Reorganized bulk loaer module directory structure to match other Tripal modules and removed setup instructions on admin page as they were incorrect

tripal_bulk_loader/tripal_bulk_loader.admin.inc → tripal_bulk_loader/includes/tripal_bulk_loader.admin.inc

@@ -5,75 +5,7 @@
  * Bulk Loader Administration (Miscellaneous)
  */
 
-/**
- * Provides a description page and quick links for the bulk loader
- *
- * @ingroup tripal_bulk_loader
- */
-function tripal_bulk_loader_admin_template() {
-  $output = '';
 
-  $output .= '<br /><h3>Quick Links:</h3>';
-  $output .= '<ul>'
-    . '<li>'
-      . t('<a href="@link">Configure settings</a>',
-        array('@link' => url('admin/tripal/tripal_bulk_loader_template/configure')))
-      . '</li>'
-    . '<li>'
-      . t('List <a href="@link">Bulk Loader Jobs</a>',
-      array('@link' => url('admin/tripal/tripal_bulk_loader_template/jobs')))
-      . '</li>'
-    . '<li>'
-      . t('List <a href="@link">Manage Templates</a>',
-      array('@link' => url('admin/tripal/tripal_bulk_loader_template/manage_templates')))
-      . '</li>'
-      . '<ul>'
-      . '<li>'
-        . t('<a href="@create">Create</a> a new template',
-        array('@create' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/create')))
-        . '</li>'
-      . '<li>'
-        . t('<a href="@edit">Edit</a> an existing template',
-        array('@edit' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/edit')))
-        . '</li>'
-      . '<li>'
-        . t('<a href="@delete">Delete</a> an existing template',
-        array('@delete' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/delete')))
-        . '</li>'
-      . '<li>'
-        . t('<a href="@import">Import</a> a new template',
-        array('@import' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/import')))
-        . '</li>'
-      . '<li>'
-        . t('<a href="@export">Export</a> an existing template',
-        array('@export' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/export')))
-        . '</li>'
-      . '</ul>'
-    . '</ul>';
-
-  $output .= '<h3>Module Description:</h3>';
-  $output .= '<p>This module provides the ability to create loading templates for any tab-delimited '
-    . 'data file allowing it to be loaded into chado. The Loading Templates are a direct mapping '
-    . 'between the columns in your file and the columns in chado tables. As such to use this tool '
-    . 'you need to be very familar with the chado schema -See '
-    . l(t('Chado -Getting Started'), 'http://gmod.org/wiki/Chado_-_Getting_Started')
-    . '. The ability to add constants and specify foreign key contraints is also provided '
-    . 'in order for the loader to fill chado columns which may be required but are not specified '
-    . 'in your input file.</p>';
-  $output .= '<br />';
-
-  $output .= '<h3>Setup Instructions</h3>';
-  $output .= '<p>After intallation of the bulk loader module, the following tasks should be performed:</p>';
-  $output .= '<ol>';
-  $output .= '<li><b>Install Theme:</b> In order for Bulk Loading pages to be displayed correctly, '
-    .'the contents of the Tripal Bulk Loader theme directory ([drupal root]/sites/all/modules/tripal/tripal_bulk_loader/theme) '
-    .'should be moved to the base directory of the Tripal theme ([drupal root]/sites/all/themes/tripal). '
-    .'Finally the drupal cache should be cleared for the new theme to take effect -navigate to admin/settings/performance '
-    .'and click the Clear Cached Data button.</li>';
-  $output .= '</ol>';
-
-  return $output;
-}
 
 /**
  * Provides a description page and quick links for template management

tripal_bulk_loader/theme/tripal_bulk_loader_admin.tpl.php

@@ -0,0 +1,26 @@
+<h3>Quick Links:</h3>
+<ul>
+  <li><?php print l('Configure settings', 'admin/tripal/tripal_bulk_loader_template/configure') ?></li>
+  <li><?php print l('List Bulk Loader Jobs', 'admin/tripal/tripal_bulk_loader_template/jobs') ?></li>
+  <li><?php print l('Manage Templates', 'admin/tripal/tripal_bulk_loader_template/manage_templates')?>
+    <ul>
+      <li><?php print l('Create a new template', 'admin/tripal/tripal_bulk_loader_template/manage_templates/create')?></li>
+      <li><?php print l('Edit an existing template', 'admin/tripal/tripal_bulk_loader_template/manage_templates/edit')?></li>
+      <li><?php print l('Delete an existing template', 'admin/tripal/tripal_bulk_loader_template/manage_templates/delete')?></li>        
+      <li><?php print l('Import a new template', 'admin/tripal/tripal_bulk_loader_template/manage_templates/import')?></li>
+      <li><?php print l('Export an existing template', 'admin/tripal/tripal_bulk_loader_template/manage_templates/export')?></li>
+    </ul>
+  </li>
+</ul>
+<br>
+<h3>Module Description:</h3>
+<p>This module allows you to create loading templates for any tab-delimited 
+   data file which can be used repetitively for loading data into chado. The Loading Templates are a direct mapping 
+   between the columns in your file and the columns in chado tables. To use this tool 
+   you need to be very familar with the chado schema -See 
+   <?php  l(t('Chado -Getting Started'), 'http://gmod.org/wiki/Chado_-_Getting_Started') ?>.
+   The ability to add constants and specify values via foreign key contraints is also provided 
+   in order for the loader to fill chado columns which may be required but are not specified 
+   in your input file.
+</p>
+<br />

tripal_bulk_loader/tripal_bulk_loader.module

@@ -6,10 +6,10 @@
  * @defgroup tripal_bulk_loader Tripal Bulk Loader Module
  * @ingroup tripal_modules
  */
-include('tripal_bulk_loader.loader.inc');
-include('tripal_bulk_loader.constants.inc');
-include('tripal_bulk_loader.admin.inc');
-include('tripal_bulk_loader.admin.templates.inc');
+include('includes/tripal_bulk_loader.loader.inc');
+include('includes/tripal_bulk_loader.constants.inc');
+include('includes/tripal_bulk_loader.admin.inc');
+include('includes/tripal_bulk_loader.admin.templates.inc');
 
 // API
 include('api/tripal_bulk_loader.api.templates.inc');
@@ -39,7 +39,7 @@ function tripal_bulk_loader_menu() {
     'description' => 'Edit a group of constants associated with the current bulk loader',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_edit_constant_set_form', 1, 3),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
   $items['node/%node/constants/%/delete'] = array(
@@ -47,7 +47,7 @@ function tripal_bulk_loader_menu() {
     'description' => 'Delete a group of constants associated with the current bulk loader',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_delete_constant_set_form', 1, 3),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
 
@@ -55,8 +55,9 @@ function tripal_bulk_loader_menu() {
   $items['admin/tripal/tripal_bulk_loader_template'] = array(
     'title' => 'Bulk Loader',
     'description' => 'Templates for loading tab-delimited data',
-    'page callback' => 'tripal_bulk_loader_admin_template',
-    'access arguments' => array('administer site configuration'),
+    'page callback' => 'theme',
+    'page arguments' => array('tripal_bulk_loader_admin'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_bulk_loader_template/configure'] = array(
@@ -64,21 +65,21 @@ function tripal_bulk_loader_menu() {
     'description' => 'Configuration of global options related to bulk loading jobs',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_configuration_form'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_bulk_loader_template/manage_templates'] = array(
     'title' => 'Manage Templates',
     'description' => 'Create/Update/Delete/Import/Export Templates',
     'page callback' => 'tripal_bulk_loader_admin_manage_templates',
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_bulk_loader_template/jobs'] = array(
     'title' => 'Bulk Loader Jobs',
     'description' => 'Listing of Bulk Loading Jobs',
     'page callback' => 'tripal_bulk_loader_admin_jobs',
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
 
@@ -88,7 +89,7 @@ function tripal_bulk_loader_menu() {
     'description' => 'Create loader template for loading tab-delimited data',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'create'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_bulk_loader_template/manage_templates/edit'] = array(
@@ -96,7 +97,7 @@ function tripal_bulk_loader_menu() {
     'description' => 'Edit loader template for loading tab-delimited data',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'edit'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_bulk_loader_template/edit_record'] = array(
@@ -104,7 +105,7 @@ function tripal_bulk_loader_menu() {
     'description' => 'Edit a record in an existing tripal bulk loader template.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_edit_template_record_form'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/tripal_bulk_loader_template/add_field'] = array(
@@ -112,7 +113,7 @@ function tripal_bulk_loader_menu() {
     'description' => 'Add a template field to an existing tripal bulk loader template.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_add_template_field_form'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/tripal_bulk_loader_template/edit_field'] = array(
@@ -120,7 +121,7 @@ function tripal_bulk_loader_menu() {
     'description' => 'Edit an existing field from a tripal bulk loader template.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_edit_template_field_form'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
   // Delete Template -----
@@ -129,7 +130,7 @@ function tripal_bulk_loader_menu() {
     'description' => 'Delete bulk loader template',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_delete_template_base_form'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
   // Import/Export ---------
@@ -138,7 +139,7 @@ function tripal_bulk_loader_menu() {
     'description' => 'Import Loaders',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'import'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_bulk_loader_template/manage_templates/export'] = array(
@@ -146,18 +147,18 @@ function tripal_bulk_loader_menu() {
     'description' => 'Export Loaders',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'export'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
   // AHAH ---------
   $items['admin/tripal/tripal_bulk_loader_template/add_field_ahah'] = array(
     'page callback' => 'tripal_bulk_loader_add_field_ahah',
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/tripal_bulk_loader_template/edit_field_ahah'] = array(
     'page callback' => 'tripal_bulk_loader_edit_field_ahah',
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
 
@@ -191,6 +192,11 @@ function tripal_bulk_loader_theme() {
       'arguments' => array('form' => NULL),
       'template' => 'tripal_bulk_loader_add_template_field_form',
     ),
+    'tripal_bulk_loader_admin' => array(
+      'template' => 'tripal_bulk_loader_admin',
+      'arguments' =>  array(NULL),
+      'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme'
+    ),
   );
 }
 
@@ -252,6 +258,7 @@ function tripal_bulk_loader_perm() {
       'create tripal_bulk_loader',
       'delete tripal_bulk_loader',
       'edit tripal_bulk_loader',
+      'administer tripal_bulk_loader',
   );
 }
 

tripal_cv/api/tripal_cv.api.inc

@@ -831,6 +831,7 @@ function tripal_cv_get_custom_tables($table = NULL) {
  *   
  * @ingroup tripal_cv_api
  */
+
 function tripal_cv_submit_obo_job($obo_id = NULL, $obo_name = NULL, $obo_url = NULL, $obo_file = NULL) {
   global $user;
 
@@ -875,7 +876,7 @@ function tripal_cv_add_obo_ref($name, $path) {
   $record->name = $name;
   $record->path = $path;
   drupal_write_record('tripal_cv_obo', $record);
-  return $record->obo_id;
+  return $record->obo_id;  
 }
 
 /**