Fixed Issue #110

tripal/api/tripal.entities.api.inc

@@ -339,9 +339,8 @@ function tripal_create_bundle($args, &$error = '') {
   }
   catch (Exception $e) {
     $transaction->rollback();
-    $error = _drupal_decode_exception($e);
     drupal_set_message(t("Failed to create content type: %message.",
-        array('%message' => $error['!message'])), 'error');
+      array('%message' => $e->getMessage())), 'error');
     return FALSE;
   }
 

tripal/includes/TripalBundleUIController.inc

@@ -487,7 +487,6 @@ function tripal_bundle_access($op, $type = NULL, $account = NULL) {
  */
 function tripal_admin_add_type_form($form, &$form_state) {
 
-
   $stores = module_invoke_all('vocab_storage_info');
   if (!is_array($stores) or count($stores) == 0) {
     tripal_set_message('A storage backend is not enabled for managing
@@ -529,6 +528,8 @@ function tripal_admin_add_type_form($form, &$form_state) {
       'method' => 'replace'
     ),
   );
+  $form['#prefix'] = '<div id = "tripal-vocab-select-form">';
+  $form['#suffix'] = '</div>';
 
   // If the term has been provided by the user then we want to search for
   // matching terms in the database and let them select among any matches.
@@ -588,6 +589,7 @@ function tripal_admin_add_type_form($form, &$form_state) {
         '#type' => 'item',
         '#markup' => '<i>' . t('There is no term that matches the entered text.') . '</i>'
       );
+      return $form;
     }
 
     // Now let the user select where the data type will be stored.
@@ -644,9 +646,6 @@ function tripal_admin_add_type_form($form, &$form_state) {
     }
   }
 
-  $form['#prefix'] = '<div id = "tripal-vocab-select-form">';
-  $form['#suffix'] = '</div>';
-
 
   return $form;
 }

tripal_chado/api/tripal_chado.schema.api.inc

@@ -633,6 +633,7 @@ function chado_get_cvterm_mapping($params) {
   $cvterm_id = array_key_exists('cvterm_id', $params) ? $params['cvterm_id'] : NULL;
   $vocabulary = array_key_exists('vocabulary', $params) ? $params['vocabulary'] : NULL;
   $accession = array_key_exists('accession', $params) ? $params['accession'] : NULL;
+  $cvterm = NULL;
 
   if ($cvterm_id) {
     $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $cvterm_id));
@@ -649,13 +650,16 @@ function chado_get_cvterm_mapping($params) {
     $cvterm = chado_generate_var('cvterm', $match);
   }
 
-  $result = db_select('chado_cvterm_mapping', 'tcm')
-    ->fields('tcm')
-    ->condition('cvterm_id', $cvterm->cvterm_id)
-    ->execute();
-  $result = $result->fetchObject();
-  if ($result) {
-    $result->cvterm = $cvterm;
+  if ($cvterm) {
+    $result = db_select('chado_cvterm_mapping', 'tcm')
+      ->fields('tcm')
+      ->condition('cvterm_id', $cvterm->cvterm_id)
+      ->execute();
+    $result = $result->fetchObject();
+    if ($result) {
+      $result->cvterm = $cvterm;
+    }
+    return $result;
   }
-  return $result;
+  return NULL;
 }

tripal_chado/includes/TripalFields/chado_linker__prop/chado_linker__prop_formatter.inc

@@ -24,40 +24,28 @@ class chado_linker__prop_formatter extends ChadoFieldFormatter {
     $field_name = $this->field['field_name'];
     $chado_table = $this->instance['settings']['chado_table'];
 
-    $content = array();
-    // If $items is not empty and it has more than one value all values need to
-    // be added to an array for display.
-    if ($items) {
-      if (count($items) > 1) {
-        foreach ($items as $index => $item) {
-          $content[$index] = $item['value'];
-        }
-      }
-      else {
-        $content = $items[0]['value'];
-      }
+    $list = array();
+    foreach ($items as $index => $item) {
+      $list[$index] = $item['value'];
     }
+
     // If more than one value has been found display all values in an unordered
     // list.
-    if (count($content) > 1) {
-      $bullets = '<ul>';
-      $bullets .= '<li>';
-      $bullets .= implode("</li><li>", $content);
-      $bullets .= '</li>';
-      $bullets .= '</ul>';
-      $element[0] = array(
-        // We create a render array to produce the desired markup,
-        '#type' => 'markup',
-        '#markup' => $bullets,
-      );
+    if (count($list) > 1) {
+      $content = theme_item_list(array(
+        'items' => $list,
+        'title' => '',
+        'attributes' => array('class' => array($entity->bundle . '-properties-list', 'properties-field-list')),
+        'type' => 'ul'
+      ));
     }
-    // If it's a single value field display without bullets.
     else {
-      $element[0] = array(
-        // We create a render array to produce the desired markup,
-        '#type' => 'markup',
-        '#markup' => $content,
-      );
+      $content = $list[0];
     }
+    $element[0] = array(
+      // We create a render array to produce the desired markup,
+      '#type' => 'markup',
+      '#markup' => $content,
+    );
   }
 }

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -1246,7 +1246,7 @@ function tripal_chado_field_storage_bundle_mapping_form_submit($form,
 
   // If we have a type_column then we know this type uses a column in the
   // base table, so we can set the storage args and return.
-  if ($default['type_column']) {
+  if ($default['type_column'] and $default['type_column'] != 'none') {
     $storage_args['data_table'] = $default['table'];
     $storage_args['type_column'] = $default['type_column'];
     return;

tripal_chado/includes/tripal_chado.fields.inc

@@ -20,6 +20,7 @@ function tripal_chado_bundle_fields_info($entity_type, $bundle) {
     'chado_table' => $chado_bundle->data_table,
     'chado_type_table' => $chado_bundle->type_linker_table,
     'chado_type_column' => $chado_bundle->type_column,
+    'chado_type_value' => $chado_bundle->type_value,
   );
 
   $info = array();
@@ -44,8 +45,9 @@ function tripal_chado_bundle_fields_info_base(&$info, $details, $entity_type, $b
 
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
-  $type_field = $details['chado_type_column'];
+  $type_column = $details['chado_type_column'];
   $cvterm_id  = $details['chado_cvterm_id'];
+  $type_value = $details['chado_type_value'];
 
   // Iterate through the columns of the table and see if fields have been
   // created for each one. If not, then create them.
@@ -74,7 +76,7 @@ function tripal_chado_bundle_fields_info_base(&$info, $details, $entity_type, $b
     }
 
     // Don't create base fields for the primary key and the type_id field.
-    if ($column_name == $pkey or $column_name == $type_field) {
+    if ($column_name == $pkey or $column_name == $type_column) {
       continue;
     }
     $cvterm = tripal_get_chado_semweb_term($table_name, $column_name, array('return_object' => TRUE));
@@ -95,7 +97,7 @@ function tripal_chado_bundle_fields_info_base(&$info, $details, $entity_type, $b
     }
 
     // Skip the type field that will always be custom
-    if (($table_name == $type_table and $column_name == $type_field) or
+    if (($table_name == $type_table and $column_name == $type_column) or
          $column_name == 'type_id') {
       continue;
     }
@@ -179,8 +181,9 @@ function tripal_chado_bundle_fields_info_base(&$info, $details, $entity_type, $b
 function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type, $bundle) {
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
-  $type_field = $details['chado_type_column'];
+  $type_column = $details['chado_type_column'];
   $cvterm_id  = $details['chado_cvterm_id'];
+  $type_value = $details['chado_type_value'];
 
   $schema = chado_get_schema($table_name);
 
@@ -189,7 +192,7 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
   // by the type_id field or on the organism table where the type_id is mean
   // as an infraspecific name type.
   if (array_key_exists('type_id', $schema['fields']) and
-      $table_name != 'organism' and $type_field != 'type_id') {
+      $table_name != 'organism' and $type_column != 'type_id') {
     $field_name = 'schema__additional_type';
     $field_type = 'schema__additional_type';
     $info[$field_name] = array(
@@ -409,8 +412,9 @@ function tripal_chado_bundle_fields_info_linker(&$info, $details, $entity_type,
 
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
-  $type_field = $details['chado_type_column'];
+  $type_column = $details['chado_type_column'];
   $cvterm_id  = $details['chado_cvterm_id'];
+  $type_value = $details['chado_type_value'];
 
   // CONTACTS
   $contact_table = $table_name . '_contact';
@@ -537,7 +541,7 @@ function tripal_chado_bundle_fields_info_linker(&$info, $details, $entity_type,
       // The tripal_analysis_KEGG, tripal_analysis_blast, and
       // tripal_analysis_interpro modules store results in the analysisprop
       // table which is probably not the best place, but we don't want to
-      // create a ton of fields for this.
+      // create a ton of fields for this, so skip them.
       if ($prop_table == 'analysisprop' and
           ($term->dbxref_id->db_id->name == 'KEGG_BRITE' or
            $term->dbxref_id->db_id->name == 'tripal')) {
@@ -647,6 +651,7 @@ function tripal_chado_bundle_instances_info($entity_type, $bundle) {
     'chado_table' => $chado_bundle->data_table,
     'chado_type_table' => $chado_bundle->type_linker_table,
     'chado_type_column' => $chado_bundle->type_column,
+    'chado_type_value' => $chado_bundle->type_value,
   );
 
   $info = array();
@@ -674,8 +679,9 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
   // Get Chado information
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
-  $type_field = $details['chado_type_column'];
+  $type_column = $details['chado_type_column'];
   $cvterm_id  = $details['chado_cvterm_id'];
+  $type_value = $details['chado_type_value'];
 
   // Iterate through the columns of the table and see if fields have been
   // created for each one. If not, then create them.
@@ -697,12 +703,12 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
     }
 
     // Don't create base fields for the primary key and the type_id field.
-    if ($column_name == $pkey or $column_name == $type_field) {
+    if ($column_name == $pkey or $column_name == $type_column) {
       continue;
     }
 
     // Skip the type field that will always be custom
-    if (($table_name == $type_table and $column_name == $type_field) or
+    if (($table_name == $type_table and $column_name == $type_column) or
         $column_name == 'type_id') {
       continue;
     }
@@ -723,7 +729,7 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
     }
 
     // Skip the type field.
-    if ($table_name == $type_table and $column_name == $type_field) {
+    if ($table_name == $type_table and $column_name == $type_column) {
       continue;
     }
 
@@ -890,8 +896,9 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
 function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle, $details) {
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
-  $type_field = $details['chado_type_column'];
+  $type_column = $details['chado_type_column'];
   $cvterm_id  = $details['chado_cvterm_id'];
+  $type_value = $details['chado_type_value'];
   $schema = chado_get_schema($table_name);
 
   // BASE TYPE_ID
@@ -899,7 +906,7 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
   // by the type_id field or on the organism table where the type_id is mean
   // as an infraspecific name type.
   if (array_key_exists('type_id', $schema['fields']) and
-      $table_name != 'organism' and $type_field != 'type_id') {
+      $table_name != 'organism' and $type_column != 'type_id') {
     $field_name = 'schema__additional_type';
     $is_required = FALSE;
     if (array_key_exists('not null', $schema['fields']['type_id']) and
@@ -1370,8 +1377,9 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
 
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
-  $type_field = $details['chado_type_column'];
+  $type_column = $details['chado_type_column'];
   $cvterm_id  = $details['chado_cvterm_id'];
+  $type_value = $details['chado_type_value'];
 
   // CONTACTS
   $contact_table = $table_name . '_contact';
@@ -1624,69 +1632,113 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
      $schema = chado_get_schema($prop_table);
      $tpkey = $tschema['primary key'][0];
      $pkey = $schema['primary key'][0];
-     // Get the list of existing property types for this table.
+
+     // Property tables can be a bit tricky because not all property types
+     // in the prop table are appropriate for each type of data.  Also som
+     // bundle types are resolved via a property.  So, we have to distinguish
+     // between these two cases.
+     $sql = '';
      $args = array();
-     $sql = 'SELECT DISTINCT type_id FROM {' . $prop_table . '}';
-
-//       $sql = "
-//         SELECT DISTINCT P.type_id
-//         FROM {" . $prop_table . "} P
-//       ";
-//       if (array_key_exists('type_id', $tschema['fields'])) {
-//         $sql .= "
-//             INNER JOIN {" . $table_name . "} T on T.$tpkey = P.$tpkey
-//           WHERE T.type_id = :cvterm_id
-//         ";
-//         $args[':cvterm_id'] = $cvterm_id;
-//       }
-
-     $props = chado_query($sql, $args);
-     while ($prop = $props->fetchObject()) {
-
-       $term = chado_generate_var('cvterm', array('cvterm_id' => $prop->type_id));
-
-       // The tripal_analysis_KEGG, tripal_analysis_blast, and
-       // tripal_analysis_interpro modules store results in the analysisprop
-       // table which is probably not the best place, but we don't want to
-       // create a ton of fields for this.
-       if ($prop_table == 'analysisprop' and
-           ($term->dbxref_id->db_id->name == 'KEGG_BRITE' or
-            $term->dbxref_id->db_id->name == 'tripal')) {
-         continue;
-       }
 
-       $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
-       $field_name = substr($field_name, 0, 32);
-       $info[$field_name] = array(
-         'field_name' => $field_name,
-         'entity_type' => $entity_type,
-         'bundle' => $bundle->name,
-         'label' => ucwords(preg_replace('/_/', ' ', $term->name)),
-         'description' => $term->definition,
-         'required' => FALSE,
-         'settings' => array(
-           'auto_attach' => TRUE,
-           'term_vocabulary' => $term->dbxref_id->db_id->name,
-           'term_accession' => $term->dbxref_id->accession,
-           'term_name' => $term->name,
-           'base_table' => $table_name,
-           'chado_table' => $prop_table,
-           'chado_column' => $pkey,
-         ),
-         'widget' => array(
-           'type' => 'chado_linker__prop_widget',
+     // First, is this the case where all of the records in the table are
+     // of this type?  If so, then all properties apply
+     if (!$type_column) {
+        $sql = 'SELECT DISTINCT type_id FROM {' . $prop_table . '}';
+        $props = chado_query($sql, $args);
+     }
+     // Second, if this is the case where a content type is uniquely identified
+     // by a type_id value in the base table, then only properties associated
+     // with that type ID should be used.
+     else if ($type_column and !$type_table) {
+      $sql = "
+        SELECT DISTINCT P.type_id
+        FROM {" . $prop_table . "} P
+          INNER JOIN {" . $table_name . "} T on T.$tpkey = P.$tpkey
+        WHERE T.$type_column = :cvterm_id
+      ";
+      $args[':cvterm_id'] = $cvterm_id;
+      $props = chado_query($sql, $args);
+     }
+     // Third, if this is the case where a content type is uniquely identified
+     // via a term/value pair in the prop table.
+     else if ($type_column and $type_table == $prop_table and !empty($type_value)) {
+       $sql = "
+        SELECT DISTINCT P2.type_id
+        FROM {" . $prop_table . "} P1
+          INNER JOIN {" . $table_name . "} T on T.$tpkey = P1.$tpkey
+          INNER JOIN {" . $prop_table . "} P2 on T.$tpkey = P2.$tpkey
+        WHERE P1.$type_column = :cvterm_id AND P1.value = :prop_value AND
+          P2.type_id != P1.type_id
+       ";
+       $args[':cvterm_id'] = $cvterm_id;
+       $args[':prop_value'] = $type_value;
+       $props = chado_query($sql, $args);
+     }
+     // Fourth, if this is the case where the content type is uinquely identifed
+     // via another table (e.g. cvterm linking table) and not this prop table.
+     else if ($type_column and $type_table != $prop_table and empty($type_value)) {
+       $sql = "
+         SELECT DISTINCT P.type_id
+         FROM {" . $prop_table . "} P
+           INNER JOIN {" . $table_name . "} T on T.$tpkey = P.$tpkey
+           INNER JOIN {" . $type_table . "} TT on TT.$tpkey = T.$tpkey
+         WHERE TT.$type_column = :cvterm_id
+       ";
+       $args[':cvterm_id'] = $cvterm_id;
+       $props = chado_query($sql, $args);
+     }
+     else {
+       // Do nothing;
+     }
+
+     if ($props) {
+       while ($prop = $props->fetchObject()) {
+
+         $term = chado_generate_var('cvterm', array('cvterm_id' => $prop->type_id));
+
+         // The tripal_analysis_KEGG, tripal_analysis_blast, and
+         // tripal_analysis_interpro modules store results in the analysisprop
+         // table which is probably not the best place, but we don't want to
+         // create a ton of fields for this.
+         if ($prop_table == 'analysisprop' and
+             ($term->dbxref_id->db_id->name == 'KEGG_BRITE' or
+              $term->dbxref_id->db_id->name == 'tripal')) {
+           continue;
+         }
+
+         $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
+         $field_name = substr($field_name, 0, 32);
+         $info[$field_name] = array(
+           'field_name' => $field_name,
+           'entity_type' => $entity_type,
+           'bundle' => $bundle->name,
+           'label' => ucwords(preg_replace('/_/', ' ', $term->name)),
+           'description' => $term->definition,
+           'required' => FALSE,
            'settings' => array(
-             'display_label' => 1,
+             'auto_attach' => TRUE,
+             'term_vocabulary' => $term->dbxref_id->db_id->name,
+             'term_accession' => $term->dbxref_id->accession,
+             'term_name' => $term->name,
+             'base_table' => $table_name,
+             'chado_table' => $prop_table,
+             'chado_column' => $pkey,
            ),
-         ),
-         'display' => array(
-           'default' => array(
-             'label' => 'hidden',
-             'type' => 'chado_linker__prop_formatter',
-             'settings' => array(),
+           'widget' => array(
+             'type' => 'chado_linker__prop_widget',
+             'settings' => array(
+               'display_label' => 1,
+             ),
            ),
-         ),
-       );
+           'display' => array(
+             'default' => array(
+               'label' => 'hidden',
+               'type' => 'chado_linker__prop_formatter',
+               'settings' => array(),
+             ),
+           ),
+         );
+       }
      }
    }
 

tripal_chado/theme/css/tripal_chado.css

@@ -57,4 +57,8 @@
 
 #autocomplete {
   width: 600px !important;
+}
+
+.properties-field-list {
+  margin: 0px;
 }