remove temporary upload if count dicom failure, prevent timout script

Pixilib · Jun 6, 2023 · 36f6665 · 36f6665
1 parent 7dfa8d4
commit 36f6665
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Showing 3 changed files with 17 additions and 13 deletions.
diff --git a/GaelO2/app/GaelO/Services/TusService.php b/GaelO2/app/GaelO/Services/TusService.php
@@ -21,7 +21,7 @@ public function __construct(HttpClientInterface $httpClientInterface, FrameworkI
 
     public function getFile(string $tusFileId) : string {
 
-        $downloadedFileName = tempnam(sys_get_temp_dir(), 'TusDicom');
+        $downloadedFileName = tempnam(sys_get_temp_dir(), 'TusDicom_');
 
         $resource  = fopen( $downloadedFileName, 'r+');
 

diff --git a/GaelO2/app/GaelO/UseCases/CreateFileToFormFromTus/CreateFileToFormFromTus.php b/GaelO2/app/GaelO/UseCases/CreateFileToFormFromTus/CreateFileToFormFromTus.php
@@ -79,6 +79,9 @@ public function execute(CreateFileToFormFromTusRequest $createFileToFormFromTusR
 
             $this->checkAuthorization($local, $validated, $reviewId, $visitId, $currentUserId, $studyName);
 
+            //Set Time Limit at 30min as operation could be really long
+            set_time_limit(1800);
+
             $file = null;
 
             //Several file, expected ziped dicom upload, unzip and merge in a single zipe
@@ -110,12 +113,14 @@ public function execute(CreateFileToFormFromTusRequest $createFileToFormFromTusR
 
                 $this->orthancService->setOrthancServer(false);
                 $orthancStudyImport = $this->orthancService->importDicomFolder($unzipedPath);
-                if ($expectedNumberOfInstances !== $orthancStudyImport->getNumberOfInstances()) {
+                $importedNumberOfInstances = $orthancStudyImport->getNumberOfInstances();
+                $importedOrthancStudyID = $orthancStudyImport->getStudyOrthancId();
+
+                if ($expectedNumberOfInstances !== $importedNumberOfInstances) {
+                    $this->orthancService->deleteFromOrthanc("studies", $importedOrthancStudyID);
                     throw new GaelOValidateDicomException("Imported DICOM not matching announced number of Instances");
                 }
 
-                $importedOrthancStudyID = $orthancStudyImport->getStudyOrthancId();
-
                 $tempFileLocation = tempnam(ini_get('upload_tmp_dir'), 'TMPZIP_');
                 $this->orthancService->getZipStreamToFile([$importedOrthancStudyID], $tempFileLocation);
                 $file = $tempFileLocation;
@@ -124,8 +129,7 @@ public function execute(CreateFileToFormFromTusRequest $createFileToFormFromTusR
                 if (sizeof($tusIds) === 1) {
                     $file = $this->tusService->getFile($tusIds[0]);
                     $this->tusService->deleteFile($tusIds[0]);
-                }
-                else throw new GaelOBadRequestException("A single TUS Id is expected for non-DICOM upload");
+                } else throw new GaelOBadRequestException("A single TUS Id is expected for non-DICOM upload");
             }
 
             //Send file to associated file

diff --git a/GaelO2/app/GaelO/UseCases/ValidateDicomUpload/ValidateDicomUpload.php b/GaelO2/app/GaelO/UseCases/ValidateDicomUpload/ValidateDicomUpload.php
@@ -56,10 +56,6 @@ public function execute(ValidateDicomUploadRequest $validateDicomUploadRequest,
     {
 
         try {
-
-            //Set Time Limit at 30min as operation could be really long
-            set_time_limit(1800);
-
             //Retrieve Visit Context
             $this->visitService->setVisitId($validateDicomUploadRequest->visitId);
             $visitContext = $this->visitService->getVisitContext();
@@ -81,6 +77,8 @@ public function execute(ValidateDicomUploadRequest $validateDicomUploadRequest,
             //Make Visit as being upload processing
             $this->visitService->updateUploadStatus(UploadStatusEnum::PROCESSING->value);
 
+            //Set Time Limit at 30min as operation could be really long
+            set_time_limit(1800);
             //Create Temporary folder to work
             $unzipedPath = Util::getUploadTemporaryFolder();
 
@@ -106,11 +104,13 @@ public function execute(ValidateDicomUploadRequest $validateDicomUploadRequest,
             $this->orthancService->setOrthancServer(false);
 
             $orthancStudyImport = $this->orthancService->importDicomFolder($unzipedPath);
-            if ($expectedNumberOfInstances !== $orthancStudyImport->getNumberOfInstances()) {
-                throw new GaelOValidateDicomException("Imported DICOM not matching announced number of Instances");
-            }
+            $importedNumberOfInstances = $orthancStudyImport->getNumberOfInstances();
             $importedOrthancStudyID = $orthancStudyImport->getStudyOrthancId();
 
+            if ($expectedNumberOfInstances !== $importedNumberOfInstances) {
+                $this->orthancService->deleteFromOrthanc("studies", $importedOrthancStudyID);
+                throw new GaelOValidateDicomException("Imported DICOM not matching announced number of Instances");
+            }
 
             //Anonymize and store new anonymized study Orthanc ID
             $anonymizedOrthancStudyID = $this->orthancService->anonymize(