add extra fields to formatter for gene transcript

tripal_chado/includes/TripalFields/so__transcript/so__transcript.inc

@@ -331,7 +331,7 @@ class so__transcript extends ChadoField {
     $fset = [];
     $fset['fields'] = [
       '#type' => 'fieldset',
-      '#title' => 'Transcipt (mRNA) Field Selection',
+      '#title' => 'Transcript (mRNA) Field Selection',
       '#description' => t('Select the fields that you want displayed on the gene page for each transcript.  If no fields are selected then a default display is provided.'),
       '#collapsible' => TRUE,
       '#collapsed' => TRUE,

tripal_chado/includes/TripalFields/so__transcript/so__transcript_formatter.inc

@@ -7,7 +7,7 @@ class so__transcript_formatter extends ChadoFieldFormatter {
 
   // The list of field types for which this formatter is appropriate.
   public static $field_types = ['so__transcript'];
-
+    
   /**
    *
    * @see TripalFieldFormatter::view()
@@ -16,15 +16,20 @@ class so__transcript_formatter extends ChadoFieldFormatter {
 
     // Get the settings
     $settings = $display['settings'];
-    dpm($this->instance['settings']);
-
+    $_entity = $entity;
+    
+    // if no transcript (mRNA) fields are selected in the transcript fields edit page, use a table to list the mRNA name, id, type and location only
     $headers = ['Transcript Name', 'Identifier', 'Type', 'Location'];
     $rows = [];
+    
+    $mRNA_fieldset = [];
+    $fields_exist = FALSE; 
     foreach ($items as $delta => $item) {
 
       if (!$item['value']) {
         continue;
       }
+      
       $transcript = $item['value'];
 
       // Get the field values
@@ -32,18 +37,120 @@ class so__transcript_formatter extends ChadoFieldFormatter {
       $feature_uname = $transcript['data:0842'];
       $loc = $transcript['SO:0000735'];
       $type = $transcript['rdfs:type'];
-
+      
       // Add a link if there is an entity.
       if (array_key_exists('entity', $item['value']) and $item['value']['entity']) {
+      
         list($entity_type, $entity_id) = explode(':', $item['value']['entity']);
+        
+        $transcript_name = $feature_name;
+        // the transcript id is the identifier for the mRNA transcript
+        $transcript_id = $entity_id; 
+        $mRNA_fieldset[$transcript_id] = [
+          '#type' => 'fieldset',
+          '#title' => $transcript_name,
+          '#description' => '',
+          '#collapsible' => TRUE,
+          '#collapsed' => TRUE,
+          '#attributes' => ['class' => ['collapsible', 'collapsed']],
+        ];
+        drupal_add_library('system', 'drupal.collapse');
+        $mRNA_fieldset[$transcript_id]['table'] = [];
+        
+        $transcript_fields_header = [];
+        $transcript_field_rows = [];
+        $single_cardinality_fields_exist = FALSE;
+        
+        // mRNA expanded fields
+        // obtain each field for the mRNA as specified in the transcripts field edit configuration
+        $fields = $this->instance['settings']['transcript_fields'];
+        $entity = TripalEntity_load($entity_id);
+        foreach ($fields as $field_name => $field_value) {
+
+          if (array_key_exists('show', $field_value) and ($field_value['show'] != 1)) {
+            // this field is not selected for display in the transcripts field edit configuration page  
+            continue;
+          }
+          $fields_exist = TRUE;
+          
+          // Load the field info.
+          $field_info = field_info_field($field_name);
+          $field_instance = field_info_instance('TripalEntity', $field_name, $entity->bundle); // get title and description
+          $field_items = field_get_items('TripalEntity', $entity, $field_name);
+          $field_element = field_view_field('TripalEntity', $entity, $field_name, $field_instance['display']['default']);
+          $field_element['#label_display'] = 'hidden';
+          
+          // use $_entity parameter for gene to obtain the 'hide empty' gene field setting
+          $bundle = tripal_load_bundle_entity(['name'=> $_entity->bundle]);
+          $hide_empty = tripal_get_bundle_variable('hide_empty_field', $bundle->id);
+          $cardinality = array_key_exists('cardinality', $field_info) ? $field_info['cardinality'] : 1; 
+          $field_is_empty = $this->isFieldEmpty($field_items);
+          
+          // do not show this field if empty and specified to be hidden from the gene edit page
+          if ($field_is_empty and $hide_empty) {
+            continue;
+          }
+          
+          // check field cardinality 
+          if ($cardinality == 1) {
+            // add field to a special transcripts table, where fields have cardinality of 1
+            $single_cardinality_fields_exist = TRUE;
+            $transcript_field_rows[] = [
+              [
+                'data' => $field_instance['label'], 
+                'header' => TRUE,
+              ],
+              [
+                'data' => drupal_render($field_element),
+              ]  
+            ];
+          }
+          else {
+            // render the fields with cardinality not 1 individually after the special transcripts table.  
+            $mRNA_fieldset[$transcript_id][$field_name] = [
+              '#type' => 'item',
+              '#title' => $field_instance['label'],
+              '#description' => $field_instance['description'],  
+              '#markup' => drupal_render($field_element),
+            ];
+          }
+        }
+        
         $feature_name = l($feature_name, "bio_data/" . $entity_id, ['attributes' => ['target' => "_blank"]]);
+      
+        if ($single_cardinality_fields_exist) {
+          // display fields of single cardinality in a special transcripts table
+          $transcript_fields_table = [
+            'header' => $transcript_fields_header,
+            'rows' => $transcript_field_rows,
+            'attributes' => [
+              'id' => 'tripal_feature-table-transcript-fields-object',
+              'class' => 'tripal-data-table',
+            ],
+            'sticky' => FALSE,
+            'caption' => "",
+            'colgroups' => [],
+            'empty' => 'This feature has no single cardinality transcript fields',
+          ];
+          
+          $mRNA_fieldset[$transcript_id]['table'] = [
+            '#type' => 'markup',
+            '#markup' => theme_table($transcript_fields_table),
+          ];
+        }
       }
+      
+      $mRNA_fieldset[$transcript_id]['mRNA_link'] = [
+        '#type' => 'markup',
+        '#markup' => "For further details go to ".$feature_name,
+      ];
       $rows[] = [$feature_name, $feature_uname, $type, $loc];
     }
+    
     $table = [
       'header' => $headers,
-      'rows' => $rows,
-      'attributes' => [
+        'rows' => $rows,
+        'attributes' => [
         'id' => 'tripal_feature-table-transcripts-object',
         'class' => 'tripal-data-table',
       ],
@@ -52,15 +159,69 @@ class so__transcript_formatter extends ChadoFieldFormatter {
       'colgroups' => [],
       'empty' => 'This feature has no transcripts',
     ];
-    $content = theme_table($table);
-
+       
     // once we have our table array structure defined, we call Drupal's theme_table()
     // function to generate the table.
     if (count($items) > 0) {
-      $element[0] = [
-        '#type' => 'markup',
-        '#markup' => $content,
-      ];
+      if ($fields_exist) {
+        $content = $mRNA_fieldset;
+        $element[0] = $content;
+      }
+      else {
+        $content = theme_table($table);
+        $element[0] = [
+          '#type' => 'markup',
+          '#markup' => $content,
+        ];
+      }
     }
   }
+  
+  /**
+   * Checks if the field is empty. 
+   *
+   * @param $field_items
+   *   The TripalEntity field items, holds the value for the field.
+   *
+   * @return bool 
+   *   TRUE if field is empty, otherwise FALSE.
+   */
+  public function isFieldEmpty($field_items) {
+      
+    $field_is_empty = FALSE;
+
+    // handle when field_items is an array with single of multiple values
+    if (is_array($field_items)) {
+      if (sizeof($field_items) == 1) {
+        if (sizeof($field_items[0]) == 1) {
+          if (is_string($field_items[0]['value'])) {
+            if (strlen($field_items[0]['value']) == 0) {
+              // the value is of zero length  
+              $field_is_empty = TRUE;
+            }
+          }
+        }
+        else {
+          $all_empty = TRUE;
+          foreach ($field_items[0] as $key=>$val) {
+            if ((is_string($val) and (strlen($val) != 0)) or (!is_string($val))) {
+              // the value is a string of non-zero length, or not a string at all  
+              $all_empty = FALSE;
+            }
+          }
+          if ($all_empty) {
+            $field_is_empty = TRUE;
+          }
+        }
+      }
+    }
+    elseif ($field_items == null) {
+      $field_is_empty = TRUE;
+    }
+    
+    return $field_is_empty;
+    
+  }
+  
 }
+