Fixed bug with cvtermynonym being wiped out after OBO loading in Chado prepare step

tripal/api/tripal.entities.api.inc

@@ -284,6 +284,9 @@ function tripal_create_bundle($args, &$error = '') {
       foreach ($info as $field_name => $details) {
         $field_type = $details['type'];
 
+        // TODO: make sure the field term exits. If not then
+        // skip it.
+
         // If the field already exists then skip it.
         $field = field_info_field($details['field_name']);
         if ($field) {

tripal/includes/TripalFields/TripalField.inc

@@ -111,6 +111,7 @@ class TripalField {
         $accession = $instance['settings']['term_accession'];
         $term = tripal_get_term_details($vocabulary, $accession);
         if (!$term) {
+          dpm(debug_backtrace());
           throw new Error(t('Cannot create TripalField of type "%term" as that
               term does not exist.', array('%term' => "$vocabulary:$accession")));
         }

tripal_chado/api/tripal_chado.schema.api.inc

@@ -38,14 +38,10 @@
  */
 function chado_table_exists($table) {
   global $databases;
+
+  global $databases;
+
   $default_db = $databases['default']['default']['database'];
-  $cached_obj = cache_get('chado_tables', 'cache');
-  if ($cached_obj) {
-    $cached_tables = $cached_obj->data;
-    if (is_array($cached_tables) and array_key_exists($table, $cached_tables)) {
-      return $cached_tables[$table]['exists'];
-    }
-  }
 
   $sql = "
     SELECT 1
@@ -63,12 +59,8 @@ function chado_table_exists($table) {
   $results = db_query($sql, $args);
   $exists = $results->fetchObject();
   if (!$exists) {
-    $cached_tables[$table]['exists'] = FALSE;
-    cache_set('chado_tables', $cached_tables, 'cache', CACHE_TEMPORARY);
     return FALSE;
   }
-  $cached_tables[$table]['exists'] = TRUE;
-  cache_set('chado_tables', $cached_tables, 'cache', CACHE_TEMPORARY);
   return TRUE;
 }
 /**

tripal_chado/includes/loaders/tripal_chado.obo_loader.inc

@@ -634,9 +634,11 @@ function tripal_cv_obo_load_typedefs($defaultcv, $newcvs, $default_db, $jobid) {
     $term = unserialize(base64_decode($typedef->stanza));
 
     // update the job status every interval
-    if ($jobid and $i % $interval == 0) {
+    if ($i % $interval == 0) {
       $complete = ($i / $count) * 33.33333333;
-      tripal_set_job_progress($jobid, intval($complete + 33.33333333));
+      if ($jobid) {
+        tripal_set_job_progress($jobid, intval($complete + 33.33333333));
+      }
       printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
     }
 
@@ -644,17 +646,19 @@ function tripal_cv_obo_load_typedefs($defaultcv, $newcvs, $default_db, $jobid) {
 
     $i++;
   }
-    // set the final status
+
+  // Set the final status.
+  if ($count > 0) {
+    $complete = ($i / $count) * 33.33333333;
+  }
+  else {
+    $complete = 33.33333333;
+  }
   if ($jobid) {
-    if ($count > 0) {
-      $complete = ($i / $count) * 33.33333333;
-    }
-    else {
-      $complete = 33.33333333;
-    }
     tripal_set_job_progress($jobid, intval($complete + 33.33333333));
-    printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
   }
+  printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
+
   return 1;
 }
 
@@ -703,9 +707,11 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
     $term = unserialize(base64_decode($t->stanza));
 
     // update the job status every interval
-    if ($jobid and $i % $interval == 0) {
+    if ($i % $interval == 0) {
       $complete = ($i / $count) * 33.33333333;
-      tripal_set_job_progress($jobid, intval($complete + 66.666666));
+      if ($jobid) {
+        tripal_set_job_progress($jobid, intval($complete + 66.666666));
+      }
       printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
     }
 
@@ -718,16 +724,17 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
   }
 
   // set the final status
+  if ($count > 0) {
+    $complete = ($i / $count) * 33.33333333;
+  }
+  else {
+    $complete = 33.33333333;
+  }
   if ($jobid) {
-    if ($count > 0) {
-      $complete = ($i / $count) * 33.33333333;
-    }
-    else {
-      $complete = 33.33333333;
-    }
     tripal_set_job_progress($jobid, intval($complete + 66.666666));
-    printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
   }
+  printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
+
 
   return 1;
 }
@@ -1164,10 +1171,12 @@ function tripal_cv_obo_parse($obo_file, &$header, $jobid) {
     $line = trim($line);
 
     // update the job status every 1% features
-    if ($jobid and $intv_read >= $interval) {
+    if ($intv_read >= $interval) {
       $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
       print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
-      tripal_set_job_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
+      if ($jobid) {
+        tripal_set_job_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
+      }
       $intv_read = 0;
     }
 
@@ -1252,7 +1261,9 @@ function tripal_cv_obo_parse($obo_file, &$header, $jobid) {
     }
     $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
     print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
-    tripal_set_job_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
+    if ($jobid) {
+      tripal_set_job_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
+    }
   }
   return $default_db;
 }

tripal_chado/includes/tripal_chado.fields.inc

@@ -400,20 +400,21 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   }
 
   // EXPRESSION
-  $expression_table = $table_name . '_expression';
-  if (chado_table_exists($expression_table)) {
-    $field_name = 'go__gene_expression';
-    $field_type = 'go__gene_expression';
-    $info[$field_name] = array(
-      'field_name' => $field_name,
-      'type' => $field_type,
-      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
-      'locked' => FALSE,
-      'storage' => array(
-        'type' => 'field_chado_storage',
-      ),
-    );
-  }
+  // TODO: this should only show up on gene or mRNA bunldes, not every feature.
+//   $expression_table = $table_name . '_expression';
+//   if (chado_table_exists($expression_table)) {
+//     $field_name = 'go__gene_expression';
+//     $field_type = 'go__gene_expression';
+//     $info[$field_name] = array(
+//       'field_name' => $field_name,
+//       'type' => $field_type,
+//       'cardinality' => FIELD_CARDINALITY_UNLIMITED,
+//       'locked' => FALSE,
+//       'storage' => array(
+//         'type' => 'field_chado_storage',
+//       ),
+//     );
+//   }
 
   // FEATURELOC
   if ($table_name == 'feature') {
@@ -1286,39 +1287,41 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
   }
 
   // EXPRESSION
-  $expression_table = $table_name . '_expression';
-  if (chado_table_exists($expression_table)) {
-    $field_name = 'go__gene_expression';
-    $schema = chado_get_schema($expression_table);
-    $pkey = $schema['primary key'][0];
-    $info[$field_name] = array(
-      'field_name' => $field_name,
-      'entity_type' => $entity_type,
-      'bundle' => $bundle->name,
-      'label' => 'Gene expression',
-      'description' => 'Information about the expression of this record.',
-      'required' => FALSE,
-      'settings' => array(
-        'auto_attach' => FALSE,
-        'chado_table' => $expression_table,
-        'chado_column' => $pkey,
-        'base_table' => $table_name,
-      ),
-      'widget' => array(
-        'type' => 'go__gene_expression_widget',
-        'settings' => array(
-          'display_label' => 1,
-        ),
-      ),
-      'display' => array(
-        'default' => array(
-          'label' => 'above',
-          'type' => 'go__gene_expression_formatter',
-          'settings' => array(),
-        ),
-      ),
-    );
-  }
+  // TODO: this should only show up on gene or mRNA and the GO must be
+  // laoded or this field will crash things.
+//   $expression_table = $table_name . '_expression';
+//   if (chado_table_exists($expression_table)) {
+//     $field_name = 'go__gene_expression';
+//     $schema = chado_get_schema($expression_table);
+//     $pkey = $schema['primary key'][0];
+//     $info[$field_name] = array(
+//       'field_name' => $field_name,
+//       'entity_type' => $entity_type,
+//       'bundle' => $bundle->name,
+//       'label' => 'Gene expression',
+//       'description' => 'Information about the expression of this record.',
+//       'required' => FALSE,
+//       'settings' => array(
+//         'auto_attach' => FALSE,
+//         'chado_table' => $expression_table,
+//         'chado_column' => $pkey,
+//         'base_table' => $table_name,
+//       ),
+//       'widget' => array(
+//         'type' => 'go__gene_expression_widget',
+//         'settings' => array(
+//           'display_label' => 1,
+//         ),
+//       ),
+//       'display' => array(
+//         'default' => array(
+//           'label' => 'above',
+//           'type' => 'go__gene_expression_formatter',
+//           'settings' => array(),
+//         ),
+//       ),
+//     );
+//   }
 
   // FEATURELOC
   if ($table_name == 'feature') {

tripal_chado/includes/tripal_chado.semweb.inc

@@ -31,7 +31,6 @@ function tripal_chado_populate_chado_semweb_table() {
   tripal_chado_populate_vocab_SBO();
   tripal_chado_populate_vocab_SCHEMA();
   tripal_chado_populate_vocab_SIO();
-  tripal_chado_populate_vocab_SO();
   tripal_chado_populate_vocab_SWO();
   tripal_chado_populate_vocab_TAXRANK();
   tripal_chado_populate_vocab_TCONTACT();
@@ -45,14 +44,16 @@ function tripal_chado_populate_chado_semweb_table() {
  */
 function tripal_chado_populate_vocab_FOAF() {
 
-  tripal_insert_cv('foaf','Friend of a Friend');
   tripal_insert_db(array(
     'name' => 'foaf',
     'description' => 'Friend of a Friend',
     'url' => 'http://www.foaf-project.org/',
     'urlprefix' => 'http://xmlns.com/foaf/spec/#',
   ));
-  tripal_insert_cv('foaf','Friend of a Friend. A dictionary of people-related terms that can be used in structured data).');
+  tripal_insert_cv(
+    'foaf',
+    'Friend of a Friend. A dictionary of people-related terms that can be used in structured data).'
+  );
 }
 
 /**
@@ -65,7 +66,10 @@ function tripal_chado_populate_vocab_RDFS() {
     'url' => 'https://www.w3.org/TR/rdf-schema/',
     'urlprefix' => 'https://www.w3.org/TR/rdf-schema/#ch_',
   ));
-  tripal_insert_cv('rdfs','Resource Description Framework Schema');
+  tripal_insert_cv(
+    'rdfs',
+    'Resource Description Framework Schema'
+  );
 
   $name = tripal_insert_cvterm(array(
     'id' => 'rdfs:type',
@@ -90,7 +94,10 @@ function tripal_chado_populate_vocab_SCHEMA() {
     'url' => 'https://schema.org/',
     'urlprefix' => 'https://schema.org/{accession}',
   ));
-  tripal_insert_cv('schema','Schema.org. Schema.org is sponsored by Google, Microsoft, Yahoo and Yandex. The vocabularies are developed by an open community process.');
+  tripal_insert_cv(
+    'schema',
+    'Schema.org. Schema.org is sponsored by Google, Microsoft, Yahoo and Yandex. The vocabularies are developed by an open community process.'
+  );
 
 
   $term = tripal_insert_cvterm(array(
@@ -218,7 +225,10 @@ function tripal_chado_populate_vocab_EDAM() {
     'url' => 'http://edamontology.org/page',
     'urlprefix' => 'http://edamontology.org/{db}_{accession}',
   ));
-  tripal_insert_cv('data','Bioinformatics operations, data types, formats, identifiers and topics.');
+  tripal_insert_cv(
+    'data',
+    'Bioinformatics operations, data types, formats, identifiers and topics.'
+  );
 
 
   $term = tripal_insert_cvterm(array(
@@ -327,7 +337,10 @@ function tripal_chado_populate_vocab_ERO() {
     'url' => 'http://purl.bioontology.org/ontology/ERO',
     'urlprefix' => 'http://purl.bioontology.org/ontology/ERO/{db}:{accession}',
   ));
-  tripal_insert_cv('ero','The Eagle-I Research Resource Ontology models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/).');
+  tripal_insert_cv(
+      'ero',
+      'The Eagle-I Research Resource Ontology models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/).'
+  );
 
   $term = tripal_insert_cvterm(array(
     'id' => 'ERO:0001716',
@@ -347,7 +360,10 @@ function tripal_chado_populate_vocab_OBI() {
     'url' => 'http://obi-ontology.org/page/Main_Page',
     'urlprefix' => 'http://purl.obolibrary.org/obo/{db}_{accession}',
   ));
-  tripal_insert_cv('obi','Ontology for Biomedical Investigation. The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.');
+  tripal_insert_cv(
+    'obi',
+    'Ontology for Biomedical Investigation. The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.'
+  );
 
   $term = tripal_insert_cvterm(array(
     'id' => 'OBI:0100026',
@@ -368,7 +384,10 @@ function tripal_chado_populate_vocab_OGI() {
     'url' => 'http://purl.bioontology.org/ontology/OGI',
     'urlprefix' => 'http://purl.obolibrary.org/obo/{db}_{accession}',
   ));
-  tripal_insert_cv('obi','Ontology for Biomedical Investigation. The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.');
+  tripal_insert_cv(
+    'ogi',
+    'Ontology for Biomedical Investigation. The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.'
+  );
 
   $term = tripal_insert_cvterm(array(
     'id' => 'OGI:0000021',
@@ -389,14 +408,17 @@ function tripal_chado_populate_vocab_IAO() {
     'url' => 'https://github.com/information-artifact-ontology/IAO/',
     'urlprefix' => 'http://purl.obolibrary.org/obo/IAO_',
   ));
-  tripal_insert_cv('IAO','Information Artifact Ontology  is a new ' .
+  tripal_insert_cv(
+    'IAO',
+    'Information Artifact Ontology  is a new ' .
       'ontology of information entities, originally driven by work by the ' .
-      'OBI digital entity and realizable information entity branch.');
+      'OBI digital entity and realizable information entity branch.'
+  );
 
   $term = tripal_insert_cvterm(array(
     'id' => 'IAO:0000115',
     'name' => 'definition',
-    'cv_name' => 'iao',
+    'cv_name' => 'IAO',
     'definition' => 'The official OBI definition, explaining the meaning of ' .
       'a class or property. Shall be Aristotelian, formalized and normalized. ' .
       'Can be augmented with colloquial definitions.',
@@ -459,10 +481,6 @@ function tripal_chado_populate_vocab_LOCAL() {
     'tripal_phylogeny',
     'Terms used by the Tripal phylotree module for phylogenetic and taxonomic trees.'
   );
-  tripal_insert_cv(
-    'synonym_type',
-    'A local vocabulary that contains synonym types (e.g. exact, broad, narrow, related).'
-  );
   // Add cv for relationship types
   tripal_insert_cv(
     'feature_relationship',
@@ -727,7 +745,6 @@ function tripal_chado_populate_vocab_LOCAL() {
       'name' => $term,
       'definition' => '',
       'cv_name' => 'organism_property',
-      'is_relationship' => 0,
       'db_name' => 'local'
     );
     tripal_insert_cvterm($value, $options);
@@ -738,16 +755,13 @@ function tripal_chado_populate_vocab_LOCAL() {
   //---------------------
 
   // Add the terms used to identify nodes in the tree.
-  tripal_insert_cvterm(
-      array(
-        'name' => 'phylo_leaf',
-        'definition' => 'A leaf node in a phylogenetic tree.',
-        'cv_name' => 'tripal_phylogeny',
-        'is_relationship' => 0,
-        'db_name' => 'local'
-      ),
-      array('update_existing' => TRUE)
-  );
+  tripal_insert_cvterm(array(
+    'name' => 'phylo_leaf',
+    'definition' => 'A leaf node in a phylogenetic tree.',
+    'cv_name' => 'tripal_phylogeny',
+    'is_relationship' => 0,
+    'db_name' => 'local'
+  ));
   // Add the terms used to identify nodes in the tree.
   tripal_insert_cvterm(array(
     'name' => 'phylo_root',
@@ -775,36 +789,6 @@ function tripal_chado_populate_vocab_LOCAL() {
     'db_name' => 'local'
   ));
 
-  //---------------------
-  // Synonym Types Terms
-  //---------------------
-  tripal_insert_cvterm(array(
-    'name' => 'exact',
-    'definition' => 'An exact equivalent; interchangeable with the term name.',
-    'cv_name' => 'synonym_type',
-    'db_name' => 'local',
-  ), array('force_db_change' => TRUE));
-
-  tripal_insert_cvterm(array(
-    'name' => 'broad',
-    'definition' => 'The synonym is broader than the name.',
-    'cv_name' => 'synonym_type',
-    'db_name' => 'local',
-  ), array('force_db_change' => TRUE));
-  tripal_insert_cvterm(array(
-    'name' => 'narrow',
-    'definition' => 'The synonym is narrower or more precise than the name.',
-    'cv_name' => 'synonym_type',
-    'db_name' => 'local',
-  ), array('force_db_change' => TRUE));
-
-  tripal_insert_cvterm(array(
-    'name' => 'related',
-    'definition' => 'The synonym is related in some way.',
-    'cv_name' => 'synonym_type',
-    'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
-
 
   //--------------
   // Project Terms
@@ -817,7 +801,7 @@ function tripal_chado_populate_vocab_LOCAL() {
     'definition'  => 'Description of a project',
     'cv_name' => 'project_property',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
 
   //--------------
   // Natural Diversity Terms
@@ -828,21 +812,21 @@ function tripal_chado_populate_vocab_LOCAL() {
     'definition' => 'An experiment where genotypes of individuals are identified.',
     'cv_name' => 'nd_experiment_types',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
 
   tripal_insert_cvterm(array(
     'name' => 'Phenotyping',
     'definition' => 'An experiment where phenotypes of individuals are identified.',
     'cv_name' => 'nd_experiment_types',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
 
   tripal_insert_cvterm(array(
     'name' => 'Location',
     'definition' => 'The name of the location.',
     'cv_name' => 'nd_geolocation_property',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
 
 
   //--------------
@@ -857,7 +841,7 @@ function tripal_chado_populate_vocab_LOCAL() {
     'definition' => 'Description of a library',
     'cv_name' => 'library_property',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
 
   // add cvterms for the map unit types
   tripal_insert_cvterm(array(
@@ -866,42 +850,42 @@ function tripal_chado_populate_vocab_LOCAL() {
     'definition' => 'cDNA library',
     'cv_name' => 'library_type',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'id' => 'local:bac_library',
     'name' => 'bac_library',
     'definition' => 'Bacterial Artifical Chromsome (BAC) library',
     'cv_name' => 'library_type',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'id' => 'local:fosmid_library',
     'name' => 'fosmid_library',
     'definition' => 'Fosmid library',
     'cv_name' => 'library_type',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'id' => 'local:cosmid_library',
     'name' => 'cosmid_library',
     'definition' => 'Cosmid library',
     'cv_name' => 'library_type',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'id' => 'local:yac_library',
     'name' => 'yac_library',
     'definition' => 'Yeast Artificial Chromosome (YAC) library',
     'cv_name' => 'library_type',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'id' => 'local:genomic_library',
     'name' => 'genomic_library',
     'definition' => 'Genomic Library',
     'cv_name' => 'library_type',
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
 
   //--------------
   // Feature Map
@@ -913,35 +897,35 @@ function tripal_chado_populate_vocab_LOCAL() {
     'cv_name' => 'featuremap_units',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'bp',
     'definition' => 'Base pairs units',
     'cv_name' => 'featuremap_units',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'bin_unit',
     'definition' => 'The bin unit',
     'cv_name' => 'featuremap_units',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'marker_order',
     'definition' => 'Units simply to define marker order.',
     'cv_name' => 'featuremap_units',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'undefined',
     'definition' => 'A catch-all for an undefined unit type',
     'cv_name' => 'featuremap_units',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   // featurepos properties
   tripal_insert_cvterm(array(
     'name' => 'start',
@@ -949,14 +933,14 @@ function tripal_chado_populate_vocab_LOCAL() {
     'cv_name' => 'featurepos_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'stop',
     'definition' => 'The end coordinate for a map feature',
     'cv_name' => 'featurepos_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   // add cvterms for map properties
   tripal_insert_cvterm(array(
     'name' => 'Map Dbxref',
@@ -966,21 +950,21 @@ function tripal_chado_populate_vocab_LOCAL() {
     'cv_name' => 'featuremap_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'Map Type',
     'definition' => 'The type of Map (e.g. QTL, Physical, etc.)',
     'cv_name' => 'featuremap_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'Genome Group',
     'definition' => '',
     'cv_name' => 'featuremap_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'URL',
     'definition' => 'A univeral resource locator (URL) reference where the '
@@ -989,7 +973,7 @@ function tripal_chado_populate_vocab_LOCAL() {
     'cv_name' => 'featuremap_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'Population Type',
     'definition' => 'A brief description of the population type used to generate '
@@ -997,28 +981,28 @@ function tripal_chado_populate_vocab_LOCAL() {
     'cv_name' => 'featuremap_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'Population Size',
     'definition' => 'The size of the population used to construct the map.',
     'cv_name' => 'featuremap_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'Methods',
     'definition' => 'A brief description of the methods used to construct the map.',
     'cv_name' => 'featuremap_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
   tripal_insert_cvterm(array(
     'name' => 'Software',
     'definition' => 'The software used to construct the map.',
     'cv_name' => 'featuremap_property',
     'is_relationship' => 0,
     'db_name' => 'local'
-  ), array('force_db_change' => TRUE));
+  ));
 
 
   //--------------
@@ -1123,7 +1107,10 @@ function tripal_chado_populate_vocab_SBO() {
     'url' => 'http://www.ebi.ac.uk/sbo/main/',
     'urlprefix' => 'http://purl.obolibrary.org/obo/{db}_{accession}',
   ));
-  tripal_insert_cv('sbo','Systems Biology.  Terms commonly used in Systems Biology, and in particular in computational modeling.');
+  tripal_insert_cv(
+    'sbo',
+    'Systems Biology.  Terms commonly used in Systems Biology, and in particular in computational modeling.'
+  );
 
   $dbxref = tripal_insert_cvterm(array(
     'id' => 'SBO:0000358',
@@ -1147,35 +1134,6 @@ function tripal_chado_populate_vocab_SBO() {
   ));
 }
 
-/**
- * Adds the Sequence Ontology
- */
-function tripal_chado_populate_vocab_SO() {
-  tripal_insert_db(array(
-    'name' => 'SO',
-    'description' => 'Sequence Ontology',
-    'url' => 'http://www.sequenceontology.org',
-    'urlprefix' => 'http://www.sequenceontology.org/browser/current_svn/term/{db}:{accession}',
-  ));
-  tripal_insert_cv('sequence','The Sequence Ontology.');
-
-  // Add the terms we need for default content types.  This needs to be
-  // done because the sequence ontology may not already be loaded but we
-  // still want to provide these default content types.
-  $term = tripal_insert_cvterm(array(
-    'id' => 'SO:0000704',
-    'name' => 'gene',
-    'cv_name' => 'sequence',
-    'definition' => 'A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. [SO:immuno_workshop]',
-  ));
-  $term = tripal_insert_cvterm(array(
-    'id' => 'SO:0000234',
-    'name' => 'mRNA',
-    'cv_name' => 'sequence',
-    'definition' => 'Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. [SO:ma]',
-  ));
-}
-
 /**
  * Adds the Software Ontology database and terms.
  */
@@ -1221,10 +1179,6 @@ function tripal_chado_populate_vocab_SWO() {
  * Adds the contact table mapping.
  */
 function tripal_chado_populate_vocab_TCONTACT() {
-  tripal_insert_db(array(
-    'name' => 'TContact',
-    'description' => 'The Tripal Contact controlled vocabulary.',
-  ));
 }
 
 /**
@@ -1232,10 +1186,8 @@ function tripal_chado_populate_vocab_TCONTACT() {
  */
 function tripal_chado_populate_vocab_TPUB() {
 
-  tripal_insert_db(array(
-    'name' => 'TPUB',
-    'description' => 'The Tripal Publication controlled vocabulary.',
-  ));
+  // No need to insert the TPUB cv/db those should already be added.
+
   // make sure we have our supported databases
   tripal_insert_db(
       array(
@@ -1307,37 +1259,14 @@ function tripal_chado_populate_vocab_UO() {
  * Adds the Taxonomic Rank Ontology database and terms.
  */
 function tripal_chado_populate_vocab_TAXRANK() {
-  tripal_insert_db(array(
-    'name' => 'TAXRANK',
-    'description' => 'Taxonomic rank vocabulary.',
-    'url' => 'https://github.com/phenoscape/taxrank',
-    'urlprefix' => 'http://purl.obolibrary.org/obo/TAXRANK_',
-  ));
-  tripal_insert_cv('taxrank','Taxonomic rank vocabulary. A vocabulary of taxonomic ranks (species, family, phylum, etc).');
-
 
-  $term = tripal_insert_cvterm(array(
-    'id' => 'TAXRANK:0000005',
-    'name' => 'genus',
-    'cv_name' => 'taxonomic_rank',
-    'description' => 'Taxonomic rank of Genus'
-  ));
+  $term = tripal_get_cvterm(array('id' => 'TAXRANK:0000005'));
   tripal_associate_chado_semweb_term('organism', 'genus', $term);
 
-  $term = tripal_insert_cvterm(array(
-    'id' => 'TAXRANK:0000006',
-    'name' => 'species',
-    'cv_name' => 'taxonomic_rank',
-    'description' => 'Taxonomic rank of species.'
-  ));
+  $term = tripal_get_cvterm(array('id' => 'TAXRANK:0000006'));
   tripal_associate_chado_semweb_term('organism', 'species', $term);
 
-  $term = tripal_insert_cvterm(array(
-    'id' => 'TAXRANK:0000045',
-    'name' => 'infraspecies',
-    'cv_name' => 'taxonomic_rank',
-    'description' => 'Taxonomic infraspecies name.'
-  ));
+  $term = tripal_get_cvterm(array('id' => 'TAXRANK:0000045'));
   tripal_associate_chado_semweb_term('organism', 'infraspecific_name', $term);
 }
 
@@ -1351,8 +1280,10 @@ function tripal_chado_populate_vocab_NCBITAXON() {
     'url' => 'http://www.berkeleybop.org/ontologies/ncbitaxon/',
     'urlprefix' => 'http://purl.obolibrary.org/obo/ncbitaxon#',
   ));
-  tripal_insert_cv('ncbitaxon','NCBI organismal classification. An ontology representation of the NCBI organismal taxonomy.');
-
+  tripal_insert_cv(
+    'ncbitaxon',
+    'NCBI organismal classification. An ontology representation of the NCBI organismal taxonomy.'
+  );
 
   $term = tripal_insert_cvterm(array(
     'id' => 'NCBITaxon:common_name',

tripal_chado/includes/tripal_chado.setup.inc

@@ -86,7 +86,7 @@ function tripal_chado_load_ontologies() {
       'name' => 'Taxonomic Rank',
       'path' => 'http://purl.obolibrary.org/obo/taxrank.obo',
       'auto_load' => TRUE,
-      'cv_name' => 'taxrank'
+      'cv_name' => 'taxonomic_rank'
     ),
     array(
       'name' => 'Tripal Contact',
@@ -100,18 +100,18 @@ function tripal_chado_load_ontologies() {
       'auto_load' => TRUE,
       'cv_name' => 'tripal_pub'
     ),
-    array(
-      'name' => 'Sequence Ontology',
-      'path' => 'http://purl.obolibrary.org/obo/so.obo',
-      'auto_load' => TRUE,
-      'cv_name' => 'sequence'
-    ),
+     array(
+       'name' => 'Sequence Ontology',
+       'path' => 'http://purl.obolibrary.org/obo/so.obo',
+       'auto_load' => TRUE,
+       'cv_name' => 'sequence'
+     ),
 
   );
   for ($i = 0; $i < count($ontologies); $i++) {
     $obo_id = tripal_insert_obo($ontologies[$i]['name'], $ontologies[$i]['path']);
     if ($ontologies[$i]['auto_load'] == TRUE) {
-      // Only load ontolgogies that are not already in the cv table.
+      // Only load ontologies that are not already in the cv table.
       $cv = tripal_get_cv(array('name' => $ontologies[$i]['cv_name']));
       if (!$cv) {
         tripal_chado_load_obo_v1_2_id($obo_id);
@@ -131,6 +131,7 @@ function tripal_chado_prepare_chado() {
     // formats.
     module_load_include('inc', 'tripal', 'api/tripal.api');
     module_load_include('inc', 'tripal', 'includes/tripal.admin');
+    module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.semweb');
 
     // Get the effective version.  Pass true as second argument
     // to warn the user if the current version is not compatible.
@@ -146,7 +147,6 @@ function tripal_chado_prepare_chado() {
     tripal_chado_load_ontologies();
 
     // Populate the semantic web associations for Chado tables/fields.
-    module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.semweb');
     tripal_chado_populate_chado_semweb_table();
 
     // Initialize the population of the chado_cvterm_mapping table.  This will

tripal_chado/tripal_chado.module

@@ -87,7 +87,7 @@ function tripal_chado_init() {
     }
     else {
       drupal_set_message('Tripal cannot find a Chado installation. Please ' .
-          l('install Chado', 'admin/tripal/storage/chado/chado_install') .
+          l('install Chado', 'admin/tripal/storage/chado/install') .
           ' before continuing.', 'warning');
     }
   }