Merge pull request #9013 from driusan/Pushv2416Tov25

Push v24.1.6 changes into 25 branch

Author: driusan

SQL/New_patches/2023-04-25-FixIssueWrongModuleID.sql

@@ -0,0 +1,8 @@
+-- NOTE: This SQL patch follows up the running of single use tool `tools/single_use/Convert_LorisMenuID_to_ModuleID.php`
+-- that was necessary to upgrade the `issues` table from LORIS version 22 to version 23. The tool forgot
+-- to include an upgrade of the `issues_history` table, which is now tackled by this SQL patch.
+
+-- delete from issues_history any orphaned module IDs
+DELETE FROM issues_history WHERE fieldChanged='module' AND issueID IN (SELECT issueID FROM issues WHERE module IS NULL);
+-- set issues history module ID to correct moduleID, replacing old LorisMenu ID
+UPDATE issues_history ih SET newValue=(SELECT i.module FROM issues i WHERE i.issueID=ih.issueID) WHERE fieldChanged='module';

modules/behavioural_qc/jsx/tabs_content/behaviouralFeedback.js

@@ -107,23 +107,32 @@ class BehaviouralFeedback extends Component {
         );
         break;
       case 'Feedback Level':
-        rowData['Instrument'] ? reactElement = (
+        let bvlLink = '';
+        let bvlLevel = '';
+        if (rowData['Instrument']) {
+          bvlLink = this.props.baseURL +
+                     '/instruments/' +
+                     rowData['Test Name'] +
+                     '/?candID=' +
+                     rowData['DCCID'] +
+                     '&sessionID=' +
+                     rowData['sessionID'] +
+                     '&commentID=' +
+                     rowData['commentID'];
+          bvlLevel ='Instrument : ' + rowData['Instrument'];
+        } else if (rowData['Visit']) {
+          bvlLink = this.props.baseURL +
+                     '/instrument_list/' +
+                     '?candID=' +
+                     rowData['DCCID'] +
+                     '&sessionID=' +
+                     rowData['sessionID'];
+          bvlLevel ='Visit : ' + rowData['Visit'];
+        }
+        reactElement = (
           <td>
-            <a href={this.props.baseURL +
-              '/instruments/' +
-              rowData['Test Name'] +
-              '/?candID=' +
-              rowData['DCCID'] +
-              '&sessionID=' +
-              rowData['sessionID'] +
-              '&commentID=' +
-              rowData['commentID']
-              }>
-                {'Instrument : ' + rowData['Instrument']}
-            </a>
+            <a href={bvlLink}>{bvlLevel}</a>
           </td>
-        ) : reactElement = (
-          <td>{''}</td>
         );
         break;
       default:

modules/genomic_browser/jsx/tabs_content/files.js

@@ -34,6 +34,7 @@ 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);
@@ -149,9 +150,16 @@ 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 'Cohort':
         reactElement = <td>{this.state.data.cohorts[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;

modules/issue_tracker/jsx/IssueForm.js

@@ -26,7 +26,7 @@ class IssueForm extends Component {
     super(props);
 
     this.state = {
-      Data: [],
+      Data: {},
       formData: {},
       submissionResult: null,
       errorMessage: null,