update

update

Revert "update"

This reverts commit 6d56db9.

Revert "update"

This reverts commit 3f8274d.

update

remove additional directory for file storage

remove additional directory for file storage

update

update

Update files.js

Author: maltheism

modules/genomic_browser/jsx/tabs_content/files.js

@@ -35,6 +35,7 @@ class Files extends Component {
       },
     };
     this.fetchData = this.fetchData.bind(this);
+    this.formatColumn = this.formatColumn.bind(this);
     this.openFileUploadModal = this.openFileUploadModal.bind(this);
     this.closeFileUploadModal = this.closeFileUploadModal.bind(this);
     this.renderFileUploadForm = this.renderFileUploadForm.bind(this);
@@ -151,9 +152,16 @@ class Files extends Component {
   formatColumn(column, cell, rowData, rowHeaders) {
     let reactElement;
     switch (column) {
+      case 'Name':
+        const fileName = rowData.Name.split('/').pop();
+        const url =
+          `${this.props.baseURL
+        }/genomic_browser/FileManager?filename=${fileName}`;
+        reactElement = <td><a href={url}>{fileName}</a></td>;
+        break;
       case 'PSCID':
-        const url = `${this.props.baseURL}/${rowData.DCCID}/`;
-        reactElement = <td><a href={url}>{rowData.PSCID}</a></td>;
+        const urlPscid = `${this.props.baseURL}/${rowData.DCCID}/`;
+        reactElement = <td><a href={urlPscid}>{rowData.PSCID}</a></td>;
         break;
       case 'Subproject':
         reactElement = <td>{this.state.data.subprojects[parseInt(cell)]}</td>;

modules/genomic_browser/php/filemanager.class.inc

@@ -54,6 +54,33 @@ class FileManager extends \NDB_Page implements ETagCalculator
      */
     private function _handleGET(ServerRequestInterface $request) : ResponseInterface
     {
+        // Parse GET query params.
+        $values = $request->getQueryParams();
+        // GET request for downloading file by ID.
+        if ($values['filename']) {
+            $factory  = \NDB_Factory::singleton();
+            $config   = $factory->config();
+            $filesDir = \Utility::appendForwardSlash(
+                $config->getSetting('GenomicDataPath')
+            );
+            try {
+                $downloadhandler = new \LORIS\FilesDownloadHandler(
+                    new \SplFileInfo($filesDir)
+                );
+                $request         = $request->withAttribute(
+                    'filename',
+                    $values['filename']
+                );
+                return $downloadhandler->handle($request);
+            } catch (\LorisException $e) {
+                // FilesUploadHandler throws an exception if there's a problem with
+                // the downloaddir.
+                return new \LORIS\Http\Response\JSON\InternalServerError(
+                    $e->getMessage()
+                );
+            }
+        }
+
         $provisioner = new FilesProvisioner();
         $user        = $request->getAttribute('user');
 

modules/genomic_browser/php/uploading/genomicfile.class.inc

@@ -468,8 +468,10 @@ class Genomicfile
     function setFullPath(&$fileToUpload) : void
     {
         $config           = \NDB_Config::singleton();
-        $genomic_data_dir = rtrim($config->getSetting('GenomicDataPath'), '/')
-            . '/genomic_uploader/';
+        $genomic_data_dir = rtrim(
+            $config->getSetting('GenomicDataPath'),
+            '/'
+        ) . '/';
 
         $fileToUpload->full_path = $genomic_data_dir
             . $fileToUpload->file_name;