Merge remote-tracking branch 'upstream/7.x-3.x' into patch-1

docs/extensions/search.rst

@@ -25,6 +25,14 @@ The Tripal ElasticSearch module allows you to easily manage the indexing and dis
 `Documentation <https://github.com/tripal/tripal_elasticsearch/blob/master/docs/README.md>`__
 `Repository <https://github.com/tripal/tripal_elasticsearch>`__
 
+Tripal MegaSearch
+---------------------
+
+Tripal MegaSearch is a tool for downloading biological data stored in a Tripal/Chado database. The module was designed to be generic and flexible so it can be used on most Tripal sites. Site administrators may choose from 1) a set of predefined materialized views or 2) chado base tables as the data source to serve data. If neither data source is desired, developers may create their own materialized views and serve them through Tripal MegaSearch via a flexible dynamic query form. This form allows filters to be added dynamically and combined using 'AND/OR' operators. The filters correspond to the underlying data source columns so the user can filter data on each column.
+
+`Documentation <https://gitlab.com/mainlabwsu/tripal_megasearch/blob/master/README.md>`__
+`Repository <https://gitlab.com/mainlabwsu/tripal_megasearch>`__
+
 Tripal Sequence Similarity Search
 ----------------------------------
 

tripal_chado/includes/tripal_chado.fields.inc

@@ -2495,6 +2495,9 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
   $prop_table = $table_name . 'prop';
   if (chado_table_exists($prop_table)) {
 
+    $schema = chado_get_schema($prop_table);
+    $pkey = $schema['primary key'][0];
+
     $props = tripal_chado_bundle_get_properties($table_name, $prop_table, $type_table, $type_column, $cvterm_id, $type_value);
     foreach ($props as $term) {
 

tripal_chado/includes/tripal_chado.publish.inc

@@ -57,6 +57,12 @@ function tripal_chado_publish_form($form, &$form_state) {
         $field = field_info_field($field_name);
         $instance = field_info_instance('TripalEntity', $field_name, $bundle_name);
 
+        // Exclude data fields from the publish form.
+        // We do this because the lack of default causes errors.
+        if ($field['type'] == 'datetime'){
+          continue;
+        }
+
         // Get the Chado mapping information.
         $base_table = array_key_exists('base_table', $instance['settings']) ? $instance['settings']['base_table'] : '';
         $chado_table = array_key_exists('chado_table', $instance['settings']) ? $instance['settings']['chado_table'] : '';
@@ -193,4 +199,3 @@ function tripal_chado_publish_form_submit($form, &$form_state) {
 function tripal_chado_publish_form_ajax_callback($form, $form_state) {
   return $form;
 }
-

tripal_chado/includes/tripal_chado.semweb.inc

@@ -759,7 +759,7 @@ function tripal_chado_populate_vocab_EFO() {
     'cv_name' => 'efo',
     'definition' => 'An instrument design which describes the design of the array.',
   ]);
-  chado_associate_semweb_term(NULL, 'arraydesign_id', $term);
+  chado_associate_semweb_term('assay', 'arraydesign_id', $term);
 
   $term = chado_insert_cvterm([
     'id' => 'EFO:0005522',
@@ -768,13 +768,7 @@ function tripal_chado_populate_vocab_EFO() {
     'definition' => 'Controlled terms for descriptors of types of array substrates.',
   ]);
   chado_associate_semweb_term('arraydesign', 'substratetype_id', $term);
-  $term = chado_insert_cvterm([
-    'id' => 'EFO:0001728',
-    'name' => 'array manufacturer',
-    'cv_name' => 'efo',
-    'definition' => '',
-  ]);
-  chado_associate_semweb_term('arraydesign', 'manufacturer_id', $term);
+
   $term = chado_insert_cvterm([
     'id' => 'EFO:0001728',
     'name' => 'array manufacturer',
@@ -785,10 +779,11 @@ function tripal_chado_populate_vocab_EFO() {
 
   $term = chado_insert_cvterm([
     'id' => 'EFO:0000269',
-    'name' => 'assay design',
+    'name' => 'array design',
     'cv_name' => 'efo',
     'definition' => 'An instrument design which describes the design of the array.',
   ]);
+  chado_associate_semweb_term('element', 'arraydesign_id', $term);
 }
 
 /**