on demand tar file download

Author: MaximeBICMTL

modules/api/php/endpoints/candidate/visit/electrophysiology/recording.class.inc

@@ -170,12 +170,9 @@ class Recording extends Endpoint implements \LORIS\Middleware\ETagCalculator
             return new \LORIS\Http\Response\JSON\NotFound($e->getMessage());
         }
 
-        $mimetype = substr($recording->getMetadata('header'), 0, 4) === 'hdf5' ?
-            'application/x.minc2' : 'application/octet-stream';
-
         $info = $recording->getFileInfo();
 
-        if (!$info->isFile()) {
+        if (!$info->isFile() && !$info->isDir()) {
             error_log('file in database but not in file system');
             return new \LORIS\Http\Response\JSON\NotFound();
         }
@@ -185,13 +182,45 @@ class Recording extends Endpoint implements \LORIS\Middleware\ETagCalculator
             return new \LORIS\Http\Response\JSON\NotFound();
         }
 
-        $body = new \LORIS\Http\FileStream($info->getRealPath(), 'r');
+        // Tar the acquisition file if it is actually a directory (such as for MEG
+        // CTF acquisitions).
+        if ($info->isDir()) {
+            $filename = $this->_filename . '.tar';
+            $mimetype = 'application/x-tar';
+
+            $tarfile = sys_get_temp_dir() . '/recording_' . uniqid() . '.tar';
+
+            try {
+                $phar = new \PharData($tarfile);
+                $phar->buildFromDirectory($info->getRealPath());
+            } catch (\Exception $e) {
+                $this->logger->error(
+                    'Failed to create tar archive: ' . $e->getMessage()
+                );
+
+                if (file_exists($tarfile)) {
+                    unlink($tarfile);
+                }
+
+                return new \LORIS\Http\Response\JSON\InternalServerError();
+            }
+
+            $filepath = $tarfile;
+        } else {
+            $filename = $this->_filename;
+            $filepath = $info->getRealPath();
+            $mimetype = substr($recording->getMetadata('header'), 0, 4) === 'hdf5'
+                ? 'application/x.minc2'
+                : 'application/octet-stream';
+        }
+
+        $body = new \LORIS\Http\FileStream($filepath, 'r', true);
 
         return (new \LORIS\Http\Response())
             ->withHeader('Content-Type', $mimetype)
             ->withHeader(
                 'Content-Disposition',
-                'attachment; filename=' . $this->_filename
+                'attachment; filename=' . $filename
             )
             ->withBody($body);
     }

modules/electrophysiology_browser/jsx/components/DownloadPanel.js

@@ -33,7 +33,7 @@ class DownloadPanel extends Component {
    * @return {JSX} - React markup for the component
    */
   render() {
-    const {t} = this.props;
+    const {t, dccid, visit, physioFileName} = this.props;
     return (
       <Panel
         id={this.props.id}
@@ -59,6 +59,24 @@ class DownloadPanel extends Component {
                 {Object.entries(panel.links).map(([type, download], j) => {
                   const disabled = (download.file === '');
 
+                  let recordingFileUrl = `/api/v0.0.3/candidates/${dccid}/`
+                    + `${visit}/recordings/${physioFileName}`;
+
+                  switch (type) {
+                  case 'physiological_event_files':
+                    recordingFileUrl += '/bidsfiles/events';
+                    break;
+                  case 'all_files':
+                    recordingFileUrl += '/bidsfiles/archive';
+                    break;
+                  case 'physiological_channel_file':
+                    recordingFileUrl += '/bidsfiles/channels';
+                    break;
+                  case 'physiological_electrode_file':
+                    recordingFileUrl += '/bidsfiles/electrodes';
+                    break;
+                  }
+
                   // Ignore physiological_coord_system_file
                   return type !== 'physiological_coord_system_file'
                     ? (
@@ -93,13 +111,13 @@ class DownloadPanel extends Component {
                           : <a
                             className='btn btn-primary download col-xs-6'
                             href={
-                              (type ==
-                                'physiological_event_files' ||
-                                type == 'all_files') ?
-                                this.state.annotationsAction
-                                + '?physioFileID=' + this.state.physioFileID
-                                + '&filePath=' + download.file
-                                : '/mri/jiv/get_file.php?file=' + download.file
+                              (type == 'physiological_event_files')
+                                ? (
+                                  this.state.annotationsAction
+                                  + '?physioFileID=' + this.state.physioFileID
+                                  + '&filePath=' + download.file
+                                )
+                                : recordingFileUrl
                             }
                             target='_blank'
                             style={{
@@ -141,7 +159,10 @@ class DownloadPanel extends Component {
 
 DownloadPanel.propTypes = {
   downloads: PropTypes.array,
+  dccid: PropTypes.string,
+  visit: PropTypes.string,
   physioFileID: PropTypes.number,
+  physioFileName: PropTypes.string,
   outputType: PropTypes.string,
   id: PropTypes.string,
   t: PropTypes.func,

modules/electrophysiology_browser/jsx/electrophysiologySessionView.js

@@ -504,7 +504,10 @@ class ElectrophysiologySessionView extends Component {
                       <DownloadPanel
                         id={'file_download_' + i}
                         downloads={this.state.database[i].file.downloads}
+                        dccid={this.state.patient.info.dccid}
+                        visit={this.state.patient.info.visit_label}
                         physioFileID={this.state.database[i].file.id}
+                        physioFileName={this.state.database[i].file.name}
                         outputType={this.state.database[i].file.output_type}
                         t={t}
                       />

src/Http/FileStream.php

@@ -27,4 +27,38 @@
  */
 class FileStream extends \Laminas\Diactoros\Stream implements \Psr\Http\Message\StreamInterface
 {
+    /**
+     * @var bool Whether the file be deleted when the stream is closed, used for
+     *           temporary files.
+     */
+    private bool $deleteOnClose;
+
+    /**
+     * Constructor
+     *
+     * @param string $stream        The path to the file or a stream resource
+     * @param string $mode          The mode to open the stream with
+     * @param bool   $deleteOnClose If true, delete the file when the stream is closed
+     */
+    public function __construct(
+        string $stream,
+        string $mode = 'r',
+        bool $deleteOnClose = false,
+    ) {
+        parent::__construct($stream, $mode);
+        $this->deleteOnClose = $deleteOnClose;
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    public function close(): void
+    {
+        if ($this->deleteOnClose
+            && is_string($this->resource)
+            && file_exists($this->resource)
+        ) {
+            unlink($this->resource);
+        }
+    }
 }