[imaging browser] Fix download of JSON, Bval and Bvec files when they…

… are on s3 (aces#8354) This fixes the error 404 users had when they tried to download a JSON, Bval or Bvec file hosted on S3 from the imaging browser. Fixing this bug also resolved aces/HBCD#227 as new API endpoints needed to be created for those files.
zaliqarosli · Mar 6, 2023 · 056b314 · 056b314
1 parent 595ccfc
commit 056b314
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Showing 6 changed files with 135 additions and 48 deletions.
diff --git a/modules/api/php/endpoints/candidate/visit/image/format.class.inc b/modules/api/php/endpoints/candidate/visit/image/format.class.inc
@@ -90,7 +90,11 @@ class Format extends Endpoint
             $handler = new Format\Brainbrowser($this->_image);
             break;
         case 'thumbnail':
-            $handler = new Format\Thumbnail($this->_image);
+        case 'nifti':
+        case 'bval':
+        case 'bvec':
+        case 'bidsjson':
+            $handler = new Format\DownloadFile($this->_image, $format);
             break;
         default:
             return new \LORIS\Http\Response\JSON\UnsupportedMediaType();

diff --git a/...te/visit/image/format/thumbnail.class.inc → ...visit/image/format/downloadfile.class.inc b/...te/visit/image/format/thumbnail.class.inc → ...visit/image/format/downloadfile.class.inc
@@ -23,24 +23,50 @@ use \LORIS\api\Endpoint;
  * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
  * @link     https://github.com/aces/Loris
  */
-class Thumbnail extends Endpoint implements \LORIS\Middleware\ETagCalculator
+class DownloadFile extends Endpoint implements \LORIS\Middleware\ETagCalculator
 {
-
-    /**
-     * The requested Image
-     *
-     * @var \LORIS\Image
-     */
-    private $_image;
+    private $_format;
+    private $_info;
+    private $_file_type;
+    private $_content_type;
 
     /**
      * Contructor
      *
-     * @param \LORIS\Image $image The requested image
+     * @param \LORIS\Image $image  The requested image
+     * @param string       $format The format user wishes to download
      */
-    public function __construct(\LORIS\Image $image)
+    public function __construct(\LORIS\Image $image, string $format)
     {
-        $this->_image = $image;
+        $this->_format = $format;
+
+        switch ($this->_format) {
+        case 'thumbnail':
+            $this->_info         = $image->getThumbnailFileInfo();
+            $this->_file_type    = "Thumbnail";
+            $this->_content_type = 'image/jpeg';
+            break;
+        case 'nifti':
+            $this->_info         = $image->getNiiFileInfo();
+            $this->_file_type    = "NIfTI";
+            $this->_content_type = 'application/octet-stream';
+            break;
+        case 'bval':
+            $this->_info         = $image->getBvalFileInfo();
+            $this->_file_type    = "NIfTI BVAL";
+            $this->_content_type = 'application/text';
+            break;
+        case 'bvec':
+            $this->_info         = $image->getBvecFileInfo();
+            $this->_file_type    = "NIfTI BVEC";
+            $this->_content_type = 'application/text';
+            break;
+        case 'bidsjson':
+            $this->_info         = $image->getBidsJsonFileInfo();
+            $this->_file_type    = "BIDS JSON";
+            $this->_content_type = 'application/json';
+            break;
+        }
     }
 
     /**
@@ -100,23 +126,22 @@ class Thumbnail extends Endpoint implements \LORIS\Middleware\ETagCalculator
      */
     private function _handleGET(): ResponseInterface
     {
-        $info = $this->_image->getThumbnailFileInfo();
-
-        if (!$info->isFile()) {
-            error_log('Thumbnail not found');
+        if (!$this->_info->isFile()) {
+            $this->logger->error("$this->_file_type file not found");
             return new \LORIS\Http\Response\JSON\NotFound();
         }
 
-        if (!$info->isReadable()) {
-            error_log('Thumbnail exists but is not readable by webserver');
+        if (!$this->_info->isReadable()) {
+            $this->logger->error(
+                "$this->_file_type file exists but is not readable by webserver"
+            );
             return new \LORIS\Http\Response\JSON\NotFound();
         }
 
-        $filename = $info->getFilename();
-
-        $realpath = $info->getRealPath();
+        $filename = $this->_info->getFilename();
+        $realpath = $this->_info->getRealPath();
         if ($realpath === false) {
-            $realpath = $info->getPath() . "/" . $info->getFilename();
+            $realpath = $this->_info->getPath() . "/" . $this->_info->getFilename();
         }
 
         $body = new \LORIS\Http\FileStream($realpath, 'r');
@@ -125,7 +150,7 @@ class Thumbnail extends Endpoint implements \LORIS\Middleware\ETagCalculator
             $body,
             200,
             [
-                'Content-Type'        => 'image/jpeg',
+                'Content-Type'        => $this->_content_type,
                 'Content-Disposition' => 'attachment; filename=' . $filename,
             ]
         );
@@ -140,16 +165,15 @@ class Thumbnail extends Endpoint implements \LORIS\Middleware\ETagCalculator
      */
     public function ETag(ServerRequestInterface $request) : string
     {
-        $info = $this->_image->getThumbnailFileInfo();
 
-        if (!$info->isFile() || !$info->isReadable()) {
+        if (!$this->_info->isFile() || !$this->_info->isReadable()) {
             return '';
         }
 
         $signature = [
-            'filename' => $info->getFilename(),
-            'size'     => $info->getSize(),
-            'mtime'    => $info->getMTime(),
+            'filename' => $this->_info->getFilename(),
+            'size'     => $this->_info->getSize(),
+            'mtime'    => $this->_info->getMTime(),
         ];
 
         return md5(json_encode($signature));

diff --git a/modules/imaging_browser/jsx/ImagePanel.js b/modules/imaging_browser/jsx/ImagePanel.js
@@ -671,6 +671,7 @@ DownloadButton.propTypes = {
   FileName: PropTypes.string,
   BaseURL: PropTypes.string,
   Label: PropTypes.string,
+  URL: PropTypes.string,
 };
 
 
@@ -828,22 +829,30 @@ class ImageDownloadButtons extends Component {
                         BaseURL={this.props.BaseURL}
                         Label="Download NRRD"
         />
-        <DownloadButton FileName={this.props.NiiFile}
-                        BaseURL={this.props.BaseURL}
-                        Label="Download NIfTI"
-        />
-        <DownloadButton FileName={this.props.BvalFile}
-                        BaseURL={this.props.BaseURL}
-                        Label="Download BVAL"
-        />
-        <DownloadButton FileName={this.props.BvecFile}
-                        BaseURL={this.props.BaseURL}
-                        Label="Download BVEC"
-        />
-        <DownloadButton FileName={this.props.JsonFile}
-                        BaseURL={this.props.BaseURL}
-                        Label="Download BIDS JSON"
-        />
+        { this.props.NiiFile ?
+          <DownloadButton URL={this.props.APIFile + '/format/nifti'}
+                          Label="Download NIfTI"
+          /> :
+          null
+        }
+        {this.props.BvalFile ?
+          <DownloadButton URL={this.props.APIFile + '/format/bval'}
+                          Label="Download BVAL"
+          /> :
+          null
+        }
+        {this.props.BvecFile ?
+          <DownloadButton URL={this.props.APIFile + '/format/bvec'}
+                          Label="Download BVEC"
+          /> :
+          null
+        }
+        {this.props.JsonFile ?
+          <DownloadButton URL={this.props.APIFile + '/format/bidsjson'}
+                          Label="Download BIDS JSON"
+          /> :
+          null
+        }
         <LongitudinalViewButton FileID={this.props.FileID}
                                 BaseURL={this.props.BaseURL}
                                 OtherTimepoints={this.props.OtherTimepoints}

diff --git a/modules/imaging_browser/php/viewsession.class.inc b/modules/imaging_browser/php/viewsession.class.inc
@@ -369,6 +369,7 @@ class ViewSession extends \NDB_Form
                 'OtherTimepoints'            => $OtherTimepoints,
                 'CaveatViolationsResolvedID' => $caveatViolationsResolvedID,
             ];
+
             $this->tpl_data['files'][] = $file;
         }
     }

diff --git a/php/libraries/Image.class.inc b/php/libraries/Image.class.inc
@@ -38,6 +38,7 @@ class Image
     private \CenterID $_centerid;
 
     private $_entitytype;
+
     /**
      * Constructor
      *
@@ -58,7 +59,7 @@ class Image
                        s.CenterID as centerid,
                        c.Entity_type as entitytype
                      FROM
-                       files f 
+                       files f
                      LEFT JOIN session s
                        ON (f.SessionID = s.ID)
                      LEFT JOIN candidate c
@@ -80,7 +81,6 @@ class Image
             $this->_filetype            = $dbrow['filetype'];
             $this->_centerid            = new \CenterID($dbrow['centerid']);
             $this->_entitytype          = $dbrow['entitytype'];
-
         }
     }
 
@@ -100,7 +100,7 @@ class Image
                        SELECT
                          Value
                        FROM
-                         parameter_file pf 
+                         parameter_file pf
                        JOIN parameter_type pt
                          USING (ParameterTypeID)
                        JOIN files f
@@ -132,7 +132,7 @@ class Image
                          pt.Name as name,
                          pf.Value as value
                        FROM
-                         parameter_file pf 
+                         parameter_file pf
                        JOIN parameter_type pt
                          USING (ParameterTypeID)
                        JOIN files f
@@ -253,6 +253,46 @@ class Image
         return $this->_getFullPath($this->_filelocation);
     }
 
+    /**
+     * Return a SPLFileInfo object based on this images's properties.
+     *
+     * @return \SplFileInfo
+     */
+    public function getNiiFileInfo(): \SplFileInfo
+    {
+        return $this->_getFullPath($this->getHeader('check_nii_filename'));
+    }
+
+    /**
+     * Return a SPLFileInfo object based on this images's properties.
+     *
+     * @return \SplFileInfo
+     */
+    public function getBvalFileInfo(): \SplFileInfo
+    {
+        return $this->_getFullPath($this->getHeader('check_bval_filename'));
+    }
+
+    /**
+     * Return a SPLFileInfo object based on this images's properties.
+     *
+     * @return \SplFileInfo
+     */
+    public function getBvecFileInfo(): \SplFileInfo
+    {
+        return $this->_getFullPath($this->getHeader('check_bvec_filename'));
+    }
+
+    /**
+     * Return a SPLFileInfo object based on this images's properties.
+     *
+     * @return \SplFileInfo
+     */
+    public function getBidsJsonFileInfo(): \SplFileInfo
+    {
+        return $this->_getFullPath($this->getHeader('bids_json_file'));
+    }
+
     /**
      * Return a SPLFileInfo object based on this images's thumbnail properties.
      *

diff --git a/src/Http/Endpoint.php b/src/Http/Endpoint.php
@@ -28,6 +28,8 @@
  */
 abstract class Endpoint implements RequestHandlerInterface
 {
+    use \PSR\Log\LoggerAwareTrait;
+
     /**
      * An Endpoint overrides the default LORIS middleware to remove the
      * PageDecorationMiddleware.
@@ -41,6 +43,13 @@ public function process(
         ServerRequestInterface $request,
         RequestHandlerInterface $handler
     ): ResponseInterface {
+        $loris    = $request->getAttribute('loris');
+        $loglevel = $loris->getConfiguration()
+            ->getLogSettings()
+            ->getRequestLogLevel();
+
+        $this->logger = new \LORIS\Log\ErrorLogLogger($loglevel);
+
         $interfaces = class_implements($handler);
         if (in_array('LORIS\Middleware\ETagCalculator', $interfaces)) {
             return (new \LORIS\Middleware\ETag())->process($request, $handler);