From: elserj <elserj@localhost>
Date: Wed, 6 Jul 2011 23:57:59 +0000 (+0000)
Subject: Moved to DbiFloret::dbconnect for db connection, and put in some versioning info
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=4617f3953e37d87204c91dd0d54a30913d07e29e;p=old-jaiswallab-svn%2F.git

Moved to DbiFloret::dbconnect for db connection, and put in some versioning info

svn path=/; revision=115
---

diff --git a/interactome_scripts/load_species_db.pl b/interactome_scripts/load_species_db.pl
index e4a4e6c..45c5fa8 100755
--- a/interactome_scripts/load_species_db.pl
+++ b/interactome_scripts/load_species_db.pl
@@ -4,14 +4,20 @@
 #  Written by Justin Elser 2/22/10                            #
 #                                                             #
 #  This program takes all fasta files in the current working  #
-#    directory and puts them in a database named protein      #
-#       sequences                                             #
+#    directory and puts them in a database                    #
 #                                                             #
 #  Initial version 0.1                                        #
 #     Shouldn't have to change much once this is done         #
 #         except to maybe add more species detection          #
 #         which is actually done in the pulled in subs        #
 #                                                             #
+#  version 0.9                                                #
+#      Switched to using the DbiFloret::dbconnect to manage   #
+#        the connection to the DB.  Also added a section to   #
+#        put in the version info into a new table.            #
+#        Can't think of much more that would need to go in    #
+#        here.                                                #
+#                                                             #
 ###############################################################
 
 use strict;
@@ -27,27 +33,11 @@ if(-e "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl") {
 	require "$ENV{HOME}/bin/find_species.pl";
 }
 
+use lib "$ENV{HOME}/scripts/jaiswallab/interactome_scripts";
 
-# define the database handle to be used 
-
-my $screen = Term::Screen::ReadLine->new();
-	# clear the screen
-	$screen->clrscr;
-	# ask for username
-	$screen->at(0,0)->puts("Username: ");
-	my $username = $screen->readline(ROW => 0, COL=>11);
-
-	# ask for password, replace character presses with stars
-	$screen->at(1,0)->puts("Password: ");
-	my $password = $screen->readline(ROW => 1, COL => 11, PASSWORD => 1);
-
-	$screen->at(2,0);
-	undef $screen;
-
-my $dbh = DBI->connect('DBI:mysql:protein_sequences;host=floret.cgrb.oregonstate.edu', $username, $password,
-	{ RaiseError=> 1, AutoCommit=>1 }
-	) or die "Failed to connect to database: $DBI::errstr";
+use DbiFloret;
 
+my $dbh = DbiFloret::dbconnect;
 
 my @files = glob("*.fa");
 
@@ -55,6 +45,13 @@ foreach my $file (@files) {
 	my $species = find_species($file);
 	print "on species $species\n";
 	
+	my ($retrieval_location, $retrieval_date) = retrieval_info($file);
+	$retrieval_date =~ /(\d+)\_(\d+)\_(\d\d)/;
+	my $formatted_date = "20".$1."-".$2."-".$3;
+	
+	my $safe_info_table = $dbh->quote_identifier("version_info");
+	$dbh->do("insert into $safe_info_table (?,?,?)  on duplicate key update retrieval_location=$retrieval_location,date=$formatted_date",$species,$retrieval_location,$formatted_date);
+	
 	# create the database table
 	my $safe_table = $dbh->quote_identifier($species);
 	
@@ -69,7 +66,8 @@ foreach my $file (@files) {
 	# and the statement handler to do the inserts
 	my $insert_sth = $dbh->prepare("insert into $safe_table (gene_id, gene_header, sequence) values (?,?,?)");
 	
-	# create the variables
+	# create the variables:q!
+	
 	my %seq_hash; # keys is $gene, values are $seq and $gene_header
 	my $gene;
 	my $seq;