Small changes to messages and display and added in-code documentation.

tripal_entities/includes/TripalBundleUIController.inc

@@ -25,7 +25,7 @@ class TripalBundleUIController extends EntityDefaultUIController {
     unset($items[$this->path . '/import']);
 
     $items[$this->path . '/add'] = array(
-      'title' => 'Add new biological data type',
+      'title' => 'Add Biological Data Type',
       'description' => 'Add new biological data type',
       'page callback' => 'drupal_get_form',
       'page arguments' => array('tripal_entities_admin_add_type_form'),

tripal_entities/includes/tripal_entities.admin.inc

@@ -1,59 +1,35 @@
 <?php
 
 /**
- * Launchpad for feature administration.
- *
- * @ingroup tripal_feature
+ * Launchpad for biological data administration.
  */
 function tripal_entities_admin_view() {
 
+  // Render the tripal entites bundle form.
   $form = drupal_get_form('tripal_entities_admin_bundles_form');
   $output = drupal_render($form) . "<br>[ Image Place Holder for Data Type Summary ]<br>";
 
-  // set the breadcrumb
+  // Set the breadcrumb.
   $breadcrumb = array();
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Biological Data', 'admin/tripal/bundles');
   drupal_set_breadcrumb($breadcrumb);
 
-/*   // Add the view
-  $view = views_embed_view('tripal_feature_admin_features','default');
-  if (isset($view)) {
-    $output .= $view;
-  }
-  else {
-    $output .= '<p>The Feature module uses primarily views to provide an '
-      . 'administrative interface. Currently one or more views needed for this '
-        . 'administrative interface are disabled. <strong>Click each of the following links to '
-          . 'enable the pertinent views</strong>:</p>';
-    $output .= '<ul>';
-    $output .= '<li>'.l('Features View', 'admin/tripal/chado/tripal_feature/views/features/enable').'</li>';
-    $output .= '</ul>';
-  }
-
-  // Add a summary chart.
-  //-----------------------------------
-  $output .= theme('tripal_feature_bar_chart_type_organism_summary');
-  drupal_add_js('
-    Drupal.behaviors.tripalFeature_moveAdminSummaryChart = {
-      attach: function (context, settings) {
-        jQuery("#tripal-feature-admin-summary").insertBefore( jQuery(".view-filters") );
-    }};
-  ', 'inline'); */
-
   return $output;
 }
 
 /**
- *
+ * Provide a data listing for tripal entites (ie: biological data).
+ * Note: This hook returns a rendered page but we want a form.
  */
 function tripal_entities_content_view() {
+
+  // Retrieve our data listing form and render it.
   $form = drupal_get_form('tripal_entities_content_overview_form');
   $output = drupal_render($form);
 
-  // set the breadcrumb
+  // Set the breadcrumb.
   $breadcrumb = array();
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
@@ -64,14 +40,22 @@ function tripal_entities_content_view() {
 }
 
 /**
+ * Display a listing of Biological Data to the administrator.
  *
- * @param unknown $form
- * @param unknown $form_state
- * @return multitype:
+ * @TODO Filters and bulk operations needed to be added to this form.
+ *
+ * @param array $form
+ * @param array $form_state
+ * @return 
+ *   A form array describing this listing to the Form API.
  */
 function tripal_entities_content_overview_form($form, &$form_state) {
-  $form = array();
 
+  // Set the title to be informative (defaults to content for some reason).
+  drupal_set_title('Biological Data');
+  
+  // Retrieve a pages list of all tripal entitles (ie: biological data).
+  // This will return the 25 most recently created entities.
   $entities = db_select('tripal_entity', 'td')
     ->fields('td')
     ->orderBy('created', 'DESC')//ORDER BY created
@@ -80,9 +64,17 @@ function tripal_entities_content_overview_form($form, &$form_state) {
 
   $headers = array('Title', 'Vocabulary', 'Term', 'Author', 'Status', 'Updated', 'Operations');
   $rows = array();
+  
+  // For each entity retrieved add a row to the data listing.
   while ($entity = $entities->fetchObject()) {
+  
+    // Retrieve details about the term this entity is based on.
     $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $entity->cvterm_id));
+    
+    // Retrieve details about the user who created this data.
     $author = user_load($entity->uid);
+    
+    // Add information to the table.
     $rows[] = array(
       l($entity->title, 'BioData/' . $entity->id),
       $cvterm->cv_id->name . ' (' . $cvterm->dbxref_id->db_id->name . ')',
@@ -94,7 +86,19 @@ function tripal_entities_content_overview_form($form, &$form_state) {
       l('delete', 'BioData/' . $entity->id . '/delete')
     );
   }
+  
+  // If there are no entites created yet then add a message to the table to
+  // provide guidance to administrators.
+  if (empty($rows)) {
+    $rows[] = array(
+      array(
+        'data' => t('No biological data available.'),
+        'colspan' => 7
+      )
+    );
+  }
 
+  // Render the data listing.
   $table_vars = array(
     'header'     => $headers,
     'rows'       => $rows,
@@ -104,15 +108,18 @@ function tripal_entities_content_overview_form($form, &$form_state) {
     'colgroups'  => array(),
     'empty'      => '',
   );
-  $results_table = theme('table', $table_vars);
-
   $form['results'] = array(
-    '#markup' => $results_table
+    '#type' => 'markup',
+    '#markup' => theme('table', $table_vars),
   );
+  
   return $form;
 }
 
 /**
+ * Tripal administration form for Biological data (Admin > Tripal > Biological Data).
+ *
+ * @TODO Add graph showing available data types.
  *
  * @param unknown $form
  * @param unknown $form_state
@@ -189,10 +196,12 @@ function tripal_entities_admin_bundles_form_submit($form, $form_state) {
 }
 
 /**
+ * Form for creating biological data types (ie: tripal entity types).
  *
- * @param unknown $form
- * @param unknown $form_state
- * @return multitype:
+ * @param array $form
+ * @param array $form_state
+ * @return 
+ *    An array describing this form to the Form API.
  */
 function tripal_entities_admin_add_type_form($form, &$form_state) {
 

tripal_entities/includes/tripal_entities.entity_form.inc

@@ -39,7 +39,12 @@ function theme_tripal_entities_add_list($variables) {
     $output .= '</dl>';
   }
   else {
-    $output = '<p>' . t('You have not created any biological types yet. Go to the <a href="@create-content">content type creation page</a> to add a new content type.', array('@create-content' => url('admin/structure/BioData/add'))) . '</p>';
+    $output = tripal_set_message(
+      t('This page is for adding biological data to your site. However, before you can add data you have to specify what types of data your site will support. For example, if you want to add genes to be displayed to users, you must first create a data type "gene".'),
+      TRIPAL_INFO,
+      array('return_html' => TRUE)
+    );
+    $output .= '<p>' . t('You have not created any biological data types yet. Go to the <a href="@create-content">data type creation page</a> to add a new biological data type.', array('@create-content' => url('admin/structure/BioData/add'))) . '</p>';
   }
   return $output;
 }