Added Default Views for all modules

theme_tripal/tripal_feature/tripal_feature_genotypes.tpl.php

@@ -2,7 +2,6 @@
 <?php
 $feature = $variables['node']->feature;
 $genotypes = $variables['tripal_feature']['genotype_experiments'];
-dpm($feature, 'feature');
 ?>
 
 <?php if(count($genotypes) > 0){ ?>

tripal_analysis/tripal_analysis.views.inc

@@ -60,3 +60,446 @@ function chado_analysis_views_views_handlers() {
   );
 }
 
+function tripal_analysis_views_default_views () {
+  $views = array();
+  
+  // Main default view
+  // List all cvterms based on cv
+  $view = new view;
+  $view->name = 'all_analysis';
+  $view->description = 'A listing of all analysis\'';
+  $view->tag = 'chado';
+  $view->view_php = '';
+  $view->base_table = 'analysis';
+  $view->is_cacheable = FALSE;
+  $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' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'name',
+      'table' => 'analysis',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'algorithm' => array(
+      'label' => 'Algorithm',
+      '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' => 'algorithm',
+      'table' => 'analysis',
+      'field' => 'algorithm',
+      'relationship' => 'none',
+    ),
+    'program' => array(
+      'label' => 'Program',
+      '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' => 'program',
+      'table' => 'analysis',
+      'field' => 'program',
+      'relationship' => 'none',
+    ),
+    'programversion' => array(
+      'label' => 'Program Version',
+      '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' => 'programversion',
+      'table' => 'analysis',
+      'field' => 'programversion',
+      'relationship' => 'none',
+    ),
+    'description' => array(
+      'label' => 'Description',
+      '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' => 'description',
+      'table' => 'analysis',
+      'field' => 'description',
+      'relationship' => 'none',
+    ),
+    'sourcename' => array(
+      'label' => 'Source Name',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'exclude' => 0,
+      'id' => 'sourcename',
+      'table' => 'analysis',
+      'field' => 'sourcename',
+      'relationship' => 'none',
+    ),
+    'sourceuri' => array(
+      'label' => 'Source URL',
+      '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' => 'sourceuri',
+      'table' => 'analysis',
+      'field' => 'sourceuri',
+      'relationship' => 'none',
+    ),
+    'sourceversion' => array(
+      'label' => 'Source Version',
+      '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' => 'sourceversion',
+      'table' => 'analysis',
+      'field' => 'sourceversion',
+      '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',
+      'table' => 'analysis',
+      'field' => 'num_features',
+      'relationship' => 'none',
+    ),
+    'timeexecuted' => array(
+      'label' => 'Time Executed',
+      '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,
+      'date_format' => 'large',
+      'custom_date_format' => '',
+      'exclude' => 0,
+      'id' => 'timeexecuted',
+      'table' => 'analysis',
+      'field' => 'timeexecuted',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'program' => array(
+      'operator' => '=',
+      'value' => 'All',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'program_op',
+        'identifier' => 'program',
+        'label' => 'Program',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'program',
+      'table' => 'analysis',
+      'field' => 'program',
+      'relationship' => 'none',
+    ),
+    'sourcename' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'sourcename_op',
+        'identifier' => 'sourcename',
+        'label' => 'Source Name Contains',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'sourcename',
+      'table' => 'analysis',
+      'field' => 'sourcename',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_analysis content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Analysis');
+  $handler->override_option('empty', 'No analysis match the supplied criteria.');
+  $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(
+    'grouping' => '',
+    'override' => 1,
+    'sticky' => 0,
+    'order' => 'asc',
+    'columns' => array(
+      'algorithm' => 'algorithm',
+      'description' => 'description',
+      'name' => 'name',
+      'num_features' => 'num_features',
+      'program' => 'program',
+      'programversion' => 'programversion',
+      'sourcename' => 'sourcename',
+      'sourceuri' => 'sourceuri',
+      'sourceversion' => 'sourceversion',
+      'timeexecuted' => 'timeexecuted',
+    ),
+    'info' => array(
+      'algorithm' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'description' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'num_features' => array(
+        'separator' => '',
+      ),
+      'program' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'programversion' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'sourcename' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'sourceuri' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'sourceversion' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'timeexecuted' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+    ),
+    'default' => 'timeexecuted',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'analyses');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Analyses',
+    '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;
+}

tripal_core/views/handlers/views_handler_field_dbxref_accession_link.inc

@@ -23,7 +23,7 @@ class views_handler_field_dbxref_accession_link extends views_handler_field {
    $accession = $values->{$this->aliases['accession']}; 
    $db_id = $values->{$this->aliases['db_id']};
 
-   if (!empty($db_id)) {
+   if (!empty($db_id) AND !empty($accession)) {
      $previous_db = tripal_db_set_active('chado');
      $result = db_fetch_object(db_query('SELECT urlprefix FROM db WHERE db_id=%d', $db_id));
      tripal_db_set_active($previous_db);   

tripal_core/views/handlers/views_handler_field_node_optional.inc

@@ -57,8 +57,10 @@ class views_handler_field_node_optional extends views_handler_field_node {
 
       if ($this->query->table_queue['node']['join']) {
         $drupal_node_table_join['join'] = clone($this->query->table_queue['node']['join']);
-      } else {
+      } elseif ($this->query->table_queue[$drupal_chado_table_name]['join']) {
         $drupal_node_table_join['join'] = clone($this->query->table_queue[$drupal_chado_table_name]['join']);
+      } else {
+        
       }
       $drupal_node_table_join['join']->table = 'node';
       $drupal_node_table_join['join']->field = 'nid';
@@ -83,7 +85,6 @@ class views_handler_field_node_optional extends views_handler_field_node {
     } else {
       $this->aliases['nid'] = 'node_nid';
     }
-
   }
 
   /**

tripal_cv/tripal_cv.views.inc

@@ -53,4 +53,300 @@ function tripal_cv_views_handlers() {
      ),
    ),
  );
+}
+
+function tripal_genetic_views_default_views () {
+  $views = array();
+  
+  // Main default view
+  // List all cvterms based on cv
+  $view = new view;
+  $view->name = 'all_cvterms';
+  $view->description = 'A listing of all controlled vocabulary terms filtered by controlled vocabulary';
+  $view->tag = 'chado';
+  $view->view_php = '';
+  $view->base_table = 'cvterm';
+  $view->is_cacheable = FALSE;
+  $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' => '',
+        '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' => 'name',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'definition' => array(
+      'label' => 'Definition',
+      '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' => 'definition',
+      'table' => 'cvterm',
+      'field' => 'definition',
+      'relationship' => 'none',
+    ),
+    'is_obsolete' => array(
+      'label' => 'Is Obsolete',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'type' => 'yes-no',
+      'not' => 0,
+      'exclude' => 0,
+      'id' => 'is_obsolete',
+      'table' => 'cvterm',
+      'field' => 'is_obsolete',
+      'relationship' => 'none',
+    ),
+    'is_relationshiptype' => array(
+      'label' => 'Is Relationship',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'type' => 'yes-no',
+      'not' => 0,
+      'exclude' => 0,
+      'id' => 'is_relationshiptype',
+      'table' => 'cvterm',
+      'field' => 'is_relationshiptype',
+      'relationship' => 'none',
+    ),
+    'accession_link' => array(
+      'label' => 'Accession Link',
+      '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' => 'accession_link',
+      'table' => 'dbxref',
+      'field' => 'accession_link',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'name' => array(
+      'operator' => '=',
+      'value' => '<select cv>',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'name_op',
+        'identifier' => 'cv',
+        'label' => 'Vocabulary',
+        'optional' => 0,
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'name',
+      'table' => 'cv',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'name_1' => array(
+      'operator' => '~',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => '',
+        'identifier' => 'name',
+        'label' => 'Name Contains',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'name_1',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+      'values_form_type' => 'textfield',
+    ),
+    'definition' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'definition_op',
+        'identifier' => 'definition',
+        'label' => 'Definition Contains',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'definition',
+      'table' => 'cvterm',
+      'field' => 'definition',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_cv content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Controlled Vocabulary Terms');
+  $handler->override_option('empty', 'There are no terms associated with the selected controlled vocabulary. Please select a different vocabulary from the list above.');
+  $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(
+    'grouping' => '',
+    'override' => 1,
+    'sticky' => 0,
+    'order' => 'asc',
+    'columns' => array(
+      'definition' => 'definition',
+      'is_obsolete' => 'is_obsolete',
+      'is_relationshiptype' => 'is_relationshiptype',
+      'name' => 'name',
+      'accession_link' => 'accession_link',
+    ),
+    'info' => array(
+      'definition' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'is_obsolete' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'is_relationshiptype' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'accession_link' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'admin/tripal/tripal_cv/list_cvterms');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Term Listing',
+    'description' => 'A listing of a controlled vocabulary terms for a given vocabulary',
+    '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_db/tripal_db.views.inc

@@ -50,3 +50,270 @@ function tripal_db_views_handlers() {
  );
 }
 
+function tripal_db_views_default_views () {
+  $views = array();
+  
+  // Main default view
+  // List all cvterms based on cv
+  $view = new view;
+  $view = new view;
+  $view->name = 'all_dbxrefs';
+  $view->description = 'A listing of all database references filtered by database';
+  $view->tag = 'chado';
+  $view->view_php = '';
+  $view->base_table = 'dbxref';
+  $view->is_cacheable = FALSE;
+  $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' => 'Database',
+      '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' => 'name',
+      'table' => 'db',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'accession' => array(
+      'label' => 'Accession',
+      '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' => 'accession',
+      'table' => 'dbxref',
+      'field' => 'accession',
+      'relationship' => 'none',
+    ),
+    'description' => array(
+      'label' => 'Description',
+      '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' => 'description',
+      'table' => 'dbxref',
+      'field' => 'description',
+      'relationship' => 'none',
+    ),
+    'version' => array(
+      'label' => 'Version',
+      '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' => 'version',
+      'table' => 'dbxref',
+      'field' => 'version',
+      'relationship' => 'none',
+    ),
+    'accession_link' => array(
+      'label' => 'External Link',
+      'alter' => array(
+        'alter_text' => 1,
+        'text' => 'link',
+        'make_link' => 1,
+        'path' => '[accession_link]',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 1,
+      'empty_zero' => 0,
+      'exclude' => 0,
+      'id' => 'accession_link',
+      'table' => 'dbxref',
+      'field' => 'accession_link',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'name' => array(
+      'operator' => '=',
+      'value' => '<select db>',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'name_op',
+        'identifier' => 'db',
+        'label' => 'Database',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'name',
+      'table' => 'db',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'accession' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'accession_op',
+        'identifier' => 'accession',
+        'label' => 'Accession Contains',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'accession',
+      'table' => 'dbxref',
+      'field' => 'accession',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_db content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Database References');
+  $handler->override_option('empty', 'There are no database references matching the above criteria. Please select a database in order to display all references to that database.');
+  $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(
+    'grouping' => '',
+    'override' => 1,
+    'sticky' => 0,
+    'order' => 'asc',
+    'columns' => array(
+      'name' => 'name',
+      'accession' => 'accession',
+      'description' => 'description',
+      'version' => 'version',
+    ),
+    'info' => array(
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'accession' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'description' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'version' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'admin/tripal/tripal_db/list_dbxrefs');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'DB Reference Listing',
+    'description' => 'A listing of all database references associated with a given database',
+    '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_feature/tripal_feature.views.inc

@@ -66,3 +66,338 @@ function tripal_feature_views_handlers() {
  );
 }
 
+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->base_table = 'feature';
+  $view->is_cacheable = FALSE;
+  $view->api_version = 2;
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+  $handler = $view->new_display('default', 'Defaults', 'default');
+  $handler->override_option('fields', array(
+    'uniquename' => array(
+      'label' => 'Unique Name',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'uniquename',
+      'table' => 'feature',
+      'field' => 'uniquename',
+      'relationship' => 'none',
+    ),
+    'name' => array(
+      'label' => 'Name',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'name',
+      'table' => 'feature',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'common_name' => array(
+      'label' => 'Organism',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
+      'relationship' => 'none',
+    ),
+    'name_3' => array(
+      'label' => 'Type',
+      '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' => 'name_3',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'accession_link' => array(
+      'label' => 'External Reference',
+      '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' => 'accession_link',
+      'table' => 'dbxref',
+      'field' => 'accession_link',
+      'relationship' => 'none',
+    ),
+    'name_1' => array(
+      'label' => 'Library',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'name_1',
+      'table' => 'library',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'name_2' => array(
+      'label' => 'Analysis',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'name_2',
+      'table' => 'analysis',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'common_name' => array(
+      'operator' => '=',
+      'value' => '<select organism>',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'common_name_op',
+        'identifier' => 'organism',
+        'label' => 'Organism',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
+      'relationship' => 'none',
+    ),
+    'name' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'name_op',
+        'identifier' => 'name',
+        'label' => 'Name Contains',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'name',
+      'table' => 'feature',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'name_1' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'name_1_op',
+        'identifier' => 'library',
+        'label' => 'Library Name Contains',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'name_1',
+      'table' => 'library',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'name_2' => array(
+      'operator' => 'contains',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'name_2_op',
+        'identifier' => 'analysis',
+        'label' => 'Analysis Name Contains',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'name_2',
+      'table' => 'analysis',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_feature content',
+  ));
+  $handler->override_option('cache', array(
+    '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('items_per_page', 50);
+  $handler->override_option('style_plugin', 'table');
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'features');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Sequence Features',
+    '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;
+}

tripal_library/tripal_library.views.inc

@@ -26,6 +26,7 @@ function tripal_library_views_data()  {
   $data = array();
   
   $data = array_merge($data, retrieve_library_views_data());
+  $data = array_merge($data, retrieve_chado_library_views_data());
   $data = array_merge($data, retrieve_library_misc_tables_views_data());
   
   return $data;
@@ -57,3 +58,302 @@ function tripal_library_views_handlers() {
  );
 }
 
+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->description = 'A listing of all libraries';
+  $view->tag = 'chado';
+  $view->view_php = '';
+  $view->base_table = 'library';
+  $view->is_cacheable = FALSE;
+  $view->api_version = 2;
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+  $handler = $view->new_display('default', 'Defaults', 'default');
+  $handler->override_option('fields', array(
+    'uniquename' => array(
+      'label' => 'Unique Name',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'uniquename',
+      'table' => 'library',
+      'field' => 'uniquename',
+      'relationship' => 'none',
+    ),
+    'name_1' => array(
+      'label' => 'Name',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'name_1',
+      'table' => 'library',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'common_name' => array(
+      'label' => 'Organism',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
+      'relationship' => 'none',
+    ),
+    'name' => array(
+      'label' => 'Type',
+      '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' => 'name',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'is_obsolete' => array(
+      'label' => 'Is Obsolete?',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'type' => 'yes-no',
+      'not' => 0,
+      'exclude' => 0,
+      'id' => 'is_obsolete',
+      'table' => 'library',
+      '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',
+      'table' => 'library',
+      'field' => 'num_features',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'common_name' => array(
+      'operator' => '=',
+      'value' => 'All',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'common_name_op',
+        'identifier' => 'organism_common_name',
+        'label' => 'Organism',
+        'optional' => 1,
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_library content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Libraries');
+  $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('use_pager', '1');
+  $handler->override_option('style_plugin', 'table');
+  $handler->override_option('style_options', array(
+    'grouping' => '',
+    'override' => 1,
+    'sticky' => 0,
+    'order' => 'asc',
+    'columns' => array(
+      'name' => 'name',
+      'timeaccessioned' => 'timeaccessioned',
+      'timelastmodified' => 'timelastmodified',
+      'is_obsolete' => 'is_obsolete',
+      'name_1' => 'name_1',
+      'uniquename' => 'uniquename',
+      'common_name' => 'common_name',
+      'num_libraries' => 'num_libraries',
+    ),
+    'info' => array(
+      'name' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'timeaccessioned' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'timelastmodified' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'is_obsolete' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'name_1' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'uniquename' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'common_name' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'num_libraries' => array(
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'libraries');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Sequence Libraries',
+    '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;
+}

tripal_organism/tripal_organism.views.inc

@@ -52,3 +52,289 @@ function tripal_organism_views_handlers() {
    ),
  );
 }
+
+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->description = 'A listing of all organism in chado';
+  $view->tag = 'chado';
+  $view->view_php = '';
+  $view->base_table = 'organism';
+  $view->is_cacheable = FALSE;
+  $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(
+    'common_name' => array(
+      'label' => 'Common Name',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'link_class' => '',
+        'alt' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        'help' => '',
+        'trim' => 0,
+        'max_length' => '',
+        'word_boundary' => 1,
+        'ellipsis' => 1,
+        'html' => 0,
+        'strip_tags' => 0,
+      ),
+      'empty' => '',
+      'hide_empty' => 0,
+      'empty_zero' => 0,
+      'link_to_node' => 1,
+      'exclude' => 0,
+      'id' => 'common_name',
+      'table' => 'organism',
+      '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(
+        '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' => 'genus',
+      'table' => 'organism',
+      'field' => 'genus',
+      'relationship' => 'none',
+    ),
+    'species' => array(
+      'label' => 'Species',
+      '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' => 'species',
+      'table' => 'organism',
+      'field' => 'species',
+      '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',
+      'table' => 'organism',
+      'field' => 'num_features',
+      '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',
+      'table' => 'organism',
+      'field' => 'num_stocks',
+      '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',
+      'table' => 'organism',
+      'field' => 'num_libraries',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_organism content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Organisms');
+  $handler->override_option('empty', 'No organism currently in your chado database.');
+  $handler->override_option('empty_format', '1');
+  $handler->override_option('items_per_page', 0);
+  $handler->override_option('style_plugin', 'table');
+  $handler->override_option('style_options', array(
+    'grouping' => '',
+    'override' => 1,
+    'sticky' => 0,
+    'order' => 'asc',
+    'columns' => array(
+      'abbreviation' => 'abbreviation',
+      'common_name' => 'common_name',
+      'genus' => 'genus',
+      'species' => 'species',
+    ),
+    'info' => array(
+      'abbreviation' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'common_name' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'genus' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+      'species' => array(
+        'sortable' => 0,
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'organisms');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Organisms',
+    '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;
+}