Added stored procedures file

svn path=/; revision=473

diff --git a/image_annotation_db/ia_upload/annotation_data_importer.pl b/image_annotation_db/ia_upload/annotation_data_importer.pl
index 6b8a151b97c3754adea01acf166715c8d6e6245c..9dd9b212b41953957889870d5640e79d3f7e201d 100644 (file)
--- a/image_annotation_db/ia_upload/annotation_data_importer.pl
+++ b/image_annotation_db/ia_upload/annotation_data_importer.pl
@@ -37,6 +37,35 @@ sub establish_db_connection
         );
 }
 
+
+sub insert_collection_data_into_database
+{
+  my($dbh, $collection_data) = @_;
+  my @collection_data_fields = split(/\t/, $collection_data);
+
+
+  #creating image_source
+  my($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 insert_image_data_into_database
 {  
 
@@ -46,26 +75,35 @@ sub insert_image_data_into_database
 
 
   # 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                     = $image_data_fields[8];
+  my($curator_first_name, $curator_last_name) = split(/ /, trim($image_data_fields[6]), 2);
+  my $curator_email                          = trim($image_data_fields[7]);
+  my $curator_affiliation                     = trim($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'};
+  my $curator_id =  $dbh->{mysql_insert_id};
 
 
 
   # Creating taxon data and storing the respective id
-  my $species               = $image_data_fields[4];
+  my $species               = trim($image_data_fields[4]);
+  my $species               = "temp";
   my ($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 =  $dbh->{'mysql_insertid'};
+
+  #$dbh->do('INSERT INTO taxon (species_id, species_name, genus) VALUES(?, ?, ?)', undef, $species_id, $species_name, $genus);
+  #$dbh->do("call import_taxon($species_id, $species_name, $genus);");
+  my $taxon_id;
+  my $sth = $dbh->prepare("call import_taxon('temp_id', 'temp_name', 'temp_genus');");
+  $sth->execute();
+  $sth->bind_col(1, \$taxon_id);
+  $sth->fetch();
+  print "taxon_id is $taxon_id";
+
+  #my $taxon_id =  $dbh->{mysql_insert_id};
 
   # 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]);
 
@@ -76,14 +114,15 @@ sub insert_image_data_into_database
   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];
+  my $doi                = trim($image_data_fields[13]);
+  my $collection_location = trim($image_data_fields[9]);
+  my $collection_date     = trim($image_data_fields[11]);
+  my $comments                   = trim($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);
@@ -109,34 +148,6 @@ sub insert_image_data_into_database
 }
 
 
-sub insert_collection_data_into_database
-{
-  my($dbh, $collection_data) = @_;
-  my @collection_data_fields = split(/\t/, $collection_data);
-
-
-  #creating image_source
-  my($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
 {
   

diff --git a/image_annotation_db/ia_upload/stored_procedures.sql b/image_annotation_db/ia_upload/stored_procedures.sql
new file mode 100644 (file)
index 0000000..47a3736
--- /dev/null
+++ b/image_annotation_db/ia_upload/stored_procedures.sql
@@ -0,0 +1,7 @@
+# create stored procedure for importing taxon table
+
+delimiter //
+create procedure import_taxon (species_id varchar(45), species_name varchar(80), genus varchar(80))
+insert into taxon (species_id, species_name, genus) values (species_id, species_name, genus);
+select last_insert_id();
+end //
\ No newline at end of file