Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x

tripal_analysis/includes/tripal_analysis.admin.inc

@@ -5,6 +5,38 @@
  * Contains functions displaying administrative pages and forms
  */
 
+/**
+ *
+ */
+function tripal_analysis_admin_analysis_view() {
+  $output = '';
+
+  // set the breadcrumb
+  $breadcrumb = array();
+  $breadcrumb[] = l('Home', '<front>');
+  $breadcrumb[] = l('Administration', 'admin');
+  $breadcrumb[] = l('Tripal', 'admin/tripal');
+  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
+  $breadcrumb[] = l('Analysis', 'admin/tripal/chado/tripal_analysis');
+  drupal_set_breadcrumb($breadcrumb);
+
+  // Add the view
+  $view = views_embed_view('tripal_analysis_admin_analyses','default');
+  if (isset($view)) {
+    $output .= $view;
+  }
+  else {
+    $output .= '<p>The Analysis module uses primarily views to provide an '
+      . 'administrative interface. Currently one or more views needed for this '
+      . 'administrative interface are disabled. <strong>Click each of the following links to '
+      . 'enable the pertinent views</strong>:</p>';
+    $output .= '<ul>';
+      $output .= '<li>'.l('Analysis View', 'admin/tripal/chado/tripal_analysis/views/analyses/enable').'</li>';
+    $output .= '</ul>';
+  }
+
+  return $output;
+}
 
 /**
  * Administration page callbacks for the Tripal Analysis module
@@ -53,7 +85,7 @@ function tripal_analysis_admin() {
     }
     $counter++;
   }
-  
+
   if($counter == 0) {
     $form['nothing'] = array(
       '#markup' => t('There are currently no settings to configure. However, analysis extension modules may add items here when they are installed.')

tripal_analysis/tripal_analysis.info

@@ -7,5 +7,6 @@ version = 7.x-2.0-beta1
 configure = admin/tripal/chado/tripal_analysis/configuration
 
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_db
 dependencies[] = tripal_cv

tripal_analysis/tripal_analysis.install

@@ -5,7 +5,21 @@
  */
 
 /**
- * Implementation of hook_requirements(). 
+ * Disable default views when module is disabled
+ */
+function tripal_analysis_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_analysis.views_default.inc");
+  $views = tripal_analysis_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
+/**
+ * Implementation of hook_requirements().
  */
 function tripal_analysis_requirements($phase) {
   $requirements = array();
@@ -32,10 +46,10 @@ function tripal_analysis_install() {
 
   // we may need the analysisfeatureprop table if it doesn't already exist
   tripal_analysis_create_analysisfeatureprop();
-  
+
   // add cvterms
   tripal_analysis_add_cvterms();
-  
+
   // add materialized views
   tripal_analysis_add_mview_analysis_organism();
 }
@@ -57,52 +71,52 @@ function tripal_analysis_uninstall() {
   }
 }
 /*
- * 
+ *
  */
 function tripal_analysis_create_analysisfeatureprop() {
-  
-  // Create analysisfeatureprop table in chado.  This is needed for Chado 
-  // version 1.11, the table exists in Chado 1.2. 
+
+  // Create analysisfeatureprop table in chado.  This is needed for Chado
+  // version 1.11, the table exists in Chado 1.2.
   if (!db_table_exists('chado.analysisfeatureprop')) {
     $sql = "
       CREATE TABLE chado.analysisfeatureprop (
-        analysisfeatureprop_id SERIAL PRIMARY KEY, 
-        analysisfeature_id     INTEGER NOT NULL REFERENCES chado.analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, 
-        type_id                INTEGER NOT NULL REFERENCES chdo.cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, 
-        value                  TEXT, 
-        rank                   INTEGER NOT NULL, 
+        analysisfeatureprop_id SERIAL PRIMARY KEY,
+        analysisfeature_id     INTEGER NOT NULL REFERENCES chado.analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
+        type_id                INTEGER NOT NULL REFERENCES chdo.cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
+        value                  TEXT,
+        rank                   INTEGER NOT NULL,
         CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank)
       )
     ";
     chado_query($sql);
-  } 
+  }
 }
 /*
- * 
+ *
  */
 function tripal_analysis_add_cvterms() {
-  
+
   tripal_cv_add_cv('tripal_analysis', 'Terms used for managing analyses in Tripal');
 
   // add analysis_date.  This is no longer used (as far as we can tell) but we don't
   // get rid of it in case it is used, so just keep it in the Tripal CV
   $term = array(
-    'name' => 'analysis_date', 
+    'name' => 'analysis_date',
     'def' => 'The date that an analysis was performed.'
   );
   tripal_cv_add_cvterm($term, 'tripal', 0, 1, 'tripal');
-  
+
   // add analysis_short_name.  This is no longer used (as far as we can tell) but we don't
   // get rid of it in case it is used, so just keep it in the Tripal CV
   $term = array(
-    'name' => 'analysis_short_name', 
+    'name' => 'analysis_short_name',
     'def' => 'A computer legible (no spaces or special characters) abbreviation for the analysis.'
-  );     
-  tripal_cv_add_cvterm($term, 'tripal', 0, 1 , 'tripal');     
-  
-  
+  );
+  tripal_cv_add_cvterm($term, 'tripal', 0, 1 , 'tripal');
+
+
   // the 'analysis_property' vocabulary is for user definable properties.
-  tripal_cv_add_cvterm(array('name' => 'Analysis Type', 'def' => 'The type of analysis that was performed.'), 
+  tripal_cv_add_cvterm(array('name' => 'Analysis Type', 'def' => 'The type of analysis that was performed.'),
      'analysis_property', 0, 1, 'tripal');
 }
 
@@ -116,7 +130,7 @@ function tripal_analysis_add_cvterms() {
  *     with this module.
  */
 function tripal_analysis_schema() {
-  
+
   // chado_analysis table
   $schema['chado_analysis'] = array(
     'fields' => array(
@@ -168,13 +182,13 @@ function tripal_analysis_schema() {
 }
 
 /*
- * 
+ *
  * @ingroup tripal_network
  */
 function tripal_analysis_add_mview_analysis_organism() {
   $view_name = 'analysis_organism';
   $comment = t('This view is for associating an organism (via it\'s associated features) to an analysis.');
-  
+
   // this is the SQL used to identify the organism to which an analsysis
   // has been used.  This is obtained though the analysisfeature -> feature -> organism
   // joins
@@ -185,12 +199,12 @@ function tripal_analysis_add_mview_analysis_organism() {
       INNER JOIN feature F          ON AF.feature_id = F.feature_id
       INNER JOIN organism O         ON O.organism_id = F.organism_id
   ";
-  
+
   // the schema array for describing this view
   $schema = array(
     'table' => $view_name,
     'description' => $comment,
-    'fields' => array(  
+    'fields' => array(
       'analysis_id' => array(
         'type' => 'int',
         'not null' => TRUE,
@@ -198,7 +212,7 @@ function tripal_analysis_add_mview_analysis_organism() {
       'organism_id' => array(
         'type' => 'int',
         'not null' => TRUE,
-      ),       
+      ),
     ),
     'indexes' => array(
       'networkmod_qtl_indx0' => array('analysis_id'),
@@ -216,10 +230,10 @@ function tripal_analysis_add_mview_analysis_organism() {
         'columns' => array(
           'organism_id' => 'organism_id',
         ),
-      ),      
+      ),
     ),
   );
-  
+
   // add the view
   tripal_add_mview($view_name, 'tripal_analysis', $schema, $sql, $comment);
 }

tripal_analysis/tripal_analysis.module

@@ -56,11 +56,12 @@ function tripal_analysis_node_info() {
  * @ingroup tripal_analysis
  */
 function tripal_analysis_menu() {
-  
+
   // Tripal Analysis administrative settings
   $items['admin/tripal/chado/tripal_analysis'] = array(
     'title' => 'Analyses',
     'description' => 'A bioinformatics analysis producing features.',
+    'page callback' => 'tripal_analysis_admin_analysis_view',
     'access arguments' => array('administer tripal analyses'),
     'type' => MENU_NORMAL_ITEM,
   );
@@ -71,25 +72,28 @@ function tripal_analysis_menu() {
     'page callback' => 'theme',
     'page arguments' => array('tripal_analysis_help'),
     'access arguments' => array('administer tripal analyses'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 10,
   );
 
   $items['admin/tripal/chado/tripal_analysis/configuration'] = array(
-    'title' => 'Configuration',
+    'title' => 'Settings',
     'description' => 'Settings for the displays of analysis results.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_analysis_admin'),
     'access arguments' => array('administer tripal analyses'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 5
   );
-  
+
   $items['admin/tripal/chado/tripal_analysis/sync'] = array(
-    'title' => 'Sync Analyses',
+    'title' => 'Sync',
     'description' => 'Sync Chado analyses with Drupal.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_analysis_sync_form'),
     'access arguments' => array('administer tripal analyses'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 0
   );
 
   return $items;
@@ -177,7 +181,7 @@ function tripal_analysis_theme($existing, $type, $theme, $path) {
     'chado_analysis_form' => array(
       'render element' => 'form',
     )
-    
+
   );
 
   return $items;
@@ -284,19 +288,19 @@ function chado_analysis_insert($node) {
   $node->sourcename = trim($node->sourcename);
   $node->sourceversion = trim($node->sourceversion);
   $node->sourceuri = trim($node->sourceuri);
-  
+
   // if there is an analysis_id in the $node object then this must be a sync so
   // we can skip adding the analysis as it is already there, although
   // we do need to proceed with the rest of the insert
   if (!property_exists($node,'analysis_id')) {
-    
+
     // Create a timestamp so we can insert it into the chado database
     $time  = $node->timeexecuted;
     $month = $time['month'];
     $day   = $time['day'];
     $year  = $time['year'];
     $timestamp = $month . '/' . $day . '/' . $year;
-    
+
     // insert and then get the newly inserted analysis record
     $values = array(
       'name'           => $node->analysisname,
@@ -321,10 +325,10 @@ function chado_analysis_insert($node) {
   else {
     $analysis_id = $node->analysis_id;
   }
-  
+
   // Make sure the entry for this analysis doesn't already exist in the
   // chado_analysis table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('analysis', $node->nid);  
+  $check_org_id = chado_get_id_for_node('analysis', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -435,7 +439,7 @@ function chado_analysis_update($node) {
   $node->sourcename = trim($node->sourcename);
   $node->sourceversion = trim($node->sourceversion);
   $node->sourceuri = trim($node->sourceuri);
-    
+
   if ($node->revision) {
     // TODO -- decide what to do about revisions
   }
@@ -586,7 +590,7 @@ function chado_analysis_load($nodes) {
     // build the analysis variable
     $values = array('analysis_id' => $analysis_id);
     $analysis = tripal_core_generate_chado_var('analysis', $values);
-    
+
 
     // add in the description field
     $analysis = tripal_core_expand_chado_vars($analysis, 'field', 'analysis.description');

tripal_analysis/tripal_analysis.views.inc

@@ -14,424 +14,3 @@
  * @defgroup tripal_analysis_views Analysis Views Integration
  * @ingroup views
  */
-
-/**
- * Implements hook_views_default_views().
- *
- * @ingroup tripal_analysis_views
- */
-function tripal_analysis_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // Main default view
-  $view = new view;
-  $view->name = 'analysis_listing';
-  $view->description = 'A default listing of analyses provided by Tripal';
-  $view->tag = 'chado default';
-  $view->base_table = 'analysis';
-  $view->core = 0;
-  $view->api_version = '2';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->override_option('fields', array(
-    '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,
-      'link_to_node' => 1,
-      'id' => 'name',
-      'table' => 'analysis',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'program' => array(
-      'label' => 'Program',
-      '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,
-      'exclude' => 0,
-      'id' => 'program',
-      'table' => 'analysis',
-      'field' => 'program',
-      'relationship' => 'none',
-    ),
-    'sourcename' => array(
-      'label' => 'Source',
-      '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,
-      'exclude' => 0,
-      'id' => 'sourcename',
-      'table' => 'analysis',
-      'field' => 'sourcename',
-      'relationship' => 'none',
-    ),
-    'timeexecuted' => array(
-      'label' => 'Time Executed',
-      '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,
-      'date_format' => 'custom',
-      'custom_date_format' => 'F j, Y',
-      'exclude' => 0,
-      'id' => 'timeexecuted',
-      'table' => 'analysis',
-      'field' => 'timeexecuted',
-      'override' => array(
-        'button' => 'Override',
-      ),
-      'relationship' => 'none',
-    ),
-  ));
-  $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 analysis matching the entered criteria. If you leave a any of the criteria blank then the analysis will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all analysis will be listed.',
-    ),
-    'program' => array(
-      'operator' => '=',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'program_op',
-        'identifier' => 'program',
-        'label' => 'Program',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'program',
-      'table' => 'analysis',
-      'field' => 'program',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 0,
-      ),
-    ),
-    'timeexecuted' => array(
-      'operator' => '>',
-      'value' => array(
-        'type' => 'date',
-        'value' => '',
-        'min' => '',
-        'max' => '',
-      ),
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 1,
-        'operator' => 'timeexecuted_op',
-        'identifier' => 'timeexecuted',
-        'label' => 'Time Executed',
-        'optional' => 1,
-        'remember' => 0,
-      ),
-      'id' => 'timeexecuted',
-      'table' => 'analysis',
-      'field' => 'timeexecuted',
-      'relationship' => 'none',
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 0,
-      ),
-    ),
-    'name' => array(
-      'operator' => '~',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'name_op',
-        'identifier' => 'name',
-        'label' => 'Name Contains',
-        'bef_filter_description' => '',
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'name',
-      'table' => 'analysis',
-      'field' => 'name',
-      'relationship' => 'none',
-      'values_form_type' => 'textfield',
-      'multiple' => 0,
-      'optional' => 0,
-    ),
-    'sourcename' => array(
-      'operator' => '~',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'sourcename_op',
-        'identifier' => 'sourcename',
-        'label' => 'Source Contains',
-        'bef_filter_description' => '',
-        '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('header', 'Click "Show" to see a list of all analysis matching the entered criteria. If you leave a any of the criteria blank then the analysis will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all analysis will be listed.');
-  $handler->override_option('header_format', '2');
-  $handler->override_option('header_empty', 1);
-  $handler->override_option('empty', 'No analyses 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',
-    'summary' => '',
-    'columns' => array(
-      'name' => 'name',
-      'program' => 'program',
-      'sourcename' => 'sourcename',
-      'num_features' => 'num_features',
-      'timeexecuted' => 'timeexecuted',
-    ),
-    'info' => array(
-      'name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'program' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'sourcename' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'num_features' => array(
-        'separator' => '',
-      ),
-      'timeexecuted' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-    ),
-    'default' => 'name',
-  ));
-  // this is needed so that fields/filters can be added to the default display later
-  $default_handler = $handler;
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/analyses');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Analyses',
-    'description' => 'An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        '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,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Adds analysis => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Analysis to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_analysis',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Change analysis.name to have a link to the node
-    $fields['name']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // Only show records with published nodes
-    /**
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-    */
-  }
-  $views[$view->name] = $view;
-
-  return $views;
-}

tripal_analysis/tripal_analysis.views_default.inc

@@ -0,0 +1,195 @@
+<?php
+
+/**
+ * Implements hook_views_default_views().
+ *
+ * @ingroup tripal_analysis_views
+ */
+function tripal_analysis_views_default_views() {
+  $views = array();
+
+  $view = tripal_analysis_defaultvalue_admin_analysis();
+  $views[$view->name] = $view;
+
+  return $views;
+}
+
+function tripal_analysis_defaultvalue_admin_analysis() {
+
+  $view = new view();
+  $view->name = 'tripal_analysis_admin_analyses';
+  $view->description = 'DO NOT DISABLE';
+  $view->tag = 'tripal admin';
+  $view->base_table = 'analysis';
+  $view->human_name = 'Analysis Admin';
+  $view->core = 0;
+  $view->api_version = '3.0';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+
+  /* Display: Defaults */
+  $handler = $view->new_display('default', 'Defaults', 'default');
+  $handler->display->display_options['title'] = 'Analysis';
+  $handler->display->display_options['use_more_always'] = FALSE;
+  $handler->display->display_options['access']['type'] = 'perm';
+  $handler->display->display_options['access']['perm'] = 'access chado_analysis content';
+  $handler->display->display_options['cache']['type'] = 'none';
+  $handler->display->display_options['query']['type'] = 'views_query';
+  $handler->display->display_options['exposed_form']['type'] = 'basic';
+  $handler->display->display_options['pager']['type'] = 'full';
+  $handler->display->display_options['pager']['options']['items_per_page'] = '25';
+  $handler->display->display_options['pager']['options']['offset'] = '0';
+  $handler->display->display_options['pager']['options']['id'] = '0';
+  $handler->display->display_options['pager']['options']['quantity'] = '9';
+  $handler->display->display_options['style_plugin'] = 'table';
+  $handler->display->display_options['style_options']['grouping'] = '';
+  $handler->display->display_options['style_options']['columns'] = array(
+    'name' => 'name',
+    'program' => 'program',
+    'sourcename' => 'sourcename',
+    'num_features' => 'num_features',
+    'timeexecuted' => 'timeexecuted',
+  );
+  $handler->display->display_options['style_options']['default'] = 'name';
+  $handler->display->display_options['style_options']['info'] = array(
+    'name' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'program' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'sourcename' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'num_features' => array(
+      'separator' => '',
+    ),
+    'timeexecuted' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+  );
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Analysis',
+    'path-1' => 'node/add/tripal-analysis',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-2'] = array(
+    'label-2' => '',
+    'path-2' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-3'] = array(
+    'label-3' => '',
+    'path-3' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-4'] = array(
+    'label-4' => '',
+    'path-4' => '',
+  );
+  /* No results behavior: Global: Text area */
+  $handler->display->display_options['empty']['text']['id'] = 'text';
+  $handler->display->display_options['empty']['text']['table'] = 'views';
+  $handler->display->display_options['empty']['text']['field'] = 'area';
+  $handler->display->display_options['empty']['text']['empty'] = TRUE;
+  $handler->display->display_options['empty']['text']['content'] = 'No analyses match the supplied criteria.';
+  $handler->display->display_options['empty']['text']['format'] = 'full_html';
+  /* Relationship: Analysis: Analysis => Node */
+  $handler->display->display_options['relationships']['analysis_id']['id'] = 'analysis_id';
+  $handler->display->display_options['relationships']['analysis_id']['table'] = 'chado_analysis';
+  $handler->display->display_options['relationships']['analysis_id']['field'] = 'analysis_id';
+  /* Field: Content: Nid */
+  $handler->display->display_options['fields']['nid']['id'] = 'nid';
+  $handler->display->display_options['fields']['nid']['table'] = 'node';
+  $handler->display->display_options['fields']['nid']['field'] = 'nid';
+  $handler->display->display_options['fields']['nid']['relationship'] = 'analysis_id';
+  $handler->display->display_options['fields']['nid']['exclude'] = TRUE;
+  /* Field: Chado Analysis: Name */
+  $handler->display->display_options['fields']['name']['id'] = 'name';
+  $handler->display->display_options['fields']['name']['table'] = 'analysis';
+  $handler->display->display_options['fields']['name']['field'] = 'name';
+  /* Field: Chado Analysis: Program */
+  $handler->display->display_options['fields']['program']['id'] = 'program';
+  $handler->display->display_options['fields']['program']['table'] = 'analysis';
+  $handler->display->display_options['fields']['program']['field'] = 'program';
+  /* Field: Chado Analysis: Sourcename */
+  $handler->display->display_options['fields']['sourcename']['id'] = 'sourcename';
+  $handler->display->display_options['fields']['sourcename']['table'] = 'analysis';
+  $handler->display->display_options['fields']['sourcename']['field'] = 'sourcename';
+  $handler->display->display_options['fields']['sourcename']['label'] = 'Source';
+  /* Field: Content: Delete link */
+  $handler->display->display_options['fields']['delete_node']['id'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['delete_node']['field'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['relationship'] = 'analysis_id';
+  $handler->display->display_options['fields']['delete_node']['exclude'] = TRUE;
+  /* Field: Content: Edit link */
+  $handler->display->display_options['fields']['edit_node']['id'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['edit_node']['field'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['relationship'] = 'analysis_id';
+  $handler->display->display_options['fields']['edit_node']['exclude'] = TRUE;
+  /* Field: Global: Custom text */
+  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['table'] = 'views';
+  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['label'] = '';
+  $handler->display->display_options['fields']['nothing']['alter']['text'] = '[edit_node]   [delete_node]';
+  $handler->display->display_options['fields']['nothing']['element_label_colon'] = FALSE;
+  /* Filter criterion: Chado Analysis: Name */
+  $handler->display->display_options['filters']['name']['id'] = 'name';
+  $handler->display->display_options['filters']['name']['table'] = 'analysis';
+  $handler->display->display_options['filters']['name']['field'] = 'name';
+  $handler->display->display_options['filters']['name']['operator'] = '~';
+  $handler->display->display_options['filters']['name']['group'] = 1;
+  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['name']['expose']['operator_id'] = 'name_op';
+  $handler->display->display_options['filters']['name']['expose']['label'] = 'Name Contains';
+  $handler->display->display_options['filters']['name']['expose']['operator'] = 'name_op';
+  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'name';
+  /* Filter criterion: Chado Analysis: Program */
+  $handler->display->display_options['filters']['program']['id'] = 'program';
+  $handler->display->display_options['filters']['program']['table'] = 'analysis';
+  $handler->display->display_options['filters']['program']['field'] = 'program';
+  $handler->display->display_options['filters']['program']['operator'] = 'contains';
+  $handler->display->display_options['filters']['program']['group'] = 1;
+  $handler->display->display_options['filters']['program']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['program']['expose']['operator_id'] = 'program_op';
+  $handler->display->display_options['filters']['program']['expose']['label'] = 'Program Name Contains';
+  $handler->display->display_options['filters']['program']['expose']['operator'] = 'program_op';
+  $handler->display->display_options['filters']['program']['expose']['identifier'] = 'program';
+  $handler->display->display_options['filters']['program']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Analysis: Sourcename */
+  $handler->display->display_options['filters']['sourcename']['id'] = 'sourcename';
+  $handler->display->display_options['filters']['sourcename']['table'] = 'analysis';
+  $handler->display->display_options['filters']['sourcename']['field'] = 'sourcename';
+  $handler->display->display_options['filters']['sourcename']['operator'] = '~';
+  $handler->display->display_options['filters']['sourcename']['group'] = 1;
+  $handler->display->display_options['filters']['sourcename']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['sourcename']['expose']['operator_id'] = 'sourcename_op';
+  $handler->display->display_options['filters']['sourcename']['expose']['label'] = 'Source Contains';
+  $handler->display->display_options['filters']['sourcename']['expose']['operator'] = 'sourcename_op';
+  $handler->display->display_options['filters']['sourcename']['expose']['identifier'] = 'sourcename';
+
+  /* Display: Page */
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_analysis/analysis';
+  $handler->display->display_options['menu']['type'] = 'default tab';
+  $handler->display->display_options['menu']['title'] = 'Analyses';
+  $handler->display->display_options['menu']['weight'] = '-10';
+  $handler->display->display_options['menu']['context'] = 0;
+  $handler->display->display_options['menu']['context_only_inline'] = 0;
+  $handler->display->display_options['tab_options']['weight'] = '0';
+
+  return $view;
+}

tripal_bulk_loader/tripal_bulk_loader.info

@@ -6,3 +6,4 @@ package = Tripal
 version = 7.x-2.0-beta1
 
 dependencies[] = tripal_core
+dependencies[] = tripal_views

tripal_bulk_loader/tripal_bulk_loader.install

@@ -4,6 +4,20 @@
  * @todo Add file header description
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_bulk_loader_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_bulk_loader.views_default.inc");
+  $views = tripal_bulk_loader_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implements hook_schema
  *

tripal_bulk_loader/tripal_bulk_loader.views_default.inc

@@ -23,7 +23,7 @@ function tripal_bulk_loader_defaultview_admin_job_listing() {
 
   $view = new view();
   $view->name = 'tripal_bulk_loading_jobs';
-  $view->description = 'Administration of Tripal Bulk Loading Jobs (add, edit, delete).';
+  $view->description = 'DO NOT DISABLE';
   $view->tag = 'tripal admin';
   $view->base_table = 'tripal_bulk_loader';
   $view->human_name = 'Tripal Bulk Loading Jobs';
@@ -102,16 +102,28 @@ function tripal_bulk_loader_defaultview_admin_job_listing() {
       'empty_column' => 0,
     ),
   );
-  /* Header: Global: Text area */
-  $handler->display->display_options['header']['area']['id'] = 'area';
-  $handler->display->display_options['header']['area']['table'] = 'views';
-  $handler->display->display_options['header']['area']['field'] = 'area';
-  $handler->display->display_options['header']['area']['label'] = 'Add Job';
-  $handler->display->display_options['header']['area']['empty'] = TRUE;
-  $handler->display->display_options['header']['area']['content'] = '<ul class="action-links">
-    <li><a href="../../../../node/add/tripal-bulk-loader">Add Bulk Loading Job</a></li>
-    </ul>';
-  $handler->display->display_options['header']['area']['format'] = 'full_html';
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Bulk Loading Job',
+    'path-1' => 'node/add/tripal-bulk-loader',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-2'] = array(
+    'label-2' => '',
+    'path-2' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-3'] = array(
+    'label-3' => '',
+    'path-3' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-4'] = array(
+    'label-4' => '',
+    'path-4' => '',
+  );
   /* No results behavior: Global: Text area */
   $handler->display->display_options['empty']['area']['id'] = 'area';
   $handler->display->display_options['empty']['area']['table'] = 'views';
@@ -251,6 +263,7 @@ function tripal_bulk_loader_defaultview_admin_job_listing() {
   $handler->display->display_options['menu']['context_only_inline'] = 0;
   $handler->display->display_options['tab_options']['weight'] = '0';
 
+
   return $view;
 }
 
@@ -261,7 +274,7 @@ function tripal_bulk_loader_defaultview_admin_template_listing() {
 
   $view = new view();
   $view->name = 'tripal_bulk_loader_templates';
-  $view->description = 'Administration of Tripal Bulk Loading Templates (add, import, edit, delete, export).';
+  $view->description = 'DO NOT DISABLE';
   $view->tag = 'tripal admin';
   $view->base_table = 'tripal_bulk_loader_template';
   $view->human_name = 'Tripal Bulk Loader Templates';
@@ -282,17 +295,20 @@ function tripal_bulk_loader_defaultview_admin_template_listing() {
   $handler->display->display_options['pager']['type'] = 'full';
   $handler->display->display_options['pager']['options']['items_per_page'] = '25';
   $handler->display->display_options['style_plugin'] = 'table';
-  /* Header: Global: Text area */
-  $handler->display->display_options['header']['area']['id'] = 'area';
-  $handler->display->display_options['header']['area']['table'] = 'views';
-  $handler->display->display_options['header']['area']['field'] = 'area';
-  $handler->display->display_options['header']['area']['label'] = 'Add Template';
-  $handler->display->display_options['header']['area']['empty'] = TRUE;
-  $handler->display->display_options['header']['area']['content'] = '<ul class="action-links">
-      <li><a href="template/create">Add Template</a></li>
-      <li><a href="templates/import">Import Template</a></li>
-      </ul>';
-  $handler->display->display_options['header']['area']['format'] = 'full_html';
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Template',
+    'path-1' => 'admin/tripal/loaders/bulk/template/create',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-2'] = array(
+    'label-2' => 'Import Template',
+    'path-2' => 'admin/tripal/loaders/bulk/templates/import',
+  );
   /* Field: Tripal Bulk Loader Templates: Name */
   $handler->display->display_options['fields']['name']['id'] = 'name';
   $handler->display->display_options['fields']['name']['table'] = 'tripal_bulk_loader_template';

tripal_contact/includes/tripal_contact.admin.inc

@@ -1,4 +1,39 @@
 <?php
+
+/**
+ *
+ */
+function tripal_contact_admin_contact_view() {
+  $output = '';
+
+  // set the breadcrumb
+  $breadcrumb = array();
+  $breadcrumb[] = l('Home', '<front>');
+  $breadcrumb[] = l('Administration', 'admin');
+  $breadcrumb[] = l('Tripal', 'admin/tripal');
+  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
+  $breadcrumb[] = l('Contacts', 'admin/tripal/chado/tripal_contact');
+  drupal_set_breadcrumb($breadcrumb);
+
+  // Add the view
+  $view = views_embed_view('tripal_contact_admin_contacts','default');
+  if (isset($view)) {
+    $output .= $view;
+  }
+  else {
+    $output .= '<p>The Contact module uses primarily views to provide an '
+      . 'administrative interface. Currently one or more views needed for this '
+      . 'administrative interface are disabled. <strong>Click each of the following links to '
+      . 'enable the pertinent views</strong>:</p>';
+    $output .= '<ul>';
+      $output .= '<li>'.l('Contacts View', 'admin/tripal/chado/tripal_contact/views/contacts/enable').'</li>';
+    $output .= '</ul>';
+  }
+
+  return $output;
+}
+
+
 /**
  * Administrative settings form
  *
@@ -18,7 +53,7 @@ function tripal_contact_admin() {
   // add the field set for syncing maps
   if (!$active_jobs) {
     get_tripal_contact_admin_form_cleanup_set($form);
-// TODO: complete coding of indexing and taxonomy assignment to features.    
+// TODO: complete coding of indexing and taxonomy assignment to features.
 //    get_tripal_contact_admin_form_reindex_set($form);
 //    get_tripal_contact_admin_form_taxonomy_set($form);
   }
@@ -125,7 +160,7 @@ function tripal_contact_admin_validate($form, &$form_state) {
       }
     }
   }
-  
+
   // -------------------------------------
   // Submit the Cleanup Job if selected
   if ($form_state['values']['op'] == t('Clean up orphaned maps')) {
@@ -148,7 +183,7 @@ function tripal_contact_admin_validate($form, &$form_state) {
 function tripal_contact_cleanup($dummy = NULL, $job_id = NULL) {
 
   return tripal_core_clean_orphaned_nodes('contact', $job_id);
-  
+
 }
 /**
  * Add the map as a taxonomy term for associating with map_features

tripal_contact/tripal_contact.info

@@ -4,5 +4,7 @@ core = 7.x
 project = tripal_contact
 package = Tripal
 version = 7.x-2.0-beta1
+
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_cv

tripal_contact/tripal_contact.install

@@ -10,6 +10,20 @@
  * multiple contact/mysql instances as well as manage and create such contact instances
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_contact_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_contact.views_default.inc");
+  $views = tripal_contact_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_requirements().
  *
@@ -33,13 +47,13 @@ function tripal_contact_requirements($phase) {
  * Implementation of hook_install().
  */
 function tripal_contact_install() {
-	
+
 	// create the module's data directory
   tripal_create_moddir('tripal_contact');
-  
+
   // add the contactprop table to Chado
   tripal_contact_add_custom_tables();
-  
+
   // add loading of the the tripal contact ontology to the job queue
   $obo_path = drupal_realpath(drupal_get_path('module', 'tripal_contact') . '/files/tcontact.obo');
   $obo_id = tripal_cv_add_obo_ref('Tripal Contacts', $obo_path);
@@ -91,7 +105,7 @@ function tripal_contact_schema() {
 
 
 /*
- * 
+ *
  */
 function tripal_contact_add_custom_tables(){
   $schema = array (

tripal_contact/tripal_contact.module

@@ -49,7 +49,7 @@ function tripal_contact_views_api() {
 function tripal_contact_init() {
   drupal_add_js(drupal_get_path('module', 'tripal_contact') . '/theme/js/tripal_contact.js');
   drupal_add_css(drupal_get_path('module', 'tripal_contact') . '/theme/css/tripal_contact.css');
-    
+
 }
 
 /**
@@ -87,34 +87,44 @@ function tripal_contact_menu() {
 
   $items = array();
 
-  $items[ 'admin/tripal/tripal_contact' ]= array(
+  $items['admin/tripal/chado/tripal_contact']= array(
     'title' => 'Contacts',
-    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of contacts'),
-    'page callback' => 'theme',
-    'page arguments' => array('tripal_contact_admin'),
+    'description' => ('Model persons, institutes, groups, organizations, etc.'),
+    'page callback' => 'tripal_contact_admin_contact_view',
     'access arguments' => array('administer tripal contacts'),
     'type' => MENU_NORMAL_ITEM
   );
-  
-  $items['admin/tripal/tripal_contact/configuration'] = array(
-    'title' => 'Configuration',
+
+  $items['admin/tripal/chado/tripal_contact/configuration'] = array(
+    'title' => 'Settings',
     'description' => 'Integration of Chado contacts.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_contact_admin'),
     'access arguments' => array('administer tripal contact'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 5
+  );
+
+  $items['admin/tripal/chado/tripal_contact/help']= array(
+    'title' => 'Help',
+    'description' => ('Help with the contact module.'),
+    'page callback' => 'theme',
+    'page arguments' => array('tripal_contact_help'),
+    'access arguments' => array('administer tripal contacts'),
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 10
   );
-  
-  
-  $items['admin/tripal/tripal_contact/sync'] = array(
-    'title' => ' Sync Contacts',
+
+  $items['admin/tripal/chado/tripal_contact/sync'] = array(
+    'title' => ' Sync',
     'description' => 'Sync contacts in Chado with Drupal',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_contact_sync_form'),
     'access arguments' => array('administer tripal contacts'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 0
   );
-  
+
   // AJAX calls for adding/removing properties to a contact
   $items['tripal_contact/properties/add'] = array(
     'page callback' => 'tripal_contact_property_add',
@@ -132,10 +142,10 @@ function tripal_contact_menu() {
     'access arguments' => array('edit chado_contact content'),
     'type ' => MENU_CALLBACK,
   );
-  
+
   return $items;
 }
-  
+
 /**
  * Implements hook_theme(): Register themeing functions for this module
  *
@@ -163,12 +173,12 @@ function tripal_contact_theme() {
       'arguments' => array('node' => NULL),
       'template' => 'tripal_contact_publications',
     ),
-    'tripal_contact_admin' => array(
-      'template' => 'tripal_contact_admin',  
-      'arguments' =>  array(NULL),  
-      'path' => drupal_get_path('module', 'tripal_contact') . '/theme' 
+    'tripal_contact_help' => array(
+      'template' => 'tripal_contact_help',
+      'arguments' =>  array(NULL),
+      'path' => drupal_get_path('module', 'tripal_contact') . '/theme'
     ),
-    
+
     // Themed Forms
     'chado_contact_node_form' => array(
       'arguments' => array('form'),
@@ -263,7 +273,7 @@ function tripal_contact_permissions() {
  *  @param $node
  *  The node on which the operation is to be performed, or, if it does not yet exist, the
  *  type of node to be created
- *  
+ *
  *  @param $op
  *  The operation to be performed
  *
@@ -273,7 +283,7 @@ function tripal_contact_permissions() {
  *  @return
  *  If the permission for the specified operation is not set then return FALSE. If the
  *  permission is set then return NULL as this allows other modules to disable
- *  access.  The only exception is when the $op == 'create'.  We will always 
+ *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
  */
@@ -317,8 +327,8 @@ function chado_contact_node_access($node, $op, $account ) {
  *
  */
 function chado_contact_insert($node) {
- 
-  // if a contact_id already exists for this node then it already exists in Chado and 
+
+  // if a contact_id already exists for this node then it already exists in Chado and
   // we get here because we are syncing the node.  Therefore, we can skip the insert
   if ($node->contact_id) {
     $contact['contact_id'] = $node->contact_id;
@@ -336,12 +346,12 @@ function chado_contact_insert($node) {
     if (!$contact) {
       drupal_set_message(t('Could not add the contact'), 'error');
       watchdog('tripal_contact','Could not add the contact', array(), WATCHDOG_ERROR);
-      return FALSE; 
+      return FALSE;
     }
-    
+
     // now add the properties
     $properties = array(); // stores all of the properties we need to add
-  
+
     // get the list of properties for easy lookup (without doing lots of database queries
     $properties_list = array();
     $sql = "
@@ -350,16 +360,16 @@ function chado_contact_insert($node) {
         INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
         INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
         INNER JOIN {cv} CV       ON CVTO.cv_id = CV.cv_id
-      WHERE 
-        CV.name = 'tripal_contact' AND 
-        NOT CVTO.name = 'Contact Type' 
-      ORDER BY CVTS.name ASC 
+      WHERE
+        CV.name = 'tripal_contact' AND
+        NOT CVTO.name = 'Contact Type'
+      ORDER BY CVTS.name ASC
     ";
     $prop_types = chado_query($sql);
     while ($prop = $prop_types->fetchObject()) {
       $properties_list[$prop->cvterm_id] = $prop->name;
-    }   
-  
+    }
+
     // get the properties that should be added. Properties are in one of two forms:
     //  1) prop_value-[type id]-[index]
     //  2) new_value-[type id]-[index]
@@ -377,11 +387,11 @@ function chado_contact_insert($node) {
       $index = count($properties[$name]);
       $name = $properties_list[$type_id];
       $properties[$name][$index] = trim($node->new_value);
-    } 
+    }
     // now add in the properties
     foreach ($properties as $property => $elements) {
       foreach ($elements as $rank => $value) {
-         
+
         $status = tripal_contact_insert_property($contact['contact_id'], $property, $value, FALSE);
         if (!$status) {
           drupal_set_message("Error cannot add property: $property", "error");
@@ -389,16 +399,16 @@ function chado_contact_insert($node) {
           array('%property' => $property), WATCHDOG_ERROR);
         }
       }
-    } 
+    }
   }
 
   // add the record to the chado_contact table in Drupal
-  if ($contact) {   
-   
+  if ($contact) {
+
     // add the description property
     tripal_contact_insert_property($contact['contact_id'], 'contact_description',
       $node->description, TRUE);
-    
+
     // make sure the entry for this contact doesn't already exist in the chado_contact table
     // if it doesn't exist then we want to add it.
     $contact_id = chado_get_id_for_node('contact', $node->nid) ;
@@ -435,17 +445,17 @@ function chado_contact_update($node) {
     // there is no way to handle revisions in Chado but leave
     // this here just to make not we've addressed it.
   }
-  
+
   $contact_id = chado_get_id_for_node('contact', $node->nid) ;
-  
-  // check to see if this contact name doens't already exists.    
+
+  // check to see if this contact name doens't already exists.
   $sql = "SELECT contact_id FROM {contact} WHERE NOT contact_id = :contact_id AND name = :name";
   $contact = chado_query($sql, array(':contact_id' => $contact_id, ':name' => $node->contact_name))->fetchObject();
   if ($contact) {
     drupal_set_message(t('A contact with this name already exists. Cannot perform update.'), 'warning');
-    return;  
-  }    
-  
+    return;
+  }
+
   // update the contact record
   $match = array(
      'contact_id' => $contact_id,
@@ -461,10 +471,10 @@ function chado_contact_update($node) {
     watchdog('t_contact', "Error updating contact", array(), WATCHDOG_ERROR);
     return;
   }
-  
+
   // now update the properties
   $properties = array(); // stores all of the properties we need to add
-   
+
   // get the list of properties for easy lookup (without doing lots of database queries
   $properties_list = array();
   $sql = "
@@ -473,16 +483,16 @@ function chado_contact_update($node) {
       INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
       INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
       INNER JOIN {cv} CV       ON CVTO.cv_id = CV.cv_id
-    WHERE 
-      CV.name = 'tripal_contact' AND 
-      NOT CVTO.name = 'Contact Type' 
-    ORDER BY CVTS.name ASC 
+    WHERE
+      CV.name = 'tripal_contact' AND
+      NOT CVTO.name = 'Contact Type'
+    ORDER BY CVTS.name ASC
   ";
   $prop_types = chado_query($sql);
   while ($prop = $prop_types->fetchObject()) {
     $properties_list[$prop->cvterm_id] = $prop->name;
   }
-  
+
   // get the properties that should be added. Properties are in one of three forms:
   //  1) prop_value-[type id]-[index]
   //  2) new_value-[type id]-[index]
@@ -508,7 +518,7 @@ function chado_contact_update($node) {
     $index = count($properties[$name]);
     $properties[$name][$index] = trim($node->new_value);
   }
-  
+
   // now add in the properties by first removing any the contact
   // already has and adding the ones we have
   tripal_core_chado_delete('contactprop', array('contact_id' => $contact_id));
@@ -521,8 +531,8 @@ function chado_contact_update($node) {
         array('%prop' => $property), WATCHDOG_ERROR);
       }
     }
-  } 
-  
+  }
+
   tripal_contact_update_property($contact_id, 'contact_description', $node->description, 1);
 }
 
@@ -547,7 +557,7 @@ function chado_contact_load($node) {
 
   // get the contact description and replace the contact.description field with this one
   $values = array(
-    'contact_id' => $contact->contact_id, 
+    'contact_id' => $contact->contact_id,
     'type_id' => array(
       'name' => 'contact_description',
     ),
@@ -556,12 +566,12 @@ function chado_contact_load($node) {
     'return_array' => 1,
     'include_fk' => array('type_id' => 1),
   );
-  $description = tripal_core_generate_chado_var('contactprop', $values, $options);    
+  $description = tripal_core_generate_chado_var('contactprop', $values, $options);
   if (count($description) == 1) {
-    $description = tripal_core_expand_chado_vars($description, 'field', 'contactprop.value');  
+    $description = tripal_core_expand_chado_vars($description, 'field', 'contactprop.value');
     $contact->description = $description[0]->value;
   }
-    
+
 
   $additions = new stdClass();
   $additions->contact = $contact;
@@ -676,7 +686,7 @@ function tripal_contact_preprocess_tripal_contact_relationships(&$variables) {
 }
 
 /*
- * 
+ *
  */
 function tripal_contact_form_alter(&$form, &$form_state, $form_id) {
   if ($form_id == "chado_contact_node_form") {

tripal_contact/tripal_contact.views.inc

@@ -8,283 +8,4 @@
  *
  *  Documentation on views integration can be found at
  *  http://views2.logrus.com/doc/html/index.html.
- */
-
-
-
-/**
- *
- * @ingroup tripal_feature_views
- */
-function tripal_contact_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // Main default view
-  $view = new view;
-  $view->name = 'contact_listing';
-  $view->description = 'A listing of chado contacts';
-  $view->tag = 'chado default';
-  $view->base_table = 'contact';
-  $view->core = 6;
-  $view->api_version = '2';
-  $view->disabled = TRUE; /* 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' => 'contact',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'name_1' => 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_1',
-      'table' => 'cvterm',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'description' => array(
-      'label' => 'Description',
-      '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' => 'contact',
-      'field' => 'description',
-      'relationship' => 'none',
-    ),
-  ));
-  $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 contacts matching the entered criteria. If you leave a any of the criteria blank then the contacts will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all contacts will be listed.',
-    ),
-    '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' => 'contact',
-      'field' => 'type_id',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'show_all' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'name' => array(
-      'operator' => '~',
-      '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' => 'contact',
-      'field' => 'name',
-      'relationship' => 'none',
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'description' => array(
-      'operator' => '~',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'description_op',
-        'identifier' => 'description',
-        'label' => 'Description Contains',
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'description',
-      'table' => 'contact',
-      'field' => 'description',
-      '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', 'Contacts');
-  $handler->override_option('header', 'Click "Show" to see a list of all contacts matching the entered criteria. If you leave a any of the criteria blank then the contacts will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all contacts will be listed.');
-  $handler->override_option('header_format', '2');
-  $handler->override_option('header_empty', 0);
-  $handler->override_option('empty', 'No contacts 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',
-      'name_1' => 'name_1',
-      'description' => 'description',
-    ),
-    'info' => array(
-      'name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name_1' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'description' => array(
-        'sortable' => 0,
-        'separator' => '',
-      ),
-    ),
-    'default' => 'name',
-  ));
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/contacts');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Contacts',
-    'description' => 'Contacts can be persons, institutes, groups, or organizations.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  $views[$view->name] = $view;
-
-  return $views;
-}
+ */

tripal_contact/tripal_contact.views_default.inc

@@ -0,0 +1,208 @@
+<?php
+
+/**
+ *
+ * @ingroup tripal_feature_views
+ */
+function tripal_contact_views_default_views() {
+  $views = array();
+
+  $view = tripal_contact_defaultview_admin_contacts();
+  $views[$view->name] = $view;
+
+  return $views;
+}
+
+/**
+ *
+ */
+function tripal_contact_defaultview_admin_contacts() {
+
+  $view = new view();
+  $view->name = 'tripal_contact_admin_contacts';
+  $view->description = 'DO NOT DISABLE';
+  $view->tag = 'tripal admin';
+  $view->base_table = 'contact';
+  $view->human_name = 'Contact Admin';
+  $view->core = 6;
+  $view->api_version = '3.0';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+
+  /* Display: Defaults */
+  $handler = $view->new_display('default', 'Defaults', 'default');
+  $handler->display->display_options['title'] = 'Contacts';
+  $handler->display->display_options['use_more_always'] = FALSE;
+  $handler->display->display_options['access']['type'] = 'perm';
+  $handler->display->display_options['cache']['type'] = 'none';
+  $handler->display->display_options['query']['type'] = 'views_query';
+  $handler->display->display_options['exposed_form']['type'] = 'basic';
+  $handler->display->display_options['pager']['type'] = 'full';
+  $handler->display->display_options['pager']['options']['items_per_page'] = '25';
+  $handler->display->display_options['pager']['options']['offset'] = '0';
+  $handler->display->display_options['pager']['options']['id'] = '0';
+  $handler->display->display_options['pager']['options']['quantity'] = '9';
+  $handler->display->display_options['style_plugin'] = 'table';
+  $handler->display->display_options['style_options']['grouping'] = '';
+  $handler->display->display_options['style_options']['columns'] = array(
+    'name' => 'name',
+    'name_1' => 'name_1',
+    'description' => 'description',
+  );
+  $handler->display->display_options['style_options']['default'] = 'name';
+  $handler->display->display_options['style_options']['info'] = array(
+    'name' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'name_1' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'description' => array(
+      'sortable' => 0,
+      'separator' => '',
+    ),
+  );
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Contact',
+    'path-1' => 'node/add/tripal-contact',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-2'] = array(
+    'label-2' => '',
+    'path-2' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-3'] = array(
+    'label-3' => '',
+    'path-3' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-4'] = array(
+    'label-4' => '',
+    'path-4' => '',
+  );
+  /* No results behavior: Global: Text area */
+  $handler->display->display_options['empty']['text']['id'] = 'area';
+  $handler->display->display_options['empty']['text']['table'] = 'views';
+  $handler->display->display_options['empty']['text']['field'] = 'area';
+  $handler->display->display_options['empty']['text']['content'] = 'No contacts match the current criteria.';
+  $handler->display->display_options['empty']['text']['format'] = '2';
+  /* Relationship: Contact: Contact => Node */
+  $handler->display->display_options['relationships']['contact_id']['id'] = 'contact_id';
+  $handler->display->display_options['relationships']['contact_id']['table'] = 'chado_contact';
+  $handler->display->display_options['relationships']['contact_id']['field'] = 'contact_id';
+  /* Field: Content: Nid */
+  $handler->display->display_options['fields']['nid']['id'] = 'nid';
+  $handler->display->display_options['fields']['nid']['table'] = 'node';
+  $handler->display->display_options['fields']['nid']['field'] = 'nid';
+  $handler->display->display_options['fields']['nid']['exclude'] = TRUE;
+  /* Field: Chado Contact: Name */
+  $handler->display->display_options['fields']['name']['id'] = 'name';
+  $handler->display->display_options['fields']['name']['table'] = 'contact';
+  $handler->display->display_options['fields']['name']['field'] = 'name';
+  /* Field: Chado Cvterm: Name */
+  $handler->display->display_options['fields']['name_1']['id'] = 'name_1';
+  $handler->display->display_options['fields']['name_1']['table'] = 'cvterm';
+  $handler->display->display_options['fields']['name_1']['field'] = 'name';
+  $handler->display->display_options['fields']['name_1']['label'] = 'Type';
+  /* Field: Chado Contact: Description */
+  $handler->display->display_options['fields']['description']['id'] = 'description';
+  $handler->display->display_options['fields']['description']['table'] = 'contact';
+  $handler->display->display_options['fields']['description']['field'] = 'description';
+  /* Field: Content: Delete link */
+  $handler->display->display_options['fields']['delete_node']['id'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['delete_node']['field'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['relationship'] = 'contact_id';
+  /* Field: Content: Edit link */
+  $handler->display->display_options['fields']['edit_node']['id'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['edit_node']['field'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['relationship'] = 'contact_id';
+  $handler->display->display_options['fields']['edit_node']['exclude'] = TRUE;
+  /* Field: Global: Custom text */
+  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['table'] = 'views';
+  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['label'] = '';
+  $handler->display->display_options['fields']['nothing']['alter']['text'] = '[edit_node]  [delete_node]';
+  $handler->display->display_options['fields']['nothing']['element_label_colon'] = FALSE;
+  /* Filter criterion: Chado Contact: Type Id */
+  $handler->display->display_options['filters']['type_id']['id'] = 'type_id';
+  $handler->display->display_options['filters']['type_id']['table'] = 'contact';
+  $handler->display->display_options['filters']['type_id']['field'] = 'type_id';
+  $handler->display->display_options['filters']['type_id']['value'] = 'All';
+  $handler->display->display_options['filters']['type_id']['group'] = '0';
+  $handler->display->display_options['filters']['type_id']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['type_id']['expose']['operator_id'] = 'type_id_op';
+  $handler->display->display_options['filters']['type_id']['expose']['label'] = 'Type';
+  $handler->display->display_options['filters']['type_id']['expose']['operator'] = 'type_id_op';
+  $handler->display->display_options['filters']['type_id']['expose']['identifier'] = 'type_id';
+  $handler->display->display_options['filters']['type_id']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Contact: Name */
+  $handler->display->display_options['filters']['name']['id'] = 'name';
+  $handler->display->display_options['filters']['name']['table'] = 'contact';
+  $handler->display->display_options['filters']['name']['field'] = 'name';
+  $handler->display->display_options['filters']['name']['operator'] = 'contains';
+  $handler->display->display_options['filters']['name']['group'] = '0';
+  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['name']['expose']['operator_id'] = 'name_op';
+  $handler->display->display_options['filters']['name']['expose']['label'] = 'Name Contains';
+  $handler->display->display_options['filters']['name']['expose']['operator'] = 'name_op';
+  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'name';
+  $handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Contact: Description */
+  $handler->display->display_options['filters']['description']['id'] = 'description';
+  $handler->display->display_options['filters']['description']['table'] = 'contact';
+  $handler->display->display_options['filters']['description']['field'] = 'description';
+  $handler->display->display_options['filters']['description']['operator'] = 'contains';
+  $handler->display->display_options['filters']['description']['group'] = '0';
+  $handler->display->display_options['filters']['description']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['description']['expose']['operator_id'] = 'description_op';
+  $handler->display->display_options['filters']['description']['expose']['label'] = 'Description Contains';
+  $handler->display->display_options['filters']['description']['expose']['operator'] = 'description_op';
+  $handler->display->display_options['filters']['description']['expose']['identifier'] = 'description';
+  $handler->display->display_options['filters']['description']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+
+  /** MANUALLY ADD since filter handler no exporting correctly */
+  $handler->display->display_options['filters']['type_id']['expose']['values_form_type'] = 'select';
+  $handler->display->display_options['filters']['type_id']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['type_id']['expose']['select_optional'] = TRUE;
+  $handler->display->display_options['filters']['type_id']['expose']['max_length'] = 40;
+
+  /* Display: Page */
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_contact/contacts';
+  $handler->display->display_options['menu']['type'] = 'default tab';
+  $handler->display->display_options['menu']['title'] = 'Contacts';
+  $handler->display->display_options['menu']['description'] = 'Contacts can be persons, institutes, groups, or organizations.';
+  $handler->display->display_options['menu']['weight'] = '-10';
+  $handler->display->display_options['menu']['name'] = 'management';
+  $handler->display->display_options['menu']['context'] = 0;
+  $handler->display->display_options['menu']['context_only_inline'] = 0;
+  $handler->display->display_options['tab_options']['weight'] = '0';
+
+  /** MANUALLY ADD since filter handler no exporting correctly
+  $handler->display->display_options['filters']['type_id']['expose']['values_form_type'] = 'select';
+  $handler->display->display_options['filters']['type_id']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['type_id']['expose']['select_optional'] = TRUE;
+  $handler->display->display_options['filters']['type_id']['expose']['max_length'] = 40;
+  */
+  return $view;
+}

tripal_cv/includes/cv_form.inc

@@ -1,4 +1,4 @@
-<?php 
+<?php
 /**
  * Purpose: Provides the actual "Select CV" form on the Update/Delete Controlled
  *   Vocabulary page. This form also triggers the edit javascript
@@ -12,8 +12,11 @@ function tripal_cv_cv_edit_form($form, &$form_state) {
   $cv_id = 0;
   if (array_key_exists('values', $form_state)) {
     $cv_id = $form_state['values']['cv_id'];
-  }    
-  
+  }
+  elseif (isset($form_state['build_info']['args'][0])) {
+    $cv_id = $form_state['build_info']['args'][0];
+  }
+
   // get a list of db from chado for user to choose
   $sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
   $results = chado_query($sql);
@@ -35,15 +38,15 @@ function tripal_cv_cv_edit_form($form, &$form_state) {
       'event'    => 'change',
       'method'   => 'replace',
     ),
-    '#default_value' => $cv_id, 
+    '#default_value' => $cv_id,
   );
 
-        
+
   // if we don't have a db_id then we can  return the form, otherwise
   // add in the other fields
   if ($cv_id) {
     tripal_cv_add_cv_form_fields($form, $form_state, $cv_id);
-        
+
     $form['update'] = array(
       '#type'         => 'submit',
       '#value'        => t('Update'),
@@ -51,7 +54,7 @@ function tripal_cv_cv_edit_form($form, &$form_state) {
     $form['delete'] = array(
       '#type'         => 'submit',
       '#value'        => t('Delete'),
-      '#attributes'   => array('onclick' => 'if(!confirm("Really Delete?")){return false;}'), 
+      '#attributes'   => array('onclick' => 'if(!confirm("Really Delete?")){return false;}'),
     );
   }
   else {
@@ -62,21 +65,21 @@ function tripal_cv_cv_edit_form($form, &$form_state) {
       '#prefix' => '<div id="cv-edit-div">',
       '#suffix' => '</div>',
     );
-  } 
+  }
   return $form;
 }
 /**
- * 
+ *
  * @param $form
  * @param $form_state
- * 
+ *
  * @ingroup tripal_db
  */
 function tripal_cv_cv_add_form($form, $form_state) {
-  
+
   // add in the form fields to this form
   tripal_cv_add_cv_form_fields($form, $form_state);
-  
+
   $form['add'] = array(
     '#type'         => 'submit',
     '#value'        => t('Add'),
@@ -85,11 +88,11 @@ function tripal_cv_cv_add_form($form, $form_state) {
   return $form;
 }
 /**
- * 
+ *
  * @param $form
  * @param $form_state
  * @param $cv_id
- * 
+ *
  * @ingroup tripal_db
  */
 function tripal_cv_add_cv_form_fields(&$form, $form_state, $cv_id = NULL) {
@@ -100,17 +103,17 @@ function tripal_cv_add_cv_form_fields(&$form, $form_state, $cv_id = NULL) {
   if ($cv_id) {
     $values = array('cv_id' => $cv_id);
     $result = tripal_core_chado_select('cv', array('*'), $values);
-    $cv = $result[0]; 
+    $cv = $result[0];
     $default_name = $cv->name;
-    $default_desc = $cv->definition; 
-  }   
-  
+    $default_desc = $cv->definition;
+  }
+
   // add a fieldset for the Drupal Schema API
   $form['fields'] = array(
     '#type' => 'fieldset',
     '#title' => 'Controlled Vocabulary Details',
     '#collapsible' => 0,
-  );      
+  );
 
   $form['fields']['name']= array(
     '#type'          => 'textfield',
@@ -118,7 +121,7 @@ function tripal_cv_add_cv_form_fields(&$form, $form_state, $cv_id = NULL) {
     '#description'   => t('Please enter the name for this vocabulary.'),
     '#required'      => TRUE,
     '#default_value' => $default_name,
-    '#maxlength'     => 255,  
+    '#maxlength'     => 255,
   );
 
   $form['fields']['definition']= array(
@@ -135,44 +138,44 @@ function tripal_cv_add_cv_form_fields(&$form, $form_state, $cv_id = NULL) {
  * Validation fucntion for tripal_cv_cv_add_form
  * @param $form
  * @param $form_state
- * 
+ *
  * @ingroup tripal_cv
  */
 function tripal_cv_cv_add_form_validate($form, &$form_state) {
-  tripal_cv_form_fields_validate($form, $form_state); 
+  tripal_cv_form_fields_validate($form, $form_state);
 }
 /**
  * Validation fucntion for tripal_cv_cv_edit_form
  * @param unknown_type $form
  * @param unknown_type $form_state
- * 
+ *
  * @ingroup tripal_cv
  */
 function tripal_cv_cv_edit_form_validate($form, &$form_state) {
-  tripal_cv_form_fields_validate($form, $form_state); 
+  tripal_cv_form_fields_validate($form, $form_state);
 }
 /**
  * Genetic validation form for shared fields of both the edit and add forms
  * @param $form
  * @param $form_state
- * 
+ *
  * @ingroup tripal_cv
  */
 function tripal_cv_form_fields_validate($form, &$form_state) {
   $name =  array_key_exists('name', $form_state['values'])       ? trim($form_state['values']['name']) : '';
   $desc =  array_key_exists('definition', $form_state['values']) ? trim($form_state['values']['definition']) : '';
   $cv_id = array_key_exists('cv_id', $form_state['values'])      ? trim($form_state['values']['cv_id']) : '';
-  
-   
+
+
   // make sure the cv name is unique
   $values = array('name' => $name);
-  $results = tripal_core_chado_select('cv', array('cv_id'), $values);   
+  $results = tripal_core_chado_select('cv', array('cv_id'), $values);
   if (count($results) > 0 and $results[0]->cv_id != $cv_id) {
     form_set_error('name', 'The vocabulary name must be unique');
   }
 }
 /**
- * 
+ *
  * @param $form
  * @param $form_state
  */
@@ -191,10 +194,10 @@ function tripal_cv_cv_add_form_submit($form, &$form_state) {
   }
   else {
     drupal_set_message(t("Failed to add controlled vocabulary."));
-  }     
+  }
 }
 /**
- * 
+ *
  * @param unknown_type $form
  * @param unknown_type $form_state
  */
@@ -203,12 +206,12 @@ function tripal_cv_cv_edit_form_submit($form, &$form_state) {
   $desc  = array_key_exists('definition', $form_state['values']) ? trim($form_state['values']['definition']) : '';
   $cv_id = array_key_exists('cv_id', $form_state['values'])      ? trim($form_state['values']['cv_id']) : '';
   $op    = array_key_exists('op', $form_state['values'])         ? trim($form_state['values']['op']) : '';
-  
+
   $values = array(
     'name' => $name,
     'definition' => $desc,
   );
-  if (strcmp($op, 'Update')==0) {      
+  if (strcmp($op, 'Update')==0) {
     $match = array('cv_id' => $cv_id);
     $success = tripal_core_chado_update('cv', $match, $values);
     if ($success) {
@@ -235,25 +238,25 @@ function tripal_cv_cv_edit_form_submit($form, &$form_state) {
  * @ingroup tripal_cv
  */
 function tripal_cv_edit_form_ajax($form, $form_state) {
-  
+
   $elements = array();
-  
-  // add in the form fields and the buttons 
+
+  // add in the form fields and the buttons
   if (array_key_exists('cv_id', $form_state['values'])) {
     $elements['fields'] = $form['fields'];
     $elements['update'] = $form['update'];
     $elements['delete'] = $form['delete'];
   }
-  
+
    // add back in the cv-edit-div that is used for the next round of AJAX
   $elements['fields']['#prefix'] =  '<div id="cv-edit-div">';
   $elements['fields']['#suffix'] =  '</div">';
-  
+
   // reset the values for the fields to the defaults
   $elements['fields']['name']['#value']        = $elements['fields']['name']['#default_value'];
   $elements['fields']['definition']['#value']  = $elements['fields']['definition']['#default_value'];
-  
+
   //drupal_set_message('<pre>' . print_r($elements, TRUE) . '</pre>', "status");
-  
+
   return $elements;
 }

tripal_cv/includes/cvterm_form.inc

@@ -1,7 +1,7 @@
-<?php 
+<?php
 
 /**
- * 
+ *
  * @param $form
  * @param $form_state
  */
@@ -20,16 +20,28 @@ function tripal_cv_cvterm_edit_form($form, &$form_state) {
     $cv_id = $form_state['storage']['cv_id'];
     $cvterm_name = $form_state['storage']['name'];
     $cvterm_id = $form_state['storage']['cvterm_id'];
-  }  
+  }
   // get the cv if form was submitted via AJAX
   $cvterm = '';
   if (array_key_exists('values', $form_state)) {
-    $cv_id = $form_state['values']['cv_id'];   
+    $cv_id = $form_state['values']['cv_id'];
     if (array_key_exists('cvterm', $form_state['values'])) {
       $cvterm = $form_state['values']['cvterm'];
-    }    
-  }   
-    
+    }
+  }
+  elseif (isset($form_state['build_info']['args'][0])) {
+    $cv_id = $form_state['build_info']['args'][0];
+    $cvterm_id = $form_state['build_info']['args'][1];
+    if ($form_state['build_info']['args'][1]) {
+      $result = db_select('chado.cvterm','c')
+        ->fields('c', array('name'))
+        ->condition('c.cvterm_id',$cvterm_id)
+        ->execute();
+      $cvterm_name = $result->fetchObject()->name;
+      $step = 1;
+    }
+  }
+
   // get a list of CVs
   $cvs = array();
   $sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
@@ -37,7 +49,7 @@ function tripal_cv_cvterm_edit_form($form, &$form_state) {
   $cvs[] = 'Select a vocabulary';
   foreach ($results as $cv) {
     $cvs[$cv->cv_id] = $cv->name;
-  }    
+  }
   $form['cv_id'] = array(
     '#title' => t('Controlled Vocabulary (Ontology) Name'),
     '#type' => 'select',
@@ -50,11 +62,11 @@ function tripal_cv_cvterm_edit_form($form, &$form_state) {
        'event'   => 'change',
        'method'  => 'replace',
        'event'    => 'change',
-    ),    
+    ),
   );
-    
+
   if ($cv_id and $step == 0) {
-    
+
     $form['name']= array(
       '#type'          => 'textfield',
       '#title'         => t("Term Name"),
@@ -68,16 +80,16 @@ function tripal_cv_cvterm_edit_form($form, &$form_state) {
       '#value'         => 'continue',
     );
   }
-  elseif ($step == 1) {    
-       
+  elseif ($step == 1) {
+
     tripal_cv_add_cvterm_form_fields($form, $form_state, $cv_id, $cvterm_name);
-    
+
     // when editing there are certain fields the user should not change for a term
     // let's mark those as disabled
     $form['cv_id']['#disabled'] = TRUE;
     $form['fields']['db_id']['#disabled'] = TRUE;
     $form['fields']['accession']['#disabled'] = TRUE;
-    
+
     // add in the div for replacing the fields if needed
     $form['fields']['#prefix'] = '<div id="cvterm-edit-div">';
     $form['fields']['#suffix'] = '</div>';
@@ -87,7 +99,7 @@ function tripal_cv_cvterm_edit_form($form, &$form_state) {
       '#type' => 'hidden',
       '#value' =>  $cvterm_id,
     );
-    
+
     $form['update'] = array(
       '#type'         => 'submit',
       '#value'        => t('Update'),
@@ -95,10 +107,10 @@ function tripal_cv_cvterm_edit_form($form, &$form_state) {
     $form['delete'] = array(
       '#type'         => 'submit',
       '#value'        => t('Delete'),
-      '#attributes'   => array('onclick' => 'if(!confirm("Really Delete?")){return false;}'), 
-    );    
-  } 
-  
+      '#attributes'   => array('onclick' => 'if(!confirm("Really Delete?")){return false;}'),
+    );
+  }
+
   if ($step == 0) {
     // if we don't have a cv_id then this is the first time the form has
     // benn loaded and we need to create the div where ajax replacement elements get stored
@@ -111,16 +123,19 @@ function tripal_cv_cvterm_edit_form($form, &$form_state) {
   return $form;
 }
 /**
- * 
+ *
  * @param $form
  * @param $form_state
  */
 function tripal_cv_cvterm_add_form($form, &$form_state) {
   $cv_id = 0;
   if (array_key_exists('values', $form_state)) {
-    $cv_id = $form_state['values']['cv_id'];   
+    $cv_id = $form_state['values']['cv_id'];
   }
-  
+  elseif (isset($form_state['build_info']['args'][0])) {
+    $cv_id = $form_state['build_info']['args'][0];
+  }
+
   // get a list of CVs
   $cvs = array();
   $sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
@@ -128,7 +143,7 @@ function tripal_cv_cvterm_add_form($form, &$form_state) {
   $cvs[] = 'Select a vocabulary';
   foreach ($results as $cv) {
     $cvs[$cv->cv_id] = $cv->name;
-  }    
+  }
   $form['cv_id'] = array(
     '#title' => t('Controlled Vocabulary (Ontology) Name'),
     '#type' => 'select',
@@ -137,21 +152,21 @@ function tripal_cv_cvterm_add_form($form, &$form_state) {
     '#default_value' => $cv_id,
   );
   tripal_cv_add_cvterm_form_fields($form, $form_state);
-  
+
   $form['add'] = array(
     '#type'         => 'submit',
     '#value'        => t('Add Term'),
   );
-  
+
   return $form;
 }
 
 /**
- * 
+ *
  * @param $form
  * @param $form_state
  * @param $cv_id
- * 
+ *
  * @ingroup tripal_db
  */
 function tripal_cv_add_cvterm_form_fields(&$form, $form_state, $cv_id = 0, $cvterm_name = '') {
@@ -168,47 +183,47 @@ function tripal_cv_add_cvterm_form_fields(&$form, $form_state, $cv_id = 0, $cvte
     $values = array('cv_id' => $cv_id, 'name' => $cvterm_name);
     $cvterm = tripal_core_generate_chado_var('cvterm', $values);
     $name = $cvterm->name;
-    $definition = $cvterm->definition; 
+    $definition = $cvterm->definition;
     $is_relationship = $cvterm->is_relationshiptype;
     $is_obsolete = $cvterm->is_obsolete;
     $db_id = $cvterm->dbxref_id->db_id->db_id;
     $accession = $cvterm->dbxref_id->accession;
-  }    
-  
+  }
+
   // add a fieldset for the Drupal Schema API
   $form['fields'] = array(
     '#type' => 'fieldset',
     '#title' => 'Term Details',
     '#collapsible' => 0,
-  );      
-  
-  
+  );
+
+
   $form['fields']['name']= array(
     '#type'          => 'textfield',
     '#title'         => t("Term Name"),
     '#default_value' => $name,
     '#required'      => TRUE,
   );
-  
+
   $form['fields']['definition']= array(
     '#type'          => 'textarea',
     '#title'         => t('Description'),
     '#description'   => t('Please enter a description for this term'),
     '#default_value' => $definition,
   );
-  
+
   $form['fields']['is_relationship'] = array(
     '#type'          => 'checkbox',
     '#title'         => t('This term describes a relationship?'),
     '#default_value' => $is_relationship,
   );
-  
+
   $form['fields']['is_obsolete'] = array(
     '#type'          => 'checkbox',
     '#title'         => t('This term is obsolete?'),
     '#default_value' => $is_obsolete,
   );
-  
+
   $values = array();
   $columns = array('db_id', 'name');
   $options = array('order_by' => array('name' => 'ASC'));
@@ -228,22 +243,22 @@ function tripal_cv_add_cvterm_form_fields(&$form, $form_state, $cv_id = 0, $cvte
     '#default_value' => $db_id,
     '#required' => TRUE,
   );
-  
+
   $form['fields']['accession']= array(
     '#type'          => 'textfield',
     '#title'         => t("Accession"),
-    '#description'   => t('If this term has an existing accession (unique identifier) in the database 
+    '#description'   => t('If this term has an existing accession (unique identifier) in the database
        please enter that here.  If the accession is numeric with a database prefix (e.g. GO:003023), please
-       enter just the numeric value.  The database prefix will be appended whenever the term is displayed. 
-       If the accession is not numeric then enter it as is.  If no value is provied, the term name 
+       enter just the numeric value.  The database prefix will be appended whenever the term is displayed.
+       If the accession is not numeric then enter it as is.  If no value is provied, the term name
        provided above will be used as the accession.'),
     '#required'      => TRUE,
     '#default_value' => $accession,
-  );     
+  );
 }
 
 /**
- * 
+ *
  * @param $form
  * @param $form_state
  */
@@ -253,14 +268,14 @@ function tripal_cv_cvterm_edit_form_validate($form, &$form_state) {
   $name = array_key_exists('name', $form_state['values']) ? $form_state['values']['name'] : '';
   $cvterm_id = array_key_exists('cvterm_id', $form_state['values']) ? $form_state['values']['cvterm_id'] : '';
   $accession = array_key_exists('accession', $form_state['values']) ? $form_state['values']['accession'] : '';
-  
+
   $step = $form_state['storage']['step'];
-   
+
   // make sure the cv term name is unique for this vocabulary
   if ($step == 1) {
     $values = array('name' => $name, 'cv_id' => $cv_id);
     $results = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
-    foreach ($results as $r) {   
+    foreach ($results as $r) {
       if ($r->cvterm_id != $cvterm_id) {
         form_set_error('name', 'The term name must be unique for this vocabulary. Another term with this name already exists.');
       }
@@ -268,7 +283,7 @@ function tripal_cv_cvterm_edit_form_validate($form, &$form_state) {
   }
 }
 /**
- * 
+ *
  * @param $form
  * @param $form_state
  */
@@ -277,7 +292,7 @@ function tripal_cv_cvterm_add_form_validate($form, &$form_state) {
   $db_id = array_key_exists('db_id', $form_state['values']) ? $form_state['values']['db_id'] : '';
   $name = array_key_exists('name', $form_state['values']) ? $form_state['values']['name'] : '';
   $accession = array_key_exists('accession', $form_state['values']) ? $form_state['values']['accession'] : '';
-    
+
   $values = array('cv_id' => $cv_id);
   $results = tripal_core_chado_select('cv', array('name'), $values);
   if (!$results or count($results) == 0) {
@@ -290,20 +305,20 @@ function tripal_cv_cvterm_add_form_validate($form, &$form_state) {
   if (!$results or count($results) == 0) {
     form_set_error('db_id', 'The database name does not exist');
   }
-  
+
   // make sure the cv term name is unique for this vocabulary
   $values = array('name' => $name, 'cv_id' => $cv_id);
-  $results = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);   
+  $results = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
   if (count($results) > 0) {
     form_set_error('name', 'The term name must be unique for this vocabulary. Another term with this name already exists.');
   }
-  
+
   // make sure this accession is unique for the database
   $values = array('accession' => $accession, 'db_id' => $db_id);
-  $results = tripal_core_chado_select('dbxref', array('dbxref_id'), $values);   
+  $results = tripal_core_chado_select('dbxref', array('dbxref_id'), $values);
   if (count($results) > 0 ) {
     form_set_error('accession', 'The accession is not uniuqe for this vocabulary\'s database.');
-  }  
+  }
 
 }
 
@@ -314,85 +329,85 @@ function tripal_cv_cvterm_add_form_validate($form, &$form_state) {
  * @ingroup tripal_cv
  */
 function tripal_cv_cvterm_edit_form_submit($form, &$form_state) {
-  
+
   $cv_id = array_key_exists('cv_id', $form_state['values']) ? $form_state['values']['cv_id'] : '';
   $name = array_key_exists('name', $form_state['values']) ? $form_state['values']['name'] : '';
   $definition = array_key_exists('definition', $form_state['values']) ? $form_state['values']['definition'] : '';
   $is_relationship = array_key_exists('is_relationship', $form_state['values']) ? $form_state['values']['is_relationship'] : '';
   $is_obsolete = array_key_exists('is_obsolete', $form_state['values']) ? $form_state['values']['is_obsolete'] : '';
   $cvterm_id = array_key_exists('cvterm_id', $form_state['values']) ? $form_state['values']['cvterm_id'] : '';
-  
+
   $db_id = array_key_exists('db_id', $form_state['values']) ? $form_state['values']['db_id'] : '';
   $accession = array_key_exists('accession', $form_state['values']) ? $form_state['values']['accession'] : '';
-  
+
   $op    = array_key_exists('op', $form_state['values'])         ? trim($form_state['values']['op']) : '';
-  
-  
+
+
   $step = $form_state['storage']['step'];
 
   switch ($step) {
     case 0:  // a cvterm name has been selected
       $cv_id = array_key_exists('cv_id', $form_state['values']) ? trim($form_state['values']['cv_id']) : '';
       $name  = array_key_exists('name', $form_state['values'])  ? trim($form_state['values']['name'])  : '';
-      
+
       // get the original cvterm_id
       $values = array('name' => $name, 'cv_id' => $cv_id);
-      $results = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);  
-      $cvterm = $results[0]; 
-    
+      $results = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
+      $cvterm = $results[0];
+
       $form_state['storage']['cv_id'] = $cv_id;
       $form_state['storage']['name'] = $name;
       $form_state['storage']['step'] = 1;
       $form_state['storage']['cvterm_id'] = $cvterm->cvterm_id;
       $form_state['rebuild'] = TRUE;
       break;
-      
-    case 1:  // update/delete button has been clicked          
-      
+
+    case 1:  // update/delete button has been clicked
+
       if ($op == 'Update') {
         // get the cv
         $values = array('cv_id' => $cv_id);
         $results = tripal_core_chado_select('cv', array('name'), $values);
         $cv = $results[0];
-        
+
         // get the db
         $values = array('db_id' => $db_id);
         $results = tripal_core_chado_select('db', array('name'), $values);
         $db = $results[0];
-        
+
         // now add the term
-        $term = array(    
+        $term = array(
           'name' => $name,
           'namespace' => $cv->name,
           'id' => $accession,
           'def' => $definition,
           'is_obsolete' => $is_obsolete,
-        );  
-        
+        );
+
         $cvterm = tripal_cv_add_cvterm($term, $cv->name, $is_relationship, TRUE, $db->name);
         if ($cvterm) {
           drupal_set_message('Term updated successfully.');
-        } 
+        }
         else {
-          drupal_set_message('Could not add term. Check Drupal recent logs for error messages.', 'error');  
+          drupal_set_message('Could not add term. Check Drupal recent logs for error messages.', 'error');
         }
       }
       if ($op == 'Delete') {
         $values = array('cvterm_id' => $cvterm_id);
         $success = tripal_core_chado_delete('cvterm', $values);
         if ($success) {
-          drupal_set_message('Term deleted successfully.');  
-        } 
+          drupal_set_message('Term deleted successfully.');
+        }
         else {
-          drupal_set_message('Could not delete term term. Check Drupal recent logs for error messages.', 'error');  
-        }             
+          drupal_set_message('Could not delete term term. Check Drupal recent logs for error messages.', 'error');
+        }
       }
       break;
-  }      
+  }
 }
 
 /**
- * 
+ *
  * @param unknown_type $form
  * @param unknown_type $form_state
  */
@@ -402,36 +417,36 @@ function tripal_cv_cvterm_add_form_submit($form, &$form_state) {
   $definition = array_key_exists('definition', $form_state['values']) ? $form_state['values']['definition'] : '';
   $is_relationship = array_key_exists('is_relationship', $form_state['values']) ? $form_state['values']['is_relationship'] : '';
   $is_obsolete = array_key_exists('is_obsolete', $form_state['values']) ? $form_state['values']['is_obsolete'] : '';
-  
+
   $db_id = array_key_exists('db_id', $form_state['values']) ? $form_state['values']['db_id'] : '';
   $accession = array_key_exists('accession', $form_state['values']) ? $form_state['values']['accession'] : '';
-  
+
   // get the database
   $values = array('db_id' => $db_id);
   $results = tripal_core_chado_select('db', array('name'), $values);
   $db = $results[0];
-      
+
   // get the cv
   $values = array('cv_id' => $cv_id);
   $results = tripal_core_chado_select('cv', array('name'), $values);
   $cv = $results[0];
 
   // now add the term
-  $term = array(    
+  $term = array(
     'name' => $name,
     'namespace' => $cv->name,
     'id' => $accession,
     'def' => $definition,
     'is_obsolete' => $is_obsolete,
-  );  
-      
+  );
+
   $cvterm = tripal_cv_add_cvterm($term, $cv->name, $is_relationship, TRUE, $db->name);
   if ($cvterm) {
     drupal_set_message('Term added successfully.');
-  } 
+  }
   else {
-    drupal_set_message('Could not add term. Check Drupal recent logs for error messages.', 'error');  
-  }    
+    drupal_set_message('Could not add term. Check Drupal recent logs for error messages.', 'error');
+  }
 }
 /**
  * Ajax callback for the tripal_cv_form
@@ -440,14 +455,14 @@ function tripal_cv_cvterm_add_form_submit($form, &$form_state) {
 function tripal_cv_cvterm_edit_form_ajax($form, $form_state) {
 
   $elements = array();
-  
+
   $elements['name'] = $form['name'];
-  $elements['continue'] = $form['continue'];   
-  
+  $elements['continue'] = $form['continue'];
+
   // add back in the cv-edit-div that is used for the next round of AJAX
   $elements['name']['#prefix'] =  '<div id="cvterm-edit-div">';
-  $elements['name']['#suffix'] =  '</div">';  
-  
-    
+  $elements['name']['#suffix'] =  '</div">';
+
+
   return $elements;
 }

tripal_cv/includes/tripal_cv_admin.inc

@@ -37,573 +37,4 @@ function tripal_cv_admin_cv_listing() {
   }
 
   return $output;
-}
-
-/**
- * Purpose: Provides the form for Updating and Deleteing existing
- *   chado controlled vocabularies (See chado cv table)
- *
- * @ingroup tripal_cv
- *
-function tripal_cv_edit_page() {
-  $output .= drupal_get_form('tripal_cv_select_form');
-  $output .= '<div id="cv-edit-div">Please select a vocabulary above to view or edit</div>';
-
-  return $output;
-}
-*/
-
-/**
- * Purpose: Provides the actual "Select CV" form on the Update/Delete Controlled
- *   Vocabulary page. This form also triggers the edit javascript
- * @todo Modify this form to use Drupal AJAX
- *
- * @ingroup tripal_cv
- *
-function tripal_cv_select_form() {
-
-  // get a list of db from chado for user to choose
-  $sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
-  $results = chado_query($sql);
-
-  $cvs = array();
-  $cvs[] = '';
-  while ($cv = db_fetch_object($results)) {
-    $cvs[$cv->cv_id] = $cv->name;
-  }
-
-  $form['cvid'] = array(
-    '#title' => t('Controlled Vocabulary/Ontology Name'),
-    '#type' => 'select',
-    '#options' => $cvs,
-    '#ahah' => array(
-      'path' => 'admin/tripal/tripal_cv/cv/edit/js',
-      'wrapper' => 'cv-edit-div',
-      'effect' => 'fade',
-      'event' => 'change',
-      'method' => 'replace',
-    ),
-  );
-
-  return $form;
-}
-*/
-
-/**
- * Purpose: The edit controlled vocabulary javascript
- *
- * @ingroup tripal_cv
- *
-function tripal_ajax_cv_edit() {
-
-  // get the database id, build the form and then return the JSON object
-  $cvid = filter_xss($_POST['cvid']);
-  $form = drupal_get_form('tripal_cv_edit_form', $cvid);
-  drupal_json(array('status' => TRUE, 'data' => $form));
-
-}
-*/
-
-/**
- * Purpose: Provides a form to allow updating/deleteing of controlled vocabularies
- *
- * @ingroup tripal_cv
- *
-function tripal_cv_edit_form(&$form_state = NULL, $cvid = NULL) {
-
-  $sql = "SELECT * FROM {cv} WHERE cv_id = :cv_id ";
-  $cv = chado_query($sql, array(':cv_id' => $cvid));
-  $cv = $cv->fetch_object();
-
-  // set the default values.  If there is a value set in the
-  // form_state then let's use that, otherwise, we'll pull
-  // the values from the database
-  $default_db = $form_state['values']['name'];
-  $default_desc = $form_state['values']['description'];
-  $default_url = $form_state['values']['url'];
-  $default_urlprefix = $form_state['values']['urlprefix'];
-  if (!$default_db) {
-    $default_cv = $cv->name;
-  }
-  if (!$default_desc) {
-    $default_desc = $cv->definition;
-  }
-
-  $form['cvid'] = array(
-    '#type' => 'hidden',
-    '#value' => $cvid
-  );
-
-  $form['name']= array(
-    '#type'          => 'textfield',
-    '#title'         => t("Controlled Vocabulary name"),
-    '#description'   => t('Please enter the name for this vocabulary.'),
-    '#required'      => FALSE,
-    '#default_value' => $default_cv,
-    '#weight'        => 1
-  );
-
-  $form['definition']= array(
-    '#type'          => 'textarea',
-    '#title'         => t('Description'),
-    '#description'   => t('Please enter a description for this vocabulary'),
-    '#default_value' => $default_desc,
-    '#weight'        => 2
-  );
-
-  $form['update'] = array(
-    '#type'         => 'submit',
-    '#value'        => t('Update'),
-    '#weight'       => 5,
-    '#executes_submit_callback' => TRUE,
-  );
-  $form['delete'] = array(
-    '#type'         => 'submit',
-    '#value'        => t('Delete'),
-    '#weight'       => 6,
-    '#executes_submit_callback' => TRUE,
-  );
-
-  $form['#redirect'] = 'admin/tripal/tripal_cv';
-
-
-  return $form;
-}
-*/
-
-/**
- * Purpose: The submit function of the update/delete controlled vocabulary form
- *
- * @ingroup tripal_cv
- *
-function tripal_cv_edit_form_submit($form, &$form_state) {
-
-  $name =  $form_state['values']['name'];
-  $desc =  $form_state['values']['definition'];
-  $cvid =  $form_state['values']['cvid'];
-  $op   =  $form_state['values']['op'];
-
-  if (strcmp($op, 'Update') == 0) {
-    $sql = "
-       UPDATE {cv} SET
-         name = :name,
-         definition = :description
-       WHERE cv_id = :cv_id
-    ";
-    $db = chado_query($sql, array(':name' => $name, ':description' => $desc, ':cv_id' => $cvid));
-    if ($db) {
-      drupal_set_message(t("Controlled vocabulary updated"));
-    }
-    else {
-      drupal_set_message(t("Failed to update controlled vocabulary."), 'error');
-    }
-  }
-  if (strcmp($op, 'Delete')==0) {
-    $sql = "
-       DELETE FROM {cv}
-       WHERE cv_id = :cv_id
-    ";
-    $db = chado_query($sql, array(':cv_id' => $cvid));
-    if ($db) {
-      drupal_set_message(t("Controlled vocabulary deleted"));
-    }
-    else {
-      drupal_set_message(t("Failed to delete controlled vocabulary."), 'error');
-    }
-  }
-
-}
-*/
-
-/**
- * Purpose: Provides the Add controlled vocabulary form
- *
-  * @ingroup tripal_cv
- *
-function tripal_cv_add_form(&$form_state = NULL) {
-
-  $form['cvid'] = array(
-    '#type' => 'hidden',
-    '#value' => $cvid
-  );
-
-  $form['name']= array(
-    '#type'          => 'textfield',
-    '#title'         => t("Controlled Vocabulary name"),
-    '#description'   => t('Please enter the name for this vocabulary.  This field will be ignored if an OBO file or URL is provided above'),
-    '#required'      => FALSE,
-    '#default_value' => $default_cv,
-    '#weight'        => 1
-  );
-
-  $form['definition']= array(
-    '#type'          => 'textarea',
-    '#title'         => t('Description'),
-    '#description'   => t('Please enter a description for this vocabulary'),
-    '#default_value' => $default_desc,
-    '#weight'        => 2
-  );
-
-  $form['add'] = array(
-    '#type'         => 'submit',
-    '#value'        => t('Add'),
-    '#weight'       => 5,
-    '#executes_submit_callback' => TRUE,
-  );
-
-  $form['#redirect'] = 'admin/tripal/tripal_cv';
-
-  return $form;
-}
-*/
-/**
- * Purpose: The submit function for the add controlled vocabulary form
- *
- * @ingroup tripal_cv
- *
-function tripal_cv_add_form_submit($form, &$form_state) {
-
-  $name =  $form_state['values']['name'];
-  $desc =  $form_state['values']['definition'];
-
-  $sql = "
-    INSERT INTO {cv}
-     (name,definition)
-    VALUES
-     (:name, :description)
-  ";
-  $db = chado_query($sql, array(':name' => $name, ':description' => $desc));
-  if ($db) {
-    drupal_set_message(t("Controlled vocabulary added"));
-  }
-  else {
-    drupal_set_message(t("Failed to add controlled vocabulary."), 'error');
-  }
-
-}
-*/
-/**
- * Purpose: Provides the form that allows adding of terms to an existing
- *   controlled vocabulary
- *
-  * @ingroup tripal_cv
- *
-function tripal_cv_cvterm_form(&$form_state, $action = 'add') {
-  tripal_core_ahah_init_form();
-
-  $form = array();
-
-  // get defaults
-  $cv_id = $form_state['values']['cv_id'] ? $form_state['values']['cv_id'] : FALSE;
-  $name  = $form_state['values']['name'] ? $form_state['values']['name'] : '';
-
-  // if we have a cv_id and a term name then get the rest of the term details
-  if ($cv_id and $name) {
-     $values = array(
-       'cv_id' => $cv_id,
-       'name' => $name,
-     );
-     $results = tripal_core_chado_select('cvterm', array('*'), $values);
-     if (!$results or count($results) == 0) {
-       // we can't find the cvterm so reset the name to blank
-       $name = '';
-     }
-     else {
-       $cvterm = $results[0];
-       $definition = $cvterm->definition;
-       $is_relationshiptype = $cvterm->is_relationshiptype;
-       $is_obsolete = $cvterm->is_obsolete;
-
-       // now get the database
-       $values = array('dbxref_id' => $cvterm->dbxref_id);
-       $results = tripal_core_chado_select('dbxref', array('*'), $values);
-       $dbxref = $results[0];
-       $accession = $dbxref->accession;
-       $db_id = $dbxref->db_id;
-     }
-  }
-
-  $values = array();
-  $columns = array('cv_id', 'name');
-  $options = array('order_by' => array('name' => 'ASC'));
-  $results = tripal_core_chado_select('cv', $columns, $values, $options);
-  $cvs = array();
-  $cvs[] = '';
-  foreach ($results as $cv) {
-    $cvs[$cv->cv_id] = $cv->name;
-  }
-
-  $form['wrapper-top'] = array(
-    '#type' => 'markup',
-    '#value' => '<div id="cvterm-form">',
-  );
-
-  $form['form_action'] = array(
-    '#type' => 'hidden',
-    '#value' => $action,
-  );
-
-  $form['cv_id'] = array(
-    '#title' => t('Controlled Vocabulary (Ontology) Name'),
-    '#type' => 'select',
-    '#options' => $cvs,
-    '#required' => TRUE,
-    '#default_value' => $cv_id,
-    '#ahah' => array(
-       'path'    => 'admin/tripal/tripal_cv/cvterm/ahah',
-       'wrapper' => 'cvterm-form',
-       'event'   => 'change',
-       'method'  => 'replace',
-    ),
-  );
-
-  if ($cv_id) {
-    $form['add_cvterm'] = array(
-      '#type'           => 'fieldset',
-      '#title'          => t('Term Details'),
-      '#prefix'         => '<div id="cvterm-add-div">',
-      '#suffix'         => '</div>'
-    );
-    $description = t('Please enter the name for this vocabulary term.');
-    if ($action == 'edit') {
-      $description = t('Enter the name of the term to edit.  This field will update automatically as you type. Click outside of the box after entering the term.');
-    }
-    $form['add_cvterm']['name']= array(
-      '#type'          => 'textfield',
-      '#title'         => t("Term Name"),
-      '#description'   => $description,
-      '#default_value' => $name,
-      '#required'      => TRUE,
-    );
-    if ($action == 'edit') {
-      if ($name) {
-        $form['add_cvterm']['name']['#attributes'] = array('readonly' => 'readonly');
-        $form['add_cvterm']['name']['#description'] = 'The term name cannot be changed. If the name is incorrect, please create a new term and make this one as obsolete.';
-      }
-      else {
-        $form['add_cvterm']['name']['#autocomplete_path'] = "admin/tripal/tripal_cv/cvterm/auto_name/$cv_id";
-        $form['add_cvterm']['name']['#ahah'] = array(
-           'path'    => 'admin/tripal/tripal_cv/cvterm/ahah',
-           'wrapper' => 'cvterm-form',
-           'method'  => 'replace',
-        );
-      }
-    }
-
-    if ($action == 'add' or $name) {
-
-
-      $form['add_cvterm']['definition']= array(
-        '#type'          => 'textarea',
-        '#title'         => t('Description'),
-        '#description'   => t('Please enter a description for this term'),
-        '#default_value' => $definition,
-      );
-
-      $form['add_cvterm']['is_relationshiptype'] = array(
-        '#type'          => 'checkbox',
-        '#title'         => t('This term describes a relationship?'),
-        '#default_value' => $is_relationshiptype,
-      );
-
-      $form['add_cvterm']['is_obsolete'] = array(
-        '#type'          => 'checkbox',
-        '#title'         => t('This term is obsolete?'),
-        '#default_value' => $is_obsolete,
-      );
-
-      $values = array();
-      $columns = array('db_id', 'name');
-      $options = array('order_by' => array('name' => 'ASC'));
-      $results = tripal_core_chado_select('db', $columns, $values, $options);
-      $dbs = array();
-      $dbs[] = '';
-      foreach ($results as $db) {
-        $dbs[$db->db_id] = $db->name;
-      }
-      $form['add_cvterm']['db_id'] = array(
-        '#type'         => 'select',
-        '#title'         => t('Database'),
-        '#description'   => t('All terms must be assocated with an external database.
-                            Please select the external database to associate with
-                            this term'),
-        '#options'      => $dbs,
-        '#default_value' => $db_id,
-        '#required' => TRUE,
-      );
-      if ($action == 'edit') {
-        // we don't want to allow the user to change the database on an edit.
-        $form['add_cvterm']['db_id']['#disabled'] = TRUE;
-        $form['add_cvterm']['db_id']['#description'] = 'The database to which this term belongs cannot be changed.';
-      }
-
-      $form['add_cvterm']['accession']= array(
-        '#type'          => 'textfield',
-        '#title'         => t("Accession"),
-        '#description'   => t('If this term has an existing accession (unique identifier) in the database
-           please enter that here.  If the accession is numeric with a database prefix (e.g. GO:003023), please
-           enter just the numeric value.  The database prefix will be appended whenever the term is displayed.
-           If the accession is not numeric then enter it as is.  If no value is provied, the term name
-           provided above will be used as the accession.'),
-        '#required'      => FALSE,
-        '#default_value' => $accession,
-      );
-      if ($action == 'edit') {
-        $form['add_cvterm']['accession']['#attributes'] = array('readonly' => 'readonly');
-        $form['add_cvterm']['accession']['#description'] = 'Cannot change the term accession.';
-      }
-      $button_text = 'Add Term';
-      if ($action == 'edit') {
-        $button_text = 'Update Term';
-      }
-      $form['add_cvterm']['submit'] = array(
-        '#type'  => 'submit',
-        '#value' => $button_text,
-      );
-    } // end if name selected (or action == 'add')
-  } //end of if cv selected
-
-
-  $form['wrapper-bottom'] = array(
-    '#type' => 'markup',
-    '#value' => '</div>',
-  );
-
-  return $form;
-}
-*/
-
-/**
- * Purpose: Validates the input for adding a cvterm
- *
-  * @ingroup tripal_cv
- *
-function tripal_cv_cvterm_form_validate($form, &$form_state) {
-
-  // Ensure that submit does not get called unless the AHAH in the form was called
-  if (!empty($form_state['ahah_submission'])) {
-    return;
-  }
-
-}
-*/
-/**
- * Purpose: Adds terms to an existing controlled vocabulary
- *
- * @ingroup tripal_cv
- *
-function tripal_cv_cvterm_form_submit($form, &$form_state) {
-
-  // Ensure the AHAH in the form was called
-  if (!empty($form_state['ahah_submission'])) {
-    return;
-  }
-
-  // get the database
-  $values = array('db_id' => $form_state['values']['db_id']);
-  $results = tripal_core_chado_select('db', array('name'), $values);
-  if (!$results or count($results) == 0) {
-    drupal_set_message(t('Unable to add term.  Cannot find the database.'), 'error');
-    return;
-  }
-  $db = $results[0];
-
-  // get the cv
-  $values = array('cv_id' => $form_state['values']['cv_id']);
-  $results = tripal_core_chado_select('cv', array('name'), $values);
-  if (!$results or count($results) == 0) {
-    drupal_set_message(t('Unable to add term.  Cannot find the vocabulary.'), 'error');
-    return;
-  }
-  $cv = $results[0];
-
-  // get the accession for this term
-  $accession = $form_state['values']['accession'];
-  if (!$accession) {
-    $accession = $form_state['values']['name'];
-  }
-  if (is_numeric($accession)) {
-    $accession = $db->name . ":" . $accession;
-  }
-
-
-  $update = 0;
-  if ($form_state['values']['form_action'] == 'edit') {
-    $update = 1;
-  }
-
-  // now add the term
-  $term = array(
-    'name' => $form_state['values']['name'],
-    'namespace' => $cv->name,
-    'id' => $accession,
-    'def' => $form_state['values']['definition'],
-    'is_obsolete' => $form_state['values']['is_obsolete'],
-  );
-
-  $is_relationship = $form_state['values']['is_relationshiptype'];
-  $cvterm = tripal_cv_add_cvterm($term, $cv->name, $is_relationship, $update, $db->name);
-  if ($cvterm) {
-    if (!$update) {
-      drupal_set_message('Term added successfully.');
-    }
-    else {
-      drupal_set_message('Term updated successfully.');
-    }
-  }
-  else {
-    drupal_set_message('Could not add term. Check Drupal recent logs for error messages.', 'error');
-  }
-
-}
-*/
-/**
- * Purpose: This function gets called when the selecting of a cv from
- *   the select list triggers it. This function simply rebuilds the form
- *   with new information. No elements are created here
- *
- * @ingroup tripal_cv
- *
-function tripal_cv_cvterm_callback() {
-  $status = TRUE;
-
-  // prepare and render the form
-  $form = tripal_core_ahah_prepare_form();
-  $data = drupal_render($form);
-
-  // bind javascript events to the new objects that will be returned
-  // so that AHAH enabled elements will work.
-  $settings = tripal_core_ahah_bind_events();
-
-  // return the updated JSON
-  drupal_json(
-    array(
-      'status'   => $status,
-      'data'     => $data,
-      'settings' => $settings,
-    )
-  );
-}
-*/
-/**
- * Cvterm path form submit
- *
- * @ingroup tripal_cv
- *
-function tripal_cv_cvtermpath_form_submit($form, &$form_state) {
-  global $user;
-
-  $cvid =  $form_state['values']['cvid'];
-
-  // first get the controlled vocabulary name:
-  $cv = chado_query("SELECT * FROM {cv} WHERE cv_id = :cv_id", array(':cv_id' => $cvid));
-  $cv = $cv->fetch_object();
-
-  // Submit a job to update cvtermpath
-  $job_args = array($cvid);
-  if ($form_state['values']['op'] == t('Update cvtermpath')) {
-    tripal_add_job("Update cvtermpath: $cv->name", 'tripal_cv',
-       'tripal_cv_update_cvtermpath', $job_args, $user->uid);
-  }
-}
-*/
+}

tripal_cv/tripal_cv.info

@@ -7,4 +7,5 @@ version = 7.x-2.0-beta1
 configure = admin/tripal/chado/tripal_cv
 
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_db

tripal_cv/tripal_cv.install

@@ -5,6 +5,20 @@
  * Contains functions executed only on install/uninstall of this module
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_cv_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_cv.views_default.inc");
+  $views = tripal_cv_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_requirements().
  */
@@ -31,10 +45,10 @@ function tripal_cv_install() {
 
   // create the module's data directory
   tripal_create_moddir('tripal_cv');
-    
-  // add the cv_root_mview 
+
+  // add the cv_root_mview
   tripal_cv_add_cv_root_mview();
-  
+
   // create the tables that correlate OBO files/references with a chado CV
   tripal_cv_add_obo_defaults();
 }
@@ -45,9 +59,12 @@ function tripal_cv_install() {
  */
 function tripal_cv_uninstall() {
   // remove the materialized view
+  // D7 @todo Fix tripal_mviews_get_mview_id()
+  /**
   if ($mview = tripal_mviews_get_mview_id('cv_root_mview')) {
     tripal_mviews_action('delete', $mview);
   }
+  */
 }
 
 /**
@@ -56,20 +73,20 @@ function tripal_cv_uninstall() {
  * @ingroup tripal_cv
  */
 function tripal_cv_schema() {
-  
+
   $schema['tripal_cv_obo'] = array(
     'fields' => array(
       'obo_id' => array(
-        'type' => 'serial', 
-        'unsigned' => TRUE, 
+        'type' => 'serial',
+        'unsigned' => TRUE,
         'not null' => TRUE
       ),
       'name' => array(
-        'type' => 'varchar', 
+        'type' => 'varchar',
          'length' => 255
        ),
       'path'  => array(
-        'type' => 'varchar', 
+        'type' => 'varchar',
         'length' => 1024
       ),
     ),
@@ -83,7 +100,7 @@ function tripal_cv_schema() {
 }
 
 /**
- * 
+ *
  * @ingroup tripal_cv
  */
 function tripal_cv_add_cv_root_mview() {
@@ -104,7 +121,7 @@ function tripal_cv_add_cv_root_mview() {
       ),
       'cv_id' => array(
         'type' => 'int',
-        'not null' => TRUE, 
+        'not null' => TRUE,
       ),
       'cv_name' => array(
         'type' => 'varchar',
@@ -117,7 +134,7 @@ function tripal_cv_add_cv_root_mview() {
       'cv_root_mview_indx2' => array('cv_id'),
     ),
   );
-  
+
   $sql = "
     SELECT DISTINCT CVT.name,CVT.cvterm_id, CV.cv_id, CV.name
     FROM cvterm_relationship CVTR
@@ -126,7 +143,7 @@ function tripal_cv_add_cv_root_mview() {
     WHERE CVTR.object_id not in
       (SELECT subject_id FROM cvterm_relationship)
   ";
-  
+
   // Create the MView
   tripal_add_mview($mv_name, 'tripal_cv', $schema, $sql, $comment);
 }

tripal_cv/tripal_cv.module

@@ -58,7 +58,7 @@ function tripal_cv_menu() {
     'title' => 'Help',
     'description' => "A description of the Tripal Controlled Vocabulary module including a short description of it's usage.",
     'page callback' => 'theme',
-    'page arguments' => array('tripal_cv_help'),
+    'page arguments' => array('tripal_cv_admin'),
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
@@ -89,17 +89,17 @@ function tripal_cv_menu() {
   /*
    * Menu items for adding and editing CVs
    */
-  $items['admin/tripal/chado/tripal_cv/edit_cv'] = array(
+  $items['admin/tripal/chado/tripal_cv/cv/edit/%'] = array(
     'title' => 'Edit a Controlled Vocabulary',
     'description' => 'Edit the details such as name and description for an existing controlled vocabulary.',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_cv_cv_edit_form'),
+    'page arguments' => array('tripal_cv_cv_edit_form', 6),
     'access callback' => 'user_access',
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
 
-  $items['admin/tripal/chado/tripal_cv/add_cv'] = array(
+  $items['admin/tripal/chado/tripal_cv/cv/add'] = array(
     'title' => 'Add a Controlled Vocabulary',
     'description' => 'Manually a new controlled vocabulary.',
     'page callback' => 'drupal_get_form',
@@ -112,6 +112,14 @@ function tripal_cv_menu() {
   /*
    * Menu items for adding and editing CVterms
    */
+  $items['admin/tripal/chado/tripal_cv/cv/%/cvterm/add'] = array(
+    'title' => 'Add a Controlled Vocabulary Term',
+    'description' => 'Add a new controlled vocabulary term.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_cv_cvterm_add_form',5),
+    'access arguments' => array('administer controlled vocabularies'),
+    'type' => MENU_CALLBACK,
+  );
   $items['admin/tripal/chado/tripal_cv/cvterm/add'] = array(
     'title' => 'Add a Controlled Vocabulary Term',
     'description' => 'Add a new controlled vocabulary term.',
@@ -120,11 +128,11 @@ function tripal_cv_menu() {
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/chado/tripal_cv/cvterm/edit/%'] = array(
+  $items['admin/tripal/chado/tripal_cv/cv/%/cvterm/edit/%'] = array(
     'title' => 'Edit a Controlled Vocabulary Term',
     'description' => 'Edit an existing controlled vocabulary term.',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_cv_cvterm_edit_form'),
+    'page arguments' => array('tripal_cv_cvterm_edit_form',5,8),
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
@@ -287,8 +295,8 @@ function tripal_cv_form_alter(&$form, &$form_state, $form_id) {
 function tripal_cv_theme() {
   $theme_path = drupal_get_path('module', 'tripal_cv') . '/theme';
   $items = array(
-    'tripal_cv_help' => array(
-      'template' => 'tripal_cv_help',
+    'tripal_cv_admin' => array(
+      'template' => 'tripal_cv_admin',
       'arguments' =>  array(NULL),
       'path' => $theme_path,
     ),

tripal_cv/tripal_cv.views_default.inc

@@ -21,159 +21,185 @@ function tripal_cv_views_default_views() {
  */
 function tripal_cv_defaultview_admin_cvs_listing() {
 
-  $view = new view();
-  $view->name = 'tripal_cv_admin_cvs';
-  $view->description = 'A listing of all controlled vocabularies';
-  $view->tag = 'tripal admin';
-  $view->base_table = 'cv';
-  $view->human_name = 'CVs Admin';
-  $view->core = 6;
-  $view->api_version = '3.0';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+$view = new view();
+$view->name = 'tripal_cv_admin_cvs';
+$view->description = 'DO NOT DISABLE';
+$view->tag = 'tripal admin';
+$view->base_table = 'cv';
+$view->human_name = 'CVs Admin';
+$view->core = 6;
+$view->api_version = '3.0';
+$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
 
-  /* Display: Defaults */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->display->display_options['title'] = 'Controlled Vocabularies';
-  $handler->display->display_options['use_more_always'] = FALSE;
-  $handler->display->display_options['access']['type'] = 'perm';
-  $handler->display->display_options['access']['perm'] = 'administer controlled vocabularies';
-  $handler->display->display_options['cache']['type'] = 'none';
-  $handler->display->display_options['query']['type'] = 'views_query';
-  $handler->display->display_options['exposed_form']['type'] = 'basic';
-  $handler->display->display_options['pager']['type'] = 'full';
-  $handler->display->display_options['pager']['options']['items_per_page'] = '25';
-  $handler->display->display_options['pager']['options']['offset'] = '0';
-  $handler->display->display_options['pager']['options']['id'] = '0';
-  $handler->display->display_options['pager']['options']['quantity'] = '9';
-  $handler->display->display_options['style_plugin'] = 'table';
-  $handler->display->display_options['style_options']['grouping'] = '';
-  $handler->display->display_options['style_options']['columns'] = array(
-    'name' => 'name',
-    'definition' => 'definition',
-    'nothing' => 'nothing',
+/* Display: Defaults */
+$handler = $view->new_display('default', 'Defaults', 'default');
+$handler->display->display_options['title'] = 'Controlled Vocabularies';
+$handler->display->display_options['use_more_always'] = FALSE;
+$handler->display->display_options['access']['type'] = 'perm';
+$handler->display->display_options['access']['perm'] = 'administer controlled vocabularies';
+$handler->display->display_options['cache']['type'] = 'none';
+$handler->display->display_options['query']['type'] = 'views_query';
+$handler->display->display_options['exposed_form']['type'] = 'basic';
+$handler->display->display_options['pager']['type'] = 'full';
+$handler->display->display_options['pager']['options']['items_per_page'] = '25';
+$handler->display->display_options['pager']['options']['offset'] = '0';
+$handler->display->display_options['pager']['options']['id'] = '0';
+$handler->display->display_options['pager']['options']['quantity'] = '9';
+$handler->display->display_options['style_plugin'] = 'table';
+$handler->display->display_options['style_options']['grouping'] = '';
+$handler->display->display_options['style_options']['columns'] = array(
+  'name' => 'name',
+  'definition' => 'definition',
+  'nothing' => 'nothing',
+);
+$handler->display->display_options['style_options']['default'] = 'name';
+$handler->display->display_options['style_options']['info'] = array(
+  'name' => array(
+    'sortable' => 1,
+    'separator' => '',
+  ),
+  'definition' => array(
+    'sortable' => 0,
+    'separator' => '',
+  ),
+  'nothing' => array(
+    'separator' => '',
+  ),
+);
+/* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Vocabulary',
+    'path-1' => 'admin/tripal/chado/tripal_cv/cv/add',
   );
-  $handler->display->display_options['style_options']['default'] = 'name';
-  $handler->display->display_options['style_options']['info'] = array(
-    'name' => array(
-      'sortable' => 1,
-      'separator' => '',
-    ),
-    'definition' => array(
-      'sortable' => 0,
-      'separator' => '',
-    ),
-    'nothing' => array(
-      'separator' => '',
-    ),
-  );
-  /* Header: Global: Text area */
-  $handler->display->display_options['header']['text']['id'] = 'text';
-  $handler->display->display_options['header']['text']['table'] = 'views';
-  $handler->display->display_options['header']['text']['field'] = 'area';
-  $handler->display->display_options['header']['text']['label'] = 'Add Cv';
-  $handler->display->display_options['header']['text']['empty'] = TRUE;
-  $handler->display->display_options['header']['text']['content'] = '<ul class="action-links">
-          <li><a href="tripal_cv/add_cv">Add Vocabulary</a></li>
-          <li><a href="tripal_cv/obo_loader">Load Ontology</a></li>
-     </ul>';
-  $handler->display->display_options['header']['text']['format'] = 'full_html';
-  /* No results behavior: Global: Text area */
-  $handler->display->display_options['empty']['text']['id'] = 'area';
-  $handler->display->display_options['empty']['text']['table'] = 'views';
-  $handler->display->display_options['empty']['text']['field'] = 'area';
-  $handler->display->display_options['empty']['text']['content'] = 'No controlled vocabularies match the supplied criteria.';
-  $handler->display->display_options['empty']['text']['format'] = '2';
-  /* Field: Chado Cv: Cv Id */
-  $handler->display->display_options['fields']['cv_id']['id'] = 'cv_id';
-  $handler->display->display_options['fields']['cv_id']['table'] = 'cv';
-  $handler->display->display_options['fields']['cv_id']['field'] = 'cv_id';
-  $handler->display->display_options['fields']['cv_id']['exclude'] = TRUE;
-  $handler->display->display_options['fields']['cv_id']['separator'] = '';
-  /* Field: Chado Cv: Name */
-  $handler->display->display_options['fields']['name']['id'] = 'name';
-  $handler->display->display_options['fields']['name']['table'] = 'cv';
-  $handler->display->display_options['fields']['name']['field'] = 'name';
-  /* Field: Chado Cv: Definition */
-  $handler->display->display_options['fields']['definition']['id'] = 'definition';
-  $handler->display->display_options['fields']['definition']['table'] = 'cv';
-  $handler->display->display_options['fields']['definition']['field'] = 'definition';
-  /* Field: Global: Custom text */
-  $handler->display->display_options['fields']['nothing_1']['id'] = 'nothing_1';
-  $handler->display->display_options['fields']['nothing_1']['table'] = 'views';
-  $handler->display->display_options['fields']['nothing_1']['field'] = 'nothing';
-  $handler->display->display_options['fields']['nothing_1']['label'] = 'Edit Link';
-  $handler->display->display_options['fields']['nothing_1']['exclude'] = TRUE;
-  $handler->display->display_options['fields']['nothing_1']['alter']['text'] = 'edit';
-  $handler->display->display_options['fields']['nothing_1']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'tripal_cv/edit_cv/[cv_id]';
-  /* Field: Global: Custom text */
-  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
-  $handler->display->display_options['fields']['nothing']['table'] = 'views';
-  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
-  $handler->display->display_options['fields']['nothing']['label'] = 'View Terms link';
-  $handler->display->display_options['fields']['nothing']['exclude'] = TRUE;
-  $handler->display->display_options['fields']['nothing']['alter']['text'] = 'View Terms';
-  $handler->display->display_options['fields']['nothing']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/tripal_cv/list_cvterms?cv%5B%5D=[name]';
-  $handler->display->display_options['fields']['nothing']['hide_alter_empty'] = TRUE;
-  /* Field: Global: Custom text */
-  $handler->display->display_options['fields']['nothing_2']['id'] = 'nothing_2';
-  $handler->display->display_options['fields']['nothing_2']['table'] = 'views';
-  $handler->display->display_options['fields']['nothing_2']['field'] = 'nothing';
-  $handler->display->display_options['fields']['nothing_2']['label'] = '';
-  $handler->display->display_options['fields']['nothing_2']['alter']['text'] = '[nothing_1]<br />
-  [nothing]';
-  $handler->display->display_options['fields']['nothing_2']['element_class'] = 'short-column';
-  $handler->display->display_options['fields']['nothing_2']['element_label_class'] = 'short-column';
-  $handler->display->display_options['fields']['nothing_2']['element_label_colon'] = FALSE;
-  /* Sort criterion: Chado Cv: Name */
-  $handler->display->display_options['sorts']['name']['id'] = 'name';
-  $handler->display->display_options['sorts']['name']['table'] = 'cv';
-  $handler->display->display_options['sorts']['name']['field'] = 'name';
-  /* Filter criterion: Chado Cv: Name */
-  $handler->display->display_options['filters']['name']['id'] = 'name';
-  $handler->display->display_options['filters']['name']['table'] = 'cv';
-  $handler->display->display_options['filters']['name']['field'] = 'name';
-  $handler->display->display_options['filters']['name']['operator'] = 'contains';
-  $handler->display->display_options['filters']['name']['group'] = '0';
-  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['name']['expose']['operator_id'] = 'name_op';
-  $handler->display->display_options['filters']['name']['expose']['label'] = 'Name Contains';
-  $handler->display->display_options['filters']['name']['expose']['operator'] = 'name_op';
-  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'name';
-  $handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
-  );
-  /* Filter criterion: Chado Cv: Definition */
-  $handler->display->display_options['filters']['definition']['id'] = 'definition';
-  $handler->display->display_options['filters']['definition']['table'] = 'cv';
-  $handler->display->display_options['filters']['definition']['field'] = 'definition';
-  $handler->display->display_options['filters']['definition']['operator'] = 'contains';
-  $handler->display->display_options['filters']['definition']['group'] = '0';
-  $handler->display->display_options['filters']['definition']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['definition']['expose']['operator_id'] = 'definition_op';
-  $handler->display->display_options['filters']['definition']['expose']['label'] = 'Definition Contains';
-  $handler->display->display_options['filters']['definition']['expose']['operator'] = 'definition_op';
-  $handler->display->display_options['filters']['definition']['expose']['identifier'] = 'definition';
-  $handler->display->display_options['filters']['definition']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
+  $handler->display->display_options['header']['action_links_area']['link-2'] = array(
+    'label-2' => 'Load Ontology',
+    'path-2' => 'admin/tripal/chado/tripal_cv/obo_loader',
   );
+/* No results behavior: Global: Text area */
+$handler->display->display_options['empty']['text']['id'] = 'area';
+$handler->display->display_options['empty']['text']['table'] = 'views';
+$handler->display->display_options['empty']['text']['field'] = 'area';
+$handler->display->display_options['empty']['text']['content'] = 'No controlled vocabularies match the supplied criteria.';
+$handler->display->display_options['empty']['text']['format'] = '2';
+/* Field: Chado Cv: Cv Id */
+$handler->display->display_options['fields']['cv_id']['id'] = 'cv_id';
+$handler->display->display_options['fields']['cv_id']['table'] = 'cv';
+$handler->display->display_options['fields']['cv_id']['field'] = 'cv_id';
+$handler->display->display_options['fields']['cv_id']['exclude'] = TRUE;
+$handler->display->display_options['fields']['cv_id']['separator'] = '';
+/* Field: Chado Cv: Name */
+$handler->display->display_options['fields']['name']['id'] = 'name';
+$handler->display->display_options['fields']['name']['table'] = 'cv';
+$handler->display->display_options['fields']['name']['field'] = 'name';
+/* Field: Chado Cv: Definition */
+$handler->display->display_options['fields']['definition']['id'] = 'definition';
+$handler->display->display_options['fields']['definition']['table'] = 'cv';
+$handler->display->display_options['fields']['definition']['field'] = 'definition';
+/* Field: Global: Custom text */
+$handler->display->display_options['fields']['nothing_1']['id'] = 'nothing_1';
+$handler->display->display_options['fields']['nothing_1']['table'] = 'views';
+$handler->display->display_options['fields']['nothing_1']['field'] = 'nothing';
+$handler->display->display_options['fields']['nothing_1']['label'] = 'Edit Link';
+$handler->display->display_options['fields']['nothing_1']['exclude'] = TRUE;
+$handler->display->display_options['fields']['nothing_1']['alter']['text'] = 'edit';
+$handler->display->display_options['fields']['nothing_1']['alter']['make_link'] = TRUE;
+$handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'admin/tripal/chado/tripal_cv/cv/edit/[cv_id]';
+/* Field: Global: Custom text */
+$handler->display->display_options['fields']['nothing']['id'] = 'nothing';
+$handler->display->display_options['fields']['nothing']['table'] = 'views';
+$handler->display->display_options['fields']['nothing']['field'] = 'nothing';
+$handler->display->display_options['fields']['nothing']['label'] = 'View Terms link';
+$handler->display->display_options['fields']['nothing']['exclude'] = TRUE;
+$handler->display->display_options['fields']['nothing']['alter']['text'] = 'View Terms';
+$handler->display->display_options['fields']['nothing']['alter']['make_link'] = TRUE;
+$handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/chado/tripal_cv/cvterms?cv=[name]';
+$handler->display->display_options['fields']['nothing']['hide_alter_empty'] = TRUE;
+/* Field: Global: Custom text */
+$handler->display->display_options['fields']['nothing_3']['id'] = 'nothing_3';
+$handler->display->display_options['fields']['nothing_3']['table'] = 'views';
+$handler->display->display_options['fields']['nothing_3']['field'] = 'nothing';
+$handler->display->display_options['fields']['nothing_3']['label'] = 'Add term';
+$handler->display->display_options['fields']['nothing_3']['exclude'] = TRUE;
+$handler->display->display_options['fields']['nothing_3']['alter']['text'] = 'Add Term';
+$handler->display->display_options['fields']['nothing_3']['alter']['make_link'] = TRUE;
+$handler->display->display_options['fields']['nothing_3']['alter']['path'] = 'admin/tripal/chado/tripal_cv/cv/[cv_id]/cvterm/add';
+/* Field: Global: Custom text */
+$handler->display->display_options['fields']['nothing_2']['id'] = 'nothing_2';
+$handler->display->display_options['fields']['nothing_2']['table'] = 'views';
+$handler->display->display_options['fields']['nothing_2']['field'] = 'nothing';
+$handler->display->display_options['fields']['nothing_2']['label'] = '';
+$handler->display->display_options['fields']['nothing_2']['alter']['text'] = '[nothing_1]<br />
+  [nothing]   [nothing_3]';
+$handler->display->display_options['fields']['nothing_2']['element_class'] = 'short-column';
+$handler->display->display_options['fields']['nothing_2']['element_label_class'] = 'short-column';
+$handler->display->display_options['fields']['nothing_2']['element_label_colon'] = FALSE;
+/* Sort criterion: Chado Cv: Name */
+$handler->display->display_options['sorts']['name']['id'] = 'name';
+$handler->display->display_options['sorts']['name']['table'] = 'cv';
+$handler->display->display_options['sorts']['name']['field'] = 'name';
+/* Filter criterion: Chado Cv: Name */
+$handler->display->display_options['filters']['name']['id'] = 'name';
+$handler->display->display_options['filters']['name']['table'] = 'cv';
+$handler->display->display_options['filters']['name']['field'] = 'name';
+$handler->display->display_options['filters']['name']['operator'] = 'contains';
+$handler->display->display_options['filters']['name']['group'] = '0';
+$handler->display->display_options['filters']['name']['exposed'] = TRUE;
+$handler->display->display_options['filters']['name']['expose']['operator_id'] = 'name_op';
+$handler->display->display_options['filters']['name']['expose']['label'] = 'Name Contains';
+$handler->display->display_options['filters']['name']['expose']['operator'] = 'name_op';
+$handler->display->display_options['filters']['name']['expose']['identifier'] = 'name';
+$handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
+  2 => '2',
+  1 => 0,
+  3 => 0,
+);
+/* Filter criterion: Chado Cv: Definition */
+$handler->display->display_options['filters']['definition']['id'] = 'definition';
+$handler->display->display_options['filters']['definition']['table'] = 'cv';
+$handler->display->display_options['filters']['definition']['field'] = 'definition';
+$handler->display->display_options['filters']['definition']['operator'] = 'contains';
+$handler->display->display_options['filters']['definition']['group'] = '0';
+$handler->display->display_options['filters']['definition']['exposed'] = TRUE;
+$handler->display->display_options['filters']['definition']['expose']['operator_id'] = 'definition_op';
+$handler->display->display_options['filters']['definition']['expose']['label'] = 'Definition Contains';
+$handler->display->display_options['filters']['definition']['expose']['operator'] = 'definition_op';
+$handler->display->display_options['filters']['definition']['expose']['identifier'] = 'definition';
+$handler->display->display_options['filters']['definition']['expose']['remember_roles'] = array(
+  2 => '2',
+  1 => 0,
+  3 => 0,
+);
+
+  /** MANUALLY ADD since filter handler no exporting correctly */
+  $handler->display->display_options['filters']['name']['expose']['values_form_type'] = 'textfield';
+  $handler->display->display_options['filters']['name']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['name']['expose']['select_optional'] = FALSE;
+  $handler->display->display_options['filters']['name']['expose']['max_length'] = 40;
 
-  /* Display: Page */
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_cv/cvs';
-  $handler->display->display_options['menu']['type'] = 'default tab';
-  $handler->display->display_options['menu']['title'] = 'Vocabularies';
-  $handler->display->display_options['menu']['description'] = 'A listing of all controlled vocabularies';
-  $handler->display->display_options['menu']['weight'] = '-10';
-  $handler->display->display_options['menu']['name'] = 'management';
-  $handler->display->display_options['menu']['context'] = 0;
-  $handler->display->display_options['menu']['context_only_inline'] = 0;
-  $handler->display->display_options['tab_options']['weight'] = '0';
+/* Display: Page */
+$handler = $view->new_display('page', 'Page', 'page_1');
+$handler->display->display_options['path'] = 'admin/tripal/chado/tripal_cv/cvs';
+$handler->display->display_options['menu']['type'] = 'default tab';
+$handler->display->display_options['menu']['title'] = 'Vocabularies';
+$handler->display->display_options['menu']['description'] = 'A listing of all controlled vocabularies';
+$handler->display->display_options['menu']['weight'] = '-10';
+$handler->display->display_options['menu']['name'] = 'management';
+$handler->display->display_options['menu']['context'] = 0;
+$handler->display->display_options['menu']['context_only_inline'] = 0;
+$handler->display->display_options['tab_options']['weight'] = '0';
+
+
+  /** MANUALLY ADD since filter handler no exporting correctly
+  $handler->display->display_options['filters']['name']['expose']['values_form_type'] = 'textfield';
+  $handler->display->display_options['filters']['name']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['name']['expose']['select_optional'] = FALSE;
+  $handler->display->display_options['filters']['name']['expose']['max_length'] = 40;
+  */
 
   return $view;
 }
@@ -183,217 +209,238 @@ function tripal_cv_defaultview_admin_cvs_listing() {
  */
 function tripal_cv_defaultview_admin_cvterms_listing() {
 
-  $view = new view();
-  $view->name = 'tripal_cv_admin_cvterms';
-  $view->description = 'A listing of all controlled vocabulary terms filtered by controlled vocabulary';
-  $view->tag = 'tripal admin';
-  $view->base_table = 'cvterm';
-  $view->human_name = 'CV Terms Admin';
-  $view->core = 0;
-  $view->api_version = '3.0';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+$view = new view();
+$view->name = 'tripal_cv_admin_cvterms';
+$view->description = 'DO NOT DISABLE';
+$view->tag = 'tripal admin';
+$view->base_table = 'cvterm';
+$view->human_name = 'CV Terms Admin';
+$view->core = 0;
+$view->api_version = '3.0';
+$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
 
-  /* Display: Defaults */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->display->display_options['title'] = 'Controlled Vocabulary Terms';
-  $handler->display->display_options['use_more_always'] = FALSE;
-  $handler->display->display_options['access']['type'] = 'perm';
-  $handler->display->display_options['access']['perm'] = 'administer controlled vocabularies';
-  $handler->display->display_options['cache']['type'] = 'none';
-  $handler->display->display_options['query']['type'] = 'views_query';
-  $handler->display->display_options['exposed_form']['type'] = 'basic';
-  $handler->display->display_options['pager']['type'] = 'full';
-  $handler->display->display_options['pager']['options']['items_per_page'] = '25';
-  $handler->display->display_options['pager']['options']['offset'] = '0';
-  $handler->display->display_options['pager']['options']['id'] = '0';
-  $handler->display->display_options['pager']['options']['quantity'] = '9';
-  $handler->display->display_options['style_plugin'] = 'table';
-  $handler->display->display_options['style_options']['grouping'] = '';
-  $handler->display->display_options['style_options']['columns'] = array(
-    'name_1' => 'name_1',
-    'name' => 'name',
-    'definition' => 'definition',
-    'is_obsolete' => 'is_obsolete',
-    'is_relationshiptype' => 'is_relationshiptype',
+/* Display: Defaults */
+$handler = $view->new_display('default', 'Defaults', 'default');
+$handler->display->display_options['title'] = 'Controlled Vocabulary Terms';
+$handler->display->display_options['use_more_always'] = FALSE;
+$handler->display->display_options['access']['type'] = 'perm';
+$handler->display->display_options['access']['perm'] = 'administer controlled vocabularies';
+$handler->display->display_options['cache']['type'] = 'none';
+$handler->display->display_options['query']['type'] = 'views_query';
+$handler->display->display_options['exposed_form']['type'] = 'basic';
+$handler->display->display_options['pager']['type'] = 'full';
+$handler->display->display_options['pager']['options']['items_per_page'] = '25';
+$handler->display->display_options['pager']['options']['offset'] = '0';
+$handler->display->display_options['pager']['options']['id'] = '0';
+$handler->display->display_options['pager']['options']['quantity'] = '9';
+$handler->display->display_options['style_plugin'] = 'table';
+$handler->display->display_options['style_options']['grouping'] = '';
+$handler->display->display_options['style_options']['columns'] = array(
+  'name_1' => 'name_1',
+  'name' => 'name',
+  'definition' => 'definition',
+  'is_obsolete' => 'is_obsolete',
+  'is_relationshiptype' => 'is_relationshiptype',
+);
+$handler->display->display_options['style_options']['default'] = '-1';
+$handler->display->display_options['style_options']['info'] = array(
+  'name_1' => array(
+    'sortable' => 1,
+    'separator' => '',
+  ),
+  'name' => array(
+    'sortable' => 1,
+    'separator' => '',
+  ),
+  'definition' => array(
+    'sortable' => 0,
+    'separator' => '',
+  ),
+  'is_obsolete' => array(
+    'sortable' => 1,
+    'separator' => '',
+  ),
+  'is_relationshiptype' => array(
+    'sortable' => 1,
+    'separator' => '',
+  ),
+);
+/* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Term',
+    'path-1' => 'admin/tripal/chado/tripal_cv/cvterm/add',
   );
-  $handler->display->display_options['style_options']['default'] = '-1';
-  $handler->display->display_options['style_options']['info'] = array(
-    'name_1' => array(
-      'sortable' => 1,
-      'separator' => '',
-    ),
-    'name' => array(
-      'sortable' => 1,
-      'separator' => '',
-    ),
-    'definition' => array(
-      'sortable' => 0,
-      'separator' => '',
-    ),
-    'is_obsolete' => array(
-      'sortable' => 1,
-      'separator' => '',
-    ),
-    'is_relationshiptype' => array(
-      'sortable' => 1,
-      'separator' => '',
-    ),
-  );
-  /* Header: Global: Text area */
-  $handler->display->display_options['header']['text']['id'] = 'text';
-  $handler->display->display_options['header']['text']['table'] = 'views';
-  $handler->display->display_options['header']['text']['field'] = 'area';
-  $handler->display->display_options['header']['text']['label'] = 'Add cvterm';
-  $handler->display->display_options['header']['text']['empty'] = TRUE;
-  $handler->display->display_options['header']['text']['content'] = '<ul class="action-links">
-        <li><a href="cvterm/add">Add Term</a></li>
-   </ul>';
-  $handler->display->display_options['header']['text']['format'] = 'full_html';
-  /* No results behavior: Global: Text area */
-  $handler->display->display_options['empty']['text']['id'] = 'area';
-  $handler->display->display_options['empty']['text']['table'] = 'views';
-  $handler->display->display_options['empty']['text']['field'] = 'area';
-  $handler->display->display_options['empty']['text']['content'] = 'There are no terms associated with the selected controlled vocabulary. Please select a different vocabulary from the list above.';
-  $handler->display->display_options['empty']['text']['format'] = '1';
-  /* Field: Chado Cv: Name */
-  $handler->display->display_options['fields']['name_1']['id'] = 'name_1';
-  $handler->display->display_options['fields']['name_1']['table'] = 'cv';
-  $handler->display->display_options['fields']['name_1']['field'] = 'name';
-  $handler->display->display_options['fields']['name_1']['label'] = 'Vocabulary';
-  $handler->display->display_options['fields']['name_1']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['name_1']['alter']['path'] = 'cvs?name=[name_1]';
-  /* Field: Chado Cvterm: Cvterm Id */
-  $handler->display->display_options['fields']['cvterm_id']['id'] = 'cvterm_id';
-  $handler->display->display_options['fields']['cvterm_id']['table'] = 'cvterm';
-  $handler->display->display_options['fields']['cvterm_id']['field'] = 'cvterm_id';
-  $handler->display->display_options['fields']['cvterm_id']['exclude'] = TRUE;
-  $handler->display->display_options['fields']['cvterm_id']['separator'] = '';
-  /* Field: Chado Cvterm: Name */
-  $handler->display->display_options['fields']['name']['id'] = 'name';
-  $handler->display->display_options['fields']['name']['table'] = 'cvterm';
-  $handler->display->display_options['fields']['name']['field'] = 'name';
-  /* Field: Chado Cvterm: Definition */
-  $handler->display->display_options['fields']['definition']['id'] = 'definition';
-  $handler->display->display_options['fields']['definition']['table'] = 'cvterm';
-  $handler->display->display_options['fields']['definition']['field'] = 'definition';
-  $handler->display->display_options['fields']['definition']['element_class'] = 'wide-column';
-  $handler->display->display_options['fields']['definition']['element_label_class'] = 'wide-column';
-  /* Field: Chado Cvterm: Is Obsolete */
-  $handler->display->display_options['fields']['is_obsolete']['id'] = 'is_obsolete';
-  $handler->display->display_options['fields']['is_obsolete']['table'] = 'cvterm';
-  $handler->display->display_options['fields']['is_obsolete']['field'] = 'is_obsolete';
-  $handler->display->display_options['fields']['is_obsolete']['label'] = 'Obsolete?';
-  $handler->display->display_options['fields']['is_obsolete']['alter']['alter_text'] = TRUE;
-  $handler->display->display_options['fields']['is_obsolete']['alter']['text'] = 'Yes';
-  $handler->display->display_options['fields']['is_obsolete']['element_class'] = 'short-column';
-  $handler->display->display_options['fields']['is_obsolete']['element_label_class'] = 'short-column';
-  $handler->display->display_options['fields']['is_obsolete']['empty'] = 'No';
-  $handler->display->display_options['fields']['is_obsolete']['empty_zero'] = TRUE;
-  $handler->display->display_options['fields']['is_obsolete']['separator'] = '';
-  /* Field: Chado Cvterm: Is Relationshiptype */
-  $handler->display->display_options['fields']['is_relationshiptype']['id'] = 'is_relationshiptype';
-  $handler->display->display_options['fields']['is_relationshiptype']['table'] = 'cvterm';
-  $handler->display->display_options['fields']['is_relationshiptype']['field'] = 'is_relationshiptype';
-  $handler->display->display_options['fields']['is_relationshiptype']['label'] = 'Relation-ship?';
-  $handler->display->display_options['fields']['is_relationshiptype']['alter']['alter_text'] = TRUE;
-  $handler->display->display_options['fields']['is_relationshiptype']['alter']['text'] = 'Yes';
-  $handler->display->display_options['fields']['is_relationshiptype']['element_class'] = 'short-column';
-  $handler->display->display_options['fields']['is_relationshiptype']['element_label_class'] = 'short-column';
-  $handler->display->display_options['fields']['is_relationshiptype']['empty'] = 'No';
-  $handler->display->display_options['fields']['is_relationshiptype']['empty_zero'] = TRUE;
-  $handler->display->display_options['fields']['is_relationshiptype']['separator'] = '';
-  /* Field: Global: Custom text */
-  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
-  $handler->display->display_options['fields']['nothing']['table'] = 'views';
-  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
-  $handler->display->display_options['fields']['nothing']['label'] = 'Edit Link';
-  $handler->display->display_options['fields']['nothing']['exclude'] = TRUE;
-  $handler->display->display_options['fields']['nothing']['alter']['text'] = 'edit';
-  $handler->display->display_options['fields']['nothing']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/chado/tripal_cv/cvterm/edit/[cvterm_id]';
-  /* Field: Global: Custom text */
-  $handler->display->display_options['fields']['nothing_1']['id'] = 'nothing_1';
-  $handler->display->display_options['fields']['nothing_1']['table'] = 'views';
-  $handler->display->display_options['fields']['nothing_1']['field'] = 'nothing';
-  $handler->display->display_options['fields']['nothing_1']['label'] = '';
-  $handler->display->display_options['fields']['nothing_1']['alter']['text'] = '[nothing]';
-  $handler->display->display_options['fields']['nothing_1']['element_class'] = 'short-column';
-  $handler->display->display_options['fields']['nothing_1']['element_label_class'] = 'short-column';
-  $handler->display->display_options['fields']['nothing_1']['element_label_colon'] = FALSE;
-  /* Sort criterion: Chado Cv: Name */
-  $handler->display->display_options['sorts']['name']['id'] = 'name';
-  $handler->display->display_options['sorts']['name']['table'] = 'cv';
-  $handler->display->display_options['sorts']['name']['field'] = 'name';
-  /* Sort criterion: Chado Cvterm: Name */
-  $handler->display->display_options['sorts']['name_1']['id'] = 'name_1';
-  $handler->display->display_options['sorts']['name_1']['table'] = 'cvterm';
-  $handler->display->display_options['sorts']['name_1']['field'] = 'name';
-  /* Filter criterion: Chado Cv: Name */
-  $handler->display->display_options['filters']['name']['id'] = 'name';
-  $handler->display->display_options['filters']['name']['table'] = 'cv';
-  $handler->display->display_options['filters']['name']['field'] = 'name';
-  $handler->display->display_options['filters']['name']['value'] = 'All';
-  $handler->display->display_options['filters']['name']['group'] = '0';
-  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['name']['expose']['operator_id'] = 'name_op';
-  $handler->display->display_options['filters']['name']['expose']['label'] = 'Vocabulary';
-  $handler->display->display_options['filters']['name']['expose']['operator'] = 'name_op';
-  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'cv';
+/* No results behavior: Global: Text area */
+$handler->display->display_options['empty']['text']['id'] = 'area';
+$handler->display->display_options['empty']['text']['table'] = 'views';
+$handler->display->display_options['empty']['text']['field'] = 'area';
+$handler->display->display_options['empty']['text']['content'] = 'There are no terms associated with the selected controlled vocabulary. Please select a different vocabulary from the list above.';
+$handler->display->display_options['empty']['text']['format'] = '1';
+/* Field: Chado Cv: Cv Id */
+$handler->display->display_options['fields']['cv_id']['id'] = 'cv_id';
+$handler->display->display_options['fields']['cv_id']['table'] = 'cv';
+$handler->display->display_options['fields']['cv_id']['field'] = 'cv_id';
+$handler->display->display_options['fields']['cv_id']['exclude'] = TRUE;
+$handler->display->display_options['fields']['cv_id']['separator'] = '';
+/* Field: Chado Cv: Name */
+$handler->display->display_options['fields']['name_1']['id'] = 'name_1';
+$handler->display->display_options['fields']['name_1']['table'] = 'cv';
+$handler->display->display_options['fields']['name_1']['field'] = 'name';
+$handler->display->display_options['fields']['name_1']['label'] = 'Vocabulary';
+$handler->display->display_options['fields']['name_1']['alter']['make_link'] = TRUE;
+$handler->display->display_options['fields']['name_1']['alter']['path'] = 'admin/tripal/chado/tripal_cv/cvs?name=[name_1]';
+/* Field: Chado Cvterm: Cvterm Id */
+$handler->display->display_options['fields']['cvterm_id']['id'] = 'cvterm_id';
+$handler->display->display_options['fields']['cvterm_id']['table'] = 'cvterm';
+$handler->display->display_options['fields']['cvterm_id']['field'] = 'cvterm_id';
+$handler->display->display_options['fields']['cvterm_id']['exclude'] = TRUE;
+$handler->display->display_options['fields']['cvterm_id']['separator'] = '';
+/* Field: Chado Cvterm: Name */
+$handler->display->display_options['fields']['name']['id'] = 'name';
+$handler->display->display_options['fields']['name']['table'] = 'cvterm';
+$handler->display->display_options['fields']['name']['field'] = 'name';
+/* Field: Chado Cvterm: Definition */
+$handler->display->display_options['fields']['definition']['id'] = 'definition';
+$handler->display->display_options['fields']['definition']['table'] = 'cvterm';
+$handler->display->display_options['fields']['definition']['field'] = 'definition';
+$handler->display->display_options['fields']['definition']['element_class'] = 'wide-column';
+$handler->display->display_options['fields']['definition']['element_label_class'] = 'wide-column';
+/* Field: Chado Cvterm: Is Obsolete */
+$handler->display->display_options['fields']['is_obsolete']['id'] = 'is_obsolete';
+$handler->display->display_options['fields']['is_obsolete']['table'] = 'cvterm';
+$handler->display->display_options['fields']['is_obsolete']['field'] = 'is_obsolete';
+$handler->display->display_options['fields']['is_obsolete']['label'] = 'Obsolete?';
+$handler->display->display_options['fields']['is_obsolete']['alter']['alter_text'] = TRUE;
+$handler->display->display_options['fields']['is_obsolete']['alter']['text'] = 'Yes';
+$handler->display->display_options['fields']['is_obsolete']['element_class'] = 'short-column';
+$handler->display->display_options['fields']['is_obsolete']['element_label_class'] = 'short-column';
+$handler->display->display_options['fields']['is_obsolete']['empty'] = 'No';
+$handler->display->display_options['fields']['is_obsolete']['empty_zero'] = TRUE;
+$handler->display->display_options['fields']['is_obsolete']['separator'] = '';
+/* Field: Chado Cvterm: Is Relationshiptype */
+$handler->display->display_options['fields']['is_relationshiptype']['id'] = 'is_relationshiptype';
+$handler->display->display_options['fields']['is_relationshiptype']['table'] = 'cvterm';
+$handler->display->display_options['fields']['is_relationshiptype']['field'] = 'is_relationshiptype';
+$handler->display->display_options['fields']['is_relationshiptype']['label'] = 'Relation-ship?';
+$handler->display->display_options['fields']['is_relationshiptype']['alter']['alter_text'] = TRUE;
+$handler->display->display_options['fields']['is_relationshiptype']['alter']['text'] = 'Yes';
+$handler->display->display_options['fields']['is_relationshiptype']['element_class'] = 'short-column';
+$handler->display->display_options['fields']['is_relationshiptype']['element_label_class'] = 'short-column';
+$handler->display->display_options['fields']['is_relationshiptype']['empty'] = 'No';
+$handler->display->display_options['fields']['is_relationshiptype']['empty_zero'] = TRUE;
+$handler->display->display_options['fields']['is_relationshiptype']['separator'] = '';
+/* Field: Global: Custom text */
+$handler->display->display_options['fields']['nothing']['id'] = 'nothing';
+$handler->display->display_options['fields']['nothing']['table'] = 'views';
+$handler->display->display_options['fields']['nothing']['field'] = 'nothing';
+$handler->display->display_options['fields']['nothing']['label'] = 'Edit Link';
+$handler->display->display_options['fields']['nothing']['exclude'] = TRUE;
+$handler->display->display_options['fields']['nothing']['alter']['text'] = 'edit';
+$handler->display->display_options['fields']['nothing']['alter']['make_link'] = TRUE;
+$handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/chado/tripal_cv/cv/[cv_id]/cvterm/edit/[cvterm_id]';
+/* Field: Global: Custom text */
+$handler->display->display_options['fields']['nothing_1']['id'] = 'nothing_1';
+$handler->display->display_options['fields']['nothing_1']['table'] = 'views';
+$handler->display->display_options['fields']['nothing_1']['field'] = 'nothing';
+$handler->display->display_options['fields']['nothing_1']['label'] = '';
+$handler->display->display_options['fields']['nothing_1']['alter']['text'] = '[nothing]';
+$handler->display->display_options['fields']['nothing_1']['element_class'] = 'short-column';
+$handler->display->display_options['fields']['nothing_1']['element_label_class'] = 'short-column';
+$handler->display->display_options['fields']['nothing_1']['element_label_colon'] = FALSE;
+/* Sort criterion: Chado Cv: Name */
+$handler->display->display_options['sorts']['name']['id'] = 'name';
+$handler->display->display_options['sorts']['name']['table'] = 'cv';
+$handler->display->display_options['sorts']['name']['field'] = 'name';
+/* Sort criterion: Chado Cvterm: Name */
+$handler->display->display_options['sorts']['name_1']['id'] = 'name_1';
+$handler->display->display_options['sorts']['name_1']['table'] = 'cvterm';
+$handler->display->display_options['sorts']['name_1']['field'] = 'name';
+/* Filter criterion: Chado Cv: Name */
+$handler->display->display_options['filters']['name']['id'] = 'name';
+$handler->display->display_options['filters']['name']['table'] = 'cv';
+$handler->display->display_options['filters']['name']['field'] = 'name';
+$handler->display->display_options['filters']['name']['value'] = 'All';
+$handler->display->display_options['filters']['name']['group'] = '0';
+$handler->display->display_options['filters']['name']['exposed'] = TRUE;
+$handler->display->display_options['filters']['name']['expose']['operator_id'] = 'name_op';
+$handler->display->display_options['filters']['name']['expose']['label'] = 'Vocabulary';
+$handler->display->display_options['filters']['name']['expose']['operator'] = 'name_op';
+$handler->display->display_options['filters']['name']['expose']['identifier'] = 'cv';
+$handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
+  2 => '2',
+  1 => 0,
+  3 => 0,
+);
+/* Filter criterion: Chado Cvterm: Name */
+$handler->display->display_options['filters']['name_1']['id'] = 'name_1';
+$handler->display->display_options['filters']['name_1']['table'] = 'cvterm';
+$handler->display->display_options['filters']['name_1']['field'] = 'name';
+$handler->display->display_options['filters']['name_1']['operator'] = 'contains';
+$handler->display->display_options['filters']['name_1']['group'] = '0';
+$handler->display->display_options['filters']['name_1']['exposed'] = TRUE;
+$handler->display->display_options['filters']['name_1']['expose']['operator_id'] = '';
+$handler->display->display_options['filters']['name_1']['expose']['label'] = 'Name Contains';
+$handler->display->display_options['filters']['name_1']['expose']['identifier'] = 'name';
+$handler->display->display_options['filters']['name_1']['expose']['remember_roles'] = array(
+  2 => '2',
+  1 => 0,
+  3 => 0,
+);
+/* Filter criterion: Chado Cvterm: Definition */
+$handler->display->display_options['filters']['definition']['id'] = 'definition';
+$handler->display->display_options['filters']['definition']['table'] = 'cvterm';
+$handler->display->display_options['filters']['definition']['field'] = 'definition';
+$handler->display->display_options['filters']['definition']['operator'] = 'contains';
+$handler->display->display_options['filters']['definition']['group'] = '0';
+$handler->display->display_options['filters']['definition']['exposed'] = TRUE;
+$handler->display->display_options['filters']['definition']['expose']['operator_id'] = 'definition_op';
+$handler->display->display_options['filters']['definition']['expose']['label'] = 'Definition Contains';
+$handler->display->display_options['filters']['definition']['expose']['operator'] = 'definition_op';
+$handler->display->display_options['filters']['definition']['expose']['identifier'] = 'definition';
+$handler->display->display_options['filters']['definition']['expose']['remember_roles'] = array(
+  2 => '2',
+  1 => 0,
+  3 => 0,
+);
+
+/** MANUALLY ADDED since filter handler no exporting correctly */
   $handler->display->display_options['filters']['name']['expose']['values_form_type'] = 'select';
   $handler->display->display_options['filters']['name']['expose']['select_multiple'] = FALSE;
   $handler->display->display_options['filters']['name']['expose']['select_optional'] = TRUE;
   $handler->display->display_options['filters']['name']['expose']['max_length'] = 40;
-  $handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
-  );
-  /* Filter criterion: Chado Cvterm: Name */
-  $handler->display->display_options['filters']['name_1']['id'] = 'name_1';
-  $handler->display->display_options['filters']['name_1']['table'] = 'cvterm';
-  $handler->display->display_options['filters']['name_1']['field'] = 'name';
-  $handler->display->display_options['filters']['name_1']['operator'] = 'contains';
-  $handler->display->display_options['filters']['name_1']['group'] = '0';
-  $handler->display->display_options['filters']['name_1']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['name_1']['expose']['operator_id'] = '';
-  $handler->display->display_options['filters']['name_1']['expose']['label'] = 'Name Contains';
-  $handler->display->display_options['filters']['name_1']['expose']['identifier'] = 'name';
-  $handler->display->display_options['filters']['name']['expose']['values_form_type'] = 'textfield';
+
+  $handler->display->display_options['filters']['name_1']['expose']['values_form_type'] = 'textfield';
+  $handler->display->display_options['filters']['name_1']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['name_1']['expose']['select_optional'] = FALSE;
+  $handler->display->display_options['filters']['name_1']['expose']['max_length'] = 40;
+
+/* Display: Page */
+$handler = $view->new_display('page', 'Page', 'page_1');
+$handler->display->display_options['path'] = 'admin/tripal/chado/tripal_cv/cvterms';
+$handler->display->display_options['menu']['type'] = 'tab';
+$handler->display->display_options['menu']['title'] = 'Terms';
+$handler->display->display_options['menu']['description'] = 'A listing of a controlled vocabulary terms for a given vocabulary';
+$handler->display->display_options['menu']['weight'] = '-8';
+$handler->display->display_options['menu']['name'] = 'management';
+$handler->display->display_options['menu']['context'] = 0;
+$handler->display->display_options['menu']['context_only_inline'] = 0;
+
+  /** MANUALLY ADD since filter handler no exporting correctly
+  $handler->display->display_options['filters']['name']['expose']['values_form_type'] = 'select';
   $handler->display->display_options['filters']['name']['expose']['select_multiple'] = FALSE;
-  $handler->display->display_options['filters']['name']['expose']['select_optional'] = FALSE;
+  $handler->display->display_options['filters']['name']['expose']['select_optional'] = TRUE;
   $handler->display->display_options['filters']['name']['expose']['max_length'] = 40;
-  $handler->display->display_options['filters']['name_1']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
-  );
-  /* Filter criterion: Chado Cvterm: Definition */
-  $handler->display->display_options['filters']['definition']['id'] = 'definition';
-  $handler->display->display_options['filters']['definition']['table'] = 'cvterm';
-  $handler->display->display_options['filters']['definition']['field'] = 'definition';
-  $handler->display->display_options['filters']['definition']['operator'] = 'contains';
-  $handler->display->display_options['filters']['definition']['group'] = '0';
-  $handler->display->display_options['filters']['definition']['exposed'] = TRUE;
-  $handler->display->display_options['filters']['definition']['expose']['operator_id'] = 'definition_op';
-  $handler->display->display_options['filters']['definition']['expose']['label'] = 'Definition Contains';
-  $handler->display->display_options['filters']['definition']['expose']['operator'] = 'definition_op';
-  $handler->display->display_options['filters']['definition']['expose']['identifier'] = 'definition';
-  $handler->display->display_options['filters']['definition']['expose']['remember_roles'] = array(
-    2 => '2',
-    1 => 0,
-    3 => 0,
-  );
 
-  /* Display: Page */
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_cv/cvterms';
-  $handler->display->display_options['menu']['type'] = 'tab';
-  $handler->display->display_options['menu']['title'] = 'Terms';
-  $handler->display->display_options['menu']['description'] = 'A listing of a controlled vocabulary terms for a given vocabulary';
-  $handler->display->display_options['menu']['weight'] = '-8';
-  $handler->display->display_options['menu']['name'] = 'management';
-  $handler->display->display_options['menu']['context'] = 0;
-  $handler->display->display_options['menu']['context_only_inline'] = 0;
+  $handler->display->display_options['filters']['name_1']['expose']['values_form_type'] = 'textfield';
+  $handler->display->display_options['filters']['name_1']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['name_1']['expose']['select_optional'] = FALSE;
+  $handler->display->display_options['filters']['name_1']['expose']['max_length'] = 40;
+  */
 
   return $view;
 }

tripal_db/tripal_db.info

@@ -7,3 +7,4 @@ version = 7.x-2.0-beta1
 configure = admin/tripal/chado/tripal_db
 
 dependencies[] = tripal_core
+dependencies[] = tripal_views

tripal_db/tripal_db.install

@@ -5,6 +5,20 @@
  * Contains functions related to the installation of this module
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_db_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_db.views_default.inc");
+  $views = tripal_db_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_requirements().
  */

tripal_db/tripal_db.module

@@ -37,7 +37,7 @@ function tripal_db_menu() {
     'title' => 'Help',
     'description' => "A description of the Tripal Database module including a short description of it's usage.",
     'page callback' => 'theme',
-    'page arguments' => array('tripal_db_help'),
+    'page arguments' => array('tripal_db_admin'),
     'access arguments' => array('administer db cross-references'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
@@ -131,8 +131,8 @@ function tripal_db_views_api() {
 function tripal_db_theme() {
   $theme_path = drupal_get_path('module', 'tripal_db') . '/theme';
   $items = array(
-    'tripal_db_help' => array(
-      'template' => 'tripal_db_help',
+    'tripal_db_admin' => array(
+      'template' => 'tripal_db_admin',
       'arguments' =>  array(NULL),
       'path' => $theme_path,
     ),

tripal_db/tripal_db.views_default.inc

@@ -23,7 +23,7 @@ function tripal_db_defaultview_admin_db_listing() {
 
   $view = new view();
   $view->name = 'tripal_db_admin_dbs';
-  $view->description = 'A listing of all databases.';
+  $view->description = 'DO NOT DISABLE';
   $view->tag = 'tripal admin';
   $view->base_table = 'db';
   $view->human_name = 'DB Admin';
@@ -72,15 +72,16 @@ function tripal_db_defaultview_admin_db_listing() {
       'separator' => '',
     ),
   );
-  /* Header: Global: Text area */
-  $handler->display->display_options['header']['text']['id'] = 'text';
-  $handler->display->display_options['header']['text']['table'] = 'views';
-  $handler->display->display_options['header']['text']['field'] = 'area';
-  $handler->display->display_options['header']['text']['label'] = 'Add DB';
-  $handler->display->display_options['header']['text']['content'] = '<ul class="action-links">
-        <li><a href="tripal_db/add">Add Database</a></li>
-    </ul>';
-  $handler->display->display_options['header']['text']['format'] = 'full_html';
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Database',
+    'path-1' => 'admin/tripal/chado/tripal_db/add',
+  );
   /* No results behavior: Global: Text area */
   $handler->display->display_options['empty']['text']['id'] = 'area';
   $handler->display->display_options['empty']['text']['table'] = 'views';
@@ -201,7 +202,7 @@ function tripal_db_defaultview_admin_dbxref_listing() {
 
   $view = new view();
   $view->name = 'tripal_db_admin_dbxrefs';
-  $view->description = '';
+  $view->description = 'DO NOT DISABLE';
   $view->tag = 'tripal admin';
   $view->base_table = 'dbxref';
   $view->human_name = 'DB Reference Admin';

tripal_feature/tripal_feature.info

@@ -8,6 +8,7 @@ version = 7.x-2.0-beta1
 dependencies[] = search
 dependencies[] = path
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_db
 dependencies[] = tripal_cv
 dependencies[] = tripal_organism

tripal_feature/tripal_feature.install

@@ -4,6 +4,20 @@
  * @todo Add file header description
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_feature_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_feature.views_default.inc");
+  $views = tripal_feature_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_requirements().
  */
@@ -33,7 +47,7 @@ function tripal_feature_install() {
 
   // add the materialized view
   tripal_feature_add_organism_count_mview();
-  
+
   // add a job to the job queue so this view gets updated automatically next
   // time the job facility is run
   if ($mview_id = tripal_mviews_get_mview_id('organism_feature_count')) {
@@ -48,40 +62,43 @@ function tripal_feature_install() {
  */
 function tripal_feature_uninstall() {
   // Drop the MView table if it exists
+  // D7 @todo Fix tripal_mviews_get_mview_id()
+  /**
   if ($mview_id = tripal_mviews_get_mview_id('organism_feature_count')) {
     tripal_mviews_action("delete", $mview_id);
   }
+  */
 }
- 
+
 /**
  * Implementation of hook_schema().
  *
  * @ingroup tripal_feature
  */
 function tripal_feature_schema() {
-  
+
   $schema['chado_feature'] = array(
     'fields' => array(
       'vid' => array(
-        'type' => 'int', 
-        'unsigned' => TRUE, 
-        'not null' => TRUE, 
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
         'default' => 0
        ),
       'nid' => array(
-        'type' => 'int', 
-        'unsigned' => TRUE, 
-        'not null' => TRUE, 
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
         'default' => 0
        ),
       'feature_id' => array(
-        'type' => 'int', 
-        'not null' => TRUE, 
+        'type' => 'int',
+        'not null' => TRUE,
         'default' => 0
       ),
       'sync_date' => array(
-        'type' => 'int', 
-        'not null' => FALSE, 
+        'type' => 'int',
+        'not null' => FALSE,
         'description' => 'UNIX integer sync date/time'
       ),
     ),
@@ -94,7 +111,7 @@ function tripal_feature_schema() {
     ),
     'primary key' => array('nid'),
   );
-  
+
   return $schema;
 };
 
@@ -142,7 +159,7 @@ function tripal_feature_add_organism_count_mview() {
         'length' => '255',
         'not null' => TRUE,
       ),
-    ),      
+    ),
     'indexes' => array(
       'organism_feature_count_idx1' => array('organism_id'),
       'organism_feature_count_idx2' => array('cvterm_id'),

tripal_feature/tripal_feature.views.inc

@@ -38,550 +38,3 @@ function tripal_feature_views_handlers() {
     ),
   );
 }
-/**
- *
- * @ingroup tripal_feature_views
- */
-function tripal_feature_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // Main default view
-  $view = new view;
-  $view->name = 'feature_listing';
-  $view->description = 'A listing of chado sequence features.';
-  $view->tag = 'chado default';
-  $view->base_table = 'feature';
-  $view->core = 0;
-  $view->api_version = '2';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  $handler = $view->new_display('default', 'features_all', 'default');
-  $handler->override_option('fields', array(
-    'uniquename' => array(
-      'label' => 'Unique Name',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => 'node/[nid]',
-        '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' => 'uniquename',
-      'table' => 'feature',
-      'field' => 'uniquename',
-      'relationship' => 'none',
-      'override' => array(
-        'button' => 'Override',
-      ),
-    ),
-    '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',
-      'override' => array(
-        'button' => 'Override',
-      ),
-    ),
-    'name_1' => 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_1',
-      'table' => 'cvterm',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    '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',
-      'override' => array(
-        'button' => 'Override',
-      ),
-    ),
-    'seqlen' => array(
-      'label' => 'Sequence Length',
-      '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,
-      'set_precision' => FALSE,
-      'precision' => 0,
-      'decimal' => '.',
-      'separator' => ',',
-      'prefix' => '',
-      'suffix' => '',
-      'exclude' => 0,
-      'id' => 'seqlen',
-      'table' => 'feature',
-      'field' => 'seqlen',
-      'relationship' => 'none',
-    ),
-    'is_obsolete' => array(
-      'label' => 'Is Obsolete',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'absolute' => 0,
-        'link_class' => '',
-        'alt' => '',
-        'rel' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        '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',
-      'not' => 0,
-      'separator' => ', ',
-      'exclude' => 0,
-      'id' => 'is_obsolete',
-      'table' => 'feature',
-      'field' => 'is_obsolete',
-      'relationship' => 'none',
-    ),
-    'timeaccessioned' => array(
-      'label' => 'Accessioned On',
-      '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,
-      'date_format' => 'large',
-      'custom_date_format' => '',
-      'type' => 'separator',
-      'separator' => ', ',
-      'exclude' => 0,
-      'id' => 'timeaccessioned',
-      'table' => 'feature',
-      'field' => 'timeaccessioned',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('sorts', array(
-    'common_name' => array(
-      'order' => 'ASC',
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-    ),
-    'name' => array(
-      'order' => 'ASC',
-      'id' => 'name',
-      'table' => 'cvterm',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'name_1' => array(
-      'order' => 'ASC',
-      'id' => 'name_1',
-      'table' => 'feature',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('filters', array(
-    'common_name' => array(
-      'operator' => '=',
-      'value' => array(),
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'common_name_op',
-        'identifier' => 'organism',
-        'label' => 'Organism Common Name',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'override' => array(
-        'button' => 'Override',
-      ),
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'type_id' => array(
-      'operator' => '=',
-      'value' => array(),
-      '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' => 'feature',
-      'field' => 'type_id',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'show_all' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'name_1' => array(
-      'operator' => '~',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'name_1_op',
-        'identifier' => 'name',
-        'label' => 'Name Contains',
-        'bef_filter_description' => '',
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'name_1',
-      'table' => 'feature',
-      '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 features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.',
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_feature content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Sequence Features');
-  $handler->override_option('header', 'Click "Show" to see a list of all features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.');
-  $handler->override_option('header_format', '2');
-  $handler->override_option('header_empty', 0);
-  $handler->override_option('empty', 'No features matched the supplied 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',
-    'columns' => array(
-      'accession' => 'accession',
-      'accession_link' => 'accession_link',
-      'name' => 'name',
-      'uniquename' => 'uniquename',
-      'name_1' => 'name_1',
-      'common_name' => 'common_name',
-      'seqlen' => 'seqlen',
-      'is_obsolete' => 'is_obsolete',
-      'is_analysis' => 'is_analysis',
-      'nid' => 'nid',
-    ),
-    'info' => array(
-      'accession' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'accession_link' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'uniquename' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name_1' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'common_name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'seqlen' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'is_obsolete' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'is_analysis' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'nid' => array(
-        'separator' => '',
-      ),
-    ),
-    'default' => '-1',
-  ));
-  $default_handler = $handler;
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/features');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Features',
-    'description' => 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        '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,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Adds feature => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Feature to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_feature',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Change analysis.name to have a link to the node
-    $fields['name']['alter']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // Only show records with published nodes
-    /**
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-    */
-  }
-  $views[$view->name] = $view;
-
-  return $views;
-}

tripal_feature/tripal_feature.views_default.inc

@@ -0,0 +1,549 @@
+<?php
+
+/**
+ *
+ * @ingroup tripal_feature_views
+ */
+function tripal_feature_views_default_views() {
+  $views = array();
+
+  if (!module_exists('tripal_views')) {
+    return $views;
+  }
+
+  // Main default view
+  $view = new view;
+  $view->name = 'feature_listing';
+  $view->description = 'A listing of chado sequence features.';
+  $view->tag = 'chado default';
+  $view->base_table = 'feature';
+  $view->core = 0;
+  $view->api_version = '2';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+  $handler = $view->new_display('default', 'features_all', 'default');
+  $handler->override_option('fields', array(
+    'uniquename' => array(
+      'label' => 'Unique Name',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => 'node/[nid]',
+        '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' => 'uniquename',
+      'table' => 'feature',
+      'field' => 'uniquename',
+      'relationship' => 'none',
+      'override' => array(
+        'button' => 'Override',
+      ),
+    ),
+    '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',
+      'override' => array(
+        'button' => 'Override',
+      ),
+    ),
+    'name_1' => 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_1',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    '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',
+      'override' => array(
+        'button' => 'Override',
+      ),
+    ),
+    'seqlen' => array(
+      'label' => 'Sequence Length',
+      '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,
+      'set_precision' => FALSE,
+      'precision' => 0,
+      'decimal' => '.',
+      'separator' => ',',
+      'prefix' => '',
+      'suffix' => '',
+      'exclude' => 0,
+      'id' => 'seqlen',
+      'table' => 'feature',
+      'field' => 'seqlen',
+      'relationship' => 'none',
+    ),
+    'is_obsolete' => array(
+      'label' => 'Is Obsolete',
+      'alter' => array(
+        'alter_text' => 0,
+        'text' => '',
+        'make_link' => 0,
+        'path' => '',
+        'absolute' => 0,
+        'link_class' => '',
+        'alt' => '',
+        'rel' => '',
+        'prefix' => '',
+        'suffix' => '',
+        'target' => '',
+        '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',
+      'not' => 0,
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'is_obsolete',
+      'table' => 'feature',
+      'field' => 'is_obsolete',
+      'relationship' => 'none',
+    ),
+    'timeaccessioned' => array(
+      'label' => 'Accessioned On',
+      '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,
+      'date_format' => 'large',
+      'custom_date_format' => '',
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'timeaccessioned',
+      'table' => 'feature',
+      'field' => 'timeaccessioned',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('sorts', array(
+    'common_name' => array(
+      'order' => 'ASC',
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
+      'relationship' => 'none',
+    ),
+    'name' => array(
+      'order' => 'ASC',
+      'id' => 'name',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'name_1' => array(
+      'order' => 'ASC',
+      'id' => 'name_1',
+      'table' => 'feature',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'common_name' => array(
+      'operator' => '=',
+      'value' => array(),
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'common_name_op',
+        'identifier' => 'organism',
+        'label' => 'Organism Common Name',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'override' => array(
+        'button' => 'Override',
+      ),
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'type_id' => array(
+      'operator' => '=',
+      'value' => array(),
+      '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' => 'feature',
+      'field' => 'type_id',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'name_1' => array(
+      'operator' => '~',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'name_1_op',
+        'identifier' => 'name',
+        'label' => 'Name Contains',
+        'bef_filter_description' => '',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'name_1',
+      'table' => 'feature',
+      '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 features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_feature content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Sequence Features');
+  $handler->override_option('header', 'Click "Show" to see a list of all features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'No features matched the supplied 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',
+    'columns' => array(
+      'accession' => 'accession',
+      'accession_link' => 'accession_link',
+      'name' => 'name',
+      'uniquename' => 'uniquename',
+      'name_1' => 'name_1',
+      'common_name' => 'common_name',
+      'seqlen' => 'seqlen',
+      'is_obsolete' => 'is_obsolete',
+      'is_analysis' => 'is_analysis',
+      'nid' => 'nid',
+    ),
+    'info' => array(
+      'accession' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'accession_link' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'uniquename' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name_1' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'common_name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'seqlen' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'is_obsolete' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'is_analysis' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'nid' => array(
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
+  $default_handler = $handler;
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'chado/features');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Features',
+    'description' => 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on.',
+    'weight' => '10',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  // Add code specific to a local chado installation
+  // NOTE: Edit $handler above to $default_handler for the default display
+  if (tripal_core_chado_schema_exists()) {
+    // Add nid field
+    $fields = $view->get_items('field', 'default');
+    $new_fields = array(
+      'nid' => array(
+        'label' => 'Nid',
+        '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,
+        'link_to_node' => 0,
+        'exclude' => 1,
+        'id' => 'nid',
+        'table' => 'node',
+        'field' => 'nid',
+        'relationship' => 'none',
+      )
+    );
+    $fields = $new_fields + $fields;
+    // Adds feature => Node relationship
+    $default_handler->override_option('relationships', array(
+      'nid' => array(
+        'label' => 'Feature to Node',
+        'required' => 0,
+        'id' => 'nid',
+        'table' => 'chado_feature',
+        'field' => 'nid',
+        'relationship' => 'none',
+      ),
+    ));
+    // Change analysis.name to have a link to the node
+    $fields['name']['alter']['link_to_node'] = 1;
+    $default_handler->override_option('fields', $fields);
+    // Only show records with published nodes
+    /**
+    $filters = $view->get_items('filter', 'default');
+    $filters['status'] = array(
+      'operator' => '=',
+      'value' => '1',
+      'group' => '0',
+      'exposed' => FALSE,
+      'expose' => array(
+        'operator' => FALSE,
+        'label' => '',
+      ),
+      'id' => 'status',
+      'table' => 'node',
+      'field' => 'status',
+      'relationship' => 'none',
+    );
+    $default_handler->override_option('filters', $filters);
+    */
+  }
+  $views[$view->name] = $view;
+
+  return $views;
+}

tripal_featuremap/tripal_featuremap.info

@@ -4,7 +4,9 @@ core = 7.x
 project = tripal_featuremap
 package = Tripal
 version = 7.x-2.0-beta1
+
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_organism
 dependencies[] = tripal_feature
 dependencies[] = search

tripal_featuremap/tripal_featuremap.install

@@ -4,6 +4,20 @@
  * @todo Add file header description
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_featuremap_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_featuremap.views_default.inc");
+  $views = tripal_featuremap_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_requirements().
  */
@@ -33,7 +47,7 @@ function tripal_featuremap_install() {
 
   // add the featuremapprop table to Chado
   tripal_featuremap_add_custom_tables();
-  
+
   // Add cvterms
   tripal_featuremap_add_cvterms();
 
@@ -89,49 +103,49 @@ function tripal_featuremap_schema() {
 
 
 /*
- * 
+ *
  */
 function tripal_featuremap_add_cvterms() {
-  
+
    // add cvterms for the map unit types
-   tripal_cv_add_cvterm(array('name' => 'cM','def' => 'Centimorgan units'), 
+   tripal_cv_add_cvterm(array('name' => 'cM','def' => 'Centimorgan units'),
+     'featuremap_units', 0, 1, 'tripal');
+   tripal_cv_add_cvterm(array('name' => 'bp','def' => 'Base pairs units'),
      'featuremap_units', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'bp','def' => 'Base pairs units'), 
+   tripal_cv_add_cvterm(array('name' => 'bin_unit','def' => 'The bin unit'),
      'featuremap_units', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'bin_unit','def' => 'The bin unit'), 
-     'featuremap_units', 0, 1, 'tripal');   
-   tripal_cv_add_cvterm(array('name' => 'marker_order','def' => 'Units simply to define marker order.'), 
+   tripal_cv_add_cvterm(array('name' => 'marker_order','def' => 'Units simply to define marker order.'),
      'featuremap_units', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'undefined','def' => 'A catch-all for an undefined unit type'), 
+   tripal_cv_add_cvterm(array('name' => 'undefined','def' => 'A catch-all for an undefined unit type'),
      'featuremap_units', 0, 1, 'tripal');
-   
-   tripal_cv_add_cvterm(array('name' => 'start','def' => 'The start coordinate for a map feature.'), 
+
+   tripal_cv_add_cvterm(array('name' => 'start','def' => 'The start coordinate for a map feature.'),
      'featurepos_property', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'stop','def' => 'The end coordinate for a map feature'), 
+   tripal_cv_add_cvterm(array('name' => 'stop','def' => 'The end coordinate for a map feature'),
      'featurepos_property', 0, 1, 'tripal');
-   
+
    // add cvterms for map properties
-   tripal_cv_add_cvterm(array('name' => 'Map Dbxref','def' => 'A unique identifer for the map in a remote database.  The format is a database abbreviation and a unique accession separated by a colon.  (e.g. Gramene:tsh1996a)'), 
+   tripal_cv_add_cvterm(array('name' => 'Map Dbxref','def' => 'A unique identifer for the map in a remote database.  The format is a database abbreviation and a unique accession separated by a colon.  (e.g. Gramene:tsh1996a)'),
      'featuremap_property', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'Map Type','def' => 'The type of Map (e.g. QTL, Physical, etc.)'), 
+   tripal_cv_add_cvterm(array('name' => 'Map Type','def' => 'The type of Map (e.g. QTL, Physical, etc.)'),
      'featuremap_property', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'Genome Group','def' => ''), 
+   tripal_cv_add_cvterm(array('name' => 'Genome Group','def' => ''),
      'featuremap_property', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'URL','def' => 'A univeral resource locator (URL) reference where the publication can be found.  For maps found online, this would be the web address for the map.'), 
+   tripal_cv_add_cvterm(array('name' => 'URL','def' => 'A univeral resource locator (URL) reference where the publication can be found.  For maps found online, this would be the web address for the map.'),
      'featuremap_property', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'Population Type','def' => 'A brief descriptoin of the population type used to generate the map (e.g. RIL, F2, BC1, etc).'), 
+   tripal_cv_add_cvterm(array('name' => 'Population Type','def' => 'A brief descriptoin of the population type used to generate the map (e.g. RIL, F2, BC1, etc).'),
      'featuremap_property', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'Population Size','def' => 'The size of the population used to construct the map.'), 
+   tripal_cv_add_cvterm(array('name' => 'Population Size','def' => 'The size of the population used to construct the map.'),
      'featuremap_property', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'Methods','def' => 'A brief description of the methods used to construct the map.'), 
+   tripal_cv_add_cvterm(array('name' => 'Methods','def' => 'A brief description of the methods used to construct the map.'),
      'featuremap_property', 0, 1, 'tripal');
-   tripal_cv_add_cvterm(array('name' => 'Software','def' => 'The software used to construct the map.'), 
+   tripal_cv_add_cvterm(array('name' => 'Software','def' => 'The software used to construct the map.'),
      'featuremap_property', 0, 1, 'tripal');
 
 }
 
 /*
- * 
+ *
  */
 function tripal_featuremap_add_custom_tables(){
   // add the featuremaprop table to Chado
@@ -192,9 +206,9 @@ function tripal_featuremap_add_custom_tables(){
         ),
       ),
     ),
-  );  
+  );
   tripal_core_create_custom_table('featuremapprop', $schema, TRUE);
-  
+
   // add the featuremap_dbxref table to Chado
   $schema = array (
     'table' => 'featuremap_dbxref',
@@ -246,7 +260,7 @@ function tripal_featuremap_add_custom_tables(){
     'referring_tables' => NULL,
   );
   tripal_core_create_custom_table('featuremap_dbxref', $schema, TRUE);
-  
+
   $schema = array (
     'table' => 'featureposprop',
     'fields' => array (

tripal_featuremap/tripal_featuremap.views.inc

@@ -13,375 +13,4 @@
 /**
  * @defgroup tripal_featuremap_views Map Views Integration
  * @ingroup views
- */
-
-/**
- *
- *
- * @ingroup tripal_featuremap_views
- */
-function tripal_featuremap_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // Main default view
-  $view = new view;
-  $view->name = 'featuremap_listing';
-  $view->description = 'A listing of all chado feature maps';
-  $view->tag = 'chado default';
-  $view->base_table = 'featuremap';
-  $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' => 'node/[nid]',
-        '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,
-      'link_to_node' => 1,
-      'hide_alter_empty' => 1,
-      'type' => 'separator',
-      'separator' => ', ',
-      'exclude' => 0,
-      'id' => 'name',
-      'table' => 'featuremap',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'description' => array(
-      'label' => 'Description',
-      '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,
-      'link_to_node' => 0,
-      'empty_zero' => 0,
-      'hide_alter_empty' => 1,
-      'type' => 'separator',
-      'separator' => ', ',
-      'exclude' => 0,
-      'id' => 'description',
-      'table' => 'featuremap',
-      'field' => 'description',
-      'relationship' => 'none',
-    ),
-    'name_1' => array(
-      'label' => 'Map Units',
-      '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,
-      'link_to_node' => 0,
-      'empty_zero' => 0,
-      'hide_alter_empty' => 1,
-      'type' => 'separator',
-      'separator' => ', ',
-      'exclude' => 0,
-      'id' => 'name_1',
-      'table' => 'cvterm',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('sorts', array(
-    'name' => array(
-      'order' => 'ASC',
-      'id' => 'name',
-      'table' => 'featuremap',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('filters', array(
-    'unittype_id' => array(
-      'operator' => '=',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'unittype_id_op',
-        'identifier' => 'unittype_id',
-        'label' => 'Map Units',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'unittype_id',
-      'table' => 'featuremap',
-      'field' => 'unittype_id',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'show_all' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'name_1' => array(
-      'operator' => '~',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'name_1_op',
-        'identifier' => 'name_1',
-        'label' => 'Name',
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'name_1',
-      'table' => 'featuremap',
-      'field' => 'name',
-      'relationship' => 'none',
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'description' => array(
-      'operator' => '~',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'description_op',
-        'identifier' => 'description',
-        'label' => 'Description',
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'description',
-      'table' => 'featuremap',
-      '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 feature maps matching the entered criteria. If you leave a any of the criteria blank then the maps will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all maps will be listed.',
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_featuremap content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Maps');
-  $handler->override_option('header', 'Click "Show" to see a list of all feature maps matching the entered criteria. If you leave a any of the criteria blank then the maps will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all maps will be listed.');
-  $handler->override_option('header_format', '1');
-  $handler->override_option('header_empty', 1);
-  $handler->override_option('empty', 'No feature maps match the current criteria.');
-  $handler->override_option('empty_format', '1');
-  $handler->override_option('items_per_page', 25);
-  $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',
-      'name_1' => 'name_1',
-      'nid' => 'nid',
-    ),
-    'info' => array(
-      'name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'description' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name_1' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'nid' => array(
-        'separator' => '',
-      ),
-    ),
-    'default' => '-1',
-  ));
-  $default_handler = $handler;
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/featuremaps');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Maps',
-    'description' => 'A listing of chado feature maps.',
-    'weight' => '0',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        '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,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Adds feature => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Map to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_featuremap',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Change analysis.name to have a link to the node
-    $fields['name']['alter']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // Only show records with published nodes
-    /**
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-    */
-  }
-  $views[$view->name] = $view;
-
-  return $views;
-}
+ */

tripal_featuremap/tripal_featuremap.views_default.inc

@@ -0,0 +1,372 @@
+<?php
+
+/**
+ *
+ *
+ * @ingroup tripal_featuremap_views
+ */
+function tripal_featuremap_views_default_views() {
+  $views = array();
+
+  if (!module_exists('tripal_views')) {
+    return $views;
+  }
+
+  // Main default view
+  $view = new view;
+  $view->name = 'featuremap_listing';
+  $view->description = 'A listing of all chado feature maps';
+  $view->tag = 'chado default';
+  $view->base_table = 'featuremap';
+  $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' => 'node/[nid]',
+        '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,
+      'link_to_node' => 1,
+      'hide_alter_empty' => 1,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'name',
+      'table' => 'featuremap',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'description' => array(
+      'label' => 'Description',
+      '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,
+      'link_to_node' => 0,
+      'empty_zero' => 0,
+      'hide_alter_empty' => 1,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'description',
+      'table' => 'featuremap',
+      'field' => 'description',
+      'relationship' => 'none',
+    ),
+    'name_1' => array(
+      'label' => 'Map Units',
+      '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,
+      'link_to_node' => 0,
+      'empty_zero' => 0,
+      'hide_alter_empty' => 1,
+      'type' => 'separator',
+      'separator' => ', ',
+      'exclude' => 0,
+      'id' => 'name_1',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('sorts', array(
+    'name' => array(
+      'order' => 'ASC',
+      'id' => 'name',
+      'table' => 'featuremap',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'unittype_id' => array(
+      'operator' => '=',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'unittype_id_op',
+        'identifier' => 'unittype_id',
+        'label' => 'Map Units',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'unittype_id',
+      'table' => 'featuremap',
+      'field' => 'unittype_id',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'name_1' => array(
+      'operator' => '~',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'name_1_op',
+        'identifier' => 'name_1',
+        'label' => 'Name',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'name_1',
+      'table' => 'featuremap',
+      'field' => 'name',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'description' => array(
+      'operator' => '~',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'description_op',
+        'identifier' => 'description',
+        'label' => 'Description',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'description',
+      'table' => 'featuremap',
+      '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 feature maps matching the entered criteria. If you leave a any of the criteria blank then the maps will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all maps will be listed.',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_featuremap content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Maps');
+  $handler->override_option('header', 'Click "Show" to see a list of all feature maps matching the entered criteria. If you leave a any of the criteria blank then the maps will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all maps will be listed.');
+  $handler->override_option('header_format', '1');
+  $handler->override_option('header_empty', 1);
+  $handler->override_option('empty', 'No feature maps match the current criteria.');
+  $handler->override_option('empty_format', '1');
+  $handler->override_option('items_per_page', 25);
+  $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',
+      'name_1' => 'name_1',
+      'nid' => 'nid',
+    ),
+    'info' => array(
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'description' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name_1' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'nid' => array(
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
+  $default_handler = $handler;
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'chado/featuremaps');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Maps',
+    'description' => 'A listing of chado feature maps.',
+    'weight' => '0',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+
+  // Add code specific to a local chado installation
+  // NOTE: Edit $handler above to $default_handler for the default display
+  if (tripal_core_chado_schema_exists()) {
+    // Add nid field
+    $fields = $view->get_items('field', 'default');
+    $new_fields = array(
+      'nid' => array(
+        'label' => 'Nid',
+        '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,
+        'link_to_node' => 0,
+        'exclude' => 1,
+        'id' => 'nid',
+        'table' => 'node',
+        'field' => 'nid',
+        'relationship' => 'none',
+      )
+    );
+    $fields = $new_fields + $fields;
+    // Adds feature => Node relationship
+    $default_handler->override_option('relationships', array(
+      'nid' => array(
+        'label' => 'Map to Node',
+        'required' => 0,
+        'id' => 'nid',
+        'table' => 'chado_featuremap',
+        'field' => 'nid',
+        'relationship' => 'none',
+      ),
+    ));
+    // Change analysis.name to have a link to the node
+    $fields['name']['alter']['link_to_node'] = 1;
+    $default_handler->override_option('fields', $fields);
+    // Only show records with published nodes
+    /**
+    $filters = $view->get_items('filter', 'default');
+    $filters['status'] = array(
+      'operator' => '=',
+      'value' => '1',
+      'group' => '0',
+      'exposed' => FALSE,
+      'expose' => array(
+        'operator' => FALSE,
+        'label' => '',
+      ),
+      'id' => 'status',
+      'table' => 'node',
+      'field' => 'status',
+      'relationship' => 'none',
+    );
+    $default_handler->override_option('filters', $filters);
+    */
+  }
+  $views[$view->name] = $view;
+
+  return $views;
+}

tripal_genetic/tripal_genetic.info

@@ -4,7 +4,9 @@ core = 7.x
 project = tripal_genetic
 package = Tripal
 version = 7.x-2.0-beta1
+
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_cv
 dependencies[] = tripal_feature
 dependencies[] = tripal_phenotype

tripal_genetic/tripal_genetic.install

@@ -0,0 +1,15 @@
+<?php
+
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_genetic_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_genetic.views_default.inc");
+  $views = tripal_genetic_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}

tripal_genetic/tripal_genetic.views.inc

@@ -13,256 +13,4 @@
 /**
  * @defgroup tripal_genetic_views Genetic Views Integration
  * @ingroup views
- */
-
-/**
- * Implements hook_views_default_views().
- *
- * @ingroup tripal_genetic
- */
-function tripal_genetic_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // Main default view
-  $view = new view;
-  $view->name = 'genotype_listing';
-  $view->description = 'A listing of observed genotypes and the features displaying them';
-  $view->tag = 'chado default';
-  $view->base_table = 'genotype';
-  $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' => 'Uniquename',
-      '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' => 'genotype',
-      'field' => 'uniquename',
-      'relationship' => 'none',
-    ),
-    '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' => 'genotype',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'description' => array(
-      'label' => 'Description',
-      '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' => 'genotype',
-      'field' => 'description',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('filters', array(
-    'uniquename' => array(
-      'operator' => '~',
-      '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' => 'genotype',
-      'field' => 'uniquename',
-      'relationship' => 'none',
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'description' => array(
-      'operator' => '~',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'description_op',
-        'identifier' => 'description',
-        'label' => 'Description Contains',
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'description',
-      'table' => 'genotype',
-      '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 genotypes matching the entered criteria. If you leave a any of the criteria blank then the genotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all genotypes will be listed.',
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Genotypes Observed');
-  $handler->override_option('header', 'Click "Show" to see a list of all genotypes matching the entered criteria. If you leave a any of the criteria blank then the genotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all genotypes will be listed.');
-  $handler->override_option('header_format', '2');
-  $handler->override_option('header_empty', 0);
-  $handler->override_option('empty', 'No genotypes 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',
-      'name' => 'name',
-      'description' => 'description',
-    ),
-    'info' => array(
-      'uniquename' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'description' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-    ),
-    'default' => 'uniquename',
-  ));
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/genotypes');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Genotypes',
-    'description' => 'A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  $views[$view->name] = $view;
-
-  return $views;
-}
+ */

tripal_genetic/tripal_genetic.views_default.inc

@@ -0,0 +1,253 @@
+<?php
+
+/**
+ * Implements hook_views_default_views().
+ *
+ * @ingroup tripal_genetic
+ */
+function tripal_genetic_views_default_views() {
+  $views = array();
+
+  if (!module_exists('tripal_views')) {
+    return $views;
+  }
+
+  // Main default view
+  $view = new view;
+  $view->name = 'genotype_listing';
+  $view->description = 'A listing of observed genotypes and the features displaying them';
+  $view->tag = 'chado default';
+  $view->base_table = 'genotype';
+  $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' => 'Uniquename',
+      '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' => 'genotype',
+      'field' => 'uniquename',
+      'relationship' => 'none',
+    ),
+    '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' => 'genotype',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+    'description' => array(
+      'label' => 'Description',
+      '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' => 'genotype',
+      'field' => 'description',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'uniquename' => array(
+      'operator' => '~',
+      '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' => 'genotype',
+      'field' => 'uniquename',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'description' => array(
+      'operator' => '~',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'description_op',
+        'identifier' => 'description',
+        'label' => 'Description Contains',
+        'remember' => 0,
+      ),
+      'case' => 0,
+      'id' => 'description',
+      'table' => 'genotype',
+      '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 genotypes matching the entered criteria. If you leave a any of the criteria blank then the genotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all genotypes will be listed.',
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Genotypes Observed');
+  $handler->override_option('header', 'Click "Show" to see a list of all genotypes matching the entered criteria. If you leave a any of the criteria blank then the genotypes will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all genotypes will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'No genotypes 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',
+      'name' => 'name',
+      'description' => 'description',
+    ),
+    'info' => array(
+      'uniquename' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'description' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+    ),
+    'default' => 'uniquename',
+  ));
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'chado/genotypes');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Genotypes',
+    'description' => 'A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.',
+    'weight' => '10',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  $views[$view->name] = $view;
+
+  return $views;
+}

tripal_library/includes/tripal_library.admin.inc

@@ -1,5 +1,34 @@
-<?php 
+<?php
+
+function tripal_library_admin_libraries_listing() {
+  $output = '';
+
+  // set the breadcrumb
+  $breadcrumb = array();
+  $breadcrumb[] = l('Home', '<front>');
+  $breadcrumb[] = l('Administration', 'admin');
+  $breadcrumb[] = l('Tripal', 'admin/tripal');
+  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
+  $breadcrumb[] = l('Libraries', 'admin/tripal/chado/tripal_library');
+  drupal_set_breadcrumb($breadcrumb);
+
+  // Add the view
+  $view = views_embed_view('tripal_library_admin_libraries','default');
+  if (isset($view)) {
+    $output .= $view;
+  }
+  else {
+    $output .= '<p>The Tripal Library Module uses primarily views to provide an '
+      . 'administrative interface. Currently one or more views needed for this '
+      . 'administrative interface are disabled. <strong>Click each of the following links to '
+      . 'enable the pertinent views</strong>:</p>';
+    $output .= '<ul>';
+      $output .= '<li>'.l('Library Admin', 'admin/tripal/chado/tripal_library/views/libraries/enable').'</li>';
+    $output .= '</ul>';
+  }
 
+  return $output;
+}
 
 /**
  * Administrative settings form
@@ -311,14 +340,14 @@ function tripal_library_add_taxonomy($node, $library_id) {
   // do this because Drupal 6 fails to do this globally for us and
   // the drupal_execute function below won't work
   module_load_include('inc', 'taxonomy', 'taxonomy.admin');
-    
+
    // add the vocabulary
   $vocab_form['values']['name'] = 'DNA Libraries';
   $vocab_form['values']['description'] = 'Allows for associating/searching of library features by library name';
   $vocab_form['values']['help'] = '';
   $vocab_form['values']['module'] = 'taxonomy';
   drupal_form_submit('taxonomy_form_vocabulary', $vocab_form);
-  return;   
+  return;
 
    // make sure this term doesn't already exist.  If it doesn't then add it
   if ($vid) {
@@ -428,10 +457,10 @@ function tripal_library_feature_set_taxonomy($library_id = NULL) {
   if ($library_id) {
     print "Finding features for library with ID: $library_id\n";
     $sql = "
-      SELECT LF.feature_id, L.library_id, L.name as libname 
-      FROM {library_feature} LF 
-        INNER JOIN {library} L ON LF.library_id = L.library_id 
-      WHERE L.library_id = :library_id 
+      SELECT LF.feature_id, L.library_id, L.name as libname
+      FROM {library_feature} LF
+        INNER JOIN {library} L ON LF.library_id = L.library_id
+      WHERE L.library_id = :library_id
       ORDER BY LF.feature_id
     ";
     $features = chado_query($sql, array(':library_id' => $library_id));
@@ -439,18 +468,18 @@ function tripal_library_feature_set_taxonomy($library_id = NULL) {
   else {
     print "Finding features for all libraries\n";
     $sql = "
-      SELECT LF.feature_id, L.library_id, L.name as libname 
-      FROM {library_feature} LF 
-        INNER JOIN {library} L ON LF.library_id = L.library_id 
+      SELECT LF.feature_id, L.library_id, L.name as libname
+      FROM {library_feature} LF
+        INNER JOIN {library} L ON LF.library_id = L.library_id
       ORDER BY LF.feature_id
     ";
     $features = chado_query($sql);
   }
 
   $node_sql = "
-    SELECT * 
-    FROM {chado_feature} CF 
-      INNER JOIN {node} N ON CF.nid = N.nid 
+    SELECT *
+    FROM {chado_feature} CF
+      INNER JOIN {node} N ON CF.nid = N.nid
     WHERE feature_id = :feature_id
   ";
   // iterate through the features and add the taxonomy
@@ -474,19 +503,19 @@ function tripal_library_reindex_features($library_id = NULL, $job_id = NULL) {
   // with all libraries.
   if ($library_id) {
     $sql = "
-      SELECT LF.feature_id, L.library_id, L.name as libname 
-      FROM {library_feature} LF 
+      SELECT LF.feature_id, L.library_id, L.name as libname
+      FROM {library_feature} LF
         INNER JOIN {library} L ON LF.library_id = L.library_id
-      WHERE L.library_id = :library_id 
+      WHERE L.library_id = :library_id
       ORDER BY LF.feature_id
     ";
     $results = chado_query($sql, array(':library_id' => $library_id));
   }
   else {
     $sql = "
-      SELECT LF.feature_id, L.library_id, L.name as libname 
-      FROM {library_feature} LF 
-        INNER JOIN {library} L ON LF.library_id = L.library_id 
+      SELECT LF.feature_id, L.library_id, L.name as libname
+      FROM {library_feature} LF
+        INNER JOIN {library} L ON LF.library_id = L.library_id
       ORDER BY LF.feature_id
     ";
     $results = chado_query($sql);
@@ -521,19 +550,19 @@ function tripal_library_taxonify_features($library_id = NULL, $job_id = NULL) {
   // with all libraries.
   if ($library_id) {
     $sql = "
-      SELECT LF.feature_id, L.library_id, L.name as libname 
-      FROM {library_feature} LF 
-        INNER JOIN {library} L ON LF.library_id = L.library_id 
-      WHERE L.library_id = :library_id 
+      SELECT LF.feature_id, L.library_id, L.name as libname
+      FROM {library_feature} LF
+        INNER JOIN {library} L ON LF.library_id = L.library_id
+      WHERE L.library_id = :library_id
       ORDER BY LF.feature_id
     ";
     $results = chado_query($sql, array(':library_id' => $library_id));
   }
   else {
     $sql = "
-      SELECT LF.feature_id, L.library_id, L.name as libname 
-      FROM {library_feature} LF 
-        INNER JOIN {library} L ON LF.library_id = L.library_id 
+      SELECT LF.feature_id, L.library_id, L.name as libname
+      FROM {library_feature} LF
+        INNER JOIN {library} L ON LF.library_id = L.library_id
       ORDER BY LF.feature_id
     ";
     $results = chado_query($sql);
@@ -552,9 +581,9 @@ function tripal_library_taxonify_features($library_id = NULL, $job_id = NULL) {
 
   // use this SQL for getting the nodes
   $nsql =  "
-    SELECT * 
-    FROM {chado_feature} CF 
-      INNER JOIN {node} N ON N.nid = CF.nid 
+    SELECT *
+    FROM {chado_feature} CF
+      INNER JOIN {node} N ON N.nid = CF.nid
     WHERE feature_id = :feature_id
   ";
    // iterate through the features and set the taxonomy
@@ -584,6 +613,6 @@ function tripal_library_taxonify_features($library_id = NULL, $job_id = NULL) {
 function tripal_library_cleanup($dummy = NULL, $job_id = NULL) {
 
   return tripal_core_clean_orphaned_nodes('library', $job_id);
-  
+
 }
 

tripal_library/tripal_library.info

@@ -4,9 +4,11 @@ core = 7.x
 project = tripal_library
 package = Tripal
 version = 7.x-2.0-beta1
+
 dependencies[] = search
 dependencies[] = path
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_organism
 dependencies[] = tripal_cv
 

tripal_library/tripal_library.install

@@ -4,6 +4,20 @@
  * @todo Add file header description
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_library_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_library.views_default.inc");
+  $views = tripal_library_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_requirements().
  */
@@ -27,13 +41,13 @@ function tripal_library_requirements($phase) {
  * @ingroup tripal_library
  */
 function tripal_library_install() {
-  
+
   // create the module's data directory
   tripal_create_moddir('tripal_library');
 
   // add the materialized view
   tripal_library_add_mview_library_feature_count();
-  
+
   // add cvterms
   tripal_library_add_cvterms();
 }
@@ -45,9 +59,12 @@ function tripal_library_install() {
  */
 function tripal_library_uninstall() {
   // Drop the MView table if it exists
+  // D7 @todo Fix tripal_mviews_get_mview_id()
+  /**
   if ($mview_id = tripal_mviews_get_mview_id('library_feature_count')) {
     tripal_mviews_action("delete", $mview_id);
   }
+  */
 }
 
 /**
@@ -94,7 +111,7 @@ function tripal_library_schema() {
 function tripal_library_add_mview_library_feature_count(){
   $view_name = 'library_feature_count';
   $comment = 'Provides count of feature by type that are associated with all libraries';
-  
+
   $schema = array(
     'table' => $view_name,
     'description' => $comment,
@@ -122,19 +139,19 @@ function tripal_library_add_mview_library_feature_count(){
       'library_feature_count_idx1' => array('library_id'),
     ),
   );
-  
+
   $sql = "
-    SELECT 
-      L.library_id, L.name, 
-      count(F.feature_id) as num_features, 
-      CVT.name as feature_type 
-    FROM library L 
-      INNER JOIN library_feature LF  ON LF.library_id = L.library_id 
-      INNER JOIN feature F           ON LF.feature_id = F.feature_id 
-      INNER JOIN cvterm CVT          ON F.type_id     = CVT.cvterm_id 
+    SELECT
+      L.library_id, L.name,
+      count(F.feature_id) as num_features,
+      CVT.name as feature_type
+    FROM library L
+      INNER JOIN library_feature LF  ON LF.library_id = L.library_id
+      INNER JOIN feature F           ON LF.feature_id = F.feature_id
+      INNER JOIN cvterm CVT          ON F.type_id     = CVT.cvterm_id
     GROUP BY L.library_id, L.name, CVT.name
   ";
-  
+
   tripal_add_mview($view_name, 'tripal_library', $schema, $sql, $comment);
 }
 
@@ -142,24 +159,24 @@ function tripal_library_add_mview_library_feature_count(){
  * @ingroup tripal_library
  */
 function tripal_library_add_cvterms() {
-  
+
   // Insert cvterm 'library_description' into cvterm table of chado
   // database. This CV term is used to keep track of the library
   // description in the libraryprop table.
-  tripal_cv_add_cvterm(array('name' => 'library_description', 'def' => 'Description of a library'), 
+  tripal_cv_add_cvterm(array('name' => 'library_description', 'def' => 'Description of a library'),
     'tripal', 0, 1, 'tripal');
-  
+
   // add cvterms for the map unit types
-  tripal_cv_add_cvterm(array('name' => 'cdna_library','def' => 'cDNA library'), 
+  tripal_cv_add_cvterm(array('name' => 'cdna_library','def' => 'cDNA library'),
+    'tripal_library_types', 0, 1, 'tripal');
+  tripal_cv_add_cvterm(array('name' => 'bac_library','def' => 'Bacterial Artifical Chromsome (BAC) library'),
     'tripal_library_types', 0, 1, 'tripal');
-  tripal_cv_add_cvterm(array('name' => 'bac_library','def' => 'Bacterial Artifical Chromsome (BAC) library'), 
+  tripal_cv_add_cvterm(array('name' => 'fosmid_library','def' => 'Fosmid library'),
     'tripal_library_types', 0, 1, 'tripal');
-  tripal_cv_add_cvterm(array('name' => 'fosmid_library','def' => 'Fosmid library'), 
-    'tripal_library_types', 0, 1, 'tripal');   
-  tripal_cv_add_cvterm(array('name' => 'cosmid_library','def' => 'Cosmid library'), 
+  tripal_cv_add_cvterm(array('name' => 'cosmid_library','def' => 'Cosmid library'),
     'tripal_library_types', 0, 1, 'tripal');
-  tripal_cv_add_cvterm(array('name' => 'yac_library','def' => 'Yeast Artificial Chromosome (YAC) library'), 
+  tripal_cv_add_cvterm(array('name' => 'yac_library','def' => 'Yeast Artificial Chromosome (YAC) library'),
     'tripal_library_types', 0, 1, 'tripal');
-  tripal_cv_add_cvterm(array('name' => 'genomic_library','def' => 'Genomic Library'), 
+  tripal_cv_add_cvterm(array('name' => 'genomic_library','def' => 'Genomic Library'),
     'tripal_library_types', 0, 1, 'tripal');
 }

tripal_library/tripal_library.module

@@ -119,22 +119,33 @@ function chado_library_node_access($node, $op, $account) {
 function tripal_library_menu() {
   $items = array();
   // The administative settings menu
-  $items['admin/tripal/tripal_library'] = array(
+  $items['admin/tripal/chado/tripal_library'] = array(
     'title' => 'Libraries',
+    'description' => 'A grouping of genetic data',
+    'page callback' => 'tripal_library_admin_libraries_listing',
+    'access arguments' => array('administer tripal libraries'),
+    'type' => MENU_NORMAL_ITEM,
+    'weight' => 0
+  );
+
+  $items['admin/tripal/chado/tripal_library/help'] = array(
+    'title' => 'Help',
     'description' => 'Basic Description of Tripal Library Module Functionality',
     'page callback' => 'theme',
-    'page arguments' => array('tripal_library_help'),
+    'page arguments' => array('tripal_library_admin'),
     'access arguments' => array('administer tripal libraries'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 4
   );
 
-  $items['admin/tripal/tripal_library/configuration'] = array(
-    'title' => 'Configuration',
+  $items['admin/tripal/chado/tripal_library/configuration'] = array(
+    'title' => 'Settings',
     'description' => 'Configure the Tripal Library module',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_library_help'),
+    'page arguments' => array('tripal_library_admin'),
     'access arguments' => array('administer tripal libraries'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 2
   );
 
   // Synchronizing libraries from Chado to Drupal
@@ -242,8 +253,8 @@ function tripal_library_theme() {
       'path' => "$theme_path/tripal_library",
     ),
     // help template
-    'tripal_library_help' => array(
-      'template' => 'tripal_library_help',
+    'tripal_library_admin' => array(
+      'template' => 'tripal_library_admin',
       'arguments' =>  array(NULL),
       'path' => $theme_path,
     ),

tripal_library/tripal_library.views.inc

@@ -15,386 +15,3 @@
  * @ingroup views
  */
 
-/**
- *
- *
- * @ingroup tripal_library_views
- */
-function tripal_library_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // Main default view
-  $view = new view;
-  $view->name = 'library_listing';
-  $view->description = 'A listing of all libraries';
-  $view->tag = 'chado default';
-  $view->base_table = 'library';
-  $view->core = 0;
-  $view->api_version = '2';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->override_option('fields', array(
-    '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',
-    ),
-  ));
-  $handler->override_option('sorts', array(
-    'name' => array(
-      'id' => 'name',
-      'table' => 'library',
-      'field' => 'name',
-    ),
-  ));
-  $handler->override_option('filters', array(
-    'common_name' => array(
-      'operator' => '=',
-      'value' => array(),
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'common_name_op',
-        'identifier' => 'organism_common_name',
-        'label' => 'Organism',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'type_id' => array(
-      'operator' => '=',
-      'value' => array(),
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'type_id_op',
-        'identifier' => 'type_id',
-        'label' => 'Type',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'type_id',
-      'table' => 'library',
-      'field' => 'type_id',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'show_all' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 0,
-      ),
-    ),
-  ));
-  $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('header', 'Click "Show" to see a list of all libraries matching the entered criteria. If you leave a any of the criteria blank then the libraries will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all libraries will be listed.');
-  $handler->override_option('header_format', '2');
-  $handler->override_option('header_empty', 0);
-  $handler->override_option('empty', 'No libraries 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',
-    'summary' => '',
-    'columns' => array(
-      'uniquename' => 'uniquename',
-      'name_1' => 'name_1',
-      'common_name' => 'common_name',
-      'name' => 'name',
-      'is_obsolete' => 'is_obsolete',
-    ),
-    'info' => array(
-      'uniquename' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name_1' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'common_name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'is_obsolete' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-    ),
-    'default' => 'uniquename',
-  ));
-  $default_handler = $handler;
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/libraries');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Libraries',
-    'description' => 'A library is a collection of features of a given type. For example, a cDNA or BAC clone library.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        '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,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Adds library => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Library to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_library',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Change analysis.name to have a link to the node
-    $fields['name_1']['alter']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // Only show records with published nodes
-    /**
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-    */
-  }
-  $views[$view->name] = $view;
-
-  return $views;
-}

tripal_library/tripal_library.views_default.inc

@@ -0,0 +1,219 @@
+<?php
+
+/**
+ *
+ *
+ * @ingroup tripal_library_views
+ */
+function tripal_library_views_default_views() {
+  $views = array();
+
+  $view = tripal_library_admin_defaultviews_library();
+  $views[$view->name] = $view;
+
+  return $views;
+}
+
+function tripal_library_admin_defaultviews_library() {
+
+  $view = new view();
+  $view->name = 'tripal_library_admin_libraries';
+  $view->description = 'DO NOT DISABLE';
+  $view->tag = 'tripal admin';
+  $view->base_table = 'library';
+  $view->human_name = 'Library Admin';
+  $view->core = 0;
+  $view->api_version = '3.0';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+
+  /* Display: Defaults */
+  $handler = $view->new_display('default', 'Defaults', 'default');
+  $handler->display->display_options['title'] = 'Libraries';
+  $handler->display->display_options['use_more_always'] = FALSE;
+  $handler->display->display_options['access']['type'] = 'perm';
+  $handler->display->display_options['access']['perm'] = 'access chado_library content';
+  $handler->display->display_options['cache']['type'] = 'none';
+  $handler->display->display_options['query']['type'] = 'views_query';
+  $handler->display->display_options['exposed_form']['type'] = 'basic';
+  $handler->display->display_options['pager']['type'] = 'none';
+  $handler->display->display_options['style_plugin'] = 'table';
+  $handler->display->display_options['style_options']['grouping'] = '';
+  $handler->display->display_options['style_options']['columns'] = array(
+    'uniquename' => 'uniquename',
+    'name_1' => 'name_1',
+    'common_name' => 'common_name',
+    'name' => 'name',
+    'is_obsolete' => 'is_obsolete',
+  );
+  $handler->display->display_options['style_options']['default'] = 'uniquename';
+  $handler->display->display_options['style_options']['info'] = array(
+    'uniquename' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'name_1' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'common_name' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'name' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'is_obsolete' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+  );
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Library',
+    'path-1' => 'node/add/tripal-library',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-2'] = array(
+    'label-2' => '',
+    'path-2' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-3'] = array(
+    'label-3' => '',
+    'path-3' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-4'] = array(
+    'label-4' => '',
+    'path-4' => '',
+  );
+  /* No results behavior: Global: Text area */
+  $handler->display->display_options['empty']['text']['id'] = 'area';
+  $handler->display->display_options['empty']['text']['table'] = 'views';
+  $handler->display->display_options['empty']['text']['field'] = 'area';
+  $handler->display->display_options['empty']['text']['content'] = 'No libraries match the supplied criteria.';
+  $handler->display->display_options['empty']['text']['format'] = '1';
+  /* Relationship: Library: Library => Node */
+  $handler->display->display_options['relationships']['library_id']['id'] = 'library_id';
+  $handler->display->display_options['relationships']['library_id']['table'] = 'chado_library';
+  $handler->display->display_options['relationships']['library_id']['field'] = 'library_id';
+  /* Field: Content: Nid */
+  $handler->display->display_options['fields']['nid']['id'] = 'nid';
+  $handler->display->display_options['fields']['nid']['table'] = 'node';
+  $handler->display->display_options['fields']['nid']['field'] = 'nid';
+  $handler->display->display_options['fields']['nid']['relationship'] = 'library_id';
+  $handler->display->display_options['fields']['nid']['exclude'] = TRUE;
+  /* Field: Chado Library: Uniquename */
+  $handler->display->display_options['fields']['uniquename']['id'] = 'uniquename';
+  $handler->display->display_options['fields']['uniquename']['table'] = 'library';
+  $handler->display->display_options['fields']['uniquename']['field'] = 'uniquename';
+  $handler->display->display_options['fields']['uniquename']['label'] = 'Unique Name';
+  /* Field: Chado Library: Name */
+  $handler->display->display_options['fields']['name_1']['id'] = 'name_1';
+  $handler->display->display_options['fields']['name_1']['table'] = 'library';
+  $handler->display->display_options['fields']['name_1']['field'] = 'name';
+  /* Field: Chado Organism: Common Name */
+  $handler->display->display_options['fields']['common_name']['id'] = 'common_name';
+  $handler->display->display_options['fields']['common_name']['table'] = 'organism';
+  $handler->display->display_options['fields']['common_name']['field'] = 'common_name';
+  $handler->display->display_options['fields']['common_name']['label'] = 'Organism';
+  /* Field: Chado Cvterm: Name */
+  $handler->display->display_options['fields']['name']['id'] = 'name';
+  $handler->display->display_options['fields']['name']['table'] = 'cvterm';
+  $handler->display->display_options['fields']['name']['field'] = 'name';
+  $handler->display->display_options['fields']['name']['label'] = 'Type';
+  /* Field: Chado Library: Is Obsolete */
+  $handler->display->display_options['fields']['is_obsolete']['id'] = 'is_obsolete';
+  $handler->display->display_options['fields']['is_obsolete']['table'] = 'library';
+  $handler->display->display_options['fields']['is_obsolete']['field'] = 'is_obsolete';
+  $handler->display->display_options['fields']['is_obsolete']['label'] = 'Obsolete?';
+  $handler->display->display_options['fields']['is_obsolete']['alter']['alter_text'] = TRUE;
+  $handler->display->display_options['fields']['is_obsolete']['alter']['text'] = 'Yes';
+  $handler->display->display_options['fields']['is_obsolete']['empty'] = 'No';
+  $handler->display->display_options['fields']['is_obsolete']['empty_zero'] = TRUE;
+  $handler->display->display_options['fields']['is_obsolete']['separator'] = '';
+  /* Field: Content: Delete link */
+  $handler->display->display_options['fields']['delete_node']['id'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['delete_node']['field'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['relationship'] = 'library_id';
+  $handler->display->display_options['fields']['delete_node']['exclude'] = TRUE;
+  /* Field: Content: Edit link */
+  $handler->display->display_options['fields']['edit_node']['id'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['edit_node']['field'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['relationship'] = 'library_id';
+  $handler->display->display_options['fields']['edit_node']['exclude'] = TRUE;
+  /* Field: Global: Custom text */
+  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['table'] = 'views';
+  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['label'] = '';
+  $handler->display->display_options['fields']['nothing']['alter']['text'] = '[edit_node]   [delete_node]';
+  $handler->display->display_options['fields']['nothing']['element_label_colon'] = FALSE;
+  /* Sort criterion: Chado Library: Name */
+  $handler->display->display_options['sorts']['name']['id'] = 'name';
+  $handler->display->display_options['sorts']['name']['table'] = 'library';
+  $handler->display->display_options['sorts']['name']['field'] = 'name';
+  /* Filter criterion: Chado Organism: Common Name */
+  $handler->display->display_options['filters']['common_name']['id'] = 'common_name';
+  $handler->display->display_options['filters']['common_name']['table'] = 'organism';
+  $handler->display->display_options['filters']['common_name']['field'] = 'common_name';
+  $handler->display->display_options['filters']['common_name']['value'] = 'All';
+  $handler->display->display_options['filters']['common_name']['group'] = '0';
+  $handler->display->display_options['filters']['common_name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['common_name']['expose']['operator_id'] = 'common_name_op';
+  $handler->display->display_options['filters']['common_name']['expose']['label'] = 'Organism';
+  $handler->display->display_options['filters']['common_name']['expose']['operator'] = 'common_name_op';
+  $handler->display->display_options['filters']['common_name']['expose']['identifier'] = 'organism_common_name';
+  $handler->display->display_options['filters']['common_name']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Library: Type Id */
+  $handler->display->display_options['filters']['type_id']['id'] = 'type_id';
+  $handler->display->display_options['filters']['type_id']['table'] = 'library';
+  $handler->display->display_options['filters']['type_id']['field'] = 'type_id';
+  $handler->display->display_options['filters']['type_id']['group'] = '0';
+  $handler->display->display_options['filters']['type_id']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['type_id']['expose']['operator_id'] = 'type_id_op';
+  $handler->display->display_options['filters']['type_id']['expose']['label'] = 'Type';
+  $handler->display->display_options['filters']['type_id']['expose']['operator'] = 'type_id_op';
+  $handler->display->display_options['filters']['type_id']['expose']['identifier'] = 'type_id';
+  $handler->display->display_options['filters']['type_id']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+
+  /** MANUALLY ADD since filter handler no exporting correctly */
+  $handler->display->display_options['filters']['common_name']['expose']['values_form_type'] = 'select';
+  $handler->display->display_options['filters']['common_name']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['common_name']['expose']['select_optional'] = TRUE;
+  $handler->display->display_options['filters']['common_name']['expose']['max_length'] = 40;
+
+  /* Display: Page */
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_library/libraries';
+  $handler->display->display_options['menu']['type'] = 'default tab';
+  $handler->display->display_options['menu']['title'] = 'Libraries';
+  $handler->display->display_options['menu']['description'] = 'A library is a collection of features of a given type. For example, a cDNA or BAC clone library.';
+  $handler->display->display_options['menu']['weight'] = '0';
+  $handler->display->display_options['menu']['name'] = 'management';
+  $handler->display->display_options['menu']['context'] = 0;
+  $handler->display->display_options['menu']['context_only_inline'] = 0;
+  $handler->display->display_options['tab_options']['weight'] = '0';
+
+  /** MANUALLY ADD since filter handler no exporting correctly
+  $handler->display->display_options['filters']['common_name']['expose']['values_form_type'] = 'select';
+  $handler->display->display_options['filters']['common_name']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['common_name']['expose']['select_optional'] = TRUE;
+  $handler->display->display_options['filters']['common_name']['expose']['max_length'] = 40;
+  */
+
+  return $view;
+}

tripal_natural_diversity/tripal_natural_diversity.info

@@ -4,7 +4,9 @@ core = 7.x
 project = tripal_natural_diversity
 package = Tripal
 version = 7.x-2.0-beta1
+
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_cv
 dependencies[] = tripal_db
 dependencies[] = tripal_genetic

tripal_natural_diversity/tripal_natural_diversity.install

@@ -4,7 +4,19 @@
  * Implements hooks from the Schema API
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_natural_diversity_disable() {
 
+  // Disable all default views provided by this module
+  require_once("tripal_natural_diversity.views_default.inc");
+  $views = tripal_natural_diversity_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
 
 /**
  * Implementation of hook_requirements().
@@ -31,10 +43,10 @@ function tripal_natural_diversity_install() {
 
   // create the module's data directory
   tripal_create_moddir('tripal_natural_diversity');
-  
+
   // add cvterms
   tripal_natural_diversity_add_cvterms();
-  
+
 }
 
 /**
@@ -45,16 +57,16 @@ function tripal_natural_diversity_uninstall() {
 }
 
 /*
- * 
+ *
  */
 function tripal_natural_diversity_add_cvterms(){
-   
-  // add cvterms for the nd_experiment_types 
-  tripal_cv_add_cvterm(array('name' => 'Genotyping','def' => 'An experiment where genotypes of individuals are identified.'), 
+
+  // add cvterms for the nd_experiment_types
+  tripal_cv_add_cvterm(array('name' => 'Genotyping','def' => 'An experiment where genotypes of individuals are identified.'),
     'nd_experiment_types', 0, 1, 'tripal');
-  tripal_cv_add_cvterm(array('name' => 'Phenotyping','def' => 'An experiment where phenotypes of individuals are identified.'), 
+  tripal_cv_add_cvterm(array('name' => 'Phenotyping','def' => 'An experiment where phenotypes of individuals are identified.'),
     'nd_experiment_types', 0, 1, 'tripal');
-  
-  tripal_cv_add_cvterm(array('name' => 'Location','def' => 'The name of the location.'), 
+
+  tripal_cv_add_cvterm(array('name' => 'Location','def' => 'The name of the location.'),
     'nd_geolocation_property', 0, 1, 'tripal');
 }

tripal_natural_diversity/tripal_natural_diversity.views.inc

@@ -12,955 +12,4 @@
 /**
  * @defgroup tripal_natural_diversity_views Natural Diversity Views Integration
  * @ingroup views
- */
-
-
-
-/**
- * Created Default views related to the tables integrated by this module
- *
- * @ingroup tripal_natural_diversity_views
- */
-
-
-/* -- SPF Jun 13, 2013 removed as a search by ND experiment 
- * results in a huge return list.  As in the case of a genotyping
- * GWAS experiment where tens of thousands of SNP genotypes are
- * present.  --
-function tripal_natural_diversity_views_default_views() {
-  $views = array();
-
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-
-  // 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; 
-  $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' => '=',
-      'value' => array(),
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'description_op',
-        'identifier' => 'geolocation',
-        'label' => 'Location Experiment Performed',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'description',
-      'table' => 'nd_geolocation',
-      'field' => 'description',
-      'relationship' => 'none',
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 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 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', 'chado/natdiv_experiments');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Natural Diversity Experiments',
-    'description' => 'A single assay resulting in a single genotype or phenotype. Multiple assays resulting in an entire experiment should be grouped together as a project.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $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; 
-  $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(
-    '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' => '=',
-      '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' => '=',
-      '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' => '=',
-      '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,
-      ),
-    ),
-    'description' => array(
-      'operator' => '~',
-      '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', 'chado/natdiv_geolocations');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Locations',
-    'description' => 'Geographical locations in which natural diversity experiments might be performed.',
-    'weight' => '10',
-    '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; 
-  $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' => '~',
-      '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', 'chado/natdiv_protocols');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Protocols',
-    'description' => 'The protcols used for natural diversity experiments',
-    'weight' => '10',
-    '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; 
-  $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',
-    ),
-  ));
-  $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' => '~',
-      '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', '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', 'chado/natdiv_reagents');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Reagents',
-    'description' => 'Reagents used in natural diversity experiments',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  $views[$view->name] = $view;
-
-  return $views;
-}
-*/
-
+ */

tripal_natural_diversity/tripal_natural_diversity.views_default.inc

@@ -0,0 +1,942 @@
+<?php
+
+/* -- SPF Jun 13, 2013 removed as a search by ND experiment
+ * results in a huge return list.  As in the case of a genotyping
+ * GWAS experiment where tens of thousands of SNP genotypes are
+ * present.  --
+ */
+function tripal_natural_diversity_views_default_views() {
+  $views = array();
+
+
+  if (!module_exists('tripal_views')) {
+    return $views;
+  }
+
+
+  // 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;
+  $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' => '=',
+      'value' => array(),
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'description_op',
+        'identifier' => 'geolocation',
+        'label' => 'Location Experiment Performed',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'description',
+      'table' => 'nd_geolocation',
+      'field' => 'description',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 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 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', 'chado/natdiv_experiments');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Natural Diversity Experiments',
+    'description' => 'A single assay resulting in a single genotype or phenotype. Multiple assays resulting in an entire experiment should be grouped together as a project.',
+    'weight' => '10',
+    'name' => 'navigation',
+  ));
+  $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;
+  $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(
+    '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' => '=',
+      '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' => '=',
+      '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' => '=',
+      '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,
+      ),
+    ),
+    'description' => array(
+      'operator' => '~',
+      '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', 'chado/natdiv_geolocations');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Locations',
+    'description' => 'Geographical locations in which natural diversity experiments might be performed.',
+    'weight' => '10',
+    '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;
+  $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' => '~',
+      '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', 'chado/natdiv_protocols');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Protocols',
+    'description' => 'The protcols used for natural diversity experiments',
+    'weight' => '10',
+    '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;
+  $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',
+    ),
+  ));
+  $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' => '~',
+      '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', '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', 'chado/natdiv_reagents');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Reagents',
+    'description' => 'Reagents used in natural diversity experiments',
+    'weight' => '10',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  $views[$view->name] = $view;
+
+  return $views;
+}

tripal_organism/includes/tripal_organism.admin.inc

@@ -1,5 +1,38 @@
 <?php
 
+/**
+ *
+ */
+function tripal_organism_admin_organism_view() {
+  $output = '';
+
+  // set the breadcrumb
+  $breadcrumb = array();
+  $breadcrumb[] = l('Home', '<front>');
+  $breadcrumb[] = l('Administration', 'admin');
+  $breadcrumb[] = l('Tripal', 'admin/tripal');
+  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
+  $breadcrumb[] = l('Organisms', 'admin/tripal/chado/tripal_organism');
+  drupal_set_breadcrumb($breadcrumb);
+
+  // Add the view
+  $view = views_embed_view('tripal_organism_admin_organisms','default');
+  if (isset($view)) {
+    $output .= $view;
+  }
+  else {
+    $output .= '<p>The Organism module uses primarily views to provide an '
+      . 'administrative interface. Currently one or more views needed for this '
+      . 'administrative interface are disabled. <strong>Click each of the following links to '
+      . 'enable the pertinent views</strong>:</p>';
+    $output .= '<ul>';
+      $output .= '<li>'.l('Organisms View', 'admin/tripal/chado/tripal_organism/views/organisms/enable').'</li>';
+    $output .= '</ul>';
+  }
+
+  return $output;
+}
+
 /**
  * Administrative settings for chado_orgnism
  *
@@ -10,7 +43,7 @@ function tripal_organism_admin() {
   $form = array();
 
   get_tripal_organism_admin_form_reindex_set($form);
-  get_tripal_organism_admin_form_taxonomy_set($form);  
+  get_tripal_organism_admin_form_taxonomy_set($form);
 
   return system_settings_form($form);
 }
@@ -41,7 +74,7 @@ function get_tripal_organism_admin_form_taxonomy_set(&$form) {
     '#value' => t(
       "Drupal allows for assignment of \"taxonomy\" or catagorical terms to " .
       "nodes. These terms allow for advanced filtering during searching. This option allows " .
-      "for setting taxonomy only for features that belong to the selected organisms below.  All " . 
+      "for setting taxonomy only for features that belong to the selected organisms below.  All " .
       "other features will be unaffected.  To set taxonomy for all features in the site see the Feature Administration page."),
     '#weight' => 1,
   );
@@ -161,9 +194,9 @@ function tripal_organism_reindex_features($organism_id = NULL, $job_id = NULL) {
   }
 
   $sql = "
-    SELECT * 
-    FROM {feature} 
-    WHERE organism_id = :organism_id 
+    SELECT *
+    FROM {feature}
+    WHERE organism_id = :organism_id
     ORDER BY feature_id";
   $results = chado_query($sql, array(':organism_id' => $organism_id));
 
@@ -196,9 +229,9 @@ function tripal_organism_taxonify_features($organism_id = NULL, $job_id = NULL)
   }
 
   $sql = "
-    SELECT * 
-    FROM {feature} 
-    WHERE organism_id = :organism_id 
+    SELECT *
+    FROM {feature}
+    WHERE organism_id = :organism_id
     ORDER BY feature_id
   ";
   $results = chado_query($sql, array(':organism_id' => $organism_id));

tripal_organism/tripal_organism.info

@@ -7,5 +7,6 @@ version = 7.x-2.0-beta1
 configure = admin/tripal/chado/tripal_organism
 
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = search
 dependencies[] = path

tripal_organism/tripal_organism.install

@@ -5,6 +5,20 @@
  * Functions pertaining to the install/uninstall of this module
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_organism_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_organism.views_default.inc");
+  $views = tripal_organism_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_install().
  *
@@ -54,7 +68,7 @@ function tripal_organism_schema() {
       ),
       'primary key' => array('nid'),
   );
-  return $schema;  
+  return $schema;
 }
 
 /**
@@ -66,8 +80,8 @@ function tripal_organism_uninstall() {
 
   // Get the list of nodes to remove
   $sql_lib_id = "
-    SELECT nid, vid 
-    FROM {node} 
+    SELECT nid, vid
+    FROM {node}
     WHERE type='chado_organism'
   ";
   $result = db_query($sql_lib_id);
@@ -77,7 +91,7 @@ function tripal_organism_uninstall() {
 }
 
 /**
- * Implementation of hook_requirements(). 
+ * Implementation of hook_requirements().
  *
  */
 function tripal_organism_requirements($phase) {

tripal_organism/tripal_organism.module

@@ -100,7 +100,8 @@ function tripal_organism_menu() {
   // the administative settings menu
   $items['admin/tripal/chado/tripal_organism'] = array(
    'title' => 'Organisms',
-   'description' => 'Basic Description of Tripal Organism Module Functionality',
+   'description' => 'Any living biological entity, such as an animal, plant, fungus, or bacterium.',
+   'page callback' => 'tripal_organism_admin_organism_view',
    'access arguments' => array('adminster tripal organism'),
    'type' => MENU_NORMAL_ITEM,
   );
@@ -111,25 +112,33 @@ function tripal_organism_menu() {
    'page callback' => 'theme',
    'page arguments' => array('tripal_organism_help'),
    'access arguments' => array('adminster tripal organism'),
-   'type' => MENU_NORMAL_ITEM,
+   'type' => MENU_LOCAL_TASK,
   );
 
   $items['admin/tripal/chado/tripal_organism/configuration'] = array(
-   'title' => 'Configuration',
+   'title' => 'Settings',
    'description' => 'Manage integration of Chado organisms including associated features',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_organism_admin'),
    'access arguments' => array('adminster tripal organism'),
-   'type' => MENU_NORMAL_ITEM,
+   'type' => MENU_LOCAL_TASK,
   );
 
   $items['admin/tripal/chado/tripal_organism/sync'] = array(
-    'title' => 'Sync Organisms',
+    'title' => 'Sync',
     'description' => 'Sync Chado organisms with Drupal',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_organism_sync'),
     'access arguments' => array('adminster tripal organism'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+  );
+
+  $items['admin/tripal/chado/tripal_organism/views/organisms/enable'] = array(
+    'title' => 'Enable Organism Administrative View',
+    'page callback' => 'tripal_views_admin_enable_view',
+    'page arguments' => array('tripal_organism_admin_organisms', 'admin/tripal/chado/tripal_organism'),
+    'access arguments' => array('administer tripal_bulk_loader'),
+    'type' => MENU_CALLBACK,
   );
 
   return $items;
@@ -154,7 +163,7 @@ function tripal_organism_help ($path, $arg) {
  */
 function tripal_organism_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
-  
+
   $items = array(
     'node__chado_organism' => array(
       'template' => 'node--chado-generic',
@@ -329,7 +338,7 @@ function chado_organism_validate($node, $form, &$form_state) {
   $node->abbreviation = trim($node->abbreviation);
   $node->common_name  = trim($node->common_name);
   $node->description  = trim($node->description);
-  
+
   // if this is an update, we want to make sure that a different organism doesn't
   // already have this genus and speces
   if (property_exists($node, 'organism_id')) {
@@ -383,7 +392,7 @@ function chado_organism_insert($node) {
   $node->abbreviation = trim($node->abbreviation);
   $node->common_name  = trim($node->common_name);
   $node->description  = trim($node->description);
-  
+
   // if there is an organism_id in the $node object then this must be a sync so
   // we can skip adding the organism as it is already there, although
   // we do need to proceed with the rest of the insert
@@ -410,7 +419,7 @@ function chado_organism_insert($node) {
 
   // Make sure the entry for this organism doesn't already exist in the
   // chado_organism table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('organism', $node->nid);  
+  $check_org_id = chado_get_id_for_node('organism', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -441,7 +450,7 @@ function chado_organism_update($node) {
   $node->abbreviation = trim($node->abbreviation);
   $node->common_name  = trim($node->common_name);
   $node->description  = trim($node->description);
-  
+
   if ($node->revision) {
     // there is no way to handle revisions in Chado but leave
     // this here just to make not we've addressed it.
@@ -546,17 +555,17 @@ function chado_organism_add_image($node) {
  */
 function chado_organism_form($node, $form_state) {
   $form = array();
-  
+
   // we have a file upload element on the form soe we need the multipart encoding type
   $form['#attributes']['enctype'] = 'multipart/form-data';
-  
+
   // if the organism is part of the node object then we are editing. If not we are inserting
   if (property_exists($node, 'organism')) {
     $organism = $node->organism;
 
     // add in the comment since it is a text field and may not be included if too big
     $organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');
-    
+
     // get form defaults
     $abbreviation   = property_exists($node, 'abbreviation')   ? property_exists($node, 'abbreviation')   : $organism->abbreviation;
     $genus          = property_exists($node, 'genus')          ? property_exists($node, 'genus')          : $organism->genus;
@@ -564,7 +573,7 @@ function chado_organism_form($node, $form_state) {
     $common_name    = property_exists($node, 'common_name')    ? property_exists($node, 'common_name')    : $organism->common_name;
     $description    = property_exists($node, 'description')    ? property_exists($node, 'description')    : $organism->comment;
     $organism_image = property_exists($node, 'organism_image') ? property_exists($node, 'organism_image') : '';
-    
+
     // set the organism_id in the form
     $form['organism_id'] = array(
       '#type' => 'value',
@@ -635,7 +644,7 @@ function chado_organism_load($nodes) {
     // build the organism variable
     $values = array('organism_id' => $organism_id);
     $organism = tripal_core_generate_chado_var('organism', $values);
-    
+
 
     // add in the description field
     $organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');

tripal_organism/tripal_organism.views.inc

@@ -14,301 +14,3 @@
  * @defgroup tripal_organism_views Organism Views Integration
  * @ingroup views
  */
-
-/**
- *
- * @ingroup tripal_organism_views
- */
-function tripal_organism_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // Main default view
-  $view = new view;
-  $view->name = 'organism_listing';
-  $view->description = 'A listing of all organism in chado';
-  $view->tag = 'chado default';
-  $view->base_table = 'organism';
-  $view->core = 0;
-  $view->api_version = '2';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->override_option('fields', array(
-    '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',
-    ),
-    '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',
-    ),
-    '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',
-    ),
-  ));
-  $handler->override_option('sorts', array(
-    'genus' => array(
-      'order' => 'ASC',
-      'id' => 'genus',
-      'table' => 'organism',
-      'field' => 'genus',
-      'relationship' => 'none',
-    ),
-    'species' => array(
-      'order' => 'ASC',
-      'id' => 'species',
-      'table' => 'organism',
-      'field' => 'species',
-      '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 organisms matched the supplied criteria.');
-  $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',
-    'summary' => '',
-    'columns' => array(
-      'common_name' => 'common_name',
-      'genus' => 'genus',
-      'species' => 'species',
-      'abbreviation' => 'abbreviation',
-    ),
-    'info' => array(
-      'common_name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'genus' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'species' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'abbreviation' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-    ),
-    'default' => '-1',
-  ));
-  $default_handler = $handler;
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/organisms');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Organisms',
-    'description' => 'A biological organism.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        '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,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Adds organism => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Organism to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_organism',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Change analysis.name to have a link to the node
-    $fields['common_name']['alter']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // Only show records with published nodes
-    /**
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-    */
-  }
-  $views[$view->name] = $view;
-
-  return $views;
-}

tripal_organism/tripal_organism.views_default.inc

@@ -0,0 +1,209 @@
+<?php
+
+/**
+ *
+ * @ingroup tripal_organism_views
+ */
+function tripal_organism_views_default_views() {
+  $views = array();
+
+  $view = tripal_organism_admin_defaultview_organisms();
+  $views[$view->name] = $view;
+
+  return $views;
+}
+
+function tripal_organism_admin_defaultview_organisms() {
+
+  $view = new view();
+  $view->name = 'tripal_organism_admin_organisms';
+  $view->description = 'DO NOT DISABLE';
+  $view->tag = 'tripal admin';
+  $view->base_table = 'organism';
+  $view->human_name = 'Organism Admin';
+  $view->core = 0;
+  $view->api_version = '3.0';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+
+  /* Display: Defaults */
+  $handler = $view->new_display('default', 'Defaults', 'default');
+  $handler->display->display_options['title'] = 'Organisms';
+  $handler->display->display_options['use_more_always'] = FALSE;
+  $handler->display->display_options['access']['type'] = 'perm';
+  $handler->display->display_options['access']['perm'] = 'adminster tripal organism';
+  $handler->display->display_options['cache']['type'] = 'none';
+  $handler->display->display_options['query']['type'] = 'views_query';
+  $handler->display->display_options['exposed_form']['type'] = 'basic';
+  $handler->display->display_options['exposed_form']['options']['submit_button'] = 'Filter';
+  $handler->display->display_options['pager']['type'] = 'full';
+  $handler->display->display_options['pager']['options']['items_per_page'] = '25';
+  $handler->display->display_options['pager']['options']['offset'] = '0';
+  $handler->display->display_options['pager']['options']['id'] = '0';
+  $handler->display->display_options['pager']['options']['quantity'] = '9';
+  $handler->display->display_options['style_plugin'] = 'table';
+  $handler->display->display_options['style_options']['grouping'] = '';
+  $handler->display->display_options['style_options']['columns'] = array(
+    'common_name' => 'common_name',
+    'genus' => 'genus',
+    'species' => 'species',
+    'abbreviation' => 'abbreviation',
+  );
+  $handler->display->display_options['style_options']['default'] = '-1';
+  $handler->display->display_options['style_options']['info'] = array(
+    'common_name' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'genus' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'species' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+    'abbreviation' => array(
+      'sortable' => 1,
+      'separator' => '',
+    ),
+  );
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Organism',
+    'path-1' => 'node/add/tripal_organism',
+  );
+  /* No results behavior: Global: Text area */
+  $handler->display->display_options['empty']['text']['id'] = 'area';
+  $handler->display->display_options['empty']['text']['table'] = 'views';
+  $handler->display->display_options['empty']['text']['field'] = 'area';
+  $handler->display->display_options['empty']['text']['content'] = 'No organisms matched the supplied criteria.';
+  $handler->display->display_options['empty']['text']['format'] = '1';
+  /* Relationship: Organism: Organism => Node */
+  $handler->display->display_options['relationships']['organism_id']['id'] = 'organism_id';
+  $handler->display->display_options['relationships']['organism_id']['table'] = 'chado_organism';
+  $handler->display->display_options['relationships']['organism_id']['field'] = 'organism_id';
+  /* Field: Content: Nid */
+  $handler->display->display_options['fields']['nid']['id'] = 'nid';
+  $handler->display->display_options['fields']['nid']['table'] = 'node';
+  $handler->display->display_options['fields']['nid']['field'] = 'nid';
+  $handler->display->display_options['fields']['nid']['exclude'] = TRUE;
+  /* Field: Chado Organism: Common Name */
+  $handler->display->display_options['fields']['common_name']['id'] = 'common_name';
+  $handler->display->display_options['fields']['common_name']['table'] = 'organism';
+  $handler->display->display_options['fields']['common_name']['field'] = 'common_name';
+  $handler->display->display_options['fields']['common_name']['alter']['make_link'] = TRUE;
+  $handler->display->display_options['fields']['common_name']['alter']['path'] = 'node/[nid]';
+  /* Field: Chado Organism: Genus */
+  $handler->display->display_options['fields']['genus']['id'] = 'genus';
+  $handler->display->display_options['fields']['genus']['table'] = 'organism';
+  $handler->display->display_options['fields']['genus']['field'] = 'genus';
+  /* Field: Chado Organism: Species */
+  $handler->display->display_options['fields']['species']['id'] = 'species';
+  $handler->display->display_options['fields']['species']['table'] = 'organism';
+  $handler->display->display_options['fields']['species']['field'] = 'species';
+  /* Field: Chado Organism: Abbreviation */
+  $handler->display->display_options['fields']['abbreviation']['id'] = 'abbreviation';
+  $handler->display->display_options['fields']['abbreviation']['table'] = 'organism';
+  $handler->display->display_options['fields']['abbreviation']['field'] = 'abbreviation';
+  /* Field: Content: Delete link */
+  $handler->display->display_options['fields']['delete_node']['id'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['delete_node']['field'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['relationship'] = 'organism_id';
+  $handler->display->display_options['fields']['delete_node']['exclude'] = TRUE;
+  /* Field: Content: Edit link */
+  $handler->display->display_options['fields']['edit_node']['id'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['edit_node']['field'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['relationship'] = 'organism_id';
+  $handler->display->display_options['fields']['edit_node']['exclude'] = TRUE;
+  /* Field: Global: Custom text */
+  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['table'] = 'views';
+  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['label'] = '';
+  $handler->display->display_options['fields']['nothing']['alter']['text'] = '[edit_node]   [delete_node]';
+  $handler->display->display_options['fields']['nothing']['element_label_colon'] = FALSE;
+  /* Sort criterion: Chado Organism: Genus */
+  $handler->display->display_options['sorts']['genus']['id'] = 'genus';
+  $handler->display->display_options['sorts']['genus']['table'] = 'organism';
+  $handler->display->display_options['sorts']['genus']['field'] = 'genus';
+  /* Sort criterion: Chado Organism: Species */
+  $handler->display->display_options['sorts']['species']['id'] = 'species';
+  $handler->display->display_options['sorts']['species']['table'] = 'organism';
+  $handler->display->display_options['sorts']['species']['field'] = 'species';
+  /* Filter criterion: Chado Organism: Common Name */
+  $handler->display->display_options['filters']['common_name']['id'] = 'common_name';
+  $handler->display->display_options['filters']['common_name']['table'] = 'organism';
+  $handler->display->display_options['filters']['common_name']['field'] = 'common_name';
+  $handler->display->display_options['filters']['common_name']['operator'] = 'contains';
+  $handler->display->display_options['filters']['common_name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['common_name']['expose']['operator_id'] = '';
+  $handler->display->display_options['filters']['common_name']['expose']['label'] = 'Common Name Contains';
+  $handler->display->display_options['filters']['common_name']['expose']['identifier'] = 'common_name';
+  $handler->display->display_options['filters']['common_name']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Organism: Genus */
+  $handler->display->display_options['filters']['genus']['id'] = 'genus';
+  $handler->display->display_options['filters']['genus']['table'] = 'organism';
+  $handler->display->display_options['filters']['genus']['field'] = 'genus';
+  $handler->display->display_options['filters']['genus']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['genus']['expose']['operator_id'] = 'genus_op';
+  $handler->display->display_options['filters']['genus']['expose']['label'] = 'Genus';
+  $handler->display->display_options['filters']['genus']['expose']['operator'] = 'genus_op';
+  $handler->display->display_options['filters']['genus']['expose']['identifier'] = 'genus';
+  $handler->display->display_options['filters']['genus']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Organism: Species */
+  $handler->display->display_options['filters']['species']['id'] = 'species';
+  $handler->display->display_options['filters']['species']['table'] = 'organism';
+  $handler->display->display_options['filters']['species']['field'] = 'species';
+  $handler->display->display_options['filters']['species']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['species']['expose']['operator_id'] = 'species_op';
+  $handler->display->display_options['filters']['species']['expose']['label'] = 'Species';
+  $handler->display->display_options['filters']['species']['expose']['operator'] = 'species_op';
+  $handler->display->display_options['filters']['species']['expose']['identifier'] = 'species';
+  $handler->display->display_options['filters']['species']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+
+  /** MANUALLY ADD since filter handler no exporting correctly */
+  $handler->display->display_options['filters']['common_name']['expose']['values_form_type'] = 'textfield';
+  $handler->display->display_options['filters']['common_name']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['common_name']['expose']['select_optional'] = FALSE;
+  $handler->display->display_options['filters']['common_name']['expose']['max_length'] = 40;
+
+  /* Display: Page */
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_organism/organisms';
+  $handler->display->display_options['menu']['type'] = 'default tab';
+  $handler->display->display_options['menu']['title'] = 'Organisms';
+  $handler->display->display_options['menu']['description'] = 'A biological organism.';
+  $handler->display->display_options['menu']['weight'] = '-10';
+  $handler->display->display_options['menu']['name'] = 'management';
+  $handler->display->display_options['menu']['context'] = 0;
+  $handler->display->display_options['menu']['context_only_inline'] = 0;
+  $handler->display->display_options['tab_options']['weight'] = '0';
+
+  /** MANUALLY ADD since filter handler no exporting correctly
+  $handler->display->display_options['filters']['common_name']['expose']['values_form_type'] = 'textfield';
+  $handler->display->display_options['filters']['common_name']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['common_name']['expose']['select_optional'] = FALSE;
+  $handler->display->display_options['filters']['common_name']['expose']['max_length'] = 40;
+  */
+
+  return $view;
+}

tripal_phenotype/tripal_phenotype.info

@@ -4,6 +4,8 @@ core = 7.x
 project = tripal_phenotype
 package = Tripal
 version = 7.x-2.0-beta1
+
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_cv
 dependencies[] = tripal_feature

tripal_phenotype/tripal_phenotype.install

@@ -0,0 +1,15 @@
+<?php
+
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_phenotype_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_phenotype.views_default.inc");
+  $views = tripal_phenotype_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}

tripal_phenotype/tripal_phenotype.views.inc

@@ -15,490 +15,3 @@
  * @ingroup views
  */
 
-/**
- *
- *
- * @ingroup tripal_phenotype_views
- */
-function tripal_phenotype_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // 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('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',
-      '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',
-    ),
-    '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(
-        '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',
-    ),
-    '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' => '~',
-      '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' => '~',
-      '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,
-      ),
-    ),
-  ));
-  $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 supplied 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', 'chado/phenotypes');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Phenotypes',
-    'description' => 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function.',
-    'weight' => '10',
-    '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_default.inc

@@ -0,0 +1,488 @@
+<?php
+
+/**
+ *
+ *
+ * @ingroup tripal_phenotype_views
+ */
+function tripal_phenotype_views_default_views() {
+  $views = array();
+
+  if (!module_exists('tripal_views')) {
+    return $views;
+  }
+
+  // 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('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',
+      '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',
+    ),
+    '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(
+        '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',
+    ),
+    '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' => '~',
+      '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' => '~',
+      '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,
+      ),
+    ),
+  ));
+  $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 supplied 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', 'chado/phenotypes');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Phenotypes',
+    'description' => 'A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function.',
+    'weight' => '10',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  $views[$view->name] = $view;
+
+  return $views;
+}

tripal_project/includes/tripal_project.admin.inc

@@ -4,6 +4,40 @@
  * @todo Add file header description
  */
 
+/**
+ *
+ */
+function tripal_project_admin_project_view() {
+  $output = '';
+
+  // set the breadcrumb
+  $breadcrumb = array();
+  $breadcrumb[] = l('Home', '<front>');
+  $breadcrumb[] = l('Administration', 'admin');
+  $breadcrumb[] = l('Tripal', 'admin/tripal');
+  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
+  $breadcrumb[] = l('Projects', 'admin/tripal/chado/tripal_project');
+  drupal_set_breadcrumb($breadcrumb);
+
+  // Add the view
+  $view = views_embed_view('tripal_project_admin_projects','default');
+  if (isset($view)) {
+    $output .= $view;
+  }
+  else {
+    $output .= '<p>The Project module uses primarily views to provide an '
+      . 'administrative interface. Currently one or more views needed for this '
+      . 'administrative interface are disabled. <strong>Click each of the following links to '
+      . 'enable the pertinent views</strong>:</p>';
+    $output .= '<ul>';
+      $output .= '<li>'.l('Projects View', 'admin/tripal/chado/tripal_project/views/projects/enable').'</li>';
+    $output .= '</ul>';
+  }
+
+  return $output;
+}
+
+
 function tripal_project_admin($form_state = NULL) {
   $form = array();
 
@@ -94,7 +128,7 @@ function get_tripal_project_admin_form_sync_set(&$form) {
       // check to see if the project is already present as a node in drupal.
       // if so, then skip it.
       $sql = "SELECT * FROM {chado_project} WHERE project_id = :project_id";
-      if (!db_query($sql, array(':project_id' => $project->project_id))->fetchObject()) { 
+      if (!db_query($sql, array(':project_id' => $project->project_id))->fetchObject()) {
         $proj_boxes[$project->project_id] = $project->name;
         $added++;
       }
@@ -270,7 +304,7 @@ function tripal_project_sync_projects($project_id = NULL, $job_id = NULL) {
   return $page_content;
 }
 /*
- * 
+ *
  */
 function tripal_project_sync_projects_form_submit($form, &$form_state) {
   global $user;
@@ -282,7 +316,7 @@ function tripal_project_sync_projects_form_submit($form, &$form_state) {
 }
 
 /*
- * 
+ *
  */
 function tripal_project_sync_all_projects() {
 

tripal_project/tripal_project.info

@@ -7,4 +7,5 @@ version = 7.x-2.0-beta1
 configure = admin/tripal/chado/tripal_project
 
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_cv

tripal_project/tripal_project.install

@@ -10,6 +10,20 @@
  * multiple project/mysql instances as well as manage and create such project instances
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_project_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_project.views_default.inc");
+  $views = tripal_project_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_requirements().
  *
@@ -32,10 +46,10 @@ function tripal_project_requirements($phase) {
  * Implementation of hook_install().
  */
 function tripal_project_install() {
-  
+
   // create the module's data directory
   tripal_create_moddir('tripal_project');
-  
+
   tripal_project_add_cvterms();
 }
 
@@ -73,13 +87,13 @@ function tripal_project_schema() {
 }
 
 /*
- * 
+ *
  */
 function tripal_project_add_cvterms() {
-  
+
   // Insert cvterm 'library_description' into cvterm table of chado
   // database. This CV term is used to keep track of the library
   // description in the libraryprop table.
-  tripal_cv_add_cvterm(array('name' => 'project_description', 'def' => 'Description of a project'), 
-    'tripal', 0, 1, 'tripal'); 
+  tripal_cv_add_cvterm(array('name' => 'project_description', 'def' => 'Description of a project'),
+    'tripal', 0, 1, 'tripal');
 }

tripal_project/tripal_project.module

@@ -63,7 +63,8 @@ function tripal_project_views_api() {
 function tripal_project_menu() {
   $items[ 'admin/tripal/chado/tripal_project' ]= array(
     'title' => 'Projects',
-    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of projects'),
+    'description' => ('A grouping of a variety of data (ie: group natural diversity experiment).'),
+    'page callback' => 'tripal_project_admin_project_view',
     'access arguments' => array('adminster tripal projects'),
     'type' => MENU_NORMAL_ITEM
   );
@@ -74,15 +75,25 @@ function tripal_project_menu() {
     'page callback' => 'theme',
     'page arguments' => array('tripal_project_help'),
     'access arguments' => array('adminster tripal projects'),
-    'type' => MENU_NORMAL_ITEM
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 6
   );
 
   $items[ 'admin/tripal/chado/tripal_project/configuration' ]= array(
-    'title' => 'Configuration',
+    'title' => 'Settings',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_project_help'),
+    'page arguments' => array('tripal_project_admin'),
     'access arguments' => array('adminster tripal projects'),
-    'type' => MENU_NORMAL_ITEM
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 4
+  );
+
+  $items['admin/tripal/chado/tripal_project/views/projects/enable'] = array(
+    'title' => 'Enable Project Administrative View',
+    'page callback' => 'tripal_views_admin_enable_view',
+    'page arguments' => array('tripal_project_admin_projects', 'admin/tripal/chado/tripal_project'),
+    'access arguments' => array('administer tripal_bulk_loader'),
+    'type' => MENU_CALLBACK,
   );
 
   return $items;
@@ -191,7 +202,7 @@ function chado_project_node_access($node, $op, $account) {
  */
 function tripal_project_theme() {
   $theme_path = drupal_get_path('module', 'tripal_project') . '/theme';
-  
+
   $items = array(
     'tripal_project_base' => array(
       'arguments' => array('node' => NULL),

tripal_project/tripal_project.views.inc

@@ -13,312 +13,4 @@
 /**
  * @defgroup tripal_project_views Project Views Integration
  * @ingroup views
- */
-
-/**
- *
- *
- * @ingroup tripal_project_views
- */
-function tripal_project_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  $values = array('name' => 'project_description');
-  $description_type_id = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
-  $description_type_id = $description_type_id[0]->cvterm_id;
-
-  // Main default view
-  $view = new view;
-  $view->name = 'project_listing';
-  $view->description = 'A listing of chado projects';
-  $view->tag = 'chado default';
-  $view->base_table = 'project';
-  $view->core = 6;
-  $view->api_version = '2';
-  $view->disabled = FALSE;
-  $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' => 'project',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'value' => array(
-      'label' => 'Description',
-      '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' => 'projectprop',
-      'field' => 'value',
-      'override' => array(
-        'button' => 'Override',
-      ),
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('filters', array(
-    'name' => array(
-      'operator' => '~',
-      '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,
-      ),
-    ),
-    'type_id' => array(
-      'operator' => '=',
-      'value' => $description_type_id,
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-        'optional' => FALSE,
-      ),
-      'case' => 1,
-      'id' => 'type_id',
-      'table' => 'projectprop',
-      'field' => 'type_id',
-      'override' => array(
-        'button' => 'Override',
-      ),
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 0,
-      'optional' => 0,
-      'show_all' => 0,
-      'agg' => array(
-        'records_with' => 0,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'value' => array(
-      'operator' => '~',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'value_op',
-        'identifier' => 'description',
-        'label' => 'Description Contains',
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'value',
-      'table' => 'projectprop',
-      'field' => 'value',
-      'override' => array(
-        'button' => 'Override',
-      ),
-      'relationship' => 'none',
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_projects',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Projects');
-  $handler->override_option('empty', 'No projects match the supplied 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' => 0,
-        'separator' => '',
-      ),
-    ),
-    'default' => 'name',
-  ));
-  $default_handler = $handler;
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/projects');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Projects',
-    'description' => 'A project is a collection of data resulting from a biological experiment.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        '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,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Adds project => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Project to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_project',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Change project.name to have a link to the node
-    $fields['name']['alter']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // Only show records with published nodes
-/**
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-*/
-  }
-  $views[$view->name] = $view;
-
-  return $views;
-}
+ */

tripal_project/tripal_project.views_default.inc

@@ -0,0 +1,192 @@
+<?php
+
+/**
+ *
+ *
+ * @ingroup tripal_project_views
+ */
+function tripal_project_views_default_views() {
+  $views = array();
+
+  $view = tripal_project_defaultview_admin_projects();
+  $views[$view->name] = $view;
+
+  return $views;
+}
+
+function tripal_project_defaultview_admin_projects() {
+
+  $view = new view();
+  $view->name = 'tripal_project_admin_projects';
+  $view->description = 'DO NOT DISABLE';
+  $view->tag = 'tripal admin';
+  $view->base_table = 'project';
+  $view->human_name = 'Project Admin';
+  $view->core = 7;
+  $view->api_version = '3.0';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+
+  /* Display: Master */
+  $handler = $view->new_display('default', 'Master', 'default');
+  $handler->display->display_options['title'] = 'Projects';
+  $handler->display->display_options['use_more_always'] = FALSE;
+  $handler->display->display_options['access']['type'] = 'none';
+  $handler->display->display_options['cache']['type'] = 'none';
+  $handler->display->display_options['query']['type'] = 'views_query';
+  $handler->display->display_options['exposed_form']['type'] = 'basic';
+  $handler->display->display_options['pager']['type'] = 'full';
+  $handler->display->display_options['pager']['options']['items_per_page'] = '25';
+  $handler->display->display_options['style_plugin'] = 'table';
+  $handler->display->display_options['style_options']['columns'] = array(
+    'nid' => 'nid',
+    'name' => 'name',
+    'description' => 'description',
+    'delete_node' => 'delete_node',
+    'edit_node' => 'edit_node',
+    'nothing' => 'nothing',
+  );
+  $handler->display->display_options['style_options']['default'] = 'name';
+  $handler->display->display_options['style_options']['info'] = array(
+    'nid' => array(
+      'sortable' => 0,
+      'default_sort_order' => 'asc',
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+    'name' => array(
+      'sortable' => 1,
+      'default_sort_order' => 'asc',
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+    'description' => array(
+      'sortable' => 0,
+      'default_sort_order' => 'asc',
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+    'delete_node' => array(
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+    'edit_node' => array(
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+    'nothing' => array(
+      'align' => '',
+      'separator' => '',
+      'empty_column' => 0,
+    ),
+  );
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Project',
+    'path-1' => 'node/add/tripal-project',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-2'] = array(
+    'label-2' => '',
+    'path-2' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-3'] = array(
+    'label-3' => '',
+    'path-3' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-4'] = array(
+    'label-4' => '',
+    'path-4' => '',
+  );
+  /* Relationship: Project: Project => Node */
+  $handler->display->display_options['relationships']['project_id']['id'] = 'project_id';
+  $handler->display->display_options['relationships']['project_id']['table'] = 'chado_project';
+  $handler->display->display_options['relationships']['project_id']['field'] = 'project_id';
+  /* Field: Content: Nid */
+  $handler->display->display_options['fields']['nid']['id'] = 'nid';
+  $handler->display->display_options['fields']['nid']['table'] = 'node';
+  $handler->display->display_options['fields']['nid']['field'] = 'nid';
+  $handler->display->display_options['fields']['nid']['exclude'] = TRUE;
+  /* Field: Chado Project: Name */
+  $handler->display->display_options['fields']['name']['id'] = 'name';
+  $handler->display->display_options['fields']['name']['table'] = 'project';
+  $handler->display->display_options['fields']['name']['field'] = 'name';
+  /* Field: Chado Project: Description */
+  $handler->display->display_options['fields']['description']['id'] = 'description';
+  $handler->display->display_options['fields']['description']['table'] = 'project';
+  $handler->display->display_options['fields']['description']['field'] = 'description';
+  $handler->display->display_options['fields']['description']['element_class'] = 'wide-column';
+  $handler->display->display_options['fields']['description']['element_label_class'] = 'wide-column';
+  /* Field: Content: Delete link */
+  $handler->display->display_options['fields']['delete_node']['id'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['delete_node']['field'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['relationship'] = 'project_id';
+  $handler->display->display_options['fields']['delete_node']['exclude'] = TRUE;
+  /* Field: Content: Edit link */
+  $handler->display->display_options['fields']['edit_node']['id'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['edit_node']['field'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['relationship'] = 'project_id';
+  $handler->display->display_options['fields']['edit_node']['exclude'] = TRUE;
+  /* Field: Global: Custom text */
+  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['table'] = 'views';
+  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['label'] = '';
+  $handler->display->display_options['fields']['nothing']['alter']['text'] = '[edit_node]   [delete_node]';
+  $handler->display->display_options['fields']['nothing']['element_class'] = 'short-column';
+  $handler->display->display_options['fields']['nothing']['element_label_class'] = 'short-column';
+  $handler->display->display_options['fields']['nothing']['element_label_colon'] = FALSE;
+  /* Filter criterion: Chado Project: Name */
+  $handler->display->display_options['filters']['name']['id'] = 'name';
+  $handler->display->display_options['filters']['name']['table'] = 'project';
+  $handler->display->display_options['filters']['name']['field'] = 'name';
+  $handler->display->display_options['filters']['name']['operator'] = 'contains';
+  $handler->display->display_options['filters']['name']['group'] = 1;
+  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['name']['expose']['operator_id'] = '';
+  $handler->display->display_options['filters']['name']['expose']['label'] = 'Name Contains';
+  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'name';
+  $handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Project: Description */
+  $handler->display->display_options['filters']['description']['id'] = 'description';
+  $handler->display->display_options['filters']['description']['table'] = 'project';
+  $handler->display->display_options['filters']['description']['field'] = 'description';
+  $handler->display->display_options['filters']['description']['operator'] = 'contains';
+  $handler->display->display_options['filters']['description']['group'] = 1;
+  $handler->display->display_options['filters']['description']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['description']['expose']['operator_id'] = 'description_op';
+  $handler->display->display_options['filters']['description']['expose']['label'] = 'Description Contains';
+  $handler->display->display_options['filters']['description']['expose']['operator'] = 'description_op';
+  $handler->display->display_options['filters']['description']['expose']['identifier'] = 'description';
+  $handler->display->display_options['filters']['description']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+
+  /* Display: Page */
+  $handler = $view->new_display('page', 'Page', 'page');
+  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_project/projects';
+  $handler->display->display_options['menu']['type'] = 'default tab';
+  $handler->display->display_options['menu']['title'] = 'Projects';
+  $handler->display->display_options['menu']['weight'] = '0';
+  $handler->display->display_options['menu']['name'] = 'management';
+  $handler->display->display_options['menu']['context'] = 0;
+  $handler->display->display_options['menu']['context_only_inline'] = 0;
+  $handler->display->display_options['tab_options']['weight'] = '0';
+
+  return $view;
+}

tripal_pub/tripal_pub.info

@@ -4,7 +4,9 @@ core = 7.x
 project = tripal_pub
 package = Tripal
 version = 7.x-2.0-beta1
+
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_cv
 dependencies[] = tripal_db
 dependencies[] = tripal_contact

tripal_pub/tripal_pub.install

@@ -10,6 +10,20 @@
  * multiple project/mysql instances as well as manage and create such project instances
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_pub_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_pub.views_default.inc");
+  $views = tripal_pub_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_requirements().
  */
@@ -55,7 +69,7 @@ function tripal_pub_uninstall() {
 }
 
 /**
- * 
+ *
  */
 function tripal_pub_enable() {
   // make sure we have our supported databases
@@ -74,24 +88,24 @@ function tripal_pub_schema() {
   $schema['chado_pub'] = array(
     'fields' => array(
       'vid' => array(
-        'type' => 'int', 
-        'unsigned' => TRUE, 
+        'type' => 'int',
+        'unsigned' => TRUE,
         'not null' => TRUE, 'default' => 0
       ),
       'nid' => array(
-        'type' => 'int', 
-        'unsigned' => TRUE, 
-        'not null' => TRUE, 
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
         'default' => 0
       ),
       'pub_id' => array(
-        'type' => 'int', 
-        'not null' => TRUE, 
+        'type' => 'int',
+        'not null' => TRUE,
         'default' => 0
       ),
       'sync_date' => array(
-        'type' => 'int', 
-        'not null' => FALSE, 
+        'type' => 'int',
+        'not null' => FALSE,
         'description' => 'UNIX integer sync date/time'
       ),
     ),
@@ -104,34 +118,34 @@ function tripal_pub_schema() {
     ),
     'primary key' => array('nid'),
   );
-  
+
   $schema['tripal_pub_import'] = array(
     'fields' => array(
       'pub_import_id' => array(
-        'type' => 'serial', 
+        'type' => 'serial',
         'not null' => TRUE
       ),
       'name' => array(
-        'type' => 'varchar', 
-        'length' => 255, 
+        'type' => 'varchar',
+        'length' => 255,
         'not null' => TRUE
       ),
       'criteria' => array(
-        'type' => 'text', 
-        'size' => 'normal', 
-        'not null' => TRUE, 
+        'type' => 'text',
+        'size' => 'normal',
+        'not null' => TRUE,
         'description' => 'Contains a serialized PHP array containing the search criteria'
       ),
       'disabled'  => array(
-        'type' => 'int', 
-        'unsigned' => TRUE, 
-        'not NULL' => TRUE, 
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not NULL' => TRUE,
         'default' => 0
-      ),      
+      ),
       'do_contact'  => array(
-        'type' => 'int', 
-        'unsigned' => TRUE, 
-        'not NULL' => TRUE, 
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not NULL' => TRUE,
         'default' => 0
       ),
     ),
@@ -140,7 +154,7 @@ function tripal_pub_schema() {
       'name' => array('name')
     ),
   );
-   
+
   return $schema;
 }
 

tripal_pub/tripal_pub.views.inc

@@ -9,376 +9,3 @@
  *  Documentation on views integration can be found at
  *  http://views2.logrus.com/doc/html/index.html.
  */
-
-/**
- *
- * @ingroup tripal_pub_views
- */
-function tripal_pub_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // Main default view
-  $view = new view;
-  $view->name = 'pub_listing';
-  $view->description = 'This view lists all pubs by default.';
-  $view->tag = 'chado default';
-  $view->base_table = 'pub';
-  $view->core = 0;
-  $view->api_version = '2';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->override_option('fields', array(
-    'title' => array(
-      'label' => 'Title',
-      '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' => 'title',
-      'table' => 'pub',
-      'field' => 'title',
-      'relationship' => 'none',
-    ),
-    'pyear' => array(
-      'label' => 'Year',
-      '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' => 'pub',
-      'field' => 'pyear',
-      'relationship' => 'none',
-    ),
-    'type' => 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' => 'type',
-      'table' => 'cvterm',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('sorts', array(
-    'pyear' => array(
-      'order' => 'ASC',
-      'id' => 'year',
-      'table' => 'pub',
-      'field' => 'pyear',
-      'relationship' => 'none',
-    ),
-    'title' => array(
-      'order' => 'ASC',
-      'id' => 'title',
-      'table' => 'pub',
-      'field' => 'title',
-      'relationship' => 'none',
-    ),
-    'type' => array(
-      'order' => 'ASC',
-      'id' => 'type',
-      'table' => 'cvterm',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-  ));
-  $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 pubs matching the entered criteria. If you leave a any of the criteria blank then the pubs will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all pubs will be listed.',
-    ),
-    'title' => array(
-      'operator' => '=',
-      'value' => array(),
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'title_op',
-        'identifier' => 'pub_title',
-        'label' => 'Title',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'title',
-      'table' => 'pub',
-      'field' => 'title',
-      'relationship' => 'none',
-    ),
-    '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' => 'pub',
-      'field' => 'type_id',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'show_all' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'year' => array(
-      'operator' => '=',
-      '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' => 'pub',
-      'field' => 'name',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'show_all' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_pub content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Publications');
-  $handler->override_option('header', 'Click "Show" to see a list of all publications matching the entered criteria. If you leave a any of the criteria blank then the pubs will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all publications will be listed.');
-  $handler->override_option('header_format', '2');
-  $handler->override_option('header_empty', 0);
-  $handler->override_option('empty', 'No publications 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(
-      'title' => 'title',
-      'pyear' => 'pyear',
-      'type' => 'type',
-      'all_dbxref' => 'all_dbxref',
-      'all_properties' => 'all_properties',
-      'all_relationships' => 'all_relationships',
-    ),
-    'info' => array(
-      'title' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'type' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'pyear' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'all_dbxref' => array(
-        'separator' => '',
-      ),
-      'all_properties' => array(
-        'separator' => '',
-      ),
-      'all_relationships' => array(
-        'separator' => '',
-      ),
-    ),
-    'default' => '-1',
-  ));
-  $default_handler = $handler;
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/pubs');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Publications',
-    'description' => 'A published article, book, conference proceeding, etc.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        '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,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Change analysis.name to have a link to the node
-    $fields['name_2']['alter']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // Adds pub => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Publication to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_pub',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Only show records with published nodes
-    /**
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-    */
-  }
-  $views[$view->name] = $view;
-
-  return $views;
-}

tripal_pub/tripal_pub.views_default.inc

@@ -0,0 +1,374 @@
+<?php
+
+/**
+ *
+ * @ingroup tripal_pub_views
+ */
+function tripal_pub_views_default_views() {
+  $views = array();
+
+  if (!module_exists('tripal_views')) {
+    return $views;
+  }
+
+  // Main default view
+  $view = new view;
+  $view->name = 'pub_listing';
+  $view->description = 'This view lists all pubs by default.';
+  $view->tag = 'chado default';
+  $view->base_table = 'pub';
+  $view->core = 0;
+  $view->api_version = '2';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+  $handler = $view->new_display('default', 'Defaults', 'default');
+  $handler->override_option('fields', array(
+    'title' => array(
+      'label' => 'Title',
+      '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' => 'title',
+      'table' => 'pub',
+      'field' => 'title',
+      'relationship' => 'none',
+    ),
+    'pyear' => array(
+      'label' => 'Year',
+      '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' => 'pub',
+      'field' => 'pyear',
+      'relationship' => 'none',
+    ),
+    'type' => 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' => 'type',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('sorts', array(
+    'pyear' => array(
+      'order' => 'ASC',
+      'id' => 'year',
+      'table' => 'pub',
+      'field' => 'pyear',
+      'relationship' => 'none',
+    ),
+    'title' => array(
+      'order' => 'ASC',
+      'id' => 'title',
+      'table' => 'pub',
+      'field' => 'title',
+      'relationship' => 'none',
+    ),
+    'type' => array(
+      'order' => 'ASC',
+      'id' => 'type',
+      'table' => 'cvterm',
+      'field' => 'name',
+      'relationship' => 'none',
+    ),
+  ));
+  $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 pubs matching the entered criteria. If you leave a any of the criteria blank then the pubs will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all pubs will be listed.',
+    ),
+    'title' => array(
+      'operator' => '=',
+      'value' => array(),
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'title_op',
+        'identifier' => 'pub_title',
+        'label' => 'Title',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'title',
+      'table' => 'pub',
+      'field' => 'title',
+      'relationship' => 'none',
+    ),
+    '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' => 'pub',
+      'field' => 'type_id',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'year' => array(
+      'operator' => '=',
+      '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' => 'pub',
+      'field' => 'name',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_pub content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Publications');
+  $handler->override_option('header', 'Click "Show" to see a list of all publications matching the entered criteria. If you leave a any of the criteria blank then the pubs will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all publications will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'No publications 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(
+      'title' => 'title',
+      'pyear' => 'pyear',
+      'type' => 'type',
+      'all_dbxref' => 'all_dbxref',
+      'all_properties' => 'all_properties',
+      'all_relationships' => 'all_relationships',
+    ),
+    'info' => array(
+      'title' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'type' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'pyear' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'all_dbxref' => array(
+        'separator' => '',
+      ),
+      'all_properties' => array(
+        'separator' => '',
+      ),
+      'all_relationships' => array(
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
+  $default_handler = $handler;
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'chado/pubs');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Publications',
+    'description' => 'A published article, book, conference proceeding, etc.',
+    'weight' => '10',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  // Add code specific to a local chado installation
+  // NOTE: Edit $handler above to $default_handler for the default display
+  if (tripal_core_chado_schema_exists()) {
+    // Add nid field
+    $fields = $view->get_items('field', 'default');
+    $new_fields = array(
+      'nid' => array(
+        'label' => 'Nid',
+        '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,
+        'link_to_node' => 0,
+        'exclude' => 1,
+        'id' => 'nid',
+        'table' => 'node',
+        'field' => 'nid',
+        'relationship' => 'none',
+      )
+    );
+    $fields = $new_fields + $fields;
+    // Change analysis.name to have a link to the node
+    $fields['name_2']['alter']['link_to_node'] = 1;
+    $default_handler->override_option('fields', $fields);
+    // Adds pub => Node relationship
+    $default_handler->override_option('relationships', array(
+      'nid' => array(
+        'label' => 'Publication to Node',
+        'required' => 0,
+        'id' => 'nid',
+        'table' => 'chado_pub',
+        'field' => 'nid',
+        'relationship' => 'none',
+      ),
+    ));
+    // Only show records with published nodes
+    /**
+    $filters = $view->get_items('filter', 'default');
+    $filters['status'] = array(
+      'operator' => '=',
+      'value' => '1',
+      'group' => '0',
+      'exposed' => FALSE,
+      'expose' => array(
+        'operator' => FALSE,
+        'label' => '',
+      ),
+      'id' => 'status',
+      'table' => 'node',
+      'field' => 'status',
+      'relationship' => 'none',
+    );
+    $default_handler->override_option('filters', $filters);
+    */
+  }
+  $views[$view->name] = $view;
+
+  return $views;
+}

tripal_stock/tripal_stock.info

@@ -4,5 +4,7 @@ core = 7.x
 project = tripal_stock
 package = Tripal
 version = 7.x-2.0-beta1
+
 dependencies[] = tripal_core
+dependencies[] = tripal_views
 dependencies[] = tripal_organism

tripal_stock/tripal_stock.install

@@ -6,6 +6,20 @@
  * @file
  */
 
+/**
+ * Disable default views when module is disabled
+ */
+function tripal_stock_disable() {
+
+  // Disable all default views provided by this module
+  require_once("tripal_stock.views_default.inc");
+  $views = tripal_stock_views_default_views();
+  foreach (array_keys($views) as $view_name) {
+    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+  }
+
+}
+
 /**
  * Implementation of hook_requirements().
  *

tripal_stock/tripal_stock.views.inc

@@ -14,408 +14,3 @@
  * @defgroup tripal_stock_views Stock Views Integration
  * @ingroup views
  */
-
-/**
- *
- * @ingroup tripal_stock_views
- */
-function tripal_stock_views_default_views() {
-  $views = array();
-
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
-
-  // Main default view
-  $view = new view;
-  $view->name = 'stock_listing';
-  $view->description = 'This view lists all stocks by default.';
-  $view->tag = 'chado default';
-  $view->base_table = 'stock';
-  $view->core = 0;
-  $view->api_version = '2';
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->override_option('fields', array(
-    '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' => 'stock',
-      'field' => 'uniquename',
-      'relationship' => 'none',
-    ),
-    'name_2' => 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_2',
-      'table' => 'stock',
-      'field' => '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',
-    ),
-    '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',
-    ),
-  ));
-  $handler->override_option('sorts', array(
-    'common_name' => array(
-      'order' => 'ASC',
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-    ),
-    'uniquename' => array(
-      'order' => 'ASC',
-      'id' => 'uniquename',
-      'table' => 'stock',
-      'field' => 'uniquename',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('filters', array(
-    'common_name' => array(
-      'operator' => '=',
-      'value' => array(),
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'common_name_op',
-        'identifier' => 'organism_common_name',
-        'label' => 'Organism',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 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 stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.',
-    ),
-    'type_id' => array(
-      'operator' => '=',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'type_id_op',
-        'identifier' => 'type_id',
-        'label' => 'Type',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'type_id',
-      'table' => 'stock',
-      'field' => 'type_id',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'show_all' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'name' => array(
-      'operator' => '~',
-      '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' => 'stock',
-      'field' => 'name',
-      'relationship' => 'none',
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_stock content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Stocks');
-  $handler->override_option('header', 'Click "Show" to see a list of all stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.');
-  $handler->override_option('header_format', '2');
-  $handler->override_option('header_empty', 0);
-  $handler->override_option('empty', 'No stocks 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(
-      'uniquename' => 'uniquename',
-      'name_2' => 'name_2',
-      'name' => 'name',
-      'common_name' => 'common_name',
-      'all_dbxref' => 'all_dbxref',
-      'all_properties' => 'all_properties',
-      'all_relationships' => 'all_relationships',
-    ),
-    'info' => array(
-      'uniquename' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name_2' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'common_name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'all_dbxref' => array(
-        'separator' => '',
-      ),
-      'all_properties' => array(
-        'separator' => '',
-      ),
-      'all_relationships' => array(
-        'separator' => '',
-      ),
-    ),
-    'default' => '-1',
-  ));
-  $default_handler = $handler;
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/stocks');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Stocks',
-    'description' => 'A stock is the physical entities, either living or preserved, held by collections and can be globally identified by the combination of organism, uniquename and stock type.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        '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,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Change analysis.name to have a link to the node
-    $fields['name_2']['alter']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // Adds stock => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Stock to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_stock',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Only show records with published nodes
-    /**
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-    */
-  }
-  $views[$view->name] = $view;
-
-  return $views;
-}

tripal_stock/tripal_stock.views_default.inc

@@ -0,0 +1,406 @@
+<?php
+
+/**
+ *
+ * @ingroup tripal_stock_views
+ */
+function tripal_stock_views_default_views() {
+  $views = array();
+
+  if (!module_exists('tripal_views')) {
+    return $views;
+  }
+
+  // Main default view
+  $view = new view;
+  $view->name = 'stock_listing';
+  $view->description = 'This view lists all stocks by default.';
+  $view->tag = 'chado default';
+  $view->base_table = 'stock';
+  $view->core = 0;
+  $view->api_version = '2';
+  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+  $handler = $view->new_display('default', 'Defaults', 'default');
+  $handler->override_option('fields', array(
+    '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' => 'stock',
+      'field' => 'uniquename',
+      'relationship' => 'none',
+    ),
+    'name_2' => 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_2',
+      'table' => 'stock',
+      'field' => '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',
+    ),
+    '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',
+    ),
+  ));
+  $handler->override_option('sorts', array(
+    'common_name' => array(
+      'order' => 'ASC',
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
+      'relationship' => 'none',
+    ),
+    'uniquename' => array(
+      'order' => 'ASC',
+      'id' => 'uniquename',
+      'table' => 'stock',
+      'field' => 'uniquename',
+      'relationship' => 'none',
+    ),
+  ));
+  $handler->override_option('filters', array(
+    'common_name' => array(
+      'operator' => '=',
+      'value' => array(),
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'common_name_op',
+        'identifier' => 'organism_common_name',
+        'label' => 'Organism',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'common_name',
+      'table' => 'organism',
+      'field' => 'common_name',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 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 stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.',
+    ),
+    'type_id' => array(
+      'operator' => '=',
+      'value' => '',
+      'group' => '0',
+      'exposed' => TRUE,
+      'expose' => array(
+        'use_operator' => 0,
+        'operator' => 'type_id_op',
+        'identifier' => 'type_id',
+        'label' => 'Type',
+        'remember' => 0,
+      ),
+      'case' => 1,
+      'id' => 'type_id',
+      'table' => 'stock',
+      'field' => 'type_id',
+      'relationship' => 'none',
+      'values_form_type' => 'select',
+      'multiple' => 1,
+      'optional' => 0,
+      'show_all' => 0,
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+    'name' => array(
+      'operator' => '~',
+      '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' => 'stock',
+      'field' => 'name',
+      'relationship' => 'none',
+      'agg' => array(
+        'records_with' => 1,
+        'aggregates_with' => 1,
+      ),
+    ),
+  ));
+  $handler->override_option('access', array(
+    'type' => 'perm',
+    'perm' => 'access chado_stock content',
+  ));
+  $handler->override_option('cache', array(
+    'type' => 'none',
+  ));
+  $handler->override_option('title', 'Stocks');
+  $handler->override_option('header', 'Click "Show" to see a list of all stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.');
+  $handler->override_option('header_format', '2');
+  $handler->override_option('header_empty', 0);
+  $handler->override_option('empty', 'No stocks 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(
+      'uniquename' => 'uniquename',
+      'name_2' => 'name_2',
+      'name' => 'name',
+      'common_name' => 'common_name',
+      'all_dbxref' => 'all_dbxref',
+      'all_properties' => 'all_properties',
+      'all_relationships' => 'all_relationships',
+    ),
+    'info' => array(
+      'uniquename' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name_2' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'common_name' => array(
+        'sortable' => 1,
+        'separator' => '',
+      ),
+      'all_dbxref' => array(
+        'separator' => '',
+      ),
+      'all_properties' => array(
+        'separator' => '',
+      ),
+      'all_relationships' => array(
+        'separator' => '',
+      ),
+    ),
+    'default' => '-1',
+  ));
+  $default_handler = $handler;
+  $handler = $view->new_display('page', 'Page', 'page_1');
+  $handler->override_option('path', 'chado/stocks');
+  $handler->override_option('menu', array(
+    'type' => 'normal',
+    'title' => 'Stocks',
+    'description' => 'A stock is the physical entities, either living or preserved, held by collections and can be globally identified by the combination of organism, uniquename and stock type.',
+    'weight' => '10',
+    'name' => 'navigation',
+  ));
+  $handler->override_option('tab_options', array(
+    'type' => 'none',
+    'title' => '',
+    'description' => '',
+    'weight' => 0,
+    'name' => 'navigation',
+  ));
+  // Add code specific to a local chado installation
+  // NOTE: Edit $handler above to $default_handler for the default display
+  if (tripal_core_chado_schema_exists()) {
+    // Add nid field
+    $fields = $view->get_items('field', 'default');
+    $new_fields = array(
+      'nid' => array(
+        'label' => 'Nid',
+        '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,
+        'link_to_node' => 0,
+        'exclude' => 1,
+        'id' => 'nid',
+        'table' => 'node',
+        'field' => 'nid',
+        'relationship' => 'none',
+      )
+    );
+    $fields = $new_fields + $fields;
+    // Change analysis.name to have a link to the node
+    $fields['name_2']['alter']['link_to_node'] = 1;
+    $default_handler->override_option('fields', $fields);
+    // Adds stock => Node relationship
+    $default_handler->override_option('relationships', array(
+      'nid' => array(
+        'label' => 'Stock to Node',
+        'required' => 0,
+        'id' => 'nid',
+        'table' => 'chado_stock',
+        'field' => 'nid',
+        'relationship' => 'none',
+      ),
+    ));
+    // Only show records with published nodes
+    /**
+    $filters = $view->get_items('filter', 'default');
+    $filters['status'] = array(
+      'operator' => '=',
+      'value' => '1',
+      'group' => '0',
+      'exposed' => FALSE,
+      'expose' => array(
+        'operator' => FALSE,
+        'label' => '',
+      ),
+      'id' => 'status',
+      'table' => 'node',
+      'field' => 'status',
+      'relationship' => 'none',
+    );
+    $default_handler->override_option('filters', $filters);
+    */
+  }
+  $views[$view->name] = $view;
+
+  return $views;
+}

tripal_views/tripal_views.views.inc

@@ -1,7 +1,7 @@
 <?php
 
 include('api/tripal_views.api.inc');
-
+include('views/handlers/tripal_views_handler_area_action_links.inc');
 
 /**
  * @file
@@ -71,6 +71,11 @@ function tripal_views_views_handlers() {
       ),
       */
 
+      // Custom area handler
+      'tripal_views_handler_area_action_links' => array(
+        'parent' => 'views_handler_area',
+      ),
+
       // Custom Tripal Filter Handlers
       'tripal_views_handler_filter_no_results' => array(
         'parent' => 'views_handler_filter'
@@ -156,6 +161,14 @@ function tripal_views_views_data() {
     ),
   );
 
+  $data['views']['action_links_area'] = array(
+    'title' => t('Action Links'),
+    'help' => t('Add action links to the view.'),
+    'area' => array(
+      'handler' => 'tripal_views_handler_area_action_links',
+    ),
+  );
+
   $tvi_query = db_query('SELECT * FROM {tripal_views}');
 
   // INTEGRATE THE LIGHTEST SETUP FOR EACH TABLE

tripal_views/views/handlers/tripal_views_handler_area_action_links.inc

@@ -0,0 +1,151 @@
+<?php
+
+class tripal_views_handler_area_action_links extends views_handler_area {
+
+  function option_definition() {
+    $options = parent::option_definition();
+
+    $options['link-1']['label-1'] = array('default' => '');
+    $options['link-1']['path-1'] = array('default' => '');
+
+    $options['link-2']['label-2'] = array('default' => '');
+    $options['link-2']['path-2'] = array('default' => '');
+
+    $options['link-3']['label-3'] = array('default' => '');
+    $options['link-3']['path-3'] = array('default' => '');
+
+    $options['link-4']['label-4'] = array('default' => '');
+    $options['link-4']['path-4'] = array('default' => '');
+
+    return $options;
+  }
+
+  function options_form(&$form, &$form_state) {
+    parent::options_form($form, $form_state);
+
+    $form['label']['#default_value'] = 'Action Links';
+
+    $form['link-1'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Link #1')
+    );
+
+    $form['link-1']['label-1'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Label'),
+      '#description' => t('The text that will be displayed as the link'),
+      '#default_value' => $this->options['link-1']['label-1'],
+    );
+
+    $form['link-1']['path-1'] = array(
+      '#type' => 'textfield',
+      '#title' => t('URL'),
+      '#description' => t('The path that the link will link to'),
+      '#default_value' => $this->options['link-1']['path-1']
+    );
+
+    $form['link-2'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Link #2')
+    );
+
+    $form['link-2']['label-2'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Label'),
+      '#description' => t('The text that will be displayed as the link'),
+      '#default_value' => $this->options['link-2']['label-2'],
+    );
+
+    $form['link-2']['path-2'] = array(
+      '#type' => 'textfield',
+      '#title' => t('URL'),
+      '#description' => t('The path that the link will link to'),
+      '#default_value' => $this->options['link-2']['path-2']
+    );
+
+    $form['link-3'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Link #3')
+    );
+
+    $form['link-3']['label-3'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Label'),
+      '#description' => t('The text that will be displayed as the link'),
+      '#default_value' => $this->options['link-3']['label-3'],
+    );
+
+    $form['link-3']['path-3'] = array(
+      '#type' => 'textfield',
+      '#title' => t('URL'),
+      '#description' => t('The path that the link will link to'),
+      '#default_value' => $this->options['link-3']['path-3']
+    );
+
+    $form['link-4'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Link #4')
+    );
+
+    $form['link-4']['label-4'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Label'),
+      '#description' => t('The text that will be displayed as the link'),
+      '#default_value' => $this->options['link-4']['label-4'],
+    );
+
+    $form['link-4']['path-4'] = array(
+      '#type' => 'textfield',
+      '#title' => t('URL'),
+      '#description' => t('The path that the link will link to'),
+      '#default_value' => $this->options['link-4']['path-4']
+    );
+
+  }
+
+  function options_submit(&$form, &$form_state) {
+    parent::options_submit($form, $form_state);
+    ddl($form_state, 'form state in submit');
+    $this->options['link-1']['label-1'] = $form_state['values']['options']['link-1']['label-1'];
+    $this->options['link-1']['path-1'] = $form_state['values']['options']['link-1']['path-1'];
+
+    $this->options['link-2']['label-2'] = $form_state['values']['options']['link-2']['label-2'];
+    $this->options['link-2']['path-2'] = $form_state['values']['options']['link-2']['path-2'];
+
+    $this->options['link-3']['label-3'] = $form_state['values']['options']['link-3']['label-3'];
+    $this->options['link-3']['path-3'] = $form_state['values']['options']['link-3']['path-3'];
+
+    $this->options['link-4']['label-4'] = $form_state['values']['options']['link-4']['label-4'];
+    $this->options['link-4']['path-4'] = $form_state['values']['options']['link-4']['path-4'];
+  }
+
+  function render($empty = FALSE) {
+    if (!$empty || !empty($this->options['empty'])) {
+      $output = '<ul class="action-links">';
+
+      // First link
+      if (!empty($this->options['link-1']['label-1']) AND !empty($this->options['link-1']['path-1'])) {
+        $output .= '<li>' . l($this->options['link-1']['label-1'], $this->options['link-1']['path-1']) . '</li>';
+      }
+
+      // Second link
+      if (!empty($this->options['link-2']['label-2']) AND !empty($this->options['link-2']['path-2'])) {
+        $output .= '<li>' . l($this->options['link-2']['label-2'], $this->options['link-2']['path-2']) . '</li>';
+      }
+
+      // Third link
+      if (!empty($this->options['link-3']['label-3']) AND !empty($this->options['link-3']['path-3'])) {
+        $output .= '<li>' . l($this->options['link-3']['label-3'], $this->options['link-3']['path-3']) . '</li>';
+      }
+
+      // Fourth link
+      if (!empty($this->options['link-4']['label-4']) AND !empty($this->options['link-4']['path-4'])) {
+        $output .= '<li>' . l($this->options['link-4']['label-4'], $this->options['link-4']['path-4']) . '</li>';
+      }
+      $output .= '</ul>';
+      return $output;
+    }
+    return '';
+  }
+
+}

tripal_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc

@@ -35,13 +35,13 @@ class tripal_views_handler_filter_select_cvterm extends tripal_views_handler_fil
       else {
         //get a list of cvs currently used
         if ($this->view->base_table == 'cvterm') {
-          $sql = 'SELECT distinct(cv.cv_id) FROM {' . $this->view->base_table . '}'
-            .' LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
+          $sql = 'SELECT distinct(cv.cv_id) FROM chado.' . $this->view->base_table
+            .' LEFT JOIN chado.cv cv ON cv.cv_id=cvterm.cv_id';
         }
         else {
-          $sql = 'SELECT distinct(cv.cv_id) FROM {' . $this->view->base_table . '}'
-            .' LEFT JOIN cvterm cvterm ON cvterm.cvterm_id=' . $this->view->base_table . '.type_id '
-            .'LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
+          $sql = 'SELECT distinct(cv.cv_id) FROM chado.' . $this->view->base_table
+            .' LEFT JOIN chado.cvterm cvterm ON cvterm.cvterm_id=' . $this->view->base_table . '.type_id '
+            .'LEFT JOIN chado.cv cv ON cv.cv_id=cvterm.cv_id';
         }
         // D7 TODO: Check DBTNG changes work
         $resource = chado_query($sql);
@@ -71,7 +71,11 @@ class tripal_views_handler_filter_select_cvterm extends tripal_views_handler_fil
     //sort cvterms by name (case insensitive)
     natcasesort($cvterms);
 
-    return $cvterms;
+    if ($this->options['expose']['select_optional']) {
+      $options['All'] = '--Any--';
+    }
+
+    return $options + $cvterms;
 
   }