databaes cross reference field now working

tripal_chado/includes/TripalFields/sbo__database_cross_reference/sbo__database_cross_reference.inc

@@ -70,24 +70,25 @@ class sbo__database_cross_reference extends ChadoField {
     return array(
       $field_term => array(
         'operations' => array(),
+        'label' => 'Cross Reference',
         'sortable' => FALSE,
         'searchable' => FALSE,
         'elements' => array(
           $dbname_term => array(
             'searchable' => TRUE,
-            'label' => 'Database Name',
+            'label' => 'Cross Reference Database Name',
             'help' => 'The name of the remote database that houses the cross reference.',
             'sortable' => TRUE,
           ),
           $accession_term => array(
             'searchable' => TRUE,
-            'label' => 'Database Accession',
+            'label' => 'Cross Reference Database Accession',
             'help' => 'The unique accession (identifier) in the database that houses the cross reference.',
             'sortable' => TRUE,
           ),
           $dburl_term => array(
             'searchable' => FALSE,
-            'label' => 'Database URL',
+            'label' => 'Cross Reference Database URL',
             'help' => 'The URL of the database that houses the cross reference.',
             'sortable' => FALSE,
           ),
@@ -182,11 +183,11 @@ class sbo__database_cross_reference extends ChadoField {
     $this->queryJoinOnce($query, 'dbxref', $alias . '_DBX', $alias . "_DBX.dbxref_id = $alias.dbxref_id");
 
     if ($condition['column'] == $dbname_term) {
-      $this->queryJoinOnce($query, $alias . '_DB', $alias . "_DB.db_id = " . $alias . "_DBX.db_id");
+      $this->queryJoinOnce($query, 'db', $alias . '_DB', $alias . "_DB.db_id = " . $alias . "_DBX.db_id");
       $query->condition($alias . "_DB.name", $condition['value'], $operator);
     }
     if ($condition['column'] == $accession_term) {
-      $query->condition($alias . "_DBX.dbxref", $condition['value'], $operator);
+      $query->condition($alias . "_DBX.accession", $condition['value'], $operator);
     }
   }
 
@@ -194,7 +195,30 @@ class sbo__database_cross_reference extends ChadoField {
    * @see ChadoField::queryOrder()
    */
   public function queryOrder($query, $order) {
+    $dbxref_linker = $this->instance['settings']['chado_table'];
+    $base_table = $this->instance['settings']['base_table'];
+    $field_table = $this->instance['settings']['chado_table'];
+
+    $bschema = chado_get_schema($base_table);
+    $bpkey = $bschema['primary key'][0];
+
+    $alias = $this->field['field_name'];
 
+    $field_term_id = $this->getFieldTermID();
+    $dbname_term = $field_term_id . ',' . tripal_get_chado_semweb_term('db', 'name');
+    $accession_term = $field_term_id . ',' . tripal_get_chado_semweb_term('dbxref', 'accession');
+    $dburl_term = $field_term_id . ',' . tripal_get_chado_semweb_term('db', 'url');
+
+    $this->queryJoinOnce($query, $field_table, $alias, "base.$bpkey = $alias.$bpkey", "LEFT OUTER");
+    $this->queryJoinOnce($query, 'dbxref', $alias . '_DBX', $alias . "_DBX.dbxref_id = $alias.dbxref_id", "LEFT OUTER");
+
+    if ($order['column'] == $dbname_term) {
+      $this->queryJoinOnce($query, 'db', $alias . '_DB', $alias . "_DB.db_id = " . $alias . "_DBX.db_id", "LEFT OUTER");
+      $query->orderBy($alias . "_DB.name", $order['direction']);
+    }
+    if ($order['column'] == $accession_term) {
+      $query->orderBy($alias . "_DBX.accession", $order['direction']);
+    }
   }
 
   /**

tripal_chado/includes/TripalFields/sbo__database_cross_reference/sbo__database_cross_reference_formatter.inc

@@ -12,9 +12,15 @@ class sbo__database_cross_reference_formatter extends ChadoFieldFormatter {
    * @see TripalFieldFormatter::view()
    */
   public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
-    $chado_table = $this->instance['settings']['chado_table'];
     $content = '';
 
+    $field_name = $this->field['field_name'];
+    $field_type = $this->field['type'];
+    $field_table = $this->instance['settings']['chado_table'];
+    $field_column = $this->instance['settings']['chado_column'];
+    $base_table = $this->instance['settings']['base_table'];
+    $linker_table = $base_table . '_dbxref';
+
     $dbname_term = tripal_get_chado_semweb_term('db', 'name');
     $accession_term = tripal_get_chado_semweb_term('dbxref', 'accession');
     $dburl_term = tripal_get_chado_semweb_term('db', 'url');
@@ -25,7 +31,7 @@ class sbo__database_cross_reference_formatter extends ChadoFieldFormatter {
       }
       $content = $item['value'][$dbname_term] . ':' . $item['value'][$accession_term];
       if ($item['value'][$dburl_term]) {
-        $dbxref = tripal_get_dbxref(array('dbxref_id' => $item['chado-feature_dbxref__dbxref_id']));
+        $dbxref = tripal_get_dbxref(array('dbxref_id' => $item['chado-' . $linker_table . '__dbxref_id']));
         $url = tripal_get_dbxref_url($dbxref);
         $content = l($content, $url, array('attributes' => array('target' => '_blank')));
       }

tripal_chado/includes/TripalFields/sbo__database_cross_reference/sbo__database_cross_reference_widget.inc

@@ -164,8 +164,19 @@ class sbo__database_cross_reference_widget extends ChadoFieldWidget {
  * An Ajax callback for the dbxref widget.
  */
 function sbo__database_cross_reference_widget_form_ajax_callback($form, $form_state) {
-
-  $field_name = $form_state['triggering_element']['#parents'][0];
-
-  return $form[$field_name]['und'][$delta];
+  // Get the triggering element
+  $form_element_name = $form_state['triggering_element']['#name'];
+  preg_match('/(.+?)\[(.+?)\]\[(.+?)\]/', $form_element_name, $matches);
+  $field = $matches[1];
+  $lang = $matches[2];
+  $delta = $matches[3];
+
+  // Return the widget that triggered the AJAX call
+  if (isset($form[$field][$lang][$delta])) {
+    return $form[$field][$lang][$delta];
+  }
+  // Alternatively, return the default value widget for the widget setting form
+  else {
+    return $form['instance']['default_value_widget'][$field];
+  }
 }

tripal_chado/includes/TripalFields/taxrank__infraspecific_taxon/taxrank__infraspecific_taxon.inc

@@ -66,11 +66,11 @@ class taxrank__infraspecific_taxon extends ChadoField {
 
     return array(
       $field_term => array(
-        'sortable' => TRUE,
+        'sortable' => FALSE,
         'searchable' => TRUE,
         'elements' => array(
           $label_term => array(
-            'sortable' => TRUE,
+            'sortable' => FALSE,
             'searchable' => TRUE,
             'label' => 'Infraspecific Full Name',
             'help' => 'The full infraspecific name including the rank and name.',
@@ -120,7 +120,20 @@ class taxrank__infraspecific_taxon extends ChadoField {
    * @see ChadoField::queryOrder()
    */
   public function queryOrder($query, $order) {
+    $alias = $this->field['field_name'];
 
+    $field_term_id = $this->getFieldTermID();
+    $label_term = $field_term_id . ',' . 'rdfs:label';
+    $infraspecific_name_term = $field_term_id . ',' . tripal_get_chado_semweb_term('organism', 'infraspecific_name');
+    $infraspecific_type_term = $field_term_id . ',' . tripal_get_chado_semweb_term('organism', 'type_id');
+
+    if ($order['column'] == $infraspecific_name_term) {
+      $query->orderBy('base.infraspecific_name', $order['direction']);
+    }
+    if ($order['column'] == $infraspecific_type_term) {
+      $this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . "_cvterm.cvterm_id = base.type_id", "LEFT OUTER");
+      $query->orderBy($alias . '_cvterm.name', $order['direction']);
+    }
   }
 
   /**

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -628,8 +628,8 @@ 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();