Issue #122: Updated Tripal3 Search API integration. It now conforms to the standards for Tripal/ChadoField value storage and all fields are indexable for search.

tripal/includes/tripal.entity.inc

@@ -260,6 +260,134 @@ function tripal_entity_info_alter(&$entity_info){
   }
 }
 
+/**
+ * Implements hook_entity_property_info_alter().
+ *
+ * For some reason not all our TripalFields end up in the properties field for
+ * each bundle. This becomes a problem with Search API integration because only
+ * fields listed in the properties for a bundle are available to be indexed.
+ * Thus we are altering the property info to add any fields attached to
+ * TripalEntities which may have been missed.
+ *
+ * Furthermore, there are some pecularities with how TripalFields store their
+ * value that causes the default getter callback difficulties in some edge cases.
+ * Thus we are overriding that function below.
+ */
+function tripal_entity_property_info_alter(&$info) {
+
+  // For each Tripal Content Type, we want to ensure all attached fields
+  // are added to the bundle properties.
+  foreach ($info['TripalEntity']['bundles'] as $bundle_name => $bundle) {
+
+    // Retrieve information for all fields attached to this Tripal Content Type.
+    $fields = field_info_instances('TripalEntity', $bundle_name);
+    foreach ($fields as $field_name => $field_info) {
+
+      // If there is a field attached to the current Tripal Content Type that
+      // is not listed in properties, then add it. We use the full defaults here
+      // just in case it's not a TripalField or ChadoField.
+      if (!isset($info['TripalEntity']['bundles'][$bundle_name]['properties'][$field_name])) {
+        $info['TripalEntity']['bundles'][$bundle_name]['properties'][$field_name] = array(
+          'label' => $field_info['label'],
+          'type' => 'text',
+          'description' => $field_info['description'],
+          'getter callback' => 'entity_metadata_field_property_get',
+          'setter callback' => 'entity_metadata_field_property_set',
+          'access callback' => 'entity_metadata_field_access_callback',
+          'query callback' => 'entity_metadata_field_query',
+          'translatable' => FALSE,
+          'field' => TRUE,
+          'required' => $field_info['required'],
+        );
+      }
+
+      // Now, if it's a TripalField or a ChadoField, then we want to use a custom
+      // getter callback in order to ensure values are retrieved properly.
+      // ASSUMPTION: All TripalFields and ChadoFields have an ontology term
+      // defining them.
+      if (isset($field_info['settings']['term_accession'])) {
+        $info['TripalEntity']['bundles'][$bundle_name]['properties'][$field_name]['getter callback'] = 'tripal_field_property_get';
+      }
+    }
+  }
+}
+
+/**
+ * Callback for getting TripalField and ChadoField property values.
+ *
+ * This function retrieves the value from a field. Since the value has already
+ * been set by the Tripal/ChadoField class at this point, it should just be a
+ * matter of grabbing the value.
+ *
+ * @param $entity
+ *   The fully-loaded entity object to be indexed.
+ * @param $options
+ *   Options that can be ued when retrieving the value.
+ * @param $field_name
+ *   The machine name of the field we want to retrieve.
+ * @param $entity_type
+ *   The type of entity (ie: TripalEntity).
+ *
+ * @return
+ *   The rendered value of the field specified by $field_name.
+ */
+function tripal_field_property_get($entity, array $options, $field_name, $entity_type, $info) {
+
+  // Retrieve information for the field.
+  $field = field_info_field($field_name);
+
+  // Retrieve the language code.
+  $langcode = isset($options['language']) ? $options['language']->language : LANGUAGE_NONE;
+  $langcode = entity_metadata_field_get_language($entity_type, $entity, $field, $langcode, TRUE);
+
+  $values = array();
+  if (isset($entity->{$field_name}[$langcode])) {
+    // For each value of the field... (this will be multiple if cardinality is > 1).
+    foreach ($entity->{$field_name}[$langcode] as $delta => $data) {
+
+      // All Tripal/ChadoFields should have a value key. Only the information
+      // stored in this value key should be displayed on the page, available
+      // via web services or indexed for searching. This is there is no value
+      // key, we will not index anything.
+      if (!isset($data['value'])) {
+        return NULL;
+      }
+
+      // Sometimes TripalFields may return multiple pieces of information in the
+      // value field. In this case, the key should be an ontology term describing
+      // what each piece of data is and the value should be the data.
+      if (is_array($data['value'])) {
+
+        // Just include all the pieces of information seperated by spaces
+        // so they are tokenized out later on.
+        $tmp = $data['value'];
+        if (isset($tmp['entity'])) { unset($tmp['entity']); }
+        foreach ($tmp as $k => $v) { $tmp[$k] = strip_tags($v); }
+        $curr_val = implode(' ', $tmp);
+      }
+      else {
+
+        // Otherwise, assume the value is a single piece of information
+        // and add that directly to be indexed.
+        $curr_val = strip_tags($data['value']);
+
+        // Ensure that we have a clean boolean data type.
+        if ($info['type'] == 'boolean' || $info['type'] == 'list<boolean>') {
+          $curr_val = (boolean) $curr_val;
+        }
+      }
+      
+      // Only add the current value if it's not empty.
+      if (!empty(trim($curr_val))) {
+        $values[$delta] = $curr_val;
+      }
+    }
+  }
+
+  // For an empty single-valued field, we have to return NULL.
+  return $field['cardinality'] == 1 ? ($values ? reset($values) : NULL) : $values;
+}
+
 /**
  * Checks access permissions for a given entity.
  *

tripal_chado/includes/tripal_chado.entity.inc

@@ -208,72 +208,6 @@ function tripal_chado_tripal_default_title_format($bundle, $available_tokens) {
   return $format;
 }
 
-/**
- * Implements hook_entity_property_info_alter().
- *
- * This is being implemented to ensure chado fields are exposed for search api
- * indexing. All fields are available for index by default but the getter
- * function set by default is not actually capable of getting the value from
- * chado. Thus we change the getter function to one that can :-).
- */
-function tripal_chado_entity_property_info_alter(&$info) {
-
-  // Get a list of fields with the chado storage backend.
-
-  // Loop through all of the bundles.
-  if (isset($info['TripalEntity']['bundles'])) {
-    foreach ($info['TripalEntity']['bundles'] as $bundle_id => $bundle) {
-      // Loop through each of the fields for a given bundle.
-      foreach ($bundle['properties'] as $field_name => $field_info) {
-        // If the field is a chado field, then change the callback.
-        // @todo check this properly.
-        if (preg_match('/(\w+)__(\w+)/', $field_name, $matches)) {
-          $info['TripalEntity']['bundles'][$bundle_id]['properties'][$field_name]['getter callback'] =
-          'tripal_chado_entity_property_get_value';
-        }
-      }
-    }
-  }
-
-}
-
-/**
- * Provides a way for the search api to grab the value of a chado field.
- *
- * @param $entity
- *   The fully-loaded entity object to be indexed.
- * @param $options
- *   Options that can be ued when retrieving the value.
- * @param $field_name
- *   The machine name of the field we want to retrieve.
- * @param $entity_type
- *   The type of entity (ie: TripalEntity).
- *
- * @return
- *   The rendered value of the field specified by $field_name.
- */
-function tripal_chado_entity_property_get_value($entity, $options, $field_name, $entity_type) {
-
-  $display = array(
-    'type' => '',
-    'label' => 'hidden',
-  );
-
-  $langcode = LANGUAGE_NONE;
-  $items = field_get_items($entity_type, $entity, $field_name);
-  if (count($items) == 1) {
-    $render_array = field_view_value($entity_type, $entity, $field_name, $items[0], $display, $langcode);
-  }
-  // @todo: handle fields with multiple values.
-  else {
-    $render_array = field_view_value($entity_type, $entity, $field_name, $items[0], $display, $langcode);
-    drupal_set_message('Tripal Chado currently only supports views integration ' .
-      'for single value fields. The first value has been shown.', 'warning');
-  }
-
-  return drupal_render($render_array);
-}
-
 /**
  * Implements hook_entity_view().
  */