Merge branch '6.x-1.x' of git.drupal.org:sandbox/spficklin/1337878 into 6.x-1.x

tripal_featuremap/tripal_featuremap.views.inc

@@ -42,6 +42,9 @@ function tripal_featuremap_views_data()  {
       if (!tripal_views_is_integrated($tablename, $priority)) {
         $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);
 
+        // Add custom handle to handle type_ids
+        $table_integration_array['fields']['unittype_id']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_cvterm';
+
         // Add in node relationships if chado is in the same db as drupal
         if (tripal_core_chado_schema_exists()) {
           $integrations = tripal_views_add_node_relationship_to_chado_table_integration($table_integration_array);
@@ -137,54 +140,26 @@ function tripal_featuremap_views_default_views() {
 
   // Main default view
   $view = new view;
-  $view->name = 'map_listing';
-  $view->description = 'A listing of all maps';
+  $view->name = 'featuremap_listing';
+  $view->description = 'A listing of all chado feature maps';
   $view->tag = 'chado default';
-  $view->base_table = 'map';
-  $view->core = 0;
+  $view->base_table = 'featuremap';
+  $view->core = 6;
   $view->api_version = '2';
   $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
   $handler = $view->new_display('default', 'Defaults', 'default');
   $handler->override_option('fields', array(
-    'uniquename' => array(
-      'label' => 'Unique Name',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'uniquename',
-      'table' => 'map',
-      'field' => 'uniquename',
-      'relationship' => 'none',
-    ),
-    'name_1' => array(
+    'name' => array(
       'label' => 'Name',
       'alter' => array(
         'alter_text' => 0,
         'text' => '',
         'make_link' => 0,
         'path' => '',
+        'absolute' => 0,
         'link_class' => '',
         'alt' => '',
+        'rel' => '',
         'prefix' => '',
         'suffix' => '',
         'target' => '',
@@ -199,22 +174,26 @@ function tripal_featuremap_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
-      'link_to_node' => 1,
+      'hide_alter_empty' => 1,
+      'type' => 'separator',
+      'separator' => ', ',
       'exclude' => 0,
-      'id' => 'name_1',
-      'table' => 'map',
+      'id' => 'name',
+      'table' => 'featuremap',
       'field' => 'name',
       'relationship' => 'none',
     ),
-    'common_name' => array(
-      'label' => 'Organism',
+    'description' => array(
+      'label' => 'Description',
       'alter' => array(
         'alter_text' => 0,
         'text' => '',
         'make_link' => 0,
         'path' => '',
+        'absolute' => 0,
         'link_class' => '',
         'alt' => '',
+        'rel' => '',
         'prefix' => '',
         'suffix' => '',
         'target' => '',
@@ -229,22 +208,26 @@ function tripal_featuremap_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
-      'link_to_node' => 1,
+      'hide_alter_empty' => 1,
+      'type' => 'separator',
+      'separator' => ', ',
       'exclude' => 0,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
+      'id' => 'description',
+      'table' => 'featuremap',
+      'field' => 'description',
       'relationship' => 'none',
     ),
-    'name' => array(
-      'label' => 'Type',
+    'name_1' => array(
+      'label' => 'Map Units',
       'alter' => array(
         'alter_text' => 0,
         'text' => '',
         'make_link' => 0,
         'path' => '',
+        'absolute' => 0,
         'link_class' => '',
         'alt' => '',
+        'rel' => '',
         'prefix' => '',
         'suffix' => '',
         'target' => '',
@@ -259,118 +242,127 @@ function tripal_featuremap_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
+      'hide_alter_empty' => 1,
+      'type' => 'separator',
+      'separator' => ', ',
       'exclude' => 0,
-      'id' => 'name',
+      'id' => 'name_1',
       'table' => 'cvterm',
       'field' => 'name',
       'relationship' => 'none',
     ),
-    'is_obsolete' => array(
-      'label' => 'Is Obsolete?',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'type' => 'yes-no',
-      'not' => 0,
-      'exclude' => 0,
-      'id' => 'is_obsolete',
-      'table' => 'map',
-      'field' => 'is_obsolete',
-      'relationship' => 'none',
-    ),
   ));
   $handler->override_option('sorts', array(
     'name' => array(
+      'order' => 'ASC',
       'id' => 'name',
-      'table' => 'map',
+      'table' => 'featuremap',
       'field' => 'name',
+      'relationship' => 'none',
     ),
   ));
   $handler->override_option('filters', array(
-    'common_name' => array(
+    'unittype_id' => array(
       'operator' => '=',
-      'value' => array(),
+      'value' => '',
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
         'use_operator' => 0,
-        'operator' => 'common_name_op',
-        'identifier' => 'organism_common_name',
-        'label' => 'Organism',
+        'operator' => 'unittype_id_op',
+        'identifier' => 'unittype_id',
+        'label' => 'Map Units',
         'remember' => 0,
       ),
       'case' => 1,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
+      'id' => 'unittype_id',
+      'table' => 'featuremap',
+      'field' => 'unittype_id',
       'relationship' => 'none',
       'values_form_type' => 'select',
       'multiple' => 1,
       'optional' => 0,
+      'show_all' => 0,
       'agg' => array(
         'records_with' => 1,
         'aggregates_with' => 1,
       ),
     ),
-    'type_id' => array(
-      'operator' => '=',
-      'value' => array(),
+    'name_1' => array(
+      'operator' => 'contains',
+      'value' => '',
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
         'use_operator' => 0,
-        'operator' => 'type_id_op',
-        'identifier' => 'type_id',
-        'label' => 'Type',
+        'operator' => 'name_1_op',
+        'identifier' => 'name_1',
+        'label' => 'Name',
         'remember' => 0,
       ),
-      'case' => 1,
-      'id' => 'type_id',
-      'table' => 'map',
-      'field' => 'type_id',
+      'case' => 0,
+      'id' => 'name_1',
+      'table' => 'featuremap',
+      'field' => 'name',
       'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'show_all' => 0,
       'agg' => array(
         'records_with' => 1,
-        'aggregates_with' => 0,
+        'aggregates_with' => 1,
       ),
     ),
+    'description' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'description_op',
+        'identifier' => 'description',
+        'label' => 'Description',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'description',
+      'table' => 'featuremap',
+      'field' => 'description',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'search_results' => array(
+      'operator' => '=',
+      'value' => '',
+      'group' => '0',
+      'exposed' => FALSE,
+      'expose' => array(
+        'operator' => FALSE,
+        'label' => '',
+      ),
+      'id' => 'search_results',
+      'table' => 'views',
+      'field' => 'search_results',
+      'relationship' => 'none',
+      'apply_button' => 'Show',
+      'no_results_text' => 'Click "Show" to see a list of all feature maps matching the entered criteria. If you leave a any of the criteria blank then the maps will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all maps will be listed.',
+    ),
   ));
   $handler->override_option('access', array(
     'type' => 'perm',
-    'perm' => 'access chado_map content',
+    'perm' => 'access chado_featuremap content',
   ));
   $handler->override_option('cache', array(
     'type' => 'none',
   ));
   $handler->override_option('title', 'Maps');
-  $handler->override_option('header', 'Click "Show" to see a list of all maps matching the entered criteria. If you leave a any of the criteria blank then the maps will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all maps will be listed.');
-  $handler->override_option('header_format', '2');
-  $handler->override_option('header_empty', 0);
-  $handler->override_option('empty', 'No maps match the supplied criteria.');
+  $handler->override_option('header', 'Click "Show" to see a list of all feature maps matching the entered criteria. If you leave a any of the criteria blank then the maps will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all maps will be listed.');
+  $handler->override_option('header_format', '1');
+  $handler->override_option('header_empty', 1);
+  $handler->override_option('empty', 'No feature maps match the current criteria.');
   $handler->override_option('empty_format', '1');
-  $handler->override_option('items_per_page', 50);
+  $handler->override_option('items_per_page', 25);
   $handler->override_option('use_pager', '1');
   $handler->override_option('style_plugin', 'table');
   $handler->override_option('style_options', array(
@@ -380,44 +372,33 @@ function tripal_featuremap_views_default_views() {
     'order' => 'asc',
     'summary' => '',
     'columns' => array(
-      'uniquename' => 'uniquename',
-      'name_1' => 'name_1',
-      'common_name' => 'common_name',
       'name' => 'name',
-      'is_obsolete' => 'is_obsolete',
+      'description' => 'description',
+      'name_1' => 'name_1',
     ),
     'info' => array(
-      'uniquename' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name_1' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'common_name' => array(
+      'name' => array(
         'sortable' => 1,
         'separator' => '',
       ),
-      'name' => array(
+      'description' => array(
         'sortable' => 1,
         'separator' => '',
       ),
-      'is_obsolete' => array(
+      'name_1' => array(
         'sortable' => 1,
         'separator' => '',
       ),
     ),
-    'default' => 'uniquename',
+    'default' => '-1',
   ));
-  $default_handler = $handler;
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/maps');
+  $handler->override_option('path', 'chado/featuremaps');
   $handler->override_option('menu', array(
     'type' => 'normal',
     'title' => 'Maps',
-    'description' => 'A map is a collection of features of a given type. For example, a cDNA or BAC clone map.',
-    'weight' => '10',
+    'description' => 'A listing of chado feature maps.',
+    'weight' => '0',
     'name' => 'navigation',
   ));
   $handler->override_option('tab_options', array(
@@ -427,80 +408,6 @@ function tripal_featuremap_views_default_views() {
     'weight' => 0,
     'name' => 'navigation',
   ));
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        'alter' => array(
-          'alter_text' => 0,
-          'text' => '',
-          'make_link' => 0,
-          'path' => '',
-          'absolute' => 0,
-          'link_class' => '',
-          'alt' => '',
-          'rel' => '',
-          'prefix' => '',
-          'suffix' => '',
-          'target' => '',
-          'help' => '',
-          'trim' => 0,
-          'max_length' => '',
-          'word_boundary' => 1,
-          'ellipsis' => 1,
-          'html' => 0,
-          'strip_tags' => 0,
-        ),
-        'empty' => '',
-        'hide_empty' => 0,
-        'empty_zero' => 0,
-        'hide_alter_empty' => 1,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Adds map => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Map to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_map',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Change analysis.name to have a link to the node
-    $fields['name_1']['alter']['make_link'] = 1;
-    $fields['name_1']['alter']['path'] = 'node/[nid]';
-    $default_handler->override_option('fields', $fields);
-    // Only show records with published nodes
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-  }
   $views[$view->name] = $view;
 
   return $views;