទ្ធ - */ -$messages['km'] = array( - 'viewxml' => 'មើល XML', - 'dt_viewxml_docu' => 'ជ្រើសយកក្នុងចំណោមចំណាត់ថ្នាក់ក្រុមនិងលំហឈ្មោះដើម្បីមើលជាទម្រង់ XML ។', - 'dt_viewxml_categories' => 'ចំណាត់ថ្នាក់ក្រុម', - 'dt_viewxml_namespaces' => 'ប្រភេទ', - 'dt_viewxml_simplifiedformat' => 'ទម្រង់សាមញ្ញ', - 'dt_xml_namespace' => 'ប្រភេទ', - 'dt_xml_pages' => 'ទំព័រ', - 'dt_xml_page' => 'ទំព័រ', - 'dt_xml_template' => 'ទំព័រគំរូ', - 'dt_xml_field' => 'ផ្នែក', - 'dt_xml_name' => 'ឈ្មោះ', - 'dt_xml_title' => 'ចំណងជើង', - 'dt_xml_id' => 'អត្តសញ្ញាណ', - 'dt_xml_freetext' => 'អត្ថបទសេរី', - 'importxml' => 'នាំចូល XML', - 'dt_import_selectfile' => 'សូម​ជ្រើស​រើស​ឯកសារ $1 ដើម្បី​នាំ​ចូល​៖', - 'dt_import_encodingtype' => 'ប្រភេទនៃការធ្វើកូដ៖', - 'dt_import_forexisting' => 'សំរាប់ទំព័រដែលមានរួចហើយ៖', - 'dt_import_overwriteexisting' => 'សរសេរជាន់ពីលើខ្លឹមសារដែលមានហើយ', - 'dt_import_skipexisting' => 'រំលង', - 'dt_import_appendtoexisting' => 'សរសេរបន្ថែមទៅលើខ្លឹមសារដែលមានហើយ', - 'dt_import_summarydesc' => 'ចំណារពន្យល់ស្ដីពីការនាំចូល៖', - 'dt_import_editsummary' => '$1 នាំចូល​', - 'dt_import_importing' => 'កំពុងនាំចូល​...', - 'dt_import_success' => 'ទំព័រចំនួន $1 នឹងត្រូវបានបង្កើតពីឯកសារ $2 នេះ។', - 'importcsv' => 'នាំចូល CSV', - 'right-datatransferimport' => 'នាំចូល​ទិន្នន័យ​', -); - -/** Kannada (ಕನ್ನಡ) - * @author Nayvik - */ -$messages['kn'] = array( - 'dt_viewxml_categories' => 'ವರ್ಗಗಳು', - 'dt_xml_namespace' => 'ನಾಮವರ್ಗ', - 'dt_xml_pages' => 'ಪುಟಗಳು', - 'dt_xml_page' => 'ಪುಟ', - 'dt_xml_template' => 'ಟೆಂಪ್ಲೇಟು', - 'dt_xml_name' => 'ಹೆಸರು', - 'dt_xml_title' => 'ಶೀರ್ಷಿಕೆ', -); - -/** Kinaray-a (Kinaray-a) - * @author Jose77 - */ -$messages['krj'] = array( - 'dt_viewxml_categories' => 'Manga Kategorya', - 'dt_xml_page' => 'Pahina', -); - -/** Colognian (Ripoarisch) - * @author Purodha - */ -$messages['ksh'] = array( - 'datatransfer-desc' => 'Määt et müjjelesch, Date uß Schabloone ier Oproofe ze emporteere un ze exporteere.', - 'viewxml' => 'XML beloore', - 'dt_viewxml_docu' => 'Don ußsöke, wat fö_n Saachjruppe un Appachtemangs De em XML Fommaat aanloore wells.', - 'dt_viewxml_categories' => 'Saachjroppe', - 'dt_viewxml_namespaces' => 'Appachtemangs', - 'dt_viewxml_simplifiedformat' => 'Em eijfachere Fommaat', - 'dt_xml_namespace' => 'Appachtemang', - 'dt_xml_pages' => 'Sigge', - 'dt_xml_page' => 'Sigg', - 'dt_xml_template' => 'Schablohn', - 'dt_xml_field' => 'Felldt', - 'dt_xml_name' => 'Name', - 'dt_xml_title' => 'Tėttel', - 'dt_xml_id' => 'Kännong', - 'dt_xml_freetext' => 'Freije Täx', - 'importxml' => 'XML Empotteere', - 'dt_import_selectfile' => 'Söhk de $1-Dattei för zem Empotteere uß:', - 'dt_import_encodingtype' => 'Zoot Kodeerung för de Bohchshtahbe un Zeishe:', - 'dt_import_forexisting' => 'För Sigge, di et ald jitt:', - 'dt_import_overwriteexisting' => 'Övverschrieve, wat ald doh es', - 'dt_import_skipexisting' => 'Övverjonn', - 'dt_import_appendtoexisting' => 'An dat aanhange, wat ald doh es', - 'dt_import_summarydesc' => 'Zesammefassung vun däm Empoot:', - 'dt_import_editsummary' => 'uss ene $1-Datei empotteet', - 'dt_import_importing' => 'Ben aam Empotteere{{int:Ellipsis}}', - 'dt_import_success' => '{{PLURAL:$1|Ein Sigg weed_uß|$1 Sigge weede uß|Kein einzelne Sigg weed_uß}} dä $2-Dattei empotteet.', - 'importcsv' => 'CSV-Dattei empoteere', - 'dt_importcsv_badheader' => 'Fähler: De Shpallde-Övverschreff för $1 es „$2“, mööt ävver „$3“ udder „$4“ sin, udder dat Fommaat „Name_vun_ene_Schablohn[Name_vun_enem_Felldt]“ han.', - 'right-datatransferimport' => 'Daate empoteere', -); - -/** Kurdish (Latin) (Kurdî (Latin)) - * @author George Animal - */ -$messages['ku-latn'] = array( - 'dt_xml_page' => 'Rûpel', - 'dt_xml_name' => 'Nav', - 'dt_xml_title' => 'Sernav', - 'dt_import_summarydesc' => 'Kurteya împortê:', -); - -/** Cornish (Kernowek) - * @author Kernoweger - * @author Kw-Moon - */ -$messages['kw'] = array( - 'dt_viewxml_categories' => 'Classys', - 'dt_xml_page' => 'Folen', -); - -/** Luxembourgish (Lëtzebuergesch) - * @author Robby - */ -$messages['lb'] = array( - 'datatransfer-desc' => "Erlaabt et Daten déi an Opruffer vu schabloune benotzt ginn z'importéieren an z'exportéieren", - 'viewxml' => 'XML weisen', - 'dt_viewxml_docu' => 'Wielt w.e.g. ënnert dëse Kategorien an Nimmraim fir am XML-Format unzeweisen.', - 'dt_viewxml_categories' => 'Kategorien', - 'dt_viewxml_namespaces' => 'Nummraim', - 'dt_viewxml_simplifiedformat' => 'Vereinfachte Format', - 'dt_xml_namespace' => 'Nummraum', - 'dt_xml_pages' => 'Säiten', - 'dt_xml_page' => 'Säit', - 'dt_xml_template' => 'Schabloun', - 'dt_xml_field' => 'Feld', - 'dt_xml_name' => 'Numm', - 'dt_xml_title' => 'Titel', - 'dt_xml_id' => 'Nummer', - 'dt_xml_freetext' => 'Fräien Text', - 'importxml' => 'XML importéieren', - 'dt_import_selectfile' => "Sicht de(n) $1-Fichier eraus fir z'importéieren:", - 'dt_import_encodingtype' => 'Encoding-Typ:', - 'dt_import_forexisting' => 'Fir Säiten déi et scho gëtt:', - 'dt_import_overwriteexisting' => 'Den Inhalt den et gëtt iwwerschreiwen', - 'dt_import_skipexisting' => 'Iwwersprangen', - 'dt_import_appendtoexisting' => 'Bäi den Inhalt deen et gëtt derbäisetzen', - 'dt_import_summarydesc' => 'Resumé vum Import:', - 'dt_import_editsummary' => '$1 importéieren', - 'dt_import_importing' => 'Import am gaang ...', - 'dt_import_success' => '$1 {{PLURAL:$1|Säit gëtt|Säite ginn}} aus dem $2-Fichier ugeluecht.', - 'importcsv' => 'CSV importéieren', - 'dt_importcsv_badheader' => "Feeler: D'Iwwerschrëft vun der Kolonn $1, '$2', muss entweder '$3', '$4' oder am Format 'Numm_vun_der_Schabloun(Numm_vum_Feld)' sinn", - 'right-datatransferimport' => 'Donnéeën importéieren', -); - -/** Limburgish (Limburgs) - * @author Aelske - * @author Remember the dot - */ -$messages['li'] = array( - 'dt_xml_page' => 'Pagina', -); - -/** Lithuanian (Lietuvių) - * @author Tomasdd - */ -$messages['lt'] = array( - 'dt_viewxml_categories' => 'Kategorijos', -); - -/** Latgalian (Latgaļu) - * @author Dark Eagle - */ -$messages['ltg'] = array( - 'dt_viewxml_namespaces' => 'Vuordu pluoti', - 'dt_xml_namespace' => 'Vuordu pluots', - 'dt_xml_pages' => 'Puslopys', -); - -/** Latvian (Latviešu) - * @author GreenZeb - */ -$messages['lv'] = array( - 'dt_viewxml_categories' => 'Kategorijas', - 'dt_viewxml_namespaces' => 'Vārdtelpas', - 'dt_viewxml_simplifiedformat' => 'Vienkāršots formāts', - 'dt_xml_namespace' => 'Vārdtelpa', - 'dt_xml_pages' => 'Lapas', - 'dt_xml_page' => 'Lapa', - 'dt_xml_template' => 'Veidne', - 'dt_xml_field' => 'Lauks', - 'dt_xml_name' => 'Vārds', - 'dt_xml_title' => 'Nosaukums', - 'dt_xml_id' => 'ID', -); - -/** Eastern Mari (Олык Марий) - * @author Сай - */ -$messages['mhr'] = array( - 'dt_xml_namespace' => 'Лӱм-влакын кумдыкышт', - 'dt_xml_page' => 'Лаштык', -); - -/** Macedonian (Македонски) - * @author Bjankuloski06 - */ -$messages['mk'] = array( - 'datatransfer-desc' => 'Овозможува увоз и извоз на податоци содржани во повикувањата на шаблоните', - 'viewxml' => 'Преглед на XML', - 'dt_viewxml_docu' => 'Одберете од следиве категории и именски простори за преглед во XML формат.', - 'dt_viewxml_categories' => 'Категории', - 'dt_viewxml_namespaces' => 'Именски простори', - 'dt_viewxml_simplifiedformat' => 'Упростен формат', - 'dt_xml_namespace' => 'Именски простор', - 'dt_xml_pages' => 'Страници', - 'dt_xml_page' => 'Страница', - 'dt_xml_template' => 'Шаблон', - 'dt_xml_field' => 'Поле', - 'dt_xml_name' => 'Име', - 'dt_xml_title' => 'Наслов', - 'dt_xml_id' => 'ид. бр.', - 'dt_xml_freetext' => 'Слободен текст', - 'importxml' => 'Увоз на XML', - 'dt_import_selectfile' => 'Одберете ја $1 податотеката за увоз:', - 'dt_import_encodingtype' => 'Тип на кодирање:', - 'dt_import_forexisting' => 'За страници што веќе постојат:', - 'dt_import_overwriteexisting' => 'Презапиши врз постоечките содржини', - 'dt_import_skipexisting' => 'Прескокни', - 'dt_import_appendtoexisting' => 'Додај во постоечката содржина', - 'dt_import_summarydesc' => 'Опис на увозот:', - 'dt_import_editsummary' => 'Увоз на $1', - 'dt_import_importing' => 'Увезувам...', - 'dt_import_success' => '$1 {{PLURAL:$1|страница ќе биде создадена|страници ќе бидат создадени}} од $2 податотеката.', - 'importcsv' => 'Увоз на CSV', - 'dt_importcsv_badheader' => 'Грешка: насловот на колона $1, „$2“, мора да биде или „$3“, или „$4“, или пак од обликот „template_name[field_name]“', - 'right-datatransferimport' => 'Увезување податоци', -); - -/** Malayalam (മലയാളം) - * @author Junaidpv - * @author Praveenp - * @author Shijualex - */ -$messages['ml'] = array( - 'viewxml' => 'XML കാണുക', - 'dt_viewxml_categories' => 'വർഗ്ഗങ്ങൾ', - 'dt_viewxml_namespaces' => 'നാമമേഖലകൾ', - 'dt_viewxml_simplifiedformat' => 'ലളിതവത്ക്കരിക്കപ്പെട്ട ഫോർമാറ്റ്', - 'dt_xml_namespace' => 'നാമമേഖല', - 'dt_xml_pages' => 'താളുകൾ', - 'dt_xml_page' => 'താൾ', - 'dt_xml_template' => 'ഫലകം', - 'dt_xml_field' => 'ഫീൽഡ്', - 'dt_xml_name' => 'പേര്‌', - 'dt_xml_title' => 'ശീർഷകം', - 'dt_xml_id' => 'ഐ.ഡി.', - 'dt_xml_freetext' => 'സ്വതന്ത്ര എഴുത്ത്', - 'importxml' => 'എക്സ്.എം.എൽ. ഇറക്കുമതി', - 'dt_import_selectfile' => 'ദയവായി ഇറക്കുമതിക്കായി $1 പ്രമാണം തിരഞ്ഞെടുക്കുക:', - 'dt_import_encodingtype' => 'എൻ‌കോഡിങ് തരം:', - 'dt_import_forexisting' => 'നിലവിലുള്ള താളുകൾക്ക് വേണ്ടി:', - 'dt_import_appendtoexisting' => 'നിലവിലുള്ള ഉള്ളടക്കത്തോട് കൂട്ടിച്ചേർക്കുക', - 'dt_import_summarydesc' => 'ഇറക്കുമതിയുടെ സംഗ്രഹം:', - 'dt_import_editsummary' => '$1 ഇറക്കുമതി', - 'dt_import_importing' => 'ഇറക്കുമതി ചെയ്യുന്നു...', - 'importcsv' => 'സി.എസ്.വി. ഇറക്കുമതി', -); - -/** Mongolian (Монгол) - * @author Chinneeb - */ -$messages['mn'] = array( - 'dt_viewxml_categories' => 'Ангиллууд', - 'dt_viewxml_namespaces' => 'Нэрний зайнууд', - 'dt_xml_namespace' => 'Нэрний зай', - 'dt_xml_page' => 'Хуудас', -); - -/** Marathi (मराठी) - * @author Kaustubh - * @author V.narsikar - */ -$messages['mr'] = array( - 'datatransfer-desc' => 'साचा कॉल मध्ये असणार्‍या डाटाची आयात निर्यात करण्याची परवानगी देतो', - 'viewxml' => 'XML पहा', - 'dt_viewxml_docu' => 'कॄपया XML मध्ये पाहण्यासाठी खालीलपैकी वर्ग व नामविश्वे निवडा.', - 'dt_viewxml_categories' => 'वर्ग', - 'dt_viewxml_namespaces' => 'नामविश्वे', - 'dt_viewxml_simplifiedformat' => 'सोप्या प्रकारे', - 'dt_xml_namespace' => 'नामविश्व', - 'dt_xml_page' => 'पान', - 'dt_xml_field' => 'रकाना', - 'dt_xml_name' => 'नाव', - 'dt_xml_title' => 'शीर्षक', - 'dt_xml_id' => 'क्रमांक (आयडी)', - 'dt_xml_freetext' => 'मुक्त मजकूर', - 'importxml' => 'एक्सएमएल आयात करा', -); - -/** Mirandese (Mirandés) - * @author Malafaya - */ -$messages['mwl'] = array( - 'dt_xml_page' => 'Páigina', -); - -/** Erzya (Эрзянь) - * @author Botuzhaleny-sodamo - */ -$messages['myv'] = array( - 'dt_viewxml_categories' => 'Категорият', - 'dt_viewxml_namespaces' => 'Лем потмот', - 'dt_xml_page' => 'Лопа', - 'dt_xml_template' => 'Лопа парцун', - 'dt_xml_field' => 'Пакся', - 'dt_xml_name' => 'Лемезэ', - 'dt_xml_title' => 'Конякс', -); - -/** Mazanderani (مازِرونی) - * @author محک - */ -$messages['mzn'] = array( - 'dt_viewxml_categories' => 'رج‌ئون', -); - -/** Nahuatl (Nāhuatl) - * @author Fluence - */ -$messages['nah'] = array( - 'dt_viewxml_categories' => 'Neneuhcāyōtl', - 'dt_viewxml_namespaces' => 'Tōcātzin', - 'dt_xml_namespace' => 'Tōcātzin', - 'dt_xml_page' => 'Zāzanilli', - 'dt_xml_name' => 'Tōcāitl', - 'dt_xml_title' => 'Tōcāitl', - 'dt_xml_id' => 'ID', -); - -/** Low German (Plattdüütsch) - * @author Slomox - */ -$messages['nds'] = array( - 'dt_xml_name' => 'Naam', -); - -/** Dutch (Nederlands) - * @author Siebrand - * @author Tvdm - */ -$messages['nl'] = array( - 'datatransfer-desc' => 'Maakt het importeren en exporteren van gestructureerde gegevens in sjabloonaanroepen mogelijk', - 'viewxml' => 'XML bekijken', - 'dt_viewxml_docu' => 'Selecteer uit de volgende categorieën en naamruimten om in XML-formaat te bekijken.', - 'dt_viewxml_categories' => 'Categorieën', - 'dt_viewxml_namespaces' => 'Naamruimten', - 'dt_viewxml_simplifiedformat' => 'Vereenvoudigd formaat', - 'dt_xml_namespace' => 'Naamruimte', - 'dt_xml_pages' => "Pagina's", - 'dt_xml_page' => 'Pagina', - 'dt_xml_template' => 'Sjabloon', - 'dt_xml_field' => 'Veld', - 'dt_xml_name' => 'Naam', - 'dt_xml_title' => 'Titel', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Vrije tekst', - 'importxml' => 'XML importeren', - 'dt_import_selectfile' => 'Selecteer het te importeren bestand van het type $1:', - 'dt_import_encodingtype' => 'Coderingstype:', - 'dt_import_forexisting' => "Voor pagina's die al bestaan:", - 'dt_import_overwriteexisting' => 'Bestaande inhoud overschrijven', - 'dt_import_skipexisting' => 'Overslaan', - 'dt_import_appendtoexisting' => 'Toevoegen aan bestaande inhoud', - 'dt_import_summarydesc' => 'Samenvatting van de import:', - 'dt_import_editsummary' => '$1-import', - 'dt_import_importing' => 'Bezig met importeren…', - 'dt_import_success' => "Uit het $2-bestand {{PLURAL:$1|wordt één pagina|worden $1 pagina's}} geïmporteerd.", - 'importcsv' => 'CSV importeren', - 'dt_importcsv_badheader' => 'Fout: De kop van kolom $1, "$2", moet "$3" of "$4" zijn, of in de vorm "sjabloonnaam[veldnaam]" genoteerd worden.', - 'right-datatransferimport' => 'Gegevens importeren', -); - -/** Norwegian Nynorsk (‪Norsk (nynorsk)‬) - * @author Gunnernett - * @author Harald Khan - * @author Jon Harald Søby - */ -$messages['nn'] = array( - 'datatransfer-desc' => 'Gjer det mogleg å importera og eksportera data i maloppkallingar', - 'viewxml' => 'Syn XML', - 'dt_viewxml_docu' => 'Vel mellom følgjande kategoriar og namnerom for å syna dei i XML-format.', - 'dt_viewxml_categories' => 'Kategoriar', - 'dt_viewxml_namespaces' => 'Namnerom', - 'dt_viewxml_simplifiedformat' => 'Forenkla format', - 'dt_xml_namespace' => 'Namnerom', - 'dt_xml_pages' => 'Sider', - 'dt_xml_page' => 'Side', - 'dt_xml_template' => 'Mal', - 'dt_xml_field' => 'Felt', - 'dt_xml_name' => 'Namn', - 'dt_xml_title' => 'Tittel', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Fritekst', - 'importxml' => 'Importer XML', - 'dt_import_selectfile' => 'Ver venleg og vel $1-fila som skal verta importert:', - 'dt_import_encodingtype' => 'Teiknkodingstype:', - 'dt_import_editsummary' => '$1-importering', - 'dt_import_importing' => 'Importerer...', - 'dt_import_success' => '$1 {{PLURAL:$1|Éi side vil verta importert|$1 sider vil verta importerte}} frå $2-fila.', - 'importcsv' => 'Importer CSV', - 'dt_importcsv_badheader' => "Feil: kolonneoverskrifta $1, '$2', må vera anten '$3', '$4' eller på forma 'malnamn[feltnamn]'", - 'right-datatransferimport' => 'Importer data', -); - -/** Norwegian (bokmål)‬ (‪Norsk (bokmål)‬) - * @author Jon Harald Søby - * @author Nghtwlkr - */ -$messages['no'] = array( - 'datatransfer-desc' => 'Gjør det mulig å importere og eksportere data som finnes i maloppkallinger', - 'viewxml' => 'Se XML', - 'dt_viewxml_docu' => 'Velg blant følgende kategorier og navnerom for å se dem i XML-format', - 'dt_viewxml_categories' => 'Kategorier', - 'dt_viewxml_namespaces' => 'Navnerom', - 'dt_viewxml_simplifiedformat' => 'Forenklet format', - 'dt_xml_namespace' => 'Navnerom', - 'dt_xml_pages' => 'Sider', - 'dt_xml_page' => 'Side', - 'dt_xml_template' => 'Mal', - 'dt_xml_field' => 'Felt', - 'dt_xml_name' => 'Navn', - 'dt_xml_title' => 'Tittel', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Fritekst', - 'importxml' => 'Importer XML', - 'dt_import_selectfile' => 'Vennligst velg $1-filen som skal importeres:', - 'dt_import_encodingtype' => 'Tegnkodingstype:', - 'dt_import_forexisting' => 'For sider som allerede finnes:', - 'dt_import_overwriteexisting' => 'Skriv over eksisterende innhold', - 'dt_import_skipexisting' => 'Hopp over', - 'dt_import_appendtoexisting' => 'Tilføy til eksisterende innhold', - 'dt_import_summarydesc' => 'Importsammendrag:', - 'dt_import_editsummary' => '$1-importering', - 'dt_import_importing' => 'Importerer...', - 'dt_import_success' => '{{PLURAL:$1|Én side|$1 sider}} vil bli importert fra $2-filen.', - 'importcsv' => 'Importer CSV', - 'dt_importcsv_badheader' => "Feil: kolonneoverskriften $1, '$2', må være enten '$3', '$4' eller på formen 'malnavn[feltnavn]'", - 'right-datatransferimport' => 'Importer data', -); - -/** Occitan (Occitan) - * @author Cedric31 - */ -$messages['oc'] = array( - 'datatransfer-desc' => "Permet l’impòrt e l’expòrt de donadas contengudas dins d'apèls de modèls", - 'viewxml' => 'Veire XML', - 'dt_viewxml_docu' => 'Seleccionatz demest las categorias e los espacis de nomenatges per visionar en format XML.', - 'dt_viewxml_categories' => 'Categorias', - 'dt_viewxml_namespaces' => 'Espacis de nomenatge', - 'dt_viewxml_simplifiedformat' => 'Format simplificat', - 'dt_xml_namespace' => 'Espaci de nom', - 'dt_xml_pages' => 'Paginas', - 'dt_xml_page' => 'Pagina', - 'dt_xml_template' => 'Modèl', - 'dt_xml_field' => 'Camp', - 'dt_xml_name' => 'Nom', - 'dt_xml_title' => 'Títol', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Tèxte Liure', - 'importxml' => 'Impòrt en XML', - 'dt_import_selectfile' => "Seleccionatz lo fichièr $1 d'importar :", - 'dt_import_encodingtype' => 'Tipe d’encodatge:', - 'dt_import_editsummary' => 'Importacion $1', - 'dt_import_importing' => 'Impòrt en cors...', - 'dt_import_success' => '$1 {{PLURAL:$1|pagina serà creada|paginas seràn creadas}} dempuèi lo fichièr $2.', - 'importcsv' => 'Impòrt CSV', - 'dt_importcsv_badheader' => 'Error : lo títol de colomna $1, « $2 », deu èsser siá « $3 », « $4 » o de la forma « nom_del_modèl[nom_del_camp] »', - 'right-datatransferimport' => 'Importar de donadas', -); - -/** Ossetic (Иронау) - * @author Amikeco - */ -$messages['os'] = array( - 'dt_xml_page' => 'Фарс', - 'dt_xml_template' => 'Шаблон', - 'dt_xml_title' => 'Сæргонд', -); - -/** Deitsch (Deitsch) - * @author Xqt - */ -$messages['pdc'] = array( - 'dt_viewxml_categories' => 'Abdeelinge', - 'dt_viewxml_namespaces' => 'Blatznaame', - 'dt_xml_namespace' => 'Blatznaame', - 'dt_xml_pages' => 'Bledder', - 'dt_xml_page' => 'Blatt', - 'dt_xml_template' => 'Moddel', - 'dt_xml_name' => 'Naame', - 'dt_xml_title' => 'Titel', -); - -/** Polish (Polski) - * @author McMonster - * @author Sp5uhe - * @author Wpedzich - */ -$messages['pl'] = array( - 'datatransfer-desc' => 'Pozwala na importowanie i eksportowanie danych zawartych w wywołaniach szablonu', - 'viewxml' => 'Podgląd XML', - 'dt_viewxml_docu' => 'Wybierz, które spośród następujących kategorii i przestrzeni nazw chcesz podejrzeć w formacie XML.', - 'dt_viewxml_categories' => 'Kategorie', - 'dt_viewxml_namespaces' => 'Przestrzenie nazw', - 'dt_viewxml_simplifiedformat' => 'Format uproszczony', - 'dt_xml_namespace' => 'Przestrzeń nazw', - 'dt_xml_pages' => 'Strony', - 'dt_xml_page' => 'Strona', - 'dt_xml_template' => 'Szablon', - 'dt_xml_field' => 'Pole', - 'dt_xml_name' => 'Nazwa', - 'dt_xml_title' => 'Tytuł', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Dowolny tekst', - 'importxml' => 'Import XML', - 'dt_import_selectfile' => 'Wybierz plik $1 do zaimportowania', - 'dt_import_encodingtype' => 'Typ kodowania', - 'dt_import_forexisting' => 'Dla stron, które już istnieją:', - 'dt_import_overwriteexisting' => 'Zastąp istniejącą zawartość', - 'dt_import_skipexisting' => 'Pomiń', - 'dt_import_appendtoexisting' => 'Dołącz do istniejącej zawartości', - 'dt_import_summarydesc' => 'Podsumowanie importu', - 'dt_import_editsummary' => 'Import $1', - 'dt_import_importing' => 'Importowanie...', - 'dt_import_success' => '$1 {{PLURAL:$1|strona zostanie utworzona|strony zostaną utworzone|stron zostanie utworzonych}} z pliku $2.', - 'importcsv' => 'Import CSV', - 'dt_importcsv_badheader' => 'Błąd – w kolumnie $1 nagłówka jest „$2”, a powinno być: „$3”, „$4” lub „nazwa_szablonu[nazwa_pola]”', - 'right-datatransferimport' => 'Importowanie danych', -); - -/** Piedmontese (Piemontèis) - * @author Borichèt - * @author Dragonòt - */ -$messages['pms'] = array( - 'datatransfer-desc' => "A përmëtt d'amporté e esporté ij dat contnù ant le ciamà a stamp", - 'viewxml' => 'Varda XML', - 'dt_viewxml_docu' => 'Për piasì selession-a an tra le categorìe sota e jë spassi nominaj për vëdde an formà XLM.', - 'dt_viewxml_categories' => 'Categorìe', - 'dt_viewxml_namespaces' => 'Spassi nominaj', - 'dt_viewxml_simplifiedformat' => 'Formà semplificà', - 'dt_xml_namespace' => 'Spassi nominal', - 'dt_xml_pages' => 'Pàgine', - 'dt_xml_page' => 'Pàgina', - 'dt_xml_template' => 'Stamp', - 'dt_xml_field' => 'Camp', - 'dt_xml_name' => 'Nòm', - 'dt_xml_title' => 'Tìtol', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Test lìber', - 'importxml' => 'Ampòrta XML', - 'dt_import_selectfile' => 'Për piasì selession-a ël file $1 da amporté:', - 'dt_import_encodingtype' => 'Tipo ëd codìfica:', - 'dt_import_forexisting' => "Për pàgine ch'a esisto già:", - 'dt_import_overwriteexisting' => 'Coaté ël contnù esistent', - 'dt_import_skipexisting' => 'Saoté', - 'dt_import_appendtoexisting' => 'Gionté al contnù esistent', - 'dt_import_summarydesc' => "Somari dj'amportassion:", - 'dt_import_editsummary' => '$1 ampòrta', - 'dt_import_importing' => "An camin ch'as ampòrta...", - 'dt_import_success' => "$1 {{PLURAL:$1|pàgina|pàgine}} a saran creà da l'archivi $2.", - 'importcsv' => 'Ampòrta CSV', - 'dt_importcsv_badheader' => "Eror: l'antestassion ëd la colòna $1, '$2', a deuv esse '$3', '$4' o ëd la forma 'template_name[field_name]'", - 'right-datatransferimport' => 'Ampòrta dat', -); - -/** Pashto (پښتو) - * @author Ahmed-Najib-Biabani-Ibrahimkhel - */ -$messages['ps'] = array( - 'dt_viewxml_categories' => 'وېشنيزې', - 'dt_viewxml_namespaces' => 'نوم-تشيالونه', - 'dt_xml_namespace' => 'نوم-تشيال', - 'dt_xml_pages' => 'مخونه', - 'dt_xml_page' => 'مخ', - 'dt_xml_template' => 'کينډۍ', - 'dt_xml_name' => 'نوم', - 'dt_xml_title' => 'سرليک', - 'dt_xml_freetext' => 'خپلواکه متن', -); - -/** Portuguese (Português) - * @author Hamilton Abreu - * @author Lijealso - * @author Malafaya - */ -$messages['pt'] = array( - 'datatransfer-desc' => 'Permite importação e exportação de dados contidos em chamadas de predefinições', - 'viewxml' => 'Ver XML', - 'dt_viewxml_docu' => 'Por favor, seleccione de entre as categorias e espaços nominais seguintes para ver em formato XML.', - 'dt_viewxml_categories' => 'Categorias', - 'dt_viewxml_namespaces' => 'Espaços nominais', - 'dt_viewxml_simplifiedformat' => 'Formato simplificado', - 'dt_xml_namespace' => 'Espaço nominal', - 'dt_xml_pages' => 'Páginas', - 'dt_xml_page' => 'Página', - 'dt_xml_template' => 'Predefinição', - 'dt_xml_field' => 'Campo', - 'dt_xml_name' => 'Nome', - 'dt_xml_title' => 'Título', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Texto Livre', - 'importxml' => 'Importar XML', - 'dt_import_selectfile' => 'Por favor, selecione o ficheiro $1 a importar:', - 'dt_import_encodingtype' => 'Tipo de codificação:', - 'dt_import_forexisting' => 'Para páginas que já existem:', - 'dt_import_overwriteexisting' => 'Sobrescrever o conteúdo existente', - 'dt_import_skipexisting' => 'Saltar', - 'dt_import_appendtoexisting' => 'Acrescentar ao conteúdo existente', - 'dt_import_summarydesc' => 'Resumo da importação:', - 'dt_import_editsummary' => 'Importação de $1', - 'dt_import_importing' => 'Importando...', - 'dt_import_success' => '{{PLURAL:$1|A página será importada|As páginas serão importadas}} a partir do ficheiro $2.', - 'importcsv' => 'Importar CSV', - 'dt_importcsv_badheader' => "Erro: o cabeçalho da coluna $1, '$2', deve ser '$3', '$4' ou ter a forma 'nome_da_predefinição[nome_do_campo]'", - 'right-datatransferimport' => 'Importar dados', -); - -/** Brazilian Portuguese (Português do Brasil) - * @author Eduardo.mps - * @author Giro720 - */ -$messages['pt-br'] = array( - 'datatransfer-desc' => 'Permite a importação e exportação de dados contidos em chamadas de predefinições', - 'viewxml' => 'Ver XML', - 'dt_viewxml_docu' => 'Por favor, selecione dentre as categorias e espaços nominais seguintes para ver em formato XML.', - 'dt_viewxml_categories' => 'Categorias', - 'dt_viewxml_namespaces' => 'Espaços nominais', - 'dt_viewxml_simplifiedformat' => 'Formato simplificado', - 'dt_xml_namespace' => 'Espaço nominal', - 'dt_xml_pages' => 'Páginas', - 'dt_xml_page' => 'Página', - 'dt_xml_template' => 'Predefinição', - 'dt_xml_field' => 'Campo', - 'dt_xml_name' => 'Nome', - 'dt_xml_title' => 'Título', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Texto Livre', - 'importxml' => 'Importar XML', - 'dt_import_selectfile' => 'Por favor selecione o arquivo $1 para importar:', - 'dt_import_encodingtype' => 'Codificação:', - 'dt_import_forexisting' => 'Para páginas que já existem:', - 'dt_import_overwriteexisting' => 'Sobrescrever o conteúdo existente', - 'dt_import_skipexisting' => 'Pular', - 'dt_import_appendtoexisting' => 'Adicionar ao conteúdo existente', - 'dt_import_summarydesc' => 'Resumo da importação:', - 'dt_import_editsummary' => 'Importação de $1', - 'dt_import_importing' => 'Importando...', - 'dt_import_success' => '$1 {{PLURAL:$1|página será importada|páginas serão importadas}} do arquivo $2.', - 'importcsv' => 'Importar CSV', - 'dt_importcsv_badheader' => "Erro: o cabeçalho da coluna $1, '$2', deve ser '$3', ou '$4' ou da forma 'nome_modelo[nome_campo]'", - 'right-datatransferimport' => 'Importar dados', -); - -/** Romanian (Română) - * @author KlaudiuMihaila - * @author Stelistcristi - */ -$messages['ro'] = array( - 'viewxml' => 'Vizualizează XML', - 'dt_viewxml_categories' => 'Categorii', - 'dt_viewxml_namespaces' => 'Spații de nume', - 'dt_viewxml_simplifiedformat' => 'Format simplificat', - 'dt_xml_namespace' => 'Spațiu de nume', - 'dt_xml_pages' => 'Pagini', - 'dt_xml_page' => 'Pagină', - 'dt_xml_template' => 'Format', - 'dt_xml_field' => 'Câmp', - 'dt_xml_name' => 'Nume', - 'dt_xml_title' => 'Titlu', - 'dt_xml_id' => 'ID', - 'importxml' => 'Importă XML', - 'dt_import_summarydesc' => 'Descrierea importului:', - 'dt_import_importing' => 'Importare...', - 'importcsv' => 'Importă CSV', - 'right-datatransferimport' => 'Importă date', -); - -/** Tarandíne (Tarandíne) - * @author Joetaras - */ -$messages['roa-tara'] = array( - 'datatransfer-desc' => "Permètte de 'mbortà e esportà date strutturate ca stonne jndr'à le chiamate a le template", - 'viewxml' => "Vide l'XML", - 'dt_viewxml_docu' => "Pe piacere scacchie ìmbrà le categorije seguende e le namespace seguende pe vedè 'u formate XML.", - 'dt_viewxml_categories' => 'Categorije', - 'dt_viewxml_namespaces' => 'Namespace', - 'dt_viewxml_simplifiedformat' => 'Formate semblifichete', - 'dt_xml_namespace' => 'Namespace', - 'dt_xml_pages' => 'Pàggene', - 'dt_xml_page' => 'Pàgene', - 'dt_xml_template' => 'Template', - 'dt_xml_field' => 'Cambe', - 'dt_xml_name' => 'Nome', - 'dt_xml_title' => 'Titele', - 'dt_xml_id' => 'Codece (ID)', - 'dt_xml_freetext' => 'Teste libbere', - 'importxml' => "'Mborte XML", -); - -/** Russian (Русский) - * @author Ferrer - * @author Innv - * @author Александр Сигачёв - */ -$messages['ru'] = array( - 'datatransfer-desc' => 'Позволяет импортировать и экспортировать данные, содержащиеся в вызовах шаблонов', - 'viewxml' => 'Просмотр XML', - 'dt_viewxml_docu' => 'Пожалуйста, выберите категории и пространства имён для просмотра в формате XML.', - 'dt_viewxml_categories' => 'Категории', - 'dt_viewxml_namespaces' => 'Пространства имён', - 'dt_viewxml_simplifiedformat' => 'Упрощённый формат', - 'dt_xml_namespace' => 'Пространство имён', - 'dt_xml_pages' => 'Страницы', - 'dt_xml_page' => 'Страница', - 'dt_xml_template' => 'Шаблон', - 'dt_xml_field' => 'Поле', - 'dt_xml_name' => 'Имя', - 'dt_xml_title' => 'Заголовок', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Свободный текст', - 'importxml' => 'Импорт XML', - 'dt_import_selectfile' => 'Пожалуйста, выберите файл $1 для импорта:', - 'dt_import_encodingtype' => 'Тип кодировки:', - 'dt_import_forexisting' => 'Для страниц, которые уже существуют:', - 'dt_import_overwriteexisting' => 'Переписать существующие данные', - 'dt_import_skipexisting' => 'Пропустить', - 'dt_import_appendtoexisting' => 'Добавить к существующим данным', - 'dt_import_summarydesc' => 'Описание импорта:', - 'dt_import_editsummary' => 'импорт $1', - 'dt_import_importing' => 'Импортирование...', - 'dt_import_success' => '$1 {{PLURAL:$1|страница была|страницы были|страниц были}} созданы из файла $2.', - 'importcsv' => 'Импорт CSV', - 'dt_importcsv_badheader' => 'Ошибка. Заголовок колонки №$1 «$2» должен быть или «$3», или «$4», или в форме «template_name[field_name]»', - 'right-datatransferimport' => 'импорт информации', -); - -/** Rusyn (Русиньскый) - * @author Gazeb - */ -$messages['rue'] = array( - 'dt_viewxml_categories' => 'Катеґорії', - 'dt_viewxml_namespaces' => 'Просторы назв', - 'dt_viewxml_simplifiedformat' => 'Простый формат', - 'dt_xml_namespace' => 'Простор назв', - 'dt_xml_pages' => 'Сторінкы', - 'dt_xml_page' => 'Сторінка', - 'dt_xml_template' => 'Шаблона', - 'dt_xml_field' => 'Поле', - 'dt_xml_name' => 'Назва', - 'dt_xml_title' => 'Надпис', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Вольный текст', - 'importxml' => 'Імпортовати XML', -); - -/** Sicilian (Sicilianu) - * @author Aushulz - */ -$messages['scn'] = array( - 'dt_xml_name' => 'Nomu', - 'dt_xml_id' => 'ID', -); - -/** Slovak (Slovenčina) - * @author Helix84 - */ -$messages['sk'] = array( - 'datatransfer-desc' => 'Umožňuje import a export údajov obsiahnutých v bunkách šablón', - 'viewxml' => 'Zobraziť XML', - 'dt_viewxml_docu' => 'Prosím, vyberte ktorý spomedzi nasledovných kategórií a menných priestorov zobraziť vo formáte XML.', - 'dt_viewxml_categories' => 'Kategórie', - 'dt_viewxml_namespaces' => 'Menné priestory', - 'dt_viewxml_simplifiedformat' => 'Zjednodušený formát', - 'dt_xml_namespace' => 'Menný priestor', - 'dt_xml_pages' => 'Stránky', - 'dt_xml_page' => 'Stránka', - 'dt_xml_template' => 'Šablóna', - 'dt_xml_field' => 'Pole', - 'dt_xml_name' => 'Názov', - 'dt_xml_title' => 'Nadpis', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Voľný text', - 'importxml' => 'Importovať XML', - 'dt_import_selectfile' => 'Prosím, vyberte $1 súbor, ktorý chcete importovať:', - 'dt_import_encodingtype' => 'Typ kódovania:', - 'dt_import_editsummary' => 'Import $1', - 'dt_import_importing' => 'Prebieha import...', - 'dt_import_success' => 'Z $2 súboru sa {{PLURAL:$1|importuje $1 stránka|importujú $1 stránky|importuje $1 stránok}}.', - 'importcsv' => 'Import CSV', - 'dt_importcsv_badheader' => 'Chyba: stĺpec $1 hlavičky, „$2“ musí mať hodnotu buď „$3“, „$4“ alebo byť v tvare „názov_šablóny[názov_poľa]“', - 'right-datatransferimport' => 'Importovať údaje', -); - -/** Slovenian (Slovenščina) - * @author Dbc334 - */ -$messages['sl'] = array( - 'dt_xml_pages' => 'Strani', - 'dt_xml_page' => 'Stran', -); - -/** Serbian Cyrillic ekavian (‪Српски (ћирилица)‬) - * @author Rancher - * @author Sasa Stefanovic - * @author Жељко Тодоровић - * @author Михајло Анђелковић - */ -$messages['sr-ec'] = array( - 'viewxml' => 'Види XML', - 'dt_viewxml_categories' => 'Категорије', - 'dt_viewxml_namespaces' => 'Именски простори', - 'dt_viewxml_simplifiedformat' => 'Поједностављени формат', - 'dt_xml_namespace' => 'Именски простор', - 'dt_xml_pages' => 'Чланци', - 'dt_xml_page' => 'Страница', - 'dt_xml_template' => 'Шаблон', - 'dt_xml_field' => 'Поље', - 'dt_xml_name' => 'Име', - 'dt_xml_title' => 'Наслов', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Слободан текст', - 'importxml' => 'Увези XML', - 'dt_import_editsummary' => '$1 увоз', - 'dt_import_importing' => 'Увоз у току...', - 'importcsv' => 'Увези CSV', - 'right-datatransferimport' => 'Увези податке', -); - -/** Serbian Latin ekavian (‪Srpski (latinica)‬) - * @author Michaello - * @author Жељко Тодоровић - */ -$messages['sr-el'] = array( - 'viewxml' => 'Vidi XML', - 'dt_viewxml_categories' => 'Kategorije', - 'dt_viewxml_namespaces' => 'Imenski prostori', - 'dt_viewxml_simplifiedformat' => 'Pojednostavljeni format', - 'dt_xml_namespace' => 'Imenski prostor', - 'dt_xml_pages' => 'Članci', - 'dt_xml_page' => 'Stranica', - 'dt_xml_template' => 'Šablon', - 'dt_xml_field' => 'Polje', - 'dt_xml_name' => 'Ime', - 'dt_xml_title' => 'Naslov', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Slobodan tekst', - 'importxml' => 'Uvezi XML', - 'dt_import_editsummary' => '$1 uvoz', - 'dt_import_importing' => 'Uvoz u toku...', - 'importcsv' => 'Uvezi CSV', - 'right-datatransferimport' => 'Uvezi podatke', -); - -/** Seeltersk (Seeltersk) - * @author Pyt - */ -$messages['stq'] = array( - 'datatransfer-desc' => 'Ferlööwet dän Import un Export fon strukturierde Doaten, do der in Aproupen un Foarloagen ferwoand wäide.', - 'viewxml' => 'XML ankiekje', - 'dt_viewxml_docu' => 'Wääl uut, wäkke Kategorien in dät XML-Formoat anwiesd wäide schällen.', - 'dt_viewxml_categories' => 'Kategorien', - 'dt_viewxml_namespaces' => 'Noomensruume', - 'dt_viewxml_simplifiedformat' => 'Fereenfacht Formoat', - 'dt_xml_namespace' => 'Noomensruum', - 'dt_xml_page' => 'Siede', - 'dt_xml_field' => 'Fäild', - 'dt_xml_name' => 'Noome', - 'dt_xml_title' => 'Tittel', -); - -/** Sundanese (Basa Sunda) - * @author Irwangatot - */ -$messages['su'] = array( - 'dt_viewxml_namespaces' => 'Ngaranspasi', -); - -/** Swedish (Svenska) - * @author Fluff - * @author Gabbe.g - * @author Lejonel - * @author M.M.S. - * @author Per - */ -$messages['sv'] = array( - 'datatransfer-desc' => 'Tillåter import och export av data som finns i mallanrop', - 'viewxml' => 'Visa XML', - 'dt_viewxml_docu' => 'Välj vilka av följande kategorier och namnrymder som ska visas i XML-format.', - 'dt_viewxml_categories' => 'Kategorier', - 'dt_viewxml_namespaces' => 'Namnrymder', - 'dt_viewxml_simplifiedformat' => 'Förenklat format', - 'dt_xml_namespace' => 'Namnrymd', - 'dt_xml_pages' => 'Sidor', - 'dt_xml_page' => 'Sida', - 'dt_xml_template' => 'Mall', - 'dt_xml_field' => 'Fält', - 'dt_xml_name' => 'Namn', - 'dt_xml_title' => 'Titel', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Fritext', - 'importxml' => 'Importera XML', - 'dt_import_selectfile' => 'Vänligen välj $1-filen som skall importeras:', - 'dt_import_encodingtype' => 'Teckenkodningstyp:', - 'dt_import_editsummary' => '$1-importering', - 'dt_import_importing' => 'Importerar...', - 'dt_import_success' => '$1 {{PLURAL:$1|sida|sidor}} kommer skapas från $2-filen.', - 'importcsv' => 'Importera CSV', - 'dt_importcsv_badheader' => "Fel: Titeln $2 för kolumnen $1 måste vara antingen $3, $4 eller på formen 'mallnamn[fältnamn]'", - 'right-datatransferimport' => 'Importera data', -); - -/** Silesian (Ślůnski) - * @author Herr Kriss - */ -$messages['szl'] = array( - 'dt_xml_page' => 'Zajta', - 'dt_xml_name' => 'Mjano', -); - -/** Tamil (தமிழ்) - * @author TRYPPN - * @author Trengarasu - * @author Ulmo - */ -$messages['ta'] = array( - 'dt_viewxml_categories' => 'பகுப்புகள்', - 'dt_viewxml_namespaces' => 'பெயர்வெளிகள்', - 'dt_viewxml_simplifiedformat' => 'எளிதாக்கப்பட்ட வடிவம்', - 'dt_xml_namespace' => 'பெயர்வெளி', - 'dt_xml_pages' => 'பக்கங்கள்', - 'dt_xml_page' => 'பக்கம்', - 'dt_xml_template' => 'வார்ப்புரு', - 'dt_xml_name' => 'பெயர்', - 'dt_xml_title' => 'தலைப்பு', - 'dt_xml_id' => 'அடையாளம்', - 'dt_xml_freetext' => 'எந்த கட்டுப்பாடும் இல்லா சொற்றொடர்', - 'dt_import_importing' => 'இறக்குமதியாகிறது...', -); - -/** Telugu (తెలుగు) - * @author Veeven - */ -$messages['te'] = array( - 'viewxml' => 'XMLని చూడండి', - 'dt_viewxml_categories' => 'వర్గాలు', - 'dt_viewxml_namespaces' => 'పేరుబరులు', - 'dt_xml_namespace' => 'పేరుబరి', - 'dt_xml_pages' => 'పేజీలు', - 'dt_xml_page' => 'పేజీ', - 'dt_xml_template' => 'మూస', - 'dt_xml_name' => 'పేరు', - 'dt_xml_title' => 'శీర్షిక', - 'dt_xml_id' => 'ఐడీ', - 'dt_xml_freetext' => 'స్వేచ్ఛా పాఠ్యం', -); - -/** Tetum (Tetun) - * @author MF-Warburg - */ -$messages['tet'] = array( - 'dt_viewxml_categories' => 'Kategoria sira', - 'dt_xml_namespace' => 'Espasu pájina nian', - 'dt_xml_page' => 'Pájina', - 'dt_xml_name' => 'Naran', - 'dt_xml_title' => 'Títulu:', - 'dt_xml_id' => 'ID', -); - -/** Tajik (Cyrillic) (Тоҷикӣ (Cyrillic)) - * @author Ibrahim - */ -$messages['tg-cyrl'] = array( - 'dt_viewxml_categories' => 'Гурӯҳҳо', - 'dt_viewxml_namespaces' => 'Фазоҳои ном', - 'dt_xml_namespace' => 'Фазоином', - 'dt_xml_page' => 'Саҳифа', - 'dt_xml_name' => 'Ном', - 'dt_xml_title' => 'Унвон', - 'dt_xml_freetext' => 'Матни дилхоҳ', -); - -/** Tajik (Latin) (Тоҷикӣ (Latin)) - * @author Liangent - */ -$messages['tg-latn'] = array( - 'dt_viewxml_categories' => 'Gurūhho', - 'dt_viewxml_namespaces' => 'Fazohoi nom', - 'dt_xml_namespace' => 'Fazoinom', - 'dt_xml_page' => 'Sahifa', - 'dt_xml_name' => 'Nom', - 'dt_xml_title' => 'Unvon', - 'dt_xml_freetext' => 'Matni dilxoh', -); - -/** Thai (ไทย) - * @author Octahedron80 - */ -$messages['th'] = array( - 'dt_viewxml_categories' => 'หมวดหมู่', - 'dt_viewxml_namespaces' => 'เนมสเปซ', - 'dt_xml_namespace' => 'เนมสเปซ', -); - -/** Turkmen (Türkmençe) - * @author Hanberke - */ -$messages['tk'] = array( - 'dt_xml_page' => 'Sahypa', - 'dt_xml_name' => 'At', -); - -/** Tagalog (Tagalog) - * @author AnakngAraw - */ -$messages['tl'] = array( - 'datatransfer-desc' => 'Nagpapahintulot sa pag-aangkat at pagluluwas ng mga datong nasa loob ng mga pagtawag sa suleras', - 'viewxml' => 'Tingnan ang XML', - 'dt_viewxml_docu' => 'Pumili po lamang mula sa sumusunod na mga kaurian at mga espasyo ng pangalan upang makita ang anyong XML.', - 'dt_viewxml_categories' => 'Mga kaurian', - 'dt_viewxml_namespaces' => 'Mga espasyo ng pangalan', - 'dt_viewxml_simplifiedformat' => 'Pinapayak na anyo', - 'dt_xml_namespace' => 'Espasyo ng pangalan', - 'dt_xml_pages' => 'Mga pahina', - 'dt_xml_page' => 'Pahina', - 'dt_xml_template' => 'Suleras', - 'dt_xml_field' => 'Hanay', - 'dt_xml_name' => 'Pangalan', - 'dt_xml_title' => 'Pamagat', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Malayang Teksto', - 'importxml' => 'Angkatin ang XML', - 'dt_import_selectfile' => 'Pakipili ang talaksang $1 na aangkatin:', - 'dt_import_encodingtype' => 'Uri ng pagkokodigo:', - 'dt_import_forexisting' => 'Para sa mga pahinang umiiral na:', - 'dt_import_overwriteexisting' => 'Patungan ang umiiral na nilalaman', - 'dt_import_skipexisting' => 'Laktawan', - 'dt_import_appendtoexisting' => 'Isugpong sa umiiral na nilalaman', - 'dt_import_summarydesc' => 'Buod ng pag-angkat:', - 'dt_import_editsummary' => 'Pag-angkat ng $1', - 'dt_import_importing' => 'Inaangkat...', - 'dt_import_success' => '$1 {{PLURAL:$1|pahina|mga pahina}} ang lilikhain mula sa talaksang $2.', - 'importcsv' => 'Angkatin ang CSV', - 'dt_importcsv_badheader' => "Kamalian: ang patayong hanay ng paulong $1, '$2', ay dapat na '$3', '$4' o nasa pormang 'template_name[field_name]'", - 'right-datatransferimport' => 'Angkatin ang dato', -); - -/** Turkish (Türkçe) - * @author Joseph - * @author Karduelis - * @author Mach - * @author Manco Capac - * @author Srhat - * @author Vito Genovese - */ -$messages['tr'] = array( - 'datatransfer-desc' => 'Şablon çağrılarında içerilen verilerin içe ve dışa aktarımına izin verir', - 'viewxml' => "XML'i gör", - 'dt_viewxml_docu' => 'Lütfen, XML formatında görüntülemek için aşağıdaki kategori ve ad alanları arasından seçin.', - 'dt_viewxml_categories' => 'Kategoriler', - 'dt_viewxml_namespaces' => 'İsim alanları', - 'dt_viewxml_simplifiedformat' => 'Basitleştirilmiş format', - 'dt_xml_namespace' => 'Ad alanı', - 'dt_xml_pages' => 'Sayfalar', - 'dt_xml_page' => 'Sayfa', - 'dt_xml_template' => 'Şablon', - 'dt_xml_field' => 'Alan', - 'dt_xml_name' => 'İsim', - 'dt_xml_title' => 'Başlık', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Özgür Metin', - 'importxml' => 'XML içe aktar', - 'dt_import_selectfile' => 'Lütfen içe aktarmak için $1 dosyasını seçin:', - 'dt_import_encodingtype' => 'Kodlama türü:', - 'dt_import_summarydesc' => 'İçe aktarma özeti:', - 'dt_import_editsummary' => '$1 içe aktarımı', - 'dt_import_importing' => 'İçe aktarıyor...', - 'dt_import_success' => '$2 dosyasından $1 {{PLURAL:$1|sayfa|sayfa}} oluşturulacak.', - 'importcsv' => "CSV'yi içe aktar", - 'dt_importcsv_badheader' => "Hata: $1 kolonunun başlığı olan '$2', '$3', '$4' ya da 'şablon_adı[alan_adı]' şeklinde olmalıdır", - 'right-datatransferimport' => 'Verileri içe aktarır', -); - -/** Uighur (Latin) (ئۇيغۇرچە / Uyghurche‎ (Latin)) - * @author Jose77 - */ -$messages['ug-latn'] = array( - 'dt_xml_page' => 'Bet', -); - -/** Ukrainian (Українська) - * @author AS - * @author Arturyatsko - * @author Prima klasy4na - * @author Тест - */ -$messages['uk'] = array( - 'datatransfer-desc' => 'Дозволяє імпортувати та експортувати дані, які містяться в викликах шаблонів', - 'viewxml' => 'Перегляд XML', - 'dt_viewxml_docu' => 'Будь ласка, виберіть одну з наступних категорій та імен для перегляду в форматі XML.', - 'dt_viewxml_categories' => 'Категорії', - 'dt_viewxml_namespaces' => 'Простори назв', - 'dt_viewxml_simplifiedformat' => 'Спрощений формат', - 'dt_xml_namespace' => 'Простір назв', - 'dt_xml_pages' => 'Сторінки', - 'dt_xml_page' => 'Сторінка', - 'dt_xml_template' => 'Шаблон', - 'dt_xml_field' => 'Поле', - 'dt_xml_name' => 'Назва', - 'dt_xml_title' => 'Заголовок', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Вільний текст', - 'importxml' => 'Імпорт XML', - 'dt_import_selectfile' => 'Будь ласка, виберіть файл $1 для імпорту:', - 'dt_import_encodingtype' => 'Тип кодування:', - 'dt_import_forexisting' => 'Для сторінок, які вже існують:', - 'dt_import_overwriteexisting' => 'Перезаписати існуючий вміст', - 'dt_import_skipexisting' => 'Пропустити', - 'dt_import_appendtoexisting' => 'Додати до існуючого вмісту', - 'dt_import_summarydesc' => 'Опис імпорту:', - 'dt_import_editsummary' => 'імпорт $1', - 'dt_import_importing' => 'Імпорт ...', - 'dt_import_success' => '$1 {{PLURAL:$1|сторінка була|сторінки було|сторінок було}} створено з файлу $2.', - 'importcsv' => 'Імпорт CSV', - 'dt_importcsv_badheader' => 'Помилка. Заголовок колонки №$1 «$2» повинен бути або «$3», або «$4», або у формі «template_name[field_name]»', - 'right-datatransferimport' => 'Імпорт даних', -); - -/** Vietnamese (Tiếng Việt) - * @author Minh Nguyen - * @author Vinhtantran - */ -$messages['vi'] = array( - 'datatransfer-desc' => 'Cho phép nhập xuất dữ liệu có cấu trúc được chứa trong lời gọi bản mẫu', - 'viewxml' => 'Xem XML', - 'dt_viewxml_docu' => 'Xin hãy chọn trong những thể loại và không gian tên dưới đây để xem ở dạng XML.', - 'dt_viewxml_categories' => 'Thể loại', - 'dt_viewxml_namespaces' => 'Không gian tên', - 'dt_viewxml_simplifiedformat' => 'Định dạng đơn giản hóa', - 'dt_xml_namespace' => 'Không gian tên', - 'dt_xml_pages' => 'Trang', - 'dt_xml_page' => 'Trang', - 'dt_xml_template' => 'Bản mẫu', - 'dt_xml_field' => 'Trường', - 'dt_xml_name' => 'Tên', - 'dt_xml_title' => 'Tựa đề', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => 'Văn bản Tự do', - 'importxml' => 'Nhập XML', - 'dt_import_selectfile' => 'Xin hãy chọn tập tin $1 để nhập:', - 'dt_import_encodingtype' => 'Bảng mã:', - 'dt_import_editsummary' => 'Nhập $1', - 'dt_import_importing' => 'Đang nhập…', - 'dt_import_success' => '{{PLURAL:$1|Trang|$1 trang}} sẽ được nhập từ tập tin $2.', - 'importcsv' => 'Nhập CSV', - 'dt_importcsv_badheader' => 'Lỗi: tên của cột $1, “$2”, phải là “$3” hay “$4”, hoặc phải theo hình dạng “tên_tiêu_bản[tên_trường]”', - 'right-datatransferimport' => 'Nhập dữ liệu', -); - -/** Volapük (Volapük) - * @author Malafaya - * @author Smeira - */ -$messages['vo'] = array( - 'datatransfer-desc' => 'Dälon nüveigi e seveigi nünodas peleodüköl in samafomotilüvoks paninädöls', - 'viewxml' => 'Logön eli XML', - 'dt_viewxml_docu' => 'Välolös bevü klads e nemaspads foviks utosi, kelosi vilol logön fomätü XML.', - 'dt_viewxml_categories' => 'Klads', - 'dt_viewxml_namespaces' => 'Nemaspads', - 'dt_viewxml_simplifiedformat' => 'Fomät pebalugüköl', - 'dt_xml_namespace' => 'Nemaspad', - 'dt_xml_page' => 'Pad', - 'dt_xml_field' => 'Fel', - 'dt_xml_name' => 'Nem', - 'dt_xml_title' => 'Tiäd', - 'dt_xml_id' => 'Dientifanüm', - 'dt_xml_freetext' => 'Vödem libik', -); - -/** Yiddish (ייִדיש) - * @author פוילישער - */ -$messages['yi'] = array( - 'dt_xml_name' => 'נאָמען', - 'dt_xml_title' => 'טיטל', -); - -/** Simplified Chinese (‪中文(简体)‬) - * @author Gaoxuewei - */ -$messages['zh-hans'] = array( - 'datatransfer-desc' => '允许根据模板的要求导入导出结构化的数据', - 'viewxml' => '查看XML', - 'dt_viewxml_docu' => '请在下列分类、名称空间中选择，以使用XML格式查看。', - 'dt_viewxml_categories' => '分类', - 'dt_viewxml_namespaces' => '名称空间', - 'dt_viewxml_simplifiedformat' => '简化格式', - 'dt_xml_namespace' => '名称空间', - 'dt_xml_pages' => '页面', - 'dt_xml_page' => '页面', - 'dt_xml_template' => '模板', - 'dt_xml_field' => '事件', - 'dt_xml_name' => '名称', - 'dt_xml_title' => '标题', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => '自由文本', -); - -/** Traditional Chinese (‪中文(繁體)‬) - * @author Liangent - * @author Mark85296341 - */ -$messages['zh-hant'] = array( - 'datatransfer-desc' => '允許根據模板的要求導入導出結構化的數據', - 'viewxml' => '檢視XML', - 'dt_viewxml_docu' => '請在下列分類、名稱空間中選擇，以使用XML格式查看。', - 'dt_viewxml_categories' => '分類', - 'dt_viewxml_namespaces' => '名稱空間', - 'dt_viewxml_simplifiedformat' => '簡化格式', - 'dt_xml_namespace' => '名稱空間', - 'dt_xml_pages' => '頁面', - 'dt_xml_page' => '頁面', - 'dt_xml_template' => '模板', - 'dt_xml_name' => '名稱', - 'dt_xml_title' => '標題', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => '自由文字', -); - -/** Chinese (Taiwan) (‪中文(台灣)‬) - * @author Pbdragonwang - * @author Roc michael - */ -$messages['zh-tw'] = array( - 'datatransfer-desc' => '允許匯入及匯出引用樣板(template calls)的結構性資料', - 'viewxml' => '查看 XML', - 'dt_viewxml_docu' => '請選取以下的分類及名字空間以查看其XML格式的資料', - 'dt_viewxml_categories' => '分類', - 'dt_viewxml_namespaces' => '名字空間', - 'dt_viewxml_simplifiedformat' => '簡化的格式', - 'dt_xml_namespace' => '名字空間', - 'dt_xml_pages' => '頁面', - 'dt_xml_page' => '頁面', - 'dt_xml_template' => '模板', - 'dt_xml_field' => '欄位', - 'dt_xml_name' => '名稱', - 'dt_xml_title' => '標題(Title)', - 'dt_xml_id' => 'ID', - 'dt_xml_freetext' => '隨意文字', - 'importxml' => '匯入XML', - 'dt_import_selectfile' => '請選取$1檔以供匯入', - 'dt_import_encodingtype' => '編碼類型', - 'dt_import_summarydesc' => '輸入的摘要', - 'dt_import_editsummary' => '匯入$1', - 'dt_import_importing' => '匯入中...', - 'dt_import_success' => '將從該$2檔匯入$1{{PLURAL:$1|頁面頁面}}。', - 'importcsv' => '匯入CSV檔', - 'dt_importcsv_badheader' => "錯誤：$1欄位的標題「$2」或必須為「$3」，「$4」或表單「模板名稱[欄位名稱]」
    -Error: the column $1 header, '$2', must be either '$3', '$4' or of the form 'template_name[field_name]'", - 'right-datatransferimport' => '輸入資料', -); - diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/specials/DT_ImportCSV.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/specials/DT_ImportCSV.php deleted file mode 100644 index 30b833f..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/specials/DT_ImportCSV.php +++ /dev/null @@ -1,231 +0,0 @@ -mTemplates = array(); - } - - function setName( $name ) { - $this->mName = $name; - } - - function getName() { - return $this->mName; - } - - function addTemplateField( $template_name, $field_name, $value ) { - if ( ! array_key_exists( $template_name, $this->mTemplates ) ) { - $this->mTemplates[$template_name] = array(); - } - $this->mTemplates[$template_name][$field_name] = $value; - } - - function setFreeText( $free_text ) { - $this->mFreeText = $free_text; - } - - function createText() { - $text = ""; - foreach ( $this->mTemplates as $template_name => $fields ) { - $text .= '{{' . $template_name . "\n"; - foreach ( $fields as $field_name => $val ) { - $text .= "|$field_name=$val\n"; - } - $text .= '}}' . "\n"; - } - $text .= $this->mFreeText; - return $text; - } -} - -class DTImportCSV extends SpecialPage { - - /** - * Constructor - */ - public function DTImportCSV() { - global $wgLanguageCode; - parent::__construct( 'ImportCSV' ); - DTUtils::loadMessages(); - } - - function execute( $query ) { - global $wgUser, $wgOut, $wgRequest; - $this->setHeaders(); - - if ( ! $wgUser->isAllowed( 'datatransferimport' ) ) { - global $wgOut; - $wgOut->permissionRequired( 'datatransferimport' ); - return; - } - - if ( $wgRequest->getCheck( 'import_file' ) ) { - $text = DTUtils::printImportingMessage(); - $uploadResult = ImportStreamSource::newFromUpload( "file_name" ); - // handling changed in MW 1.17 - $uploadError = null; - if ( $uploadResult instanceof Status ) { - if ( $uploadResult->isOK() ) { - $source = $uploadResult->value; - } else { - $uploadError = $wgOut->parse( $uploadResult->getWikiText() ); - } - } elseif ( $uploadResult instanceof WikiErrorMsg ) { - $uploadError = $uploadResult->getMessage(); - } else { - $source = $uploadResult; - } - - if ( !is_null( $uploadError ) ) { - $text .= $uploadError; - $wgOut->addHTML( $text ); - return; - } - - $encoding = $wgRequest->getVal( 'encoding' ); - $pages = array(); - $error_msg = self::getCSVData( $source->mHandle, $encoding, $pages ); - if ( ! is_null( $error_msg ) ) { - $text .= $error_msg; - $wgOut->addHTML( $text ); - return; - } - - $importSummary = $wgRequest->getVal( 'import_summary' ); - $forPagesThatExist = $wgRequest->getVal( 'pagesThatExist' ); - $text .= self::modifyPages( $pages, $importSummary, $forPagesThatExist ); - } else { - $formText = DTUtils::printFileSelector( 'CSV' ); - $utf8OptionText = "\t" . Xml::element( 'option', - array( - 'selected' => 'selected', - 'value' => 'utf8' - ), 'UTF-8' ) . "\n"; - $utf16OptionText = "\t" . Xml::element( 'option', - array( - 'value' => 'utf16' - ), 'UTF-16' ) . "\n"; - $encodingSelectText = Xml::tags( 'select', - array( 'name' => 'encoding' ), - "\n" . $utf8OptionText . $utf16OptionText. "\t" ) . "\n\t"; - $formText .= "\t" . Xml::tags( 'p', null, wfMsg( 'dt_import_encodingtype', 'CSV' ) . " " . $encodingSelectText ) . "\n"; - $formText .= "\t" . '
    ' . "\n"; - $formText .= DTUtils::printExistingPagesHandling(); - $formText .= DTUtils::printImportSummaryInput( 'CSV' ); - $formText .= DTUtils::printSubmitButton(); - $text = "\t" . Xml::tags( 'form', - array( - 'enctype' => 'multipart/form-data', - 'action' => '', - 'method' => 'post' - ), $formText ) . "\n"; - } - - $wgOut->addHTML( $text ); - } - - - static function getCSVData( $csv_file, $encoding, &$pages ) { - if ( is_null( $csv_file ) ) - return wfMsg( 'emptyfile' ); - $table = array(); - if ( $encoding == 'utf16' ) { - // change encoding to UTF-8 - // Starting with PHP 5.3 we could use str_getcsv(), - // which would save the tempfile hassle - $tempfile = tmpfile(); - $csv_string = ''; - while ( !feof( $csv_file ) ) { - $csv_string .= fgets( $csv_file, 65535 ); - } - fwrite( $tempfile, iconv( 'UTF-16', 'UTF-8', $csv_string ) ); - fseek( $tempfile, 0 ); - while ( $line = fgetcsv( $tempfile ) ) { - array_push( $table, $line ); - } - fclose( $tempfile ); - } else { - while ( $line = fgetcsv( $csv_file ) ) { - array_push( $table, $line ); - } - } - fclose( $csv_file ); - - // Get rid of the "byte order mark", if it's there - this is - // a three-character string sometimes put at the beginning - // of files to indicate its encoding. - // Code copied from: - // http://www.dotvoid.com/2010/04/detecting-utf-bom-byte-order-mark/ - $byteOrderMark = pack( "CCC", 0xef, 0xbb, 0xbf ); - if ( 0 == strncmp( $table[0][0], $byteOrderMark, 3 ) ) { - $table[0][0] = substr( $table[0][0], 3 ); - // If there were quotation marks around this value, - // they didn't get removed, so remove them now. - $table[0][0] = trim( $table[0][0], '"' ); - } - - // check header line to make sure every term is in the - // correct format - $title_label = wfMsgForContent( 'dt_xml_title' ); - $free_text_label = wfMsgForContent( 'dt_xml_freetext' ); - foreach ( $table[0] as $i => $header_val ) { - if ( $header_val !== $title_label && $header_val !== $free_text_label && - ! preg_match( '/^[^\[\]]+\[[^\[\]]+]$/', $header_val ) ) { - $error_msg = wfMsg( 'dt_importcsv_badheader', $i, $header_val, $title_label, $free_text_label ); - return $error_msg; - } - } - foreach ( $table as $i => $line ) { - if ( $i == 0 ) continue; - $page = new DTPage(); - foreach ( $line as $j => $val ) { - if ( $val == '' ) continue; - if ( $table[0][$j] == $title_label ) { - $page->setName( $val ); - } elseif ( $table[0][$j] == $free_text_label ) { - $page->setFreeText( $val ); - } else { - list( $template_name, $field_name ) = explode( '[', str_replace( ']', '', $table[0][$j] ) ); - $page->addTemplateField( $template_name, $field_name, $val ); - } - } - $pages[] = $page; - } - } - - function modifyPages( $pages, $editSummary, $forPagesThatExist ) { - global $wgUser, $wgLang; - - $text = ""; - $jobs = array(); - $jobParams = array(); - $jobParams['user_id'] = $wgUser->getId(); - $jobParams['edit_summary'] = $editSummary; - $jobParams['for_pages_that_exist'] = $forPagesThatExist; - foreach ( $pages as $page ) { - $title = Title::newFromText( $page->getName() ); - if ( is_null( $title ) ) { - $text .= '

    ' . wfMsg( 'img-auth-badtitle', $page->getName() ) . "

    \n"; - continue; - } - $jobParams['text'] = $page->createText(); - $jobs[] = new DTImportJob( $title, $jobParams ); - } - Job::batchInsert( $jobs ); - $text .= wfMsgExt( 'dt_import_success', array( 'parse' ), $wgLang->formatNum( count( $jobs ) ), 'CSV' ); - - return $text; - } - -} diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/specials/DT_ImportXML.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/specials/DT_ImportXML.php deleted file mode 100644 index ffb4398..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/specials/DT_ImportXML.php +++ /dev/null @@ -1,82 +0,0 @@ -setHeaders(); - - if ( ! $wgUser->isAllowed( 'datatransferimport' ) ) { - global $wgOut; - $wgOut->permissionRequired( 'datatransferimport' ); - return; - } - - if ( $wgRequest->getCheck( 'import_file' ) ) { - $text = DTUtils::printImportingMessage(); - $uploadResult = ImportStreamSource::newFromUpload( "file_name" ); - // handling changed in MW 1.17 - if ( $uploadResult instanceof Status ) { - $source = $uploadResult->value; - } else { - $source = $uploadResult; - } - $importSummary = $wgRequest->getVal( 'import_summary' ); - $forPagesThatExist = $wgRequest->getVal( 'pagesThatExist' ); - $text .= self::modifyPages( $source, $importSummary, $forPagesThatExist ); - } else { - $formText = DTUtils::printFileSelector( 'XML' ); - $formText .= DTUtils::printExistingPagesHandling(); - $formText .= DTUtils::printImportSummaryInput( 'XML' ); - $formText .= DTUtils::printSubmitButton(); - $text = "\t" . Xml::tags( 'form', - array( - 'enctype' => 'multipart/form-data', - 'action' => '', - 'method' => 'post' - ), $formText ) . "\n"; - - } - - $wgOut->addHTML( $text ); - } - - function modifyPages( $source, $editSummary, $forPagesThatExist ) { - $text = ""; - $xml_parser = new DTXMLParser( $source ); - $xml_parser->doParse(); - $jobs = array(); - $job_params = array(); - global $wgUser; - $job_params['user_id'] = $wgUser->getId(); - $job_params['edit_summary'] = $editSummary; - $job_params['for_pages_that_exist'] = $forPagesThatExist; - - foreach ( $xml_parser->mPages as $page ) { - $title = Title::newFromText( $page->getName() ); - $job_params['text'] = $page->createText(); - $jobs[] = new DTImportJob( $title, $job_params ); - } - Job::batchInsert( $jobs ); - global $wgLang; - $text .= wfMsgExt( 'dt_import_success', array( 'parse' ), $wgLang->formatNum( count( $jobs ) ), 'XML' ); - return $text; - } -} diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/specials/DT_ViewXML.php b/preecej/semantic_wiki/extensions/DataTransfer_PS/specials/DT_ViewXML.php deleted file mode 100644 index cb2497f..0000000 --- a/preecej/semantic_wiki/extensions/DataTransfer_PS/specials/DT_ViewXML.php +++ /dev/null @@ -1,511 +0,0 @@ -setHeaders(); - doSpecialViewXML( $query ); - } -} - -function getCategoriesList() { - global $wgContLang, $dtgContLang; - $dt_props = $dtgContLang->getPropertyLabels(); - $exclusion_cat_name = str_replace( ' ', '_', $dt_props[DT_SP_IS_EXCLUDED_FROM_XML] ); - $exclusion_cat_full_name = $wgContLang->getNSText( NS_CATEGORY ) . ':' . $exclusion_cat_name; - $dbr = wfGetDB( DB_SLAVE ); - $categorylinks = $dbr->tableName( 'categorylinks' ); - $res = $dbr->query( "SELECT DISTINCT cl_to FROM $categorylinks" ); - $categories = array(); - while ( $row = $dbr->fetchRow( $res ) ) { - $cat_name = $row[0]; - // add this category to the list, if it's not the - // "Excluded from XML" category, and it's not a child of that - // category - if ( $cat_name != $exclusion_cat_name ) { - $title = Title::newFromText( $cat_name, NS_CATEGORY ); - $parent_categories = $title->getParentCategoryTree( array() ); - if ( ! treeContainsElement( $parent_categories, $exclusion_cat_full_name ) ) - $categories[] = $cat_name; - } - } - $dbr->freeResult( $res ); - sort( $categories ); - return $categories; -} - -function getNamespacesList() { - $dbr = wfGetDB( DB_SLAVE ); - $page = $dbr->tableName( 'page' ); - $res = $dbr->query( "SELECT DISTINCT page_namespace FROM $page" ); - $namespaces = array(); - while ( $row = $dbr->fetchRow( $res ) ) { - $namespaces[] = $row[0]; - } - $dbr->freeResult( $res ); - return $namespaces; -} - -function getGroupings() { - global $dtgContLang; - - global $smwgIP; - if ( ! isset( $smwgIP ) ) { - return array(); - } else { - $groupings = array(); - $store = smwfGetStore(); - $grouping_prop = SMWPropertyValue::makeProperty( '_DT_XG' ); - $grouped_props = $store->getAllPropertySubjects( $grouping_prop ); - foreach ( $grouped_props as $grouped_prop ) { - $res = $store->getPropertyValues( $grouped_prop, $grouping_prop ); - $num = count( $res ); - if ( $num > 0 ) { - $grouping_label = $res[0]->getShortWikiText(); - $groupings[] = array( $grouped_prop, $grouping_label ); - } - } - return $groupings; - } -} - -function getSubpagesForPageGrouping( $page_name, $relation_name ) { - $dbr = wfGetDB( DB_SLAVE ); - $smw_relations = $dbr->tableName( 'smw_relations' ); - $smw_attributes = $dbr->tableName( 'smw_attributes' ); - $res = $dbr->query( "SELECT subject_title FROM $smw_relations WHERE object_title = '$page_name' AND relation_title = '$relation_name'" ); - $subpages = array(); - while ( $row = $dbr->fetchRow( $res ) ) { - $subpage_name = $row[0]; - $query_subpage_name = str_replace( "'", "\'", $subpage_name ); - // get the display order - $res2 = $dbr->query( "SELECT value_num FROM $smw_attributes WHERE subject_title = '$query_subpage_name' AND attribute_title = 'Display_order'" ); - if ( $row2 = $dbr->fetchRow( $res2 ) ) { - $display_order = $row2[0]; - } else { - $display_order = - 1; - } - $dbr->freeResult( $res2 ); - // HACK - page name is the key, display order is the value - $subpages[$subpage_name] = $display_order; - } - $dbr->freeResult( $res ); - uasort( $subpages, "cmp" ); - return array_keys( $subpages ); -} - - -/* - * Get all the pages that belong to a category and all its subcategories, - * down a certain number of levels - heavily based on SMW's - * SMWInlineQuery::includeSubcategories() - */ - function getPagesForCategory( $top_category, $num_levels ) { - if ( 0 == $num_levels ) return $top_category; - - $db = wfGetDB( DB_SLAVE ); - $fname = "getPagesForCategory"; - $categories = array( $top_category ); - $checkcategories = array( $top_category ); - $titles = array(); - for ( $level = $num_levels; $level > 0; $level-- ) { - $newcategories = array(); - foreach ( $checkcategories as $category ) { - $res = $db->select( // make the query - array( 'categorylinks', 'page' ), - array( 'page_id', 'page_title', 'page_namespace' ), - array( 'cl_from = page_id', - 'cl_to = ' . $db->addQuotes( $category ) ), - $fname ); - if ( $res ) { - while ( $res && $row = $db->fetchRow( $res ) ) { - if ( array_key_exists( 'page_title', $row ) ) { - $page_namespace = $row['page_namespace']; - if ( $page_namespace == NS_CATEGORY ) { - $new_category = $row[ 'page_title' ]; - if ( !in_array( $new_category, $categories ) ) { - $newcategories[] = $new_category; - } - } else { - $titles[] = Title::newFromID( $row['page_id'] ); - } - } - } - $db->freeResult( $res ); - } - } - if ( count( $newcategories ) == 0 ) { - return $titles; - } else { - $categories = array_merge( $categories, $newcategories ); - } - $checkcategories = array_diff( $newcategories, array() ); - } - return $titles; - } - -/* -function getPagesForCategory($category) { - $dbr = wfGetDB( DB_SLAVE ); - $categorylinks = $dbr->tableName( 'categorylinks' ); - $res = $dbr->query("SELECT cl_from FROM $categorylinks WHERE cl_to = '$category'"); - $titles = array(); - while ($row = $dbr->fetchRow($res)) { - $titles[] = Title::newFromID($row[0]); - } - $dbr->freeResult($res); - return $titles; -} -*/ - -function getPagesForNamespace( $namespace ) { - $dbr = wfGetDB( DB_SLAVE ); - $page = $dbr->tableName( 'page' ); - $res = $dbr->query( "SELECT page_id FROM $page WHERE page_namespace = '$namespace'" ); - $titles = array(); - while ( $row = $dbr->fetchRow( $res ) ) { - $titles[] = Title::newFromID( $row[0] ); - } - $dbr->freeResult( $res ); - return $titles; -} - -/** - * Helper function for getXMLForPage() - */ -function treeContainsElement( $tree, $element ) { - // escape out if there's no tree (i.e., category) - if ( $tree == null ) - return false; - - foreach ( $tree as $node => $child_tree ) { - if ( $node === $element ) { - return true; - } elseif ( count( $child_tree ) > 0 ) { - if ( treeContainsElement( $child_tree, $element ) ) { - return true; - } - } - } - // no match found - return false; -} - -function getXMLForPage( $title, $simplified_format, $groupings, $depth = 0 ) { - if ( $depth > 5 ) { return ""; } - - global $wgContLang, $dtgContLang; - - $namespace_labels = $wgContLang->getNamespaces(); - $template_label = $namespace_labels[NS_TEMPLATE]; - $namespace_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_namespace' ) ); - $page_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_page' ) ); - $field_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_field' ) ); - $name_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_name' ) ); - $title_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_title' ) ); - $id_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_id' ) ); - $free_text_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_freetext' ) ); - - // if this page belongs to the exclusion category, exit - $parent_categories = $title->getParentCategoryTree( array() ); - $dt_props = $dtgContLang->getPropertyLabels(); - // $exclusion_category = $title->newFromText($dt_props[DT_SP_IS_EXCLUDED_FROM_XML], NS_CATEGORY); - $exclusion_category = $wgContLang->getNSText( NS_CATEGORY ) . ':' . str_replace( ' ', '_', $dt_props[DT_SP_IS_EXCLUDED_FROM_XML] ); - if ( treeContainsElement( $parent_categories, $exclusion_category ) ) - return ""; - $article = new Article( $title ); - $page_title = str_replace( '"', '"', $title->getText() ); - $page_title = str_replace( '&', '&', $page_title ); - if ( $simplified_format ) - $text = "<$page_str><$id_str>{$article->getID()}<$title_str>$page_title\n"; - else - $text = "<$page_str $id_str=\"" . $article->getID() . "\" $title_str=\"" . $page_title . '" >'; - - // traverse the page contents, one character at a time - $uncompleted_curly_brackets = 0; - $page_contents = $article->getContent(); - // escape out variables like "{{PAGENAME}}" - $page_contents = str_replace( '{{PAGENAME}}', '{{PAGENAME}}', $page_contents ); - // escape out parser functions - $page_contents = preg_replace( '/{{(#.+)}}/', '{{$1}}', $page_contents ); - // escape out transclusions - $page_contents = preg_replace( '/{{(:.+)}}/', '{{$1}}', $page_contents ); - // escape out variable names - $page_contents = str_replace( '{{{', '{{{', $page_contents ); - $page_contents = str_replace( '}}}', '}}}', $page_contents ); - // escape out tables - $page_contents = str_replace( '{|', '{|', $page_contents ); - $page_contents = str_replace( '|}', '|}', $page_contents ); - $free_text = ""; - $free_text_id = 1; - $template_name = ""; - $field_name = ""; - $field_value = ""; - $field_has_name = false; - for ( $i = 0; $i < strlen( $page_contents ); $i++ ) { - $c = $page_contents[$i]; - if ( $uncompleted_curly_brackets == 0 ) { - if ( $c == "{" || $i == strlen( $page_contents ) - 1 ) { - if ( $i == strlen( $page_contents ) - 1 ) - $free_text .= $c; - $uncompleted_curly_brackets++; - $free_text = trim( $free_text ); - $free_text = str_replace( '&', '&', $free_text ); - $free_text = str_replace( '[', '[', $free_text ); - $free_text = str_replace( ']', ']', $free_text ); - $free_text = str_replace( '<', '<', $free_text ); - $free_text = str_replace( '>', '>', $free_text ); - if ( $free_text != "" ) { - $text .= "<$free_text_str id=\"$free_text_id\">$free_text"; - $free_text = ""; - $free_text_id++; - } - } elseif ( $c == "{" ) { - // do nothing - } else { - $free_text .= $c; - } - } elseif ( $uncompleted_curly_brackets == 1 ) { - if ( $c == "{" ) { - $uncompleted_curly_brackets++; - $creating_template_name = true; - } elseif ( $c == "}" ) { - $uncompleted_curly_brackets--; - // is this needed? - // if ($field_name != "") { - // $field_name = ""; - // } - if ( $page_contents[$i - 1] == '}' ) { - if ( $simplified_format ) - $text .= ""; - else - $text .= ""; - } - $template_name = ""; - } - } else { // 2 or greater - probably 2 - if ( $c == "}" ) { - $uncompleted_curly_brackets--; - } - if ( $c == "{" ) { - $uncompleted_curly_brackets++; - } else { - if ( $creating_template_name ) { - if ( $c == "|" || $c == "}" ) { - $template_name = str_replace( ' ', '_', trim( $template_name ) ); - $template_name = str_replace( '&', '&', $template_name ); - if ( $simplified_format ) { - $text .= "<" . $template_name . ">"; - } else - $text .= "<$template_label $name_str=\"$template_name\">"; - $creating_template_name = false; - $creating_field_name = true; - $field_id = 1; - } else { - $template_name .= $c; - } - } else { - if ( $c == "|" || $c == "}" ) { - if ( $field_has_name ) { - $field_value = str_replace( '&', '&', $field_value ); - if ( $simplified_format ) { - $field_name = str_replace( ' ', '_', trim( $field_name ) ); - $text .= "<" . $field_name . ">"; - $text .= trim( $field_value ); - $text .= ""; - } else { - $text .= "<$field_str $name_str=\"" . trim( $field_name ) . "\">"; - $text .= trim( $field_value ); - $text .= ""; - } - $field_value = ""; - $field_has_name = false; - } else { - // "field_name" is actually the value - if ( $simplified_format ) { - $field_name = str_replace( ' ', '_', $field_name ); - // add "Field" to the beginning of the file name, since - // XML tags that are simply numbers aren't allowed - $text .= "<" . $field_str . '_' . $field_id . ">"; - $text .= trim( $field_name ); - $text .= ""; - } else { - $text .= "<$field_str $name_str=\"$field_id\">"; - $text .= trim( $field_name ); - $text .= ""; - } - $field_id++; - } - $creating_field_name = true; - $field_name = ""; - } elseif ( $c == "=" ) { - // handle case of = in value - if ( ! $creating_field_name ) { - $field_value .= $c; - } else { - $creating_field_name = false; - $field_has_name = true; - } - } elseif ( $creating_field_name ) { - $field_name .= $c; - } else { - $field_value .= $c; - } - } - } - } - } - - // handle groupings, if any apply here; first check if SMW is installed - global $smwgIP; - if ( isset( $smwgIP ) ) { - $store = smwfGetStore(); - foreach ( $groupings as $pair ) { - list( $property_page, $grouping_label ) = $pair; - $wiki_page = SMWDataValueFactory::newTypeIDValue( '_wpg', $page_title ); - $options = new SMWRequestOptions(); - $options->sort = "subject_title"; - // get actual property from the wiki-page of the property - $property = SMWPropertyValue::makeProperty( $property_page->getTitle()->getText() ); - $res = $store->getPropertySubjects( $property, $wiki_page, $options ); - $num = count( $res ); - if ( $num > 0 ) { - $grouping_label = str_replace( ' ', '_', $grouping_label ); - $text .= "<$grouping_label>\n"; - foreach ( $res as $subject ) { - $subject_title = $subject->getTitle(); - $text .= getXMLForPage( $subject_title, $simplified_format, $groupings, $depth + 1 ); - } - $text .= "\n"; - } - } - } - - $text .= "\n"; - // escape back the curly brackets that were escaped out at the beginning - $text = str_replace( '&#123;', '{', $text ); - $text = str_replace( '&#125;', '}', $text ); - return $text; -} - -function doSpecialViewXML() { - global $wgOut, $wgRequest, $wgUser, $wgContLang; - $skin = $wgUser->getSkin(); - $namespace_labels = $wgContLang->getNamespaces(); - $category_label = $namespace_labels[NS_CATEGORY]; - $template_label = $namespace_labels[NS_TEMPLATE]; - $name_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_name' ) ); - $namespace_str = str_replace( ' ', '_', wfMsg( 'dt_xml_namespace' ) ); - $pages_str = str_replace( ' ', '_', wfMsgForContent( 'dt_xml_pages' ) ); - - $form_submitted = false; - $page_titles = array(); - $cats = $wgRequest->getArray( 'categories' ); - $nses = $wgRequest->getArray( 'namespaces' ); - if ( count( $cats ) > 0 || count( $nses ) > 0 ) { - $form_submitted = true; - } - - if ( $form_submitted ) { - $wgOut->disable(); - - // Cancel output buffering and gzipping if set - // This should provide safer streaming for pages with history - wfResetOutputBuffers(); - header( "Content-type: application/xml; charset=utf-8" ); - - $groupings = getGroupings(); - $simplified_format = $wgRequest->getVal( 'simplified_format' ); - $text = "<$pages_str>"; - if ( $cats ) { - foreach ( $cats as $cat => $val ) { - if ( $simplified_format ) - $text .= '<' . str_replace( ' ', '_', $cat ) . ">\n"; - else - $text .= "<$category_label $name_str=\"$cat\">\n"; - $titles = getPagesForCategory( $cat, 10 ); - foreach ( $titles as $title ) { - $text .= getXMLForPage( $title, $simplified_format, $groupings ); - } - if ( $simplified_format ) - $text .= '\n"; - else - $text .= "\n"; - } - } - - if ( $nses ) { - foreach ( $nses as $ns => $val ) { - if ( $ns == 0 ) { - $ns_name = "Main"; - } else { - $ns_name = MWNamespace::getCanonicalName( $ns ); - } - if ( $simplified_format ) - $text .= '<' . str_replace( ' ', '_', $ns_name ) . ">\n"; - else - $text .= "<$namespace_str $name_str=\"$ns_name\">\n"; - $titles = getPagesForNamespace( $ns ); - foreach ( $titles as $title ) { - $text .= getXMLForPage( $title, $simplified_format, $groupings ); - } - if ( $simplified_format ) - $text .= '\n"; - else - $text .= "\n"; - } - } - $text .= ""; - print $text; - } else { - // set 'title' as hidden field, in case there's no URL niceness - global $wgContLang; - $mw_namespace_labels = $wgContLang->getNamespaces(); - $special_namespace = $mw_namespace_labels[NS_SPECIAL]; - $text = << - - -END; - $text .= "

    " . wfMsg( 'dt_viewxml_docu' ) . "

    \n"; - $text .= "

    " . wfMsg( 'dt_viewxml_categories' ) . "

    \n"; - $categories = getCategoriesList(); - foreach ( $categories as $category ) { - $title = Title::makeTitle( NS_CATEGORY, $category ); - $link = $skin->makeLinkObj( $title, $title->getText() ); - $text .= " $link
    \n"; - } - $text .= "

    " . wfMsg( 'dt_viewxml_namespaces' ) . "

    \n"; - $namespaces = getNamespacesList(); - foreach ( $namespaces as $namespace ) { - if ( $namespace == 0 ) { - $ns_name = wfMsgHtml( 'blanknamespace' ); - } else { - $ns_name = htmlspecialchars( $wgContLang->getFormattedNsText( $namespace ) ); - } - $ns_name = str_replace( '_', ' ', $ns_name ); - $text .= " $ns_name
    \n"; - } - $text .= "

    " . wfMsg( 'dt_viewxml_simplifiedformat' ) . "

    \n"; - $text .= "\n"; - $text .= "\n"; - - $wgOut->addHTML( $text ); - } -} diff --git a/preecej/semantic_wiki/forms/Annotation.wiki b/preecej/semantic_wiki/forms/Annotation.wiki deleted file mode 100644 index b9c677d..0000000 --- a/preecej/semantic_wiki/forms/Annotation.wiki +++ /dev/null @@ -1,206 +0,0 @@ - -This is the "Annotation" form. -To create a page with this form, enter the page name below; -if a page with that name already exists, you will be sent to a form to edit that page. -{{#forminput:form=Annotation}} - - -{{{info|page name=Annotation:}}} -__NOTOC__ -{{#ifexist: {{PAGENAME}} - |'''{{#show:{{PAGENAME}}|?has_Gene_Symbol}} (''{{#show:{{PAGENAME}}|?has_Species_Name}}'')''' - | -}} - - -= Annotation = - -{{{for template|Annotation}}} - -{| class="formtable" -! Species Name: -| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] - [[Is Associated With Field Or Object::Species Name]] - [[Is Associated With Category::Annotations]] - |?is_Provenance - }} - | {{{field|Species Name|autocomplete on property=Has Reference Taxon|restricted}}} - | {{{field|Species Name|autocomplete on property=Has Reference Taxon}}} - }} -|- -! Gene Symbol: -| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] - [[Is Associated With Field Or Object::Gene Symbol]] - [[Is Associated With Category::Annotations]] - |?is_Provenance - }} - |{{{field|Gene Symbol|restricted}}} - |{{{field|Gene Symbol}}} - }} -|- -! Gene Name: -| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] - [[Is Associated With Field Or Object::Gene Name]] - [[Is Associated With Category::Annotations]] - |?is_Provenance - }} - | {{{field|Gene Name|restricted}}} - | {{{field|Gene Name}}} - }} -|- -! Gene Synonyms: -| {{#ifexist: {{PAGENAME}} - | {{#if: {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]] }} - | {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]] - | ?is_Gene_Synonym - | headers=hide - | mainlabel=- - | format=list - }} {{#formlink:form=Gene_Synonyms|link text=Edit|link type=button|target={{PAGENAME}}/Gene_Synonyms }} - | {{#formlink:form=Gene_Synonyms|link text=Add Synonyms|link type=button|query string=Gene_Synonyms[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} - }} - | To add gene synonyms, first save your basic annotation information on this "Annotation" tab. -}} -|- -! Gene Locus: -| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] - [[Is Associated With Field Or Object::Gene Locus]] - [[Is Associated With Category::Annotations]] - |?is_Provenance - }} - | {{{field|Gene Locus|restricted}}} - | {{{field|Gene Locus}}} - }} -|- -! Gene Type: -| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] - [[Is Associated With Field Or Object::Gene Type]] - [[Is Associated With Category::Annotations]] - |?is_Provenance - }} - | {{{field|Gene Type|restricted}}} - | {{{field|Gene Type}}} - }} -|- -! EC Number(s): -| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] - [[Is Associated With Field Or Object::EC Numbers]] - [[Is Associated With Category::Annotations]] - |?is_Provenance - }} - | {{{field|EC Numbers|restricted|list|delimiter=,}}} - | {{{field|EC Numbers|list|delimiter=,}}} - }} -|- -! Chromosome: -| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] - [[Is Associated With Field Or Object::Chromosome]] - [[Is Associated With Category::Annotations]] - |?is_Provenance - }} - |{{{field|Chromosome|restricted}}} - |{{{field|Chromosome}}} - }} -|- -! Has Phenotype: -| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] - [[Is Associated With Field Or Object::Has Phenotype]] - [[Is Associated With Category::Annotations]] - |?is_Provenance - }} - | {{{field|Has Phenotype|restricted}}} - | {{{field|Has Phenotype}}} - }} -|- -! Description: -| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]] - [[Is Associated With Field Or Object::Annotation Description]] - [[Is Associated With Category::Annotations]] - |?is_Provenance - }} - | {{{field|Annotation Description|restricted}}} - | {{{field|Annotation Description}}} - }} -|} - -{{{end template}}} - -= External References = - -{{#ifexist: {{PAGENAME}} - | {{#if: {{#ask:[[Category:External_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} - | Add, edit, or remove external reference data {{#formlink:form=External_References|link text=here|target={{PAGENAME}}/External_References }}. - {{#ask:[[Is External Reference::~{{PAGENAME}}/External_References* ]] - | mainlabel=- - |? from_External_Source - |? has_External_Accession_ID - }} - | Add external references for this annotation.
    {{#formlink:form=External_References|link text=Add|link type=button|query string=External_References[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} - }} - | To add external references, first save your basic annotation information on the "Annotation" tab. -}} - -= Ontologies = - -{{#ifexist: {{PAGENAME}} - | {{#if: {{#ask:[[Category:Ontological_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} - | Add, edit, or remove ontology references {{#formlink:form=Ontological_References|link text=here|target={{PAGENAME}}/Ontologies }}. - {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies*]] - | mainlabel=- - |? from_Ontology - |? has_Term_ID - |? has_Term_Name - |? has_Aspect - |? has_Evidence_Code - |? has_Evidence - }} - | Add ontological associations for this annotation.
    {{#formlink:form=Ontological_References|link text=Add|link type=button|query string=Ontological_References[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} - }} - | To add ontological references, first save your basic annotation information on the "Annotation" tab. -}} - -= Sequences = - -{{#ifexist: {{PAGENAME}} - | {{#if: {{#ask:[[Category:Sequences]][[Is Associated With Annotation::{{PAGENAME}} ]] }} - | Add, edit, or remove sequence references {{#formlink:form=Sequences|link text=here|target={{PAGENAME}}/Sequences }}. - {{#ask:[[Is Sequence Reference::~{{PAGENAME}}/Sequences*]] - | mainlabel=- - |? has_Sequence_Type - |? has_Sequence_Source - |? has_External_Accession_ID - }} - | Add sequence references for this annotation.
    {{#formlink:form=Sequences|link text=Add|link type=button|query string=Sequences[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} - }} - | To add sequence references, first save your basic annotation information on the "Annotation" tab. -}} - -= Literature = - -{{#ifexist: {{PAGENAME}} - | Add a reference to a publication listed with PubMed or the DOI registry {{#formlink:form=Reference_Publication|link text=here|link type=|query string=Reference_Publication[New Annotation Reference]={{PAGENAME}} }}.
    - -Need to add a reference to a publication without a PubMed ID or DOI (Digital Object Identifier)?
    -{{#formlink:form=Publication|link text=Add a new publication reference|link type=|query string=Publication[New Annotation Reference]={{PAGENAME}} }} - - {{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] }} - | {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] - |? has First Author - |? has Publication Title - |? has Journal Name - |? has Publication ID - }} - | - }} - | To add publication references, first save your basic annotation information on the "Annotation" tab. -}} - - -{{{standard input|summary}}} - -{{{standard input|watch}}} - -{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} - -     - diff --git a/preecej/semantic_wiki/forms/External_References.wiki b/preecej/semantic_wiki/forms/External_References.wiki deleted file mode 100644 index 4796ba6..0000000 --- a/preecej/semantic_wiki/forms/External_References.wiki +++ /dev/null @@ -1,31 +0,0 @@ - -This is the "External References" form. -To create a page with this form, enter the page name below; -if a page with that name already exists, you will be sent to a form to edit that page. - - -{{#forminput:form=External References}} - - - -{{{info|page name=External_References}}} - -{{{for template|External References}}} -{| class="formtable" -! Annotation Page: -| {{{field|Annotation Page}}} -|} -{{{end template}}} - -{{{for template|External Reference Repeater|multiple}}} -'''Source:''' {{{field|External Source}}} -'''Accession ID:''' {{{field|External Accession ID}}} -{{{end template}}} - -{{{standard input|summary}}} - -{{{standard input|watch}}} - -{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} - - diff --git a/preecej/semantic_wiki/forms/Gene_Synonyms.wiki b/preecej/semantic_wiki/forms/Gene_Synonyms.wiki deleted file mode 100644 index 16add14..0000000 --- a/preecej/semantic_wiki/forms/Gene_Synonyms.wiki +++ /dev/null @@ -1,70 +0,0 @@ - -This is the "Gene Synonyms" form. -To create a page with this form, enter the page name below; -if a page with that name already exists, you will be sent to a form to edit that page. - -{{#forminput:form=Gene Synonyms}} - - - -{{{info|page name=Gene_Synonyms}}} - -{{{for template|Gene Synonyms}}} -{| class="formtable" -! Annotation Page: -| {{{field|Annotation Page}}} -|} -{{{end template}}} - -{{{for template|Gene Synonym Repeater|multiple}}} - - - -'''Gene Synonym:''' {{{field|Gene Synonym}}} - - - -{{{end template}}} - -{{{standard input|summary}}} - -{{{standard input|watch}}} - -{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} - - diff --git a/preecej/semantic_wiki/forms/Ontological_References.wiki b/preecej/semantic_wiki/forms/Ontological_References.wiki deleted file mode 100644 index eef09a0..0000000 --- a/preecej/semantic_wiki/forms/Ontological_References.wiki +++ /dev/null @@ -1,54 +0,0 @@ - -This is the "Ontological References" form. -To create a page with this form, enter the page name below; -if a page with that name already exists, you will be sent to a form to edit that page. - - -{{#forminput:form=Ontological References}} - - - -{{{info|page name=Ontologies}}} -__NOTOC__ - -{{{for template|Ontological References}}} -{| class="formtable" -! Annotation Page: -| {{{field|Annotation Page}}} -|} -{{{end template}}} - -=== Plant Ontology === -{{{for template|Plant Ontology Reference Repeater|multiple}}} -'''Term Name:''' {{{field|Term Name|autocomplete from url=remote_PO_terms}}} '''or''' '''Term ID:''' {{{field|Term ID|autocomplete from url=remote_PO_ids}}} -

    '''Evidence Code:'''
    -{{{field|Evidence Code|list}}} -

    '''Evidence:''' {{{field|Evidence|}}} -{{{end template}}} - -=== Gene Ontology === -{{{for template|Gene Ontology Reference Repeater|multiple}}} -'''Term Name:''' {{{field|Term Name|autocomplete from url=remote_GO_terms}}} '''or''' '''Term ID:''' {{{field|Term ID|autocomplete from url=remote_GO_ids}}} -

    '''Evidence Code:'''
    -{{{field|Evidence Code|list}}} -

    '''Evidence:''' {{{field|Evidence|}}} -{{{end template}}} - -=== Other Ontologies === -{{{for template|Ontological Reference Repeater|multiple}}} -'''Ontology:''' {{{field|Ontology|}}} -'''Term Name:''' {{{field|Term Name|}}} -'''Term ID:''' {{{field|Term ID|}}} -'''Branch:''' {{{field|Aspect|}}} -

    '''Evidence Code:'''
    -{{{field|Evidence Code|list}}} -

    '''Evidence:''' {{{field|Evidence|}}} -{{{end template}}} - -{{{standard input|summary}}} - -{{{standard input|watch}}} - -{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} -     - diff --git a/preecej/semantic_wiki/forms/Provenance.wiki b/preecej/semantic_wiki/forms/Provenance.wiki deleted file mode 100644 index 6baec4b..0000000 --- a/preecej/semantic_wiki/forms/Provenance.wiki +++ /dev/null @@ -1,32 +0,0 @@ - -This is the "Provenance" form. -To create a page with this form, enter the page name below; -if a page with that name already exists, you will be sent to a form to edit that page. - -{{#forminput:form=Provenance}} - - - -{{{info|page name=Provenance}}} - -{{{for template|Provenance}}} -{| class="formtable" -! Annotation Page: -| {{{field|Annotation Page}}} -|} -{{{end template}}} - -{{{for template|Provenance Repeater|multiple}}} -'''Field or Object:''' {{{field|Source Field or Object}}} -'''Category:''' {{{field|Source Category}}} -'''Accession ID:''' {{{field|Source Accession ID}}} -'''Source:''' {{{field|Source}}} -{{{end template}}} - -{{{standard input|summary}}} - -{{{standard input|watch}}} - -{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} - - diff --git a/preecej/semantic_wiki/forms/Publication.wiki b/preecej/semantic_wiki/forms/Publication.wiki deleted file mode 100644 index b86c6e8..0000000 --- a/preecej/semantic_wiki/forms/Publication.wiki +++ /dev/null @@ -1,55 +0,0 @@ - -This is the "Publication" form. -To create a page with this form, enter the page name below; -if a page with that name already exists, you will be sent to a form to edit that page. - - -{{#forminput:form=Publication}} - - - -{{{info|page name=Publication:}}} -{{{for template|Publication}}} - -{{#set:Annotation References={{{Annotation References|}}}, {{{New Annotation Reference|}}} }} - -{| class="formtable" -! Publication: -| {{{field|Publication}}} -|- -! Publication ID: -| {{{field|Publication ID}}} -|- -! Publication Title: -| {{{field|Publication Title}}} -|- -! First Author: -| {{{field|First Author}}} -|- -! Journal Name: -| {{{field|Journal Name}}} -|- -! Volume: -| {{{field|Volume}}} -|- -! Year: -| {{{field|Year}}} -|- -! Pages: -| {{{field|Pages}}} -|- -! Annotation References: -| {{{field|Annotation References}}} -|- -! New Annotation Reference (to be hidden): -| {{{field|New Annotation Reference}}} -|} -{{{end template}}} - -{{{standard input|summary}}} - -{{{standard input|watch}}} - -{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} - - diff --git a/preecej/semantic_wiki/forms/Reference_Publication.wiki b/preecej/semantic_wiki/forms/Reference_Publication.wiki deleted file mode 100644 index f358e5f..0000000 --- a/preecej/semantic_wiki/forms/Reference_Publication.wiki +++ /dev/null @@ -1,52 +0,0 @@ - -This is the "Reference Publication" form. -To create a page with this form, enter the page name below; -if a page with that name already exists, you will be sent to a form to edit that page. - - -{{#forminput:form=Reference Publication}} - - - -{{{info|page name=Publication:}}} -{{{for template|Reference Publication}}} -{| class="formtable" -! Publication: -| {{{field|Publication}}} -|- -! Publication ID: -| {{{field|Publication ID}}} -|- -! Publication Title: -| {{{field|Publication Title|hidden}}} -|- -! First Author: -| {{{field|First Author|hidden}}} -|- -! Journal Name: -| {{{field|Journal Name|hidden}}} -|- -! Volume: -| {{{field|Volume|hidden}}} -|- -! Year: -| {{{field|Year|hidden}}} -|- -! Pages: -| {{{field|Pages|hidden}}} -|- -! Annotation References: -| {{{field|Annotation References}}} -|- -! New Annotation Reference (to be hidden): -| {{{field|New Annotation Reference}}} -|} -{{{end template}}} - -{{{standard input|summary}}} - -{{{standard input|watch}}} - -{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} - - diff --git a/preecej/semantic_wiki/forms/Sequences.wiki b/preecej/semantic_wiki/forms/Sequences.wiki deleted file mode 100644 index e2127df..0000000 --- a/preecej/semantic_wiki/forms/Sequences.wiki +++ /dev/null @@ -1,32 +0,0 @@ - -This is the "Sequences" form. -To create a page with this form, enter the page name below; -if a page with that name already exists, you will be sent to a form to edit that page. - - -{{#forminput:form=Sequences}} - - - -{{{info|page name=Sequences}}} - -{{{for template|Sequences}}} -{| class="formtable" -! Annotation Page: -| {{{field|Annotation Page}}} -|} -{{{end template}}} - -{{{for template|Sequence Repeater|multiple}}} -'''Sequence Type:''' {{{field|Sequence Type}}} -'''Sequence Source:''' {{{field|Sequence Source}}} -'''Accession ID:''' {{{field|External Accession ID}}} -{{{end template}}} - -{{{standard input|summary}}} - -{{{standard input|watch}}} - -{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} - - diff --git a/preecej/semantic_wiki/forms/Source.wiki b/preecej/semantic_wiki/forms/Source.wiki deleted file mode 100644 index 62f26d6..0000000 --- a/preecej/semantic_wiki/forms/Source.wiki +++ /dev/null @@ -1,38 +0,0 @@ - -This is the "Source" form. -To create a page with this form, enter the page name below; -if a page with that name already exists, you will be sent to a form to edit that page. - - -{{#forminput:form=Source}} - - - -{{{info|page name=Source:}}} - -{{{for template|Source}}} -{| class="formtable" -! Source Date Stamp: -| {{{field|Source Date Stamp}}} -|- -! Source Database: -| {{{field|Source Database}}} -|- -! Source Version: -| {{{field|Source Version}}} -|- -! Source URI: -| {{{field|Source URI}}} -|- -! Source File: -| {{{field|Source File}}} -|} -{{{end template}}} - -{{{standard input|summary}}} - -{{{standard input|watch}}} - -{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} - - diff --git a/preecej/semantic_wiki/local_settings/dev.LocalSettings.php b/preecej/semantic_wiki/local_settings/dev.LocalSettings.php deleted file mode 100644 index 3b264e1..0000000 --- a/preecej/semantic_wiki/local_settings/dev.LocalSettings.php +++ /dev/null @@ -1,173 +0,0 @@ -&format=json&max=20'; -$sfgAutocompletionURLs['remote_PO_ids'] = 'http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=acc&ontology=po&qval=&format=json&max=20'; - -# GO web service calls -$sfgAutocompletionURLs['remote_GO_terms'] = 'http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&ontology=go&qval=&format=json&max=25'; -$sfgAutocompletionURLs['remote_GO_ids'] = 'http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=acc&ontology=go&qval=&format=json&max=25'; - -$sfgAutocompleteOnAllChars = false; - -# END: Justin Preece - Semantic Bundle (SMW and other extensions) - -/** Allow client-side caching of pages */ -$wgCachePages = false; - -/** - * * Set this to current time to invalidate all prior cached pages. Affects both - * * client- and server-side caching. - * * You can get the current date on your server by using the command: - * * date +%Y%m%d%H%M%S - * */ -$wgCacheEpoch = 'date +%Y%m%d%H%M%S'; - - -# When you make changes to this configuration file, this will make -# sure that cached pages are cleared. -$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) ); diff --git a/preecej/semantic_wiki/local_settings/proto.LocalSettings.php b/preecej/semantic_wiki/local_settings/proto.LocalSettings.php deleted file mode 100644 index 15b7902..0000000 --- a/preecej/semantic_wiki/local_settings/proto.LocalSettings.php +++ /dev/null @@ -1,175 +0,0 @@ -&format=json&max=20'; -$sfgAutocompleteOnAllChars = false; - -# END 02/22/11: Justin Preece - Semantic Bundle (SMW and other extensions) - -/** Allow client-side caching of pages */ -$wgCachePages = false; - -/** - * * Set this to current time to invalidate all prior cached pages. Affects both - * * client- and server-side caching. - * * You can get the current date on your server by using the command: - * * date +%Y%m%d%H%M%S - * */ -$wgCacheEpoch = 'date +%Y%m%d%H%M%S'; - - -# When you make changes to this configuration file, this will make -# sure that cached pages are cleared. -$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) ); diff --git a/preecej/semantic_wiki/local_settings/test.LocalSettings.php b/preecej/semantic_wiki/local_settings/test.LocalSettings.php deleted file mode 100644 index 5bf519d..0000000 --- a/preecej/semantic_wiki/local_settings/test.LocalSettings.php +++ /dev/null @@ -1,170 +0,0 @@ -&format=json&max=20'; -$sfgAutocompletionURLs['remote_PO_ids'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=acc&ontology=po&qval=&format=json&max=20'; - -# GO web service calls -$sfgAutocompletionURLs['remote_GO_terms'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&ontology=go&qval=&format=json&max=25'; -$sfgAutocompletionURLs['remote_GO_ids'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=acc&ontology=go&qval=&format=json&max=25'; - -$sfgAutocompleteOnAllChars = false; - -# END: Justin Preece - Semantic Bundle (SMW and other extensions) - -/** Allow client-side caching of pages */ -$wgCachePages = false; - -/** - * * Set this to current time to invalidate all prior cached pages. Affects both - * * client- and server-side caching. - * * You can get the current date on your server by using the command: - * * date +%Y%m%d%H%M%S - * */ -$wgCacheEpoch = 'date +%Y%m%d%H%M%S'; - -# When you make changes to this configuration file, this will make -# sure that cached pages are cleared. -$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) ); diff --git a/preecej/semantic_wiki/local_settings/test.SemanticBundleSettings.php b/preecej/semantic_wiki/local_settings/test.SemanticBundleSettings.php deleted file mode 100644 index 966e4d2..0000000 --- a/preecej/semantic_wiki/local_settings/test.SemanticBundleSettings.php +++ /dev/null @@ -1,93 +0,0 @@ - - -=cut - -# TODO: file size check and clip -# TODO: file numbering - -# --------------------------------------------------------------------------- -# modules -# --------------------------------------------------------------------------- - -# general -use strict; -use Cwd; -use Switch; -use Getopt::Std; -use Data::Dumper; - -# specific -use XML::Smart; -use XML::Writer; -use IO::File; -use Encode; - -# --------------------------------------------------------------------------- -# declarations -# --------------------------------------------------------------------------- - -my %opts; # arg options -my $file_type; # tab, csv, gaf -my $file_del; # data delimeter -my $input_file; -my $output_file; -my $verbose = 0; # flag for verbose output -my $debug = 0; # debugging switch - -# global data storage ---------- - -# universal -my %source; -my $output_data; - -# tab, csv -my $template_name; -my @field_names; -my @field_data; -my $xml; # represents the xml doc - -# gaf -my %ontology_info; # holds ontology names and aspects, keyed by abbreviation -my $curr_ontology_type; # flag to track the proper ontology to reference, line by line -my %annotation_universals; # holds values assumed not to vary across the file -my %annotations; # keyed on Gene Symbol - -# other config constants (including temporary arrangements) - -# default page id seeds, until I can figure out how to auto-increment w/in the -# an import/update script -my $SOURCE_TITLE_SEED = 1; -my $ANNOT_TITLE_SEED = 1; -my $PUB_TITLE_SEED = 1; - -$Data::Dumper::Pad = "... "; - -# --------------------------------------------------------------------------- -# functions -# --------------------------------------------------------------------------- - - -# --------------------------------------------------------------------------- -sub init -{ - # read and set options - getopts('i:t:o:s:vd', \%opts); - - foreach my $key (keys %opts) { - my $value = $opts{$key}; - switch ($key) { - case "i" { - if ($value =~ /\//) { # assume path - $input_file = $value; - } else { - $input_file = getcwd() . "\/$value"; - } - } - case "t" { $file_type = $value; } - - case "o" { - if ($value =~ /\//) { # assume path - $output_file = $value; - } else { - $output_file = getcwd() . "\/$value"; - } - } - case "s" { - my @seeds = split(',',$value); - if (scalar @seeds == 3) { - $SOURCE_TITLE_SEED = $seeds[0]; - $ANNOT_TITLE_SEED = $seeds[1]; - $PUB_TITLE_SEED = $seeds[2]; - } else { - die("Please supply three consecutive, comma-delimited seed" - . "values for the 's' option."); - } - } - case "v" { $verbose = 1; } - - case "d" { $debug = 1; } - } - } - - # split data on either commas or tabs - switch ($file_type) { - case "csv" { $file_del = ','; } - case "tab" { $file_del = '\t'; } - case "gaf" { $file_del = '\t'; } - else { - die(uc($file_type) . " is not a valid file type. Please supply " - . "a tab, csv, or gaf file.\n"); - } - } - - system "clear"; - print "\n" - . "------------------------------------------------------------\n" - . "-- Planteome Annotation Wiki Import Transformation Script --\n" - . "------------------------------------------------------------\n" - . "\n" - . "Input File: $input_file\n" - . "Designated input file type: $file_type\n" - . "Output File (Template): $output_file\n" - . "Source ID Seed: $SOURCE_TITLE_SEED\n" - . "Annotations ID Seed: $ANNOT_TITLE_SEED\n" - . "Publications ID Seed: $PUB_TITLE_SEED\n" - . "Running in verbose mode? " . ($verbose ? "Yes" : "No") . "\n" - . "Running in debug mode? " . ($debug ? "Yes" : "No") . "\n" - . "\n" - . "------------------------------------------------------------\n" - . "------------------------------------------------------------\n" - . "------------------------------------------------------------\n" - . "\n"; -} - - -# read, parse, and store generic CSV and tab templates and annotations -# --------------------------------------------------------------------------- -sub import_generic -{ - # read in "[Format] section... - my $line; - my $count = 0; - - while () - { - $count++; - $line = $_; - chomp $line; - my $data_val = (split('=',$line))[1]; - switch ($count) { - case 2 { $template_name = $data_val; } - case 3 { @field_names = split($file_del,$data_val); } - else {;} - } - if ($count == 3) { last; } - } - - # loop through data rows and add all data fields to an array of hashes - while () - { - $line = $_; - chomp $line; - - my @tmp_data_ary = split($file_del, $line); - my %tmp_hash; - - if ($debug) { print join(',',@tmp_data_ary) . "\n"; } - - for (my $i=0; $i { - name => "Gene Ontology", - aspects => { - P => "Biological Process", - C => "Cellular Component", - F => "Molecular Function" - } - }, - PO => { - name => "Plant Ontology", - aspects => { - A => "Plant Anatomy", - G => "Plant Growth and Development Stage" - } - } - ); - - if ($debug) { print "...\n" - . Dumper(\%ontology_info) . "\n\n"; } -} - -# read, parse, and store GAF annotations -# --------------------------------------------------------------------------- -sub import_gaf -{ - #[GAF implied data structure] - # singletons: db/Source (not really, but OK for now), taxon/Species ID, - # assigned_by, gene_type/Gene Type (later: proteins, too) - # lower priority: db_object_id, date - # not needed: qualifier - # unvaried fields (gene-level): db_object_symbol/Gene Symbol, - # db_object_name/Gene Name, - # db_object_synonym/Gene Locus|Source Accession ID|Chromosome|Gene Synonyms (see below), - # varied fields (gene synonyms): db_object_synonym/Gene Synonym - # varied fields (ontology-level): term_id/Term ID, evidence_code/Evidence Code, - # aspect/Aspect, db_reference (multi-, get PMID from here), with_or_from (multi-) - - # [Annotation Object Structure] - # %annotation_universals - # "Source" - # "Species ID" - # "Gene Type" - # %annotations - # "$Gene Symbol" => %annotation_properties - # "Gene Name" => string - # "Gene Locus"/"Source Accession ID" (first uc("AT.G")) => string - # "Chromosome" (AT#G in "Gene Locus") => string - # "Gene Synonyms" => % strings - # "Ontological References" => % "$Term ID" => %annotation_ontology_ref - # "Aspect" => string (assumes only one) - # "Evidence Codes" => % strings - # "Evidence" => % strings ("with_or_from" ) - # "Publications" => % PMID's from "db:reference", used to create separate Pub pages - - # set up a hash of ontology types and aspects to be referenced during data import - initialize_ontology(); - - # loop through data rows and build hashed annotation data structure - my $count = 0; - - # regex for locating a useable accession id from a locus (species-specific) - my $locus_finder_expr; - - while () - { - $count++; - my $line = $_; - chomp $line; - - my @curr_line_ary = split("\t", $line); - if ($debug) { print "...\n" - . Dumper(\@curr_line_ary) . "\n\n"; } - - my %curr_line_hash = ( - "db" => $curr_line_ary[0], # Source - "db_object_symbol" => $curr_line_ary[2], # Gene Symbol - "term_id" => $curr_line_ary[4], # Term ID - "db_reference" => $curr_line_ary[5], # inc. Publication info (PMID) - "evidence_code" => $curr_line_ary[6], # Evidence Code - "with_or_from" => $curr_line_ary[7], # Evidence (data) - "aspect" => $curr_line_ary[8], # Aspect - "db_object_name" => $curr_line_ary[9], # Gene Name - - # Gene Locus, Source Accession ID, Chromosome, Gene Synonyms - "db_object_synonym" => $curr_line_ary[10], - "db_object_type" => $curr_line_ary[11], # Gene Type - "taxon" => $curr_line_ary[12] # Species ID - ); - - if ($debug) { print "...\n" - . Dumper(\%curr_line_hash) . "\n\n"; } - - # grab the unvaried values from the first line - if ($count == 1) { - %annotation_universals = ( - "Source" => $curr_line_hash{"db"}, # currently not in use - "Gene Type" => $curr_line_hash{"db_object_type"}, - "Species ID" => "NCBI:" . (split(':',$curr_line_hash{"taxon"}))[1]#, - #"Species Name" => $species_name # TODO: get this from NCBI - ); - - # set species-specific values - switch ($annotation_universals{"Species ID"}) { - case "NCBI:3702" { - $locus_finder_expr = "^([Aa][Tt].[Gg])"; - $annotation_universals{"Species Name"} = "Arabidopsis thaliana"; # temp; need an NCBI lookup - } - case "NCBI:4530" { - $locus_finder_expr = "^(LOC_|[Oo][Ss]|osa-)"; - $annotation_universals{"Species Name"} = "Oryza sativa"; # temp; need an NCBI lookup - } - else { - die($annotation_universals{"Species ID"} - . " is not a valid NCBI taxon ID.\n"); - } - } - - if ($debug) { print "...\n" - . Dumper(\%annotation_universals) . "\n\n"; } - - } - - # set the ontology for the current line - $curr_ontology_type = uc((split(':',$curr_line_hash{"term_id"}))[0]); - - # check to see if Gene Symbol hash key exists (for grouping) - # if not, add the new Gene Symbol and its associated props - if (!exists $annotations{$curr_line_hash{"db_object_symbol"}}) - { - - # print "\n*** NEW SYMBOL: $curr_line_hash{'db_object_symbol'} ***\n"; # TEST - - # prepare Gene Locus, Source Accession ID, Chromosome, Gene Synonyms - my @loci; - my $locus = ""; - - if (exists $curr_line_hash{"db_object_synonym"}) - { - my @synonyms = split('\|',$curr_line_hash{"db_object_synonym"}); - - if ($debug) { print "...\n" - . Dumper(\@synonyms) . "\n\n"; } - - # find the gene locus, if it is listed - @loci = grep /$locus_finder_expr/, @synonyms; - - if ($debug) { print "...\n" - . Dumper(\@loci) . "\n\n"; } - } - - if (scalar(@loci) > 0) # we have at least one match; use the first one - { - $locus = $loci[0]; - } - else # no match; attempt to use the Gene Symbol instead - { - if ($curr_line_hash{"db_object_symbol"} =~ $locus_finder_expr) - { - # the split drops the variant/allele signifier, if present - if (!(split('.',$curr_line_hash{"db_object_symbol"}))[0]) - { - $locus = $curr_line_hash{"db_object_symbol"}; - } - else - { - $locus = (split('.',$curr_line_hash{"db_object_symbol"}))[0]; - } - } - else # no match; attempt to use the Gene Name instead - { - if ($curr_line_hash{"db_object_name"} =~ $locus_finder_expr) - { - $locus = (split('.',$curr_line_hash{"db_object_name"}))[0]; - } - } - } - - my $chromosome = ""; - if ($locus) { - if ($annotation_universals{"Species ID"} eq "NCBI:3702") { - # for Ath, third char in locus, if it exists - $chromosome = ($locus ne "" ? (split('',$locus))[2] : ""); - } - } - - # set some sort of pseudo-unique value as the accession id, - # in order of succession: locus, then symbol - # (NOTE: this is dangerous; a stable identifier is preferred) - my $accession_id = - $locus ? $locus : $curr_line_hash{"db_object_symbol"}; - - # set up props - my $annotation_properties = { - "Accession ID" => $accession_id, - "Gene Name" => $curr_line_hash{"db_object_name"}, - "Gene Locus" => $locus, - "Chromosome" => $chromosome - }; - - # add synonyms - for (split('\|', $curr_line_hash{"db_object_synonym"})) { - $$annotation_properties{"Gene Synonyms"}{$_} = ""; } - - if ($debug) { print "...\n" - . Dumper($annotation_properties) . "\n\n"; } - - # add new gene annotation and assign props - $annotations{$curr_line_hash{"db_object_symbol"}} = $annotation_properties; - - add_ontology_ref_data(\%curr_line_hash, $curr_ontology_type); # add the first ontology reference (every time) - } - # that Gene Symbol does exist, so we just need to roll-up multi-line - # annotation information, like gene synonyms and ontology refs - else - { - #print "\n*** EXISTING SYMBOL: $curr_line_hash{'db_object_symbol'} ***\n"; # TEST - - # add any add'l synonyms - for (split('\|', $curr_line_hash{"db_object_synonym"})) { - $annotations{$curr_line_hash{"db_object_symbol"}} - {"Gene Synonyms"}{$_} = ""; } - - add_ontology_ref_data(\%curr_line_hash, $curr_ontology_type); # add add'l ontology reference data - } - } - if ($debug) { print "...\n" - . Dumper(\%annotations) . "\n\n"; } -} - - -# read, parse, and store source -# --------------------------------------------------------------------------- -sub import_data -{ - print "Opening input file and reading header info...\n\n"; - - # open file - open(INPUT_FILE,$input_file) or die("Could not open input file."); - - # read in the source data - my $count = 0; - my $line; - while () - { - $count++; - $line = $_; - chomp $line; - my $data_val = (split('=',$line))[1]; - switch ($count) { - case 2 { $source{'SourceDateStamp'} = $data_val; } - case 3 { $source{'SourceDatabase'} = $data_val; } - case 4 { $source{'SourceVersion'} = $data_val; } - case 5 { $source{'SourceURI'} = $data_val; } - case 6 { $source{'SourceFile'} = $data_val; } - else {;} - } - if ($count == 6) { last; } - } - - print "Reading data...\n\n"; - $line = ; # skip "[Data]" - - switch ($file_type) { - case ('csv' || 'tab') { import_generic(); } - case 'gaf' { import_gaf(); } - } - - close INPUT_FILE; -} - - -# spit out the data to make sure you've read in the files correctly -# --------------------------------------------------------------------------- -sub show_input -{ - print "\n[Source]\n"; - foreach my $key (keys %source) { - print "$key: $source{$key}\n"; - } - print "\n"; - - switch ($file_type) { - case ('csv' || 'tab') { - print "[Template]\n$template_name\n\n"; - print "[Fields]\n" . join(', ',@field_names) . "\n\n"; - - print "[Data]\n"; - foreach my $row (@field_data) { - foreach my $key (keys %$row) { - print "$key => " . $row->{$key} . "\n"; - } - print "\n"; - } - } - case 'gaf' { - print "[Data]\n"; - - for my $key (keys %annotation_universals) { - print "$key: " . $annotation_universals{$key} . "\n"; - } - print "\n"; - - print "[Annotations]\n" . Dumper(\%annotations) . "\n\n"; - } - } - print "\n"; -} - -# xml transformation for generic tab or CSV-templated data -# (currently uses XML::Smart) -# --------------------------------------------------------------------------- -sub transform_generic -{ - my $curr_node; # placeholder for general node cursor - my $curr_prov_node; # placeholder for node cursor in provenance pages - my $curr_annot_node; # placeholder for node cursor in annotation pages - my $curr_accession_id; # holds each rows accession id for provenance marking - - - $xml = new XML::Smart($output_data, 'XML::Smart::Parser'); - - # set root element, source page and elements - # (temp set of page title until moved to import extension) - $xml->{Pages}{Page} = {Title => "Source:$SOURCE_TITLE_SEED"}; - - $curr_node = $xml->{Pages}{Page}; - $curr_node->{Template} = {Name => 'Source'}; - $curr_node = $curr_node->{Template}; - - $curr_node->{Field}[0] = {Name => 'Source Date Stamp'}; - $curr_node->{Field}[0]->content(0,$source{'SourceDateStamp'}); - $curr_node->{Field}[1] = {Name => 'Source Database'}; - $curr_node->{Field}[1]->content(0,$source{'SourceDatabase'}); - $curr_node->{Field}[2] = {Name => 'Source Version'}; - $curr_node->{Field}[2]->content(0,$source{'SourceVersion'}); - $curr_node->{Field}[3] = {Name => 'Source URI'}; - $curr_node->{Field}[3]->content(0,$source{'SourceURI'}); - $curr_node->{Field}[4] = {Name => 'Source File'}; - $curr_node->{Field}[4]->content(0,$source{'SourceFile'}); - - $curr_node = $curr_node->back->back; # return to node - - if ($debug) { print "Current node: " . $curr_node->path . "\n"; } - - my $next_page_title_id = $ANNOT_TITLE_SEED; - - # iterate through the data - foreach my $row (@field_data) { - - # set up next annotation page - my $next_page = { Title => "Annotation:$next_page_title_id" }; - push(@{$curr_node->{Page}}, $next_page); - - $curr_annot_node = $curr_node->{Page}( - "Title","eq","Annotation:$next_page_title_id"); - - if ($debug) { print "Curr annot node: ".$curr_annot_node->path."\n";} - - $curr_annot_node->{Template} = {Name => "$template_name"}; - $curr_annot_node = $curr_annot_node->{Template}; - - # set up next provenance page - $next_page = { Title => "Annotation:$next_page_title_id/Provenance" }; - push(@{$curr_node->{Page}}, $next_page); - - $curr_prov_node = $curr_node->{Page}( - "Title","eq","Annotation:$next_page_title_id/Provenance"); - - if ($debug) {print "Curr prov node: " . $curr_prov_node->path . "\n"; } - - $curr_prov_node->{Template} = {Name => 'Provenance'}; - $curr_prov_node = $curr_prov_node->{Template}; - $curr_prov_node->{Field} = {Name => 'Annotation Page'}; - $curr_prov_node->{Field}->content(0,"Annotation:$next_page_title_id"); - $curr_prov_node = $curr_prov_node->back; - - my $field_ct = 0; # counter for field position in pages - - # grab the Accession ID for the current row of data - foreach my $key (keys %$row) { - if ($key eq "Accession ID") { - $curr_accession_id = $row->{$key}; - if ($debug) { - print "* Found Accession ID: $curr_accession_id *\n"; - } - } - } - if (!(defined $curr_accession_id)) { - die "Error: No Accession ID available. Ending program.\n"; - } - - # iterate through the annotation data and assign to elements - foreach my $key (keys %$row) { - if ($debug) { print "$key => " . $row->{$key} . "\n"; } - - # build the annotation page - $curr_annot_node->{Field}[$field_ct] = {Name => $key}; - $curr_annot_node->{Field}[$field_ct]->content(0,$row->{$key}); - $field_ct++; - - # add a corresponding template to the annotation provenance page - my $next_prov_node = {Name => 'Provenance_Repeater'}; - push(@{$curr_prov_node->{Template}}, $next_prov_node); - - # grab the last template you added - $curr_prov_node = @{$curr_prov_node->{Template}}[-1]; - - # assign the relevant provenance field data - $curr_prov_node->{Field}[0] = {Name => 'Source'}; - $curr_prov_node->{Field}[0]->content(0,"Source:$SOURCE_TITLE_SEED"); - $curr_prov_node->{Field}[1] = {Name => 'Source Accession ID'}; - $curr_prov_node->{Field}[1]->content(0,$curr_accession_id); - $curr_prov_node->{Field}[2] = {Name => 'Source Template'}; - $curr_prov_node->{Field}[2]->content(0,$template_name); - $curr_prov_node->{Field}[3] = {Name => 'Source Field'}; - $curr_prov_node->{Field}[3]->content(0,$key); - - $curr_prov_node = $curr_prov_node->back; - } - $next_page_title_id++; - } - - # write out xml doc to a single ImportXML file - print "Writing data to output file...\n\n"; - $xml->save($output_file); - $output_data = $xml->data; -} - -# xml transformation for GAF data -# (currently uses XML::DOM) -# --------------------------------------------------------------------------- -sub transform_gaf -{ - # define templates and their fields for Provenance-generation - my $template_field_map = { - Annotation => [ - 'Species Name', - 'Species ID', - 'Gene Symbol', - 'Gene Name', - 'Gene Locus', - 'Gene Type', - 'Chromosome', - 'Has Phenotype' - ] - }; - - my %ref_pubs; # list of non-duplicate publication references - - # create new xml doc, write to string - my $writer = new XML::Writer( - OUTPUT => \$output_data, - DATA_MODE => 1, - DATA_INDENT => 4, - ENCODING => 'utf-8' - ); - - # create root elements - $writer->xmlDecl; - $writer->startTag("Pages"); - - # create source page - $writer->startTag("Page",Title=>"Source:$SOURCE_TITLE_SEED"); - $writer->startTag("Template",Name=>"Source"); - - # iterate the source hash for element name attribs and vals - my @pretty_elements; - foreach my $element (keys %source) - { - # split on CamelCase (saves a few lines and was fun to write) - for ($element) { - @pretty_elements = /[A-Z](?:[A-Z]+|[a-z]*)(?=$|[A-Z])/g; - } - $writer->dataElement("Field", $source{$element}, Name=>"@pretty_elements"); - } - - $writer->endTag("Template"); - $writer->endTag("Page"); - - # iterate %annotations - my $annot_title_count = $ANNOT_TITLE_SEED; - - foreach my $annotation (keys %annotations) - { - # create annotation page - $writer->startTag("Page",Title=>"Annotation:$annot_title_count"); - $writer->startTag("Template",Name=>"Annotation"); - $writer->dataElement("Field", $annotation_universals{"Species Name"}, Name=>"Species Name"); - $writer->dataElement("Field", $annotation_universals{"Species ID"}, Name=>"Species ID"); - $writer->dataElement("Field", $annotation, Name=>"Gene Symbol"); - $writer->dataElement("Field", $annotations{$annotation}{"Gene Name"}, Name=>"Gene Name"); - $writer->dataElement("Field", $annotations{$annotation}{"Gene Locus"}, Name=>"Gene Locus"); - $writer->dataElement("Field", ucfirst($annotation_universals{"Gene Type"}), Name=>"Gene Type"); - $writer->dataElement("Field", $annotations{$annotation}{"Chromosome"}, Name=>"Chromosome"); - $writer->dataElement("Field", "No", Name=>"Has Phenotype"); - $writer->endTag("Template"); - $writer->endTag("Page"); - - # create gene synonyms page - if (scalar keys (%{$annotations{$annotation}{'Gene Synonyms'}}) > 0) - { - $writer->startTag("Page",Title=>"Annotation:$annot_title_count/Gene Synonyms"); - $writer->startTag("Template",Name=>"Gene_Synonyms"); - $writer->dataElement("Field", "Annotation:$annot_title_count", Name=>"Annotation Page"); - $writer->endTag("Template"); - - foreach my $synonym (keys %{$annotations{$annotation}{'Gene Synonyms'}}) - { - $writer->startTag("Template",Name=>"Gene_Synonym_Repeater"); - $writer->dataElement("Field", $synonym, Name=>"Gene Synonym"); - $writer->endTag("Template"); - } - $writer->endTag("Page"); - } - - # create ont refs page - if (scalar keys (%{$annotations{$annotation}{"Ontological References"}}) > 0) - { - $writer->startTag("Page",Title=>"Annotation:$annot_title_count/Ontologies"); - $writer->startTag("Template",Name=>"Ontological_References"); - $writer->dataElement("Field", "Annotation:$annot_title_count", Name=>"Annotation Page"); - $writer->endTag("Template"); - - foreach my $ont_term (keys %{$annotations{$annotation}{"Ontological References"}}) - { - # gather PMID's for separate Ref Publication page creation (avoid dupes) - if (scalar keys (%{$annotations{$annotation}{"Ontological References"}{$ont_term}{"Publications"}}) > 0) { - foreach my $pub_term (keys %{$annotations{$annotation}{"Ontological References"}{$ont_term}{"Publications"}}) - { - if (!exists $ref_pubs{$pub_term}) { - $ref_pubs{$pub_term} = { "Annotation:$annot_title_count" => "" }; - } - else - { - $ref_pubs{$pub_term}{"Annotation:$annot_title_count"} = ""; - } - } - } - - $writer->startTag("Template",Name=>"$ontology_info{$curr_ontology_type}{name} Reference Repeater"); - $writer->dataElement("Field", $ontology_info{$curr_ontology_type}{"name"}, Name=>"Ontology"); - $writer->dataElement("Field", $ont_term, Name=>"Term ID"); - $writer->dataElement("Field", $annotations{$annotation}{"Ontological References"}{$ont_term}{"Aspect"}, Name=>"Aspect"); - - my @evidence_codes; - foreach my $evidence_code (keys %{$annotations{$annotation}{"Ontological References"}{$ont_term}{"Evidence Codes"}}) { - push @evidence_codes, $evidence_code; - } - $writer->dataElement("Field", join(', ',@evidence_codes), Name=>"Evidence Code"); - - my @ary_evidence; - foreach my $evidence (keys %{$annotations{$annotation}{"Ontological References"}{$ont_term}{"Evidence"}}) { - push @ary_evidence, $evidence; - } - $writer->dataElement("Field", join(', ',@ary_evidence), Name=>"Evidence"); - - $writer->endTag("Template"); - } - $writer->endTag("Page"); - } - - # create provenance page - $writer->startTag("Page",Title=>"Annotation:$annot_title_count/Provenance"); - $writer->startTag("Template",Name=>"Provenance"); - $writer->dataElement("Field", "Annotation:$annot_title_count", Name=>"Annotation Page"); - $writer->endTag("Template"); - - # items on the Annotation page - foreach (@{@$template_field_map{"Annotation"}}) - { - $writer->startTag("Template",Name=>"Provenance_Repeater"); - $writer->dataElement("Field", $_, Name=>"Source Field or Object"); - $writer->dataElement("Field", "Annotations", Name=>"Source Category"); - $writer->dataElement("Field", $annotations{$annotation}{"Accession ID"}, Name=>"Source Accession ID"); - $writer->dataElement("Field", "Source:$SOURCE_TITLE_SEED", Name=>"Source"); - $writer->endTag("Template"); - } - - # items on the Gene Synonyms subpage - if (scalar keys (%{$annotations{$annotation}{'Gene Synonyms'}}) > 0) - { - foreach my $synonym (keys %{$annotations{$annotation}{'Gene Synonyms'}}) - { - $writer->startTag("Template",Name=>"Provenance_Repeater"); - $writer->dataElement("Field", $synonym, Name=>"Source Field or Object"); - $writer->dataElement("Field", "Gene Synonyms", Name=>"Source Category"); - $writer->dataElement("Field", $annotations{$annotation}{"Accession ID"}, Name=>"Source Accession ID"); - $writer->dataElement("Field", "Source:$SOURCE_TITLE_SEED", Name=>"Source"); - $writer->endTag("Template"); - } - } - - # items on the Ontologies subpage - if (scalar keys (%{$annotations{$annotation}{"Ontological References"}}) > 0) - { - foreach my $ont_term (keys %{$annotations{$annotation}{"Ontological References"}}) - { - $writer->startTag("Template",Name=>"Provenance_Repeater"); - $writer->dataElement("Field", $ont_term, Name=>"Source Field or Object"); - $writer->dataElement("Field", "Ontological References", Name=>"Source Category"); - $writer->dataElement("Field", $annotations{$annotation}{"Accession ID"}, Name=>"Source Accession ID"); - $writer->dataElement("Field", "Source:$SOURCE_TITLE_SEED", Name=>"Source"); - $writer->endTag("Template"); - } - } - - - $writer->endTag("Page"); - - $annot_title_count++; - } - - if ($debug) { print "...\n" - . Dumper(\%ref_pubs) . "\n\n"; } - - # create Reference Publication pages - my $pub_title_count = $PUB_TITLE_SEED; - - if (scalar keys (%ref_pubs) > 0) { - - foreach my $ref_pub (keys %ref_pubs) - { - $writer->startTag("Page",Title=>"Publication:$pub_title_count"); - $writer->startTag("Template",Name=>"Reference_Publication"); - $writer->dataElement("Field", "PubMed", Name=>"Publication"); # TODO: replace hard-coded pub type w/ something dynamic - $writer->dataElement("Field", $ref_pub, Name=>"Publication ID"); - my @annot_refs; # holds com-del string of annotation page references - foreach my $annot_ref (keys %{$ref_pubs{$ref_pub}}) - { - push @annot_refs, $annot_ref; - } - $writer->dataElement("Field", join(',',@annot_refs), Name=>"Annotation References"); - $writer->endTag("Template"); - $writer->endTag("Page"); - - $pub_title_count++; - } - } - - # close doc - $writer->endTag("Pages"); - $writer->end(); - - # write out the file - open(OUTPUT_FILE,">$output_file"); - print OUTPUT_FILE $output_data; - close OUTPUT_FILE; -} - - -# loop through the hash and build annotation data and source xml doc -# --------------------------------------------------------------------------- -sub write_xml -{ - print "Transforming " . uc($file_type) . " data to SMW/SF XML...\n\n"; - - switch ($file_type) { - case ('csv' || 'tab') { transform_generic(); } - case 'gaf' { transform_gaf(); } - } -} - - -# print the transformed data (as xml) -# --------------------------------------------------------------------------- -sub show_output -{ - print "[XML]\n"; - print $output_data; - print "\n"; -} - -# --------------------------------------------------------------------------- -# main -# --------------------------------------------------------------------------- - -init; -import_data; -if ($verbose) { show_input; } -write_xml(); -if ($verbose) { show_output; } - -exit; - diff --git a/preecej/semantic_wiki/prototyping/NCBI_eDocSummary.php b/preecej/semantic_wiki/prototyping/NCBI_eDocSummary.php deleted file mode 100644 index 7e38a66..0000000 --- a/preecej/semantic_wiki/prototyping/NCBI_eDocSummary.php +++ /dev/null @@ -1,49 +0,0 @@ -"); // inst. new xml doc for output - -// build xml doc with NCBI data -$DocSum = $xml_out->addChild("DocSum"); -$DocSum->addChild("Id",$NCBI_doc->DocSum->Id); - -foreach ($NCBI_doc->xpath("//Item") as $item) { - switch((string) $item["Name"]) { // Get attributes as element indices - case "PubDate": - $DocSum->addChild("PubDate",$item); - break; - case "Author": - $authorList[] = $item; - break; - case "LastAuthor": - $DocSum->addChild("LastAuthor",$item); - break; - case "Title": - $DocSum->addChild("Title",$item); - break; - case "Volume": - $DocSum->addChild("Volume",$item); - break; - case "Pages": - $DocSum->addChild("Pages",$item); - break; - case "FullJournalName": - $DocSum->addChild("FullJournalName",$item); - break; - } -} - -$author_list = ""; -foreach ($authorList as $author) { - $author_list = $author_list . $author . ", "; -} -$DocSum->addChild("AuthorList",rtrim($author_list,", ")); - - -header('Content-Type: text/xml'); // output xml doctype in your response -echo $xml_out->asXML(); -?> - diff --git a/preecej/semantic_wiki/prototyping/TermSearch_JSON.php b/preecej/semantic_wiki/prototyping/TermSearch_JSON.php deleted file mode 100644 index 89c1033..0000000 --- a/preecej/semantic_wiki/prototyping/TermSearch_JSON.php +++ /dev/null @@ -1,106 +0,0 @@ - 50) { $number_of_terms = 50; } - - $qval = $_GET['qval']; - - $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0 - ? strtolower($_GET['qval']) - : die('Please provide a searchable value'); - - $format = strtolower($_GET['format']) != 'json' - ? strtolower($_GET['format']) - : 'json'; //json is the default - - /* connect to the db */ - $link = mysql_connect($_SERVER['mysql_host'], $_SERVER['mysql_user'], $_SERVER['mysql_pw']) or die('Cannot connect to the DB'); - mysql_select_db($_SERVER['mysql_db'],$link) or die('Cannot select the DB'); - - switch ($type) { - case 'autocomplete': - /* grab the terms from the db */ - $query = "SELECT t.$field FROM term t" - . " LEFT JOIN term_definition d ON d.term_id = t.id" - . " WHERE t.$field LIKE '%$qval%'" - . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')" - . " AND t.is_obsolete = 0" - . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" - . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" - . " ORDER BY name LIMIT $number_of_terms"; - $result = mysql_query($query,$link) or die('Errant query: '.$query); - - /* create one master array of the records */ - $terms = array(); - if(mysql_num_rows($result)) { - while($term = mysql_fetch_assoc($result)) { - $terms[] = array('title'=>$term[$field]); - } - } - - /* output in necessary format */ - if($format == 'json') { - header('Content-type: application/json'); - echo json_encode(array('sfautocomplete'=>$terms)); - } - else { - die('Sorry, this request cannot be fulfilled in '.$format.' format.'); - } - break; - - case 'term_detail': - /* grab the ontology data from the db */ - $query = "SELECT DISTINCT t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'" - . " FROM term t" - . " LEFT JOIN term_definition d ON d.term_id = t.id" - . " WHERE t.name = '$qval'" - . " AND t.term_type in ('plant_anatomy','plant_growth_and_development_stage')" - . " AND t.is_obsolete = 0" - . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" - . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" - . " ORDER BY t.name LIMIT 1"; - $result = mysql_query($query,$link) or die('Errant query: '.$query); - - /* create one master array of the records */ - $terms = array(); - if(mysql_num_rows($result)) { - while($term = mysql_fetch_assoc($result)) { - $terms[] = array( - 'id'=>$term['acc'], - 'aspect'=>$term['type'] == "plant_anatomy" ? "Plant Anatomy" : "Plant Growth and Development Stage", - 'definition'=>$term['definition'], - 'comment'=>$term['comment']); - } - } - /* output in necessary format */ - if($format == 'json') { - header('Content-type: application/json'); - echo json_encode(array('PO_result'=>$terms)); - } - else { - die('Sorry, this request cannot be fulfilled in '.$format.' format.'); - } - break; - default: - die('Sorry, this web service method is not available.'); - } - /* disconnect from the db */ - @mysql_close($link); -} -else { die('Not authorized.'); } -?> - diff --git a/preecej/semantic_wiki/prototyping/remote_autocomplete.php b/preecej/semantic_wiki/prototyping/remote_autocomplete.php deleted file mode 100755 index a0f1f3e..0000000 --- a/preecej/semantic_wiki/prototyping/remote_autocomplete.php +++ /dev/null @@ -1,7 +0,0 @@ - - diff --git a/preecej/semantic_wiki/prototyping/sample_species.xml b/preecej/semantic_wiki/prototyping/sample_species.xml deleted file mode 100644 index 62badaa..0000000 --- a/preecej/semantic_wiki/prototyping/sample_species.xml +++ /dev/null @@ -1,7 +0,0 @@ - - - - - - - diff --git a/preecej/semantic_wiki/prototyping/simple_forms_ajax.php b/preecej/semantic_wiki/prototyping/simple_forms_ajax.php deleted file mode 100644 index 3c8fcd3..0000000 --- a/preecej/semantic_wiki/prototyping/simple_forms_ajax.php +++ /dev/null @@ -1 +0,0 @@ - diff --git a/preecej/semantic_wiki/services/NCBI_eDocSummary.php b/preecej/semantic_wiki/services/NCBI_eDocSummary.php deleted file mode 100644 index 7e38a66..0000000 --- a/preecej/semantic_wiki/services/NCBI_eDocSummary.php +++ /dev/null @@ -1,49 +0,0 @@ -"); // inst. new xml doc for output - -// build xml doc with NCBI data -$DocSum = $xml_out->addChild("DocSum"); -$DocSum->addChild("Id",$NCBI_doc->DocSum->Id); - -foreach ($NCBI_doc->xpath("//Item") as $item) { - switch((string) $item["Name"]) { // Get attributes as element indices - case "PubDate": - $DocSum->addChild("PubDate",$item); - break; - case "Author": - $authorList[] = $item; - break; - case "LastAuthor": - $DocSum->addChild("LastAuthor",$item); - break; - case "Title": - $DocSum->addChild("Title",$item); - break; - case "Volume": - $DocSum->addChild("Volume",$item); - break; - case "Pages": - $DocSum->addChild("Pages",$item); - break; - case "FullJournalName": - $DocSum->addChild("FullJournalName",$item); - break; - } -} - -$author_list = ""; -foreach ($authorList as $author) { - $author_list = $author_list . $author . ", "; -} -$DocSum->addChild("AuthorList",rtrim($author_list,", ")); - - -header('Content-Type: text/xml'); // output xml doctype in your response -echo $xml_out->asXML(); -?> - diff --git a/preecej/semantic_wiki/services/dev.TermSearch_JSON.php b/preecej/semantic_wiki/services/dev.TermSearch_JSON.php deleted file mode 100644 index cffbdaf..0000000 --- a/preecej/semantic_wiki/services/dev.TermSearch_JSON.php +++ /dev/null @@ -1,140 +0,0 @@ - 50) { $number_of_terms = 50; } - - $ont = isset($_GET['ontology']) && in_array(strtolower($_GET['ontology']),$arr_ontologies) - ? strtolower($_GET['ontology']) - : die('"ontology" is a required parameter and must match an available data field.'); - - $qval = $_GET['qval']; - - $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0 - ? strtolower($_GET['qval']) - : die('Please provide a searchable value'); - - $format = strtolower($_GET['format']) != 'json' - ? strtolower($_GET['format']) - : 'json'; //json is the default - - /* connect to the appropriate db */ - switch ($ont) { - case 'po': - $link = mysql_connect($_SERVER['dev_po_host'], $_SERVER['dev_po_user'], $_SERVER['dev_po_pw']) or die('Cannot connect to the DB'); - mysql_select_db($_SERVER['dev_po_db'],$link) or die('Cannot select the DB'); - - $term_types = "'plant_anatomy','plant_growth_and_development_stage'"; - break; - - case 'go': - $link = mysql_connect($_SERVER['dev_go_host'], $_SERVER['dev_go_user'], $_SERVER['dev_go_pw']) or die('Cannot connect to the DB'); - mysql_select_db($_SERVER['dev_go_db'],$link) or die('Cannot select the DB'); - - $term_types = "'biological_process','cellular_component','molecular_function'"; - break; - - default: - die('Sorry, this ontology type is not available.'); - } - - switch ($type) { - case 'autocomplete': - /* grab the terms from the db */ - $query = "SELECT t.$field FROM term t" - . " LEFT JOIN term_definition d ON d.term_id = t.id" - . " WHERE t.$field LIKE '%$qval%'" - . " AND t.term_type in ($term_types)" - . " AND t.is_obsolete = 0" - . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" - . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" - . " ORDER BY name LIMIT $number_of_terms"; - $result = mysql_query($query,$link) or die('Errant query: '.$query); - - /* create one master array of the records */ - $terms = array(); - if(mysql_num_rows($result)) { - while($term = mysql_fetch_assoc($result)) { - $terms[] = array('title'=>$term[$field]); - } - } - - /* output in necessary format */ - if($format == 'json') { - header('Content-type: application/json'); - echo json_encode(array('sfautocomplete'=>$terms)); - } - else { - die('Sorry, this request cannot be fulfilled in '.$format.' format.'); - } - break; - - case 'term_detail': - /* grab the ontology data from the db */ - $query = "SELECT DISTINCT t.name as 'name', t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'" - . " FROM term t" - . " LEFT JOIN term_definition d ON d.term_id = t.id" - . " WHERE t.$field = '$qval'" - . " AND t.term_type in ($term_types)" - . " AND t.is_obsolete = 0" - . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" - . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" - . " ORDER BY t.name LIMIT 1"; - $result = mysql_query($query,$link) or die('Errant query: '.$query); - - /* create one master array of the records */ - $terms = array(); - if(mysql_num_rows($result)) { - while($term = mysql_fetch_assoc($result)) { - switch($term['type']) { - case 'plant_anatomy': - $term_type_formal = "Plant Anatomy"; break; - case 'plant_growth_and_development_stage': - $term_type_formal = "Plant Growth and Development Stage"; break; - case 'biological_process': - $term_type_formal = "Biological Process"; break; - case 'cellular_component': - $term_type_formal = "Cellular Component"; break; - case 'molecular_function': - $term_type_formal = "Molecular Function"; break; - } - $terms[] = array( - 'name'=>$term['name'], - 'id'=>$term['acc'], - 'aspect'=>$term_type_formal, - 'definition'=>$term['definition'], - 'comment'=>$term['comment']); - } - } - /* output in necessary format */ - if($format == 'json') { - header('Content-type: application/json'); - echo json_encode(array('term_detail_result'=>$terms)); - } - else { - die('Sorry, this request cannot be fulfilled in '.$format.' format.'); - } - break; - default: - die('Sorry, this web service method is not available.'); - } - /* disconnect from the db */ - @mysql_close($link); -} -else { die('Not authorized.'); } -?> - diff --git a/preecej/semantic_wiki/services/test.TermSearch_JSON.php b/preecej/semantic_wiki/services/test.TermSearch_JSON.php deleted file mode 100644 index f60dcc5..0000000 --- a/preecej/semantic_wiki/services/test.TermSearch_JSON.php +++ /dev/null @@ -1,140 +0,0 @@ - 50) { $number_of_terms = 50; } - - $ont = isset($_GET['ontology']) && in_array(strtolower($_GET['ontology']),$arr_ontologies) - ? strtolower($_GET['ontology']) - : die('"ontology" is a required parameter and must match an available data field.'); - - $qval = $_GET['qval']; - - $qval = isset($_GET['qval']) && strlen($_GET['qval']) > 0 - ? strtolower($_GET['qval']) - : die('Please provide a searchable value'); - - $format = strtolower($_GET['format']) != 'json' - ? strtolower($_GET['format']) - : 'json'; //json is the default - - /* connect to the appropriate db */ - switch ($ont) { - case 'po': - $link = mysql_connect($_SERVER['test_po_host'], $_SERVER['test_po_user'], $_SERVER['test_po_pw']) or die('Cannot connect to the DB'); - mysql_select_db($_SERVER['test_po_db'],$link) or die('Cannot select the DB'); - - $term_types = "'plant_anatomy','plant_growth_and_development_stage'"; - break; - - case 'go': - $link = mysql_connect($_SERVER['test_go_host'], $_SERVER['test_go_user'], $_SERVER['test_go_pw']) or die('Cannot connect to the DB'); - mysql_select_db($_SERVER['test_go_db'],$link) or die('Cannot select the DB'); - - $term_types = "'biological_process','cellular_component','molecular_function'"; - break; - - default: - die('Sorry, this ontology type is not available.'); - } - - switch ($type) { - case 'autocomplete': - /* grab the terms from the db */ - $query = "SELECT t.$field FROM term t" - . " LEFT JOIN term_definition d ON d.term_id = t.id" - . " WHERE t.$field LIKE '%$qval%'" - . " AND t.term_type in ($term_types)" - . " AND t.is_obsolete = 0" - . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" - . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" - . " ORDER BY name LIMIT $number_of_terms"; - $result = mysql_query($query,$link) or die('Errant query: '.$query); - - /* create one master array of the records */ - $terms = array(); - if(mysql_num_rows($result)) { - while($term = mysql_fetch_assoc($result)) { - $terms[] = array('title'=>$term[$field]); - } - } - - /* output in necessary format */ - if($format == 'json') { - header('Content-type: application/json'); - echo json_encode(array('sfautocomplete'=>$terms)); - } - else { - die('Sorry, this request cannot be fulfilled in '.$format.' format.'); - } - break; - - case 'term_detail': - /* grab the ontology data from the db */ - $query = "SELECT DISTINCT t.name as 'name', t.acc as 'acc', t.term_type as 'type', d.term_definition as 'definition', d.term_comment as 'comment'" - . " FROM term t" - . " LEFT JOIN term_definition d ON d.term_id = t.id" - . " WHERE t.$field = '$qval'" - . " AND t.term_type in ($term_types)" - . " AND t.is_obsolete = 0" - . " AND UCASE(t.name) NOT LIKE 'OBSOLETE%'" - . " AND UCASE(d.term_definition) NOT LIKE 'OBSOLETE%'" - . " ORDER BY t.name LIMIT 1"; - $result = mysql_query($query,$link) or die('Errant query: '.$query); - - /* create one master array of the records */ - $terms = array(); - if(mysql_num_rows($result)) { - while($term = mysql_fetch_assoc($result)) { - switch($term['type']) { - case 'plant_anatomy': - $term_type_formal = "Plant Anatomy"; break; - case 'plant_growth_and_development_stage': - $term_type_formal = "Plant Growth and Development Stage"; break; - case 'biological_process': - $term_type_formal = "Biological Process"; break; - case 'cellular_component': - $term_type_formal = "Cellular Component"; break; - case 'molecular_function': - $term_type_formal = "Molecular Function"; break; - } - $terms[] = array( - 'name'=>$term['name'], - 'id'=>$term['acc'], - 'aspect'=>$term_type_formal, - 'definition'=>$term['definition'], - 'comment'=>$term['comment']); - } - } - /* output in necessary format */ - if($format == 'json') { - header('Content-type: application/json'); - echo json_encode(array('term_detail_result'=>$terms)); - } - else { - die('Sorry, this request cannot be fulfilled in '.$format.' format.'); - } - break; - default: - die('Sorry, this web service method is not available.'); - } - /* disconnect from the db */ - @mysql_close($link); -} -else { die('Not authorized.'); } -?> - diff --git a/preecej/semantic_wiki/skins/Planteome.deps.php b/preecej/semantic_wiki/skins/Planteome.deps.php deleted file mode 100644 index 7a8c288..0000000 --- a/preecej/semantic_wiki/skins/Planteome.deps.php +++ /dev/null @@ -1,11 +0,0 @@ -addStyle( 'planteome/main-rtl.css', 'screen', '', 'rtl' ); - $out->addStyle( 'planteome/main-ltr.css', 'screen', '', 'ltr' ); - // Append CSS which includes IE only behavior fixes for hover support - - // this is better than including this in a CSS fille since it doesn't - // wait for the CSS file to load before fetching the HTC file. - $out->addScript( - '' - ); - // Add extra stylesheets - // THIS IS ONLY USEFUL FOR EXPERIMENTING WITH DIFFERNT STYLE OPTIONS! THIS WILL BE REMOVED IN THE NEAR FUTURE. - if ( is_array( $wgPlanteomeExtraStyles ) ) { - foreach ( $wgPlanteomeExtraStyles as $style ) { - $out->addStyle( 'planteome/' . $style, 'screen' ); - } - } - } - /** - * Builds a structured array of links used for tabs and menus - * @return array - * @private - */ - function buildNavigationUrls() { - global $wgContLang, $wgLang, $wgOut, $wgUser, $wgRequest, $wgArticle, $wgStylePath; - global $wgDisableLangConversion, $wgPlanteomeUseIconWatch; - - wfProfileIn( __METHOD__ ); - - $links = array( - 'namespaces' => array(), - 'views' => array(), - 'actions' => array(), - 'variants' => array() - ); - - // Detects parameters - $action = $wgRequest->getVal( 'action', 'view' ); - $section = $wgRequest->getVal( 'section' ); - - // Checks if page is some kind of content - if( $this->iscontent ) { - - // Gets page objects for the related namespaces - $subjectPage = $this->mTitle->getSubjectPage(); - $talkPage = $this->mTitle->getTalkPage(); - - // Determines if this is a talk page - $isTalk = $this->mTitle->isTalkPage(); - - // Generates XML IDs from namespace names - $subjectId = $this->mTitle->getNamespaceKey( '' ); - - if ( $subjectId == 'main' ) { - $talkId = 'talk'; - } else { - $talkId = "{$subjectId}_talk"; - } - $currentId = $isTalk ? $talkId : $subjectId; - - // Adds namespace links - $links['namespaces'][$subjectId] = $this->tabAction( - $subjectPage, 'vector-namespace-' . $subjectId, !$isTalk, '', true - ); - $links['namespaces'][$subjectId]['context'] = 'subject'; - $links['namespaces'][$talkId] = $this->tabAction( - $talkPage, 'vector-namespace-talk', $isTalk, '', true - ); - $links['namespaces'][$talkId]['context'] = 'talk'; - - // Adds view view link - if ( $this->mTitle->exists() ) { - $links['views']['view'] = $this->tabAction( - $isTalk ? $talkPage : $subjectPage, - 'vector-view-view', ( $action == 'view' ), '', true - ); - } - - wfProfileIn( __METHOD__ . '-edit' ); - - // Checks if user can... - if ( - // edit the current page - $this->mTitle->quickUserCan( 'edit' ) && - ( - // if it exists - $this->mTitle->exists() || - // or they can create one here - $this->mTitle->quickUserCan( 'create' ) - ) - ) { - // Builds CSS class for talk page links - $isTalkClass = $isTalk ? ' istalk' : ''; - - // Determines if we're in edit mode - $selected = ( - ( $action == 'edit' || $action == 'submit' ) && - ( $section != 'new' ) - ); - $links['views']['edit'] = array( - 'class' => ( $selected ? 'selected' : '' ) . $isTalkClass, - 'text' => $this->mTitle->exists() - ? wfMsg( 'vector-view-edit' ) - : wfMsg( 'vector-view-create' ), - 'href' => - $this->mTitle->getLocalUrl( $this->editUrlOptions() ) - ); - // Checks if this is a current rev of talk page and we should show a new - // section link - if ( ( $isTalk && $wgArticle->isCurrent() ) || ( $wgOut->showNewSectionLink() ) ) { - // Checks if we should ever show a new section link - if ( !$wgOut->forceHideNewSectionLink() ) { - // Adds new section link - //$links['actions']['addsection'] - $links['views']['addsection'] = array( - 'class' => 'collapsible ' . ( $section == 'new' ? 'selected' : false ), - 'text' => wfMsg( 'vector-action-addsection' ), - 'href' => $this->mTitle->getLocalUrl( - 'action=edit§ion=new' - ) - ); - } - } - // Checks if the page is known (some kind of viewable content) - } elseif ( $this->mTitle->isKnown() ) { - // Adds view source view link - $links['views']['viewsource'] = array( - 'class' => ( $action == 'edit' ) ? 'selected' : false, - 'text' => wfMsg( 'vector-view-viewsource' ), - 'href' => - $this->mTitle->getLocalUrl( $this->editUrlOptions() ) - ); - } - wfProfileOut( __METHOD__ . '-edit' ); - - wfProfileIn( __METHOD__ . '-live' ); - - // Checks if the page exists - if ( $this->mTitle->exists() ) { - // Adds history view link - $links['views']['history'] = array( - 'class' => 'collapsible ' . ( ($action == 'history') ? 'selected' : false ), - 'text' => wfMsg( 'vector-view-history' ), - 'href' => $this->mTitle->getLocalUrl( 'action=history' ), - 'rel' => 'archives', - ); - - if( $wgUser->isAllowed( 'delete' ) ) { - $links['actions']['delete'] = array( - 'class' => ($action == 'delete') ? 'selected' : false, - 'text' => wfMsg( 'vector-action-delete' ), - 'href' => $this->mTitle->getLocalUrl( 'action=delete' ) - ); - } - if ( $this->mTitle->quickUserCan( 'move' ) ) { - $moveTitle = SpecialPage::getTitleFor( - 'Movepage', $this->thispage - ); - $links['actions']['move'] = array( - 'class' => $this->mTitle->isSpecial( 'Movepage' ) ? - 'selected' : false, - 'text' => wfMsg( 'vector-action-move' ), - 'href' => $moveTitle->getLocalUrl() - ); - } - - if ( - $this->mTitle->getNamespace() !== NS_MEDIAWIKI && - $wgUser->isAllowed( 'protect' ) - ) { - if ( !$this->mTitle->isProtected() ){ - $links['actions']['protect'] = array( - 'class' => ($action == 'protect') ? - 'selected' : false, - 'text' => wfMsg( 'vector-action-protect' ), - 'href' => - $this->mTitle->getLocalUrl( 'action=protect' ) - ); - - } else { - $links['actions']['unprotect'] = array( - 'class' => ($action == 'unprotect') ? - 'selected' : false, - 'text' => wfMsg( 'vector-action-unprotect' ), - 'href' => - $this->mTitle->getLocalUrl( 'action=unprotect' ) - ); - } - } - } else { - // article doesn't exist or is deleted - if ( - $wgUser->isAllowed( 'deletedhistory' ) && - $wgUser->isAllowed( 'undelete' ) - ) { - if( $n = $this->mTitle->isDeleted() ) { - $undelTitle = SpecialPage::getTitleFor( 'Undelete' ); - $links['actions']['undelete'] = array( - 'class' => false, - 'text' => wfMsgExt( - 'vector-action-undelete', - array( 'parsemag' ), - $wgLang->formatNum( $n ) - ), - 'href' => $undelTitle->getLocalUrl( - 'target=' . urlencode( $this->thispage ) - ) - ); - } - } - - if ( - $this->mTitle->getNamespace() !== NS_MEDIAWIKI && - $wgUser->isAllowed( 'protect' ) - ) { - if ( !$this->mTitle->getRestrictions( 'create' ) ) { - $links['actions']['protect'] = array( - 'class' => ($action == 'protect') ? - 'selected' : false, - 'text' => wfMsg( 'vector-action-protect' ), - 'href' => - $this->mTitle->getLocalUrl( 'action=protect' ) - ); - - } else { - $links['actions']['unprotect'] = array( - 'class' => ($action == 'unprotect') ? - 'selected' : false, - 'text' => wfMsg( 'vector-action-unprotect' ), - 'href' => - $this->mTitle->getLocalUrl( 'action=unprotect' ) - ); - } - } - } - wfProfileOut( __METHOD__ . '-live' ); - /** - * The following actions use messages which, if made particular to - * the Planteome skin, would break the Ajax code which makes this - * action happen entirely inline. Skin::makeGlobalVariablesScript - * defines a set of messages in a javascript object - and these - * messages are assumed to be global for all skins. Without making - * a change to that procedure these messages will have to remain as - * the global versions. - */ - // Checks if the user is logged in - if ( $this->loggedin ) { - if ( $wgPlanteomeUseIconWatch ) { - $class = 'icon '; - $place = 'views'; - } else { - $class = ''; - $place = 'actions'; - } - $mode = $this->mTitle->userIsWatching() ? 'unwatch' : 'watch'; - $links[$place][$mode] = array( - 'class' => $class . ( ( $action == 'watch' || $action == 'unwatch' ) ? ' selected' : false ), - 'text' => wfMsg( $mode ), // uses 'watch' or 'unwatch' message - 'href' => $this->mTitle->getLocalUrl( 'action=' . $mode ) - ); - } - // This is instead of SkinTemplateTabs - which uses a flat array - wfRunHooks( 'SkinTemplateNavigation', array( &$this, &$links ) ); - - // If it's not content, it's got to be a special page - } else { - $links['namespaces']['special'] = array( - 'class' => 'selected', - 'text' => wfMsg( 'vector-namespace-special' ), - 'href' => $wgRequest->getRequestURL() - ); - } - - // Gets list of language variants - $variants = $wgContLang->getVariants(); - // Checks that language conversion is enabled and variants exist - if( !$wgDisableLangConversion && count( $variants ) > 1 ) { - // Gets preferred variant - $preferred = $wgContLang->getPreferredVariant(); - // Loops over each variant - foreach( $variants as $code ) { - // Gets variant name from language code - $varname = $wgContLang->getVariantname( $code ); - // Checks if the variant is marked as disabled - if( $varname == 'disable' ) { - // Skips this variant - continue; - } - // Appends variant link - $links['variants'][] = array( - 'class' => ( $code == $preferred ) ? 'selected' : false, - 'text' => $varname, - 'href' => $this->mTitle->getLocalURL( '', $code ) - ); - } - } - - wfProfileOut( __METHOD__ ); - - return $links; - } -} - -/** - * QuickTemplate class for Planteome skin - * @ingroup Skins - */ -class PlanteomeTemplate extends QuickTemplate { - - /* Members */ - - /** - * @var Cached skin object - */ - var $skin; - - /* Functions */ - - /** - * Outputs the entire contents of the XHTML page - */ - public function execute() { - global $wgRequest, $wgOut, $wgContLang; - - $this->skin = $this->data['skin']; - $action = $wgRequest->getText( 'action' ); - - // Build additional attributes for navigation urls - $nav = $this->skin->buildNavigationUrls(); - foreach ( $nav as $section => $links ) { - foreach ( $links as $key => $link ) { - $xmlID = $key; - if ( isset( $link['context'] ) && $link['context'] == 'subject' ) { - $xmlID = 'ca-nstab-' . $xmlID; - } else if ( isset( $link['context'] ) && $link['context'] == 'talk' ) { - $xmlID = 'ca-talk'; - } else { - $xmlID = 'ca-' . $xmlID; - } - $nav[$section][$key]['attributes'] = - ' id="' . Sanitizer::escapeId( $xmlID ) . '"'; - if ( $nav[$section][$key]['class'] ) { - $nav[$section][$key]['attributes'] .= - ' class="' . htmlspecialchars( $link['class'] ) . '"'; - unset( $nav[$section][$key]['class'] ); - } - // We don't want to give the watch tab an accesskey if the page - // is being edited, because that conflicts with the accesskey on - // the watch checkbox. We also don't want to give the edit tab - // an accesskey, because that's fairly superfluous and conflicts - // with an accesskey (Ctrl-E) often used for editing in Safari. - if ( - in_array( $action, array( 'edit', 'submit' ) ) && - in_array( $key, array( 'edit', 'watch', 'unwatch' ) ) - ) { - $nav[$section][$key]['key'] = - $this->skin->tooltip( $xmlID ); - } else { - $nav[$section][$key]['key'] = - $this->skin->tooltipAndAccesskey( $xmlID ); - } - } - } - $this->data['namespace_urls'] = $nav['namespaces']; - $this->data['view_urls'] = $nav['views']; - $this->data['action_urls'] = $nav['actions']; - $this->data['variant_urls'] = $nav['variants']; - // Build additional attributes for personal_urls - foreach ( $this->data['personal_urls'] as $key => $item) { - $this->data['personal_urls'][$key]['attributes'] = - ' id="' . Sanitizer::escapeId( "pt-$key" ) . '"'; - if ( isset( $item['active'] ) && $item['active'] ) { - $this->data['personal_urls'][$key]['attributes'] .= - ' class="active"'; - } - $this->data['personal_urls'][$key]['key'] = - $this->skin->tooltipAndAccesskey('pt-'.$key); - } - - // Generate additional footer links - $footerlinks = array( - 'info' => array( - 'lastmod', - 'viewcount', - 'numberofwatchingusers', - 'credits', - 'copyright', - 'tagline', - ), - 'places' => array( - 'privacy', - 'about', - 'disclaimer', - ), - ); - // Reduce footer links down to only those which are being used - $validFooterLinks = array(); - foreach( $footerlinks as $category => $links ) { - $validFooterLinks[$category] = array(); - foreach( $links as $link ) { - if( isset( $this->data[$link] ) && $this->data[$link] ) { - $validFooterLinks[$category][] = $link; - } - } - } - // Reverse horizontally rendered navigation elements - if ( $wgContLang->isRTL() ) { - $this->data['view_urls'] = - array_reverse( $this->data['view_urls'] ); - $this->data['namespace_urls'] = - array_reverse( $this->data['namespace_urls'] ); - $this->data['personal_urls'] = - array_reverse( $this->data['personal_urls'] ); - } - // Output HTML Page - $this->html( 'headelement' ); -?> -
    -
    - -
    html('specialpageattributes') ?>> - - - data['sitenotice'] ): ?> - -
    html( 'sitenotice' ) ?>
    - - - -

    html( 'title' ) ?>

    - - -
    - -

    msg( 'tagline' ) ?>

    - - -
    html('userlangattributes') ?>>html( 'subtitle' ) ?>
    - - data['undelete'] ): ?> - -
    html( 'undelete' ) ?>
    - - - data['newtalk'] ): ?> - -
    html( 'newtalk' ) ?>
    - - - data['showjumplinks'] ): ?> - - - - - - html( 'bodytext' ) ?> - - data['catlinks'] ): ?> - - html( 'catlinks' ); ?> - - - data['dataAfterContent'] ): ?> - - html( 'dataAfterContent' ); ?> - - -
    -
    - -
    - - -
    - renderNavigation( 'PERSONAL' ); ?> -
    - renderNavigation( array( 'NAMESPACES', 'VARIANTS' ) ); ?> -
    -
    - renderNavigation( array( 'VIEWS', 'ACTIONS', 'SEARCH' ) ); ?> -
    -
    - - -
    - - - - renderPortals( $this->data['sidebar'] ); ?> -
    - - - - - - - - html( 'bottomscripts' ); /* JS call to runBodyOnloadHook */ ?> - html( 'reporttime' ) ?> - data['debug'] ): ?> - - - - - $content ) { - echo "\n\n"; - switch( $name ) { - case 'SEARCH': - break; - case 'TOOLBOX': -?> -
    - html('userlangattributes') ?>>msg( 'toolbox' ) ?>

    -
    - -
    - -data['language_urls'] ) { -?> -
    - html('userlangattributes') ?>>msg( 'otherlanguages' ) ?> -
    -
      - data['language_urls'] as $langlink ): ?> -
      • - -
    -
    -
    - -
    skin->tooltip( 'p-' . $name ) ?>> - html('userlangattributes') ?>> -
    - - - - - -
    -
    -\n"; - } - } - - /** - * Render one or more navigations elements by name, automatically reveresed - * when UI is in RTL mode - */ - private function renderNavigation( $elements ) { - global $wgContLang, $wgPlanteomeUseSimpleSearch, $wgStylePath; - - // If only one element was given, wrap it in an array, allowing more - // flexible arguments - if ( !is_array( $elements ) ) { - $elements = array( $elements ); - // If there's a series of elements, reverse them when in RTL mode - } else if ( $wgContLang->isRTL() ) { - $elements = array_reverse( $elements ); - } - // Render elements - foreach ( $elements as $name => $element ) { - echo "\n\n"; - switch ( $element ) { - case 'NAMESPACES': -?> -
    -
    msg('namespaces') ?>
    - html('userlangattributes') ?>> - data['namespace_urls'] as $key => $link ): ?> -
  • >>
    • - - -
    - -
    -
    msg('variants') ?>
    -
    - html('userlangattributes') ?>> - data['variant_urls'] as $key => $link ): ?> - >> - - -
    -
    - -
    -
    msg('views') ?>
    - html('userlangattributes') ?>> - data['view_urls'] as $key => $link ): ?> - >>' : ''.htmlspecialchars( $link['text'] ).'') ?> - - -
    - -
    -
    msg('actions') ?>
    -
    - html('userlangattributes') ?>> - data['action_urls'] as $key => $link ): ?> - >> - - -
    -
    - -
    -
    msg('personaltools') ?>
    - html('userlangattributes') ?>> - data['personal_urls'] as $key => $item): ?> -
  • > class="">
    • - - -
    - - -\n"; - } - } -} diff --git a/preecej/semantic_wiki/skins/planteome/Makefile b/preecej/semantic_wiki/skins/planteome/Makefile deleted file mode 100644 index 74e36c4..0000000 --- a/preecej/semantic_wiki/skins/planteome/Makefile +++ /dev/null @@ -1,18 +0,0 @@ -# -# Handy makefile to build the RTL variant with cssjanus -# - -all: main-rtl.css - -main-rtl.css: main-ltr.css cssjanus/cssjanus.py - python cssjanus/cssjanus.py --swap_ltr_rtl_in_url < main-ltr.css > main-rtl.css - -# SVN version is broken; checking in our own. -#cssjanus/cssjanus.py: -# svn co http://cssjanus.googlecode.com/svn/trunk cssjanus - -#distclean: clean -# rm -rf cssjanus - -clean: - rm -f main-rtl.css diff --git a/preecej/semantic_wiki/skins/planteome/csshover.htc b/preecej/semantic_wiki/skins/planteome/csshover.htc deleted file mode 100644 index a88fa08..0000000 --- a/preecej/semantic_wiki/skins/planteome/csshover.htc +++ /dev/null @@ -1,262 +0,0 @@ - - \ No newline at end of file diff --git a/preecej/semantic_wiki/skins/planteome/cssjanus/COPYING b/preecej/semantic_wiki/skins/planteome/cssjanus/COPYING deleted file mode 100644 index 3f2c895..0000000 --- a/preecej/semantic_wiki/skins/planteome/cssjanus/COPYING +++ /dev/null @@ -1,13 +0,0 @@ - Copyright 2008 Google Inc. - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/preecej/semantic_wiki/skins/planteome/cssjanus/LICENSE b/preecej/semantic_wiki/skins/planteome/cssjanus/LICENSE deleted file mode 100644 index d645695..0000000 --- a/preecej/semantic_wiki/skins/planteome/cssjanus/LICENSE +++ /dev/null @@ -1,202 +0,0 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/preecej/semantic_wiki/skins/planteome/cssjanus/README b/preecej/semantic_wiki/skins/planteome/cssjanus/README deleted file mode 100644 index 9b92215..0000000 --- a/preecej/semantic_wiki/skins/planteome/cssjanus/README +++ /dev/null @@ -1,91 +0,0 @@ -=CSSJanus= - -_Flips CSS from LTR to an RTL orienation and vice-versa_ - -Author: `Lindsey Simon ` - -==Introduction== - -CSSJanus is CSS parser utility designed to aid the conversion of a website's -layout from left-to-right(LTR) to right-to-left(RTL). The script was born out of -a need to convert CSS for RTL languages when tables are not being used for layout (since tables will automatically reorder TD's in RTL). -CSSJanus will change most of the obvious CSS property names and their values as -well as some not-so-obvious ones (cursor, background-position %, etc...). -The script is designed to offer flexibility to account for cases when you do -not want to change certain rules which exist to account for bidirectional text -display bugs, as well as situations where you may or may not want to flip annotations inside of the background url string. -Note that you can disable CSSJanus from running on an entire class or any -rule within a class by prepending a /* @noflip */ comment before the rule(s) -you want CSSJanus to ignore. - -CSSJanus itself is not always enough to make a website that works in a LTR -language context work in a RTL language all the way, but it is a start. - -==Getting the code== - -View the trunk at: - - http://cssjanus.googlecode.com/svn/trunk/ - -Check out the latest development version anonymously with: - -{{{ - $ svn checkout http://cssjanus.googlecode.com/svn/trunk/ cssjanus -}}} - -==Using== - -Usage: - ./cssjanus.py < file.css > file-rtl.css -Flags: - --swap_left_right_in_url: Fixes "left"/"right" string within urls. - Ex: ./cssjanus.py --swap_left_right_in_url < file.css > file_rtl.css - --swap_ltr_rtl_in_url: Fixes "ltr"/"rtl" string within urls. - Ex: ./cssjanus.py --swap_ltr_rtl_in_url < file.css > file_rtl.css - -If you'd like to make use of the webapp version of cssjanus, you'll need to -download the Google App Engine SDK - http://code.google.com/appengine/downloads.html -and also drop a "django" directory into this directory, with the latest svn -from django. You should be good to go with that setup. Please let me know -otherwise. - -==Bugs, Patches== - -Patches and bug reports are welcome, just please keep the style -consistent with the original source. If you find a bug, please include a diff -of cssjanus_test.py with the bug included as a new unit test which fails. It -will make understanding and fixing the bug easier. - -==Todo== - -* Include some helpers for some typical bidi text solutions? -* Aural CSS (azimuth) swapping? - -==Contributors== - -Additional thanks to Mike Samuel for his work on csslex.py, Andy Perelson for -his help coding and reviewing, Stephen Zabel for his help with i18n and my sanity, -and to Eric Meyer for his thoughtful input. -Thanks to Junyu Wang for the Chinese translation. -Thanks to Masashi Kawashima for the Japanese translation. -Thanks to Taaryk Taar and Tariq Al-Omaireeni for an updated Arabic translation. -Thanks to Jens Meiert for the German translation. - -==License== - -{{{ - Copyright 2008 Google Inc. All Rights Reserved. - - Licensed under the Apache License, Version 2.0 (the 'License'); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an 'AS IS' BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. -}}} diff --git a/preecej/semantic_wiki/skins/planteome/cssjanus/cssjanus.py b/preecej/semantic_wiki/skins/planteome/cssjanus/cssjanus.py deleted file mode 100755 index dd14bd5..0000000 --- a/preecej/semantic_wiki/skins/planteome/cssjanus/cssjanus.py +++ /dev/null @@ -1,574 +0,0 @@ -#!/usr/bin/python -# -# Copyright 2008 Google Inc. All Rights Reserved. - -"""Converts a LeftToRight Cascading Style Sheet into a RightToLeft one. - - This is a utility script for replacing "left" oriented things in a CSS file - like float, padding, margin with "right" oriented values. - It also does the opposite. - The goal is to be able to conditionally serve one large, cat'd, compiled CSS - file appropriate for LeftToRight oriented languages and RightToLeft ones. - This utility will hopefully help your structural layout done in CSS in - terms of its RTL compatibility. It will not help with some of the more - complicated bidirectional text issues. -""" - -__author__ = 'elsigh@google.com (Lindsey Simon)' -__version__ = '0.1' - -import logging -import re -import sys -import getopt -import os - -import csslex - -logging.getLogger().setLevel(logging.INFO) - -# Global for the command line flags. -SWAP_LTR_RTL_IN_URL_DEFAULT = False -SWAP_LEFT_RIGHT_IN_URL_DEFAULT = False -FLAGS = {'swap_ltr_rtl_in_url': SWAP_LTR_RTL_IN_URL_DEFAULT, - 'swap_left_right_in_url': SWAP_LEFT_RIGHT_IN_URL_DEFAULT} - -# Generic token delimiter character. -TOKEN_DELIMITER = '~' - -# This is a temporary match token we use when swapping strings. -TMP_TOKEN = '%sTMP%s' % (TOKEN_DELIMITER, TOKEN_DELIMITER) - -# Token to be used for joining lines. -TOKEN_LINES = '%sJ%s' % (TOKEN_DELIMITER, TOKEN_DELIMITER) - -# Global constant text strings for CSS value matches. -LTR = 'ltr' -RTL = 'rtl' -LEFT = 'left' -RIGHT = 'right' - -# This is a lookbehind match to ensure that we don't replace instances -# of our string token (left, rtl, etc...) if there's a letter in front of it. -# Specifically, this prevents replacements like 'background: url(bright.png)'. -LOOKBEHIND_NOT_LETTER = r'(?)*?{)' % - (csslex.NMCHAR, TOKEN_LINES, csslex.SPACE)) - - -# These two lookaheads are to test whether or not we are within a -# background: url(HERE) situation. -# Ref: http://www.w3.org/TR/CSS21/syndata.html#uri -VALID_AFTER_URI_CHARS = r'[\'\"]?%s' % csslex.WHITESPACE -LOOKAHEAD_NOT_CLOSING_PAREN = r'(?!%s?%s\))' % (csslex.URL_CHARS, - VALID_AFTER_URI_CHARS) -LOOKAHEAD_FOR_CLOSING_PAREN = r'(?=%s?%s\))' % (csslex.URL_CHARS, - VALID_AFTER_URI_CHARS) - -# Compile a regex to swap left and right values in 4 part notations. -# We need to match negatives and decimal numeric values. -# ex. 'margin: .25em -2px 3px 0' becomes 'margin: .25em 0 3px -2px'. -POSSIBLY_NEGATIVE_QUANTITY = r'((?:-?%s)|(?:inherit|auto))' % csslex.QUANTITY -POSSIBLY_NEGATIVE_QUANTITY_SPACE = r'%s%s%s' % (POSSIBLY_NEGATIVE_QUANTITY, - csslex.SPACE, - csslex.WHITESPACE) -FOUR_NOTATION_QUANTITY_RE = re.compile(r'%s%s%s%s' % - (POSSIBLY_NEGATIVE_QUANTITY_SPACE, - POSSIBLY_NEGATIVE_QUANTITY_SPACE, - POSSIBLY_NEGATIVE_QUANTITY_SPACE, - POSSIBLY_NEGATIVE_QUANTITY), - re.I) -COLOR = r'(%s|%s)' % (csslex.NAME, csslex.HASH) -COLOR_SPACE = r'%s%s' % (COLOR, csslex.SPACE) -FOUR_NOTATION_COLOR_RE = re.compile(r'(-color%s:%s)%s%s%s(%s)' % - (csslex.WHITESPACE, - csslex.WHITESPACE, - COLOR_SPACE, - COLOR_SPACE, - COLOR_SPACE, - COLOR), - re.I) - -# Compile the cursor resize regexes -CURSOR_EAST_RE = re.compile(LOOKBEHIND_NOT_LETTER + '([ns]?)e-resize') -CURSOR_WEST_RE = re.compile(LOOKBEHIND_NOT_LETTER + '([ns]?)w-resize') - -# Matches the condition where we need to replace the horizontal component -# of a background-position value when expressed in horizontal percentage. -# Had to make two regexes because in the case of position-x there is only -# one quantity, and otherwise we don't want to match and change cases with only -# one quantity. -BG_HORIZONTAL_PERCENTAGE_RE = re.compile(r'background(-position)?(%s:%s)' - '([^%%]*?)(%s)%%' - '(%s(?:%s|%s))' % (csslex.WHITESPACE, - csslex.WHITESPACE, - csslex.NUM, - csslex.WHITESPACE, - csslex.QUANTITY, - csslex.IDENT)) - -BG_HORIZONTAL_PERCENTAGE_X_RE = re.compile(r'background-position-x(%s:%s)' - '(%s)%%' % (csslex.WHITESPACE, - csslex.WHITESPACE, - csslex.NUM)) - -# Matches the opening of a body selector. -BODY_SELECTOR = r'body%s{%s' % (csslex.WHITESPACE, csslex.WHITESPACE) - -# Matches anything up until the closing of a selector. -CHARS_WITHIN_SELECTOR = r'[^\}]*?' - -# Matches the direction property in a selector. -DIRECTION_RE = r'direction%s:%s' % (csslex.WHITESPACE, csslex.WHITESPACE) - -# These allow us to swap "ltr" with "rtl" and vice versa ONLY within the -# body selector and on the same line. -BODY_DIRECTION_LTR_RE = re.compile(r'(%s)(%s)(%s)(ltr)' % - (BODY_SELECTOR, CHARS_WITHIN_SELECTOR, - DIRECTION_RE), - re.I) -BODY_DIRECTION_RTL_RE = re.compile(r'(%s)(%s)(%s)(rtl)' % - (BODY_SELECTOR, CHARS_WITHIN_SELECTOR, - DIRECTION_RE), - re.I) - - -# Allows us to swap "direction:ltr" with "direction:rtl" and -# vice versa anywhere in a line. -DIRECTION_LTR_RE = re.compile(r'%s(ltr)' % DIRECTION_RE) -DIRECTION_RTL_RE = re.compile(r'%s(rtl)' % DIRECTION_RE) - -# We want to be able to switch left with right and vice versa anywhere -# we encounter left/right strings, EXCEPT inside the background:url(). The next -# two regexes are for that purpose. We have alternate IN_URL versions of the -# regexes compiled in case the user passes the flag that they do -# actually want to have left and right swapped inside of background:urls. -LEFT_RE = re.compile('%s(%s)%s%s' % (LOOKBEHIND_NOT_LETTER, - LEFT, - LOOKAHEAD_NOT_CLOSING_PAREN, - LOOKAHEAD_NOT_OPEN_BRACE), - re.I) -RIGHT_RE = re.compile('%s(%s)%s%s' % (LOOKBEHIND_NOT_LETTER, - RIGHT, - LOOKAHEAD_NOT_CLOSING_PAREN, - LOOKAHEAD_NOT_OPEN_BRACE), - re.I) -LEFT_IN_URL_RE = re.compile('%s(%s)%s' % (LOOKBEHIND_NOT_LETTER, - LEFT, - LOOKAHEAD_FOR_CLOSING_PAREN), - re.I) -RIGHT_IN_URL_RE = re.compile('%s(%s)%s' % (LOOKBEHIND_NOT_LETTER, - RIGHT, - LOOKAHEAD_FOR_CLOSING_PAREN), - re.I) -LTR_IN_URL_RE = re.compile('%s(%s)%s' % (LOOKBEHIND_NOT_LETTER, - LTR, - LOOKAHEAD_FOR_CLOSING_PAREN), - re.I) -RTL_IN_URL_RE = re.compile('%s(%s)%s' % (LOOKBEHIND_NOT_LETTER, - RTL, - LOOKAHEAD_FOR_CLOSING_PAREN), - re.I) - -COMMENT_RE = re.compile('(%s)' % csslex.COMMENT, re.I) - -NOFLIP_TOKEN = r'\@noflip' -# The NOFLIP_TOKEN inside of a comment. For now, this requires that comments -# be in the input, which means users of a css compiler would have to run -# this script first if they want this functionality. -NOFLIP_ANNOTATION = r'/\*%s%s%s\*/' % (csslex.WHITESPACE, - NOFLIP_TOKEN, - csslex. WHITESPACE) - -# After a NOFLIP_ANNOTATION, and within a class selector, we want to be able -# to set aside a single rule not to be flipped. We can do this by matching -# our NOFLIP annotation and then using a lookahead to make sure there is not -# an opening brace before the match. -NOFLIP_SINGLE_RE = re.compile(r'(%s%s[^;}]+;?)' % (NOFLIP_ANNOTATION, - LOOKAHEAD_NOT_OPEN_BRACE), - re.I) - -# After a NOFLIP_ANNOTATION, we want to grab anything up until the next } which -# means the entire following class block. This will prevent all of its -# declarations from being flipped. -NOFLIP_CLASS_RE = re.compile(r'(%s%s})' % (NOFLIP_ANNOTATION, - CHARS_WITHIN_SELECTOR), - re.I) - - -class Tokenizer: - """Replaces any CSS comments with string tokens and vice versa.""" - - def __init__(self, token_re, token_string): - """Constructor for the Tokenizer. - - Args: - token_re: A regex for the string to be replace by a token. - token_string: The string to put between token delimiters when tokenizing. - """ - logging.debug('Tokenizer::init token_string=%s' % token_string) - self.token_re = token_re - self.token_string = token_string - self.originals = [] - - def Tokenize(self, line): - """Replaces any string matching token_re in line with string tokens. - - By passing a function as an argument to the re.sub line below, we bypass - the usual rule where re.sub will only replace the left-most occurrence of - a match by calling the passed in function for each occurrence. - - Args: - line: A line to replace token_re matches in. - - Returns: - line: A line with token_re matches tokenized. - """ - line = self.token_re.sub(self.TokenizeMatches, line) - logging.debug('Tokenizer::Tokenize returns: %s' % line) - return line - - def DeTokenize(self, line): - """Replaces tokens with the original string. - - Args: - line: A line with tokens. - - Returns: - line with any tokens replaced by the original string. - """ - - # Put all of the comments back in by their comment token. - for i, original in enumerate(self.originals): - token = '%s%s_%s%s' % (TOKEN_DELIMITER, self.token_string, i + 1, - TOKEN_DELIMITER) - line = line.replace(token, original) - logging.debug('Tokenizer::DeTokenize i:%s w/%s' % (i, token)) - logging.debug('Tokenizer::DeTokenize returns: %s' % line) - return line - - def TokenizeMatches(self, m): - """Replaces matches with tokens and stores the originals. - - Args: - m: A match object. - - Returns: - A string token which replaces the CSS comment. - """ - logging.debug('Tokenizer::TokenizeMatches %s' % m.group(1)) - self.originals.append(m.group(1)) - return '%s%s_%s%s' % (TOKEN_DELIMITER, - self.token_string, - len(self.originals), - TOKEN_DELIMITER) - - -def FixBodyDirectionLtrAndRtl(line): - """Replaces ltr with rtl and vice versa ONLY in the body direction. - - Args: - line: A string to replace instances of ltr with rtl. - Returns: - line with direction: ltr and direction: rtl swapped only in body selector. - line = FixBodyDirectionLtrAndRtl('body { direction:ltr }') - line will now be 'body { direction:rtl }'. - """ - - line = BODY_DIRECTION_LTR_RE.sub('\\1\\2\\3%s' % TMP_TOKEN, line) - line = BODY_DIRECTION_RTL_RE.sub('\\1\\2\\3%s' % LTR, line) - line = line.replace(TMP_TOKEN, RTL) - logging.debug('FixBodyDirectionLtrAndRtl returns: %s' % line) - return line - - -def FixLeftAndRight(line): - """Replaces left with right and vice versa in line. - - Args: - line: A string in which to perform the replacement. - - Returns: - line with left and right swapped. For example: - line = FixLeftAndRight('padding-left: 2px; margin-right: 1px;') - line will now be 'padding-right: 2px; margin-left: 1px;'. - """ - - line = LEFT_RE.sub(TMP_TOKEN, line) - line = RIGHT_RE.sub(LEFT, line) - line = line.replace(TMP_TOKEN, RIGHT) - logging.debug('FixLeftAndRight returns: %s' % line) - return line - - -def FixLeftAndRightInUrl(line): - """Replaces left with right and vice versa ONLY within background urls. - - Args: - line: A string in which to replace left with right and vice versa. - - Returns: - line with left and right swapped in the url string. For example: - line = FixLeftAndRightInUrl('background:url(right.png)') - line will now be 'background:url(left.png)'. - """ - - line = LEFT_IN_URL_RE.sub(TMP_TOKEN, line) - line = RIGHT_IN_URL_RE.sub(LEFT, line) - line = line.replace(TMP_TOKEN, RIGHT) - logging.debug('FixLeftAndRightInUrl returns: %s' % line) - return line - - -def FixLtrAndRtlInUrl(line): - """Replaces ltr with rtl and vice versa ONLY within background urls. - - Args: - line: A string in which to replace ltr with rtl and vice versa. - - Returns: - line with left and right swapped. For example: - line = FixLtrAndRtlInUrl('background:url(rtl.png)') - line will now be 'background:url(ltr.png)'. - """ - - line = LTR_IN_URL_RE.sub(TMP_TOKEN, line) - line = RTL_IN_URL_RE.sub(LTR, line) - line = line.replace(TMP_TOKEN, RTL) - logging.debug('FixLtrAndRtlInUrl returns: %s' % line) - return line - - -def FixCursorProperties(line): - """Fixes directional CSS cursor properties. - - Args: - line: A string to fix CSS cursor properties in. - - Returns: - line reformatted with the cursor properties substituted. For example: - line = FixCursorProperties('cursor: ne-resize') - line will now be 'cursor: nw-resize'. - """ - - line = CURSOR_EAST_RE.sub('\\1' + TMP_TOKEN, line) - line = CURSOR_WEST_RE.sub('\\1e-resize', line) - line = line.replace(TMP_TOKEN, 'w-resize') - logging.debug('FixCursorProperties returns: %s' % line) - return line - - -def FixFourPartNotation(line): - """Fixes the second and fourth positions in 4 part CSS notation. - - Args: - line: A string to fix 4 part CSS notation in. - - Returns: - line reformatted with the 4 part notations swapped. For example: - line = FixFourPartNotation('padding: 1px 2px 3px 4px') - line will now be 'padding: 1px 4px 3px 2px'. - """ - line = FOUR_NOTATION_QUANTITY_RE.sub('\\1 \\4 \\3 \\2', line) - line = FOUR_NOTATION_COLOR_RE.sub('\\1\\2 \\5 \\4 \\3', line) - logging.debug('FixFourPartNotation returns: %s' % line) - return line - - -def FixBackgroundPosition(line): - """Fixes horizontal background percentage values in line. - - Args: - line: A string to fix horizontal background position values in. - - Returns: - line reformatted with the 4 part notations swapped. - """ - line = BG_HORIZONTAL_PERCENTAGE_RE.sub(CalculateNewBackgroundPosition, line) - line = BG_HORIZONTAL_PERCENTAGE_X_RE.sub(CalculateNewBackgroundPositionX, - line) - logging.debug('FixBackgroundPosition returns: %s' % line) - return line - - -def CalculateNewBackgroundPosition(m): - """Fixes horizontal background-position percentages. - - This function should be used as an argument to re.sub since it needs to - perform replacement specific calculations. - - Args: - m: A match object. - - Returns: - A string with the horizontal background position percentage fixed. - BG_HORIZONTAL_PERCENTAGE_RE.sub(FixBackgroundPosition, - 'background-position: 75% 50%') - will return 'background-position: 25% 50%'. - """ - - # The flipped value is the offset from 100% - new_x = str(100-int(m.group(4))) - - # Since m.group(1) may very well be None type and we need a string.. - if m.group(1): - position_string = m.group(1) - else: - position_string = '' - - return 'background%s%s%s%s%%%s' % (position_string, m.group(2), m.group(3), - new_x, m.group(5)) - - -def CalculateNewBackgroundPositionX(m): - """Fixes percent based background-position-x. - - This function should be used as an argument to re.sub since it needs to - perform replacement specific calculations. - - Args: - m: A match object. - - Returns: - A string with the background-position-x percentage fixed. - BG_HORIZONTAL_PERCENTAGE_X_RE.sub(CalculateNewBackgroundPosition, - 'background-position-x: 75%') - will return 'background-position-x: 25%'. - """ - - # The flipped value is the offset from 100% - new_x = str(100-int(m.group(2))) - - return 'background-position-x%s%s%%' % (m.group(1), new_x) - - -def ChangeLeftToRightToLeft(lines, - swap_ltr_rtl_in_url=None, - swap_left_right_in_url=None): - """Turns lines into a stream and runs the fixing functions against it. - - Args: - lines: An list of CSS lines. - swap_ltr_rtl_in_url: Overrides this flag if param is set. - swap_left_right_in_url: Overrides this flag if param is set. - - Returns: - The same lines, but with left and right fixes. - """ - - global FLAGS - - # Possibly override flags with params. - logging.debug('ChangeLeftToRightToLeft swap_ltr_rtl_in_url=%s, ' - 'swap_left_right_in_url=%s' % (swap_ltr_rtl_in_url, - swap_left_right_in_url)) - if swap_ltr_rtl_in_url is None: - swap_ltr_rtl_in_url = FLAGS['swap_ltr_rtl_in_url'] - if swap_left_right_in_url is None: - swap_left_right_in_url = FLAGS['swap_left_right_in_url'] - - # Turns the array of lines into a single line stream. - logging.debug('LINES COUNT: %s' % len(lines)) - line = TOKEN_LINES.join(lines) - - # Tokenize any single line rules with the /* noflip */ annotation. - noflip_single_tokenizer = Tokenizer(NOFLIP_SINGLE_RE, 'NOFLIP_SINGLE') - line = noflip_single_tokenizer.Tokenize(line) - - # Tokenize any class rules with the /* noflip */ annotation. - noflip_class_tokenizer = Tokenizer(NOFLIP_CLASS_RE, 'NOFLIP_CLASS') - line = noflip_class_tokenizer.Tokenize(line) - - # Tokenize the comments so we can preserve them through the changes. - comment_tokenizer = Tokenizer(COMMENT_RE, 'C') - line = comment_tokenizer.Tokenize(line) - - # Here starteth the various left/right orientation fixes. - line = FixBodyDirectionLtrAndRtl(line) - - if swap_left_right_in_url: - line = FixLeftAndRightInUrl(line) - - if swap_ltr_rtl_in_url: - line = FixLtrAndRtlInUrl(line) - - line = FixLeftAndRight(line) - line = FixCursorProperties(line) - line = FixFourPartNotation(line) - line = FixBackgroundPosition(line) - - # DeTokenize the single line noflips. - line = noflip_single_tokenizer.DeTokenize(line) - - # DeTokenize the class-level noflips. - line = noflip_class_tokenizer.DeTokenize(line) - - # DeTokenize the comments. - line = comment_tokenizer.DeTokenize(line) - - # Rejoin the lines back together. - lines = line.split(TOKEN_LINES) - - return lines - -def usage(): - """Prints out usage information.""" - - print 'Usage:' - print ' ./cssjanus.py < file.css > file-rtl.css' - print 'Flags:' - print ' --swap_left_right_in_url: Fixes "left"/"right" string within urls.' - print ' Ex: ./cssjanus.py --swap_left_right_in_url < file.css > file_rtl.css' - print ' --swap_ltr_rtl_in_url: Fixes "ltr"/"rtl" string within urls.' - print ' Ex: ./cssjanus --swap_ltr_rtl_in_url < file.css > file_rtl.css' - -def setflags(opts): - """Parse the passed in command line arguments and set the FLAGS global. - - Args: - opts: getopt iterable intercepted from argv. - """ - - global FLAGS - - # Parse the arguments. - for opt, arg in opts: - logging.debug('opt: %s, arg: %s' % (opt, arg)) - if opt in ("-h", "--help"): - usage() - sys.exit() - elif opt in ("-d", "--debug"): - logging.getLogger().setLevel(logging.DEBUG) - elif opt == '--swap_ltr_rtl_in_url': - FLAGS['swap_ltr_rtl_in_url'] = True - elif opt == '--swap_left_right_in_url': - FLAGS['swap_left_right_in_url'] = True - - -def main(argv): - """Sends stdin lines to ChangeLeftToRightToLeft and writes to stdout.""" - - # Define the flags. - try: - opts, args = getopt.getopt(argv, 'hd', ['help', 'debug', - 'swap_left_right_in_url', - 'swap_ltr_rtl_in_url']) - except getopt.GetoptError: - usage() - sys.exit(2) - - # Parse and set the flags. - setflags(opts) - - # Call the main routine with all our functionality. - fixed_lines = ChangeLeftToRightToLeft(sys.stdin.readlines()) - sys.stdout.write(''.join(fixed_lines)) - -if __name__ == '__main__': - main(sys.argv[1:]) diff --git a/preecej/semantic_wiki/skins/planteome/cssjanus/csslex.py b/preecej/semantic_wiki/skins/planteome/cssjanus/csslex.py deleted file mode 100755 index 1fc7304..0000000 --- a/preecej/semantic_wiki/skins/planteome/cssjanus/csslex.py +++ /dev/null @@ -1,114 +0,0 @@ -#!/usr/bin/python -# -# Copyright 2007 Google Inc. All Rights Reserved. - -"""CSS Lexical Grammar rules. - -CSS lexical grammar from http://www.w3.org/TR/CSS21/grammar.html -""" - -__author__ = ['elsigh@google.com (Lindsey Simon)', - 'msamuel@google.com (Mike Samuel)'] - -# public symbols -__all__ = [ "NEWLINE", "HEX", "NON_ASCII", "UNICODE", "ESCAPE", "NMSTART", "NMCHAR", "STRING1", "STRING2", "IDENT", "NAME", "HASH", "NUM", "STRING", "URL", "SPACE", "WHITESPACE", "COMMENT", "QUANTITY", "PUNC" ] - -# The comments below are mostly copied verbatim from the grammar. - -# "@import" {return IMPORT_SYM;} -# "@page" {return PAGE_SYM;} -# "@media" {return MEDIA_SYM;} -# "@charset" {return CHARSET_SYM;} -KEYWORD = r'(?:\@(?:import|page|media|charset))' - -# nl \n|\r\n|\r|\f ; a newline -NEWLINE = r'\n|\r\n|\r|\f' - -# h [0-9a-f] ; a hexadecimal digit -HEX = r'[0-9a-f]' - -# nonascii [\200-\377] -NON_ASCII = r'[\200-\377]' - -# unicode \\{h}{1,6}(\r\n|[ \t\r\n\f])? -UNICODE = r'(?:(?:\\' + HEX + r'{1,6})(?:\r\n|[ \t\r\n\f])?)' - -# escape {unicode}|\\[^\r\n\f0-9a-f] -ESCAPE = r'(?:' + UNICODE + r'|\\[^\r\n\f0-9a-f])' - -# nmstart [_a-z]|{nonascii}|{escape} -NMSTART = r'(?:[_a-z]|' + NON_ASCII + r'|' + ESCAPE + r')' - -# nmchar [_a-z0-9-]|{nonascii}|{escape} -NMCHAR = r'(?:[_a-z0-9-]|' + NON_ASCII + r'|' + ESCAPE + r')' - -# ident -?{nmstart}{nmchar}* -IDENT = r'-?' + NMSTART + NMCHAR + '*' - -# name {nmchar}+ -NAME = NMCHAR + r'+' - -# hash -HASH = r'#' + NAME - -# string1 \"([^\n\r\f\\"]|\\{nl}|{escape})*\" ; "string" -STRING1 = r'"(?:[^\"\\]|\\.)*"' - -# string2 \'([^\n\r\f\\']|\\{nl}|{escape})*\' ; 'string' -STRING2 = r"'(?:[^\'\\]|\\.)*'" - -# string {string1}|{string2} -STRING = '(?:' + STRING1 + r'|' + STRING2 + ')' - -# num [0-9]+|[0-9]*"."[0-9]+ -NUM = r'(?:[0-9]*\.[0-9]+|[0-9]+)' - -# s [ \t\r\n\f] -SPACE = r'[ \t\r\n\f]' - -# w {s}* -WHITESPACE = '(?:' + SPACE + r'*)' - -# url special chars -URL_SPECIAL_CHARS = r'[!#$%&*-~]' - -# url chars ({url_special_chars}|{nonascii}|{escape})* -URL_CHARS = r'(?:%s|%s|%s)*' % (URL_SPECIAL_CHARS, NON_ASCII, ESCAPE) - -# url -URL = r'url\(%s(%s|%s)%s\)' % (WHITESPACE, STRING, URL_CHARS, WHITESPACE) - -# comments -# see http://www.w3.org/TR/CSS21/grammar.html -COMMENT = r'/\*[^*]*\*+([^/*][^*]*\*+)*/' - -# {E}{M} {return EMS;} -# {E}{X} {return EXS;} -# {P}{X} {return LENGTH;} -# {C}{M} {return LENGTH;} -# {M}{M} {return LENGTH;} -# {I}{N} {return LENGTH;} -# {P}{T} {return LENGTH;} -# {P}{C} {return LENGTH;} -# {D}{E}{G} {return ANGLE;} -# {R}{A}{D} {return ANGLE;} -# {G}{R}{A}{D} {return ANGLE;} -# {M}{S} {return TIME;} -# {S} {return TIME;} -# {H}{Z} {return FREQ;} -# {K}{H}{Z} {return FREQ;} -# % {return PERCENTAGE;} -UNIT = r'(?:em|ex|px|cm|mm|in|pt|pc|deg|rad|grad|ms|s|hz|khz|%)' - -# {num}{UNIT|IDENT} {return NUMBER;} -QUANTITY = '%s(?:%s%s|%s)?' % (NUM, WHITESPACE, UNIT, IDENT) - -# "" {return CDC;} -# "~=" {return INCLUDES;} -# "|=" {return DASHMATCH;} -# {w}"{" {return LBRACE;} -# {w}"+" {return PLUS;} -# {w}">" {return GREATER;} -# {w}"," {return COMMA;} -PUNC = r'|~=|\|=|[\{\+>,:;]' diff --git a/preecej/semantic_wiki/skins/planteome/experiments/babaco-colors-a.css b/preecej/semantic_wiki/skins/planteome/experiments/babaco-colors-a.css deleted file mode 100644 index ce6f67d..0000000 --- a/preecej/semantic_wiki/skins/planteome/experiments/babaco-colors-a.css +++ /dev/null @@ -1,109 +0,0 @@ -/* Babaco Color Scheme A */ - - -a:visited, -a:visited div.vectorTabs li.selected a:visited span { - color: #260e9c; -} - -html .thumbimage, -#toc, .toc, .mw-warning, div.thumbinner { - border-color: #cccccc; - background-color: #f7f7f7; -} - -/* Framework */ -#mw-page-base { - background-color: inherit !important; - background-image: none !important; -} -body { - background-color: #f9f9f9 !important; - background-image:url(images/page-base-updated.png); -} - -/* Links */ -a { - color: #0066cc; -} -a:visited { - color: #004d99; -} -a:active { - color: #ff6600; -} -a.stub { - color: #56228b; -} -a.new, #p-personal a.new { - color: #a31205 !important; -} -a.new:visited, #p-personal a.new:visited { - color: #a31205; -} - -h1, -h2, -h3, -h4, -h5, -h6 { - border-color:#999999; - font-family:georgia, times, serif; - font-weight:bold; -} -#firstHeading { - font-size:1.5em; -} -h2 .editsection, -.portal h5{ - font-family:sans-serif; - font-weight:normal; - -} -#toc h2, .toc h2 { - font-family:sans-serif; - font-weight:normal; -} -body #mw-panel div.portal div.body { - background-image:url(images/new-portal-break-ltr.png); -} -body.rtl #mw-panel div.portal div.body { - background-image:url(images/new-portal-break-rtl.png); -} -body div.vectorTabs li a, div.vectorTabs li a span{ - color:#4d4d4d; -} -body div.vectorTabs li.selected a, -body div.vectorTabs li.selected a span, -body div.vectorTabs li.selected a:visited -body div.vectorTabs li.selected a:visited span { - color: #ff9900 !important; - font-weight:bold; -} -div.vectorTabs li.new a, -div.vectorTabs li.new a span, -div.vectorTabs li.new a:visited, -div.vectorTabs li.new a:visited span { - color:#a31205; -} -#toc, -.toc, -.mw-warning, -div.gallerybox div.thumb, -table.gallery, -#preferences fieldset.prefsection fieldset, -#preferences, -html .thumbimage, -.usermessage, -img.thumbborder, -div.thumbinner{ - border: 1px solid #cccccc; - background-color: #f7f7f7; -} -#mw-panel div.portal h5 { - font-weight:bold; - margin-bottom:0; - padding-bottom:0.05em; - color:#000000; -} diff --git a/preecej/semantic_wiki/skins/planteome/experiments/babaco-colors-b.css b/preecej/semantic_wiki/skins/planteome/experiments/babaco-colors-b.css deleted file mode 100644 index 227e197..0000000 --- a/preecej/semantic_wiki/skins/planteome/experiments/babaco-colors-b.css +++ /dev/null @@ -1,67 +0,0 @@ -/* Babaco Color Scheme A */ - - -html .thumbimage, -#toc, .toc, .mw-warning, div.thumbinner { - border-color: #cccccc; - background-color: #f7f7f7; -} - -/* Framework */ -#mw-page-base { - background-color: inherit !important; - background-image: none !important; -} -body { - background-color: #f9f9f9 !important; - background-image:url(images/page-base-updated.png); -} -/* Links */ -a { - color: #003cb3; -} -a.stub { - color: #772233; -} -a.new, #p-personal a.new { - color: #a31205 !important; -} -{ - color: #260e9c; -} -a:visited, -a:visited div.vectorTabs li.selected a:visited span, -a.new:visited, -#p-personal a.new:visited { - color: #260e9c; -} -h1, -h2, -h3, -h4, -h5, -h6 { - border-color:#999999; -} - -div.vectorTabs li.new a, -div.vectorTabs li.new a span, -div.vectorTabs li.new a:visited, -div.vectorTabs li.new a:visited span { - color:#a31205; -} - -#toc, -.toc, -.mw-warning, -div.gallerybox div.thumb, -table.gallery, -#preferences fieldset.prefsection fieldset, -#preferences, -html .thumbimage, -.usermessage, -img.thumbborder, -div.thumbinner{ - border: 1px solid #cccccc; - background-color: #f7f7f7; -} diff --git a/preecej/semantic_wiki/skins/planteome/experiments/babaco-colors-c.css b/preecej/semantic_wiki/skins/planteome/experiments/babaco-colors-c.css deleted file mode 100644 index d2dabf7..0000000 --- a/preecej/semantic_wiki/skins/planteome/experiments/babaco-colors-c.css +++ /dev/null @@ -1,91 +0,0 @@ -/* Babaco Color Scheme C */ - -/* ridding ourselves of the gradient */ -#mw-page-base { - background-color: inherit !important; - background-image: none !important; -} - -a:visited, -a:visited div.vectorTabs li.selected a:visited span { - color: #260e9c; -} - -html .thumbimage, -#toc, .toc, .mw-warning, div.thumbinner { - border-color: #cccccc; - background-color: #f7f7f7; -} - -/* Framework */ -body { - background-color: #f9f9f9 !important; - background-image:url(images/page-base-updated.png); -} - -/* Links */ -a { - color: #0066cc; -} -a:visited { - color: #004d99; -} -a:active { - color: #ff6600; -} -a.stub { - color: #56228b; -} -a.new, #p-personal a.new { - color: #a31205 !important; -} -a.new:visited, #p-personal a.new:visited { - color: #a31205; -} - -#firstHeading { - font-size:1.5em; -} -h2 .editsection, -.portal h5 { - font-weight:normal; -} -#toc h2, .toc h2 { - font-weight:normal; -} -body #mw-panel div.portal div.body { - background-image:url(images/new-portal-break-ltr.png); -} - -div.vectorTabs li.new a, -div.vectorTabs li.new a span, -div.vectorTabs li.new a:visited, -div.vectorTabs li.new a:visited span { - color:#a31205; -} -#toc, -.toc, -.mw-warning, -div.gallerybox div.thumb, -table.gallery, -#preferences fieldset.prefsection fieldset, -#preferences, -html .thumbimage, -.usermessage, -img.thumbborder, -div.thumbinner { - border: 1px solid #cccccc; - background-color: #f7f7f7; -} -#mw-panel div.portal h5 { - font-weight:bold; - margin-bottom:0; - padding-bottom:0.05em; - color:#000000; -} -div.vectorTabs li.selected a, -div.vectorTabs li.selected a span, -div.vectorTabs li.selected a:visited -div.vectorTabs li.selected a:visited span { - color: #333333 !important; -} \ No newline at end of file diff --git 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diff --git a/preecej/semantic_wiki/skins/planteome/main-ltr.css b/preecej/semantic_wiki/skins/planteome/main-ltr.css deleted file mode 100644 index 0b0f46d..0000000 --- a/preecej/semantic_wiki/skins/planteome/main-ltr.css +++ /dev/null @@ -1,1200 +0,0 @@ -/* - * main-rtl.css is automatically generated using CSSJanus, a python script for - * creating RTL versions of otherwise LTR stylesheets. - * - * You may download the tool to rebuild this stylesheet - * http://code.google.com/p/cssjanus/ - * - * An online version of this tool can be used at: - * http://cssjanus.commoner.com/ - * - * The following command is used to generate the RTL version of this file - * ./cssjanus.py --swap_ltr_rtl_in_url < main-ltr.css > main-rtl.css - * - * Any rules which should not be flipped should be prepended with @noflip in - * a comment block. - */ -/* Framework */ -html, -body { - height: 100%; - margin: 0; - padding: 0; - font-family: sans-serif; - font-size: 1em; -} -body { - /*background-color: #f3f3f3;*/ - /*background-color: #b7c8b7;*/ - /*background-image: url(images/page-base.png);*/ - - /* thanks to http://blog.fakedarren.com/2010/01/cross-browser-css-gradients/ */ - /* and http://www.puremango.co.uk/2010/04/css-gradient/ */ - /* fallback (Opera) */ - background: #b7c8b7; - /* Mozilla: */ - background: -moz-linear-gradient(top, #b7c8b7, #e7f8e7); - /* Chrome, Safari:*/ - background: -webkit-gradient(linear, - left top, left bottom, from(#b7c8b7), to(#e7f8e7)); - /* MSIE */ - filter: progid:DXImageTransform.Microsoft.Gradient( - StartColorStr='#b7c8b7', EndColorStr='#e7f8e7', GradientType=0); -} - -/* Content */ -#content { - margin-left: 10em; - padding: 1em; - background-image: url(images/border.png); - background-position: top left; - background-repeat: repeat-y; - /* fallback (Opera) */ - background: white; - /* Mozilla: */ - background: -moz-linear-gradient(top, white, #c7b3cc); - /* Chrome, Safari:*/ - background: -webkit-gradient(linear, - left top, left bottom, from(white), to(#c7b3cc)); - /* MSIE */ - filter: progid:DXImageTransform.Microsoft.Gradient( - StartColorStr='white', EndColorStr='#c7b3cc', GradientType=0); - /*background-color: white;*/ -} -/* Head */ -#mw-page-base { - height: 5em; - /*background-color: grey;*/ - background-image: url(images/page-fade.png); - opacity: 0.0; - background-position: bottom left; - background-repeat: repeat-x; -} -#mw-head-base { - margin-top: -5em; - margin-left: 10em; - height: 5em; - background-image: url(images/border.png); - background-position: bottom left; - background-repeat: repeat-x; -} -#mw-head { - position: absolute; - top: 0; - right: 0; - width: 100%; -} -#mw-head h5 { - margin: 0; - padding: 0; -} - /* Hide empty portlets */ - div.emptyPortlet { - display: none; - } - /* Personal */ - #p-personal { - position: absolute; - top: 0; - margin-left: 10em; - right: 0.75em; - } - #p-personal h5 { - display: none; - } - #p-personal ul { - list-style: none; - margin: 0; - padding: 0; - } - /* @noflip */ - #p-personal li { - line-height: 1.125em; - float: left; - } - #p-personal li { - margin-left: 0.75em; - margin-top: 0.5em; - font-size: 0.75em; - } - /* Navigation Containers */ - #left-navigation { - position: absolute; - left: 10em; - top: 2.5em; - } - #right-navigation { - float: right; - margin-top: 2.5em; - } - /* Navigation Labels */ - div.vectorTabs h5, - div.vectorMenu h5 span { - display: none; - } - /* Namespaces and Views */ - /* @noflip */ - div.vectorTabs { - float: left; - } - div.vectorTabs { - background-image: url(images/tab-break.png); - background-position: bottom left; - background-repeat: no-repeat; - padding-left: 1px; - } - /* @noflip */ - div.vectorTabs ul { - float: left; - } - div.vectorTabs ul { - height: 100%; - list-style: none; - margin: 0; - padding: 0; - } - /* @noflip */ - div.vectorTabs ul li { - float: left; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - div.vectorTabs ul li { - line-height: 1.125em; - display: inline-block; - height: 100%; - margin: 0; - padding: 0; - - /* thanks to http://blog.fakedarren.com/2010/01/cross-browser-css-gradients/ */ - /* and http://www.puremango.co.uk/2010/04/css-gradient/ */ - /* fallback (Opera) */ - background: #b7c8b7; - /* Mozilla: */ - background: -moz-linear-gradient(top, #b7c8b7, #aaaaaa); - /* Chrome, Safari:*/ - background: -webkit-gradient(linear, - left top, left bottom, from(#b7c8b7), to(#aaaaaa)); - /* MSIE */ - filter: progid:DXImageTransform.Microsoft.Gradient( - StartColorStr='#b7c8b7', EndColorStr='#aaaaaa', GradientType=0); - - /*background-color: #f3f3f3;*/ - /*background-color: #b7c8b7;*/ - /*background-image: url(images/tab-normal-fade.png);*/ - background-position: bottom left; - background-repeat: repeat-x; - white-space:nowrap; - } - /* IGNORED BY IE6 */ - div.vectorTabs ul > li { - display: block; - } - div.vectorTabs li.selected { - - /* thanks to http://blog.fakedarren.com/2010/01/cross-browser-css-gradients/ */ - /* and http://www.puremango.co.uk/2010/04/css-gradient/ */ - /* fallback (Opera) */ - background: #b7c8b7; - /* Mozilla: */ - background: -moz-linear-gradient(top, #b7c8b7, white); - /* Chrome, Safari:*/ - background: -webkit-gradient(linear, - left top, left bottom, from(#b7c8b7), to(white)); - /* MSIE */ - filter: progid:DXImageTransform.Microsoft.Gradient( - StartColorStr='#b7c8b7', EndColorStr='white', GradientType=0); - - /*background-image: url(images/tab-current-fade.png);*/ - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - div.vectorTabs li a { - display: inline-block; - height: 2.5em; - padding-left: 0.4em; - padding-right: 0.4em; - background-image: url(images/tab-break.png); - background-position: bottom right; - background-repeat: no-repeat; - } - div.vectorTabs li a, - div.vectorTabs li a span { - /*color: #0645ad;*/ - color: #67536c; - cursor: pointer; - } - div.vectorTabs li a span { - font-size: 0.8em; - } - /* IGNORED BY IE6 */ - div.vectorTabs li > a { - display: block; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - div.vectorTabs a span { - display: inline-block; - padding-top: 1.25em; - } - /* IGNORED BY IE6 */ - /* @noflip */ - div.vectorTabs a > span { - float: left; - display: block; - } - div.vectorTabs li.selected a, - div.vectorTabs li.selected a span, - div.vectorTabs li.selected a:visited - div.vectorTabs li.selected a:visited span { - color: #333333; - text-decoration: none; - } - div.vectorTabs li.new a, - div.vectorTabs li.new a span, - div.vectorTabs li.new a:visited, - div.vectorTabs li.new a:visited span { - color: #a55858; - } - /* Variants and Actions */ - /* @noflip */ - div.vectorMenu { - direction: ltr; - float: left; - background-image: url(images/arrow-down-icon.png); - background-position: center center; - background-repeat: no-repeat; - } - /* @noflip */ - body.rtl div.vectorMenu { - direction: rtl; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - /* @noflip */ - #mw-head div.vectorMenu h5 { - float: left; - background-image: url(images/tab-break.png); - background-repeat: no-repeat; - } - /* IGNORED BY IE6 */ - #mw-head div.vectorMenu > h5 { - background-image: none; - } - #mw-head div.vectorMenu h5 { - background-position: bottom left; - margin-left: -1px; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - /* @noflip */ - div.vectorMenu h5 a { - display: inline-block; - width: 24px; - height: 2.5em; - text-decoration: none; - background-image: url(images/tab-break.png); - background-repeat: no-repeat; - } - div.vectorMenu h5 a{ - background-position: bottom right; - } - /* IGNORED BY IE6 */ - div.vectorMenu h5 > a { - display: block; - } - div.vectorMenu div.menu { - position: relative; - display: none; - clear: both; - text-align: left; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - /* @noflip */ - body.rtl div.vectorMenu div.menu { - margin-left: 24px; - } - /* IGNORED BY IE6 */ - /* @noflip */ - body.rtl div.vectorMenu > div.menu { - margin-left: auto; - } - /* Fixes old versions of FireFox */ - /* @noflip */ - body.rtl div.vectorMenu > div.menu, - x:-moz-any-link { - margin-left: 23px; - } - div.vectorMenu:hover div.menu { - display: block; - } - div.vectorMenu ul { - position: absolute; - - /* thanks to http://blog.fakedarren.com/2010/01/cross-browser-css-gradients/ */ - /* and http://www.puremango.co.uk/2010/04/css-gradient/ */ - /* fallback (Opera) */ - background: white; - /* Mozilla: */ - background: -moz-linear-gradient(top, white, #b7c8b7); - /* Chrome, Safari:*/ - background: -webkit-gradient(linear, - left top, left bottom, from(white), to(#b7c8b7)); - /* MSIE */ - filter: progid:DXImageTransform.Microsoft.Gradient( - StartColorStr='white', EndColorStr='#b7c8b7', GradientType=0); - - /*background-color: white;*/ - border: solid 1px silver; - border-top-width: 0; - list-style: none; - list-style-image: none; - list-style-type: none; - padding: 0; - margin: 0; - margin-left: -1px; - text-align: left; - } - /* Fixes old versions of FireFox */ - div.vectorMenu ul, - x:-moz-any-link { - min-width: 5em; - } - /* Returns things back to normal in modern versions of FireFox */ - div.vectorMenu ul, - x:-moz-any-link, - x:default { - min-width: 0; - } - div.vectorMenu li { - padding: 0; - margin: 0; - text-align: left; - line-height: 1em; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - div.vectorMenu li a { - display: inline-block; - padding: 0.5em; - white-space: nowrap; - } - /* IGNORED BY IE6 */ - div.vectorMenu li > a { - display: block; - } - div.vectorMenu li a { - color: #0645ad; - cursor: pointer; - font-size: 0.8em; - } - div.vectorMenu li.selected a, - div.vectorMenu li.selected a:visited { - color: #333333; - text-decoration: none; - } - /* Search */ - #p-search h5 { - display: none; - } - /* @noflip */ - #p-search { - float: left; - } - #p-search { - margin-right: 0.5em; - margin-left: 0.5em; - } - #p-search form, - #p-search input { - margin: 0; - margin-top: 0.4em; - } - #simpleSearch { - margin-top: 0.5em; - position: relative; - border: solid 1px #AAAAAA; - background-color: white; - background-image: url(images/search-fade.png); - background-position: top left; - background-repeat: repeat-x; - } - #simpleSearch label { - font-size: 0.8em; - top: 0.25em; - } - #simpleSearch input#searchInput { - margin: 0; - border-width: 0; - padding: 0.25em; - line-height: 1em; - font-size: 0.8em; - width: 9em; - background-color: transparent; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - #simpleSearch button#searchButton { - margin: 0; - padding: 0; - width: 1.75em; - height: 1.5em; - border: none; - cursor: pointer; - background-color: transparent; - background-image: url(images/search-ltr.png); - background-position: center center; - background-repeat: no-repeat; - } - /* IGNORED BY IE6 */ - #simpleSearch > button#searchButton { - height: 100%; - } - .suggestions-special .special-label { - font-size: 0.8em; - color: gray; - } - .suggestions-special .special-query { - color: black; - font-style: italic; - } - .suggestions-special .special-hover { - background-color: silver; - } -/* Panel */ -#mw-panel { - position: absolute; - top: 160px; - padding-top: 1em; - width: 10em; - left: 0; -} - #mw-panel div.portal { - padding-bottom: 1.5em; - } - #mw-panel div.portal h5 { - font-weight: normal; - color: #444444; - padding: 0.25em; - padding-top: 0; - padding-left: 1.75em; - cursor: default; - border: none; - font-size: 0.75em; - } - #mw-panel div.portal div.body { - margin: 0; - padding-top: 0.5em; - margin-left: 1.25em; - background-image: url(images/portal-break.png); - background-repeat: no-repeat; - background-position: top left; - } - #mw-panel div.portal div.body ul { - list-style: none; - list-style-image: none; - list-style-type: none; - padding: 0; - margin: 0; - } - #mw-panel div.portal div.body ul li { - line-height: 1.125em; - padding: 0; - padding-bottom: 0.5em; - margin: 0; - overflow: hidden; - font-size: 0.75em; - } - #mw-panel div.portal div.body ul li a { - color: #0645ad; - } - #mw-panel div.portal div.body ul li a:visited { - color: #0b0080; - } -/* Footer */ -#footer { - margin-left: 10em; - margin-top: 0; - padding: 0.75em; - background-image: url(images/border.png); - background-position: top left; - background-repeat: repeat-x; -} -#footer ul { - list-style: none; - list-style-image: none; - list-style-type: none; - margin: 0; - padding: 0; -} -#footer ul li { - margin: 0; - padding: 0; - padding-top: 0.5em; - padding-bottom: 0.5em; - color: #333333; - font-size: 0.7em; -} -#footer #footer-icons { - float: right; -} -/* @noflip */ -body.ltr #footer #footer-places { - float: left; -} -#footer #footer-info li { - line-height: 1.4em; -} -#footer #footer-icons li { - float: left; - margin-left: 0.5em; - line-height: 2em; -} -#footer #footer-places li { - float: left; - margin-right: 1em; - line-height: 2em; -} -/* Logo */ -#p-logo { - position: absolute; - top: -160px; - left: 0; - width: 10em; - height: 160px; -} -#p-logo a { - display: block; - width: 10em; - height: 160px; - background-repeat: no-repeat; - background-position: center center; - text-decoration: none; -} - -/* - * - * The following code is highly modified from monobook. It would be nice if the - * preftoc id was more human readable like preferences-toc for instance, - * howerver this would require backporting the other skins. - */ - -/* Preferences */ -#preftoc { - /* Tabs */ - width: 100%; - float: left; - clear: both; - margin: 0 !important; - padding: 0 !important; - background-image: url(images/preferences-break.png); - background-position: bottom left; - background-repeat: no-repeat; -} - #preftoc li { - /* Tab */ - float: left; - margin: 0; - padding: 0; - padding-right: 1px; - height: 2.25em; - white-space: nowrap; - list-style-type: none; - list-style-image: none; - background-image: url(images/preferences-break.png); - background-position: bottom right; - background-repeat: no-repeat; - } - /* IGNORED BY IE6 */ - #preftoc li:first-child { - margin-left: 1px; - } - #preftoc a, - #preftoc a:active { - display: inline-block; - position: relative; - color: #0645ad; - padding: 0.5em; - text-decoration: none; - background-image: none; - font-size: 0.9em; - } - #preftoc a:hover { - text-decoration: underline; - } - #preftoc li.selected a { - background-image: url(images/preferences-fade.png); - background-position: bottom; - background-repeat: repeat-x; - color: #333333; - text-decoration: none; - } -#preferences { - float: left; - width: 100%; - margin: 0; - margin-top: -2px; - clear: both; - border: solid 1px #cccccc; - background-color: #f9f9f9; - background-image: url(images/preferences-base.png); -} -#preferences fieldset.prefsection { - border: none; - padding: 0; - margin: 1em; -} -#preferences fieldset.prefsection fieldset { - border: none; - border-top: solid 1px #cccccc; -} -#preferences legend { - color: #666666; -} -#preferences fieldset.prefsection legend.mainLegend { - display: none; -} -#preferences td { - padding-left: 0.5em; - padding-right: 0.5em; -} -#preferences td.htmlform-tip { - font-size: x-small; - padding: .2em 2em; - color: #666666; -} -#preferences div.mw-prefs-buttons { - padding: 1em; -} -#preferences div.mw-prefs-buttons input { - margin-right: 0.25em; -} - -/* - * Styles for the user login and create account forms - */ -#userlogin, #userloginForm { - border: solid 1px #cccccc; - padding: 1.2em; - margin: .5em; - float: left; -} - -#userlogin { - min-width: 20em; - max-width: 90%; - width: 40em; -} - -/* - * - * The following code is slightly modified from monobook - * - */ -#content { - line-height: 1.5em; -} -#bodyContent { - font-size: 0.8em; -} -/* Links */ -a { - text-decoration: none; - color: #0645ad; - /*color: #67536c;*/ - background: none; -} -a:visited { - color: #0b0080; -} -a:active { - color: #faa700; -} -a:hover { - text-decoration: underline; -} -a.stub { - color: #772233; -} -a.new, #p-personal a.new { - color: #ba0000; -} -a.new:visited, #p-personal a.new:visited { - color: #a55858; -} - -/* Inline Elements */ -img { - border: none; - vertical-align: middle; -} -hr { - height: 1px; - color: #aaa; - background-color: #aaa; - border: 0; - margin: .2em 0 .2em 0; -} - -/* Structural Elements */ -h1, -h2, -h3, -h4, -h5, -h6 { - /*color: black;*/ - color: #67536c; - background: none; - font-weight: normal; - margin: 0; - padding-top: .5em; - padding-bottom: .17em; - border-bottom: 1px solid #aaa; - width: auto; -} -h1 { font-size: 188%; } -h1 .editsection { font-size: 53%; } -h2 { font-size: 150%; } -h2 .editsection { font-size: 67%; } -h3, -h4, -h5, -h6 { - border-bottom: none; - font-weight: bold; -} -h3 { font-size: 132%; } -h3 .editsection { font-size: 76%; font-weight: normal; } -h4 { font-size: 116%; } -h4 .editsection { font-size: 86%; font-weight: normal; } -h5 { font-size: 100%; } -h5 .editsection { font-weight: normal; } -h6 { font-size: 80%; } -h6 .editsection { font-size: 125%; font-weight: normal; } -p { - margin: .4em 0 .5em 0; - line-height: 1.5em; -} - p img { - margin: 0; - } -abbr, -acronym, -.explain { - border-bottom: 1px dotted black; - color: black; - background: none; - cursor: help; -} -q { - font-family: Times, "Times New Roman", serif; - font-style: italic; -} -/* Disabled for now -blockquote { - font-family: Times, "Times New Roman", serif; - font-style: italic; -}*/ -code { - background-color: #f9f9f9; -} -pre { - padding: 1em; - border: 1px dashed #2f6fab; - color: black; - background-color: #f9f9f9; - line-height: 1.1em; -} -ul { - line-height: 1.5em; - list-style-type: square; - margin: .3em 0 0 1.5em; - padding: 0; - list-style-image: url(images/bullet-icon.png); -} -ol { - line-height: 1.5em; - margin: .3em 0 0 3.2em; - padding: 0; - list-style-image: none; -} -li { - margin-bottom: .1em; -} -dt { - font-weight: bold; - margin-bottom: .1em; -} -dl { - margin-top: .2em; - margin-bottom: .5em; -} -dd { - line-height: 1.5em; - margin-left: 2em; - margin-bottom: .1em; -} -/* Tables */ -table { - font-size: 100%; - color: black; - /* we don't want the bottom borders of

    s to be visible through - * floated tables */ - background-color: white; -} -fieldset table { - /* but keep table layouts in forms clean... */ - background: none; -} -/* Forms */ -fieldset { - border: 1px solid #2f6fab; - margin: 1em 0 1em 0; - padding: 0 1em 1em; - line-height: 1.5em; -} - fieldset.nested { - margin: 0 0 0.5em 0; - padding: 0 0.5em 0.5em; - } -legend { - padding: .5em; - font-size: 95%; -} -form { - border: none; - margin: 0; -} -textarea { - width: 100%; - padding: .1em; -} -select { - vertical-align: top; -} -/* Table of Contents */ -#toc, -.toc, -.mw-warning { - border: 1px solid #aaa; - background-color: #f9f9f9; - padding: 5px; - font-size: 95%; -} -#toc h2, -.toc h2 { - display: inline; - border: none; - padding: 0; - font-size: 100%; - font-weight: bold; -} -#toc #toctitle, -.toc #toctitle, -#toc .toctitle, -.toc .toctitle { - text-align: center; -} -#toc ul, -.toc ul { - list-style-type: none; - list-style-image: none; - margin-left: 0; - padding-left: 0; - text-align: left; -} -#toc ul ul, -.toc ul ul { - margin: 0 0 0 2em; -} -#toc .toctoggle, -.toc .toctoggle { - font-size: 94%; -} -/* Images */ -div.floatright, table.floatright { - clear: right; - float: right; - position: relative; - margin: 0 0 .5em .5em; - border: 0; -} -div.floatright p { font-style: italic; } -div.floatleft, table.floatleft { - float: left; - clear: left; - position: relative; - margin: 0 .5em .5em 0; - border: 0; -} -div.floatleft p { font-style: italic; } -/* Thumbnails */ -div.thumb { - margin-bottom: .5em; - border-style: solid; - border-color: white; - width: auto; - background-color: transparent; -} -div.thumbinner { - border: 1px solid #cccccc; - padding: 3px !important; - background-color: #f9f9f9; - font-size: 94%; - text-align: center; - overflow: hidden; -} -html .thumbimage { - border: 1px solid #ccc; -} -html .thumbcaption { - border: none; - text-align: left; - line-height: 1.4em; - padding: 3px !important; - font-size: 94%; -} -div.magnify { - float: right; - border: none !important; - background: none !important; -} -div.magnify a, div.magnify img { - display: block; - border: none !important; - background: none !important; -} -div.tright { - clear: right; - float: right; - border-width: .5em 0 .8em 1.4em; -} -div.tleft { - float: left; - clear: left; - margin-right: .5em; - border-width: .5em 1.4em .8em 0; -} -img.thumbborder { - border: 1px solid #dddddd; -} -.hiddenStructure { - display: none; -} -/* Warning */ -.mw-warning { - margin-left: 50px; - margin-right: 50px; - text-align: center; -} -/* User Message */ -.usermessage { - background-color: #ffce7b; - border: 1px solid #ffa500; - color: black; - font-weight: bold; - margin: 2em 0 1em; - padding: .5em 1em; - vertical-align: middle; -} -/* Site Notice */ -#siteNotice { - text-align: center; - font-size: 0.8em; - margin: 0; -} - #siteNotice div, - #siteNotice p { - margin: 0; - padding: 0; - margin-bottom: 0.9em; - } -/* Categories */ -.catlinks { - border: 1px solid #888; - background-color: #cccccc; - padding: 5px; - margin-top: 1em; - clear: both; -} -/* Sub-navigation */ -#siteSub { - display: none; -} -#jump-to-nav { - display: none; -} -#contentSub, #contentSub2 { - font-size: 84%; - line-height: 1.2em; - margin: 0 0 1.4em 1em; - color: #7d7d7d; - width: auto; -} -span.subpages { - display: block; -} -/* Emulate Center */ -.center { - width: 100%; - text-align: center; -} -*.center * { - margin-left: auto; - margin-right: auto; -} -/* Small for tables and similar */ -.small, .small * { - font-size: 94%; -} -table.small { - font-size: 100%; -} -/* Edge Cases for Content */ -h1, h2 { - margin-bottom: .6em; -} -h3, h4, h5 { - margin-bottom: .3em; -} -#firstHeading { - padding-top: 0; - margin-top: 0; - padding-top: 0; - margin-bottom: 0.1em; - line-height: 1.2em; - font-size: 1.6em; - padding-bottom: 0; -} -#content a.external, -#content a[href ^="gopher://"] { - background: url(images/external-link-ltr-icon.png) center right no-repeat; - padding: 0 13px 0 0; -} -#content a[href ^="https://"], -.link-https { - background: url(images/lock-icon.png) center right no-repeat; - padding: 0 18px 0 0; -} -#content a[href ^="mailto:"], -.link-mailto { - background: url(images/mail-icon.png) center right no-repeat; - padding: 0 18px 0 0; -} -#content a[href ^="news://"] { - background: url(images/news-icon.png) center right no-repeat; - padding: 0 18px 0 0; -} -#content a[href ^="ftp://"], -.link-ftp { - background: url(images/file-icon.png) center right no-repeat; - padding: 0 18px 0 0; -} -#content a[href ^="irc://"], -#content a.extiw[href ^="irc://"], -.link-irc { - background: url(images/talk-icon.png) center right no-repeat; - padding: 0 18px 0 0; -} -#content a.external[href $=".ogg"], #content a.external[href $=".OGG"], -#content a.external[href $=".mid"], #content a.external[href $=".MID"], -#content a.external[href $=".midi"], #content a.external[href $=".MIDI"], -#content a.external[href $=".mp3"], #content a.external[href $=".MP3"], -#content a.external[href $=".wav"], #content a.external[href $=".WAV"], -#content a.external[href $=".wma"], #content a.external[href $=".WMA"], -.link-audio { - background: url("images/audio-icon.png") center right no-repeat; - padding: 0 18px 0 0; -} -#content a.external[href $=".ogm"], #content a.external[href $=".OGM"], -#content a.external[href $=".avi"], #content a.external[href $=".AVI"], -#content a.external[href $=".mpeg"], #content a.external[href $=".MPEG"], -#content a.external[href $=".mpg"], #content a.external[href $=".MPG"], -.link-video { - background: url("images/video-icon.png") center right no-repeat; - padding: 0 18px 0 0; -} -#content a.external[href $=".pdf"], #content a.external[href $=".PDF"], -#content a.external[href *=".pdf#"], #content a.external[href *=".PDF#"], -#content a.external[href *=".pdf?"], #content a.external[href *=".PDF?"], -.link-document { - background: url("images/document-icon.png") center right no-repeat; - padding: 0 18px 0 0; -} -/* Interwiki Styling (Disabled) */ -#content a.extiw, -#content a.extiw:active { - color: #36b; - background: none; - padding: 0; -} -#content a.external { - color: #36b; -} -#content .printfooter { - display: none; -} -/* Icon for Usernames */ -#pt-userpage, -#pt-anonuserpage, -#pt-login { - background: url(images/user-icon.png) left top no-repeat; - padding-left: 15px !important; - text-transform: none; -} - -.toccolours { - border: 1px solid #aaa; - background-color: #f9f9f9; - padding: 5px; - font-size: 95%; -} -#bodyContent { - position: relative; - width: 100%; -} -#mw-js-message { - font-size: 0.8em; -} -div#bodyContent { - line-height: 1.5em; -} - -/* Watch/Unwatch Icon Styling */ -#ca-unwatch.icon, -#ca-watch.icon { - margin-right:1px; -} -#ca-unwatch.icon a, -#ca-watch.icon a { - margin: 0; - padding: 0; - outline: none; - display: block; - width: 26px; - height: 2.5em; -} -#ca-unwatch.icon a { - background-image: url(images/watch-icons.png); - background-position: -43px 60%; -} -#ca-watch.icon a { - background-image: url(images/watch-icons.png); - background-position: 5px 60%; -} -#ca-unwatch.icon a:hover { - background-image: url(images/watch-icons.png); - background-position: -67px 60%; -} -#ca-watch.icon a:hover { - background-image: url(images/watch-icons.png); - background-position: -19px 60%; -} -#ca-unwatch.icon a.loading, -#ca-watch.icon a.loading { - background-image: url(images/watch-icon-loading.gif); - background-position: center 60%; -} -#ca-unwatch.icon a span, -#ca-watch.icon a span { - display: none; -} -div.vectorTabs ul { - background-image:url(images/tab-break.png); - background-position:right bottom; - background-repeat:no-repeat; -} diff --git a/preecej/semantic_wiki/skins/planteome/main-rtl.css b/preecej/semantic_wiki/skins/planteome/main-rtl.css deleted file mode 100644 index 5387289..0000000 --- a/preecej/semantic_wiki/skins/planteome/main-rtl.css +++ /dev/null @@ -1,1128 +0,0 @@ -/* - * main-rtl.css is automatically generated using CSSJanus, a python script for - * creating RTL versions of otherwise LTR stylesheets. - * - * You may download the tool to rebuild this stylesheet - * http://code.google.com/p/cssjanus/ - * - * An online version of this tool can be used at: - * http://cssjanus.commoner.com/ - * - * The following command is used to generate the RTL version of this file - * ./cssjanus.py --swap_ltr_rtl_in_url < main-ltr.css > main-rtl.css - * - * Any rules which should not be flipped should be prepended with @noflip in - * a comment block. - */ -/* Framework */ -html, -body { - height: 100%; - margin: 0; - padding: 0; - font-family: sans-serif; - font-size: 1em; -} -body { - background-color: #f3f3f3; - background-image: url(images/page-base.png); -} -/* Content */ -#content { - margin-right: 10em; - padding: 1em; - background-image: url(images/border.png); - background-position: top right; - background-repeat: repeat-y; - background-color: white; -} -/* Head */ -#mw-page-base { - height: 5em; - background-color: white; - background-image: url(images/page-fade.png); - background-position: bottom right; - background-repeat: repeat-x; -} -#mw-head-base { - margin-top: -5em; - margin-right: 10em; - height: 5em; - background-image: url(images/border.png); - background-position: bottom right; - background-repeat: repeat-x; -} -#mw-head { - position: absolute; - top: 0; - left: 0; - width: 100%; -} -#mw-head h5 { - margin: 0; - padding: 0; -} - /* Hide empty portlets */ - div.emptyPortlet { - display: none; - } - /* Personal */ - #p-personal { - position: absolute; - top: 0; - margin-right: 10em; - left: 0.75em; - } - #p-personal h5 { - display: none; - } - #p-personal ul { - list-style: none; - margin: 0; - padding: 0; - } - /* @noflip */ - #p-personal li { - line-height: 1.125em; - float: left; - } - #p-personal li { - margin-right: 0.75em; - margin-top: 0.5em; - font-size: 0.75em; - } - /* Navigation Containers */ - #left-navigation { - position: absolute; - right: 10em; - top: 2.5em; - } - #right-navigation { - float: left; - margin-top: 2.5em; - } - /* Navigation Labels */ - div.vectorTabs h5, - div.vectorMenu h5 span { - display: none; - } - /* Namespaces and Views */ - /* @noflip */ - div.vectorTabs { - float: left; - } - div.vectorTabs { - background-image: url(images/tab-break.png); - background-position: bottom right; - background-repeat: no-repeat; - padding-right: 1px; - } - /* @noflip */ - div.vectorTabs ul { - float: left; - } - div.vectorTabs ul { - height: 100%; - list-style: none; - margin: 0; - padding: 0; - } - /* @noflip */ - div.vectorTabs ul li { - float: left; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - div.vectorTabs ul li { - line-height: 1.125em; - display: inline-block; - height: 100%; - margin: 0; - padding: 0; - background-color: #f3f3f3; - background-image: url(images/tab-normal-fade.png); - background-position: bottom right; - background-repeat: repeat-x; - white-space:nowrap; - } - /* IGNORED BY IE6 */ - div.vectorTabs ul > li { - display: block; - } - div.vectorTabs li.selected { - background-image: url(images/tab-current-fade.png); - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - div.vectorTabs li a { - display: inline-block; - height: 2.5em; - padding-right: 0.4em; - padding-left: 0.4em; - background-image: url(images/tab-break.png); - background-position: bottom left; - background-repeat: no-repeat; - } - div.vectorTabs li a, - div.vectorTabs li a span { - color: #0645ad; - cursor: pointer; - } - div.vectorTabs li a span { - font-size: 0.8em; - } - /* IGNORED BY IE6 */ - div.vectorTabs li > a { - display: block; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - div.vectorTabs a span { - display: inline-block; - padding-top: 1.25em; - } - /* IGNORED BY IE6 */ - /* @noflip */ - div.vectorTabs a > span { - float: left; - display: block; - } - div.vectorTabs li.selected a, - div.vectorTabs li.selected a span, - div.vectorTabs li.selected a:visited - div.vectorTabs li.selected a:visited span { - color: #333333; - text-decoration: none; - } - div.vectorTabs li.new a, - div.vectorTabs li.new a span, - div.vectorTabs li.new a:visited, - div.vectorTabs li.new a:visited span { - color: #a55858; - } - /* Variants and Actions */ - /* @noflip */ - div.vectorMenu { - direction: ltr; - float: left; - background-image: url(images/arrow-down-icon.png); - background-position: center center; - background-repeat: no-repeat; - } - /* @noflip */ - body.rtl div.vectorMenu { - direction: rtl; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - /* @noflip */ - #mw-head div.vectorMenu h5 { - float: left; - background-image: url(images/tab-break.png); - background-repeat: no-repeat; - } - /* IGNORED BY IE6 */ - #mw-head div.vectorMenu > h5 { - background-image: none; - } - #mw-head div.vectorMenu h5 { - background-position: bottom right; - margin-right: -1px; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - /* @noflip */ - div.vectorMenu h5 a { - display: inline-block; - width: 24px; - height: 2.5em; - text-decoration: none; - background-image: url(images/tab-break.png); - background-repeat: no-repeat; - } - div.vectorMenu h5 a{ - background-position: bottom left; - } - /* IGNORED BY IE6 */ - div.vectorMenu h5 > a { - display: block; - } - div.vectorMenu div.menu { - position: relative; - display: none; - clear: both; - text-align: right; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - /* @noflip */ - body.rtl div.vectorMenu div.menu { - margin-left: 24px; - } - /* IGNORED BY IE6 */ - /* @noflip */ - body.rtl div.vectorMenu > div.menu { - margin-left: auto; - } - /* Fixes old versions of FireFox */ - /* @noflip */ - body.rtl div.vectorMenu > div.menu, - x:-moz-any-link { - margin-left: 23px; - } - div.vectorMenu:hover div.menu { - display: block; - } - div.vectorMenu ul { - position: absolute; - background-color: white; - border: solid 1px silver; - border-top-width: 0; - list-style: none; - list-style-image: none; - list-style-type: none; - padding: 0; - margin: 0; - margin-right: -1px; - text-align: right; - } - /* Fixes old versions of FireFox */ - div.vectorMenu ul, - x:-moz-any-link { - min-width: 5em; - } - /* Returns things back to normal in modern versions of FireFox */ - div.vectorMenu ul, - x:-moz-any-link, - x:default { - min-width: 0; - } - div.vectorMenu li { - padding: 0; - margin: 0; - text-align: right; - line-height: 1em; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - div.vectorMenu li a { - display: inline-block; - padding: 0.5em; - white-space: nowrap; - } - /* IGNORED BY IE6 */ - div.vectorMenu li > a { - display: block; - } - div.vectorMenu li a { - color: #0645ad; - cursor: pointer; - font-size: 0.8em; - } - div.vectorMenu li.selected a, - div.vectorMenu li.selected a:visited { - color: #333333; - text-decoration: none; - } - /* Search */ - #p-search h5 { - display: none; - } - /* @noflip */ - #p-search { - float: left; - } - #p-search { - margin-left: 0.5em; - margin-right: 0.5em; - } - #p-search form, - #p-search input { - margin: 0; - margin-top: 0.4em; - } - #simpleSearch { - margin-top: 0.5em; - position: relative; - border: solid 1px #AAAAAA; - background-color: white; - background-image: url(images/search-fade.png); - background-position: top right; - background-repeat: repeat-x; - } - #simpleSearch label { - font-size: 0.8em; - top: 0.25em; - } - #simpleSearch input#searchInput { - margin: 0; - border-width: 0; - padding: 0.25em; - line-height: 1em; - font-size: 0.8em; - width: 9em; - background-color: transparent; - } - /* OVERRIDDEN BY COMPLIANT BROWSERS */ - #simpleSearch button#searchButton { - margin: 0; - padding: 0; - width: 1.75em; - height: 1.5em; - border: none; - cursor: pointer; - background-color: transparent; - background-image: url(images/search-rtl.png); - background-position: center center; - background-repeat: no-repeat; - } - /* IGNORED BY IE6 */ - #simpleSearch > button#searchButton { - height: 100%; - } - .suggestions-special .special-label { - font-size: 0.8em; - color: gray; - } - .suggestions-special .special-query { - color: black; - font-style: italic; - } - .suggestions-special .special-hover { - background-color: silver; - } -/* Panel */ -#mw-panel { - position: absolute; - top: 160px; - padding-top: 1em; - width: 10em; - right: 0; -} - #mw-panel div.portal { - padding-bottom: 1.5em; - } - #mw-panel div.portal h5 { - font-weight: normal; - color: #444444; - padding: 0.25em; - padding-top: 0; - padding-right: 1.75em; - cursor: default; - border: none; - font-size: 0.75em; - } - #mw-panel div.portal div.body { - margin: 0; - padding-top: 0.5em; - margin-right: 1.25em; - background-image: url(images/portal-break.png); - background-repeat: no-repeat; - background-position: top right; - } - #mw-panel div.portal div.body ul { - list-style: none; - list-style-image: none; - list-style-type: none; - padding: 0; - margin: 0; - } - #mw-panel div.portal div.body ul li { - line-height: 1.125em; - padding: 0; - padding-bottom: 0.5em; - margin: 0; - overflow: hidden; - font-size: 0.75em; - } - #mw-panel div.portal div.body ul li a { - color: #0645ad; - } - #mw-panel div.portal div.body ul li a:visited { - color: #0b0080; - } -/* Footer */ -#footer { - margin-right: 10em; - margin-top: 0; - padding: 0.75em; - background-image: url(images/border.png); - background-position: top right; - background-repeat: repeat-x; -} -#footer ul { - list-style: none; - list-style-image: none; - list-style-type: none; - margin: 0; - padding: 0; -} -#footer ul li { - margin: 0; - padding: 0; - padding-top: 0.5em; - padding-bottom: 0.5em; - color: #333333; - font-size: 0.7em; -} -#footer #footer-icons { - float: left; -} -/* @noflip */ -body.ltr #footer #footer-places { - float: left; -} -#footer #footer-info li { - line-height: 1.4em; -} -#footer #footer-icons li { - float: right; - margin-right: 0.5em; - line-height: 2em; -} -#footer #footer-places li { - float: right; - margin-left: 1em; - line-height: 2em; -} -/* Logo */ -#p-logo { - position: absolute; - top: -160px; - right: 0; - width: 10em; - height: 160px; -} -#p-logo a { - display: block; - width: 10em; - height: 160px; - background-repeat: no-repeat; - background-position: center center; - text-decoration: none; -} - -/* - * - * The following code is highly modified from monobook. It would be nice if the - * preftoc id was more human readable like preferences-toc for instance, - * howerver this would require backporting the other skins. - */ - -/* Preferences */ -#preftoc { - /* Tabs */ - width: 100%; - float: right; - clear: both; - margin: 0 !important; - padding: 0 !important; - background-image: url(images/preferences-break.png); - background-position: bottom right; - background-repeat: no-repeat; -} - #preftoc li { - /* Tab */ - float: right; - margin: 0; - padding: 0; - padding-left: 1px; - height: 2.25em; - white-space: nowrap; - list-style-type: none; - list-style-image: none; - background-image: url(images/preferences-break.png); - background-position: bottom left; - background-repeat: no-repeat; - } - /* IGNORED BY IE6 */ - #preftoc li:first-child { - margin-right: 1px; - } - #preftoc a, - #preftoc a:active { - display: inline-block; - position: relative; - color: #0645ad; - padding: 0.5em; - text-decoration: none; - background-image: none; - font-size: 0.9em; - } - #preftoc a:hover { - text-decoration: underline; - } - #preftoc li.selected a { - background-image: url(images/preferences-fade.png); - background-position: bottom; - background-repeat: repeat-x; - color: #333333; - text-decoration: none; - } -#preferences { - float: right; - width: 100%; - margin: 0; - margin-top: -2px; - clear: both; - border: solid 1px #cccccc; - background-color: #f9f9f9; - background-image: url(images/preferences-base.png); -} -#preferences fieldset.prefsection { - border: none; - padding: 0; - margin: 1em; -} -#preferences fieldset.prefsection fieldset { - border: none; - border-top: solid 1px #cccccc; -} -#preferences legend { - color: #666666; -} -#preferences fieldset.prefsection legend.mainLegend { - display: none; -} -#preferences td { - padding-right: 0.5em; - padding-left: 0.5em; -} -#preferences td.htmlform-tip { - font-size: x-small; - padding: .2em 2em; - color: #666666; -} -#preferences div.mw-prefs-buttons { - padding: 1em; -} -#preferences div.mw-prefs-buttons input { - margin-left: 0.25em; -} - -/* - * Styles for the user login and create account forms - */ -#userlogin, #userloginForm { - border: solid 1px #cccccc; - padding: 1.2em; - margin: .5em; - float: right; -} - -#userlogin { - min-width: 20em; - max-width: 90%; - width: 40em; -} - -/* - * - * The following code is slightly modified from monobook - * - */ -#content { - line-height: 1.5em; -} -#bodyContent { - font-size: 0.8em; -} -/* Links */ -a { - text-decoration: none; - color: #0645ad; - background: none; -} -a:visited { - color: #0b0080; -} -a:active { - color: #faa700; -} -a:hover { - text-decoration: underline; -} -a.stub { - color: #772233; -} -a.new, #p-personal a.new { - color: #ba0000; -} -a.new:visited, #p-personal a.new:visited { - color: #a55858; -} - -/* Inline Elements */ -img { - border: none; - vertical-align: middle; -} -hr { - height: 1px; - color: #aaa; - background-color: #aaa; - border: 0; - margin: .2em 0 .2em 0; -} - -/* Structural Elements */ -h1, -h2, -h3, -h4, -h5, -h6 { - color: black; - background: none; - font-weight: normal; - margin: 0; - padding-top: .5em; - padding-bottom: .17em; - border-bottom: 1px solid #aaa; - width: auto; -} -h1 { font-size: 188%; } -h1 .editsection { font-size: 53%; } -h2 { font-size: 150%; } -h2 .editsection { font-size: 67%; } -h3, -h4, -h5, -h6 { - border-bottom: none; - font-weight: bold; -} -h3 { font-size: 132%; } -h3 .editsection { font-size: 76%; font-weight: normal; } -h4 { font-size: 116%; } -h4 .editsection { font-size: 86%; font-weight: normal; } -h5 { font-size: 100%; } -h5 .editsection { font-weight: normal; } -h6 { font-size: 80%; } -h6 .editsection { font-size: 125%; font-weight: normal; } -p { - margin: .4em 0 .5em 0; - line-height: 1.5em; -} - p img { - margin: 0; - } -abbr, -acronym, -.explain { - border-bottom: 1px dotted black; - color: black; - background: none; - cursor: help; -} -q { - font-family: Times, "Times New Roman", serif; - font-style: italic; -} -/* Disabled for now -blockquote { - font-family: Times, "Times New Roman", serif; - font-style: italic; -}*/ -code { - background-color: #f9f9f9; -} -pre { - padding: 1em; - border: 1px dashed #2f6fab; - color: black; - background-color: #f9f9f9; - line-height: 1.1em; -} -ul { - line-height: 1.5em; - list-style-type: square; - margin: .3em 1.5em 0 0; - padding: 0; - list-style-image: url(images/bullet-icon.png); -} -ol { - line-height: 1.5em; - margin: .3em 3.2em 0 0; - padding: 0; - list-style-image: none; -} -li { - margin-bottom: .1em; -} -dt { - font-weight: bold; - margin-bottom: .1em; -} -dl { - margin-top: .2em; - margin-bottom: .5em; -} -dd { - line-height: 1.5em; - margin-right: 2em; - margin-bottom: .1em; -} -/* Tables */ -table { - font-size: 100%; - color: black; - /* we don't want the bottom borders of

    s to be visible through - * floated tables */ - background-color: white; -} -fieldset table { - /* but keep table layouts in forms clean... */ - background: none; -} -/* Forms */ -fieldset { - border: 1px solid #2f6fab; - margin: 1em 0 1em 0; - padding: 0 1em 1em; - line-height: 1.5em; -} - fieldset.nested { - margin: 0 0 0.5em 0; - padding: 0 0.5em 0.5em; - } -legend { - padding: .5em; - font-size: 95%; -} -form { - border: none; - margin: 0; -} -textarea { - width: 100%; - padding: .1em; -} -select { - vertical-align: top; -} -/* Table of Contents */ -#toc, -.toc, -.mw-warning { - border: 1px solid #aaa; - background-color: #f9f9f9; - padding: 5px; - font-size: 95%; -} -#toc h2, -.toc h2 { - display: inline; - border: none; - padding: 0; - font-size: 100%; - font-weight: bold; -} -#toc #toctitle, -.toc #toctitle, -#toc .toctitle, -.toc .toctitle { - text-align: center; -} -#toc ul, -.toc ul { - list-style-type: none; - list-style-image: none; - margin-right: 0; - padding-right: 0; - text-align: right; -} -#toc ul ul, -.toc ul ul { - margin: 0 2em 0 0; -} -#toc .toctoggle, -.toc .toctoggle { - font-size: 94%; -} -/* Images */ -div.floatright, table.floatright { - clear: left; - float: left; - position: relative; - margin: 0 .5em .5em 0; - border: 0; -} -div.floatright p { font-style: italic; } -div.floatleft, table.floatleft { - float: right; - clear: right; - position: relative; - margin: 0 0 .5em .5em; - border: 0; -} -div.floatleft p { font-style: italic; } -/* Thumbnails */ -div.thumb { - margin-bottom: .5em; - border-style: solid; - border-color: white; - width: auto; - background-color: transparent; -} -div.thumbinner { - border: 1px solid #ccc; - padding: 3px !important; - background-color: #f9f9f9; - font-size: 94%; - text-align: center; - overflow: hidden; -} -html .thumbimage { - border: 1px solid #ccc; -} -html .thumbcaption { - border: none; - text-align: right; - line-height: 1.4em; - padding: 3px !important; - font-size: 94%; -} -div.magnify { - float: left; - border: none !important; - background: none !important; -} -div.magnify a, div.magnify img { - display: block; - border: none !important; - background: none !important; -} -div.tright { - clear: left; - float: left; - border-width: .5em 1.4em .8em 0; -} -div.tleft { - float: right; - clear: right; - margin-left: .5em; - border-width: .5em 0 .8em 1.4em; -} -img.thumbborder { - border: 1px solid #dddddd; -} -.hiddenStructure { - display: none; -} -/* Warning */ -.mw-warning { - margin-right: 50px; - margin-left: 50px; - text-align: center; -} -/* User Message */ -.usermessage { - background-color: #ffce7b; - border: 1px solid #ffa500; - color: black; - font-weight: bold; - margin: 2em 0 1em; - padding: .5em 1em; - vertical-align: middle; -} -/* Site Notice */ -#siteNotice { - text-align: center; - font-size: 0.8em; - margin: 0; -} - #siteNotice div, - #siteNotice p { - margin: 0; - padding: 0; - margin-bottom: 0.9em; - } -/* Categories */ -.catlinks { - border: 1px solid #aaa; - background-color: #f9f9f9; - padding: 5px; - margin-top: 1em; - clear: both; -} -/* Sub-navigation */ -#siteSub { - display: none; -} -#jump-to-nav { - display: none; -} -#contentSub, #contentSub2 { - font-size: 84%; - line-height: 1.2em; - margin: 0 1em 1.4em 0; - color: #7d7d7d; - width: auto; -} -span.subpages { - display: block; -} -/* Emulate Center */ -.center { - width: 100%; - text-align: center; -} -*.center * { - margin-right: auto; - margin-left: auto; -} -/* Small for tables and similar */ -.small, .small * { - font-size: 94%; -} -table.small { - font-size: 100%; -} -/* Edge Cases for Content */ -h1, h2 { - margin-bottom: .6em; -} -h3, h4, h5 { - margin-bottom: .3em; -} -#firstHeading { - padding-top: 0; - margin-top: 0; - padding-top: 0; - margin-bottom: 0.1em; - line-height: 1.2em; - font-size: 1.6em; - padding-bottom: 0; -} -#content a.external, -#content a[href ^="gopher://"] { - background: url(images/external-link-rtl-icon.png) center left no-repeat; - padding: 0 0 0 13px; -} -#content a[href ^="https://"], -.link-https { - background: url(images/lock-icon.png) center left no-repeat; - padding: 0 0 0 18px; -} -#content a[href ^="mailto:"], -.link-mailto { - background: url(images/mail-icon.png) center left no-repeat; - padding: 0 0 0 18px; -} -#content a[href ^="news://"] { - background: url(images/news-icon.png) center left no-repeat; - padding: 0 0 0 18px; -} -#content a[href ^="ftp://"], -.link-ftp { - background: url(images/file-icon.png) center left no-repeat; - padding: 0 0 0 18px; -} -#content a[href ^="irc://"], -#content a.extiw[href ^="irc://"], -.link-irc { - background: url(images/talk-icon.png) center left no-repeat; - padding: 0 0 0 18px; -} -#content a.external[href $=".ogg"], #content a.external[href $=".OGG"], -#content a.external[href $=".mid"], #content a.external[href $=".MID"], -#content a.external[href $=".midi"], #content a.external[href $=".MIDI"], -#content a.external[href $=".mp3"], #content a.external[href $=".MP3"], -#content a.external[href $=".wav"], #content a.external[href $=".WAV"], -#content a.external[href $=".wma"], #content a.external[href $=".WMA"], -.link-audio { - background: url("images/audio-icon.png") center left no-repeat; - padding: 0 0 0 18px; -} -#content a.external[href $=".ogm"], #content a.external[href $=".OGM"], -#content a.external[href $=".avi"], #content a.external[href $=".AVI"], -#content a.external[href $=".mpeg"], #content a.external[href $=".MPEG"], -#content a.external[href $=".mpg"], #content a.external[href $=".MPG"], -.link-video { - background: url("images/video-icon.png") center left no-repeat; - padding: 0 0 0 18px; -} -#content a.external[href $=".pdf"], #content a.external[href $=".PDF"], -#content a.external[href *=".pdf#"], #content a.external[href *=".PDF#"], -#content a.external[href *=".pdf?"], #content a.external[href *=".PDF?"], -.link-document { - background: url("images/document-icon.png") center left no-repeat; - padding: 0 0 0 18px; -} -/* Interwiki Styling (Disabled) */ -#content a.extiw, -#content a.extiw:active { - color: #36b; - background: none; - padding: 0; -} -#content a.external { - color: #36b; -} -#content .printfooter { - display: none; -} -/* Icon for Usernames */ -#pt-userpage, -#pt-anonuserpage, -#pt-login { - background: url(images/user-icon.png) right top no-repeat; - padding-right: 15px !important; - text-transform: none; -} - -.toccolours { - border: 1px solid #aaa; - background-color: #f9f9f9; - padding: 5px; - font-size: 95%; -} -#bodyContent { - position: relative; - width: 100%; -} -#mw-js-message { - font-size: 0.8em; -} -div#bodyContent { - line-height: 1.5em; -} - -/* Watch/Unwatch Icon Styling */ -#ca-unwatch.icon, -#ca-watch.icon { - margin-left:1px; -} -#ca-unwatch.icon a, -#ca-watch.icon a { - margin: 0; - padding: 0; - outline: none; - display: block; - width: 26px; - height: 2.5em; -} -#ca-unwatch.icon a { - background-image: url(images/watch-icons.png); - background-position: -43px 60%; -} -#ca-watch.icon a { - background-image: url(images/watch-icons.png); - background-position: 5px 60%; -} -#ca-unwatch.icon a:hover { - background-image: url(images/watch-icons.png); - background-position: -67px 60%; -} -#ca-watch.icon a:hover { - background-image: url(images/watch-icons.png); - background-position: -19px 60%; -} -#ca-unwatch.icon a.loading, -#ca-watch.icon a.loading { - background-image: url(images/watch-icon-loading.gif); - background-position: center 60%; -} -#ca-unwatch.icon a span, -#ca-watch.icon a span { - display: none; -} -div.vectorTabs ul { - background-image:url(images/tab-break.png); - background-position:left bottom; - background-repeat:no-repeat; -} diff --git a/preecej/semantic_wiki/skins/planteome/wiki-indexed.png b/preecej/semantic_wiki/skins/planteome/wiki-indexed.png deleted file mode 100644 index 189a2ae..0000000 Binary files a/preecej/semantic_wiki/skins/planteome/wiki-indexed.png and /dev/null differ diff --git a/preecej/semantic_wiki/skins/planteome/wiki.png b/preecej/semantic_wiki/skins/planteome/wiki.png deleted file mode 100644 index 2463b52..0000000 Binary files a/preecej/semantic_wiki/skins/planteome/wiki.png and /dev/null differ diff --git a/preecej/semantic_wiki/templates/Annotation.wiki b/preecej/semantic_wiki/templates/Annotation.wiki deleted file mode 100644 index f6d4f54..0000000 --- a/preecej/semantic_wiki/templates/Annotation.wiki +++ /dev/null @@ -1,133 +0,0 @@ - -This is the "Annotation" template. -It should be called in the following format: -
    -{{Annotation
-|Species Name=
-|Species ID=
-|Gene Symbol=
-|Gene Name=
-|Gene Locus=
-|Gene Type=
-|EC Number(s)=
-|Chromosome=
-|Has Phenotype=
-|Annotation Description=
-}}
-
    -Edit the page to see the template text. -    __NOTOC__ -'''[[Has Gene Symbol::{{{Gene Symbol|}}}]] (''[[Has Species Name::{{{Species Name|}}}]]'')''' - -{{#get_web_data: - |url=http://eutils.ncbi.nlm.nih.gov/entrez/eutils//esearch.fcgi?db=taxonomy&term={{{Species Name|}}} - |format=XML - |data=species_id=id -}} -{{#set:Has Species ID={{#external_value:species_id}} }} - -= Annotation = - -{| class="wikitable" -! Species Name -| [[Has Species Name::{{{Species Name|}}}]] -|- -! Species ID -| NCBI:[[Has Species ID::{{#external_value:species_id}}]] -|- -! Gene Symbol -| [[Has Gene Symbol::{{{Gene Symbol|}}}]] -|- -! Gene Name -| [[Has Gene Name::{{{Gene Name|}}}]] -|- -! Gene Synonyms -| {{#if: {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]] }} - | {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}}]] - | ?is_Gene_Synonym - | headers=hide - | mainlabel=- - | format=list - }} - | None available -}} -|- -! Gene Locus -| [[Has Gene Locus::{{{Gene Locus|}}}]] -|- -! Gene Type -| [[Has Gene Type::{{{Gene Type|}}}]] -|- -! EC number(s) -| {{#arraymap:{{{EC Numbers|}}}|,|x|[[Has EC Numbers::x]]}} -|- -! Chromosome -| [[Exists On Chromosome Number::{{{Chromosome|}}}]] -|- -! Has Phenotype? -| [[Has Phenotype::{{{Has Phenotype|}}}]] -|} - -{| class="wikitable" -! Description -| [[Has Annotation Description::{{{Annotation Description|}}}]] -|} - -{{#ifexist: {{PAGENAME}}/Provenance - | To review the provenance of this data, click [[{{PAGENAME}}/Provenance|here]]. - | -}} - -= External References = - -{{#if: {{#ask:[[Category:External_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} - | {{#ask:[[Is External Reference::~{{PAGENAME}}/External_References]] - | mainlabel=- - |? from_External_Source - |? has_External_Accession_ID - }} - | There are no external references available for this annotation. -}} - -= Ontologies = - -{{#if: {{#ask:[[Category:Ontological_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} - | {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies]] - | mainlabel=- - |? from_Ontology - |? has_Term_ID - |? has_Term_Name - |? has_Aspect - |? has_Evidence_Code - |? has_Evidence - }} - | There are no ontological associations available for this gene annotation. -}} - -= Sequences = - -{{#if: {{#ask:[[Category:Sequences]][[Is Associated With Annotation::{{PAGENAME}} ]] }} - | {{#ask:[[Is Sequence Reference::~{{PAGENAME}}/Sequences]] - | mainlabel=- - |? has_Sequence_Type - |? has_Sequence_Source - |? has_External_Accession_ID - }} - | There is no sequence data available for this gene annotation. -}} - -= Literature = - -{{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] }} - | {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] - |? has First Author - |? has Publication Title - |? has Journal Name - |? has Publication ID - }} - | There are no publications associated with this annotation. -}} - -[[Category:Annotations]] - - diff --git a/preecej/semantic_wiki/templates/External_Reference_Repeater.wiki b/preecej/semantic_wiki/templates/External_Reference_Repeater.wiki deleted file mode 100644 index 1772131..0000000 --- a/preecej/semantic_wiki/templates/External_Reference_Repeater.wiki +++ /dev/null @@ -1,24 +0,0 @@ - -This is the "External Reference Repeater" template. -It should be called in the following format: -
    -{{External Reference Repeater
-|External Source=
-|External Accession ID=
-}}
-
    -Edit the page to see the template text. -    {{#set_internal:is_External_Reference -|from_External_Source={{{External Source|}}} -|has_External_Accession_ID={{{External Accession ID|}}} -}} - -{| class="wikitable" -! Source -| [[From External Source::{{{External Source|}}}]] -|- -! Accession ID -| [[Has External Accession ID::{{{External Accession ID|}}}]] -|} - - diff --git a/preecej/semantic_wiki/templates/External_References.wiki b/preecej/semantic_wiki/templates/External_References.wiki deleted file mode 100644 index a965393..0000000 --- a/preecej/semantic_wiki/templates/External_References.wiki +++ /dev/null @@ -1,18 +0,0 @@ - -This is the "External References" template. -It should be called in the following format: -
    -{{External References
-|Annotation Page=
-}}
-
    -Edit the page to see the template text. -     -{| class="wikitable" -! Annotation Page -| [[Is Associated With Annotation::{{{Annotation Page|}}}]] -|} - -[[Category:External References]] - - diff --git a/preecej/semantic_wiki/templates/Gene_Ontology_Reference_Repeater.wiki b/preecej/semantic_wiki/templates/Gene_Ontology_Reference_Repeater.wiki deleted file mode 100644 index 019da7a..0000000 --- a/preecej/semantic_wiki/templates/Gene_Ontology_Reference_Repeater.wiki +++ /dev/null @@ -1,56 +0,0 @@ - -This is the "Gene Ontology Reference Repeater" template. -It should be called in the following format: -
    -{{Gene Ontology Reference Repeater
-|Term ID=
-|Term Name=
-|Aspect=
-|Evidence Code=
-|Evidence=
-}}
-
    -Edit the page to see the template text. -    {{#get_web_data: - |url=http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&field={{#if:{{{Term Name|}}}|name|acc}}&type=term_detail&ontology=go&qval={{#if:{{{Term Name|}}}|{{{Term Name|}}}|{{{Term ID|}}}}}&format=json - |format=JSON - |data=term_name=name,term_id=id,term_aspect=aspect,term_definition=definition,term_comment=comment -}} -{{#set_internal:is_Ontological_Reference -|from_Ontology=Gene Ontology -|has_Term_ID={{#external_value:term_id}} -|has_Term_Name={{#external_value:term_name}} -|has_Aspect={{#external_value:term_aspect}} -|has_Evidence_Code#list={{{Evidence Code|}}} -|has_Evidence#list={{{Evidence|}}} -}} -{| class="wikitable" -! Ontology -| Gene Ontology -|- -! Term Name -| [[Has Term Name::{{#external_value:term_name}}]] -|- -! Term ID -| [[Has Term ID::{{#external_value:term_id}}]] -|- -! Branch -| {{#external_value:term_aspect}} -|- -! Definition -| {{#external_value:term_definition}} -{{#if: {{#external_value:term_comment}} - | {{!}}- -! Comment -{{!}} {{#external_value:term_comment}} - | -}} -|- -! Evidence Code -| {{#arraymap:{{{Evidence Code|}}}|,|x|[[Has Evidence Code::x]]}} -|- -! Evidence -| {{#arraymap:{{{Evidence|}}}|,|x|[[Has Evidence::x]]}} -|} - - diff --git a/preecej/semantic_wiki/templates/Gene_Synonym_Repeater.wiki b/preecej/semantic_wiki/templates/Gene_Synonym_Repeater.wiki deleted file mode 100644 index 20681d1..0000000 --- a/preecej/semantic_wiki/templates/Gene_Synonym_Repeater.wiki +++ /dev/null @@ -1,14 +0,0 @@ - -This is the "Gene Synonym Repeater" template. -It should be called in the following format: -
    -{{Gene Synonym Repeater
-|Gene Synonym=
-}}
-
    -Edit the page to see the template text. -    {| class="wikitable" -! Gene Synonym -| [[Is Gene Synonym::{{{Gene Synonym|}}}]] -|} - diff --git a/preecej/semantic_wiki/templates/Gene_Synonyms.wiki b/preecej/semantic_wiki/templates/Gene_Synonyms.wiki deleted file mode 100644 index 8ed271d..0000000 --- a/preecej/semantic_wiki/templates/Gene_Synonyms.wiki +++ /dev/null @@ -1,21 +0,0 @@ - -This is the "Gene Synonyms" template. -It should be called in the following format: -
    -{{Gene Synonyms
-|Annotation Page=
-}}
-
    -Edit the page to see the template text. -     -{| class="wikitable" -! Annotation Page -| [[Is Associated With Annotation::{{{Annotation Page|}}}]] -|- -! Gene Name -| {{#show: {{{Annotation Page|}}}|?has_Gene_Name}} -|} - -[[Category:Gene Synonyms]] - - diff --git a/preecej/semantic_wiki/templates/Ontological_Reference_Repeater.wiki b/preecej/semantic_wiki/templates/Ontological_Reference_Repeater.wiki deleted file mode 100644 index 44672e9..0000000 --- a/preecej/semantic_wiki/templates/Ontological_Reference_Repeater.wiki +++ /dev/null @@ -1,43 +0,0 @@ - -This is the "Ontological Reference Repeater" template. -It should be called in the following format: -
    -{{Ontological Reference Repeater
-|Ontology=
-|Term ID=
-|Term Name=
-|Aspect=
-|Evidence Code=
-|Evidence=
-}}
-
    -Edit the page to see the template text. -    {{#set_internal:is_Ontological_Reference -|from_Ontology={{{Ontology|}}} -|has_Term_ID={{{Term ID|}}} -|has_Term_Name={{{Term Name|}}} -|has_Aspect={{{Aspect|}}} -|has_Evidence_Code#list={{{Evidence Code|}}} -|has_Evidence#list={{{Evidence|}}} -}} -{| class="wikitable" -! Ontology -| [[From Ontology::{{{Ontology|}}}]] -|- -! Term Name -| [[Has Term Name::{{{Term Name|}}}]] -|- -! Term ID -| [[Has Term ID::{{{Term ID|}}}]] -|- -! Branch -| [[Has Aspect::{{{Aspect|}}}]] -|- -! Evidence Code -| {{#arraymap:{{{Evidence Code|}}}|,|x|[[Has Evidence Code::x]]}} -|- -! Evidence -| {{#arraymap:{{{Evidence|}}}|,|x|[[Has Evidence::x]]}} -|} - - diff --git a/preecej/semantic_wiki/templates/Ontological_References.wiki b/preecej/semantic_wiki/templates/Ontological_References.wiki deleted file mode 100644 index 4e88f08..0000000 --- a/preecej/semantic_wiki/templates/Ontological_References.wiki +++ /dev/null @@ -1,18 +0,0 @@ - -This is the "Ontological References" template. -It should be called in the following format: -
    -{{Ontological References
-|Annotation Page=
-}}
-
    -Edit the page to see the template text. -     -{| class="wikitable" -! Annotation Page -| [[Is Associated With Annotation::{{{Annotation Page|}}}]] -|} - -[[Category:Ontological References]] - - diff --git a/preecej/semantic_wiki/templates/Plant_Ontology_Reference_Repeater.wiki b/preecej/semantic_wiki/templates/Plant_Ontology_Reference_Repeater.wiki deleted file mode 100644 index ecfda58..0000000 --- a/preecej/semantic_wiki/templates/Plant_Ontology_Reference_Repeater.wiki +++ /dev/null @@ -1,57 +0,0 @@ - -This is the "Plant Ontology Reference Repeater" template. -It should be called in the following format: -
    -{{Plant Ontology Reference Repeater
-|Term ID=
-|Term Name=
-|Aspect=
-|Evidence Code=
-|Evidence=
-}}
-
    -Edit the page to see the template text. -    {{#get_web_data: - |url=http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&field={{#if:{{{Term Name|}}}|name|acc}}&type=term_detail&ontology=po&qval={{#if:{{{Term Name|}}}|{{{Term Name|}}}|{{{Term ID|}}}}}&format=json - |format=JSON - |data=term_name=name,term_id=id,term_aspect=aspect,term_definition=definition,term_comment=comment -}} -{{#set_internal:is_Ontological_Reference -|from_Ontology=Plant Ontology -|has_Term_ID={{#external_value:term_id}} -|has_Term_Name={{#external_value:term_name}} -|has_Aspect={{#external_value:term_aspect}} -|has_Evidence_Code#list={{{Evidence Code|}}} -|has_Evidence#list={{{Evidence|}}} -}} -[[Has Term Search Type::{{{Term Search Type|}}}]] -{| class="wikitable" -! Ontology -| Plant Ontology -|- -! Term Name -| [[Has Term Name::{{#external_value:term_name}}]] -|- -! Term ID -| [[Has Term ID::{{#external_value:term_id}}]] -|- -! Branch -| [[Has Aspect::{{#external_value:term_aspect}}]] -|- -! Definition -| {{#external_value:term_definition}} -{{#if: {{#external_value:term_comment}} - | {{!}}- -! Comment -{{!}} {{#external_value:term_comment}} - | -}} -|- -! Evidence Code -| {{#arraymap:{{{Evidence Code|}}}|,|x|[[Has Evidence Code::x]]}} -|- -! Evidence -| {{#arraymap:{{{Evidence|}}}|,|x|[[Has Evidence::x]]}} -|} - - diff --git a/preecej/semantic_wiki/templates/Provenance.wiki b/preecej/semantic_wiki/templates/Provenance.wiki deleted file mode 100644 index 2e1764f..0000000 --- a/preecej/semantic_wiki/templates/Provenance.wiki +++ /dev/null @@ -1,18 +0,0 @@ - -This is the "Provenance" template. -It should be called in the following format: -
    -{{Provenance
-|Annotation Page=
-}}
-
    -Edit the page to see the template text. -     -{| class="wikitable" -! Annotation -| [[Is Associated With Annotation::{{{Annotation Page|}}}]] -|} - -[[Category:Provenance]] - - diff --git a/preecej/semantic_wiki/templates/Provenance_Repeater.wiki b/preecej/semantic_wiki/templates/Provenance_Repeater.wiki deleted file mode 100644 index f46fa2f..0000000 --- a/preecej/semantic_wiki/templates/Provenance_Repeater.wiki +++ /dev/null @@ -1,29 +0,0 @@ - -This is the "Provenance Repeater" template. -It should be called in the following format: -
    -{{Provenance Repeater
-|Source=
-|Source Accession ID=
-|Source Category=
-|Source Field or Object=
-}}
-
    -Edit the page to see the template text. -    {{#set_internal:is_Provenance -|has_Source={{{Source|}}} -|has_Source_Accession_ID={{{Source Accession ID|}}} -|is_Associated_With_Field_Or_Object={{{Source Field or Object|}}} -|is_Associated_With_Category={{{Source Category|}}} }} - -{| class="wikitable" -! Source -| [[Has Source::{{{Source|}}}]] -|- -! Accession ID -| [[Has Source Accession ID::{{{Source Accession ID|}}}]] -|- -! Field -| [[Is Associated With Field Or Object::{{{Source Field or Object|}}}]] (''Category'': {{{Source Category|}}}) -|} - diff --git a/preecej/semantic_wiki/templates/Publication.wiki b/preecej/semantic_wiki/templates/Publication.wiki deleted file mode 100644 index e447cd8..0000000 --- a/preecej/semantic_wiki/templates/Publication.wiki +++ /dev/null @@ -1,54 +0,0 @@ - -This is the "Publication" template. -It should be called in the following format: -
    -{{Publication
-|Publication=
-|Publication ID=
-|Publication Title=
-|First Author=
-|Journal Name=
-|Volume=
-|Year=
-|Pages=
-|Annotation References=
-|New Annotation Reference=
-}}
-
    -Edit the page to see the template text. -     -{| class="wikitable" -! Publication -| [[Has Publication Type::{{{Publication|}}}]] -|- -! Publication Identifier -| [[Has Publication ID::{{{Publication ID|}}}]] -|- -! Publication Title -| [[Has Publication Title::{{{Publication Title|}}}]] -|- -! First Author -| [[Has First Author::{{{First Author|}}}]] -|- -! Journal Name -| [[Has Journal Name::{{{Journal Name|}}}]] -|- -! Volume -| [[Has Publication Volume::{{{Volume|}}}]] -|- -! Year -| [[Has Publication Year::{{{Year|}}}]] -|- -! Pages -| [[Has Publication Pages::{{{Pages|}}}]] -|- -! Annotation References -| {{#arraymap:{{{Annotation References|}}}|,|x|[[Is Associated With Annotations::x]]}} -|- -! New Annotation Reference (to be hidden) -| [[Has New Annotation Association::{{{New Annotation Reference|}}}]] -|} - -[[Category:Publications]] - - diff --git a/preecej/semantic_wiki/templates/Reference_Publication.wiki b/preecej/semantic_wiki/templates/Reference_Publication.wiki deleted file mode 100644 index 1d22e3a..0000000 --- a/preecej/semantic_wiki/templates/Reference_Publication.wiki +++ /dev/null @@ -1,60 +0,0 @@ - -This is the "Reference Publication" template. -It should be called in the following format: -
    -{{Reference Publication
-|Publication=
-|Publication ID=
-|Publication Title=
-|First Author=
-|Journal Name=
-|Volume=
-|Year=
-|Pages=
-|Annotation References=
-|New Annotation Reference=
-}}
-
    -Edit the page to see the template text. -     - -{{#get_web_data: -url=http://dev.planteome.org/w/services/NCBI_eDocSummary.php?pub_id={{{Publication ID|}}} -|format=XML -|data=pub_id=Id,year=PubDate,first_author=LastAuthor,journal_name=FullJournalName,title=Title,volume=Volume,pages=Pages -}} - -{| class="wikitable" -! Publication Catalogue -| [[Has Publication Type::{{{Publication|}}}]] -|- -! Publication Identifier -| [[Has Publication ID::{{{Publication ID|}}}]] -|- -! Publication Title -| [[Has Publication Title::{{#for_external_table:{{{title}}} }}]] -|- -! First Author -| [[Has First Author::{{#for_external_table:{{{first_author}}} }}]] -|- -! Journal Name -| [[Has Journal Name::{{#for_external_table:{{{journal_name}}} }}]] -|- -! Volume -| [[Has Publication Volume::{{#for_external_table:{{{volume}}} }}]] -|- -! Year -| [[Has Publication Year::{{#for_external_table:{{{year}}} }}]] -|- -! Pages -| [[Has Publication Pages::{{#for_external_table:{{{pages}}} }}]] -|- -! Annotation References -| {{#arraymap:{{{Annotation References|}}}|,|x|[[Is Associated With Annotations::x]]}} -|} - - - -[[Category:Reference Publications]] - - diff --git a/preecej/semantic_wiki/templates/Sequence_Repeater.wiki b/preecej/semantic_wiki/templates/Sequence_Repeater.wiki deleted file mode 100644 index e9c84b6..0000000 --- a/preecej/semantic_wiki/templates/Sequence_Repeater.wiki +++ /dev/null @@ -1,28 +0,0 @@ - -This is the "Sequence Repeater" template. -It should be called in the following format: -
    -{{Sequence Repeater
-|Sequence Type=
-|Sequence Source=
-|External Accession ID=
-}}
-
    -Edit the page to see the template text. -    {{#set_internal:is_Sequence_Reference -|has_Sequence_Type={{{Sequence Type}}} -|has_Sequence_Source={{{Sequence Source|}}} -|has_External_Accession_ID={{{External Accession ID|}}} -}} -{| class="wikitable" -! Sequence Type -| [[Has Sequence Type::{{{Sequence Type|}}}]] -|- -! Sequence Source -| [[Has Sequence Source::{{{Sequence Source|}}}]] -|- -! Accession ID -| [[Has External Accession ID::{{{External Accession ID|}}}]] -|} - - diff --git a/preecej/semantic_wiki/templates/Sequences.wiki b/preecej/semantic_wiki/templates/Sequences.wiki deleted file mode 100644 index 2a98b35..0000000 --- a/preecej/semantic_wiki/templates/Sequences.wiki +++ /dev/null @@ -1,18 +0,0 @@ - -This is the "Sequences" template. -It should be called in the following format: -
    -{{Sequences
-|Annotation Page=
-}}
-
    -Edit the page to see the template text. -     -{| class="wikitable" -! Annotation Page -| [[Is Associated With Annotation::{{{Annotation Page|}}}]] -|} - -[[Category:Sequences]] - - diff --git a/preecej/semantic_wiki/templates/Source.wiki b/preecej/semantic_wiki/templates/Source.wiki deleted file mode 100644 index 3cb52f7..0000000 --- a/preecej/semantic_wiki/templates/Source.wiki +++ /dev/null @@ -1,34 +0,0 @@ - -This is the "Source" template. -It should be called in the following format: -
    -{{Source
-|Source Date Stamp=
-|Source Database=
-|Source Version=
-|Source URI=
-|Source File=
-}}
-
    -Edit the page to see the template text. -     -{| class="wikitable" -! Release Date -| [[Has Date Stamp::{{{Source Date Stamp|}}}]] -|- -! Data Source -| [[Has Source Database::{{{Source Database|}}}]] -|- -! Version -| [[Has Source Version::{{{Source Version|}}}]] -|- -! Web Address -| [[From Source URI::{{{Source URI|}}}]] -|- -! File -| [[From Source File::{{{Source File|}}}]] -|} - -[[Category:Sources]] - -