Merge pull request #940 from tripal/938_so_bundles

resolve SO based bundles using wrong term name

tripal/api/tripal.entities.api.inc

@@ -433,6 +433,9 @@ function tripal_add_notification($title, $details, $type, $actions, $submitter_i
  *     - term_name: A human-readable name for this term.  This will became
  *       the name that appears for the content type.  In practice, this
  *       should be the name of the term. (E.g. the name for SO:0000704 is gene).
+ *     - label: An alternative bundle label.  This will be used instead of the
+ *       term name, for cases where the vocabulary term is not human readable.
+ *
  * @param $job
  *  The job ID if this is launched via a job.
  *
@@ -446,6 +449,7 @@ function tripal_create_bundle($args, $job = NULL) {
   $accession = $args['accession'];
   $term_name = $args['term_name'];
   $storage_args = $args['storage_args'];
+  $label = $args['label'];
 
   $message_args = [
     'job' => $job,
@@ -505,9 +509,11 @@ function tripal_create_bundle($args, $job = NULL) {
     if (!in_array($bundle_name, array_keys($einfo['bundles']))) {
       // Make the label for the content type have capitalized words.  The
       // exception is 'mRNA' which we know should not be uppercased.
-      $label = ucwords(preg_replace('/_/', ' ', $term_name));
-      if ($term_name == 'mRNA') {
-        $label = $term_name;
+      if (!$label) {
+        $label = ucwords(preg_replace('/_/', ' ', $term_name));
+        if ($term_name == 'mRNA') {
+          $label = $term_name;
+        }
       }
       // Insert the bundle.
       db_insert('tripal_bundle')

tripal_chado/includes/setup/tripal_chado.setup.inc

@@ -348,7 +348,8 @@ function tripal_chado_prepare_general_types($job) {
   $args = [
     'vocabulary' => 'SIO',
     'accession' => '001066',
-    'term_name' => 'Study',
+    'term_name' => 'study',
+    'label' => 'Study',
     'storage_args' => [
       'data_table' => 'study',
     ],
@@ -501,7 +502,8 @@ function tripal_chado_prepare_genomic_types($job) {
   $args = [
     'vocabulary' => 'operation',
     'accession' => '0525',
-    'term_name' => 'Genome Assembly',
+    'term_name' => 'Genome assembly',
+    'label' => 'Genome Assembly',
     'storage_args' => [
       'data_table' => 'analysis',
       'type_linker_table' => 'analysisprop',
@@ -518,7 +520,8 @@ function tripal_chado_prepare_genomic_types($job) {
   $args = [
     'vocabulary' => 'operation',
     'accession' => '0362',
-    'term_name' => 'Genome Annotation',
+    'term_name' => 'Genome annotation',
+    'label' => 'Genome Annotation',
     'storage_args' => [
       'data_table' => 'analysis',
       'type_linker_table' => 'analysisprop',
@@ -574,7 +577,8 @@ function tripal_chado_prepare_expression_types($job) {
   $args = [
     'vocabulary' => 'OBI',
     'accession' => '0000070',
-    'term_name' => 'Assay',
+    'term_name' => 'assay',
+    'label' => 'Assay',
     'storage_args' => [
       'data_table' => 'assay',
     ],
@@ -628,7 +632,8 @@ function tripal_chado_prepare_germplasm_types($job) {
   $args = [
     'vocabulary' => 'CO_010',
     'accession' => '0000044',
-    'term_name' => 'Germplasm Accession',
+    'term_name' => 'accession',
+    'label' => 'Germplasm Accession',
     'storage_args' => [
       'data_table' => 'stock',
       'type_column' => 'type_id',
@@ -643,7 +648,8 @@ function tripal_chado_prepare_germplasm_types($job) {
   $args = [
     'vocabulary' => 'CO_010',
     'accession' => '0000255',
-    'term_name' => 'Generated germplasm (breeding cross)',
+    'label' => 'Generated Germplasm (Breeding Cross)',
+    'term_name' => 'generated germplasm',
     'storage_args' => [
       'data_table' => 'stock',
       'type_column' => 'type_id',
@@ -658,7 +664,8 @@ function tripal_chado_prepare_germplasm_types($job) {
   $args = [
     'vocabulary' => 'CO_010',
     'accession' => '0000029',
-    'term_name' => 'Cultivar (germplasm variety)',
+    'label' => 'Cultivar (Germplasm Variety)',
+    'term_name' => 'cultivar',
     'storage_args' => [
       'data_table' => 'stock',
       'type_column' => 'type_id',
@@ -673,7 +680,8 @@ function tripal_chado_prepare_germplasm_types($job) {
   $args = [
     'vocabulary' => 'CO_010',
     'accession' => '0000162',
-    'term_name' => 'Recombinant Inbred Line',
+    'label' => 'Recombinant Inbred Line',
+    'term_name' => '414 inbred line',
     'storage_args' => [
       'data_table' => 'stock',
       'type_column' => 'type_id',
@@ -695,7 +703,8 @@ function tripal_chado_prepare_genetic_types($job) {
   $args = [
     'vocabulary' => 'data',
     'accession' => '1278',
-    'term_name' => 'Genetic Map',
+    'label' => 'Genetic Map',
+    'term_name' => 'Genetic map',
     'storage_args' => [
       'data_table' => 'featuremap',
       'type_linker_table' => 'featuremapprop',
@@ -728,7 +737,8 @@ function tripal_chado_prepare_genetic_types($job) {
   $args = [
     'vocabulary' => 'SO',
     'accession' => '0001060',
-    'term_name' => 'Sequence Variant',
+    'label' => "Sequence Variant",
+    'term_name' => 'sequence_variant',
     'storage_args' => [
       'data_table' => 'feature',
       'type_column' => 'type_id',
@@ -743,7 +753,8 @@ function tripal_chado_prepare_genetic_types($job) {
   $args = [
     'vocabulary' => 'SO',
     'accession' => '0001645',
-    'term_name' => 'Genetic Marker',
+    'term_name' => 'genetic_marker',
+    'label' => "Genetic Marker",
     'storage_args' => [
       'data_table' => 'feature',
       'type_column' => 'type_id',
@@ -759,7 +770,9 @@ function tripal_chado_prepare_genetic_types($job) {
   $args = [
     'vocabulary' => 'SO',
     'accession' => '0001500',
-    'term_name' => 'Heritable Phenotypic Marker',
+    'term_name' => 'heritable_phenotypic_marker',
+    'label' => "Heritable Phenotypic Marker",
+
     'storage_args' => [
       'data_table' => 'feature',
       'type_column' => 'type_id',

tripal_chado/tripal_chado.install

@@ -1940,3 +1940,138 @@ function tripal_chado_update_7337(){
     throw new DrupalUpdateException('Could not perform update: '. $error);
   }
 }
+
+
+/**
+ * Modify the term name for Sequence Variant, Genetic Marker, and Heritable Phenotypic Marker to match the corresponding SO term.
+ */
+function tripal_chado_update_7338() {
+
+  $terms = [
+    [
+      'vocabulary' => 'SO',
+      'label' => 'Sequence Variant',
+      'term' => 'sequence_variant',
+      'accession' => '0001060',
+    ],
+    [
+      'vocabulary' => 'SO',
+      'label' => 'Genetic Marker',
+      'term' => 'genetic_marker',
+      'accession' => '0001645',
+    ],
+    [
+      'vocabulary' => 'SO',
+      'label' => 'Heritable Phenotypic Marker',
+      'term' => 'heritable_phenotypic_marker',
+      'accession' => '0001500',
+    ],
+    [
+      'vocabulary' => 'SIO',
+      'label' => 'Study',
+      'term' => 'study',
+      'accession' => '001066',
+    ],
+    [
+      'vocabulary' => 'sep',
+      'label' => 'Biological Sample',
+      'term' => '	biological sample',
+      'accession' => '00195',
+    ],
+    [
+      'vocabulary' => 'OBI',
+      'label' => 'Assay',
+      'term' => 'assay',
+      'accession' => '0000070',
+    ],
+    [
+      'vocabulary' => 'data',
+      'label' => 'Genetic Map',
+      'term' => 'Genetic map',
+      'accession' => '1278',
+    ],
+    [
+      'vocabulary' => 'operation',
+      'label' => 'Genome Annotation',
+      'term' => 'Genome annotation',
+      'accession' => '0362',
+    ],
+    [
+      'vocabulary' => 'operation',
+      'label' => 'Genome Assembly',
+      'term' => 'Genome assembly',
+      'accession' => '0525',
+    ],
+    [
+      'vocabulary' => 'CO_010',
+      'label' => 'Generated Germplasm (Breeding Cross)',
+      'term' => 'generated germplasm',
+      'accession' => '0000255',
+    ],
+    [
+      'vocabulary' => 'CO_010',
+      'label' => 'Cultivar (Germplasm Variety)',
+      'term' => 'cultivar',
+      'accession' => '0000029',
+    ],
+
+    [
+      'vocabulary' => 'CO_010',
+      'label' => 'Germplasm Accession',
+      'term' => 'accession',
+      'accession' => '0000044',
+    ],
+    [
+      'vocabulary' => 'data',
+      'label' => 'Physical Map',
+      'term' => 'Physical map',
+      'accession' => '1280',
+    ],
+    [
+      'vocabulary' => 'sep',
+      'label' => 'Protocol',
+      'term' => '	protocol',
+      'accession' => '00101',
+    ],
+    [
+      'vocabulary' => 'CO_010',
+      'label' => 'Recombinant Inbred Line',
+      'term' => '414 inbred line',
+      'accession' => '0000162',
+    ],
+  ];
+
+  try {
+    foreach ($terms as $term) {
+
+      $label = $term['label'];
+      $termName = $term['term'];
+      $accession = $term['accession'];
+      $vocabulary = $term['vocabulary']; #shortname, ie, chado.db
+      $term = tripal_load_term_entity([
+        'vocabulary' => $vocabulary,
+        'accession' => $accession
+      ]);
+
+      if (!$term) {
+        continue;
+      }
+      $term->name = $termName;
+      $term->save();
+
+      $bundle = tripal_load_bundle_entity(['term_id' => $term->id]);
+
+      if (!$bundle) {
+        continue;
+      }
+      $bundle->label = $label;
+      $bundle->save();
+
+
+    }
+  } catch (\PDOException $e) {
+    $error = $e->getMessage();
+    throw new DrupalUpdateException('Could not perform update: '. $error);
+  }
+
+}