[genomic_browser] Download button not showing up in the Files tab (#…

…8480) Made the name column a link for downloading. Note: This module needs refactoring of the upload and download logic to be more robust. Resolves #7594
aces · Dec 12, 2023 · 18707d1 · 18707d1
1 parent 5b7ddb2
commit 18707d1
Show file tree

Hide file tree

Showing 3 changed files with 41 additions and 4 deletions.
diff --git a/modules/genomic_browser/jsx/tabs_content/files.js b/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>;

diff --git a/modules/genomic_browser/php/filemanager.class.inc b/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');
 

diff --git a/modules/genomic_browser/php/uploading/genomicfile.class.inc b/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;