Filter by collection for review

UofS-Pulse-Binfo · Aug 12, 2022 · e676bcb · e676bcb
1 parent ffa66fe
commit e676bcb
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Showing 2 changed files with 25 additions and 9 deletions.
diff --git a/includes/GermplasmSearch.inc b/includes/GermplasmSearch.inc
@@ -128,7 +128,7 @@ class GermplasmSearch extends KPSEARCH {
         'help' => 'The country the seed originated from.'
       ],
       'collection' => [
-        'title' => 'Collection/Population',
+        'title' => 'Collection',
         'help' => 'The collection or population the germplasm is part of.'
       ],
       'source_institute' => [
@@ -293,13 +293,17 @@ class GermplasmSearch extends KPSEARCH {
         s.stock_id,
         tb.label as type,
         origin.value as origin,
-        source.value as source_institute
+        source.value as source_institute,
+        col.name as collection
       FROM {stock} s
       LEFT JOIN {organism} o ON o.organism_id=s.organism_id
       LEFT JOIN {stockprop} source ON source.stock_id=s.stock_id AND source.type_id=3711
       LEFT JOIN {stockprop} origin ON origin.stock_id=s.stock_id AND origin.type_id=3976
       LEFT JOIN chado_bundle cb ON cb.type_id=s.type_id
-      LEFT JOIN tripal_bundle tb ON tb.id=cb.bundle_id ";
+      LEFT JOIN tripal_bundle tb ON tb.id=cb.bundle_id 
+      LEFT JOIN {stockcollection_stock} c ON s.stock_id = c.stock_id 
+      LEFT JOIN {stockcollection} col ON c.stockcollection_id = col.stockcollection_id
+      ";
 
     $where = [];
     $joins = [];
@@ -334,6 +338,12 @@ class GermplasmSearch extends KPSEARCH {
       $args[':origin'] = $filter_results['origin'];
     }
 
+    // -- Collection: 0 - select all.
+    if ($filter_results['collection'] > 0) {
+      $where[] = "col.stockcollection_id = :collection";
+      $args[':collection'] = $filter_results['collection'];
+    }
+
     // -- Name.
     if ($filter_results['name'] != '') {
       $where[] = "(s.name ~* :name OR s.uniquename = :name)";

diff --git a/includes/KPSEARCH.inc b/includes/KPSEARCH.inc
@@ -166,14 +166,16 @@ class KPSEARCH extends ChadoCustomSearch {
     $collections = chado_query($sql_collection);    
     if ($collections->rowCount() > 0) {
       foreach($collections as $collection) {
+        // Collection id number - Collection Name: Field will return
+        // collection id number, NOT THE NAME.
         $collection_options[ $collection->id ] = $collection->name;
       }
     }
 
     $q = drupal_get_query_parameters();
 
     // Refine collection options to only collection names
-    // where registered germplasm has the genus selected.
+    // where a registered germplasm has the genus of the selected genus.
     if (isset($q) && is_array($q) && $collection_options) {
       if (isset($q['genus']) && !empty($q['genus'])) {
         $genus = $q['genus'];
@@ -192,7 +194,7 @@ class KPSEARCH extends ChadoCustomSearch {
         $new_collection_options = [0 => $default_text];
         foreach($collection_options as $i => $collection) {
           if ($i > 0) {
-            // Skip default select option.
+            // Skip default select option 0.
 
             $has_genus = chado_query($sql_new_collection, [':genus' => $genus, ':collection' => $i])
               ->fetchObject();
@@ -203,14 +205,18 @@ class KPSEARCH extends ChadoCustomSearch {
           }
         }
       }
+
+      // Use currently selected collection not the default.
+      $default_collection = $q['collection'];
     }
-
-    $options = (count($new_collection_options) > 0) ? $new_collection_options : $collection_options;
+
+    $options = (count($new_collection_options) > 1) ? $new_collection_options : $collection_options;
+    $collection_field = $class::$info['filters']['collection'];
 
     $form['collection'] = array(
       '#type' => 'select',
-      '#title' => $class::$info['filters']['collection']['title'],
-      '#description' => $class::$info['filters']['collection']['help'],
+      '#title' => t($collection_field['title']),
+      '#description' => t($collection_field['help']),
       '#options' => $options,
       '#default_value' => $default_collection
     );