Fix for major upgrades

tripal_core/api/tripal_core.jobs.api.inc

@@ -73,17 +73,21 @@ function tripal_add_job($job_name, $modulename, $callback, $arguments, $uid, $pr
     $args = serialize($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;
-
-  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')) {
       $jobs_url = url("admin/tripal/tripal_jobs");
@@ -95,10 +99,10 @@ function tripal_add_job($job_name, $modulename, $callback, $arguments, $uid, $pr
     }
   }
   else {
-    drupal_set_message(t("Failed to add job %job_name.", array('%job_name' => $job_name)), 'error');
+    drupal_set_message(t("Failed to add job: %job_name.", array('%job_name' => $job_name)), 'error');
   }
 
-  return $record->job_id;
+  return $job_id;
 }
 
 /**

tripal_core/includes/tripal_core.chado_install.inc

@@ -20,12 +20,18 @@ function tripal_core_chado_load_form() {
 
   if ($real_version == '1.2') {
     drupal_set_message('Please note: the upgrade of Chado from v1.2 to v1.3 may
-        require a fix to your materialized views.  All of the primary keys
+        require three fixes to your database. All of the primary keys
         in Chado were changed from integers to big integers to support larger
-        tables.  If your materialized views uses these fields you may need to
-        alter and repopulate those views.  Additionally, if you have made
+        tables.  First, if your site has custom materialized views that will hold
+        data derived from fields changed to big integers then you may need to
+        alter the views to change the fields from integers to big integers
+        and repopulate those views.  Second, if you have made
         any custom PL/pgSQL functions that expect primary and foreign key fields
-        to be integers, then those functions will need to be correct.
+        to be integers, then those functions will need to be altered to accept
+        big integers.  Third, if you have PostgreSQL Views that use fields
+        that are converted to big integers then most likely this upgrade will
+        fail.  You must first remove those views, perform the upgrade and then
+        recreate them with the appropriate fields change to big integers.
         The Tripal upgrader is not able to fix these problems automatically',
         'warning');
   }

tripal_cv/api/tripal_cv.api.inc

@@ -873,11 +873,13 @@ 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_organism/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_organism/tripal_organism.install

@@ -35,9 +35,8 @@ function tripal_organism_install() {
   tripal_set_default_cv('organismprop', 'type_id', 'organism_property');
 
   // Add taxonomic terms.
-  $obo_id = tripal_insert_obo('Taxonomic Rank', '{tripal_organism}/files/taxrank.obo');
+  $obo_id = tripal_insert_obo('Taxonomic Rank', 'http://purl.obolibrary.org/obo/taxrank.obo');
   tripal_submit_obo_job(array('obo_id' => $obo_id));
-
 }
 
 /**
@@ -200,13 +199,19 @@ function tripal_organism_update_7200() {
  */
 function tripal_organism_update_7201() {
   try {
+    // Make sure we have the full API loaded this will help during a
+    // site upgrade when the tripal_core module is disabled.
+    module_load_include('module', 'tripal_core', 'tripal_core');
+    tripal_core_import_api();
+    module_load_include('inc', 'tripal_cv', 'api/tripal_cv.api');
+
     // Add taxonomic terms.
-    $obo_id = tripal_insert_obo('Taxonomic Rank', '{tripal_organism}/files/taxrank.obo');
+    $obo_id = tripal_insert_obo('Taxonomic Rank', 'http://purl.obolibrary.org/obo/taxrank.obo');
     tripal_submit_obo_job(array('obo_id' => $obo_id));
   }
   catch (\PDOException $e) {
     $error = $e->getMessage();
-    throw new DrupalUpdateException('Could not move organism taxonomy terms: '. $error);
+    throw new DrupalUpdateException('Could not add taxrank ontology: '. $error);
   }
 }