use strict;
use English;
use DBI;
+use String::Util qw(:all);
# configurations
);
}
-sub insert_curator_data(my $dbh, my @image_data_fields)
-{
- my($curator_first, $curator_last) = split(/ /, $image_data_fields[6], 2);
- my $curator_email = $image_data_fields[7];
- my $curator_affiliation = $image_data_fields[8];
+sub insert_image_data_into_database
+{
+
+ my($dbh, $image_data) = @_;
+ my @image_data_fields = split(/\t/, $image_data);
+
+
+
+ # Creating curator data and storing the respective id
+ my($curator_first_name, $curator_last_name) = split(/ /, $image_data_fields[6], 2);
+ my $curator_email = $image_data_fields[7];
+ my $curator_affiliation = $image_data_fields[8];
+
+ $dbh->do('INSERT INTO curator (firstname, lastname, primary_email, affiliation) VALUES(?, ?, ?, ?)', undef, $curator_first_name, $curator_last_name, $curator_email, $curator_affiliation);
+ my $curator_id = $dbh->{'mysql_insertid'};
+
+
+
+ # Creating taxon data and storing the respective id
+ my $species = $image_data_fields[4];
+ my ($genus, $species_name) = split(/\s/, $species, 2);
+ my $species_id = trim($image_data_fields[5]);
+ $dbh->do('INSERT INTO taxon (species_id, species_name, genus) VALUES(?, ?, ?)', undef, $species_id, $species_name, $genus);
+ my $taxon_id = $dbh->{'mysql_insertid'};
+
+ # Forming image_path by concatinating import_location and filename
+ my $image_path = trim($image_data_fields[1]) . trim($image_data_fields[0]);
+
+
+ # preprocessing ip_comment data
+ my $ip_comment = trim($image_data_fields[12]);
+
+ if(undef $ip_comment){
+ $ip_comment = ""
+ }
+
+ my $source_db = trim($image_data_fields[14]);
+ my $source_db_name = "";
+ my $source_db_id = "";
+ if(defined $source_db)
+ {
+ ($source_db_name, $source_db_id) = split(/:/, $source_db, 2);
+ }
+ my $doi = $image_data_fields[13];
+ my $collection_location = $image_data_fields[9];
+ my $collection_date = $image_data_fields[11];
+ my $comments = $image_data_fields[15];
+
+ $dbh->do('INSERT INTO annotated_image (curator_id, taxon_id, image_path, collection_location, collection_date, ip_comment, doi, source_db_name, source_db_id, comments) VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?)',
+ undef, $curator_id, $taxon_id, $image_path, $collection_location, $collection_date, $ip_comment, $doi, $source_db_name, $source_db_id, $comments);
+ my $annotated_image_id = $dbh->{'mysql_insertid'};
+
+ my @keywords = split(/\|/, trim($image_data_fields[2]));
+ my @ontology_term_ids = split(/\|/, trim($image_data_fields[3]));
+
+ foreach (0..(scalar(@keywords)-1))
+ {
+
+ #creating annotated_term
+ $dbh->do('INSERT INTO annotated_term (keyword, ontology_term_id) VALUES(?, ?)', undef, $keywords[$_], $ontology_term_ids[$_]);
+ my $annotated_term_id = $dbh->{'mysql_insertid'};
- $dbh->do('INSERT INTO curator (firstname, lastname, primary_email, alternate_email, affiliation) VALUES(?, ?, ?, ?, ?)', undef, $curator_first, $curator_last , $curator_email ,'', $curator_affiliation);
+
+ #creating annotated_term_image
+ $dbh->do('INSERT INTO annotated_term_image (annotated_term_id, annotated_image_id) VALUES(?, ?)', undef, $annotated_term_id, $annotated_image_id);
+ my $annotated_term_image_id = $dbh->{'mysql_insertid'};
+
+ }
}
-sub insert_record_into_database
-{
- my $dbh = establish_db_connection;
- my @image_data_fields = split(/\t/);
+sub insert_collection_data_into_database
+{
+ my($dbh, $collection_data) = @_;
+ my @collection_data_fields = split(/\t/, $collection_data);
- insert_curator_data($dbh, @image_data_fields);
-
+ #creating image_source
+ my($source_name) = trim($collection_data_fields[0]);
+ my($url) = trim($collection_data_fields[1]);
+ my($contact_email) = trim($collection_data_fields[3]);
+ my($contributor_name) = trim($collection_data_fields[2]);
+
+ $dbh->do('INSERT INTO image_source (source_name, url, contact_email, contributor_name) VALUES(?, ?, ?, ?)', undef, $source_name, $url, $contact_email, $contributor_name);
+ my $image_source_id = $dbh->{'mysql_insertid'};
+
+
+
+ #creating image_source_version
+ my($source_version) = trim($collection_data_fields[6]);
+ my($contribution_date) = trim($collection_data_fields[4]);
+ my($publication_id) = trim($collection_data_fields[5]);
+
+ $dbh->do('INSERT INTO image_source_version (image_source_id, source_version, contribution_date, publication_id) VALUES(?, ?, ?, ?)', undef, $image_source_id, $source_version, $contribution_date, $publication_id);
+ my $image_source_version_id = $dbh->{'mysql_insertid'};
}
+
sub import_image_data
{
- print "Opening each image data(*.tsv) file and reading data...\n\n";
+ print "Connecting to the Database...\n\n";
+ my $dbh = establish_db_connection;
+
+
+ print "Reading content of each collection specification data(IADB_coll_spec_*.tsv) file and reading data...\n\n";
+
+ foreach (glob(IMAGE_DATA_DIR."/IADB_coll_spec_*.tsv"))
+ {
+
+ my $content = do {
+ local $/ = undef;
+ open (my $file, "<", $_) or die("could not open $_: $!");
+ <$file>;
+ };
+
+ chomp;
- foreach (glob(IMAGE_DATA_DIR."/*.tsv"))
+ my @collection_spec_records = split(/\n/, $content);
+
+ shift @collection_spec_records;
+
+ foreach (@collection_spec_records)
+ {
+ insert_collection_data_into_database($dbh, $_);
+ }
+
+ }
+
+
+ print "Reading content of each image data(IADB_img_data_*.tsv) file and reading data...\n\n";
+
+ foreach (glob(IMAGE_DATA_DIR."/IADB_img_data_*.tsv"))
{
my $content = do {
local $/ = undef;
+ print "file is " . $_ . "\n";
open (my $file, "<", $_) or die("could not open $_: $!");
<$file>;
};
my @image_data_records = split(/\n/, $content);
- splice @image_data_records, 0, 1;
+ shift @image_data_records;
foreach (@image_data_records)
{
- insert_record_into_database($_);
+ insert_image_data_into_database($dbh, $_);
}
- close $_ or die("Could not close '$_': $OS_ERROR");
-
}
+
}
# ---------------------------------------------------------------------------
filename import_location keywords ontology_term_ids species species_id curator_name curator_email curator_affiliation collection_location geo_coords collection_date ip_comment doi source_db comments
-Saurauia xs Ovary.jpg / locule|ovule|pericarp|septum PO:0025266|PO:0020003|PO:0009084|PO:0025262 Saurauia sp Dennis Stevenson dws@nybg.org NYBG COLOMBIA: Boyaca: Villa de Lleva, Iguaque National Park 2500-2800 M 20070429 PlantSystematics:DOL27827
-Helleborus_argutifolius_Carpels.jpg / carpel|style PO:0009030|PO:0009074 Helleborus argutifolius Dennis Stevenson dws@nybg.org NYBG AUSTRALIA: South Australia: Botanic Gardens of Adelaide Accession G880864 20110810 PlantSystematics:DOL40035
-Yucca_schidigera_flower.jpg / anther|filament|flower|ovary|petal|sepal|stigma PO:0009066|PO:0009067|PO:0009046|PO:0009072|PO:0009032|PO:0009031|PO:0009073 Yucca schidigera Lawrence M. Kelly lkelly@nybg.org NYBG USA: California:: San Diego Co. Near Miramar NAS 20040320 PlantSystematics:DOL11866
-Gunnera_tinctoria Prickle.jpg / prickle PO:0025169 Gunnera tinctoria Dennis Stevenson dws@nybg.org NYBG DENMARK: University of Copenhagen, Botanical Garden E6139 C001 A 20080813 PlantSystematics:DOL33711
- Acacia cornigera Stipules as Spines.jpg / stipule|stipule spine PO:0020041|PO:0025174 Acacia cornigera Lawrence M. Kelly lkelly@nybg.org NYBG COSTA RICA: Guanacaste: Palo Verde 2003 PlantSystematics:DOL4821
-Bougainvillea_spectabilis Thorn.jpg / thorn PO:0025172 Bougainvillea spectabilis Dennis Stevenson dws@nybg.org NYBG CHINA: Shenzhen, Fairylake Botanical Garden 20111025
-Parmentiera_cerifera Style & Stigma.jpg / stigma|style PO:0009073|PO:0009074 Parmentiera cerifera Dennis Stevenson dws@nybg.org NYBG USA: Florida:: Dade Co. Montgomery Botanical Center 20070404 PlantSystematics:DOL27681
-Leucojum_aestivum Flower.jpg / collective tepal structure|free tepal|plant ovary|stamen|tepal PO:0025021|PO:0025136PO:0009072|PO:0009029|PO:0009033 Leucojum aestivum Dennis Stevenson dws@nybg.org NYBG USA: NY:: Tompkins Co. Mins Garden, Cornell University 20050428 PlantSystematics:DOL12340|DOL12342
-Ticodendron incognitum.jpg / shoot node|petiole|shoot internode|stipule PO:0005004|PO:0020038|PO:0005005|PO:0020041| Ticodendron incognitum Lawrence M. Kelly lkelly@nybg.org NYBG COSTA RICA: Alajuela:: San Ramon Estacion Biologica Alberto M. Brenes 2003 PlantSystematics:DOL4844
-Agave sebastiana Labelled.jpg / locule|ovule|septum PO:0025266|PO:0020003|PO:0025262 Agave sebastiana Dennis Stevenson dws@nybg.org NYBG USA: California:: Santa Barbara Co. Santa Barbara Botanic Garden 20061208 PlantSystematics:DOL26528
-Acacia mangium Phyllode.JPG / inflorescence|phyllode leaf PO:0009049|PO:0025335 Acacia mangium Dennis Stevenson dws@nybg.org NYBG VIETNAM: Vinh Phuc Province: Me Linh District, Me Linh Station of the Institute of Ecology and Biological Resources, Vietnamese Academy of Science and Technology 21 23.309 N 105 42.837 E 20051210 PlantSystematics:DOL17750
-Acacia sp Phyllode.JPG / axillary inflorescence bud|phyllode leaf PO:0004711|PO:0025335 Acacia sp Dennis Stevenson dws@nybg.org NYBG AUSTRALIA: Western Australia: Kings Park, Perth 20110805 PlantSystematics:DOL39936
-EucalyptusKingsmillii6.JPG / calyptra corolla PO:0025330 Eucalyptus kingsmillii Dennis Stevenson dws@nybg.org NYBG AUSTRALIA: Western Australia: Kings Park, Perth 20110805 PlantSystematics:DOL39933
-EucalyptusKingsmillii2.JPG / calyptra corolla PO:0025330 Eucalyptus kingsmillii Dennis Stevenson dws@nybg.org NYBG AUSTRALIA: Western Australia: Kings Park, Perth 20110805 PlantSystematics:DOL39929
-GymnocalyciumMarsoneri1.JPG / areole bud|spine leaf PO:0025353|PO:0025173 Gymnocalycium marsoneri Dennis Stevenson dws@nybg.org NYBG USA: Arizona:: Maricopa Co. Desert Botanical Garden, Phoenix 20070114 PlantSystematics:DOL26949
-Anchomanes giganteus.JPG / prickle PO:0025169 Anchomanes giganteus Dennis Stevenson dws@nybg.org NYBG GERMANY: Botanical Garden, University of Bonn. Accession No. 02608 20060924
\ No newline at end of file
+Saurauia xs Ovary.jpg / locule|ovule|pericarp|septum PO:0025266|PO:0020003|PO:0009084|PO:0025262 Saurauia sp Dennis Stevenson dws@nybg.org NYBG COLOMBIA: Boyaca: Villa de Lleva, Iguaque National Park 2500-2800 M 20070429 PlantSystematics:DOL27827
+Helleborus argutifolius Carpels.jpg / carpel|style PO:0009030|PO:0009074 Helleborus argutifolius Dennis Stevenson dws@nybg.org NYBG AUSTRALIA: South Australia: Botanic Gardens of Adelaide Accession G880864 20110810 PlantSystematics:DOL40035
+Yucca_schidigera_flower.jpg / anther|filament|flower|ovary|petal|sepal|stigma PO:0009066|PO:0009067|PO:0009046|PO:0009072|PO:0009032|PO:0009031|PO:0009073 Yucca schidigera Lawrence M. Kelly lkelly@nybg.org NYBG USA: California:: San Diego Co. Near Miramar NAS 20040320 PlantSystematics:DOL11866
+Gunnera_tinctoria Prickle.jpg / prickle PO:0025169 Gunnera tinctoria Dennis Stevenson dws@nybg.org NYBG DENMARK: University of Copenhagen, Botanical Garden E6139 C001 A 20080813 PlantSystematics:DOL33711
+ Acacia cornigera Stipules as Spines.jpg / stipule|stipule spine PO:0020041|PO:0025174 Acacia cornigera Lawrence M. Kelly lkelly@nybg.org NYBG COSTA RICA: Guanacaste: Palo Verde 2003 PlantSystematics:DOL4821
+Bougainvillea_spectabilis Thorn.jpg / thorn PO:0025172 Bougainvillea spectabilis Dennis Stevenson dws@nybg.org NYBG CHINA: Shenzhen, Fairylake Botanical Garden 20111025
+Parmentiera_cerifera Style & Stigma.jpg / stigma|style PO:0009073|PO:0009074 Parmentiera cerifera Dennis Stevenson dws@nybg.org NYBG USA: Florida:: Dade Co. Montgomery Botanical Center 20070404 PlantSystematics:DOL27681
+Leucojum_aestivum Flower.jpg / collective tepal structure|free tepal|plant ovary|stamen|tepal PO:0025021|PO:0025136|PO:0009072|PO:0009029|PO:0009033 Leucojum aestivum Dennis Stevenson dws@nybg.org NYBG USA: NY:: Tompkins Co. Mins Garden, Cornell University 20050428 PlantSystematics:DOL12340|DOL12342
+Ticodendron incognitum.jpg / shoot node|petiole|shoot internode|stipule PO:0005004|PO:0020038|PO:0005005|PO:0020041| Ticodendron incognitum Lawrence M. Kelly lkelly@nybg.org NYBG COSTA RICA: Alajuela:: San Ramon Estacion Biologica Alberto M. Brenes 2003 PlantSystematics:DOL4844
+Agave sebastiana Labelled.jpg / locule|ovule|septum PO:0025266|PO:0020003|PO:0025262 Agave sebastiana Dennis Stevenson dws@nybg.org NYBG USA: California:: Santa Barbara Co. Santa Barbara Botanic Garden 20061208 PlantSystematics:DOL26528
+Acacia mangium Phyllode.JPG / inflorescence|phyllode leaf PO:0009049|PO:0025335 Acacia mangium Dennis Stevenson dws@nybg.org NYBG VIETNAM: Vinh Phuc Province: Me Linh District, Me Linh Station of the Institute of Ecology and Biological Resources, Vietnamese Academy of Science and Technology 21 23.309 N 105 42.837 E 20051210 PlantSystematics:DOL17750
+Acacia sp Phyllode.JPG / axillary inflorescence bud|phyllode leaf PO:0004711|PO:0025335 Acacia sp Dennis Stevenson dws@nybg.org NYBG AUSTRALIA: Western Australia: Kings Park, Perth 20110805 PlantSystematics:DOL39936
+EucalyptusKingsmillii6.JPG / calyptra corolla PO:0025330 Eucalyptus kingsmillii Dennis Stevenson dws@nybg.org NYBG AUSTRALIA: Western Australia: Kings Park, Perth 20110805 PlantSystematics:DOL39933
+EucalyptusKingsmillii2.JPG / calyptra corolla PO:0025330 Eucalyptus kingsmillii Dennis Stevenson dws@nybg.org NYBG AUSTRALIA: Western Australia: Kings Park, Perth 20110805 PlantSystematics:DOL39929
+GymnocalyciumMarsoneri1.JPG / areole bud|spine leaf PO:0025353|PO:0025173 Gymnocalycium marsoneri Dennis Stevenson dws@nybg.org NYBG USA: Arizona:: Maricopa Co. Desert Botanical Garden, Phoenix 20070114 PlantSystematics:DOL26949
+Anchomanes giganteus.JPG / prickle PO:0025169 Anchomanes giganteus Dennis Stevenson dws@nybg.org NYBG GERMANY: Botanical Garden, University of Bonn. Accession No. 02608 20060924
+Mickelia_nicotianifolia Diarch.jpg protoxylem PO:0000272 Mickelia nicotianifolia Dennis Stevenson dws@nybg.org NYBG USA: New York:: Bronx Co. New York Botanical Garden 20130412
+Angiopteris_evecta_root_xs Polyarch.jpg protoxylem PO:0000272 Angiopteris evecta Dennis Stevenson dws@nybg.org NYBG USA: New York:: Bronx Co. New York Botanical Garden 20130412
+Angiopteris_evecta_root_xs3 Exarch.JPG protoxylem PO:0000272 Angiopteris evecta Dennis Stevenson dws@nybg.org NYBG USA: New York:: Bronx Co. New York Botanical Garden 20130412
+PunicaGranatumThorn.jpg thorn PO:0025172 Punicata granatum Dennis Stevenson dws@nybg.org NYBG USA: Arizona:: Pima Co. Tucson Botanical Garden, Tucson 20130423
+Sciaphyllum_amoenum5 Adaxial.jpg leaf adaxial epidermis|leaf lamina adaxial epidermis PO:0006018|PO:0000050 Sciaphyllum amoenum Dennis Stevenson dws@nybg.org NYBG USA: New York:: Bronx Co. Conservatory, New York Botanical Garden 20070309 PlantSystematics DOL27401
+Sciaphyllum_amoenum4 Abaxial.jpg leaf abaxial epidermis|leaf lamina abaxial epidermis PO:0006019|PO:0000049 Sciaphyllum amoenum Dennis Stevenson dws@nybg.org NYBG USA: New York:: Bronx Co. Conservatory, New York Botanical Garden 20070309 PlantSystematics DOL21104
projects / old-jaiswallab-svn / .git / commitdiff