Merge pull request #7 from UofS-Pulse-Binfo/4-qtl_lists

4 qtl lists
UofS-Pulse-Binfo · Apr 21, 2020 · 8d1f52b · 8d1f52b
2 parents 2b6c7db + b271561
commit 8d1f52b
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Showing 3 changed files with 61 additions and 28 deletions.
diff --git a/includes/TripalFields/so__qtl/so__qtl.inc b/includes/TripalFields/so__qtl/so__qtl.inc
@@ -1,10 +1,11 @@
 <?php
 /**
  * @class
- * Purpose:
+ * Purpose: List QTL on various Tripal Content Pages including Genetic Maps,
+ *   Traits, Genetic Markers and Sequence Variants.
  *
- * Data:
- * Assumptions:
+ * Data: See https://tripal-qtl.readthedocs.io/en/latest/QTLimporter.html#data-storage
+ * Assumptions: Assumes QTL are imported by this module.
  */
 class so__qtl extends ChadoField {
 
@@ -109,12 +110,31 @@ class so__qtl extends ChadoField {
     // @debug dpm($entity, 'entity');
     $field_name = $this->instance['field_name'];
 
-    // Retrieve the QTL associated with a given trait.
+    // Retrieve the type_ids we'll need for our query.
+    $type_id_obj = [
+      'start' => chado_get_cvterm(['id' => 'MAIN:start']),
+      'end' => chado_get_cvterm(['id' => 'MAIN:end']),
+      'lod' => chado_get_cvterm(['id' => 'MAIN:lod']),
+      'addt_effect' => chado_get_cvterm(['id' => 'MAIN:additive_effect']),
+      'parent' => chado_get_cvterm(['id' => 'MAIN:direction']),
+      'instance_of' => chado_get_cvterm(['id' => 'OBO_REL:instance_of']),
+    ];
+    $type_id = [];
+    foreach ($type_id_obj as $key => $obj) {
+      $type_id[$key] = 0;
+      if (is_object($obj)) {
+        $type_id[$key] = $obj->cvterm_id;
+      }
+    }
+    // @debug dpm($type_id, 'types');
+
+    // Retrieve the QTL associated with a given TRAIT.
     if ($entity->chado_table == 'cvterm') {
       $feature_ids = chado_query('SELECT feature_id FROM {feature_cvterm} WHERE cvterm_id=:id',
         [':id' => $entity->chado_record_id])->fetchCol();
       // @debug dpm($feature_ids, 'feature_ids');
     }
+    // Retrieve the QTL associated with a given GENETIC MAP.
     elseif ($entity->chado_table == 'featuremap') {
       $feature_ids = chado_query("SELECT qtl.feature_id FROM {featurepos} pos
         LEFT JOIN {feature} qtl ON pos.feature_id=qtl.feature_id
@@ -123,24 +143,35 @@ class so__qtl extends ChadoField {
         [':id' => $entity->chado_record_id])->fetchCol();
       // @debug dpm($feature_ids, 'feature_ids');
     }
+    // Retrieve the QTL a given MARKER/VARIANT falls within.
+    elseif ($entity->chado_table == 'feature') {
 
-    if (!empty($feature_ids)) {
+      // First find the position of this marker.
+      $marker_pos = chado_query('
+        SELECT pos.mappos
+          FROM chado.feature m
+          LEFT JOIN chado.feature_relationship mrl ON mrl.object_id=m.feature_id AND mrl.type_id=:instance_of
+          LEFT JOIN chado.feature l ON l.feature_id=mrl.subject_id
+          LEFT JOIN chado.featurepos pos ON l.feature_id = pos.feature_id
+          WHERE m.feature_id=:id', [
+            ':id' => $entity->chado_record_id,
+            ':instance_of' => $type_id['instance_of'],
+          ])->fetchField();
 
-      // Retrieve the type_ids we'll need for our query.
-      $type_id_obj = [
-        'start' => chado_get_cvterm(['id' => 'MAIN:start']),
-        'end' => chado_get_cvterm(['id' => 'MAIN:end']),
-        'lod' => chado_get_cvterm(['id' => 'MAIN:lod']),
-        'addt_effect' => chado_get_cvterm(['id' => 'MAIN:additive_effect']),
-        'parent' => chado_get_cvterm(['id' => 'MAIN:direction']),
-      ];
-      $type_id = [];
-      foreach ($type_id_obj as $key => $obj) {
-        $type_id[$key] = 0;
-        if (is_object($obj)) {
-          $type_id[$key] = $obj->cvterm_id;
-        }
-      }
+      // Now grab all QTL spanning this position.
+      $feature_ids = chado_query('
+        SELECT pos.feature_id as qtl
+          FROM chado.featurepos pos
+          INNER JOIN chado.featureposprop pstart
+            ON pstart.featurepos_id=pos.featurepos_id AND pstart.type_id=:start
+          INNER JOIN chado.featureposprop pend
+            ON pend.featurepos_id=pos.featurepos_id AND pend.type_id=:end
+          WHERE cast(pstart.value as float) <= :pos AND cast(pend.value as float) >= :pos',
+          [':pos' => $marker_pos, ':start' => $type_id['start'], ':end' => $type_id['end']])->fetchCol();
+      // @debug dpm($feature_ids, 'feature_ids');
+    }
+
+    if (!empty($feature_ids)) {
 
       // Now get the generic information for each QTL.
       $entity->{$field_name}['und'] = [];

diff --git a/includes/TripalFields/so__qtl/so__qtl_widget.inc b/includes/TripalFields/so__qtl/so__qtl_widget.inc
@@ -20,9 +20,13 @@ class so__qtl_widget extends ChadoFieldWidget {
   * @see ChadoFieldWidget::form()
   *
   **/
-
   public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
     parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+
+    $widget['msg'] = [
+      '#type' => 'markup',
+      '#markup' => '<p>The QTL List field retrieves data from the database for display but does not provide a way to edit it. To load QTL data use the importer provided.</p>',
+    ];
   }
 
   /**
@@ -39,4 +43,4 @@ class so__qtl_widget extends ChadoFieldWidget {
   public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
   }
 
-}
+}
diff --git a/includes/tripal_qtl.fields.inc b/includes/tripal_qtl.fields.inc
@@ -103,7 +103,7 @@ function tripal_qtl_bundle_instances_info($entity_type, $bundle) {
         'term_accession' => '0000771',
         'auto_attach' => FALSE,
         'chado_table' => $bundle->data_table,
-        'chado_column' => 'organism_id',
+        'chado_column' => 'cvterm_id',
         'base_table' => $bundle->data_table,
       ),
       'widget' => array(
@@ -143,7 +143,7 @@ function tripal_qtl_bundle_instances_info($entity_type, $bundle) {
         'term_accession' => '0000771',
         'auto_attach' => FALSE,
         'chado_table' => $bundle->data_table,
-        'chado_column' => 'organism_id',
+        'chado_column' => 'featuremap_id',
         'base_table' => $bundle->data_table,
       ),
       'widget' => array(
@@ -163,8 +163,7 @@ function tripal_qtl_bundle_instances_info($entity_type, $bundle) {
       ),
     );
   }
-  // Feature-based Pages (e.g. genetic map, gene, etc.)
-  /*
+  // Feature-based Pages (e.g. genetic marker, gene, etc.)
   elseif (isset($bundle->data_table) AND ($bundle->data_table == 'feature')) {
 
     // Specifically, only genetic markers.
@@ -187,7 +186,7 @@ function tripal_qtl_bundle_instances_info($entity_type, $bundle) {
           'term_accession' => '0000771',
           'auto_attach' => FALSE,
           'chado_table' => $bundle->data_table,
-          'chado_column' => 'organism_id',
+          'chado_column' => 'feature_id',
           'base_table' => $bundle->data_table,
         ),
         'widget' => array(
@@ -208,7 +207,6 @@ function tripal_qtl_bundle_instances_info($entity_type, $bundle) {
       );
     }
   }
-  */
 
   return $instances;
 }