Created Phenotype and natural diversity default views

tripal_natural_diversity/tripal_natural_diversity.api.inc

@@ -553,7 +553,7 @@ function tripal_natural_diversity_chado_schema_v1_11_nd_experiment_stock() {
 function tripal_natural_diversity_chado_schema_v1_2_nd_experiment_stock() {
   $description = array();
 
-  $description = array( 
+  $description = array(
     'referring_tables' => array(
       'nd_experiment_stock_dbxref',
       'nd_experiment_stockprop',
@@ -1078,6 +1078,11 @@ function tripal_natural_diversity_chado_schema_v1_11_nd_reagent() {
         'type' => 'serial',
         'not null' => '1',
       ),
+      'name' => array(
+        'type' => 'varchar',
+        'length' => 80,
+        'not null' => TRUE
+      ),
       'type_id' => array(
         'type' => 'int',
         'not null' => '1',

tripal_natural_diversity/tripal_natural_diversity.views.inc

@@ -3,14 +3,13 @@
 /**
  *  @file
  *  This file contains the basic functions for views integration of
- *  chado/tripal_natural_diversity tables. Supplementary functions can be found in
- *  ./views/
+ *  chado/tripal_natural_diversity tables.
  *
  *  Documentation on views integration can be found at
  *  http://views2.logrus.com/doc/html/index.html.
  */
 
-/*************************************************************************
+/**
  * Implements hook_views_data()
  * Purpose: Describe chado/tripal tables & fields to views
  *
@@ -33,6 +32,18 @@ function tripal_natural_diversity_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
+        switch ($tablename) {
+          case 'nd_geolocation':
+            $table_integration_array['fields']['description']['handlers']['filter']['name'] = 'chado_views_handler_filter_select_string';
+            $table_integration_array['fields']['geodetic_datum']['handlers']['filter']['name'] = 'chado_views_handler_filter_select_string';
+            $table_integration_array['fields']['latitude']['handlers']['filter']['name'] = 'chado_views_handler_filter_float';
+            $table_integration_array['fields']['longitude']['handlers']['filter']['name'] = 'chado_views_handler_filter_float';
+            $table_integration_array['fields']['altitude']['handlers']['filter']['name'] = 'chado_views_handler_filter_float';
+            break;
+        }
+
         tripal_views_integration_add_entry($table_integration_array);
       }
     }
@@ -66,7 +77,7 @@ function tripal_natural_diversity_views_data()  {
   return $data;
 }
 
-/*************************************************************************
+/**
  * Implements hook_views_handlers()
  * Purpose: Register all custom handlers with views
  *   where a handler describes either "the type of field",
@@ -76,16 +87,983 @@ function tripal_natural_diversity_views_data()  {
  */
 function tripal_natural_diversity_views_handlers() {
   return array(
-   'info' => array(
-     'path' => drupal_get_path('module', 'tripal_natural_diversity') . '/views/handlers',
-  ),
-   'handlers' => array(
-  'views_handler_field_chado_relationship_all' => array(
+    'info' => array(
+      'path' => drupal_get_path('module', 'tripal_natural_diversity') . '/views/handlers',
+    ),
+    'handlers' => array(
+      'views_handler_field_chado_relationship_all' => array(
+        'parent' => 'views_handler_field_prerender_list',
+      ),
+      'views_handler_field_chado_relationship_by_type' => array(
        'parent' => 'views_handler_field_prerender_list',
-  ),
-  'views_handler_field_chado_relationship_by_type' => array(
-       'parent' => 'views_handler_field_prerender_list',
-  ),
-  ),
+      ),
+    ),
   );
 }
+
+/**
+ * Created Default views related to the tables integrated by this module
+ *
+ * @ingroup tripal_feature_views
+ */
+function tripal_natural_diversity_views_default_views() {
+  $views = array();
+
+  // Experiment Listing
+  $view = new view;
+  $view->name = 'natdiv_experiment_listing';
+  $view->description = 'A listing of all natural diversity experiments';
+  $view->tag = 'chado default';
+  $view->base_table = 'nd_experiment';
+  $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(
+    'name' => array(
+      'label' => 'Type',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'name',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'description' => array(
+      'label' => 'Location Experiment Performed',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'description',
+      'table' => 'nd_geolocation',
+      'field' => 'description',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('sorts', array(
+    'name' => array(
+      'order' => 'ASC',
+      'id' => 'name',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'description' => array(
+      'order' => 'ASC',
+      'id' => 'description',
+      'table' => 'nd_geolocation',
+      'field' => 'description',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'type_id' => array(
+      'operator' => '=',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'type_id_op',
+        'identifier' => 'type_id',
+        'label' => 'Experiment Type',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'type_id',
+      'table' => 'nd_experiment',
+      'field' => 'type_id',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'description' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'description_op',
+        'identifier' => 'geolocation',
+        'label' => 'Location Experiment Performed',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'description',
+      'table' => 'nd_geolocation',
+      '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 experiments matching the entered criteria. If you leave a any of the criteria blank then the experiments will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all experiments will be listed.',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Natural Diversity Experiments');
+  $handler->override_option('header', 'Click "Show" to see a list of all experiments matching the entered criteria. If you leave a any of the criteria blank then the experiments will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all experiments will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'No natural diversity experiments match the current criteria.');
+  $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',
+    'summary' => '',
+    'columns' => array(
+      'name' => 'name',
+      'description' => 'description',
+    ),
+    'info' => array(
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'description' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'natdiv_experiments');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Natural Diversity Experiments',
+    'description' => '',
+    'weight' => '0',
+    'name' => 'primary-links',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  $views[$view->name] = $view;
+
+  // List geolocations
+  $view = new view;
+  $view->name = 'geolocation_listing';
+  $view->description = 'A listing of locations where natural diversity experiments took place';
+  $view->tag = 'chado default';
+  $view->base_table = 'nd_geolocation';
+  $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(
+    'description' => array(
+      'label' => 'Name',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'description',
+      'table' => 'nd_geolocation',
+      'field' => 'description',
+      'relationship' => 'none',
+    ),
+    'latitude' => array(
+      'label' => 'Latitude',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'latitude',
+      'table' => 'nd_geolocation',
+      'field' => 'latitude',
+      'relationship' => 'none',
+    ),
+    'longitude' => array(
+      'label' => 'Longitude',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'longitude',
+      'table' => 'nd_geolocation',
+      'field' => 'longitude',
+      'relationship' => 'none',
+    ),
+    'altitude' => array(
+      'label' => 'Altitude',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'altitude',
+      'table' => 'nd_geolocation',
+      'field' => 'altitude',
+      'relationship' => 'none',
+    ),
+    'geodetic_datum' => array(
+      'label' => 'Geodetic Datum',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'geodetic_datum',
+      'table' => 'nd_geolocation',
+      'field' => 'geodetic_datum',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'latitude' => array(
+      'operator' => 'between',
+      'value' => array(
+        'value' => '',
+        'min' => '',
+        'max' => '',
+      ),
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 1,
+        'operator' => 'latitude_op',
+        'identifier' => 'latitude',
+        'label' => 'Latitude',
+        'optional' => 0,
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'latitude',
+      'table' => 'nd_geolocation',
+      'field' => 'latitude',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'longitude' => array(
+      'operator' => 'between',
+      'value' => array(
+        'value' => '',
+        'min' => '',
+        'max' => '',
+      ),
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 1,
+        'operator' => 'longitude_op',
+        'identifier' => 'longitude',
+        'label' => 'Longitude',
+        'optional' => 0,
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'longitude',
+      'table' => 'nd_geolocation',
+      'field' => 'longitude',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'altitude' => array(
+      'operator' => 'between',
+      'value' => array(
+        'value' => '',
+        'min' => '',
+        'max' => '',
+      ),
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 1,
+        'operator' => 'altitude_op',
+        'identifier' => 'altitude',
+        'label' => 'Altitude',
+        'optional' => 0,
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'altitude',
+      'table' => 'nd_geolocation',
+      'field' => 'altitude',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'geodetic_datum' => array(
+      'operator' => '=',
+      'value' => array(),
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'geodetic_datum_op',
+        'identifier' => 'geodetic_datum',
+        'label' => 'Geodetic Datum',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'geodetic_datum',
+      'table' => 'nd_geolocation',
+      'field' => 'geodetic_datum',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+    ),
+    'description' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'description_op',
+        'identifier' => 'description',
+        'label' => 'Name Contains',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'description',
+      'table' => 'nd_geolocation',
+      'field' => 'description',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+      'values_form_type' => 'textfield',
+      'multiple' => 0,
+      'optional' => 0,
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Geographical Locations');
+  $handler->override_option('header', 'Use the following criteria to limit the locations listed. If you leave a any of the criteria blank then the locations will be not be filtered based on that field.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'No locations matched the current criteria.');
+  $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',
+    'summary' => '',
+    'columns' => array(
+      'description' => 'description',
+      'latitude' => 'latitude',
+      'longitude' => 'longitude',
+      'altitude' => 'altitude',
+      'geodetic_datum' => 'geodetic_datum',
+    ),
+    'info' => array(
+      'description' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'latitude' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'longitude' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'altitude' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'geodetic_datum' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+    ),
+    'default' => 'description',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'natdiv_geolocations');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Geographical Locations',
+    'description' => '',
+    'weight' => '0',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  $views[$view->name] = $view;
+
+  // List protocols
+  $view = new view;
+  $view->name = 'natdiv_protocol_listing';
+  $view->description = 'A listing of protocols used for natural diversity experiments';
+  $view->tag = 'chado default';
+  $view->base_table = 'nd_protocol';
+  $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(
+    'name' => array(
+      'label' => 'Name',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'name',
+      'table' => 'nd_protocol',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'name' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'name_op',
+        'identifier' => 'name',
+        'label' => 'Name Contains',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'name',
+      'table' => 'nd_protocol',
+      'field' => 'name',
+      '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 protocols matching the entered criteria. If you leave a any of the criteria blank then the protocols will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all protocols will be listed.',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Protocols');
+  $handler->override_option('header', 'Click "Show" to see a list of all protocols matching the entered criteria. If you leave a any of the criteria blank then the protocols will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all protocols will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'No protocols match the current criteria.');
+  $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',
+    'summary' => '',
+    'columns' => array(
+      'name' => 'name',
+    ),
+    'info' => array(
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+    ),
+    'default' => 'name',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'natdiv_protocols');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Natural Diversity Protocols',
+    'description' => 'The protcols used for natural diversity experiments',
+    'weight' => '0',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  $views[$view->name] = $view;
+
+  // List Reagents
+  $view = new view;
+  $view->name = 'natdiv_reagent_listing';
+  $view->description = 'A listing of reagents used in natural diversity experiments';
+  $view->tag = 'chado default';
+  $view->base_table = 'nd_reagent';
+  $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(
+    'name_1' => array(
+      'label' => 'Name',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'name_1',
+      'table' => 'nd_reagent',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'name' => array(
+      'label' => 'Type',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'name',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'residues' => array(
+      'label' => 'Sequence',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'residues',
+      'table' => 'feature',
+      'field' => 'residues',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    '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' => 'nd_reagent',
+      'field' => 'type_id',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+      '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 reagents matching the entered criteria. If you leave a any of the criteria blank then the reagents will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all reagents will be listed.',
+    ),
+    'name' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'name_op',
+        'identifier' => 'name',
+        'label' => 'Name Contains',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'name',
+      'table' => 'nd_reagent',
+      'field' => 'name',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Natural Diversity Protocol Reagents');
+  $handler->override_option('header', 'Click "Show" to see a list of all reagents matching the entered criteria. If you leave a any of the criteria blank then the reagents will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all reagents will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'No reagents match the current criteria.');
+  $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 = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'natdiv_reagents');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Natural Diversity Protocol Reagents',
+    'description' => 'Reagents used in natural diversity experiments',
+    'weight' => '0',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  $views[$view->name] = $view;
+
+  return $views;
+}
+

tripal_phenotype/tripal_phenotype.views.inc

@@ -67,3 +67,212 @@ function tripal_phenotype_views_handlers() {
   ),
   );
 }
+
+/**
+ *
+ * @ingroup tripal_feature_views
+ */
+function tripal_phenotype_views_default_views() {
+  $views = array();
+
+  // Main default view
+  $view = new view;
+  $view->name = 'phenotype_listing';
+  $view->description = 'A listing of chado phenotypes';
+  $view->tag = 'chado default';
+  $view->base_table = 'phenotype';
+  $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' => '',
+        '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'uniquename',
+      'table' => 'phenotype',
+      'field' => 'uniquename',
+      'relationship' => 'none',
+    ),
+    'value' => array(
+      'label' => 'Value',
+      '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,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'value',
+      'table' => 'phenotype',
+      'field' => 'value',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'uniquename' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'uniquename_op',
+        'identifier' => 'uniquename',
+        'label' => 'Unique Name Contains',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'uniquename',
+      'table' => 'phenotype',
+      'field' => 'uniquename',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'value' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'value_op',
+        'identifier' => 'phen_value',
+        'label' => 'Value Contains',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'value',
+      'table' => 'phenotype',
+      'field' => 'value',
+      '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 phenotypes matching the entered criteria. If you leave a any of the criteria blank then the phenotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all phenotypes will be listed.',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Phenotypes');
+  $handler->override_option('header', 'Click "Show" to see a list of all phenotypes matching the entered criteria. If you leave a any of the criteria blank then the phenotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all phenotypes will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'No phenotypes match the current criteria.');
+  $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',
+    'summary' => '',
+    'columns' => array(
+      'uniquename' => 'uniquename',
+      'value' => 'value',
+    ),
+    'info' => array(
+      'uniquename' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'value' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+    ),
+    'default' => 'uniquename',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'phenotypes');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Phenotypes',
+    'description' => '',
+    'weight' => '0',
+    'name' => 'primary-links',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  $views[$view->name] = $view;
+
+  return $views;
+}
+