Merge branch 'Gaelo2' into GaelO2-dev

Pixilib · Jun 6, 2023 · c674f03 · c674f03
2 parents 92bbc19 + 4e0cc21
commit c674f03
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Showing 6 changed files with 29 additions and 16 deletions.
diff --git a/GaelO2/app/GaelO/Adapters/HttpClientAdapter.php b/GaelO2/app/GaelO/Adapters/HttpClientAdapter.php
@@ -123,7 +123,7 @@ public function requestStreamResponseToFile(string $method, string $uri, $ressou
         return new Psr7ResponseAdapter($response);
     }
 
-    public function rowRequest(string $method, string $uri, $body, ?array $headers, $ressourceDestination = null): Psr7ResponseInterface
+    public function rowRequest(string $method, string $uri, $body, ?array $headers, $ressourceDestination = null, $httpErrors = true): Psr7ResponseInterface
     {
         $options = [];
 
@@ -147,6 +147,10 @@ public function rowRequest(string $method, string $uri, $body, ?array $headers,
             $options['sink'] = $ressourceDestination;
         }
 
+        if(!$httpErrors){
+            $options['http_errors'] = false;
+        }
+
         $response = $this->client->request($method, $this->address . $uri, $options);
         return new Psr7ResponseAdapter($response);
     }

diff --git a/GaelO2/app/GaelO/Interfaces/Adapters/HttpClientInterface.php b/GaelO2/app/GaelO/Interfaces/Adapters/HttpClientInterface.php
@@ -13,7 +13,7 @@ public function setAuthorizationToken(string $authorizationToken): void;
 
     public function setBasicAuthentication(string $login, string $password): void;
 
-    public function rowRequest(string $method, string $uri, $body, ?array $headers): Psr7ResponseInterface;
+    public function rowRequest(string $method, string $uri, $body, ?array $headers, $ressourceDestination = null, $httpErrors = true): Psr7ResponseInterface;
 
     /**
      * Return array of PSR7 response adapter of multiple request, used to sent multiple files to an endpoint

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/ReverseProxyTus/ReverseProxyTus.php b/GaelO2/app/GaelO/UseCases/ReverseProxyTus/ReverseProxyTus.php
@@ -35,7 +35,7 @@ public function execute(ReverseProxyTusRequest $reverseProxyTusRequest, ReverseP
 
         //Make query of TUS
         $this->httpClientInterface->setUrl($this->frameworkInterface::getConfig(SettingsConstants::TUS_URL));
-        $response = $this->httpClientInterface->rowRequest($reverseProxyTusRequest->method, $reverseProxyTusRequest->url, $reverseProxyTusRequest->body, $headers);
+        $response = $this->httpClientInterface->rowRequest($reverseProxyTusRequest->method, $reverseProxyTusRequest->url, $reverseProxyTusRequest->body, $headers, null, false);
 
         //Output response
         $reverseProxyTusResponse->status = $response->getStatusCode();

diff --git a/GaelO2/app/GaelO/UseCases/ValidateDicomUpload/ValidateDicomUpload.php b/GaelO2/app/GaelO/UseCases/ValidateDicomUpload/ValidateDicomUpload.php
@@ -69,11 +69,16 @@ public function execute(ValidateDicomUploadRequest $validateDicomUploadRequest,
             $currentUserId = $validateDicomUploadRequest->currentUserId;
             $visitId  = $validateDicomUploadRequest->visitId;
 
+            $expectedNumberOfInstances = $validateDicomUploadRequest->numberOfInstances;
+            $originalOrthancId = $validateDicomUploadRequest->originalOrthancId;
+
             $this->checkAuthorization($currentUserId, $visitId, $studyName, $visitContext);
 
             //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();
 
@@ -98,14 +103,14 @@ public function execute(ValidateDicomUploadRequest $validateDicomUploadRequest,
             }
             $this->orthancService->setOrthancServer(false);
 
-            $expectedNumberOfInstances = $validateDicomUploadRequest->numberOfInstances;
-
             $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(
@@ -130,7 +135,7 @@ public function execute(ValidateDicomUploadRequest $validateDicomUploadRequest,
             $this->orthancService->setOrthancServer(true);
 
             $statistics = $this->orthancService->getOrthancRessourcesStatistics('studies', $anonymizedOrthancStudyID);
-            if ($statistics['CountInstances'] !== $validateDicomUploadRequest->numberOfInstances) {
+            if ($statistics['CountInstances'] !== $expectedNumberOfInstances) {
                 throw new GaelOValidateDicomException("Error during Peer transfers");
             }
 
@@ -140,7 +145,7 @@ public function execute(ValidateDicomUploadRequest $validateDicomUploadRequest,
                 $studyName,
                 $currentUserId,
                 $anonymizedOrthancStudyID,
-                $validateDicomUploadRequest->originalOrthancId
+                $originalOrthancId
             );
 
             $studyInstanceUID = $this->registerDicomStudyService->execute();