Fixed issue with non TripalField fields not working properly with filters in Drupal views. I think this is related to the issue #341

tripal/tripal_views_query.inc

@@ -132,6 +132,42 @@ class tripal_views_query extends views_plugin_query {
       $this->cquery->fieldCondition($field_name, $element_name, $value, $operator);
     }
   }
+  
+  /**
+   * Add's a where exression clause to a query.
+   * 
+   * @param $group
+   *   The WHERE group to add these to; groups are used to create AND/OR
+   *   sections. Groups cannot be nested. Use 0 as the default group. If the
+   *   group does not yet exist it will be created as an AND group.
+   * @param $snippet
+   *   The snippet to check. This can be either a column or a complex 
+   *   expression like "UPPER(table.field) = 'value'".
+   * @param $args
+   *   An associative array of arguments.
+   */
+  public function add_where_expression($group, $snippet, $args = array()) {
+    
+    // Ensure all variants of 0 are actually 0. Thus '', 0 and NULL are all
+    // the default group.
+    if (empty($group)) {
+      $group = 0;
+    }
+    
+    // TODO: this function needs to be adjusted to pull out the element from
+    // snippet (see the code for the add_where function above for an example.
+    // for now this function will not properly work.
+    
+    // Check for a group.
+    if (!isset($this->where[$group])) {
+      $this->set_where_group('AND', $group);
+    }
+    $this->where[$group]['conditions'][] = array(
+      'field' => $snippet,
+      'value' => $args,
+      'operator' => 'formula',
+    );
+  }
 
   /**
    * Overrides add_orderby().
@@ -326,4 +362,13 @@ class tripal_views_query extends views_plugin_query {
     $view->execute_time = microtime(TRUE) - $start;
   }
 
+  /**
+   * Provides a unique placeholders for handlers.
+   */
+  public function placeholder() {
+    // TODO: this function doesn't currently work. It is used by the
+    // words, all words, shorter than, longer than filters, but those
+    // are currently commented out.
+    //return $this->query->placeholder($this->options['table'] . '_' . $this->options['field']);
+  }
 }

tripal/views_handlers/tripal_views_handler_filter_string.inc

@@ -36,18 +36,20 @@ class tripal_views_handler_filter_string extends tripal_views_handler_filter {
         'method' => 'op_contains',
         'values' => 1,
       ),
-      'word' => array(
-        'title' => t('Contains any word'),
-        'short' => t('has word'),
-        'method' => 'op_word',
-        'values' => 1,
-      ),
-      'allwords' => array(
-        'title' => t('Contains all words'),
-        'short' => t('has all'),
-        'method' => 'op_word',
-        'values' => 1,
-      ),
+      // TODO: These two filters are a bit problematic with fields.
+      // The require a tripal_views_query::placeholder() function
+//       'word' => array(
+//         'title' => t('Contains any word'),
+//         'short' => t('has word'),
+//         'method' => 'op_word',
+//         'values' => 1,
+//       ),
+//       'allwords' => array(
+//         'title' => t('Contains all words'),
+//         'short' => t('has all'),
+//         'method' => 'op_word',
+//         'values' => 1,
+//       ),
       'starts' => array(
         'title' => t('Starts with'),
         'short' => t('begins'),
@@ -78,18 +80,22 @@ class tripal_views_handler_filter_string extends tripal_views_handler_filter {
         'method' => 'op_not',
         'values' => 1,
       ),
-      'shorterthan' => array(
-        'title' => t('Length is shorter than'),
-        'short' => t('shorter than'),
-        'method' => 'op_shorter',
-        'values' => 1,
-      ),
-      'longerthan' => array(
-        'title' => t('Length is longer than'),
-        'short' => t('longer than'),
-        'method' => 'op_longer',
-        'values' => 1,
-      ),
+      // TODO: These two filters are a bit problematic with fields.
+      // The require a tripal_views_query::add_where_expression function
+      // that can properly separate the field out of the "snippet". For now
+      // we'll just comment them out.
+//       'shorterthan' => array(
+//         'title' => t('Length is shorter than'),
+//         'short' => t('shorter than'),
+//         'method' => 'op_shorter',
+//         'values' => 1,
+//       ),
+//       'longerthan' => array(
+//         'title' => t('Length is longer than'),
+//         'short' => t('longer than'),
+//         'method' => 'op_longer',
+//         'values' => 1,
+//       ),
     );
     // if the definition allows for the empty operator, add it.
     if (!empty($this->definition['allow empty'])) {

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -55,7 +55,6 @@ function tripal_chado_field_storage_write($entity_type, $entity, $op, $fields) {
     $values[$type_field] = $cvterm->cvterm_id;
   }
 
-
   $base_record_id = tripal_chado_field_storage_write_table($base_table, $values, $base_table);
 
   // If this is an insert then add the chado_entity record.
@@ -537,11 +536,12 @@ function tripal_chado_field_storage_query($query) {
 
           $matches = array();
           $key = $condition['value'];
-          $op = '=';
+          $op = array_key_exists('operator', $condition) ? $condition['operator'] : '=';
           if (preg_match('/^(.+);(.+)$/', $key, $matches)) {
             $key = $matches[1];
             $op = $matches[2];
           }
+
           switch ($op) {
             case 'eq':
               $op = '=';
@@ -558,12 +558,22 @@ function tripal_chado_field_storage_query($query) {
             case 'lte':
               $op = '<=';
               break;
+            case '<>':
             case 'ne':
-              $op = '<>';
+              $op = '!=';
               break;
+            case 'LIKE':
             case 'contains':
               $op = 'LIKE';
-              $key = '%' . $key . '%';
+              if (!preg_match('/\%/', $key)) {
+                $key = '%' . $key . '%';
+              }
+              break;
+            case 'NOT LIKE':              
+              $op = 'NOT LIKE';
+              if (!preg_match('/\%/', $key)) {
+                $key = '%' . $key . '%';
+              }
               break;
             case 'starts':
               $op = 'LIKE';
@@ -718,8 +728,8 @@ function tripal_chado_field_storage_query($query) {
     } // end if ($sort['type'] == 'field') {
   } // end foreach ($query->order as $index => $sort) {
 
-// dpm($cquery->__toString());
-// dpm($cquery->getArguments());
+ //dpm($cquery->__toString());
+ //dpm($cquery->getArguments());
 
   $records = $cquery->execute();