Small fixes to genetic, library, natural diversity, phenotype, project and stock default views

tripal_genetic/tripal_genetic.views.inc

@@ -93,7 +93,7 @@ function tripal_genetic_views_default_views() {
   $view->base_table = 'genotype';
   $view->core = 6;
   $view->api_version = '2';
-  $view->disabled = TRUE; /* Edit this to true to make a default view disabled initially */
+  $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(
@@ -200,44 +200,44 @@ function tripal_genetic_views_default_views() {
     ),
   ));
   $handler->override_option('filters', array(
-    'description' => array(
+    'uniquename' => array(
       'operator' => 'contains',
       'value' => '',
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
         'use_operator' => 0,
-        'operator' => 'description_op',
-        'identifier' => 'description',
-        'label' => 'Description Contains',
+        'operator' => 'uniquename_op',
+        'identifier' => 'uniquename',
+        'label' => 'Unique Name Contains',
         'remember' => 0,
       ),
       'case' => 0,
-      'id' => 'description',
+      'id' => 'uniquename',
       'table' => 'genotype',
-      'field' => 'description',
+      'field' => 'uniquename',
       'relationship' => 'none',
       'agg' => array(
         'records_with' => 1,
         'aggregates_with' => 1,
       ),
     ),
-    'uniquename' => array(
+    'description' => array(
       'operator' => 'contains',
       'value' => '',
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
         'use_operator' => 0,
-        'operator' => 'uniquename_op',
-        'identifier' => 'uniquename',
-        'label' => 'Unique Name Contains',
+        'operator' => 'description_op',
+        'identifier' => 'description',
+        'label' => 'Description Contains',
         'remember' => 0,
       ),
       'case' => 0,
-      'id' => 'uniquename',
+      'id' => 'description',
       'table' => 'genotype',
-      'field' => 'uniquename',
+      'field' => 'description',
       'relationship' => 'none',
       'agg' => array(
         'records_with' => 1,

tripal_library/tripal_library.views.inc

@@ -305,10 +305,14 @@ function tripal_library_views_default_views() {
       'values_form_type' => 'select',
       'multiple' => 1,
       'optional' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
     ),
     'type_id' => array(
       'operator' => '=',
-      'value' => '',
+      'value' => array(),
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
@@ -332,22 +336,6 @@ function tripal_library_views_default_views() {
         '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(
     'type' => 'perm',

tripal_natural_diversity/tripal_natural_diversity.views.inc

@@ -233,8 +233,8 @@ function tripal_natural_diversity_views_default_views() {
       ),
     ),
     'description' => array(
-      'operator' => 'contains',
-      'value' => '',
+      'operator' => '=',
+      'value' => 'University of Saskatchewan',
       'group' => '0',
       'exposed' => TRUE,
       'expose' => array(
@@ -244,7 +244,7 @@ function tripal_natural_diversity_views_default_views() {
         'label' => 'Location Experiment Performed',
         'remember' => 0,
       ),
-      'case' => 0,
+      'case' => 1,
       'id' => 'description',
       'table' => 'nd_geolocation',
       'field' => 'description',
@@ -253,6 +253,9 @@ function tripal_natural_diversity_views_default_views() {
         'records_with' => 1,
         'aggregates_with' => 1,
       ),
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
     ),
     'search_results' => array(
       'operator' => '=',
@@ -510,8 +513,33 @@ function tripal_natural_diversity_views_default_views() {
     ),
   ));
   $handler->override_option('filters', array(
+    '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,
+    ),
     'latitude' => array(
-      'operator' => 'between',
+      'operator' => '=',
       'value' => array(
         'value' => '',
         'min' => '',
@@ -538,7 +566,7 @@ function tripal_natural_diversity_views_default_views() {
       ),
     ),
     'longitude' => array(
-      'operator' => 'between',
+      'operator' => '=',
       'value' => array(
         'value' => '',
         'min' => '',
@@ -565,7 +593,7 @@ function tripal_natural_diversity_views_default_views() {
       ),
     ),
     'altitude' => array(
-      'operator' => 'between',
+      'operator' => '=',
       'value' => array(
         'value' => '',
         'min' => '',
@@ -591,31 +619,6 @@ function tripal_natural_diversity_views_default_views() {
         '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' => '',
@@ -1037,7 +1040,7 @@ function tripal_natural_diversity_views_default_views() {
   $handler->override_option('cache', array(
     'type' => 'none',
   ));
-  $handler->override_option('title', 'Natural Diversity Protocol Reagents');
+  $handler->override_option('title', '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);

tripal_phenotype/tripal_phenotype.views.inc

@@ -30,6 +30,17 @@ function tripal_phenotype_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 'phenotype':
+            $table_integration_array['fields']['attr_id']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_cvterm';
+            $table_integration_array['fields']['assay_id']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_cvterm';
+            $table_integration_array['fields']['cvalue_id']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_cvterm';
+            $table_integration_array['fields']['observable_id']['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_cvterm';
+            break;
+        }
+
         tripal_views_integration_add_entry($table_integration_array);
       }
     }
@@ -85,6 +96,40 @@ function tripal_phenotype_views_default_views() {
   $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('relationships', array(
+    'assay_id' => array(
+      'label' => 'assay_id to cvterm',
+      'required' => 0,
+      'id' => 'assay_id',
+      'table' => 'phenotype',
+      'field' => 'assay_id',
+      'relationship' => 'none',
+    ),
+    'attr_id' => array(
+      'label' => 'attr_id to cvterm',
+      'required' => 0,
+      'id' => 'attr_id',
+      'table' => 'phenotype',
+      'field' => 'attr_id',
+      'relationship' => 'none',
+    ),
+    'cvalue_id' => array(
+      'label' => 'cvalue_id to cvterm',
+      'required' => 0,
+      'id' => 'cvalue_id',
+      'table' => 'phenotype',
+      'field' => 'cvalue_id',
+      'relationship' => 'none',
+    ),
+    'observable_id' => array(
+      'label' => 'observable_id to cvterm',
+      'required' => 0,
+      'id' => 'observable_id',
+      'table' => 'phenotype',
+      'field' => 'observable_id',
+      'relationship' => 'none',
+    ),
+  ));
   $handler->override_option('fields', array(
     'uniquename' => array(
       'label' => 'Unique Name',
@@ -120,6 +165,74 @@ function tripal_phenotype_views_default_views() {
       'field' => 'uniquename',
       'relationship' => 'none',
     ),
+    'name_1' => array(
+      'label' => 'Phenotypic Attribute',
+      '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' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'attr_id',
+    ),
+    'name_3' => array(
+      'label' => 'Controlled 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' => 'name_3',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'cvalue_id',
+    ),
     'value' => array(
       'label' => 'Value',
       'alter' => array(
@@ -154,8 +267,196 @@ function tripal_phenotype_views_default_views() {
       'field' => 'value',
       'relationship' => 'none',
     ),
+    'name_2' => array(
+      'label' => 'Observation 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_2',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'observable_id',
+    ),
+    'name' => array(
+      'label' => 'Evidence 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' => 'assay_id',
+    ),
   ));
   $handler->override_option('filters', 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 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.',
+    ),
+    'attr_id' => array(
+      'operator' => '=',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'attr_id_op',
+        'identifier' => 'attr_id',
+        'label' => 'Phenotypic Attribute',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'attr_id',
+      'table' => 'phenotype',
+      'field' => 'attr_id',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+    ),
+    'cvalue_id' => array(
+      'operator' => '=',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'cvalue_id_op',
+        'identifier' => 'cvalue_id',
+        'label' => 'Controlled Value',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'cvalue_id',
+      'table' => 'phenotype',
+      'field' => 'cvalue_id',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+    ),
+    'observable_id' => array(
+      'operator' => '=',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'observable_id_op',
+        'identifier' => 'observable_id',
+        'label' => 'Observation Type',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'observable_id',
+      'table' => 'phenotype',
+      'field' => 'observable_id',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+    ),
+    'assay_id' => array(
+      'operator' => '=',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'assay_id_op',
+        'identifier' => 'assay_id',
+        'label' => 'Evidence Type',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'assay_id',
+      'table' => 'phenotype',
+      'field' => 'assay_id',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+    ),
     'uniquename' => array(
       'operator' => 'contains',
       'value' => '',
@@ -200,22 +501,6 @@ function tripal_phenotype_views_default_views() {
         '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',

tripal_project/tripal_project.views.inc

@@ -81,7 +81,7 @@ function tripal_project_views_default_views() {
   $view->base_table = 'project';
   $view->core = 6;
   $view->api_version = '2';
-  $view->disabled = TRUE; /* Edit this to true to make a default view disabled initially */
+  $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(
@@ -153,6 +153,52 @@ function tripal_project_views_default_views() {
       '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' => 'project',
+      'field' => 'name',
+      'relationship' => 'none',
+      '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' => 'description',
+        'label' => 'Description Contains',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'description',
+      'table' => 'project',
+      'field' => 'description',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+  ));
   $handler->override_option('access', array(
     'type' => 'perm',
     'perm' => 'access chado_projects',

tripal_stock/tripal_stock.views.inc

@@ -422,6 +422,10 @@ function tripal_stock_views_default_views() {
       'values_form_type' => 'select',
       'multiple' => 1,
       'optional' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
     ),
     'search_results' => array(
       'operator' => '=',