Renamed 'Search Biological Data' to 'Search Data' and added the publication search to the 'Search Data' menu

tripal_analysis/theme/tripal_analysis_help.tpl.php

@@ -33,6 +33,6 @@
     <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/analyses') ?> is provided for
     finding analyses. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
     which must be installed to see the search tool.  Look for it in the navigation menu under the item
-    "Search Biological Data". </p></li>
+    "Search Data". </p></li>
 </ul>
 

tripal_analysis/tripal_analysis.module

@@ -87,7 +87,7 @@ function tripal_analysis_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_analysis_search_biological_data_views() {
   return array(

tripal_contact/theme/tripal_contact_help.tpl.php

@@ -26,5 +26,5 @@
     <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/contacts') ?> is provided for 
     finding contacts. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
     which must be installed to see the search tool.  Look for it in the navigation menu under the item 
-    "Search Biological Data". </p></li>
+    "Search Data". </p></li>
 </ul>

tripal_contact/tripal_contact.module

@@ -105,7 +105,7 @@ function tripal_contact_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_contact_search_biological_data_views() {
   return array(

tripal_feature/theme/tripal_feature_help.tpl.php

@@ -115,7 +115,7 @@
     <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/features') ?> is provided for 
     finding features. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
     which must be installed to see the search tool.  Look for it in the navigation menu under the item 
-    "Search Biological Data". </p></li>
+    "Search Data". </p></li>
 
     <li><p><b>Delete Features</b>: You can  <a href="<?php print url('admin/tripal/tripal_feature/delete') ?>">bulk delete features</a>
     by providing a list of feature names, or for a specific organism or for a specific feature type. Be sure you have

tripal_feature/tripal_feature.module

@@ -215,7 +215,7 @@ function tripal_feature_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_feature_search_biological_data_views() {
   return array(

tripal_featuremap/theme/tripal_featuremap_help.tpl.php

@@ -32,5 +32,5 @@
     <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/featuremaps') ?> is provided for 
     finding maps. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
     which must be installed to see the search tool.  Look for it in the navigation menu under the item 
-    "Search Biological Data". </p></li>
+    "Search Data". </p></li>
 </ul>

tripal_featuremap/tripal_featuremap.module

@@ -151,7 +151,7 @@ function tripal_featuremap_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_featuremap_search_biological_data_views() {
   return array(

tripal_genetic/tripal_genetic.module

@@ -78,7 +78,7 @@ function tripal_genetic_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_genetic_search_biological_data_views() {
   return array(

tripal_library/theme/tripal_library_help.tpl.php

@@ -24,5 +24,5 @@
     <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/libraries') ?> is provided for 
     finding libraries. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
     which must be installed to see the search tool.  Look for it in the navigation menu under the item 
-    "Search Biological Data". </p></li>
+    "Search Data". </p></li>
 </ul>

tripal_library/tripal_library.module

@@ -116,7 +116,7 @@ function tripal_library_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_library_search_biological_data_views() {
   return array(

tripal_organism/theme/tripal_organism_help.tpl.php

@@ -35,5 +35,5 @@
     <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/organisms') ?> is provided for
     finding organisms. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
     which must be installed to see the search tool.  Look for it in the navigation menu under the item
-    "Search Biological Data". </p></li>
+    "Search Data". </p></li>
             </ul>

tripal_organism/tripal_organism.module

@@ -121,7 +121,7 @@ function tripal_organism_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_organism_search_biological_data_views() {
   return array(

tripal_phenotype/tripal_phenotype.module

@@ -73,7 +73,7 @@ function tripal_phenotype_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_phenotype_search_biological_data_views() {
   return array(

tripal_project/theme/tripal_project_help.tpl.php

@@ -22,6 +22,6 @@
     <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/projects') ?> is provided for
     finding projects. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
     which must be installed to see the search tool.  Look for it in the navigation menu under the item
-    "Search Biological Data". </p></li>
+    "Search Data". </p></li>
 
 </ul>

tripal_project/tripal_project.module

@@ -91,7 +91,7 @@ function tripal_project_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_project_search_biological_data_views() {
   return array(

tripal_pub/tripal_pub.module

@@ -46,7 +46,18 @@ require_once 'includes/importers/tripal_pub.AGL.inc';
 function tripal_pub_menu() {
   $items = array();
 
+  // because the publication search is not views we need to manually add
+  // it to the Search Data list in the navigation menu
+  $items['chado/publication' ]= array(
+    'title' => 'Publications',
+    'description' => ('Publications such as journal articles, conference proceedings, or other media.'),
+    'page callback' => 'tripal_pub_search_page',
+    'access arguments' => array('access chado_pub content'),
+    'type' => MENU_NORMAL_ITEM
+  );
 
+  // for backwards compatibility the same chado/publications is also found
+  // at find/publications
   $items['find/publications' ]= array(
     'title' => 'Publication Search',
     'description' => ('Search for publications'),
@@ -54,6 +65,8 @@ function tripal_pub_menu() {
     'access arguments' => array('access chado_pub content'),
     'type' => MENU_CALLBACK
   );
+  
+
 
   $items['find/publications/criteria/%/%'] = array(
     'page callback' => 'tripal_pub_search_page_update_criteria',
@@ -434,4 +447,18 @@ function tripal_get_remote_pub_raw_page($dbxref) {
     return $page;
   }
   return "Cound not find the requested publication ($dbxref)";
+}
+
+/**
+ * 
+ */
+function tripal_pub_search_biological_data_views() {
+  return array(
+    'publications' => array(
+      'machine_name' => 'publications',
+      'human_name'   => 'Publications',
+      'description'  => 'Publications such as journal articles, conference proceedings, or other media.',
+      'link'         => 'find/publications'
+    ),
+  );
 }

tripal_stock/tripal_stock.module

@@ -96,7 +96,7 @@ function tripal_stock_menu() {
 /**
  * Implements hook_search_biological_data_views().
  *
- * Adds the described views to the "Search Biological Data" Page created by Tripal Views
+ * Adds the described views to the "Search Data" Page created by Tripal Views
  */
 function tripal_stock_search_biological_data_views() {
   return array(

tripal_views/theme/tripal_views_search_biological_content.tpl.php

@@ -28,7 +28,8 @@ print tripal_set_message(
 
 // Tell Tripal admin how to add views to this list
 print tripal_set_message(
-  "In order to add views to the above list you need to implement hook_search_biological_data_views().
+  "Developers: To add a view or other search tool to the above list you need to 
+    implement hook_search_biological_data_views() in your custom module.
     This hook should return an array as follows: <code><pre>array(
     '[view-machine-name]' => array(
       'machine_name' => '[view-machine-name]',

tripal_views/tripal_views.module

@@ -31,7 +31,7 @@ function tripal_views_menu() {
   $items = array();
 
   $items['chado'] = array(
-    'title' => 'Search Biological Data',
+    'title' => 'Search Data',
     'description' => 'Listings of the various biological data available categorized by type.',
     'page callback' => 'theme',
     'page arguments' => array('tripal_views_search_biological_content'),