Minor textual changes

tripal_chado/includes/tripal_chado.cv_defaults.inc

@@ -285,14 +285,14 @@ function theme_tripal_chado_admin_set_defaults_form($variables) {
   foreach ($element['settings']['existing'] as $key => $value) {
     if (is_numeric($key)) {
 
-      $action_links = '<ul class="links inline">';
-      if (!empty($value['view-terms'])) {
-        $action_links .= '<li>' . drupal_render($value['view-terms']) . '</li>';
-      }
-      if (!empty($value['add-new-term'])) {
-        $action_links .= '<li>' . drupal_render($value['add-new-term']) . '</li>';
-      }
-      $action_links .= '</li></ul>';
+//       $action_links = '<ul class="links inline">';
+//       if (!empty($value['view-terms'])) {
+//         $action_links .= '<li>' . drupal_render($value['view-terms']) . '</li>';
+//       }
+//       if (!empty($value['add-new-term'])) {
+//         $action_links .= '<li>' . drupal_render($value['add-new-term']) . '</li>';
+//       }
+//       $action_links .= '</li></ul>';
 
       $rows[] = array(
         drupal_render($value['table_name-display']),

tripal_chado/includes/tripal_chado.mapping.inc

@@ -19,7 +19,7 @@ function tripal_chado_map_cvterms() {
     // Iterate through the referring tables to see what records are there.
     foreach ($referring as $tablename) {
 
-      // We only want to look at base tables.
+      // Ignore the cvterm tables, relationships, chadoprop tables.
       if ($tablename == 'cvterm_dbxref' || $tablename == 'cvterm_relationship' ||
           $tablename == 'cvtermpath' || $tablename == 'cvtermprop' || $tablename == 'chadoprop' ||
           $tablename == 'cvtermsynonym' || preg_match('/_relationship$/', $tablename) ||
@@ -51,7 +51,7 @@ function tripal_chado_map_cvterms() {
               array(
                 'cvterm_id' => $cvterm->cvterm_id,
                 'chado_table' => $tablename,
-                'chado_field' => $remote_id
+                'chado_field' => $local_id
               )
             )
             ->execute();

tripal_chado/includes/tripal_chado.migrate.inc

@@ -316,6 +316,10 @@ function tripal_chado_migrate_form($form, &$form_state) {
  * @param $form_state
  */
 function tripal_chado_migrate_form_validate($form, &$form_state) {
+
+  // If the user selects the migrate button then we want to make sure that the
+  // the term for each content is mapped to a table and column in Chado.
+  // Otherwise creation of bundles will be bungled.
   if ($form_state['clicked_button']['#name'] == 'migrate_btn') {
     $selected_type = $form_state['values']['tv2_content_type'];
     $tv3_content_types = array();
@@ -342,6 +346,7 @@ function tripal_chado_migrate_form_validate($form, &$form_state) {
         }
       }
     }
+
     // Check if CV exists in the tripal_cv_defaults table. If not, do not proceed to migration
     foreach ($tv3_content_types AS $type) {
       $voc = $type['vocabulary'];
@@ -362,13 +367,17 @@ function tripal_chado_migrate_form_validate($form, &$form_state) {
       }
       $default = tripal_get_default_cv_table($cvterm->cv_id->cv_id);
       if (!$default) {
-        form_set_error('', 
-            t("'@voc' is not a ". l('Default Vocabulary', 'admin/tripal/storage/chado/vocab') . ". '@cvterm' can not be migrated.", 
-              array(
-                '@voc' => $voc,
-                '@cvterm' => $cvterm->name
-              )
+        form_set_error('',
+          t("The tripal content type, '@type', of subtype, '@cvterm', cannot be
+              migrated because the vocabulary, '@voc', has not been mapped to a table in Chado.
+              Please go to the ". l('Default Vocabulary settings page', 'admin/tripal/storage/chado/vocab') . "and indicate
+              which table to use for the vocabulary.",
+            array(
+              '@type' => $type,
+              '@voc' => $voc,
+              '@cvterm' => $cvterm->name
             )
+          )
         );
       }
     }
@@ -618,7 +627,7 @@ function tripal_chado_migrate_map_types($tv2_content_types) {
     $schema = chado_get_schema($table);
     $pkey = $schema['primary key'][0];
     $fkeys = $schema['foreign keys'];
-  
+
     if (key_exists('cvterm', $fkeys) && key_exists('type_id', $fkeys['cvterm']['columns'])) {
       // Get all Tripal v2 node types from the chad_* linking table
       $sql = "

tripal_chado/tripal_chado.install

@@ -54,6 +54,8 @@ function tripal_chado_uninstall() {
 //     ALTER TABLE {tripal_custom_tables}
 //     DROP CONSTRAINT tripal_custom_tables_fk1 CASCADE
 //   ');
+
+  variable_set('tripal_chado_is_prepared', FALSE);
 }
 
 function tripal_chado_chado_semweb_schema(){