Updated taxrank OBO to use PURL and removed some drupal_write_record from API functions

tripal/api/tripal.jobs.api.inc

@@ -88,18 +88,21 @@ function tripal_add_job($job_name, $modulename, $callback, $arguments, $uid,
     $args = serialize($arguments);
   }
 
-  $record = new stdClass();
-  $record->job_name = $job_name;
-  $record->modulename = $modulename;
-  $record->callback = $callback;
-  $record->status = 'Waiting';
-  $record->submit_date = REQUEST_TIME;
-  $record->uid = $uid;
-  $record->priority = $priority;  # the lower the number the higher the priority
-  $record->arguments = $args;
-  $record->includes = serialize($includes);
-
-  if (drupal_write_record('tripal_jobs', $record)) {
+  $job_id = db_insert('tripal_jobs')
+  ->fields(array(
+    'job_name' => $job_name,
+    'modulename' => $modulename,
+    'callback' => $callback,
+    'status' => 'Waiting',
+    'submit_date' => REQUEST_TIME,
+    'uid' => $uid,
+    # The lower the number the higher the priority.
+    'priority' => $priority,
+    'arguments' => $args,
+  ))
+  ->execute();
+
+  if ($job_id) {
     drupal_set_message(t("Job '%job_name' submitted.", array('%job_name' => $job_name)));
     if (user_access('administer tripal')) {
       $jobs_url = url("admin/tripal/tripal_jobs");
@@ -114,7 +117,7 @@ function tripal_add_job($job_name, $modulename, $callback, $arguments, $uid,
     drupal_set_message(t("Failed to add job %job_name.", array('%job_name' => $job_name)), 'error');
   }
 
-  return $record->job_id;
+  return $job_id;
 }
 
 /**

tripal_chado/api/modules/tripal_chado.cv.api.inc

@@ -853,11 +853,13 @@ function tripal_insert_obo($name, $path) {
     return $obo_id;
   }
   else {
-    $record = new stdClass;
-    $record->name = $name;
-    $record->path = $path;
-    drupal_write_record('tripal_cv_obo', $record);
-    return $record->obo_id;
+    $obo_id = db_insert('tripal_cv_obo')
+      ->fields(array(
+        'name' => $name,
+        'path' => $path,
+      ))
+      ->execute();
+    return $obo_id;
   }
 }
 

tripal_chado/files/taxrank.obo

@@ -1,440 +0,0 @@
-format-version: 1.2
-data-version: 2013-11-10
-default-namespace: taxonomic_rank
-remark: To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Taxonomic Rank Vocabulary (TAXRANK). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: http://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary
-ontology: taxrank
-
-[Term]
-id: TAXRANK:0000000
-name: taxonomic_rank
-def: "A level of depth of a taxon in a taxonomic hierarchy." [TAXRANK:curator]
-
-[Term]
-id: TAXRANK:0000001
-name: phylum
-synonym: "division" EXACT []
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Phylum
-xref: NCBITaxon:phylum
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000002
-name: class
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Class
-xref: NCBITaxon:class
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000003
-name: order
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Order
-xref: NCBITaxon:order
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000004
-name: family
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Family
-xref: NCBITaxon:family
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000005
-name: genus
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Genus
-xref: NCBITaxon:genus
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000006
-name: species
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Species
-xref: NCBITaxon:species
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000007
-name: subclass
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Subclass
-xref: NCBITaxon:subclass
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000008
-name: subphylum
-synonym: "subdivision" EXACT []
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#SubPhylum
-xref: NCBITaxon:subphylum
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000009
-name: subgenus
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Subgenus
-xref: NCBITaxon:subgenus
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000010
-name: species_group
-xref: NCBITaxon:species_group
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000011
-name: species_subgroup
-synonym: "species complex" EXACT []
-xref: NCBITaxon:species_subgroup
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000012
-name: species_complex
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000013
-name: infraorder
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Infraorder
-xref: NCBITaxon:infraorder
-is_a: TAXRANK:0000000 ! taxonomic_rank
-
-[Term]
-id: TAXRANK:0000014
-name: suborder
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Suborder
-xref: NCBITaxon:suborder
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000015
-name: superclass
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Superclass
-xref: NCBITaxon:superclass
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000016
-name: varietas
-synonym: "variety" EXACT []
-xref: NCBITaxon:varietas
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000017
-name: kingdom
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Kingdom
-xref: NCBITaxon:kingdom
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000018
-name: superfamily
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Superfamily
-xref: NCBITaxon:superfamily
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000019
-name: infraclass
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Infraclass
-xref: NCBITaxon:infraclass
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000020
-name: superorder
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Superorder
-xref: NCBITaxon:superorder
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000021
-name: parvorder
-xref: NCBITaxon:parvorder
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000022
-name: superkingdom
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Superkingdom
-xref: NCBITaxon:superkingdom
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000023
-name: subspecies
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Subspecies
-xref: NCBITaxon:subspecies
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000024
-name: subfamily
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Subfamily
-xref: NCBITaxon:subfamily
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000025
-name: tribe
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Tribe
-xref: NCBITaxon:tribe
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000026
-name: forma
-synonym: "form" EXACT []
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Form
-xref: NCBITaxon:forma
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000027
-name: superphylum
-synonym: "superdivision" EXACT []
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Superphylum
-xref: NCBITaxon:superphylum
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000028
-name: subtribe
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Subtribe
-xref: NCBITaxon:subtribe
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000029
-name: subkingdom
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Subkingdom
-xref: NCBITaxon:subkingdom
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000030
-name: section
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Section
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000031
-name: series
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Series
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000032
-name: bio-variety
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Bio-variety
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000033
-name: candidate
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Candidate
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000034
-name: cultivar
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Cultivar
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000035
-name: cultivar-group
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Cultivar-group
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000036
-name: denominationclass
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#DenominationClass
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000037
-name: domain
-synonym: "empire" EXACT []
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Domain
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000038
-name: graft-chimaera
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Graft-chimaera
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000039
-name: grex
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Grex
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000040
-name: infraphylum
-synonym: "infradivision" EXACT []
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Infraphylum
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000041
-name: infrafamily
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Infrafamily
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000042
-name: infragenerictaxon
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#InfragenericTaxon
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000043
-name: infragenus
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Infragenus
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000044
-name: infrakingdom
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Infrakingdom
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000045
-name: infraspecies
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Infraspecies
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000046
-name: infraspecificTaxon
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#InfraspecificTaxon
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000047
-name: infratribe
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Infratribe
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000048
-name: patho-variety
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#patho-variety
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000049
-name: specialform
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Specialform
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000050
-name: speciesaggregate
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#SpeciesAggregate
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000051
-name: subvariety
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Sub-Variety
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000052
-name: subsubvariety
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Sub-Sub-Variety
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000053
-name: subsection
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Subsection
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000054
-name: subseries
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Subseries
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000055
-name: subspecificaggregate
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#SubspecificAggregate
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000056
-name: subsubform
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Subsubform
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000057
-name: supertribe
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#Supertribe
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Term]
-id: TAXRANK:0000058
-name: supragenerictaxon
-xref: http://rs.tdwg.org/ontology/voc/TaxonRank#SupragenericTaxon
-is_a: TAXRANK:0000000 ! taxonomic_rank
-created_by: pmidford
-
-[Typedef]
-id: TAXRANK:1000000
-name: has_rank
-is_metadata_tag: true
-

tripal_chado/includes/tripal_chado.setup.inc

@@ -141,7 +141,7 @@ function tripal_chado_prepare_chado() {
     tripal_set_default_cv('organismprop', 'type_id', 'organism_property');
 
     // Add taxonomic terms.
-    $obo_id = tripal_insert_obo('Taxonomic Rank', '{tripal_chado}/files/taxrank.obo');
+    $obo_id = tripal_insert_obo('Taxonomic Rank', 'http://purl.obolibrary.org/obo/taxrank.obo');
     $cv = chado_select_record('cv', array('name'), array('name' => 'taxonomic_rank'));
     if (count($cv) == 0 and $obo_id) {
       tripal_chado_load_obo_v1_2_id($obo_id);