Latest commits. All queries are changes to use stored procedures.

svn path=/; revision=481

diff --git a/image_annotation_db/ia_upload/annotation_data_importer.pl b/image_annotation_db/ia_upload/annotation_data_importer.pl
index 600b47c61049d96c93633d522cf9734983c72c64..dfc5101668d1f9b5fb9d998d129d5505f0f94607 100644 (file)
--- a/image_annotation_db/ia_upload/annotation_data_importer.pl
+++ b/image_annotation_db/ia_upload/annotation_data_importer.pl
@@ -37,6 +37,12 @@ sub establish_db_connection
 }
 
 
+sub null_if_empty
+{
+  return (defined $_[0]) ? trim($_[0]) : 'NULL';
+}
+
+
 sub insert_collection_data_into_database
 {
   my($dbh, $collection_data) = @_;
@@ -44,10 +50,10 @@ sub insert_collection_data_into_database
 
 
   #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]);
+  my($source_name)      = null_if_empty($collection_data_fields[0]);
+  my($url)             = null_if_empty($collection_data_fields[1]);
+  my($contact_email)    = null_if_empty($collection_data_fields[3]);
+  my($contributor_name) = null_if_empty($collection_data_fields[2]);
 
   my $image_source_id;
   my $sth = $dbh->prepare("call import_image_source('$source_name', '$url', '$contact_email', '$contributor_name');");
@@ -57,9 +63,9 @@ sub insert_collection_data_into_database
 
 
   #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]);
+  my($source_version)    = null_if_empty($collection_data_fields[6]);
+  my($contribution_date) = null_if_empty($collection_data_fields[4]);
+  my($publication_id)    = null_if_empty($collection_data_fields[5]);
 
   my $image_source_version_id;
   my $sth = $dbh->prepare("call import_image_source_version('$image_source_id', '$source_version', '$contribution_date', '$publication_id');");
@@ -67,6 +73,7 @@ sub insert_collection_data_into_database
   $sth->bind_col(1, \$image_source_version_id);
   $sth->fetch();
 
+  return $image_source_version_id;
 
 }
 
@@ -74,15 +81,14 @@ sub insert_collection_data_into_database
 sub insert_image_data_into_database
 {  
 
-  my($dbh, $image_data) = @_;
+  my($dbh, $image_data, $image_source_version_id) = @_;
   my @image_data_fields = split(/\t/, $image_data);
 
 
-
   # Creating curator data and storing the respective id
   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]);
+  my $curator_email                          = null_if_empty($image_data_fields[7]);
+  my $curator_affiliation                     = null_if_empty($image_data_fields[8]);
   
   my $curator_id;
   my $sth = $dbh->prepare("call import_curator('$curator_first_name', '$curator_last_name', '$curator_email', '$curator_affiliation');");
@@ -91,11 +97,10 @@ sub insert_image_data_into_database
   $sth->fetch();
 
 
-
   # Creating taxon data and storing the respective id
-  my $species               = trim($image_data_fields[4]);
+  my $species               = null_if_empty($image_data_fields[4]);
   my ($genus, $species_name) = split(/\s/, $species, 2);
-  my $species_id             = trim($image_data_fields[5]);
+  my $species_id             = null_if_empty($image_data_fields[5]);
 
   my $taxon_id;
   my $sth = $dbh->prepare("call import_taxon('$species_id', '$species_name', '$genus');");
@@ -104,11 +109,11 @@ sub insert_image_data_into_database
   $sth->fetch();
 
   # Forming image_path by concatinating import_location and filename
-  my $image_path = trim($image_data_fields[1]) . trim($image_data_fields[0]);
+  my $image_path = null_if_empty($image_data_fields[1]) . null_if_empty($image_data_fields[0]);
 
   # preprocessing ip_comment data
-  my $ip_comment     = trim($image_data_fields[12]);
-  my $source_db      = trim($image_data_fields[14]);
+  my $ip_comment     = null_if_empty($image_data_fields[12]);
+  my $source_db      = null_if_empty($image_data_fields[14]);
   my $source_db_name;
   my $source_db_id;
 
@@ -116,13 +121,16 @@ sub insert_image_data_into_database
   {
     ($source_db_name, $source_db_id) = split(/:/, $source_db, 2);
   }
-  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]);
+
+  $source_db_name         = null_if_empty($source_db_name);
+  $source_db_id           = null_if_empty($source_db_id);
+  my $doi                = null_if_empty($image_data_fields[13]);
+  my $collection_location = null_if_empty($image_data_fields[9]);
+  my $collection_date     = null_if_empty($image_data_fields[11]);
+  my $comments                   = null_if_empty($image_data_fields[15]);
 
   my $annotated_image_id;
-  my $sth = $dbh->prepare("call import_annotated_image('$curator_id', '$taxon_id', '$image_path', '$collection_location', '$collection_date', '$ip_comment', '$doi', '$source_db_name', '$source_db_id', '$comments');");
+  my $sth = $dbh->prepare("call import_annotated_image('$curator_id', '$image_source_version_id', '$taxon_id', '$image_path', '$collection_location', '$collection_date', '$ip_comment', '$doi', '$source_db_name', '$source_db_id', '$comments');");
   $sth->execute();
   $sth->bind_col(1, \$annotated_image_id);
   $sth->fetch();
@@ -134,14 +142,18 @@ sub insert_image_data_into_database
   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'};
+    my $annotated_term_id;
+    my $sth = $dbh->prepare("call import_annotated_term('$keywords[$_]', '$ontology_term_ids[$_]');");
+    $sth->execute();
+    $sth->bind_col(1, \$annotated_term_id);
+    $sth->fetch();
 
 
-    #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'};
+    my $annotated_term_image_id;
+    my $sth = $dbh->prepare("call import_annotated_term_image('$annotated_term_id', '$annotated_image_id');");
+    $sth->execute();
+    $sth->bind_col(1, \$annotated_term_image_id);
+    $sth->fetch();
 
   }
 
@@ -155,54 +167,38 @@ sub import_image_data
   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"))
-  {
+  print "Reading content of collection specification data(IADB_coll_spec_*.tsv) file and reading data...\n\n";
 
-    my $content = do {
-       local $/ = undef;
-       open (my $file, "<", $_) or die("could not open $_: $!");
-       <$file>;
-    };
+  my @collection_files = glob(IMAGE_DATA_DIR."/IADB_coll_spec_*.tsv");
+  my $collection_content = do {
+      local $/ = undef;
+      open (my $file, "<", $collection_files[0]) or die("could not open $collection_files[0]: $!");
+      <$file>;
+  };
 
-    chomp;
+  my @collection_spec_records = split(/\n/, $collection_content);
 
-    my @collection_spec_records = split(/\n/, $content);
-    
-    shift @collection_spec_records;
+  shift @collection_spec_records;
 
-    foreach (@collection_spec_records)
-    {
-      insert_collection_data_into_database($dbh, $_);
-    }
+  my $image_source_version_id = insert_collection_data_into_database($dbh, $collection_spec_records[0]);
+  
 
-  }
+  print "Reading content of image data(IADB_img_data_*.tsv) file and reading data...\n\n";
 
+  my @image_data_files = glob(IMAGE_DATA_DIR."/IADB_img_data_*.tsv");
+  my $image_content = do {
+      local $/ = undef;
+      open (my $file, "<", $image_data_files[0]) or die("could not open $image_data_files[0]: $!");
+      <$file>;
+  };
 
-  print "Reading content of each image data(IADB_img_data_*.tsv) file and reading data...\n\n";
+  my @image_data_records = split(/\n/, $image_content);
+  
+  shift @image_data_records;
 
-  foreach (glob(IMAGE_DATA_DIR."/IADB_img_data_*.tsv"))
+  foreach (@image_data_records)
   {
-
-    my $content = do {
-       local $/ = undef;
-       print "file is " . $_ . "\n";
-       open (my $file, "<", $_) or die("could not open $_: $!");
-       <$file>;
-    };
-
-    chomp;
-
-    my @image_data_records = split(/\n/, $content);
-    
-    shift @image_data_records;
-
-    foreach (@image_data_records)
-    {
-      insert_image_data_into_database($dbh, $_);
-    }
-
+    insert_image_data_into_database($dbh, $_, $image_source_version_id);
   }
 
 }

diff --git a/image_annotation_db/ia_upload/stored_procedures.sql b/image_annotation_db/ia_upload/stored_procedures.sql
index acacc1a8dda89ab8c1ff6527e78169c5e23f0adb..fabafee7773c12ac248520b1d4074916a5ad8b2e 100644 (file)
--- a/image_annotation_db/ia_upload/stored_procedures.sql
+++ b/image_annotation_db/ia_upload/stored_procedures.sql
@@ -43,8 +43,28 @@ end //
 
 DROP procedure if exists import_annotated_image;
 delimiter //
-create procedure import_annotated_image (curator_id int(11), taxon_id int(11), image_path varchar(255), collection_location varchar(255), collection_date date, ip_comment varchar(255), doi varchar(45), source_db_name varchar(45), source_db_id varchar(30), comments varchar(255))
+create procedure import_annotated_image (curator_id int(11), image_source_version_id int(11), taxon_id int(11), image_path varchar(255), collection_location varchar(255), collection_date date, ip_comment varchar(255), doi varchar(45), source_db_name varchar(45), source_db_id varchar(30), comments varchar(255))
 begin
-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 (curator_id, taxon_id, image_path, collection_location, collection_date, ip_comment, doi, source_db_name, source_db_id, comments);
+insert into annotated_image (curator_id, image_source_version_id, taxon_id, image_path, collection_location, collection_date, ip_comment, doi, source_db_name, source_db_id, comments) values (curator_id, image_source_version_id, taxon_id, image_path, collection_location, collection_date, ip_comment, doi, source_db_name, source_db_id, comments);
+select last_insert_id();
+end //
+
+-- create(drop and create if exists) stored procedure for importing data into annotated_term table
+
+DROP procedure if exists import_annotated_term;
+delimiter //
+delimiter
+begin
+insert into annotated_term (keyword, ontology_term_id) values (keyword, ontology_term_id);
+select last_insert_id();
+end //
+
+-- create(drop and create if exists) stored procedure for importing data into annotated_term_image table
+
+DROP procedure if exists import_annotated_term_image;
+delimiter //
+create procedure import_annotated_term_image (annotated_term_id int(11), annotated_image_id int(11))
+begin
+insert into annotated_term_image (annotated_term_id, annotated_image_id) values (annotated_term_id, annotated_image_id);
 select last_insert_id();
 end //
\ No newline at end of file