Removing TRIPAL VIEWS Deprecated functions

tripal_analysis/tripal_analysis.install

@@ -18,7 +18,7 @@ function tripal_analysis_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -58,13 +58,13 @@ function tripal_analysis_install() {
 
   // add vocabularies
   tripal_analysis_add_cvs();
-  
+
   // add cvterms
   tripal_analysis_add_cvterms();
 
   // add materialized views
   tripal_analysis_add_mview_analysis_organism();
-  
+
   // set the default vocabularies
   tripal_set_default_cv('analysisprop', 'type_id', 'analysis_property');
 }
@@ -146,7 +146,7 @@ function tripal_analysis_add_cvterms() {
   // the 'analysis_property' vocabulary is for user definable properties wo we
   // will add an 'Analysis Type' to this vocubulary
   $term = array(
-    'name' => 'Analysis Type', 
+    'name' => 'Analysis Type',
     'def' => 'The type of analysis that was performed.'
   );
   tripal_cv_add_cvterm($term, 'analysis_property', 0, 1, 'tripal');
@@ -280,7 +280,7 @@ function tripal_analysis_add_mview_analysis_organism() {
 function tripal_analysis_update_7200() {
   // We cannot use the Tripal API calls in the 7200 update
   // because during upgrade the tripal_core should also be disabled
-  
+
   // set the analysis_property as default
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'analysis_property'")->fetchField();
@@ -296,8 +296,8 @@ function tripal_analysis_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add analysis_property vocabulary: '. $error);
   }
-  
-  
+
+
   // During the upgrade from D6 to D7 the vocabulary terms assigned to organisms were
   // copied to the field_data_taxonomyextra table rather than to the correct
   // field_data_taxonomy_vocabulary_[vid] table. We'll move them.
@@ -355,9 +355,9 @@ function tripal_analysis_update_dependencies() {
  *
  */
 function tripal_analysis_update_7201() {
-  
+
   // there is a bug in the Tripal v2.0-alpha release that didn't add the
-  // materialized view schema to the mviews table.  
+  // materialized view schema to the mviews table.
   // get the schema for the materialized view from the custom_tables table
   // as there is a copy there, but only if the schema is missing from the
   // materialized view table

tripal_analysis/tripal_analysis.views_default.inc

@@ -19,12 +19,12 @@ function tripal_analysis_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_analysis_search_biological_data_views()
   $view = tripal_analysis_defaultvalue_user_analysis();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin View
   $view = tripal_analysis_defaultvalue_admin_analysis();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_bulk_loader/tripal_bulk_loader.install

@@ -18,7 +18,7 @@ function tripal_bulk_loader_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }

tripal_bulk_loader/tripal_bulk_loader.module

@@ -94,7 +94,7 @@ function tripal_bulk_loader_menu() {
   $items['admin/tripal/loaders/bulk/views/jobs/enable'] = array(
     'title' => 'Enable Jobs Administrative View',
     'description' => 'Enable Jobs Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_bulk_loading_jobs','admin/tripal/loaders/bulk'),
     'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
@@ -102,7 +102,7 @@ function tripal_bulk_loader_menu() {
   $items['admin/tripal/loaders/bulk/views/templates/enable'] = array(
     'title' => 'Enable Templates Administrative View',
     'description' => 'Enable Templates Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_bulk_loader_templates', 'admin/tripal/loaders/bulk'),
     'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
@@ -285,7 +285,7 @@ function tripal_bulk_loader_views_api() {
  */
 function tripal_bulk_loader_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
-  
+
   return array(
     'node__tripal_bulk_loader' => array(
       'template' => 'node--chado-generic',
@@ -303,7 +303,7 @@ function tripal_bulk_loader_theme($existing, $type, $theme, $path) {
       'template' => 'tripal_bulk_loader_fields',
       'path' => "$path/theme/templates",
     ),
-    
+
     // form element themes
     'tripal_bulk_loader_modify_template_base_form' => array(
       'template' => 'tripal_bulk_loader_modify_template_base_form',
@@ -315,13 +315,13 @@ function tripal_bulk_loader_theme($existing, $type, $theme, $path) {
       'function' => 'tripal_bulk_loader_field_regex_fieldset',
       'render element' => 'element'
     ),
-    
+
     // admin theme
     'tripal_bulk_loader_admin' => array(
       'template' => 'tripal_bulk_loader_admin',
       'path' => "$path/theme/templates",
     ),
-    
+
 
     // themed teaser
     'tripal_bulk_loader_teaser' => array(

tripal_contact/tripal_contact.install

@@ -19,7 +19,7 @@ function tripal_contact_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -65,7 +65,7 @@ function tripal_contact_install() {
   // Add cvterms for relationship types
   tripal_contact_add_cvs();
   tripal_contact_add_cvterms();
-  
+
   // set the default vocabularies
   tripal_set_default_cv('contact', 'type_id', 'tripal_contact');
   tripal_set_default_cv('contactprop', 'type_id', 'tripal_contact');
@@ -93,27 +93,27 @@ function tripal_contact_uninstall() {
  * @ingroup tripal_contact
  */
 function tripal_contact_add_cvs() {
-  
+
   // Add the cv for contact properties. This is a default vocabulary in the event
   // that a user does not want to use the tripal_contact vocabulary
   tripal_cv_add_cv(
     'contact_property',
     'Contains properties for contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
   );
-  
+
   // add the cv for the contact type. This is a default vocabulary in the event
   // that a user does not want to use the tripal_contact vocabulary
   tripal_cv_add_cv(
     'contact_type',
     'Contains types of contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
   );
-  
+
   // Add the cv for the tripal_contact vocabulary which is loaded via the OBO
   tripal_cv_add_cv(
    'tripal_contact',
    'A heirarchical set of terms for describing a contact. It is intended to be used as the default vocabularies in Tripal for contact types and contact properties.'
   );
-  
+
   // add the cv for contact relationships
   tripal_cv_add_cv(
     'contact_relationship',
@@ -242,10 +242,10 @@ function tripal_contact_add_custom_tables(){
  *
  */
 function tripal_contact_update_7200() {
-  
-  // We cannot use the Tripal API calls in the 7200 update 
+
+  // We cannot use the Tripal API calls in the 7200 update
   // because during upgrade the tripal_core will be disabled
-  
+
   // add the contact_type CV
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'tripal_contact'")->fetchField();
@@ -278,8 +278,8 @@ function tripal_contact_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add tripal_contact vocabulary: '. $error);
   }
-  
-  
+
+
   // add the contact_relationship CV
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'contact_relationship'")->fetchField();
@@ -323,7 +323,7 @@ function tripal_contact_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add contact_type vocabulary: '. $error);
   }
-  
+
   // add the contact_property CV
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'contact_property'")->fetchField();
@@ -363,9 +363,9 @@ function tripal_contact_update_dependencies() {
  *
  */
 function tripal_contact_update_7201() {
-  // there was a bug in the function for creating a custom table that 
+  // there was a bug in the function for creating a custom table that
   // kept foreign key constraints from being added.  So, we need to add those
-  // to keep from error messages appear, we will drop the FK if it already 
+  // to keep from error messages appear, we will drop the FK if it already
   // exists and then re-add it.
   try {
     db_query('

tripal_contact/tripal_contact.views_default.inc

@@ -18,12 +18,12 @@ function tripal_contact_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_contact_search_biological_data_views()
   $view = tripal_contact_defaultvalue_user_contacts();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin view
   $view = tripal_contact_defaultview_admin_contacts();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_core/tripal_core.module

@@ -237,7 +237,7 @@ function tripal_core_menu() {
   );
   $items['admin/tripal/tripal_jobs/views/jobs/enable'] = array(
     'title' => 'Enable Jobs Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_core_admin_jobs', 'admin/tripal/tripal_jobs'),
     'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
@@ -351,7 +351,7 @@ function tripal_core_menu() {
   );
   $items['admin/tripal/schema/custom_tables/views/tables/enable'] = array(
     'title' => 'Enable Custom Tables Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_core_admin_custom_table', 'admin/tripal/schema/custom_tables'),
     'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
@@ -533,16 +533,16 @@ function tripal_core_node_view_alter(&$build) {
   if ($build['#view_mode'] != 'full' OR !array_key_exists('#tripal_generic_node_template', $build)) {
     return;
   }
-  
+
   $node_type = $build["#node"]->type;
   $nid = $build["#node"]->nid;
-  
+
 
   $cache = cache_get("theme_registry:$theme", 'cache');
   $node = $build['#node'];
   $toc = array();
   $toc_html = '';
-  
+
   // if we are looking at a Tripal node template then we want to
   // make some changes to each block of content so that we can associate
   // a table of contents and add administrator and curator messages
@@ -552,7 +552,7 @@ function tripal_core_node_view_alter(&$build) {
     // that are wanting to provide content for this node
     $markup = array();
     foreach ($build as $key => $value) {
-      
+
       // skip the body element as the Tripal node types do not use it
       if ($key == 'body') {
         continue;
@@ -583,7 +583,7 @@ function tripal_core_node_view_alter(&$build) {
         $override_hide = $toc_item_overrides->hide;
       }
       else {
-        
+
         // get the override title, weight for the general case
         $toc_item_overrides = db_select('tripal_toc', 'tc')
           ->fields('tc', array('toc_item_id', 'title', 'weight', 'hide'))
@@ -605,11 +605,11 @@ function tripal_core_node_view_alter(&$build) {
         unset($build[$key]);
         continue;
       }
-      
-      // for backwards compatibility we will handle the content type fields 
+
+      // for backwards compatibility we will handle the content type fields
       // named 'field_resource_blocks', 'field_resource_titles', and 'field_resource_links'
       // these fields can be added on the Drupal content types page and were
-      // specifically recoginzed by Tripal v1.1. 
+      // specifically recoginzed by Tripal v1.1.
       if ($key == "field_resource_links") {
         // links should just appear on the sidebar as is and not open up a panel
         foreach (element_children($build[$key]) as $index) {
@@ -658,16 +658,16 @@ function tripal_core_node_view_alter(&$build) {
         unset($build["field_resource_titles"]);
         continue;
       }
-      
-      // skip any keys we may have already handled. This is the case for 
+
+      // skip any keys we may have already handled. This is the case for
       // the field_resource_blocks where we removed the old CCK fields
       // and added new ones.  We don't want these new ones to be processed
       // again by the code below.
       if (array_key_exists('#toc_handled', $build[$key]) and $build[$key]['#toc_handled'] == TRUE) {
         continue;
       }
-      
-      // for all other fields we will handle in the following way 
+
+      // for all other fields we will handle in the following way
       //-----------------------
       // INITIALIZE THE CONTENT VARIABLES
       //-----------------------
@@ -685,7 +685,7 @@ function tripal_core_node_view_alter(&$build) {
         $toc_item_title = $build[$key]['#title'];
       }
       $toc_item_title = ucwords($toc_item_title);
-      
+
       // now override the title if a value is set in the tripal_toc table
       $toc_item_title = $override_title ? $override_title : $toc_item_title;
 
@@ -730,7 +730,7 @@ function tripal_core_node_view_alter(&$build) {
       //-----------------------
       // get the template path so we can put it in an admin message box
       $path = '';
-      if (!array_key_exists('#tripal_template_show', $build[$key]) or 
+      if (!array_key_exists('#tripal_template_show', $build[$key]) or
            $build[$key]['#tripal_template_show'] == TRUE) {
         if ($cache and array_key_exists($key, $cache->data) and array_key_exists('path', $cache->data[$key])) {
 

tripal_cv/tripal_cv.install

@@ -17,7 +17,7 @@ function tripal_cv_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -111,10 +111,10 @@ function tripal_cv_create_tripal_obo_temp() {
  */
 function tripal_cv_schema() {
   $schema = array();
-  
+
   tripal_cv_get_tripal_cv_obo_table($schema);
   tripal_cv_get_tripal_cv_defaults_table($schema);
-  
+
   return $schema;
 }
 /**

tripal_cv/tripal_cv.module

@@ -52,7 +52,7 @@ function tripal_cv_menu() {
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_NORMAL_ITEM,
   );
-  
+
   $items['admin/tripal/chado/tripal_cv/defaults'] = array(
     'title' => 'Defaults',
     'description' => 'Set the default vocabularies for properties and relationships.',
@@ -166,14 +166,14 @@ function tripal_cv_menu() {
    */
   $items['admin/tripal/chado/tripal_cv/views/cvs/enable'] = array(
     'title' => 'Enable Vocabulary Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_cv_admin_cvs', 'admin/tripal/chado/tripal_cv'),
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/chado/tripal_cv/views/cvterms/enable'] = array(
     'title' => 'Enable Vocabulary Terms Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_cv_admin_cvterms', 'admin/tripal/chado/tripal_cv'),
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,

tripal_cv/tripal_cv.views_default.inc

@@ -14,12 +14,12 @@ function tripal_cv_views_default_views() {
 
   // Default Tripal Admin View: CVs
   $view = tripal_cv_defaultview_admin_cvs_listing();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Default Tripal Admin View: CV Terms
   $view = tripal_cv_defaultview_admin_cvterms_listing();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_db/tripal_db.install

@@ -16,7 +16,7 @@ function tripal_db_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }

tripal_db/tripal_db.module

@@ -69,14 +69,14 @@ function tripal_db_menu() {
 
   $items['admin/tripal/chado/tripal_db/views/dbs/enable'] = array(
     'title' => 'Enable Database Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_db_admin_dbs', 'admin/tripal/chado/tripal_db'),
     'access arguments' => array('administer db cross-references'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/chado/tripal_db/views/dbxrefs/enable'] = array(
     'title' => 'Enable Reference Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_db_admin_dbxrefs', 'admin/tripal/chado/tripal_db'),
     'access arguments' => array('administer db cross-references'),
     'type' => MENU_CALLBACK,

tripal_db/tripal_db.views_default.inc

@@ -14,12 +14,12 @@ function tripal_db_views_default_views() {
 
   // Default Tripal Admin View: DB
   $view = tripal_db_defaultview_admin_db_listing();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Default Tripal Admin View: DB References
   $view = tripal_db_defaultview_admin_dbxref_listing();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_example/tripal_example.install

@@ -12,10 +12,10 @@
  * @ingroup tripal_example
  */
 function tripal_example_disable() {
-  
+
   // EXPLANATION: If you are using Drupal Views you want to ensure
   // that any default views that your module provides are disabled
-  // when the module is disabled.  Default views are specified in the 
+  // when the module is disabled.  Default views are specified in the
   // [module name].views.default.inc file.  The following code will disable
   // these views.  If your module does not create any default views you
   // can remove the following code.
@@ -24,30 +24,30 @@ function tripal_example_disable() {
   require_once("tripal_example.views_default.inc");
   $views = tripal_example_views_default_views();
   foreach (array_keys($views) as $view_name) {
-    tripal_views_admin_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
 
 /**
  * Implements hook_requirements().
- * 
+ *
  * Performs check to see if all required dependencies are met. Drupal will
- * automatically check for module dependencies but here you can check for 
- * other requirements. 
+ * automatically check for module dependencies but here you can check for
+ * other requirements.
  *
  * @ingroup tripal_example
  */
 function tripal_example_requirements($phase) {
-   
-  
+
+
   $requirements = array();
   if ($phase == 'install') {
     // EXPLANATION: It is essential that Chado be installed for almost all
     // Tripal modules. Therefore, the following code checks to ensure Chado
     // is installed and available.  If your module does not require that
     // Chado be installed, you can remove the following check.
-    
+
     // make sure chado is installed
     if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_example'] = array(
@@ -62,57 +62,57 @@ function tripal_example_requirements($phase) {
 
 /**
  * Implements hook_install().
- * 
- * Performs actions when the modules is first installed. 
+ *
+ * Performs actions when the modules is first installed.
  *
  * @ingroup tripal_example
  */
 function tripal_example_install() {
-  
+
   // EXPLANATION: If your module will making data publicly available for
   // download or use by the site you can create the directory using the
   // tripal_create_files_dir() function.  This will create a directory
   // in the public access directory which will typcially be in
   // sites/default/files/tripal/[module name]/
-  
+
   // create the module's data directory
   tripal_create_files_dir('tripal_example');
 
-  // EXPLANATION: Here is a good place to add any materialized views, 
+  // EXPLANATION: Here is a good place to add any materialized views,
   // controlled vocabularies CV, databases or CV terms needed by your module.
   // To keep this module code short, create functions to do each of those
   // tasks
-  
+
   // add any materialized view
   tripal_example_add_mviews();
 
   // add any external databases used by the example module.
   tripal_example_add_dbs();
-  
+
   // add any controlled vocabularies used by the example module. You may need
   // to add a vocabulary if you to set it as default (see next lines of code).
   // For example, the Sequence Ontology (SO) is used by the feature module as the
   // default vocabulary for the feature type_id field.  But, that vocabulary
-  // does not yet exist in Chado until after the SO is loaded using the 
+  // does not yet exist in Chado until after the SO is loaded using the
   // Tripal OBO loader.  But, we can add it here as a placeholder so that we can
   // then set it as a default vocabulary (see below).
   tripal_example_add_cvs();
-  
-  
+
+
   // add any controlled vocabulary terms
   tripal_example_add_cvterms();
-  
+
   // EXPLANATION: Many tables in Chado have a 'type_id' column which allows for
   // association of controlled vocabulries to describe the record.   Chado
   // places no restrictions on which vocabularies can be used, but Tripal can
-  // be instructed to provide a default vocabulary for any given field. For 
+  // be instructed to provide a default vocabulary for any given field. For
   // example, the feature.type_id column will typically use the Sequence Ontology
   // In that case, we can use the tripal_set_default_cv() function to specify
-  // the Sequence Ontology (sequence) as the default vocabulary.  
+  // the Sequence Ontology (sequence) as the default vocabulary.
   tripal_set_default_cv('example', 'type_id', 'example_type');
   tripal_set_default_cv('exampleprop', 'type_id', 'example_property');
   tripal_set_default_cv('example_relationship', 'type_id', 'example_relationship');
-  
+
   // add any custom tables. For this case we will add an 'example' table to the
   // chado schema
   tripal_example_add_custom_tables();
@@ -121,9 +121,9 @@ function tripal_example_install() {
 
 /**
  * Implements hook_uninstall().
- * 
+ *
  * Performs actions when the modules is uninstalled.
- * 
+ *
  * @ingroup tripal_example
  */
 function tripal_example_uninstall() {
@@ -132,11 +132,11 @@ function tripal_example_uninstall() {
 
 /**
  * Implementation of hook_schema().
- * 
+ *
  * Provides a list of tables to be created inside of the Drupal schema
  * (the 'public' schema by default). It uses the Drupal Schema API
  * array structure to define the table, its indexes and constraints.
- * 
+ *
  * Schema API documentation is here:
  * https://api.drupal.org/api/drupal/includes%21database%21schema.inc/group/schemaapi/7
  *
@@ -195,12 +195,12 @@ function tripal_example_schema() {
  * @ingroup tripal_example
  */
 function tripal_example_add_mviews() {
-  
+
   // EXPLANATION: use the tripal_add_mview() function to add a materialized
   // view needed by your module.  If you have more than one materialized view
   // it is best to create a single function for each one and call each
   // function here. Otherwise this function can become quite long.
-  
+
 }
 /**
  * Add cvs related to publications
@@ -211,7 +211,7 @@ function tripal_example_add_dbs() {
   // EXPLANATION: use the tripal_db_add_db() function to add any
   // external databases needed by your module.  If the database already
   // exists then the function will gracefully return.
-  
+
   tripal_db_add_db(
     'example_db',
     'An example database.'
@@ -224,26 +224,26 @@ function tripal_example_add_dbs() {
  */
 function tripal_example_add_cvs() {
 
-  // EXPLANATION: use the tripal_cv_add_cv() function to add any 
+  // EXPLANATION: use the tripal_cv_add_cv() function to add any
   // controlled vocabularies needed by your module.  If the vocabulary already
   // exists then the function will gracefully return.  Chado convensions
   // use a singluar name for CV names (not plural)/
-  
+
   tripal_cv_add_cv(
     'example_property',
     'Contains property terms for examples.'
   );
-  
+
   tripal_cv_add_cv(
     'example_type',
     'Contains terms describing types of examples.'
   );
-  
+
   tripal_cv_add_cv(
    'example_relationship',
    'Contains terms for describing relationship types between examples.'
   );
-  
+
 }
 
 /**
@@ -252,7 +252,7 @@ function tripal_example_add_cvs() {
  * @ingroup tripal_example
  */
 function tripal_example_add_cvterms() {
-  
+
   // EXPLANATION:  for our test module to work we need to add some terms to our example_type
   // controlled vocabulary.  Ideally we should have a full OBO file for loading
   // but sometimes we just have a small list that won't really change so
@@ -268,11 +268,11 @@ function tripal_example_add_cvterms() {
 
 /**
  * Add custom tables to Chado that are required by this module
- * 
+ *
  * @ingroup tripal_example
  */
 function tripal_example_add_custom_tables() {
-  
+
   // EXPLANATION: for this example module we will create a set of example tables
   // that mimic Chado tables. These tables are:
   //
@@ -281,9 +281,9 @@ function tripal_example_add_custom_tables() {
   //   3) example_relationship (for storing relationships about examples)
   //   4) example_dbxref (for storing cross-references about an example)
   //
-  // To make the code easier to read, each table is created by a separte 
+  // To make the code easier to read, each table is created by a separte
   // function called here:
-  
+
   tripal_example_add_example_table();
   tripal_example_add_exampleprop_table();
   tripal_example_add_example_relationship_table();
@@ -291,7 +291,7 @@ function tripal_example_add_custom_tables() {
 }
 /**
  * Adds the 'example' custom table to Chado.
- * 
+ *
  * @ingroup tripal_example
  */
 function tripal_example_add_example_table() {
@@ -354,7 +354,7 @@ function tripal_example_add_example_table() {
       ),
     ),
     // EXPLANATION: the 'referring_tables' array is the list of tables
-    // that have a foreign key relationships with this table. This 
+    // that have a foreign key relationships with this table. This
     // information is required for the Tripal API to be able to expand
     // tables in templates.
     'referring_tables' => array(
@@ -367,13 +367,13 @@ function tripal_example_add_example_table() {
 }
 /**
  * Adds the 'example_relationship' custom table to Chado.
- * 
+ *
  * @ingroup tripal_example
  */
 function tripal_example_add_exampleprop_table() {
   // EXPLANATION: use the Drupal Schema API to describe the custom table. Then
   // add the table using the chado_create_custom_table() function.
-  
+
   // Add the exampleprop table
   $schema =  array(
     'table' => 'exampleprop',
@@ -429,13 +429,13 @@ function tripal_example_add_exampleprop_table() {
 
 /**
  * Adds the 'example_relationship' custom table to Chado.
- * 
+ *
  * @ingroup tripal_example
  */
 function tripal_example_add_example_relationship_table() {
   // EXPLANATION: use the Drupal Schema API to describe the custom table. Then
   // add the table using the chado_create_custom_table() function.
-  
+
   $schema =  array(
     'table' => 'example_relationship',
     'fields' => array(
@@ -508,11 +508,11 @@ function tripal_example_add_example_relationship_table() {
 
 /**
  * Adds the 'example_dbxref' custom table to Chado.
- * 
+ *
  * @ingroup tripal_example
  */
 function tripal_example_add_example_dbxref_table() {
-  
+
   // EXPLANATION: use the Drupal Schema API to describe the custom table. Then
   // add the table using the chado_create_custom_table() function.
 
@@ -576,14 +576,14 @@ function tripal_example_add_example_dbxref_table() {
  * This is the required update for tripal_example.
  */
 function tripal_example_update_7200() {
-  // EXPLANATION: as you create new releases of your module you may find that 
-  // tables your module created, or data may need to be adjusted. This function 
-  // allows you to do that. This function is executed using the 
+  // EXPLANATION: as you create new releases of your module you may find that
+  // tables your module created, or data may need to be adjusted. This function
+  // allows you to do that. This function is executed using the
   // http://[your site]/update.php  URL or using the drush command 'updatedb'.
-  // This function should be named according to the instructions provided here: 
+  // This function should be named according to the instructions provided here:
   // https://api.drupal.org/api/drupal/modules%21system%21system.api.php/function/hook_update_N/7
   //
-  // It is best not to use Tripal API calls inside of this function because an 
+  // It is best not to use Tripal API calls inside of this function because an
   // upgarde from Drupal 6 to Drupal 7 requires that all modules be disabled
   // which means the Tripal API is not available.  This is an unfortunate
   // requirement, but will prevent errors during a major upgrade.
@@ -607,9 +607,9 @@ function tripal_example_update_dependencies() {
 
   // EXPLANATION: here we can specify which modules must be updated prior
   // to applying the updates in this module.  This is useful because it
-  // prevents updates from being executed out of order.  The following 
+  // prevents updates from being executed out of order.  The following
   // example code shows that the 'tripal_example' module update number 7200
-  // must be executed after the 'tripal_cv' module's 7200 update. 
+  // must be executed after the 'tripal_cv' module's 7200 update.
   $dependencies['tripal_example'][7200] = array(
     'tripal_cv' => 7200
   );

tripal_feature/tripal_feature.install

@@ -17,7 +17,7 @@ function tripal_feature_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -56,10 +56,10 @@ function tripal_feature_install() {
 
   // create the temp table we will use for loading GFF files
   tripal_cv_create_tripal_gff_temp();
-  
+
   // add the vocabularies used by the feature module:
   tripal_feature_add_cvs();
-  
+
   // set the default vocabularies
   tripal_set_default_cv('feature', 'type_id', 'sequence');
   tripal_set_default_cv('featureprop', 'type_id', 'feature_property');
@@ -231,16 +231,16 @@ function tripal_feature_add_cvs() {
     'feature_relationship',
     'Contains types of relationships between features.'
   );
-  
+
   // the feature_property CV already exists... it comes with chado, but we need to
   // add it just in case it doesn't get added before the feature module is installed
   tripal_cv_add_cv(
     'feature_property',
     'Stores properties about features'
   );
-  
+
   // the feature type vocabulary should be the sequence ontology, and even though
-  // this ontology should get loaded we will create it here just so that we can 
+  // this ontology should get loaded we will create it here just so that we can
   // set the default vocabulary for the feature.type_id field
   tripal_cv_add_cv(
     'sequence',
@@ -253,9 +253,9 @@ function tripal_feature_add_cvs() {
  * This update may take some time to complete.
  */
 function tripal_feature_update_7200() {
-  // During the upgrade from D6 to D7 the vocabulary terms assigned to features were 
+  // During the upgrade from D6 to D7 the vocabulary terms assigned to features were
   // copied to the field_data_taxonomyextra table rather than to the correct
-  // field_data_taxonomy_vocabulary_[vid] table. We'll move them. 
+  // field_data_taxonomy_vocabulary_[vid] table. We'll move them.
   $vid = db_query("SELECT vid FROM {taxonomy_vocabulary} WHERE name = 'Feature Type'")->fetchField();
   if ($vid) {
     try {
@@ -270,7 +270,7 @@ function tripal_feature_update_7200() {
       db_query($sql);
       $sql = "DELETE FROM field_data_taxonomyextra WHERE bundle = 'chado_feature'";
       db_query($sql);
-      
+
       // next move from the field_revision_taxonomyextra table
       $sql = "
         INSERT INTO {field_revision_taxonomy_vocabulary_$vid}
@@ -288,7 +288,7 @@ function tripal_feature_update_7200() {
       throw new DrupalUpdateException('Could not move feature taxonomy terms: '. $error);
     }
   }
-  
+
   // set the default feature property vocabulary
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'feature_property'")->fetchField();
@@ -304,7 +304,7 @@ function tripal_feature_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to set feature_property vocabulary as default: '. $error);
   }
-  
+
   // add the feature_relationshp CV
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'feature_relationship'")->fetchField();
@@ -330,7 +330,7 @@ function tripal_feature_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add feature_relationship vocabulary: '. $error);
   }
-  
+
   // set the feature_type as the 'sequence' ontology
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'sequence'")->fetchField();
@@ -355,8 +355,8 @@ function tripal_feature_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add sequence vocabulary which will be used for the sequence ontology: '. $error);
   }
-  
-  
+
+
 }
 
 /**

tripal_feature/tripal_feature.module

@@ -203,7 +203,7 @@ function tripal_feature_menu() {
   // Enable admin view
   $items['admin/tripal/chado/tripal_feature/views/features/enable'] = array(
     'title' => 'Enable feature Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_feature_admin_features', 'admin/tripal/chado/tripal_feature'),
     'access arguments' => array('administer tripal feature'),
     'type' => MENU_CALLBACK,
@@ -515,10 +515,10 @@ function tripal_feature_coder_ignore() {
 function tripal_feature_match_features_page($id) {
 
   // first check to see if the URL (e.g. /feature/$id) is already
-  // assigned to a node. If so, then just go there.  Otherwise, 
+  // assigned to a node. If so, then just go there.  Otherwise,
   // try to find the feature.
   $sql = "
-    SELECT source 
+    SELECT source
     FROM {url_alias}
     WHERE alias = :alias
   ";
@@ -603,7 +603,7 @@ function tripal_feature_form_alter(&$form, &$form_state, $form_id) {
   // turn off preview button for insert/updates
   if ($form_id == "chado_feature_node_form") {
     $form['actions']['preview']['#access'] = FALSE;
-    
+
     //remove the body field
     unset($form['body']);
   }

tripal_feature/tripal_feature.views_default.inc

@@ -16,12 +16,12 @@ function tripal_feature_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_feature_search_biological_data_views()
   $view = tripal_feature_defaultvalue_user_features();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin view
   $view = tripal_feature_defaultview_admin_features();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;
@@ -43,7 +43,7 @@ function tripal_feature_defaultvalue_user_features() {
   $view->core = 0;
   $view->api_version = '3.0';
   $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  
+
   /* Display: features_all */
   $handler = $view->new_display('default', 'features_all', 'default');
   $handler->display->display_options['title'] = 'Sequence Features';
@@ -248,7 +248,7 @@ function tripal_feature_defaultvalue_user_features() {
   $handler->display->display_options['filters']['common_name']['expose']['identifier'] = 'organism';
   $handler->display->display_options['filters']['common_name']['values_form_type'] = 'select';
   $handler->display->display_options['filters']['common_name']['select_optional'] = TRUE;
-  
+
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
   $handler->display->display_options['path'] = 'chado/feature';
@@ -256,8 +256,8 @@ function tripal_feature_defaultvalue_user_features() {
   $handler->display->display_options['menu']['title'] = 'Features';
   $handler->display->display_options['menu']['description'] = 'A biological sequence or a section of a biological sequence, or a collection of such sections.';
   $handler->display->display_options['menu']['weight'] = '-10';
-  
-  
+
+
   return $view;
 }
 

tripal_featuremap/tripal_featuremap.install

@@ -16,7 +16,7 @@ function tripal_featuremap_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -447,7 +447,7 @@ function tripal_featuremap_update_7200() {
 
   // set the default vocabularies
   // featuremap_units
-  try {    
+  try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'featuremap_units'")->fetchField();
     db_insert('tripal_cv_defaults')
       ->fields(array(
@@ -461,7 +461,7 @@ function tripal_featuremap_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to set featuremap_units vocabulary as default: '. $error);
   }
-  
+
   // featurepos_property
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'featurepos_property'")->fetchField();
@@ -477,7 +477,7 @@ function tripal_featuremap_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to set featurepos_property vocabulary as default: '. $error);
   }
-  
+
   // featuremap_property
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'featuremap_property'")->fetchField();
@@ -493,7 +493,7 @@ function tripal_featuremap_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to set featuremap_property vocabulary as default: '. $error);
   }
-  
+
 }
 
 /**
@@ -542,7 +542,7 @@ function tripal_featuremap_update_7201() {
       FOREIGN KEY (featuremap_id) REFERENCES chado.featuremap (featuremap_id)
       ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
     ');
-    
+
     // featuremap_dbref table
     db_query('
       ALTER TABLE chado.featuremap_dbxref
@@ -564,7 +564,7 @@ function tripal_featuremap_update_7201() {
       FOREIGN KEY (featuremap_id) REFERENCES chado.featuremap (featuremap_id)
       ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
     ');
-    
+
     // featureposprop
     db_query('
       ALTER TABLE chado.featureposprop

tripal_featuremap/tripal_featuremap.module

@@ -139,7 +139,7 @@ function tripal_featuremap_menu() {
 
   $items['admin/tripal/chado/tripal_featuremap/views/featuremaps/enable'] = array(
     'title' => 'Enable featuremap Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_featuremap_admin_featuremaps', 'admin/tripal/chado/tripal_featuremap'),
     'access arguments' => array('administer tripal featuremap'),
     'type' => MENU_CALLBACK,

tripal_featuremap/tripal_featuremap.views_default.inc

@@ -16,12 +16,12 @@ function tripal_featuremap_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_featuremap_search_biological_data_views()
   $view = tripal_featuremap_defaultvalue_user_featuremaps();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin view
   $view = tripal_featuremap_defaultview_admin_featuremaps();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_genetic/tripal_genetic.install

@@ -16,7 +16,7 @@ function tripal_genetic_disable() {
   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_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }

tripal_genetic/tripal_genetic.module

@@ -66,7 +66,7 @@ function tripal_genetic_menu() {
 
   $items['admin/tripal/chado/tripal_genetic/views/genetics/enable'] = array(
     'title' => 'Enable genetic Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_genetic_admin_genetics', 'admin/tripal/chado/tripal_genetic'),
     'access arguments' => array('administer tripal genetic'),
     'type' => MENU_CALLBACK,

tripal_genetic/tripal_genetic.views_default.inc

@@ -16,12 +16,12 @@ function tripal_genetic_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_genetic_search_biological_data_views()
   $view = tripal_genetic_defaultvalue_user_genotypes();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin view
   $view = tripal_genetic_defaultviews_admin_genotypes();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_library/tripal_library.install

@@ -16,7 +16,7 @@ function tripal_library_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -57,7 +57,7 @@ function tripal_library_install() {
   // add cvterms
   tripal_library_add_cvs();
   tripal_library_add_cvterms();
-  
+
   // set the default vocabularies
   tripal_set_default_cv('libraryprop', 'type_id', 'library_property');
   tripal_set_default_cv('library', 'type_id', 'library_type');
@@ -247,7 +247,7 @@ function tripal_library_add_cvterms() {
 function tripal_library_update_7200() {
 
   // the library types were formerly in a vocabulary named 'tripal_library_types'.
-  // rename that to just be 'library_type'. We cannot use the Tripal API calls 
+  // rename that to just be 'library_type'. We cannot use the Tripal API calls
   // because during upgrade the tripal_core should also be disabled
   try {
     $check = db_query("SELECT cv_id FROM chado.cv WHERE name = 'library_type'")->fetchObject();
@@ -260,7 +260,7 @@ function tripal_library_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to change the vocabulary from tripal_library_types to library_type: '. $error);
   }
-  
+
   // add the library_property CV
   try {
     $check = db_query("SELECT cv_id FROM chado.cv WHERE name = 'library_property'")->fetchObject();
@@ -276,7 +276,7 @@ function tripal_library_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add library_property vocabulary: '. $error);
   }
-  
+
   // add the library_type CV
   try {
     $check = db_query("SELECT cv_id FROM chado.cv WHERE name = 'library_type'")->fetchObject();
@@ -284,7 +284,7 @@ function tripal_library_update_7200() {
       $sql = "INSERT INTO chado.cv (name, definition) VALUES (
         'library_type',
         'Contains terms for types of libraries (e.g. BAC, cDNA, FOSMID, etc).')
-      ";  
+      ";
       db_query($sql);
     }
   }
@@ -292,19 +292,19 @@ function tripal_library_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add library_type vocabulary: '. $error);
   }
-  
+
   // For Tripal in Drupal 6 the library_description cvterm was stored in the
   // 'tripal' CV.  It should be stored in the new library_property CV that
   // is added by this module for Tripal 2.0 and Drupal 7.  So, we need to
-  // reset the CV ID for that term and rename the term to 'Library Description' 
-  // We cannot use the Tripal API calls in the 7000 update 
+  // reset the CV ID for that term and rename the term to 'Library Description'
+  // We cannot use the Tripal API calls in the 7000 update
   // because during upgrade the tripal_core should also be disabled
   $sql = "
-    UPDATE chado.cvterm 
-    SET 
+    UPDATE chado.cvterm
+    SET
       name = 'Library Description',
       cv_id = (SELECT cv_id FROM chado.cv WHERE name = 'library_property')
-    WHERE 
+    WHERE
       name = 'library_description' AND
       cv_id = (SELECT cv_id FROM chado.cv WHERE name = 'tripal')
   ";
@@ -315,7 +315,7 @@ function tripal_library_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to change library_description property type to the library_property CV and update the name: '. $error);
   }
-  
+
   // During the upgrade from D6 to D7 the vocabulary terms assigned to libraries were
   // copied to the field_data_taxonomyextra table rather than to the correct
   // field_data_taxonomy_vocabulary_[vid] table. We'll move them.
@@ -333,7 +333,7 @@ function tripal_library_update_7200() {
       db_query($sql);
       $sql = "DELETE FROM field_data_taxonomyextra WHERE bundle = 'chado_library'";
       db_query($sql);
-  
+
       // next move from the field_revision_taxonomyextra table
       $sql = "
         INSERT INTO {field_revision_taxonomy_vocabulary_$vid}
@@ -351,7 +351,7 @@ function tripal_library_update_7200() {
       throw new DrupalUpdateException('Could not move library taxonomy terms: '. $error);
     }
   }
-  
+
   // set the default vocabularies
   // library_type
   try {
@@ -383,7 +383,7 @@ function tripal_library_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to set the library_property vocabulary as default: '. $error);
   }
-  
+
 }
 
 /**

tripal_library/tripal_library.module

@@ -104,7 +104,7 @@ function tripal_library_menu() {
 
   $items['admin/tripal/chado/tripal_library/views/libraries/enable'] = array(
     'title' => 'Enable Library Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_library_admin_libraries', 'admin/tripal/chado/tripal_library'),
     'access arguments' => array('administer tripal library'),
     'type' => MENU_CALLBACK,

tripal_library/tripal_library.views_default.inc

@@ -16,12 +16,12 @@ function tripal_library_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_library_search_biological_data_views()
   $view = tripal_library_defaultvalue_user_library();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin view
   $view = tripal_library_admin_defaultviews_library();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_natural_diversity/tripal_natural_diversity.install

@@ -16,7 +16,7 @@ function tripal_natural_diversity_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }

tripal_natural_diversity/tripal_natural_diversity.module

@@ -67,7 +67,7 @@ function tripal_natural_diversity_menu() {
 
   $items['admin/tripal/chado/tripal_natdiv/views/natdiv_exp/enable'] = array(
     'title' => 'Enable Natural Diversity Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_natural_diversity_admin_natdiv_exp', 'admin/tripal/chado/tripal_natdiv'),
     'access arguments' => array('administer tripal nd'),
     'type' => MENU_CALLBACK,

tripal_natural_diversity/tripal_natural_diversity.views_default.inc

@@ -14,22 +14,22 @@ function tripal_natural_diversity_views_default_views() {
 
   // Experiment Listing
   $view = tripal_natural_diversity_defaultview_admin_natdiv_exp();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // List geolocations
   $view = tripal_natural_diversity_defaultview_admin_geolocations();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // List protocols
   $view = tripal_natural_diversity_defaultview_admin_protocols();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // List Reagents
   $view = tripal_natural_diversity_defaultview_admin_reagents();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_organism/tripal_organism.install

@@ -16,7 +16,7 @@ function tripal_organism_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -37,10 +37,10 @@ function tripal_organism_install() {
   // cvs & cvterms
   tripal_organism_add_cvs();
   tripal_organism_add_cvterms();
-  
+
   // set the default vocabularies
   tripal_set_default_cv('organismprop', 'type_id', 'organism_property');
-  
+
 }
 
 /**
@@ -117,7 +117,7 @@ function tripal_organism_requirements($phase) {
  */
 function tripal_organism_add_cvs() {
   tripal_cv_add_cv(
-    'organism_property', 
+    'organism_property',
     'Contains properties for organisms'
   );
 }
@@ -138,7 +138,7 @@ function tripal_organism_add_cvterms() {
 function tripal_organism_update_7200() {
 
   // add the new organism_property vocabulary
-  // We cannot use the Tripal API calls in the 7000 update 
+  // We cannot use the Tripal API calls in the 7000 update
   // because during upgrade the tripal_core should also be disabled
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'organism_property'")->fetchField();
@@ -162,7 +162,7 @@ function tripal_organism_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add organism_property vocabulary: '. $error);
   }
-  
+
 
   // During the upgrade from D6 to D7 the vocabulary terms assigned to organisms were
   // copied to the field_data_taxonomyextra table rather than to the correct
@@ -207,11 +207,11 @@ function tripal_organism_update_7200() {
  */
 function tripal_organism_update_dependencies() {
   $dependencies = array();
-  
+
   // the tripal_cv update 7200 must run prior to update 7200 of this module
   $dependencies['tripal_organism'][7200] = array(
     'tripal_cv' => 7200
   );
-  
+
   return $dependencies;
 }

tripal_organism/tripal_organism.module

@@ -108,7 +108,7 @@ function tripal_organism_menu() {
 
   $items['admin/tripal/chado/tripal_organism/views/organisms/enable'] = array(
     'title' => 'Enable Organism Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_organism_admin_organisms', 'admin/tripal/chado/tripal_organism'),
     'access arguments' => array('administer tripal organism'),
     'type' => MENU_CALLBACK,
@@ -272,7 +272,7 @@ function tripal_organism_form_alter(&$form, &$form_state, $form_id) {
   // turn of preview button for insert/updates
   if ($form_id == "chado_organism_node_form") {
     $form['actions']['preview']['#access'] = FALSE;
-    
+
     //remove the body field
     unset($form['body']);
   }

tripal_organism/tripal_organism.views_default.inc

@@ -16,12 +16,12 @@ function tripal_organism_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_organism_search_biological_data_views()
   $view = tripal_organism_defaultvalue_user_organisms();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin view
   $view = tripal_organism_admin_defaultview_organisms();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;
@@ -43,7 +43,7 @@ function tripal_organism_defaultvalue_user_organisms() {
   $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';
@@ -186,7 +186,7 @@ function tripal_organism_defaultvalue_user_organisms() {
     1 => 0,
     3 => 0,
   );
-  
+
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
   $handler->display->display_options['path'] = 'chado/organism';
@@ -194,7 +194,7 @@ function tripal_organism_defaultvalue_user_organisms() {
   $handler->display->display_options['menu']['title'] = 'Organisms';
   $handler->display->display_options['menu']['description'] = 'Any living biological entity, such as an animal, plant, fungus, or bacterium.';
   $handler->display->display_options['menu']['weight'] = '-10';
-    
+
 
   return $view;
 }

tripal_phenotype/tripal_phenotype.install

@@ -16,7 +16,7 @@ function tripal_phenotype_disable() {
   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_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }

tripal_phenotype/tripal_phenotype.module

@@ -61,7 +61,7 @@ function tripal_phenotype_menu() {
 
   $items['admin/tripal/chado/tripal_phenotype/views/phenotypes/enable'] = array(
     'title' => 'Enable Phenotype Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_phenotype_admin_phenotypes', 'admin/tripal/chado/tripal_phenotype'),
     'access arguments' => array('administer tripal phenotype'),
     'type' => MENU_CALLBACK,

tripal_phenotype/tripal_phenotype.views_default.inc

@@ -16,12 +16,12 @@ function tripal_phenotype_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_phenotype_search_biological_data_views()
   $view = tripal_phenotype_defaultvalue_user_phenotypes();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin view
   $view = tripal_phenotype_defaultview_admin_phenotypes();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_project/tripal_project.install

@@ -16,7 +16,7 @@ function tripal_project_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -53,7 +53,7 @@ function tripal_project_install() {
 
   tripal_project_add_cvs();
   tripal_project_add_cvterms();
-  
+
   // set the default vocabularies
   tripal_set_default_cv('projectprop', 'type_id', 'project_property');
   tripal_set_default_cv('project_relationship', 'type_id', 'project_relationship');
@@ -104,7 +104,7 @@ function tripal_project_schema() {
 function tripal_project_add_cvs() {
   // Add the cv for project properties
   tripal_cv_add_cv(
-    'project_property', 
+    'project_property',
     'Contains properties for projects'
   );
 
@@ -139,7 +139,7 @@ function tripal_project_add_cvterms() {
  *
  */
 function tripal_project_update_7200() {
-  
+
   // add the project_property CV
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'project_property'")->fetchField();
@@ -165,7 +165,7 @@ function tripal_project_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add project_property vocabulary: '. $error);
   }
-  
+
   // add the project_relationship CV
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'project_relationship'")->fetchField();

tripal_project/tripal_project.module

@@ -79,7 +79,7 @@ function tripal_project_menu() {
 
   $items['admin/tripal/chado/tripal_project/views/projects/enable'] = array(
     'title' => 'Enable Project Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_project_admin_projects', 'admin/tripal/chado/tripal_project'),
     'access arguments' => array('administer tripal project'),
     'type' => MENU_CALLBACK,

tripal_project/tripal_project.views_default.inc

@@ -16,12 +16,12 @@ function tripal_project_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_project_search_biological_data_views()
   $view = tripal_project_defaultvalue_user_projects();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin view
   $view = tripal_project_defaultview_admin_projects();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_pub/tripal_pub.install

@@ -16,7 +16,7 @@ function tripal_pub_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -62,7 +62,7 @@ function tripal_pub_install() {
 
   // add the custom tables
   tripal_pub_add_custom_tables();
-  
+
   // set the default vocabularies
   tripal_set_default_cv('pub', 'type_id', 'tripal_pub');
   tripal_set_default_cv('pubprop', 'type_id', 'tripal_pub');
@@ -229,25 +229,25 @@ function tripal_pub_add_custom_tables() {
  */
 function tripal_pub_add_cvs() {
 
-  
+
   // Add the cv for pub properties
   tripal_cv_add_cv(
     'tripal_pub',
     'A heirarchical set of terms for describing a publication. It is intended to be used as the default vocabularies in Tripal for publication types and contact properties.'
   );
-  
+
   // Add the cv for pub types
   tripal_cv_add_cv(
     'pub_type',
     'Contains types of publications. This can be used if the tripal_pub vocabulary (which is default for publications in Tripal) is not desired.'
   );
-  
+
   // Add the cv for pub properties
   tripal_cv_add_cv(
     'pub_property',
     'Contains properties for publications. This can be used if the tripal_pub vocabulary (which is default for publications in Tripal) is not desired.'
   );
-  
+
   // Add cv for relationship types
   tripal_cv_add_cv(
     'pub_relationship',
@@ -270,7 +270,7 @@ function tripal_pub_add_cvterms() {
  */
 function tripal_pub_update_7200() {
 
-  
+
   // add the tripal_pub CV and set it to be the default for pub types and pub properties
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'tripal_pub'")->fetchField();
@@ -304,7 +304,7 @@ function tripal_pub_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add pub_property vocabulary: '. $error);
   }
-  
+
   // add the pub_property CV
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'pub_property'")->fetchField();
@@ -322,7 +322,7 @@ function tripal_pub_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add pub_property vocabulary: '. $error);
   }
-  
+
   // add the pub_type CV
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'pub_type'")->fetchField();
@@ -340,7 +340,7 @@ function tripal_pub_update_7200() {
     $error = $e->getMessage();
     throw new DrupalUpdateException('Failed to add pub_type vocabulary: '. $error);
   }
-  
+
   // add the pub_relationship CV
   try {
     $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'pub_relationship'")->fetchField();

tripal_pub/tripal_pub.views_default.inc

@@ -14,7 +14,7 @@ function tripal_pub_views_default_views() {
 
   // Main default view
   $view = tripal_pub_defaultview_admin_publications();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_stock/tripal_stock.install

@@ -16,7 +16,7 @@ function tripal_stock_disable() {
   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));
+    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
   }
 
 }
@@ -49,10 +49,10 @@ function tripal_stock_requirements($phase) {
 function tripal_stock_install() {
   // create the module's data directory
   tripal_create_files_dir('tripal_stock');
-  
-  // add some controlled vocabularies 
+
+  // add some controlled vocabularies
   tripal_stock_add_cvs();
-  
+
   tripal_stock_add_cvterms();
 
   // set the default vocabularies

tripal_stock/tripal_stock.views_default.inc

@@ -16,12 +16,12 @@ function tripal_stock_views_default_views() {
   // Remember, if you change the name/path of this view,
   // you also want to change it's description in tripal_stock_search_biological_data_views()
   $view = tripal_stock_defaultvalue_user_stocks();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   // Admin view
   $view = tripal_stock_defaultview_admin_stocks();
-  $view = tripal_views_make_view_compatible_with_external($view);
+  $view = tripal_make_view_compatible_with_external($view);
   $views[$view->name] = $view;
 
   return $views;

tripal_views/includes/tripal_views_integration.inc

@@ -41,7 +41,7 @@ function tripal_views_integrate_all_chado_tables() {
   foreach ($tables as $tablename) {
 
     $priority = 10;
-    if (!tripal_views_is_integrated($tablename, $priority)) {
+    if (!tripal_is_table_integrated($tablename, $priority)) {
       if (in_array($tablename, $base_tables)) {
         $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);
       }
@@ -49,7 +49,7 @@ function tripal_views_integrate_all_chado_tables() {
         $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, FALSE, $priority);
       }
       if ($table_integration_array) {
-        tripal_views_integration_add_entry($table_integration_array);
+        tripal_add_views_integration($table_integration_array);
       }
     }
   }
@@ -62,7 +62,7 @@ function tripal_views_integrate_all_chado_tables() {
  *   The table to generate the tripal views integration array for
  * @return
  *   The tripal views integration array which is the parameter for
- *   tripal_views_integration_add_entry($defn_array)
+ *   tripal_add_views_integration($defn_array)
  *
  * @ingroup tripal_views
  */

tripal_views/includes/tripal_views_integration_UI.inc

@@ -131,7 +131,7 @@ function tripal_views_integration_setup_list() {
  */
 function tripal_views_integration_delete($setup_id) {
 
-  tripal_views_integration_remove_entry_by_setup_id($setup_id);
+  tripal_remove_views_integration(array('setup_id' => ($setup_id));
   drupal_set_message(t("Record Deleted"));
   drupal_goto('admin/tripal/views-integration');
 
@@ -188,7 +188,7 @@ function tripal_views_integration_delete_all_form($form, &$form_state) {
  */
 function tripal_views_integration_delete_all_form_submit($form, &$form_state) {
 
-  tripal_views_rebuild_views_integrations(TRUE);
+  tripal_rebuild_views_integrations(TRUE);
 
   $form_state['redirect'] = 'admin/tripal/views-integration/list';
 
@@ -198,7 +198,7 @@ function tripal_views_integration_delete_all_form_submit($form, &$form_state) {
  * Purpose: defines the web form used for specifing the base table, joins and
  *   handlers when integrating a table with views.  This form is used for both
  *   creating a new record and editing an existing record.
- *   
+ *
  * @param $form
  *    The form array which is passed automatically by drupal
  *
@@ -857,7 +857,7 @@ function tripal_views_integration_form($form, &$form_state) {
       ->orderBy('tvj.relationship_only','ASC')
       ->orderBy('tvj.base_field', 'ASC')
       ->orderBy('tvj.left_table', 'ASC');
-    
+
     foreach ($query->execute() as $i => $result) {
       $form['view_setup_join']["$table_id-$i"] = array(
            '#type' => 'markup',
@@ -1092,7 +1092,7 @@ function tripal_views_integration_form($form, &$form_state) {
       );
     }
   }
-  
+
   $form['#prefix'] = '<div id="tripal-views-integration-form">';
   $form['#suffix'] = '</div>';
 

tripal_views/includes/tripal_views_integration_port.inc

@@ -21,7 +21,7 @@
 function tripal_views_integration_export_form($form, &$form_state, $setup_id) {
   $form = array();
 
-  $defn_array = tripal_views_integration_export_entry($setup_id);
+  $defn_array = tripal_export_views_integration($setup_id);
 
   $t = var_export($defn_array, TRUE);
   $t = preg_replace("/\n\s+array/", "array", $t); // move array( to previous line
@@ -110,7 +110,7 @@ function tripal_views_integration_import_form_submit($form, &$form_state) {
   }
 
   // Add the views integration
-  $success = tripal_views_integration_add_entry($defn_array);
+  $success = tripal_add_views_integration($defn_array);
   if ($success) {
     drupal_set_message(t("Successfully imported %name Integration", array('%name' => $defn_array['name'])));
   }

tripal_views/tripal_views.module

@@ -135,7 +135,7 @@ function tripal_views_menu() {
 
   $items['admin/tripal/views-integrations/views/integrations/enable'] = array(
     'title' => 'Enable Integrations Administrative View',
-    'page callback' => 'tripal_views_admin_enable_view',
+    'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_views_admin_integrations', 'admin/tripal/views-integrations'),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_CALLBACK,
@@ -159,7 +159,7 @@ function tripal_views_init() {
   $tripal_views = $tripal_views->fetchObject();
   if (isset($tripal_views)) {
     if (!$tripal_views->has_rows) {
-      tripal_views_rebuild_views_integrations();
+      tripal_rebuild_views_integrations();
     }
   }
 }

tripal_views/tripal_views.views.inc

@@ -145,7 +145,7 @@ function tripal_views_views_data() {
 
     // check to see if this is the lightest (drupal-style) priority setup for this table
     // if not then don't use this definition
-    $lightest_priority_setup = tripal_views_is_lightest_priority_setup($tvi_row->setup_id, $tvi_row->table_name);
+    $lightest_priority_setup = tripal_is_lightest_priority_setup($tvi_row->setup_id, $tvi_row->table_name);
     if (!$lightest_priority_setup) {
       continue;
     }