Further cleaning up of menus including Tripal Project.

tripal_core/tripal_core.module

@@ -135,23 +135,57 @@ function tripal_core_menu() {
     'file' => 'system.admin.inc',
     'file path' => drupal_get_path('module', 'system'),
   );
-  $items['admin/tripal/customize'] = array(
+  $items['admin/tripal/schema'] = array(
+    'title' => 'Chado Schema',
+    'description' => "Tools to extend the chado schema through custom tables & materialized views.",
+    'weight' => -2,
+    'access arguments' => array('administer site configuration'),
+  );
+  $items['admin/tripal/chado'] = array(
+    'title' => 'Chado Modules',
+    'description' => 'Configuration for specific chado data types such as Vocabularies, Features, etc.',
+    'access arguments' => array('access administration pages'),
+    'type' => MENU_NORMAL_ITEM,
+    'weight' => -6
+  );
+  $items['admin/tripal/loaders'] = array(
+    'title' => 'Chado Data Loaders',
+    'description' => 'Tools facilitating loading data into the chado database. Includes a generic tab-delimited loader (Bulk Loader).',
+    'access arguments' => array('access administration pages'),
+    'type' => MENU_NORMAL_ITEM,
+    'weight' => -4
+  );
+  $items['admin/tripal/extension'] = array(
+    'title' => 'Extension Modules',
+    'description' => 'Configuration for Tripal extension modules.',
+    'access arguments' => array('access administration pages'),
+    'type' => MENU_NORMAL_ITEM,
+    'weight' => 0
+  );
+
+  // Tripal Setup
+  $items['admin/tripal/setup'] = array(
+    'title' => 'Setup Tripal',
+    'description' => 'Tools for initial setup of Tripal',
+    'access arguments' => array('administer site configuration'),
+    'weight' => -8
+  );
+  $items['admin/tripal/setup/customize'] = array(
     'title' => 'Customize Tripal',
     'description' => 'Information on how to customize tripal',
-    'position' => 'right',
     'page callback' => 'theme',
     'page arguments' => array('tripal_core_customize'),
     'access arguments' => array('administer site configuration'),
     'weight' => 10
   );
-  $items['admin/tripal/chado_install'] = array(
+  $items['admin/tripal/setup/chado_install'] = array(
     'title' => 'Install Chado Schema',
     'description' => 'Installs the Chado database tables, views, etc., inside the current Drupal database',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_core_chado_load_form'),
     'access arguments' => array('install chado'),
     'type' => MENU_NORMAL_ITEM,
-    'weight' => 10
+    'weight' => -10
   );
 
   // Jobs Management
@@ -189,14 +223,14 @@ function tripal_core_menu() {
   );
 
   // Materialized Views
-  $items['admin/tripal/mviews'] = array(
+  $items['admin/tripal/schema/mviews'] = array(
     'title' => 'Materialized Views',
     'description' => 'Materialized views are used to improve speed of large or complex queries.',
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => -10
   );
-  $items['admin/tripal/mviews/list'] = array(
+  $items['admin/tripal/schema/mviews/list'] = array(
     'title' => 'List Materialized Views',
     'description' => 'A list of existing materialized views with the ability to edit & delete existing materialized views.',
     'page callback' => 'tripal_mviews_report',
@@ -204,7 +238,7 @@ function tripal_core_menu() {
     'type' => MENU_NORMAL_ITEM,
     'weight' => -10
   );
-  $items['admin/tripal/mviews/report/%'] = array(
+  $items['admin/tripal/schema/mviews/report/%'] = array(
     'title' => 'Materialized View',
     'description' => 'Materialized views are used to improve speed of large or complex queries. These are database views as compared to Drupal views.',
     'page callback' => 'tripal_mview_report',
@@ -212,7 +246,7 @@ function tripal_core_menu() {
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/mviews/new'] = array(
+  $items['admin/tripal/schema/mviews/new'] = array(
     'title' => 'Create Materialized View',
     'description' => 'Create a new materialized view.',
     'page callback' => 'drupal_get_form',
@@ -220,14 +254,14 @@ function tripal_core_menu() {
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/mviews/edit/%'] = array(
+  $items['admin/tripal/schema/mviews/edit/%'] = array(
     'title' => 'Edit Materialized View',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_mviews_form', 4),
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/mviews/action/%/%'] = array(
+  $items['admin/tripal/schema/mviews/action/%/%'] = array(
     'title' => 'Create Materialized View',
     'description' => 'Materialized views are used to improve speed of large or complex queries.',
     'page callback' => 'tripal_mviews_action',
@@ -237,14 +271,14 @@ function tripal_core_menu() {
   );
 
   // Custom Tables
-  $items['admin/tripal/custom_tables'] = array(
+  $items['admin/tripal/schema/custom_tables'] = array(
     'title' => 'Custom Tables',
     'description' => 'Creation of custom tables that are added to Chado database.',
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => -10
   );
-  $items['admin/tripal/custom_tables/list'] = array(
+  $items['admin/tripal/schema/custom_tables/list'] = array(
     'title' => 'List of Custom Tables',
     'description' => 'Provides a list of all custom tables created by Tripal and allows for editing or removing existing custom tables.',
     'page callback' => 'tripal_custom_tables_list',
@@ -252,7 +286,7 @@ function tripal_core_menu() {
     'type' => MENU_NORMAL_ITEM,
     'weight' => -10
   );
-  $items['admin/tripal/custom_tables/view/%'] = array(
+  $items['admin/tripal/schema/custom_tables/view/%'] = array(
     'title' => 'Custom Tables',
     'description' => 'Custom tables are added to Chado.',
     'page callback' => 'tripal_custom_table_view',
@@ -260,21 +294,21 @@ function tripal_core_menu() {
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/custom_tables/new'] = array(
+  $items['admin/tripal/schema/custom_tables/new'] = array(
     'title' => 'Create Custom Table',
     'description' => 'An interface for creating your own custom tables.',
     'page callback' => 'tripal_custom_table_new_page',
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/custom_tables/edit/%'] = array(
+  $items['admin/tripal/schema/custom_tables/edit/%'] = array(
     'title' => 'Edit Custom Table',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_custom_tables_form', 4),
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/custom_tables/action/%/%'] = array(
+  $items['admin/tripal/schema/custom_tables/action/%/%'] = array(
     'title' => 'Create Custom Table',
     'description' => 'Custom tables are added to Chado.',
     'page callback' => 'tripal_custom_tables_action',
@@ -283,15 +317,6 @@ function tripal_core_menu() {
     'type' => MENU_CALLBACK,
   );
 
-  // Create menu item for chado-specific module config
-  $items['admin/tripal/chado'] = array(
-    'title' => 'Chado Module-Specific Configuration',
-    'description' => 'Configuration for specific chado data types such as Vocabularies, Features, etc.',
-    'access arguments' => array('access administration pages'),
-    'type' => MENU_NORMAL_ITEM,
-    'weight' => -10
-  );
-
   return $items;
 }
 

tripal_project/theme/tripal_project_admin.tpl.php

@@ -1,7 +1,3 @@
-<h3>Tripal Project Administrative Tools Quick Links:</h3>
-<ul>
- <li><a href="<?php print url("admin/tripal/tripal_project/configuration") ?>">Project Configuration</a></li>
-</ul>
 <h3>Module Description:</h3>
 <p>The Tripal Project module provides support for visualization of "project" pages, editing and updating.</p>
 
@@ -9,7 +5,7 @@
 <ol>
    <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
    or administer features. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
-   permissions under the 'tripal_project' section as appropriate for your site. For a simple setup, allow anonymous 
+   permissions under the 'tripal_project' section as appropriate for your site. For a simple setup, allow anonymous
    users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
 
 <li><p><b>Sync any Existing Projects</b>: Near the top of the <?php print l('Project Configuration page', 'admin/tripal/tripal_project/configuration') ?> there is
@@ -20,12 +16,12 @@
 
 <h3>Features of this Module:</h3>
 <ul>
-  <li><b>Add/Edit/Delete Projects</b>: Projects can be created <?php print l('here', 'node/add/chado-project') ?>. 
+  <li><b>Add/Edit/Delete Projects</b>: Projects can be created <?php print l('here', 'node/add/chado-project') ?>.
   After creation, projects (regardless of the method used to create them) can be
   edited or deleted by clicking the Edit tab at the top of the Project Page.</li>
-    <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/projects') ?> is provided for 
+    <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 
+    which must be installed to see the search tool.  Look for it in the navigation menu under the item
     "Search Biological Data". </p></li>
 
 </ul>

tripal_project/tripal_project.info

@@ -4,5 +4,7 @@ core = 7.x
 project = tripal_project
 package = Tripal
 version = 7.x-2.0
+configure = admin/tripal/chado/tripal_project
+
 dependencies[] = tripal_core
 dependencies[] = tripal_cv

tripal_project/tripal_project.module

@@ -37,16 +37,23 @@ function tripal_project_views_api() {
  * @ingroup tripal_project
  */
 function tripal_project_menu() {
-  $items[ 'admin/tripal/tripal_project' ]= array(
+  $items[ 'admin/tripal/chado/tripal_project' ]= array(
     'title' => 'Projects',
     'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of projects'),
+    'access arguments' => array('adminster tripal projects'),
+    'type' => MENU_NORMAL_ITEM
+  );
+
+  $items[ 'admin/tripal/chado/tripal_project/help' ]= array(
+    'title' => 'Help',
+    'description' => ("A description of the Tripal Project module including a short description of it's usage."),
     'page callback' => 'theme',
     'page arguments' => array('tripal_project_admin'),
     'access arguments' => array('adminster tripal projects'),
     'type' => MENU_NORMAL_ITEM
   );
 
-  $items[ 'admin/tripal/tripal_project/configuration' ]= array(
+  $items[ 'admin/tripal/chado/tripal_project/configuration' ]= array(
     'title' => 'Configuration',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_project_admin'),
@@ -57,6 +64,16 @@ function tripal_project_menu() {
   return $items;
 }
 
+/**
+ * Implements hook_help()
+ * Purpose: Adds a help page to the module list
+ */
+function tripal_project_help ($path, $arg) {
+  if ($path == 'admin/help#tripal_project') {
+    return theme('tripal_project_admin', array());
+  }
+}
+
 /**
  * Implements hook_perm()
  *
@@ -99,7 +116,7 @@ function tripal_project_permission() {
  *  @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
  *
@@ -110,9 +127,9 @@ function tripal_project_permission() {
  *  @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 $op == 'create'.  We will always
  *  return TRUE if the permission is set.
- *  
+ *
  * @ingroup tripal_project
  */
 function chado_project_node_access($node, $op, $account) {
@@ -444,19 +461,19 @@ function tripal_project_block_info() {
 
   $blocks['projectbase']['info'] = t('Tripal Project Details');
   $blocks['projectbase']['cache'] = BLOCK_NO_CACHE;
-  
+
   $blocks['projectprops']['info'] = t('Tripal Project Properties');
   $blocks['projectprops']['cache'] = BLOCK_NO_CACHE;
-  
+
   $blocks['projectpubs']['info'] = t('Tripal Project Publications');
   $blocks['projectpubs']['cache'] = BLOCK_NO_CACHE;
-  
+
   $blocks['projectcont']['info'] = t('Tripal Project Contact');
   $blocks['projectcont']['cache'] = BLOCK_NO_CACHE;
-  
+
   $blocks['projectrels']['info'] = t('Tripal Project Relationships');
   $blocks['projectrels']['cache'] = BLOCK_NO_CACHE;
-  
+
   return $blocks;
 }
 /**
@@ -464,11 +481,11 @@ function tripal_project_block_info() {
  * @ingroup tripal_project
  */
 function tripal_project_block_view($delta = '') {
- 
+
   if (user_access('access chado_project content') and arg(0) == 'node' and is_numeric(arg(1))) {
     $nid = arg(1);
     $node = node_load($nid);
-  
+
     $block = array();
     switch ($delta) {
       case 'projectbase':

tripal_views/tripal_views.module

@@ -30,7 +30,7 @@ function tripal_views_menu() {
     //'page arguments' => array('tripal_views_admin'),
     'access arguments' => array('manage tripal_views_integration'),
     'type' => MENU_NORMAL_ITEM,
-    'weight' => -10
+    'weight' => 2
   );
 
   $items['admin/tripal/views-integration/list'] = array(