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
aces · Mar 24, 2023 · bb76c32 · bb76c32
1 parent 488bec8
commit bb76c32
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 url_pscid = `${this.props.baseURL}/${rowData.DCCID}/`;
+        reactElement = <td><a href={url_pscid}>{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;