Updated library, stock and organism default views

tripal_library/tripal_library.views.inc

@@ -116,15 +116,13 @@ function tripal_library_views_default_views() {
   $views = array();
 
   // Main default view
-  // List all cvterms based on cv
   $view = new view;
-  $view->name = 'all_libraries';
+  $view->name = 'library_listing';
   $view->description = 'A listing of all libraries';
-  $view->tag = 'chado';
-  $view->view_php = '';
+  $view->tag = 'chado default';
   $view->base_table = 'library';
-  $view->is_cacheable = FALSE;
-  $view->api_version = 2;
+  $view->core = 0;
+  $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(
@@ -278,40 +276,18 @@ function tripal_library_views_default_views() {
       'field' => 'is_obsolete',
       'relationship' => 'none',
     ),
-    'num_features' => array(
-      'label' => 'Number of Features',
-      '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,
-      'exclude' => 0,
-      'id' => 'num_features',
+  ));
+  $handler->override_option('sorts', array(
+    'name' => array(
+      'id' => 'name',
       'table' => 'library',
-      'field' => 'num_features',
-      'relationship' => 'none',
+      'field' => 'name',
     ),
   ));
   $handler->override_option('filters', array(
     'common_name' => array(
       'operator' => '=',
-      'value' => 'All',
+      'value' => array(),
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
@@ -319,7 +295,6 @@ function tripal_library_views_default_views() {
         'operator' => 'common_name_op',
         'identifier' => 'organism_common_name',
         'label' => 'Organism',
-        'optional' => 1,
         'remember' => 0,
       ),
       'case' => 1,
@@ -327,6 +302,51 @@ function tripal_library_views_default_views() {
       'table' => 'organism',
       'field' => 'common_name',
       'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+    ),
+    'type_id' => array(
+      'operator' => '=',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'type_id_op',
+        'identifier' => 'type_id',
+        'label' => 'Type',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'type_id',
+      'table' => 'library',
+      'field' => 'type_id',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 0,
+      ),
+    ),
+    '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 libraries matching the entered criteria. If you leave a any of the criteria blank then the libraries will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all libraries will be listed.',
     ),
   ));
   $handler->override_option('access', array(
@@ -337,8 +357,12 @@ function tripal_library_views_default_views() {
     'type' => 'none',
   ));
   $handler->override_option('title', 'Libraries');
+  $handler->override_option('header', 'Click "Show" to see a list of all libraries matching the entered criteria. If you leave a any of the criteria blank then the libraries will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all libraries will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
   $handler->override_option('empty', 'There are no libraries matching the current criteria. If you think there should be, check that all chado libraries are sync\'d with your website.');
   $handler->override_option('empty_format', '1');
+  $handler->override_option('items_per_page', 50);
   $handler->override_option('use_pager', '1');
   $handler->override_option('style_plugin', 'table');
   $handler->override_option('style_options', array(
@@ -346,50 +370,37 @@ function tripal_library_views_default_views() {
     'override' => 1,
     'sticky' => 0,
     'order' => 'asc',
+    'summary' => '',
     'columns' => array(
-      'name' => 'name',
-      'timeaccessioned' => 'timeaccessioned',
-      'timelastmodified' => 'timelastmodified',
-      'is_obsolete' => 'is_obsolete',
-      'name_1' => 'name_1',
       'uniquename' => 'uniquename',
+      'name_1' => 'name_1',
       'common_name' => 'common_name',
-      'num_libraries' => 'num_libraries',
+      'name' => 'name',
+      'is_obsolete' => 'is_obsolete',
     ),
     'info' => array(
-      'name' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'timeaccessioned' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'timelastmodified' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-      'is_obsolete' => array(
-        'sortable' => 0,
+      'uniquename' => array(
+        'sortable' => 1,
         'separator' => '',
       ),
       'name_1' => array(
-        'sortable' => 0,
+        'sortable' => 1,
         'separator' => '',
       ),
-      'uniquename' => array(
-        'sortable' => 0,
+      'common_name' => array(
+        'sortable' => 1,
         'separator' => '',
       ),
-      'common_name' => array(
-        'sortable' => 0,
+      'name' => array(
+        'sortable' => 1,
         'separator' => '',
       ),
-      'num_libraries' => array(
+      'is_obsolete' => array(
+        'sortable' => 1,
         'separator' => '',
       ),
     ),
-    'default' => '-1',
+    'default' => 'uniquename',
   ));
   $handler = $view->new_display('page', 'Page', 'page_1');
   $handler->override_option('path', 'libraries');

tripal_organism/tripal_organism.views.inc

@@ -38,6 +38,13 @@ function tripal_organism_views_data()  {
     foreach ($tables as $tablename) {
       if (!tripal_views_is_integrated($tablename, 9)) {
         $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE);
+
+        // Add specialty handlers
+        $table_integration_array['fields']['common_name']['handlers']['filter']['name'] = 'views_handler_filter_chado_select_string';
+        $table_integration_array['fields']['genus']['handlers']['filter']['name'] = 'views_handler_filter_chado_select_string';
+        $table_integration_array['fields']['species']['handlers']['filter']['name'] = 'views_handler_filter_chado_select_string';
+        $table_integration_array['fields']['abbreviation']['handlers']['filter']['name'] = 'views_handler_filter_chado_select_string';
+
         tripal_views_integration_add_entry($table_integration_array);
       }
     }
@@ -117,15 +124,13 @@ function tripal_organism_views_default_views() {
   $views = array();
 
   // Main default view
-  // List all cvterms based on cv
   $view = new view;
-  $view->name = 'all_organisms';
+  $view->name = 'organism_listing';
   $view->description = 'A listing of all organism in chado';
-  $view->tag = 'chado';
-  $view->view_php = '';
+  $view->tag = 'chado default';
   $view->base_table = 'organism';
-  $view->is_cacheable = FALSE;
-  $view->api_version = 2;
+  $view->core = 0;
+  $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(
@@ -159,36 +164,6 @@ function tripal_organism_views_default_views() {
       'field' => 'common_name',
       'relationship' => 'none',
     ),
-    'abbreviation' => array(
-      'label' => 'Abbreviation',
-      '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' => 0,
-      'exclude' => 0,
-      'id' => 'abbreviation',
-      'table' => 'organism',
-      'field' => 'abbreviation',
-      'relationship' => 'none',
-    ),
     'genus' => array(
       'label' => 'Genus',
       'alter' => array(
@@ -247,8 +222,8 @@ function tripal_organism_views_default_views() {
       'field' => 'species',
       'relationship' => 'none',
     ),
-    'num_features' => array(
-      'label' => 'Number of Features',
+    'abbreviation' => array(
+      'label' => 'Abbreviation',
       'alter' => array(
         'alter_text' => 0,
         'text' => '',
@@ -270,68 +245,27 @@ function tripal_organism_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
+      'link_to_node' => 0,
       'exclude' => 0,
-      'id' => 'num_features',
+      'id' => 'abbreviation',
       'table' => 'organism',
-      'field' => 'num_features',
+      'field' => 'abbreviation',
       'relationship' => 'none',
     ),
-    'num_stocks' => array(
-      'label' => 'Number of Stocks',
-      '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,
-      'exclude' => 0,
-      'id' => 'num_stocks',
+  ));
+  $handler->override_option('sorts', array(
+    'genus' => array(
+      'order' => 'ASC',
+      'id' => 'genus',
       'table' => 'organism',
-      'field' => 'num_stocks',
+      'field' => 'genus',
       'relationship' => 'none',
     ),
-    'num_libraries' => array(
-      'label' => 'Number of Libraries',
-      '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,
-      'exclude' => 0,
-      'id' => 'num_libraries',
+    'species' => array(
+      'order' => 'ASC',
+      'id' => 'species',
       'table' => 'organism',
-      'field' => 'num_libraries',
+      'field' => 'species',
       'relationship' => 'none',
     ),
   ));
@@ -352,27 +286,28 @@ function tripal_organism_views_default_views() {
     'override' => 1,
     'sticky' => 0,
     'order' => 'asc',
+    'summary' => '',
     'columns' => array(
-      'abbreviation' => 'abbreviation',
       'common_name' => 'common_name',
       'genus' => 'genus',
       'species' => 'species',
+      'abbreviation' => 'abbreviation',
     ),
     'info' => array(
-      'abbreviation' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
       'common_name' => array(
-        'sortable' => 0,
+        'sortable' => 1,
         'separator' => '',
       ),
       'genus' => array(
-        'sortable' => 0,
+        'sortable' => 1,
         'separator' => '',
       ),
       'species' => array(
-        'sortable' => 0,
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'abbreviation' => array(
+        'sortable' => 1,
         'separator' => '',
       ),
     ),

tripal_stock/tripal_stock.views.inc

@@ -254,14 +254,14 @@ function tripal_stock_views_pre_render  (&$view) {
 function tripal_stock_views_default_views() {
   $views = array();
 
+  // Main default view
   $view = new view;
-  $view->name = 'all_stocks';
-  $view->description = 'This view lists all stocks by default. There are exposed filters available but no arguments are used.';
-  $view->tag = 'chado';
-  $view->view_php = '';
+  $view->name = 'stock_listing';
+  $view->description = 'This view lists all stocks by default.';
+  $view->tag = 'chado default';
   $view->base_table = 'stock';
-  $view->is_cacheable = FALSE;
-  $view->api_version = 2;
+  $view->core = 0;
+  $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(
@@ -384,99 +384,6 @@ function tripal_stock_views_default_views() {
       'field' => 'common_name',
       'relationship' => 'none',
     ),
-    'all_dbxref' => array(
-      'label' => 'All Database References',
-      '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' => 'ul',
-      'separator' => ', ',
-      'exclude' => 0,
-      'id' => 'all_dbxref',
-      'table' => 'stock',
-      'field' => 'all_dbxref',
-      'relationship' => 'none',
-    ),
-    'all_properties' => array(
-      'label' => 'All Properties',
-      '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' => 'ul',
-      'separator' => ', ',
-      'exclude' => 0,
-      'id' => 'all_properties',
-      'table' => 'stock',
-      'field' => 'all_properties',
-      'relationship' => 'none',
-    ),
-    'all_relationships' => array(
-      'label' => 'All Relationships',
-      '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' => 'ul',
-      'separator' => ', ',
-      'exclude' => 0,
-      'id' => 'all_relationships',
-      'table' => 'stock',
-      'field' => 'all_relationships',
-      'relationship' => 'none',
-    ),
   ));
   $handler->override_option('sorts', array(
     'common_name' => array(
@@ -497,7 +404,7 @@ function tripal_stock_views_default_views() {
   $handler->override_option('filters', array(
     'common_name' => array(
       'operator' => '=',
-      'value' => 'All',
+      'value' => array(),
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
@@ -505,7 +412,6 @@ function tripal_stock_views_default_views() {
         'operator' => 'common_name_op',
         'identifier' => 'organism_common_name',
         'label' => 'Organism',
-        'optional' => 1,
         'remember' => 0,
       ),
       'case' => 1,
@@ -513,25 +419,73 @@ function tripal_stock_views_default_views() {
       'table' => 'organism',
       'field' => 'common_name',
       'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
     ),
-    'name' => array(
+    '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 stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.',
+    ),
+    'type_id' => array(
       'operator' => '=',
-      'value' => 'All',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'type_id_op',
+        'identifier' => 'type_id',
+        'label' => 'Type',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'type_id',
+      'table' => 'stock',
+      'field' => 'type_id',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'name' => array(
+      'operator' => 'contains',
+      'value' => '',
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
         'use_operator' => 0,
         'operator' => 'name_op',
         'identifier' => 'name',
-        'label' => 'Chado CV Terms: Name',
-        'optional' => 1,
+        'label' => 'Name Contains',
         'remember' => 0,
       ),
-      'case' => 1,
+      'case' => 0,
       'id' => 'name',
-      'table' => 'cvterm',
+      'table' => 'stock',
       'field' => 'name',
       'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
     ),
   ));
   $handler->override_option('access', array(
@@ -542,9 +496,12 @@ function tripal_stock_views_default_views() {
     'type' => 'none',
   ));
   $handler->override_option('title', 'Stocks');
+  $handler->override_option('header', 'Click "Show" to see a list of all stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
   $handler->override_option('empty', 'There are no stocks that match this criteria. If you think there should be, ensure that all stocks in chado are sync\'d with your website.');
   $handler->override_option('empty_format', '1');
-  $handler->override_option('items_per_page', 25);
+  $handler->override_option('items_per_page', 50);
   $handler->override_option('use_pager', '1');
   $handler->override_option('style_plugin', 'table');
   $handler->override_option('style_options', array(