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@@ -1,53 +1,211 @@
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<?php
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-/**
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- * Provides the page with a list of files uploaded by the user.
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- *
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- * @param $uid
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- * The user ID.
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- *
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- * @return
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- * A Drupal render array.
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- */
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- function tripal_user_files_page($uid) {
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-
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- // Get all of the files that have been uploaded by the user.
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- // TODO: we should make this a paged query in case a user has a huge
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- // numbef of uploaded files.
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- $sql = "
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- SELECT FM.fid, FM.filename, TGEF.expiration_date
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+function tripal_user_get_files($uid){
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+ $directory = [];
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+
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+ // Get all of the files that have been uploaded by the user.
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+ $sql = "
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+ SELECT FM.fid, FM.filename, FM.uri, FM.uid, FM.filesize, TGEF.expiration_date
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FROM {file_managed} FM
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INNER JOIN {file_usage} FU on FM.fid = FU.fid and FM.uid = :user_id
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LEFT JOIN {tripal_expiration_files} TGEF on TGEF.fid = FU.fid
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WHERE FU.module = 'tripal'
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ORDER BY FM.filename
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";
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- $files = db_query($sql, array(':user_id' => $uid));
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- $rows = array();
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- While ($entry = $files->fetchObject()) {
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- $file = file_load($entry->fid);
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-
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+ $files = db_query($sql, array(':user_id' => $uid));
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+ $rows = array();
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+ While ($file = $files->fetchObject()) {
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+
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// Don't list files that don't exist on the file system.
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if (!file_exists($file->uri)) {
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continue;
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}
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+
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+ // Files have to be in the User's directory.
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+ if (!preg_match('/^public:\/\/tripal\/users\//', $file->uri)) {
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+ continue;
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+ }
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+
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+ // If the expiration date is somehow not set, then set it.
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+ if (!$file->expiration_date) {
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+ $file->expiration_date = tripal_reset_file_expiration($file->fid);
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+ }
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+
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+ // Organize the file into it's directory structure.
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+ $rpath = preg_replace('/^public:\/\/tripal\/users\/'. $uid . '\//', '', $file->uri);
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+ $paths = explode('/', $rpath);
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+ _tripal_user_build_files_dir($directory, $paths, $file);
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+ }
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+
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+ return $directory;
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+}
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+
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+/**
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+ * A recursive helper function for building the directory file tree.
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+ *
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+ * @param $directory
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+ * The $directory array into which the file will be placed.
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+ * @param $paths
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+ * An containing the directory path of the file. Each Directory
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+ * is a separate element of the array.
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+ * @param $file
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+ * The file object to add to the $directory object.
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+ */
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+function _tripal_user_build_files_dir(&$directory, $paths, $file) {
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+ $path = array_shift($paths);
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+ if (count($paths) == 0) {
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+ $directory[$path] = $file;
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+ }
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+ else {
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+ _tripal_user_build_files_dir($directory[$path], $paths, $file);
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+ }
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+}
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- $date_uploaded = date('Y-m-d H:i:s', $file->timestamp);
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- $expiration = $entry->expiration_date ? date('Y-m-d H:i:s', $entry->expiration_date) : '';
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- $actions = l('Delete', "user/$uid/files/$file->fid/delete") . ' | ' .
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- l('Renew', "user/$uid/files/$file->fid/renew");
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+/**
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+ * Generates an item list of the files.
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+ *
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+ * The results from this function can be passed to the theme_item_list function
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+ * and then themed as a file tree..
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+ *
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+ * @param $files_list
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+ * The array as returned by tripal_user_get_files().
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+ *
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+ * @return
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+ * An item list.
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+ */
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+function tripal_user_get_files_item_list($files_list, &$i = 0) {
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+ $items = [];
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+
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+ // Add a header row
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+ if ($i == 0) {
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+ $items[] = [
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+ 'data' => '<span><b>File</b></span>' .
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+ '<span class="file-expires"><b>Expires</b></span>' .
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+ '<span class="file-size"><b>Size</b></span>' ,
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+ ];
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+ }
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+
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+ // Iterate through each file and recursively add it to our items array.
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+ foreach ($files_list as $filename => $file) {
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+ $i++;
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+ // If this is a folder then recurse.
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+ if (is_array($file)) {
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+ $items[] = [
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+ 'data' => $filename,
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+ 'children' => tripal_user_get_files_item_list($file, $i),
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+ 'class' => ['tree-node-folder', 'tree-node-closed', ($i % 2 == 0) ? 'even' : 'odd'],
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+ ];
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+ }
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+ // If this is a file then give details for it.
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+ else {
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+ $datediff = $file->expiration_date - time();
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+ $dayleft = round($datediff / (60 * 60 * 24));
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+ if ($dayleft < 0) {
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+ $dayleft = 0;
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+ }
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+ $expiration = $file->expiration_date ? date('Y-m-d', $file->expiration_date) : '';
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+ $items[] = [
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+ 'data' => '<span class="file-name">' . $filename . '</span>' .
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+ '<span class="file-expires">' . $dayleft . ' days</span>' .
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+ '<span class="file-size">' . tripal_format_bytes($file->filesize) . '</span>' ,
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+ 'class' => ['tree-node-file', ($i % 2 == 0) ? 'even' : 'odd'],
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+ 'fid' => $file->fid,
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+ 'uid' => $file->uid,
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+ ];
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+ }
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+ }
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+
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+ return $items;
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+}
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- $rows[] = array(
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- $entry->fid,
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- l($file->filename,"/user/$uid/files/$file->fid"),
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- $date_uploaded,
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- $expiration,
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- tripal_format_bytes($file->filesize),
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- $actions,
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- );
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+/**
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+ * Gets the list of collections that have not yet generated files.
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+ *
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+ * @param $uid
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+ * The ID of the user.
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+ */
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+function tripal_user_files_get_pending_collections_table($uid) {
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+
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+ $collections = db_select('tripal_collection', 'tc')
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+ ->fields('tc', array('collection_id'))
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+ ->condition('uid', $uid)
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+ ->orderBy('tc.collection_name')
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+ ->execute();
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+
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+ $headers = array('Name', 'Download Formats', 'Actions');
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+ $rows = array();
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+
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+ while ($collection_id = $collections->fetchField()) {
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+ $collection = new TripalEntityCollection();
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+ $collection->load($collection_id);
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+
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+ $downloads = array();
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+ $formatters = $collection->getFormatters();
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+ $formatter_labels = [];
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+
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+ $status = 'complete';
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+ foreach ($formatters as $class_name => $label) {
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+ $formatter_labels[] = $label;
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+
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+ $outfile = $collection->getOutfilePath($class_name);
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+
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+ if (file_exists($outfile)) {
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+ continue;
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+ }
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+ else {
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+ $status = 'pending';
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+ }
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+ }
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+
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+ if ($status == 'pending') {
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+ $rows[] = array(
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+ 'data' => array(
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+ $collection->getName(),
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+ implode(', ', $formatters),
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+ l('Create Files', 'user/' . $uid . '/data-collections/generate/' . $collection_id) . ' | ' .
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+ l('View', 'user/' . $uid . '/data-collections/' . $collection_id . '/view') . ' | ' .
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+ l('Delete', 'user/' . $uid . '/data-collections/' . $collection_id . '/delete'),
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+ ),
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+ );
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+ }
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}
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- $header = array('ID', 'File Name', 'Upload Date', 'Expiration', 'Size', 'Actions');
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+ return theme_table(array(
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+ 'header' => $headers,
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+ 'rows' => $rows,
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+ 'attributes' => array(),
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+ 'caption' => '',
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+ 'colgroups' => array(),
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+ 'sticky' => TRUE,
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+ 'empty' => t('You currently have no pending data collections.')
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+ ));
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+}
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+/**
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+ * Provides the page with a list of files uploaded by the user.
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+ *
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+ * @param $uid
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+ * The user ID.
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+ *
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+ * @return
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+ * A Drupal render array.
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+ */
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+ function tripal_user_files_page($uid) {
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+
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+ drupal_add_css(drupal_get_path('module', 'tripal') . '/theme/css/tripal_user_files.css');
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+ drupal_add_js(drupal_get_path('module', 'tripal') . '/theme/js/tripal.user_files.js', 'file');
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+
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+ $user_files = tripal_user_get_files($uid);
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+ $items = tripal_user_get_files_item_list($user_files);
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+ $theme_files = theme_item_list([
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+ 'items' => $items,
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+ 'title' => '',
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+ 'type' => 'ul',
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+ 'attributes' => [
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+ 'id' => 'tripal-user-file-tree'
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+ ],
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+ ]);
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+
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+ $data_collections = tripal_user_files_get_pending_collections_table($uid);
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// Get the user quota settings.
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$quota = tripal_get_user_quota($uid);
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@@ -56,11 +214,11 @@
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$content = array(
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'page_title' => array(
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'#type' => 'markup',
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- '#markup' => '<h2>Your Uploaded Files</h2>',
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+ '#markup' => '<h2>Your Files</h2>',
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),
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'page_description' => array(
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'#type' => 'markup',
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- '#markup' => '<p>' . t('Each user is allowed to consume a limited amount of space with uploaded files. This page provides details about your current usage, your limits and files you\'ve uploaded.') . '</p>',
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+ '#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>',
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),
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'usage' => array(
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'#type' => 'item',
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@@ -78,20 +236,26 @@
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'#type' => 'item',
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'#title' => 'Current Days to Expire',
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'#markup' => $quota->custom_expiration,
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- '#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 using the "Renew" link in the table below.')
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+ '#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.')
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+ ),
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+ 'data_collections' => array(
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+ '#type' => 'item',
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+ '#title' => 'Pending Data Collections',
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+ '#markup' => $data_collections,
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+ '#description' => t('Data collections allow you to store custom sets of data
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+ for use on this site. Typically data collections are created using search
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+ tools. The above data collections are waiting to be generated. You must
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+ generate the files before you can use them.'),
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),
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'file_list' => array(
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'#type' => 'item',
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- '#title' => 'Uploaded Files',
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- '#markup' => theme_table(array(
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- 'header' => $header,
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- 'rows' => $rows,
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- 'attributes' => array(),
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- 'caption' => t('Click a file name for more details.'),
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- 'colgroups' => array(),
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- 'sticky' => TRUE,
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- 'empty' => 'You currently have no uploaded files.',
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- )),
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+ '#title' => 'File Browser',
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+ '#markup' => $theme_files,
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+ ),
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+ 'file_details' => array(
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+ '#type' => 'item',
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+ '#title' => 'File Details',
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+ '#markup' => '<div id="tripal-user-file-details">Click a file above for details.</div>',
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)
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);
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@@ -211,12 +375,59 @@ function tripal_delete_file_form_submit($form, &$form_state) {
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*/
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function tripal_view_file($uid, $fid) {
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$file = file_load($fid);
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+ $usage = file_usage_list($file);
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+
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+ // Check to see if this is a data collection.
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+ $collection = NULL;
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+ $collection_ctypes = [];
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+ $collection_field_list = [];
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+ $collection_formatters = [];
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+ $collection_entities = 0;
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+ if (array_key_exists('tripal', $usage)) {
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+ if (array_key_exists('data_collection', $usage['tripal'])) {
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+ $collection_id = array_keys($usage['tripal']['data_collection'])[0];
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+ $collection = new TripalEntityCollection();
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+ $collection->load($collection_id);
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+
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+ // Get the content types for this data collection.
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+ $cbundles = $collection->getBundles();
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+ foreach ($cbundles as $cbundle) {
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+ $eids = $collection->getEntityIDs($cbundle->bundle_name);
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+ $fields = $collection->getFieldIDs($cbundle->bundle_name);
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+
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+ // Convert local field IDs to their names.
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+ if (!$cbundle->site_id) {
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+ $bundle = tripal_load_bundle_entity(array('name' => $cbundle->bundle_name));
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+ $collection_ctypes[] = $bundle->label;
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+
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+ foreach ($fields as $field_id) {
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+ $field = field_info_field_by_id($field_id);
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+ $instance = field_info_instance('TripalEntity', $field['field_name'], $bundle->name);
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+ $collection_field_list[] = $instance['label'];
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+
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+ $field_formatters = tripal_get_field_field_formatters($field, $instance);
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+ foreach ($field_formatters as $class_name => $label) {
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+ tripal_load_include_downloader_class($class_name);
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+ $collection_formatters[] = $class_name::$label . ' (' . $class_name::$full_label . ')';
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+ }
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+ }
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+ }
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+ // Convert remote field IDs to their names.
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+ // TODO: add in retrieval of remote details.
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+
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+
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+ $collection_entities += count($eids);
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+ }
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+
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+ }
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+ }
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$headers = array();
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$rows = array();
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$actions = l('Delete', "user/$uid/files/$file->fid/delete") . '<br>' .
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- l('Download', "user/$uid/files/$file->fid/download");
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+ l('Download', "user/$uid/files/$file->fid/download") . '<br>' .
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+ l('Renew', "user/$uid/files/$file->fid/renew");
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// Name row
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$rows[] = array(
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@@ -231,7 +442,7 @@ function tripal_view_file($uid, $fid) {
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$date_uploaded = date('Y-m-d H:i:s', $file->timestamp);
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$rows[] = array(
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array(
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- 'data' => 'Upload Date',
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+ 'data' => 'Create Date',
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'header' => TRUE,
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'width' => '20%',
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),
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@@ -252,7 +463,18 @@ function tripal_view_file($uid, $fid) {
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),
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$expiration
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);
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-
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+
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+ $md5_file = $file->uri . '.md5';
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+ if (file_exists($md5_file)) {
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+ $rows[] = array(
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+ array(
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+ 'data' => 'MD5',
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+ 'header' => TRUE,
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+ 'width' => '20%',
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+ ),
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+ file_get_contents($md5_file),
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+ );
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+ }
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$rows[] = array(
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array(
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'data' => 'Actions',
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@@ -262,29 +484,82 @@ function tripal_view_file($uid, $fid) {
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$actions
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);
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- $content = array(
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- 'description' => array(
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- '#type' => 'markup',
|
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|
- '#markup' => '<p>' . t('The following file has been uploaded.') . '</p>',
|
|
|
- ),
|
|
|
- 'return' => array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#markup' => '<p>' . l('View all Uploaded Files', "user/$uid/files") . '</p>',
|
|
|
- ),
|
|
|
- 'file_details' => array(
|
|
|
- '#type' => 'markup',
|
|
|
- '#markup' => theme_table(array(
|
|
|
- 'header' => $headers,
|
|
|
- 'rows' => $rows,
|
|
|
- 'attributes' => array(),
|
|
|
- 'sticky' => FALSE,
|
|
|
- 'caption' => '',
|
|
|
- 'colgroups' => array(),
|
|
|
- 'empty' => '',
|
|
|
- )),
|
|
|
- ),
|
|
|
- );
|
|
|
- return $content;
|
|
|
+ $file_content = theme_table([
|
|
|
+ 'header' => $headers,
|
|
|
+ 'rows' => $rows,
|
|
|
+ 'attributes' => [],
|
|
|
+ 'sticky' => FALSE,
|
|
|
+ 'caption' => '',
|
|
|
+ 'colgroups' => [],
|
|
|
+ 'empty' => '',
|
|
|
+ ]);
|
|
|
+
|
|
|
+
|
|
|
+ $collection_content = '';
|
|
|
+ if ($collection) {
|
|
|
+ $rows = [];
|
|
|
+ $rows[] = array(
|
|
|
+ array(
|
|
|
+ 'data' => 'Description',
|
|
|
+ 'header' => TRUE,
|
|
|
+ 'width' => '20%',
|
|
|
+ ),
|
|
|
+ $collection->getDescription(),
|
|
|
+ );
|
|
|
+ $rows[] = array(
|
|
|
+ array(
|
|
|
+ 'data' => 'Content types',
|
|
|
+ 'header' => TRUE,
|
|
|
+ 'width' => '20%',
|
|
|
+ ),
|
|
|
+ join(', ', $collection_ctypes),
|
|
|
+ );
|
|
|
+
|
|
|
+ $rows[] = array(
|
|
|
+ array(
|
|
|
+ 'data' => 'Fields',
|
|
|
+ 'header' => TRUE,
|
|
|
+ 'width' => '20%',
|
|
|
+ ),
|
|
|
+ join(', ', array_unique($collection_field_list)),
|
|
|
+ );
|
|
|
+ $rows[] = array(
|
|
|
+ array(
|
|
|
+ 'data' => 'Supported File Types',
|
|
|
+ 'header' => TRUE,
|
|
|
+ 'width' => '20%',
|
|
|
+ ),
|
|
|
+ join(', ', array_unique($collection_formatters)),
|
|
|
+ );
|
|
|
+ $rows[] = array(
|
|
|
+ array(
|
|
|
+ 'data' => 'Records',
|
|
|
+ 'header' => TRUE,
|
|
|
+ 'width' => '20%',
|
|
|
+ ),
|
|
|
+ number_format($collection_entities),
|
|
|
+ );
|
|
|
+ $rows[] = array(
|
|
|
+ array(
|
|
|
+ 'data' => 'Actions',
|
|
|
+ 'header' => TRUE,
|
|
|
+ 'width' => '20%',
|
|
|
+ ),
|
|
|
+ l('Delete', 'user/' . $uid . '/data-collections/' . $collection->getCollectionID() . '/delete')
|
|
|
+ );
|
|
|
+
|
|
|
+ $collection_content = '<b>Collection Details</b>' . theme_table([
|
|
|
+ 'header' => $headers,
|
|
|
+ 'rows' => $rows,
|
|
|
+ 'attributes' => [],
|
|
|
+ 'sticky' => FALSE,
|
|
|
+ 'caption' => '',
|
|
|
+ 'colgroups' => [],
|
|
|
+ 'empty' => '',
|
|
|
+ ]);
|
|
|
+ }
|
|
|
+
|
|
|
+ drupal_json_output($file_content . $collection_content);
|
|
|
}
|
|
|
|
|
|
|
Stephen Ficklin
