Updated feature and analysis default views

tripal_analysis/tripal_analysis.views.inc

@@ -42,8 +42,6 @@ function tripal_analysis_views_data()  {
       $table_integration_array['fields']['program']['handlers']['filter']['name'] = 'chado_views_handler_filter_select_string';
       $table_integration_array['fields']['algorithm']['handlers']['filter']['name'] = 'chado_views_handler_filter_select_string';
 
-      dpm($table_integration_array, 'analysis integration');
-
       tripal_views_integration_add_entry($table_integration_array);
     }
 

tripal_feature/tripal_feature.views.inc

@@ -134,17 +134,15 @@ function tripal_feature_views_default_views() {
   $views = array();
 
   // Main default view
-  // List all cvterms based on cv
   $view = new view;
-  $view->name = 'all_features';
-  $view->description = 'A listing of all Sequence FEatures';
-  $view->tag = 'chado';
-  $view->view_php = '';
+  $view->name = 'feature_listing';
+  $view->description = 'A listing of chado sequence features.';
+  $view->tag = 'chado default';
   $view->base_table = 'feature';
-  $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 = $view->new_display('default', 'features_all', 'default');
   $handler->override_option('fields', array(
     'uniquename' => array(
       'label' => 'Unique Name',
@@ -152,7 +150,7 @@ function tripal_feature_views_default_views() {
         'alter_text' => 0,
         'text' => '',
         'make_link' => 0,
-        'path' => '',
+        'path' => 'node/[nid]',
         'link_class' => '',
         'alt' => '',
         'prefix' => '',
@@ -169,12 +167,15 @@ function tripal_feature_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
-      'link_to_node' => 1,
+      'link_to_node' => 0,
       'exclude' => 0,
       'id' => 'uniquename',
       'table' => 'feature',
       'field' => 'uniquename',
       'relationship' => 'none',
+      'override' => array(
+        'button' => 'Override',
+      ),
     ),
     'name' => array(
       'label' => 'Name',
@@ -205,9 +206,12 @@ function tripal_feature_views_default_views() {
       'table' => 'feature',
       'field' => 'name',
       'relationship' => 'none',
+      'override' => array(
+        'button' => 'Override',
+      ),
     ),
-    'common_name' => array(
-      'label' => 'Organism',
+    'name_1' => array(
+      'label' => 'Type',
       'alter' => array(
         'alter_text' => 0,
         'text' => '',
@@ -229,15 +233,14 @@ function tripal_feature_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
-      'link_to_node' => 1,
       'exclude' => 0,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
+      'id' => 'name_1',
+      'table' => 'cvterm',
+      'field' => 'name',
       'relationship' => 'none',
     ),
-    'name_3' => array(
-      'label' => 'Type',
+    'common_name' => array(
+      'label' => 'Common Name',
       'alter' => array(
         'alter_text' => 0,
         'text' => '',
@@ -259,14 +262,18 @@ function tripal_feature_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
+      'link_to_node' => 1,
       'exclude' => 0,
-      'id' => 'name_3',
-      'table' => 'cvterm',
-      'field' => 'name',
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
       'relationship' => 'none',
+      'override' => array(
+        'button' => 'Override',
+      ),
     ),
-    'accession_link' => array(
-      'label' => 'External Reference',
+    'seqlen' => array(
+      'label' => 'Sequence Length',
       'alter' => array(
         'alter_text' => 0,
         'text' => '',
@@ -288,21 +295,29 @@ function tripal_feature_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
+      'set_precision' => FALSE,
+      'precision' => 0,
+      'decimal' => '.',
+      'separator' => ',',
+      'prefix' => '',
+      'suffix' => '',
       'exclude' => 0,
-      'id' => 'accession_link',
-      'table' => 'dbxref',
-      'field' => 'accession_link',
+      'id' => 'seqlen',
+      'table' => 'feature',
+      'field' => 'seqlen',
       'relationship' => 'none',
     ),
-    'name_1' => array(
-      'label' => 'Library',
+    'is_obsolete' => array(
+      'label' => 'Is Obsolete',
       'alter' => array(
         'alter_text' => 0,
         'text' => '',
         'make_link' => 0,
         'path' => '',
+        'absolute' => 0,
         'link_class' => '',
         'alt' => '',
+        'rel' => '',
         'prefix' => '',
         'suffix' => '',
         'target' => '',
@@ -317,22 +332,27 @@ function tripal_feature_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
-      'link_to_node' => 1,
+      'hide_alter_empty' => 1,
+      'type' => 'separator',
+      'not' => 0,
+      'separator' => ', ',
       'exclude' => 0,
-      'id' => 'name_1',
-      'table' => 'library',
-      'field' => 'name',
+      'id' => 'is_obsolete',
+      'table' => 'feature',
+      'field' => 'is_obsolete',
       'relationship' => 'none',
     ),
-    'name_2' => array(
-      'label' => 'Analysis',
+    'timeaccessioned' => array(
+      'label' => 'Accessioned On',
       'alter' => array(
         'alter_text' => 0,
         'text' => '',
         'make_link' => 0,
         'path' => '',
+        'absolute' => 0,
         'link_class' => '',
         'alt' => '',
+        'rel' => '',
         'prefix' => '',
         'suffix' => '',
         'target' => '',
@@ -347,10 +367,37 @@ function tripal_feature_views_default_views() {
       'empty' => '',
       'hide_empty' => 0,
       'empty_zero' => 0,
-      'link_to_node' => 1,
+      'hide_alter_empty' => 1,
+      'date_format' => 'large',
+      'custom_date_format' => '',
+      'type' => 'separator',
+      'separator' => ', ',
       'exclude' => 0,
-      'id' => 'name_2',
-      'table' => 'analysis',
+      'id' => 'timeaccessioned',
+      'table' => 'feature',
+      'field' => 'timeaccessioned',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('sorts', array(
+    'common_name' => array(
+      'order' => 'ASC',
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
+      'relationship' => 'none',
+    ),
+    'name' => array(
+      'order' => 'ASC',
+      'id' => 'name',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'name_1' => array(
+      'order' => 'ASC',
+      'id' => 'name_1',
+      'table' => 'feature',
       'field' => 'name',
       'relationship' => 'none',
     ),
@@ -358,15 +405,14 @@ function tripal_feature_views_default_views() {
   $handler->override_option('filters', array(
     'common_name' => array(
       'operator' => '=',
-      'value' => '<select organism>',
+      'value' => array(),
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
         'use_operator' => 0,
         'operator' => 'common_name_op',
         'identifier' => 'organism',
-        'label' => 'Organism',
-        'optional' => 1,
+        'label' => 'Organism Common Name',
         'remember' => 0,
       ),
       'case' => 1,
@@ -374,63 +420,77 @@ function tripal_feature_views_default_views() {
       'table' => 'organism',
       'field' => 'common_name',
       'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'override' => array(
+        'button' => 'Override',
+      ),
     ),
-    'name' => array(
-      'operator' => 'contains',
-      'value' => '',
+    'type_id' => array(
+      'operator' => '=',
+      'value' => array(),
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
         'use_operator' => 0,
-        'operator' => 'name_op',
-        'identifier' => 'name',
-        'label' => 'Name Contains',
-        'optional' => 1,
+        'operator' => 'type_id_op',
+        'identifier' => 'type_id',
+        'label' => 'Type',
         'remember' => 0,
       ),
-      'case' => 0,
-      'id' => 'name',
+      'case' => 1,
+      'id' => 'type_id',
       'table' => 'feature',
-      'field' => 'name',
+      '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_1' => array(
-      'operator' => 'contains',
+      'operator' => 'allwords',
       'value' => '',
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
         'use_operator' => 0,
         'operator' => 'name_1_op',
-        'identifier' => 'library',
-        'label' => 'Library Name Contains',
-        'optional' => 1,
+        'identifier' => 'name',
+        'label' => 'Name Contains',
+        'bef_filter_description' => '',
         'remember' => 0,
       ),
       'case' => 0,
       'id' => 'name_1',
-      'table' => 'library',
+      'table' => 'feature',
       'field' => 'name',
       'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
     ),
-    'name_2' => array(
-      'operator' => 'contains',
+    'search_results' => array(
+      'operator' => '=',
       'value' => '',
       'group' => '0',
-      'exposed' => TRUE,
+      'exposed' => FALSE,
       'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'name_2_op',
-        'identifier' => 'analysis',
-        'label' => 'Analysis Name Contains',
-        'optional' => 1,
-        'remember' => 0,
+        'operator' => FALSE,
+        'label' => '',
       ),
-      'case' => 0,
-      'id' => 'name_2',
-      'table' => 'analysis',
-      'field' => 'name',
+      'id' => 'search_results',
+      'table' => 'views',
+      'field' => 'search_results',
       'relationship' => 'none',
+      'apply_button' => 'Show',
+      'no_results_text' => 'Click "Show" to see a list of all features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.',
     ),
   ));
   $handler->override_option('access', array(
@@ -441,16 +501,80 @@ function tripal_feature_views_default_views() {
     'type' => 'none',
   ));
   $handler->override_option('title', 'Sequence Features');
-  $handler->override_option('empty', 'There are no features matching that criteria. Please select a different organism above.');
-  $handler->override_option('empty_format', '1');
+  $handler->override_option('header', 'Click "Show" to see a list of all features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'There are currently no features sync\'d with drupal.');
+  $handler->override_option('empty_format', '2');
   $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(
+    'grouping' => '',
+    'override' => 1,
+    'sticky' => 0,
+    'order' => 'asc',
+    'columns' => array(
+      'accession' => 'accession',
+      'accession_link' => 'accession_link',
+      'name' => 'name',
+      'uniquename' => 'uniquename',
+      'name_1' => 'name_1',
+      'common_name' => 'common_name',
+      'seqlen' => 'seqlen',
+      'is_obsolete' => 'is_obsolete',
+      'is_analysis' => 'is_analysis',
+      'nid' => 'nid',
+    ),
+    'info' => array(
+      'accession' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'accession_link' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'uniquename' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name_1' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'common_name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'seqlen' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'is_obsolete' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'is_analysis' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'nid' => array(
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
   $handler = $view->new_display('page', 'Page', 'page_1');
   $handler->override_option('path', 'features');
   $handler->override_option('menu', array(
     'type' => 'normal',
-    'title' => 'Sequence Features',
-    'description' => '',
+    'title' => 'Features View',
+    'description' => 'Provides a table of sequence features',
     'weight' => '0',
     'name' => 'primary-links',
   ));