Merge branch '4.x' into tv4g1-1509-sequence-fields

pdtouch · Oct 25, 2023 · c62fa0b · c62fa0b
2 parents cef5845 + e518eb9
commit c62fa0b
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Showing 6 changed files with 706 additions and 4 deletions.
diff --git a/tripal_chado/config/install/tripal.tripalfield_collection.default_chado.yml b/tripal_chado/config/install/tripal.tripalfield_collection.default_chado.yml
@@ -1014,6 +1014,33 @@ fields:
               region: content
               weight: 90
 
+    -   name: gene_synonym
+        content_type: gene
+        label: Synonyms
+        type: chado_synonym_default
+        description: Alternate names, aliases or synonyms for this record.
+        cardinality: -1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                linker_table: feature_synonym
+                linker_fkey_column: feature_id
+        settings:
+            termIdSpace: schema
+            termAccession: alternateName
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 10
+          form:
+            default:
+              region: content
+              weight: 10
+
     -   name: mrna_name
         content_type: mRNA
         label: Name
@@ -1253,6 +1280,33 @@ fields:
               region: content
               weight: 90
 
+    -   name: mrna_synonym
+        content_type: mRNA
+        label: Synonyms
+        type: chado_synonym_default
+        description: Alternate names, aliases or synonyms for this record.
+        cardinality: -1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                linker_table: feature_synonym
+                linker_fkey_column: feature_id
+        settings:
+            termIdSpace: schema
+            termAccession: alternateName
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 10
+          form:
+            default:
+              region: content
+              weight: 10
+
     -   name: phylotree_name
         content_type: phylotree
         label: Name
@@ -1573,6 +1627,33 @@ fields:
               region: content
               weight: 20
 
+    -   name: dna_library_synonym
+        content_type: dna_library
+        label: Synonyms
+        type: chado_synonym_default
+        description: Alternate names, aliases or synonyms for this record.
+        cardinality: -1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: library
+                linker_table: library_synonym
+                linker_fkey_column: library_id
+        settings:
+            termIdSpace: schema
+            termAccession: alternateName
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 10
+          form:
+            default:
+              region: content
+              weight: 10
+
     -   name: genome_assembly_name
         content_type: genome_assembly
         label: Name
@@ -2405,6 +2486,33 @@ fields:
               region: content
               weight: 90
 
+    -   name: qtl_synonym
+        content_type: QTL
+        label: Synonyms
+        type: chado_synonym_default
+        description: Alternate names, aliases or synonyms for this record.
+        cardinality: -1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                linker_table: feature_synonym
+                linker_fkey_column: feature_id
+        settings:
+            termIdSpace: schema
+            termAccession: alternateName
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 10
+          form:
+            default:
+              region: content
+              weight: 10
+
     -   name: sequence_variant_name
         content_type: sequence_variant
         label: Name
@@ -2644,6 +2752,33 @@ fields:
               region: content
               weight: 90
 
+    -   name: sequence_variant_synonym
+        content_type: sequence_variant
+        label: Synonyms
+        type: chado_synonym_default
+        description: Alternate names, aliases or synonyms for this record.
+        cardinality: -1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                linker_table: feature_synonym
+                linker_fkey_column: feature_id
+        settings:
+            termIdSpace: schema
+            termAccession: alternateName
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 10
+          form:
+            default:
+              region: content
+              weight: 10
+
     -   name: genetic_marker_name
         content_type: genetic_marker
         label: Name
@@ -2883,6 +3018,33 @@ fields:
               region: content
               weight: 90
 
+    -   name: genetic_marker_synonym
+        content_type: genetic_marker
+        label: Synonyms
+        type: chado_synonym_default
+        description: Alternate names, aliases or synonyms for this record.
+        cardinality: -1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                linker_table: feature_synonym
+                linker_fkey_column: feature_id
+        settings:
+            termIdSpace: schema
+            termAccession: alternateName
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 10
+          form:
+            default:
+              region: content
+              weight: 10
+
     -   name: phenotypic_marker_name
         content_type: phenotypic_marker
         label: Name
@@ -3122,6 +3284,33 @@ fields:
               region: content
               weight: 90
 
+    -   name: phenotypic_marker_synonym
+        content_type: phenotypic_marker
+        label: Synonyms
+        type: chado_synonym_default
+        description: Alternate names, aliases or synonyms for this record.
+        cardinality: -1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                linker_table: feature_synonym
+                linker_fkey_column: feature_id
+        settings:
+            termIdSpace: schema
+            termAccession: alternateName
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 10
+          form:
+            default:
+              region: content
+              weight: 10
+
     -   name: germplasm_name
         content_type: germplasm
         label: Name

diff --git a/tripal_chado/src/Plugin/Field/FieldFormatter/ChadoSynonymFormatterDefault.php b/tripal_chado/src/Plugin/Field/FieldFormatter/ChadoSynonymFormatterDefault.php
@@ -0,0 +1,59 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter;
+
+use Drupal\tripal\TripalField\TripalFormatterBase;
+use Drupal\Core\Field\FieldItemListInterface;
+use Drupal\Core\Form\FormStateInterface;
+use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
+
+/**
+ * Plugin implementation of Default Tripal field formatter for sequence data
+ *
+ * @FieldFormatter(
+ *   id = "chado_synonym_formatter_default",
+ *   label = @Translation("Chado Synonym Formatter"),
+ *   description = @Translation("A chado synonym formatter"),
+ *   field_types = {
+ *     "chado_synonym_default"
+ *   }
+ * )
+ */
+class ChadoSynonymFormatterDefault extends ChadoFormatterBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function viewElements(FieldItemListInterface $items, $langcode) {
+    $elements = [];
+
+    $list = [];
+    foreach($items as $delta => $item) {
+      $value = $item->get('name')->getString();
+      $list[$delta] = $value;
+    }
+
+    // Also need to make sure to not return markup if the field is empty.
+    if (empty($list)) {
+      return $elements;
+    }
+
+    // If more than one value has been found display all values in an unordered
+    // list.
+    if (count($list) > 1) {
+      $elements[0] = [
+        '#theme' => 'item_list',
+        '#list_type' => 'ul',
+        '#items' => $list,
+        '#wrapper_attributes' => ['class' => 'container'],
+      ];
+      return $elements;
+    }
+
+    $elements[0] = [
+      '#type' => 'markup',
+      "#markup" => $list[0]
+    ];
+    return $elements;
+  }
+}