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@@ -3,7 +3,7 @@
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function tripal_user_get_files($uid){
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$directory = [];
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-
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+
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// Get all of the files that have been uploaded by the user.
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$sql = "
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SELECT FM.fid, FM.filename, FM.uri, FM.uid, FM.filesize, TGEF.expiration_date
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@@ -11,39 +11,39 @@ function tripal_user_get_files($uid){
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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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+ ORDER BY FM.uri
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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 = $files->fetchObject()) {
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-
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+
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// Don't list files that don't exist on the file system.
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if (!file_exists($file->uri)) {
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continue;
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}
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-
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+
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// Files have to be in the User's directory.
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if (!preg_match('/^public:\/\/tripal\/users\//', $file->uri)) {
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continue;
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}
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-
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+
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// If the expiration date is somehow not set, then set it.
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if (!$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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+
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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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+ $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, $file);
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+ _tripal_user_build_files_dir($directory, $paths, $file);
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}
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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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+ *
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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 $paths
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@@ -62,21 +62,21 @@ function _tripal_user_build_files_dir(&$directory, $paths, $file) {
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}
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}
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-/**
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+/**
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* Generates an item list of the files.
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- *
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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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+ *
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* @param $files_list
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* The array as returned by tripal_user_get_files().
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- *
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- * @return
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+ *
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+ * @return
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* An item list.
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*/
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function tripal_user_get_files_item_list($files_list, &$i = 0) {
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$items = [];
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-
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+
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// Add a header row
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if ($i == 0) {
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$items[] = [
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@@ -85,7 +85,7 @@ function tripal_user_get_files_item_list($files_list, &$i = 0) {
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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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+
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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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@@ -106,8 +106,8 @@ function tripal_user_get_files_item_list($files_list, &$i = 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-details"><span class="file-name">' . $filename . '</span>' .
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- '<span class="file-expires">' . $dayleft . ' days</span>' .
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+ 'data' => '<span class="file-details"><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></span>' ,
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'class' => ['tree-node-file', ($i % 2 == 0) ? 'even' : 'odd'],
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'fid' => $file->fid,
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@@ -115,18 +115,18 @@ function tripal_user_get_files_item_list($files_list, &$i = 0) {
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];
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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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/**
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* Gets the list of collections that have not yet generated files.
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- *
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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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+
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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', $uid)
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@@ -135,21 +135,21 @@ function tripal_user_files_get_pending_collections_table($uid) {
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$headers = array('Name', 'Download Formats', 'Actions');
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$rows = array();
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-
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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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+
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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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+
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$status = 'complete';
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foreach ($formatters as $class_name => $label) {
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$formatter_labels[] = $label;
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-
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+
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$outfile = $collection->getOutfilePath($class_name);
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-
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+
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if (file_exists($outfile)) {
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continue;
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}
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@@ -157,8 +157,8 @@ function tripal_user_files_get_pending_collections_table($uid) {
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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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+
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+ if ($status == 'pending') {
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$rows[] = array(
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'data' => array(
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$collection->getName(),
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@@ -193,9 +193,9 @@ function tripal_user_files_get_pending_collections_table($uid) {
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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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+
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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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+ $items = tripal_user_get_files_item_list($user_files);
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$theme_files = theme_item_list([
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'items' => $items,
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'title' => '',
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@@ -204,7 +204,7 @@ function tripal_user_files_get_pending_collections_table($uid) {
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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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+
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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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@@ -243,7 +243,7 @@ function tripal_user_files_get_pending_collections_table($uid) {
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'#title' => 'Pending Data Collections',
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'#markup' => $data_collections,
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'#description' => t('Data collections allow you to store custom sets of data
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- for use on this site. Typically data collections are created using search
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+ for use on this site. Typically data collections are created using search
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tools. The above data collections are waiting to be generated. You must
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generate the files before you can use them.'),
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),
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@@ -376,8 +376,8 @@ function tripal_delete_file_form_submit($form, &$form_state) {
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function tripal_view_file($uid, $fid) {
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$file = file_load($fid);
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$usage = file_usage_list($file);
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-
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- // Check to see if this is a data collection.
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+
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+ // Check to see if this is a data collection.
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$collection = NULL;
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$collection_ctypes = [];
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$collection_field_list = [];
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@@ -388,23 +388,23 @@ function tripal_view_file($uid, $fid) {
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$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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+
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// Get the content types for this data collection.
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- $cbundles = $collection->getBundles();
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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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+
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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[] = $bundle->label;
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-
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+
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foreach ($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[] = $instance['label'];
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-
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+
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$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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@@ -414,11 +414,11 @@ function tripal_view_file($uid, $fid) {
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}
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// Convert remote field IDs to their names.
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// TODO: add in retrieval of remote details.
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-
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-
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+
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+
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$collection_entities += count($eids);
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}
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-
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+
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}
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}
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@@ -463,7 +463,7 @@ function tripal_view_file($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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$rows[] = array(
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@@ -474,7 +474,7 @@ function tripal_view_file($uid, $fid) {
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),
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file_get_contents($md5_file),
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);
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- }
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+ }
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$rows[] = array(
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array(
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'data' => 'Actions',
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@@ -493,8 +493,8 @@ function tripal_view_file($uid, $fid) {
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'colgroups' => [],
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'empty' => '',
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]);
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-
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-
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+
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+
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$collection_content = '';
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if ($collection) {
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$rows = [];
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@@ -514,7 +514,7 @@ function tripal_view_file($uid, $fid) {
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),
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join(', ', $collection_ctypes),
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);
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-
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+
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$rows[] = array(
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array(
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'data' => 'Fields',
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@@ -547,7 +547,7 @@ function tripal_view_file($uid, $fid) {
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),
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l('Delete', 'user/' . $uid . '/data-collections/' . $collection->getCollectionID() . '/delete')
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);
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-
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+
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$collection_content = '<b>Collection Details</b>' . theme_table([
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'header' => $headers,
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'rows' => $rows,
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@@ -558,7 +558,7 @@ function tripal_view_file($uid, $fid) {
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'empty' => '',
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]);
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}
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-
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+
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drupal_json_output($file_content . $collection_content);
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}
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Lacey-Anne Sanderson