Fixed merge conflict with most recnet 7.x-3.x

tripal/tripal.install

@@ -165,6 +165,7 @@ function tripal_schema() {
   $schema['tripal_bundle'] = tripal_tripal_bundle_schema();
   $schema['tripal_import'] = tripal_tripal_import_schema();
   $schema['tripal_collection'] = tripal_tripal_collection_schema();
+  $schema['tripal_collection_bundle'] = tripal_tripal_collection_bundle_schema();
 
   // Adds a table for additional information related to bundles.
   $schema['tripal_bundle_variables'] = tripal_tripal_bundle_variables_schema();
@@ -1144,9 +1145,29 @@ function tripal_update_7309() {
 }
 
 /**
- * Adds support for file quotas.
+ * Adds the missing tripal_collection_bundle table
+ * @throws DrupalUpdateException
  */
 function tripal_update_7310() {
+  $transaction = db_transaction();
+  try {
+    if (!db_table_exists('tripal_collection_bundle')) {
+      $schema = array();
+      $schema['tripal_collection_bundle'] = tripal_tripal_collection_bundle_schema();
+      db_create_table('tripal_collection_bundle', $schema['tripal_collection_bundle']);
+    }
+  }
+  catch (\PDOException $e) {
+    $transaction->rollback();
+    $error = $e->getMessage();
+    throw new DrupalUpdateException('Could not add the tripal_collection_bundle table:' . $error);
+  }
+}
+
+/**
+ * Adds support for file quotas.
+ */
+function tripal_update_7311() {
   try {
     $schema = array();
     $schema['tripal_custom_quota'] = tripal_tripal_custom_quota_schema();
@@ -1158,4 +1179,4 @@ function tripal_update_7310() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Could not perform update: '. $error);
   }
-}
+}

tripal/tripal.views_default.inc

@@ -251,12 +251,13 @@ function tripal_admin_defaultview_jobs() {
   $view->core = 7;
   $view->api_version = '3.0';
   $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-
+  
   /* Display: Master */
   $handler = $view->new_display('default', 'Master', 'default');
   $handler->display->display_options['title'] = 'Jobs';
   $handler->display->display_options['use_more_always'] = FALSE;
-  $handler->display->display_options['access']['type'] = 'none';
+  $handler->display->display_options['access']['type'] = 'perm';
+  $handler->display->display_options['access']['perm'] = 'administer tripal';
   $handler->display->display_options['cache']['type'] = 'none';
   $handler->display->display_options['query']['type'] = 'views_query';
   $handler->display->display_options['exposed_form']['type'] = 'basic';
@@ -505,17 +506,16 @@ function tripal_admin_defaultview_jobs() {
     1 => 0,
     3 => 0,
   );
-
+  
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page');
   $handler->display->display_options['path'] = 'admin/tripal/tripal_jobs/jobs';
-  $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Jobs';
   $handler->display->display_options['menu']['description'] = 'Jobs managed by Tripal';
   $handler->display->display_options['menu']['weight'] = '-10';
   $handler->display->display_options['menu']['context'] = 0;
   $handler->display->display_options['menu']['context_only_inline'] = 0;
   $handler->display->display_options['tab_options']['weight'] = '0';
-
+  
   return $view;
 }

tripal/views_handlers/tripal_views_handler_field.inc

@@ -82,7 +82,7 @@ class tripal_views_handler_field extends views_handler_field {
     $items = $this->get_value($values);
 
     // Handle single value fields:
-    if (count($items == 1)) {
+    if (count($items) == 1) {
       $function = $field['module'] . '_field_formatter_view';
       $value = $function('TripalEntity', $entity, $field, $instance, 'und', $items, $instance['display']['default']);
       return $value;

tripal_chado/api/modules/tripal_chado.phylotree.api.inc

@@ -859,7 +859,7 @@ function tripal_phylogeny_import_tree_file($file_name, $format, $options = array
     // Parse the file according to the format indicated.
     if ($format == 'newick') {
       // Parse the tree into the expected nested node format.
-      module_load_include('inc', 'tripal_phylogeny', 'includes/parsers/tripal_phylogeny.newick_parser');
+      module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.phylotree_newick');
       $tree = tripal_phylogeny_parse_newick_file($file_name);
 
       // Assign the right and left indecies to the tree ndoes
@@ -873,4 +873,4 @@ function tripal_phylogeny_import_tree_file($file_name, $format, $options = array
     $transaction->rollback();
     watchdog_exception('tripal_phylogeny', $e);
   }
-}
+}

tripal_chado_views/views-sql-compliant-three-tier-naming-1971160-30.patch

@@ -2,7 +2,7 @@ diff --git a/includes/handlers.inc b/includes/handlers.inc
 index 680a54d..1d72aed 100644
 --- a/includes/handlers.inc
 +++ b/includes/handlers.inc
-@@ -1637,7 +1637,17 @@ class views_join {
+@@ -1729,7 +1729,17 @@ class views_join {
        }
      }
  
@@ -21,7 +21,7 @@ index 680a54d..1d72aed 100644
    }
  }
  
-@@ -1728,7 +1738,17 @@ class views_join_subquery extends views_join {
+@@ -1832,7 +1842,17 @@ class views_join_subquery extends views_join {
        }
      }
  
@@ -44,8 +44,8 @@ diff --git a/includes/view.inc b/includes/view.inc
 index d9fb43f..1cf5c50 100644
 --- a/includes/view.inc
 +++ b/includes/view.inc
-@@ -202,6 +202,11 @@ class view extends views_db_object {
-   var $base_database = NULL;
+@@ -234,6 +234,11 @@ class view extends views_db_object {
+   public $base_database = NULL;
  
    /**
 +   * Allow to set the search_path for databases which, unlike MySQL, are actually SQL-compliant
@@ -56,7 +56,7 @@ index d9fb43f..1cf5c50 100644
     * Here comes a list of the possible handler which are active on this view.
     */
  
-@@ -897,6 +902,12 @@ class view extends views_db_object {
+@@ -939,6 +944,12 @@ class view extends views_db_object {
        $this->base_database = $views_data['table']['base']['database'];
      }
  
@@ -73,10 +73,10 @@ diff --git a/plugins/views_plugin_query_default.inc b/plugins/views_plugin_query
 index 7468dd9..f092515 100644
 --- a/plugins/views_plugin_query_default.inc
 +++ b/plugins/views_plugin_query_default.inc
-@@ -1290,8 +1290,13 @@ class views_plugin_query_default extends views_plugin_query {
+@@ -1308,8 +1308,13 @@ class views_plugin_query_default extends views_plugin_query {
  
-     // Go ahead and build the query.
-     // db_select doesn't support to specify the key, so use getConnection directly.
+     // Go ahead and build the query. db_select doesn't support to specify the
+     // key, so use getConnection directly.
 +    $scoped_base_table = $this->base_table;
 +    if (isset($this->view->search_path)) {
 +      $scoped_base_table = $this->view->search_path . '.' . $this->base_table;