Tripal Bulk Loader: Fixed create/edit template form and re-did menu system

tripal_bulk_loader/api/tripal_bulk_loader.api.templates.inc

@@ -32,13 +32,7 @@ function tripal_bulk_loader_is_record_name_unique($new_record_name, $template_id
     $template = db_query("SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=:template", array(':template' => $template_id))->fetchObject();
     $template_array = unserialize($template->template_array);
     if (!is_array($template_array)) {
-      watchdog(
-        'tripal_bulk_loader',
-        'Unable to retrieve template array from database where template_id=%template_id',
-        array('%template_id' => $template_id),
-        WATCHDOG_WARNING
-      );
-      return FALSE;
+      return TRUE;
     }
   }
 

tripal_bulk_loader/includes/tripal_bulk_loader.admin.inc

@@ -14,39 +14,12 @@
  */
 function tripal_bulk_loader_admin_manage_templates() {
   $output = '';
-
-  $output .= '<br /><h3>Quick Links:</h3>';
-  $output .= '<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>';
-
   $output .= '<p>' . t('Templates, as the term is used for this module, refer to plans
   describing how the columns in the data file supplied to a bulk loading job map to tables
   and fields in chado. Templates are created independently of bulk loading jobs so that
   they can be re-used. Thus you only need one template to load any number of files of the
   same format.') . '</p>';
 
-
-
   return $output;
 }
 
@@ -91,7 +64,7 @@ function tripal_bulk_loader_admin_jobs() {
     $rows[] = array(
       l($n->job_id, 'admin/tripal/tripal_jobs/view/' . $n->job_id),
       l($n->loader_name, 'node/' . $n->nid),
-      l($n->template_name, 'admin/tripal/tripal_bulk_loader_template/manage_templates/edit', array('query' => 'template_id=' . $n->template_id)),
+      l($n->template_name, 'admin/tripal/loaders/bulk/template/'.$n->template_id.'/edit'),
       $n->job_status,
       ($n->progress) ? $n->progress . '%' : '',
       l('View', 'node/' . $n->nid) . ' | ' .  l('Edit', 'node/' . $n->nid . '/edit')

tripal_bulk_loader/theme/tripal_bulk_loader_admin.tpl.php

@@ -1,26 +1,11 @@
-<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 
+<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 
+   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/theme/tripal_bulk_loader_modify_template_base_form.tpl.php

@@ -4,11 +4,25 @@ tr.odd .form-item, tr.even .form-item {
   white-space: normal;
   word-wrap: break-word;
 }
+fieldset {
+  padding: 20px;
+}
+td.active{
+  width: 10px;
+}
+td.tbl-action-record-links {
+  width: 150px;
+}
+td.tbl-action-field-links {
+  width: 100px;
+}
 </style>
 
 <div id="tripal-bulk-loader-fields">
 <?php print drupal_render($form['template_name']); ?>
 
+<?php ddl($form, 'form in tpl'); ?>
+
 <!-- For each table display details in a draggable table -->
 <?php if (!$form['records']['no_records']['#value']) { ?>
   <fieldset><legend><?php print $form['records']['#title']; ?></legend>
@@ -16,23 +30,40 @@ tr.odd .form-item, tr.even .form-item {
     print drupal_render($form['records']['description']);
 
     // generate table
-    drupal_add_tabledrag('draggable-table', 'order', 'sibling', 'records-reorder');
-    $header = array('Record Name', 'Chado Table', 'Action', 'Order', '');
+    drupal_add_tabledrag('records-table', 'order', 'sibling', 'records-reorder');
+    $header = array(' ', ' ', 'Record Name', 'Chado Table', 'Mode', 'Order',);
     $rows = array();
     foreach (element_children($form['records']['records-data']) as $key) {
       $element = &$form['records']['records-data'][$key];
-      $element['new_priority']['#attributes']['class'] = 'records-reorder';
+      $element['new_priority']['#attributes']['class'] = array('records-reorder');
 
       $row = array();
+      $row[] = '';
+      $row[] = array(
+        'class' => array('tbl-action-record-links'),
+        'data' => drupal_render($element['submit-edit_record']) . ' | '
+          . drupal_render($element['submit-delete_record']) . ' | '
+          . drupal_render($element['submit-duplicate_record']) . '<br>'
+          . drupal_render($element['view-fields-link']) . ' | '
+          . drupal_render($element['submit-add_field'])
+        );
       $row[] = drupal_render($element['title']);
       $row[] = drupal_render($element['chado_table']);
       $row[] = drupal_render($element['mode']);
-      $row[] = drupal_render($element['new_priority']) . drupal_render($element['id']);
-      $row[] = drupal_render($element['submit-edit_record']) . '<br>' . drupal_render($element['submit-duplicate_record']) . '<br>' . drupal_render($element['submit-add_field']);
-      $rows[] = array('data' => $row, 'class' => 'draggable');
+      $row[] = drupal_render($element['new_priority'])
+        . drupal_render($element['id']);
+
+      $rows[] = array('data' => $row, 'class' => array('draggable'));
     }
 
-print theme('table', $header, $rows, array('id' => 'draggable-table', 'width' => '100%'));
+    print theme(
+      'table',
+      array(
+        'header' => $header,
+        'rows' => $rows,
+        'attributes' => array('id' => 'records-table')
+      )
+    );
 
     // Render submit
     print drupal_render($form['records']['submit-new_record']);
@@ -48,13 +79,18 @@ print theme('table', $header, $rows, array('id' => 'draggable-table', 'width' =>
 
   <?php
     // generate table
-  $header = array('','Record Name', 'Field Name', 'Chado Table', 'Chado Field', 'Data File Column', 'Constant Value', 'Foreign Record');
+    $header = array('','Record Name', 'Field Name', 'Chado Table', 'Chado Field', 'Data File Column', 'Constant Value', 'Foreign Record');
     $rows = array();
     foreach ($form['fields']['fields-data'] as $key => $element) {
       if (preg_match('/^#/', $key)) { continue; }
 
       $row = array();
-      $row[] = drupal_render($element['edit_submit']) . '<br>' . drupal_render($element['delete_submit']);
+      $row[] = array(
+        'class' => array('tbl-action-field-links', 'active'),
+        'data' => drupal_render($element['edit_submit']) . ' | '
+          . drupal_render($element['delete_submit']) . '<br />'
+          . drupal_render($element['view-record-link'])
+        );
       $row[] = drupal_render($element['record_id']);
       $row[] = drupal_render($element['field_name']);
       $row[] = drupal_render($element['chado_table_name']);
@@ -65,7 +101,14 @@ print theme('table', $header, $rows, array('id' => 'draggable-table', 'width' =>
 
       $rows[] = $row;
     }
-print theme('table', $header, $rows, array('style'=>'table-layout: fixed; width: 100%'));
+    print theme(
+      'table',
+      array(
+        'header' => $header,
+        'rows' => $rows,
+        //'attributes' => array('style'=>'table-layout: fixed; width: 100%')
+      )
+    );
 
     // Render other elements
     print drupal_render($form['fields']['add_field']);
@@ -75,5 +118,5 @@ print theme('table', $header, $rows, array('style'=>'table-layout: fixed; width:
 <?php } ?>
 
 <!-- Display Rest of form -->
-<?php print drupal_render($form); ?>
+<?php print drupal_render_children($form); ?>
 </div>

tripal_bulk_loader/tripal_bulk_loader.module

@@ -9,6 +9,8 @@
  */
 include('includes/tripal_bulk_loader.loader.inc');
 include('includes/tripal_bulk_loader.constants.inc');
+
+// Administration
 include('includes/tripal_bulk_loader.admin.inc');
 include('includes/tripal_bulk_loader.admin.templates.inc');
 
@@ -53,111 +55,157 @@ function tripal_bulk_loader_menu() {
   );
 
   // Admin pages -----------------
-  $items['admin/tripal/tripal_bulk_loader_template'] = array(
+  $items['admin/tripal/loaders/bulk'] = array(
     'title' => 'Bulk Loader',
     'description' => 'Templates for loading tab-delimited data',
-    '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(
+  $items['admin/tripal/loaders/bulk/configure'] = array(
     'title' => 'Configure',
     '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 tripal_bulk_loader'),
+    'weight' => 8,
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/tripal_bulk_loader_template/manage_templates'] = array(
-    'title' => 'Manage Templates',
-    'description' => 'Create/Update/Delete/Import/Export Templates',
+  $items['admin/tripal/loaders/bulk/help'] = array(
+    'title' => 'Help',
+    'description' => "A description of the Tripal Bulk Loader module including a short description of it's usage.",
     'page callback' => 'tripal_bulk_loader_admin_manage_templates',
     'access arguments' => array('administer tripal_bulk_loader'),
+    'weight' => 10,
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/tripal_bulk_loader_template/jobs'] = array(
+  $items['admin/tripal/loaders/bulk/jobs'] = array(
     'title' => 'Bulk Loader Jobs',
     'description' => 'Listing of Bulk Loading Jobs',
     'page callback' => 'tripal_bulk_loader_admin_jobs',
     'access arguments' => array('administer tripal_bulk_loader'),
+    'weight' => -10,
     'type' => MENU_NORMAL_ITEM,
   );
 
   // Create/Edit Template --------
-  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/create'] = array(
+  $items['admin/tripal/loaders/bulk/template/create'] = array(
     'title' => 'Create Template',
     '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 tripal_bulk_loader'),
+    'weight' => -8,
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/edit'] = array(
+  $items['admin/tripal/loaders/bulk/template/%tblid/edit'] = array(
     'title' => 'Edit Template',
     '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'),
+    'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'edit',5),
     'access arguments' => array('administer tripal_bulk_loader'),
+    'type' => MENU_CALLBACK,
+  );
+  $items['admin/tripal/loaders/bulk/template/edit'] = array(
+    'title' => 'Edit Template',
+    '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',FALSE),
+    'access arguments' => array('administer tripal_bulk_loader'),
+    'weight' => -6,
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/tripal_bulk_loader_template/edit_record'] = array(
+
+  // Add/Edit Record -----
+  $items['admin/tripal/loaders/bulk/template/%tblid/add_record'] = array(
+    'title' => 'Add Template Field',
+    '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',5),
+    'access arguments' => array('administer tripal_bulk_loader'),
+    'type' => MENU_CALLBACK,
+  );
+  $items['admin/tripal/loaders/bulk/template/%tblid/edit_record/%tblid'] = array(
     'title' => 'Edit Template Record',
     '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'),
+    'page arguments' => array('tripal_bulk_loader_edit_template_record_form',5,7),
+    'access arguments' => array('administer tripal_bulk_loader'),
+    'type' => MENU_CALLBACK,
+  );
+  $items['admin/tripal/loaders/bulk/template/%tblid/delete_record/%tblid'] = array(
+    'title' => 'Delete Template Record',
+    'description' => 'Delete a record in an existing tripal bulk loader template.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_bulk_loader_delete_template_record_form',5,7),
+    'access arguments' => array('administer tripal_bulk_loader'),
+    'type' => MENU_CALLBACK,
+  );
+  $items['admin/tripal/loaders/bulk/template/%tblid/duplicate_record/%tblid'] = array(
+    'title' => 'Duplicate Template Record',
+    'description' => 'Duplicate a record in an existing tripal bulk loader template.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_bulk_loader_duplicate_template_record_form',5,7),
     'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/tripal_bulk_loader_template/add_field'] = array(
+
+  // Add/Edit Field ------
+  $items['admin/tripal/loaders/bulk/template/%tblid/add_field/%tblid'] = array(
     'title' => 'Add Template Field',
     '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'),
+    'page arguments' => array('tripal_bulk_loader_add_template_field_form',5,7),
     'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/tripal_bulk_loader_template/edit_field'] = array(
+  $items['admin/tripal/loaders/bulk/template/%tblid/edit_field/%tblid/%tblid'] = array(
     'title' => 'Edit Template Field',
     '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'),
+    'page arguments' => array('tripal_bulk_loader_edit_template_field_form',5,7,8),
     'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
   );
+  $items['admin/tripal/loaders/bulk/template/%tblid/delete_field/%tblid/%tblid'] = array(
+    'title' => 'Delete Template Field',
+    'description' => 'Delete an existing field from a tripal bulk loader template.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_bulk_loader_delete_template_field_form',5,7,8),
+    'access arguments' => array('administer tripal_bulk_loader'),
+    'type' => MENU_CALLBACK,
+  );
+
   // Delete Template -----
-  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/delete'] = array(
+  $items['admin/tripal/loaders/bulk/manage_templates/delete'] = array(
     'title' => 'Delete Template',
     'description' => 'Delete bulk loader template',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_delete_template_base_form'),
     'access arguments' => array('administer tripal_bulk_loader'),
+    'weight' => -4,
     'type' => MENU_NORMAL_ITEM,
   );
   // Import/Export ---------
-  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/import'] = array(
+  $items['admin/tripal/loaders/bulk/manage_templates/import'] = array(
     'title' => 'Import Template',
     'description' => 'Import Loaders',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'import'),
     'access arguments' => array('administer tripal_bulk_loader'),
+    'weight' => 2,
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/export'] = array(
+  $items['admin/tripal/loaders/bulk/manage_templates/export'] = array(
     'title' => 'Export Template',
     'description' => 'Export Loaders',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'export'),
     'access arguments' => array('administer tripal_bulk_loader'),
+    'weight' => 4,
     '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 tripal_bulk_loader'),
-    'type' => MENU_CALLBACK,
-  );
-  $items['admin/tripal/tripal_bulk_loader_template/edit_field_ahah'] = array(
+  $items['admin/tripal/loaders/bulk/edit_field_ahah'] = array(
     'page callback' => 'tripal_bulk_loader_edit_field_ahah',
     'access arguments' => array('administer tripal_bulk_loader'),
     'type' => MENU_CALLBACK,
@@ -166,6 +214,11 @@ function tripal_bulk_loader_menu() {
   return $items;
 }
 
+function tblid_to_arg($arg, $map, $index) {
+  if (preg_match('/^\d+$/', $arg)) {
+    return $arg;
+  }
+}
 
 /**
  * Implements hook_theme
@@ -188,10 +241,12 @@ function tripal_bulk_loader_theme() {
       'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
     ),
     'tripal_bulk_loader_modify_template_base_form' => array(
-      'variables' => array('form' => NULL),
+      'arguments' => array('form' => NULL),
       'template' => 'tripal_bulk_loader_modify_template_base_form',
       'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
+      'render element' => 'form'
     ),
+    /**
     'tripal_bulk_loader_edit_template_field_form' => array(
       'variables' => array('form' => NULL),
       'template' => 'tripal_bulk_loader_edit_template_field_form',
@@ -202,6 +257,7 @@ function tripal_bulk_loader_theme() {
       'template' => 'tripal_bulk_loader_add_template_field_form',
       'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
     ),
+    */
     'tripal_bulk_loader_admin' => array(
       'template' => 'tripal_bulk_loader_admin',
       'variables' =>  array(NULL),