Fix for issue #1122

tripal/api/tripal.quotas.api.inc

@@ -88,6 +88,12 @@ function tripal_expire_files(TripalJob $job = NULL) {
     ->fields('tgfe')
     ->execute();
   while ($result = $results->fetchObject()) {
+    // Skip files that have an expiration date of -1.  These are files
+    // that should be permenant.
+    if ($result->expiration_date == -1) {
+      continue;
+    }
+    // For files that have exceeded the expiration date, remove those.
     if (time() > $result->expiration_date) {
 
       $file = file_load($result->fid);
@@ -112,17 +118,32 @@ function tripal_expire_files(TripalJob $job = NULL) {
  *
  * @param $fid
  *   The file ID of the file to reset.
+ * @param $is_permanent
+ *   Set to TRUE if this file should be marked to never expire.
+ * @param $days
+ *   Manually set a number of days until expirtaion. If this is NULL then
+ *   the default setting is used.
  *
  * @return
  *   The new expiration date on success, FALSE on failure.
  */
-function tripal_reset_file_expiration($fid) {
+function tripal_reset_file_expiration($fid, $is_permanent=FALSE, $days=NULL) {
 
   $file = file_load($fid);
   try {
-    $quota = tripal_get_user_quota($file->uid);
-    $custom_expiration = $quota->custom_expiration;
-    $expiration_date = time() + $custom_expiration * 24 * 60 * 60;
+    if ($is_permanent===TRUE) {
+      $expiration_date = -1;
+    }
+    else {
+      $quota = tripal_get_user_quota($file->uid);
+      $custom_expiration = $quota->custom_expiration;
+      if (is_integer($days)) {
+        $expiration_date = time() + $days * 24 * 60 * 60;
+      }
+      else {
+        $expiration_date = time() + $custom_expiration * 24 * 60 * 60;
+      }
+    }
 
     db_delete('tripal_expiration_files')
       ->condition('fid', $fid)

tripal/includes/tripal.user.inc

@@ -81,8 +81,8 @@ function tripal_user_get_files_item_list($files_list, &$i = 0) {
   if ($i == 0) {
     $items[] = [
       'data' => '<span><b>File</b></span>' .
-        '<span class="file-expires"><b>Expires</b></span>' .
-        '<span class="file-size"><b>Size</b></span>',
+        '<span class="tripal-user-file-expires tripal-user-file-browser-header"><b>Expires</b></span>' .
+        '<span class="tripal-user-file-size tripal-user-file-browser-header"><b>Size</b></span>',
     ];
   }
 
@@ -95,25 +95,31 @@ function tripal_user_get_files_item_list($files_list, &$i = 0) {
         'data' => $filename,
         'children' => tripal_user_get_files_item_list($file, $i),
         'class' => [
-          'tree-node-folder',
-          'tree-node-closed',
+          'tripal-user-tree-node-folder',
+          'tripal-user-tree-node-closed',
           ($i % 2 == 0) ? 'even' : 'odd',
         ],
       ];
     }
     // If this is a file then give details for it.
     else {
-      $datediff = $file->expiration_date - time();
-      $dayleft = round($datediff / (60 * 60 * 24));
-      if ($dayleft < 0) {
-        $dayleft = 0;
+      if ($file->expiration_date == -1) {
+        $daysleft = 'Never';
+      }
+      else {
+        $datediff = $file->expiration_date - time();
+        $daysleft = round($datediff / (60 * 60 * 24));
+        if ($daysleft < 0) {
+          $daysleft = 0;
+        }
+        $expiration = $file->expiration_date ? date('Y-m-d', $file->expiration_date) : '';
+        $daysleft = $daysleft . ' days';
       }
-      $expiration = $file->expiration_date ? date('Y-m-d', $file->expiration_date) : '';
       $items[] = [
-        'data' => '<span class="file-details"><span class="file-name">' . $filename . '</span>' .
-          '<span class="file-expires">' . $dayleft . ' days</span>' .
-          '<span class="file-size">' . tripal_format_bytes($file->filesize) . '</span></span>',
-        'class' => ['tree-node-file', ($i % 2 == 0) ? 'even' : 'odd'],
+        'data' => '<span class="tripal-user-file-details"><span class="tripal-user-file-name">' . $filename . '</span>' .
+          '<span class="tripal-user-file-expires">' . $daysleft . '</span>' .
+          '<span class="tripal-user-file-size">' . tripal_format_bytes($file->filesize) . '</span></span>',
+        'class' => ['tripal-user-tree-node-file', ($i % 2 == 0) ? 'even' : 'odd'],
         'fid' => $file->fid,
         'uid' => $file->uid,
       ];
@@ -216,32 +222,40 @@ function tripal_user_files_page($uid) {
   $quota = tripal_get_user_quota($uid);
   $usage = tripal_get_user_usage($uid);
 
+  drupal_add_library('system', 'drupal.collapse');
   $content = [
     'page_title' => [
       '#type' => 'markup',
       '#markup' => '<h2>Your Files</h2>',
     ],
-    'page_description' => [
-      '#type' => 'markup',
-      '#markup' => '<p>' . t('Each user is allowed to consume a limited amount of space for files. This page provides details about your current usage, your limits and files in your account.') . '</p>',
-    ],
-    'usage' => [
-      '#type' => 'item',
-      '#title' => 'Current Usage',
-      '#markup' => tripal_format_bytes($usage),
-      '#description' => t('The total number of bytes you currently consume.'),
-    ],
-    'quota' => [
-      '#type' => 'item',
-      '#title' => 'Current Quota',
-      '#markup' => tripal_format_bytes($quota->custom_quota),
-      '#description' => t('The maximum number of bytes of files you can upload.'),
-    ],
-    'expiration' => [
-      '#type' => 'item',
-      '#title' => 'Current Days to Expire',
-      '#markup' => $quota->custom_expiration,
-      '#description' => t('The number of days a file will remain on the server before deletion. The expiration of date of a file can be renewed by selecting the file name and then selecting the "Renew" link in the file details table.'),
+    'limits' => [
+      '#type' => 'fieldset',
+      '#title' => 'Usage and Limits',
+      '#collapsible' => TRUE,
+      '#collapsed' => TRUE,
+      '#attributes' => ['class' => ['collapsible', 'collapsed']],
+      'page_description' => [
+        '#type' => 'markup',
+        '#markup' => '<p>' . t('Each user is allowed to consume a limited amount of space for files. This page provides details about your current usage, your limits and files in your account.') . '</p>',
+      ],
+      'usage' => [
+        '#type' => 'item',
+        '#title' => 'Current Usage',
+        '#markup' => tripal_format_bytes($usage),
+        '#description' => t('The total number of bytes you currently consume.'),
+      ],
+      'quota' => [
+        '#type' => 'item',
+        '#title' => 'Current Quota',
+        '#markup' => tripal_format_bytes($quota->custom_quota),
+        '#description' => t('The maximum number of bytes of files you can upload.'),
+      ],
+      'expiration' => [
+        '#type' => 'item',
+        '#title' => 'Current Days to Expire',
+        '#markup' => $quota->custom_expiration,
+        '#description' => t('The number of days a file will remain on the server before deletion. The expiration of date of a file can be renewed by selecting the file name and then selecting the "Renew" link in the file details table.'),
+      ],
     ],
     'data_collections' => [
       '#type' => 'item',
@@ -256,11 +270,15 @@ function tripal_user_files_page($uid) {
       '#type' => 'item',
       '#title' => 'File Browser',
       '#markup' => $theme_files,
+      '#prefix' => '<div id="tripal-user-file-browser">',
+      '#suffix' => '</div>',
     ],
     'file_details' => [
       '#type' => 'item',
       '#title' => 'File Details',
-      '#markup' => '<div id="tripal-user-file-details">Click a file above for details.</div>',
+      '#markup' => 'Click a file name for details.',
+      '#prefix' => '<div id="tripal-user-file-details">',
+      '#suffix' => '</div>',
     ],
   ];
 
@@ -288,7 +306,24 @@ function tripal_renew_file($fid) {
   $success = tripal_reset_file_expiration($fid);
 
   if ($success) {
-    drupal_set_message('Successfully updated expiration date.');
+    drupal_set_message(t('The expiration date for the file, \'!fname\', is now reset.', ['!fname' => $file->filename]));
+  }
+  drupal_goto('user/' . $file->uid . '/files/');
+}
+
+/**
+ * User action to remove the expiration of a file.
+ *
+ * Sets the expriation date to a -1 value indicating that the file
+ * should not be automatically removed.
+ *
+ **/
+function tripal_set_file_permanent($fid) {
+  $file = file_load($fid);
+  $success = tripal_reset_file_expiration($fid, TRUE);
+
+  if ($success) {
+    drupal_set_message(t('The file, \'!fname\', is now permanent.', ['!fname' => $file->filename]));
   }
   drupal_goto('user/' . $file->uid . '/files/');
 }
@@ -430,10 +465,6 @@ function tripal_view_file($uid, $fid) {
   $headers = [];
   $rows = [];
 
-  $actions = l('Delete', "user/$uid/files/$file->fid/delete") . '<br>' .
-    l('Download', "user/$uid/files/$file->fid/download") . '<br>' .
-    l('Renew', "user/$uid/files/$file->fid/renew");
-
   // Name row
   $rows[] = [
     [
@@ -459,7 +490,12 @@ function tripal_view_file($uid, $fid) {
     ->condition('fid', $fid)
     ->execute()
     ->fetchField();
-  $expiration = $expiration_date ? date('Y-m-d H:i:s', $expiration_date) : '';
+  if ($expiration_date == -1) {
+    $expiration = 'Never';
+  }
+  else {
+    $expiration = $expiration_date ? date('Y-m-d H:i:s', $expiration_date) : '';
+  }
   $rows[] = [
     [
       'data' => 'Expiration Date',
@@ -480,6 +516,14 @@ function tripal_view_file($uid, $fid) {
       file_get_contents($md5_file),
     ];
   }
+
+
+  $actions = l('Delete', "user/$uid/files/$file->fid/delete") . '<br>' .
+      l('Download', "user/$uid/files/$file->fid/download") . '<br>' .
+      l('Renew Expiration', "user/$uid/files/$file->fid/renew") . '<br>';
+  if ($expiration_date != -1) {
+    $actions .= l('Make Permanent', "user/$uid/files/$file->fid/permanent");
+  }
   $rows[] = [
     [
       'data' => 'Actions',
@@ -489,6 +533,7 @@ function tripal_view_file($uid, $fid) {
     $actions,
   ];
 
+
   $file_content = theme_table([
     'header' => $headers,
     'rows' => $rows,

tripal/theme/css/tripal_user_files.css

@@ -1,16 +1,19 @@
+#tripal-user-file-browser {
+}
+#tripal-user-file-details {
+}
 #tripal-user-file-tree {
   margin: 0;
   padding: 10px;
-  height: 250px;
   overflow: auto;
   border: 1px solid #AAAAAA;
 }
-#tripal-user-file-tree li.tree-node-folder {
+#tripal-user-file-tree li.tripal-user-tree-node-folder {
   background: url(../images/directory.png) no-repeat;
   background-size: 22px 22px;
   cursor: pointer;
 }
-#tripal-user-file-tree li.tree-node-file {
+#tripal-user-file-tree li.tripal-user-tree-node-file {
   background: url(../images/txt.png) no-repeat;
   background-size: 22px 22px;
   cursor: pointer;
@@ -26,31 +29,27 @@
   padding: 0;
 }
 #tripal-user-file-tree li {
-	list-style-type: none;
+  list-style-type: none;
   margin: 0px;
   padding: 0px 0px 0px 30px;
   line-height: 22px;
 }
-#tripal-user-file-tree .file-name {
-  color: #369;	
+#tripal-user-file-tree .tripal-user-file-name {
 }
-#tripal-user-file-tree .file-size {
+#tripal-user-file-tree .tripal-user-file-size {
   float: right; 
   padding-left: 10px;
   font-size: 0.8em; 
-  width: 60px;
   text-align: right;
 }
-#tripal-user-file-tree .file-expires {
+#tripal-user-file-tree .tripal-user-file-expires {
   float: right; 
   padding-left: 10px;
   font-size: 0.8em; 
-  width: 60px;
   text-align: right;
 }
 #tripal-user-file-tree a {
   border-bottom-width: 1px;
   border-bottom-style: dotted;
 }
-#tripal-user-file-details {
-}
+

tripal/theme/js/tripal.user_files.js

@@ -9,17 +9,17 @@
       $('#tripal-user-file-tree ul').removeAttr('class');
       
       // Set default actions for closed and open folders.
-      $('.tree-node-closed').children().hide();
-      $('.tree-node-closed').click(function(event) {
+      $('.tripal-user-tree-node-closed').children().hide();
+      $('.tripal-user-tree-node-closed').click(function(event) {
         expandNode($(this));
       });
-      $('.tree-node-open').click(function(event) {
+      $('.tripal-user-tree-node-open').click(function(event) {
         collapseNode($(this));
       });
       
       // Keep clicks on the files from propagating up to folders and
       // causing collapse.
-      $('.tree-node-file').click(function(event) {
+      $('.tripal-user-tree-node-file').click(function(event) {
       	event.stopPropagation();
       	
       	// Reset the colors for all of the elements.
@@ -30,7 +30,7 @@
       	showFileDetails($(this));
       	
       	// Higlight the selected file.
-      	$(this).css("background-color", "#FFAAAA");
+      	$(this).css("background-color", "#CCCCCC");
       });
     }
   }
@@ -53,8 +53,8 @@
    * Collapses a node in the CV tree browser and removes its children.
    */
   function collapseNode(item) {
-    item.removeClass('tree-node-open');
-    item.addClass('tree-node-closed');
+    item.removeClass('tripal-user-tree-node-open');
+    item.addClass('tripal-user-tree-node-closed');
     item.children().hide()
     item.unbind('click');
     item.click(function(event){
@@ -66,8 +66,8 @@
    * Expands a node in the CV tree browser and loads it's children via AJAX.
    */
   function expandNode(item){
-    item.removeClass('tree-node-closed');
-    item.addClass('tree-node-open');
+    item.removeClass('tripal-user-tree-node-closed');
+    item.addClass('tripal-user-tree-node-open');
     item.children().show()
     item.unbind('click');
     item.click(function(event){

tripal/tripal.module

@@ -573,7 +573,7 @@ function tripal_menu() {
 
   // User file renew.
   $items['user/%/files/%/renew'] = [
-    'title' => 'Renew File',
+    'title' => 'Renew File Expiration',
     'description' => "Renew a user's file",
     'page callback' => 'tripal_renew_file',
     'page arguments' => [3],
@@ -583,6 +583,17 @@ function tripal_menu() {
     'file' => 'includes/tripal.user.inc',
     'file path' => drupal_get_path('module', 'tripal'),
   ];
+  $items['user/%/files/%/permanent'] = [
+    'title' => 'Make File Permanent',
+    'description' => "Removes the expiration date of a file. It will never be removed.",
+    'page callback' => 'tripal_set_file_permanent',
+    'page arguments' => [3, TRUE],
+    'access callback' => 'tripal_access_user_files',
+    'access arguments' => ['renew', 1, 3],
+    'type' => MENU_CALLBACK,
+    'file' => 'includes/tripal.user.inc',
+    'file path' => drupal_get_path('module', 'tripal'),
+  ];
   // User file download.
   $items['user/%/files/%/download'] = [
     'title' => 'Download File',