admin interface updates for the collections functionality

tripal/api/tripal.collections.api.inc

@@ -23,13 +23,7 @@ function tripal_create_collection($details) {
     $collection->create($details);
     $collection_id = $collection->getCollectionID();
 
-    // Add the job to write the collection download files.
-    $args = array($collection_id);
-    tripal_add_job('Create data collection files for ' . $user->name, 'tripal',
-        'tripal_create_collection_files', $args, $user->uid, 10, array());
-
-
-    drupal_set_message(t("Collection '%name' created with %num_recs record(s).  Downloadble files will be available shortly.  Check the !view for status and download links.",
+    drupal_set_message(t("Collection '%name' created with %num_recs record(s). Check the !view for generate file links.",
       array(
         '%name' => $details['collection_name'],
         '%num_recs' => count($details['ids']),
@@ -79,12 +73,12 @@ function tripal_get_user_collections($uid) {
  * Deletes all collections that have surpassed their lifespan
  */
 function tripal_expire_collections() {
-  $max_hours = variable_get('tripal_data_collections_lifespan', 7);
+  $max_days = variable_get('tripal_data_collections_lifespan', 30);
   $ctime = time();
 
   $query = db_select('tripal_collection', 'tc');
   $query->fields('tc', array('collection_id'));
-  $query->where("(($ctime - create_date) / 60) / 60 >= $max_hours");
+  $query->where("((($ctime - create_date) / 60) / 60) / 24 >= $max_days");
   $results = $query->execute();
   while ($collection_id = $results->fetchField()) {
     $collection = new TripalEntityCollection();
@@ -155,15 +149,15 @@ function tripal_get_collection($values) {
  * @param TripalEntityCollection $collection
  */
 function tripal_create_collection_files($collection_id, TripalJob $job = NULL) {
-   if($job) {
-     $job->setProgress(0);
-   }
+  if ($job) {
+    $job->setProgress(0);
+  }
 
-   $collection = new TripalEntityCollection();
-   $collection->load($collection_id);
-   $collection->writeAll();
+  $collection = new TripalEntityCollection();
+  $collection->load($collection_id);
+  $collection->writeAll();
 
-   if ($job) {
-     $job->setProgress(100);
-   }
-}
+  if ($job) {
+    $job->setProgress(100);
+  }
+}

tripal/includes/TripalEntityCollection.inc

@@ -3,7 +3,7 @@
 class TripalEntityCollection {
 
   /**
-   * The name of the bundle (i.e. content type) to which the entities belong.
+   * The name of the bundles (i.e. content type) to which the entities belong.
    */
   protected $bundles = array();
 
@@ -68,7 +68,7 @@ class TripalEntityCollection {
       foreach ($this->downloaders as $class_name => $label) {
         tripal_load_include_downloader_class($class_name);
         $outfile = $this->getOutfile($class_name);
-        $downloader = new $class_name($this->bundle_name, $this->ids, $this->fields,
+        $downloader = new $class_name($this->bundles, $this->ids, $this->fields,
             $outfile, $this->getUserID());
         $downloader->delete();
       }
@@ -117,6 +117,24 @@ class TripalEntityCollection {
     $this->description = $collection->description;
     $this->collection_id = $collection->collection_id;
 
+    /* Add the IDs, Fields, Bundles for this collection from the
+     * collection_bundle table.
+     */
+    $this->bundles = getBundles();
+    // If more than one bundle plop into associative array.
+    if (count($this->bundles) > 1) {
+      foreach ($this->bundles as $bundle) {
+        $ids[$bundle] = unserialize(getEntityIDs($this->bundle));
+        $fields[$bundle] = unserialize(getFields($this->bundle));
+      }
+      $this->ids = $ids;
+      $this->fields = $fields;
+    }
+    else {
+      $this->ids = unserialize(getEntityIDs($this->bundles));
+      $this->fields = unserialize(getFields($this->bundles));
+    }
+
     // Iterate through the fields and find out what download formats are
     // supported for this basket.
     foreach ($this->fields as $field_id) {
@@ -127,7 +145,7 @@ class TripalEntityCollection {
       $field_name = $field['field_name'];
       $field_type = $field['type'];
       $field_module = $field['module'];
-      $instance = field_info_instance('TripalEntity', $field_name, $this->bundle_name);
+      $instance = field_info_instance('TripalEntity', $field_name, $this->bundles);
       $downloaders = array();
 
       // All fields should support the Tab and CSV downloaders.
@@ -249,7 +267,15 @@ class TripalEntityCollection {
    *   An array of bundles.
    */
   public function getBundles() {
-    return $this->bundles;
+    $collection_id = $this->collection_id;
+    // Return the bundles from the collection_bundle table.
+    $result = db_select('tripal_collection_bundle')
+      ->fields('tripal_collection_bundle', array('ids'))
+      ->condition('collection_id', $collection_id, '=')
+      ->execute()
+      ->fetchAll();
+
+    return $result;
   }
 
   /**
@@ -454,7 +480,7 @@ class TripalEntityCollection {
 
     $outfile = $this->getOutfile($formatter);
 
-    $downloader = new $formatter($this->bundle_name, $this->ids, $this->fields, $outfile, $this->user->uid);
+    $downloader = new $formatter($this->bundles, $this->ids, $this->fields, $outfile, $this->user->uid);
 
     return $downloader->getURL();
   }
@@ -508,8 +534,8 @@ class TripalEntityCollection {
       }
     }
 
-    $downloader = new $formatter($this->bundle_name, $this->ids, $supported_fields, $outfile, $this->user->uid);
+    $downloader = new $formatter($this->bundles, $this->ids, $supported_fields, $outfile, $this->user->uid);
     $downloader->write();
 
   }
-}
+}

tripal/includes/tripal.admin.inc

@@ -21,11 +21,11 @@ function tripal_admin_data_collection_form($form, &$form_state) {
   $form['lifespan'] = array(
     '#type' => 'textfield',
     '#title' => t('Collection Lifespan'),
-    '#description' => t('Enter the number of hours (e.g. 24 is 1 day, 720 is 30 days)
-       that data collections exist.  Collections will be automatically removed after the lifespan
+    '#description' => t('Enter the number of days that data collections exist.  
+       Collections will be automatically removed after the lifespan
        period has passed.  Removal of data collections occurs when the
        sites Drupal cron executes.'),
-    '#default_value' => variable_get('tripal_data_collections_lifespan', 7),
+    '#default_value' => variable_get('tripal_data_collections_lifespan', 30),
     '#required' => TRUE,
   );
 

tripal/includes/tripal.collections.inc

@@ -46,6 +46,7 @@ function tripal_user_collections_page() {
         $collection->getCreateDate(),
         $download_list,
         l('Delete', 'user/' . $user->uid . '/data-collections/' . $collection_id . '/delete'),
+        l('Generate File for Download', 'user/' . $user->uid . '/data-collections/' . $collection_id . '/generate'),
       ),
     );
   }
@@ -111,4 +112,38 @@ function tripal_user_collections_delete_form_submit($form, &$form_state) {
     }
   }
   drupal_goto('user/' . $user->uid . '/data-collections');
-}
+}
+
+function tripal_user_collections_generate_file($form, &$form_state,  $uid, $collection_id) {
+  $form_state['collection_id'] = $collection_id;
+  $form['#submit'][] = 'tripal_user_collections_delete_form_submit';
+
+  $collection  = new TripalEntityCollection();
+  $collection->load($collection_id);
+
+  $form = confirm_form($form,
+      t('Click the button below to generate the collection filed: %title',
+          array('%title' => $collection->getName())), 'user/' . $uid . '/data-collections',
+      '<p>' .t('This action cannot be undone.') .'</p>', t('Generate File'), t('Cancel'), 'confirm');
+
+  return $form;
+}
+/**
+ * Deletes a user's collection.
+ *
+ * @param $collection_id
+ *   The ID of the collection to delete.
+ */
+function tripal_user_collections_generate_file_submit($form, &$form_state) {
+  global $user;
+  $collection_id = $form_state['collection_id'];
+  $collection  = new TripalEntityCollection();
+  $collection->load($collection_id);
+
+  // Add the job to write the collection download files.
+  $args = array($collection_id);
+  tripal_add_job('Create data collection files for ' . $user->name, 'tripal',
+      'tripal_create_collection_files', $args, $user->uid, 10, array());
+      
+  drupal_goto('user/' . $user->uid . '/data-collections');
+}

tripal/tripal.module

@@ -361,6 +361,17 @@ function tripal_menu() {
     'file' => 'includes/tripal.collections.inc',
     'file path' => drupal_get_path('module', 'tripal'),
   );
+  $items['user/%/data-collections/%/generate'] = array (
+    'title' => 'Generate a file for download of a Collections',
+    'description' => 'Deletes a data collection.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_user_collections_generate_file', 1, 3),
+    'access callback' => 'tripal_accesss_user_collections',
+    'access arguments' => array(1),
+    'type' => MENU_CALLBACK,
+    'file' => 'includes/tripal.collections.inc',
+    'file path' => drupal_get_path('module', 'tripal'),
+  );
 
   $items['admin/tripal/data-collections'] = array(
     'title' => 'Data Collections',