[imaging browser] Fix download of JSON, Bval and Bvec files when they are on s3

modules/api/php/endpoints/candidate/visit/image/format.class.inc

@@ -90,7 +90,12 @@ 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':
+            error_log(print_r($format, true));
+            $handler = new Format\DownloadFile($this->_image, $format);
             break;
         default:
             return new \LORIS\Http\Response\JSON\UnsupportedMediaType();

modules/api/php/endpoints/candidate/visit/image/format/thumbnail.class.inc → modules/api/php/endpoints/candidate/visit/image/format/downloadfile.class.inc

@@ -23,7 +23,7 @@ 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
 {
 
     /**
@@ -32,15 +32,17 @@ class Thumbnail extends Endpoint implements \LORIS\Middleware\ETagCalculator
      * @var \LORIS\Image
      */
     private $_image;
+    private $_format;
 
     /**
      * Contructor
      *
      * @param \LORIS\Image $image The requested image
      */
-    public function __construct(\LORIS\Image $image)
+    public function __construct(\LORIS\Image $image, string $format)
     {
         $this->_image = $image;
+        $this->_format = $format;
     }
 
     /**
@@ -100,20 +102,47 @@ class Thumbnail extends Endpoint implements \LORIS\Middleware\ETagCalculator
      */
     private function _handleGET(): ResponseInterface
     {
-        $info = $this->_image->getThumbnailFileInfo();
+        switch ($this->_format) {
+            case 'thumbnail':
+                $info         = $this->_image->getThumbnailFileInfo();
+                $file_type    = "Thumbnail";
+                $content_type = 'image/jpeg';
+                break;
+            case 'nifti':
+                $info         = $this->_image->getNiiFileInfo();
+                $file_type    = "NIfTI";
+                $content_type = 'application/octet-stream';
+                break;
+            case 'bval':
+                $info         = $this->_image->getBvalFileInfo();
+                $file_type    = "NIfTI BVAL";
+                $content_type = 'application/text';
+                break;
+            case 'bvec':
+                $info         = $this->_image->getBvecFileInfo();
+                $file_type    = "NIfTI BVEC";
+                $content_type = 'application/text';
+                break;
+            case 'bidsjson':
+                $info = $this->_image->getBidsJsonFileInfo();
+                $file_type    = "BIDS JSON";
+                $content_type = 'application/json';
+                break;
+            default:
+                return new \LORIS\Http\Response\JSON\UnsupportedMediaType();
+        }
 
         if (!$info->isFile()) {
-            error_log('Thumbnail not found');
+            error_log("$file_type file not found");
             return new \LORIS\Http\Response\JSON\NotFound();
         }
 
         if (!$info->isReadable()) {
-            error_log('Thumbnail exists but is not readable by webserver');
+            error_log("$file_type file exists but is not readable by webserver");
             return new \LORIS\Http\Response\JSON\NotFound();
         }
 
         $filename = $info->getFilename();
-
         $realpath = $info->getRealPath();
         if ($realpath === false) {
             $realpath = $info->getPath() . "/" . $info->getFilename();
@@ -125,7 +154,7 @@ class Thumbnail extends Endpoint implements \LORIS\Middleware\ETagCalculator
             $body,
             200,
             [
-                'Content-Type'        => 'image/jpeg',
+                'Content-Type'        => $content_type,
                 'Content-Disposition' => 'attachment; filename=' . $filename,
             ]
         );
@@ -140,7 +169,25 @@ class Thumbnail extends Endpoint implements \LORIS\Middleware\ETagCalculator
      */
     public function ETag(ServerRequestInterface $request) : string
     {
-        $info = $this->_image->getThumbnailFileInfo();
+        switch ($this->_format) {
+            case 'thumbnail':
+                $info = $this->_image->getThumbnailFileInfo();
+                break;
+            case 'nifti':
+                $info = $this->_image->getNiiFileInfo();
+                break;
+            case 'bval':
+                $info = $this->_image->getBvalFileInfo();
+                break;
+            case 'bvec':
+                $info = $this->_image->getBvecFileInfo();
+                break;
+            case 'bidsjson':
+                $info = $this->_image->getBidsJsonFileInfo();
+                break;
+            default:
+                return '';
+        }
 
         if (!$info->isFile() || !$info->isReadable()) {
             return '';

modules/imaging_browser/jsx/ImagePanel.js

@@ -671,6 +671,7 @@ DownloadButton.propTypes = {
   FileName: PropTypes.string,
   BaseURL: PropTypes.string,
   Label: PropTypes.string,
+  URL: PropTypes.string,
 };
 
 
@@ -826,22 +827,30 @@ 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}

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;
         }
     }

php/libraries/Image.class.inc

@@ -38,6 +38,15 @@ class Image
     private \CenterID $_centerid;
 
     private $_entitytype;
+
+    private $_check_nii_filename;
+
+    private $_check_bval_filename;
+
+    private $_check_bvec_filename;
+
+    private $_bids_json_filename;
+
     /**
      * Constructor
      *
@@ -58,7 +67,7 @@ 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 +89,10 @@ class Image
             $this->_filetype            = $dbrow['filetype'];
             $this->_centerid            = new \CenterID($dbrow['centerid']);
             $this->_entitytype          = $dbrow['entitytype'];
-
+            $this->_check_nii_filename  = $this->getHeader('check_nii_filename');
+            $this->_check_bval_filename = $this->getHeader('check_bval_filename');
+            $this->_check_bvec_filename = $this->getHeader('check_bvec_filename');
+            $this->_bids_json_filename  = $this->getHeader('bids_json_file');
         }
     }
 
@@ -100,7 +112,7 @@ class Image
                        SELECT
                          Value
                        FROM
-                         parameter_file pf 
+                         parameter_file pf
                        JOIN parameter_type pt
                          USING (ParameterTypeID)
                        JOIN files f
@@ -132,7 +144,7 @@ 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 +265,46 @@ 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->_check_nii_filename);
+    }
+
+    /**
+     * Return a SPLFileInfo object based on this images's properties.
+     *
+     * @return \SplFileInfo
+     */
+    public function getBvalFileInfo(): \SplFileInfo
+    {
+        return $this->_getFullPath($this->_check_bval_filename);
+    }
+
+    /**
+     * Return a SPLFileInfo object based on this images's properties.
+     *
+     * @return \SplFileInfo
+     */
+    public function getBvecFileInfo(): \SplFileInfo
+    {
+        return $this->_getFullPath($this->_check_bvec_filename);
+    }
+
+    /**
+     * Return a SPLFileInfo object based on this images's properties.
+     *
+     * @return \SplFileInfo
+     */
+    public function getBidsJsonFileInfo(): \SplFileInfo
+    {
+        return $this->_getFullPath($this->_bids_json_filename);
+    }
+
     /**
      * Return a SPLFileInfo object based on this images's thumbnail properties.
      *
@@ -306,7 +358,11 @@ class Image
             $this->_acquisitionprotocol,
             $this->_filetype,
             $this->_centerid,
-            $this->_entitytype
+            $this->_entitytype,
+            $this->_check_nii_filename,
+            $this->_check_bval_filename,
+            $this->_check_bvec_filename,
+            $this->_bids_json_filename
         );
     }
 }