Merge pull request #702 from Pixilib/GaelO2-dev

Gael o2 dev
Pixilib · Nov 30, 2023 · 1172a2f · 1172a2f
2 parents 2f744e4 + 90a16dc
commit 1172a2f
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Showing 26 changed files with 173 additions and 159 deletions.
diff --git a/GaelO2/app/GaelO/Adapters/FrameworkAdapter.php b/GaelO2/app/GaelO/Adapters/FrameworkAdapter.php
@@ -2,6 +2,7 @@
 
 namespace App\GaelO\Adapters;
 
+use App\GaelO\Exceptions\GaelOException;
 use App\GaelO\Interfaces\Adapters\FrameworkInterface;
 use App\Models\User;
 use Illuminate\Auth\Events\Registered;
@@ -47,7 +48,11 @@ public static function deleteFile(string $path): void
 
     public static function getFile(string $path): string
     {
-        return Storage::get($path);
+        $file = Storage::get($path);
+        if($file === null){
+            throw new GaelOException("File not found in storage");
+        }
+        return $file;
     }
 
     public static function sendRegisteredEventForEmailVerification(int $userId): void

diff --git a/GaelO2/app/GaelO/Adapters/JobAdapter.php b/GaelO2/app/GaelO/Adapters/JobAdapter.php
@@ -13,8 +13,8 @@ public function sendQcReportJob(int $visitId): void
         JobQcReport::dispatch($visitId);
     }
 
-    public function sendRadiomicsReport(int $visitId, int $behalfUserId): void
+    public function sendRadiomicsReport(int $visitId, ?int $behalfUserId, ?array $destinatorEmails): void
     {
-        JobRadiomicsReport::dispatch($visitId, $behalfUserId);
+        JobRadiomicsReport::dispatch($visitId, $behalfUserId, $destinatorEmails);
     }
 }
diff --git a/GaelO2/app/GaelO/Interfaces/Adapters/JobInterface.php b/GaelO2/app/GaelO/Interfaces/Adapters/JobInterface.php
@@ -5,5 +5,5 @@
 interface JobInterface
 {
     public function sendQcReportJob(int $visitId) : void;
-    public function sendRadiomicsReport(int $visitId, int $behalfUserId) :void;
+    public function sendRadiomicsReport(int $visitId, ?int $behalfUserId, ?array $destinatorEmails) :void;
 }
diff --git a/GaelO2/app/GaelO/Services/GaelOProcessingService/GaelOProcessingService.php b/GaelO2/app/GaelO/Services/GaelOProcessingService/GaelOProcessingService.php
@@ -38,7 +38,8 @@ public function createSeriesFromOrthanc(string $orthancSeriesId, bool $pet = fal
         return $request->getBody();
     }
 
-    public function createDicom(string $filename){
+    public function createDicom(string $filename)
+    {
         $request = $this->httpClientInterface->uploadFile('POST', "/dicoms", $filename);
         return $request->getBody();
     }
@@ -154,6 +155,12 @@ public function getStatsMask(string $maskId): array
         return $request->getJsonBody();
     }
 
+    public function getStatsMaskSeries(string $maskId, string $seriesId): array
+    {
+        $request = $this->httpClientInterface->requestJson('POST', "/tools/stats-mask-image", ["seriesId" => $seriesId, "maskId" => $maskId]);
+        return $request->getJsonBody();
+    }
+
     public function deleteRessource(string $type, string $id): void
     {
         $request = $this->httpClientInterface->requestJson('DELETE', "/" . $type . "/" . $id);

diff --git a/GaelO2/app/GaelO/Services/GaelOStudiesService/ExpectedPatient/ExpectedPatient.php b/GaelO2/app/GaelO/Services/GaelOStudiesService/ExpectedPatient/ExpectedPatient.php
@@ -6,9 +6,9 @@ class ExpectedPatient
 {
     public string $code;
     public int $centerCode;
-    public string $inclusionStatus;
+    public ?string $inclusionStatus;
 
-    public function __construct(string $code, int $centerCode, string $inclusionStatus)
+    public function __construct(string $code, int $centerCode = null, ?string $inclusionStatus = null)
     {
         $this->code = $code;
         $this->centerCode = $centerCode;

diff --git a/GaelO2/app/GaelO/Services/MailServices.php b/GaelO2/app/GaelO/Services/MailServices.php
@@ -595,7 +595,7 @@ public function sendQcReport(string $studyName, string $visitType, string $patie
         $this->mailInterface->send();
     }
 
-    public function sendRadiomicsReport(string $studyName, string $patientCode, string $visitType, string $visitDate, string $imagePath, array $stats, int $uploaderId)
+    public function sendRadiomicsReport(string $studyName, string $patientCode, string $visitType, string $visitDate, string $imagePath, array $stats, array $emailList)
     {
         $parameters = [
             'patientCode' => $patientCode,
@@ -606,11 +606,7 @@ public function sendRadiomicsReport(string $studyName, string $patientCode, stri
             'stats' => $stats
         ];
 
-        $mailListBuilder = new MailListBuilder($this->userRepositoryInterface, $this->studyRepositoryInterface);
-        $mailListBuilder->withUserEmail($uploaderId)
-            ->withUsersEmailsByRolesInStudy($studyName, Constants::ROLE_SUPERVISOR);
-
-        $this->mailInterface->setTo($mailListBuilder->get());
+        $this->mailInterface->setTo($emailList);
         $this->mailInterface->setReplyTo($this->getStudyContactEmail($studyName));
         $this->mailInterface->setParameters($parameters);
         $this->mailInterface->setBody(MailConstants::EMAIL_RADIOMICS_REPORT);

diff --git a/GaelO2/app/GaelO/UseCases/CreateFileToVisit/CreateFileToVisitRequest.php b/GaelO2/app/GaelO/UseCases/CreateFileToVisit/CreateFileToVisitRequest.php
@@ -8,7 +8,7 @@ class CreateFileToVisitRequest
     public int $visitId;
     public string $studyName;
     public string $key;
-    public string $contentType;
+    public ?string $contentType = null;
     public string $content;
     public ?string $extension = null;
 }
diff --git a/GaelO2/app/GaelO/UseCases/ReactivateDicomSeries/ReactivateDicomSeries.php b/GaelO2/app/GaelO/UseCases/ReactivateDicomSeries/ReactivateDicomSeries.php
@@ -91,11 +91,17 @@ private function checkAuthorization(int $userId, int $visitId, string $role, str
     {
         $qcStatus = $visitContext['state_quality_control'];
 
-        //If QC is done, can't reactivate series
-        if (in_array($qcStatus, [QualityControlStateEnum::ACCEPTED->value, QualityControlStateEnum::REFUSED->value, QualityControlStateEnum::NOT_NEEDED->value])) {
-            throw new GaelOForbiddenException();
+        //If QC is performed, can't reactivate series
+        if (in_array($qcStatus, [QualityControlStateEnum::ACCEPTED->value, QualityControlStateEnum::REFUSED->value])) {
+            throw new GaelOForbiddenException("Can't reactivate series on QC performed visit");
+        }
+
+        //If QC is not needed we allow supervisor to reactivate series (reactivation after a dicom study delete)
+        if($qcStatus === QualityControlStateEnum::NOT_NEEDED->value && $role !== Constants::ROLE_SUPERVISOR){
+            throw new GaelOForbiddenException("In case of not needed QC only supervisor can reactivate series");
         }
 
+        //We deny access to all other of than investigator, controller or supervisor
         if (!in_array($role, [Constants::ROLE_INVESTIGATOR, Constants::ROLE_CONTROLLER, Constants::ROLE_SUPERVISOR])) {
             throw new GaelOForbiddenException();
         }

diff --git a/GaelO2/app/GaelO/UseCases/ValidateDicomUpload/ValidateDicomUpload.php b/GaelO2/app/GaelO/UseCases/ValidateDicomUpload/ValidateDicomUpload.php
@@ -57,6 +57,9 @@ public function execute(ValidateDicomUploadRequest $validateDicomUploadRequest,
     {
 
         try {
+            //Run as a background task even if the user leave the website
+            ignore_user_abort(true);
+
             //Initialize unzipPath to avoid null pointer in catch
             $unzipedPath = null;
             //Retrieve Visit Context

diff --git a/GaelO2/app/GaelO/views/mails/mail_conclusion.blade.php b/GaelO2/app/GaelO/views/mails/mail_conclusion.blade.php
@@ -2,9 +2,8 @@
 
 @section('content')
     Review of the following visit is concluded <br>
-    Study : {{$study}}<br>
-    Patient Code : {{$patientCode}}
-    Visit : {{$visitType}}<br>
-    Conclusion Value : {{$conclusionValue}}
+    Study : {{ $study }}<br>
+    Patient Code : {{ $patientCode }}
+    Visit : {{ $visitType }}<br>
+    <b>Conclusion Value : {{ $conclusionValue }}</b>
 @endsection
-
diff --git a/GaelO2/app/GaelO/views/mails/mail_radiomics_report.blade.php b/GaelO2/app/GaelO/views/mails/mail_radiomics_report.blade.php
@@ -231,6 +231,30 @@
       </table>
     </div>
     <!--[if mso | IE]></td></tr></table><table align="center" border="0" cellpadding="0" cellspacing="0" class="" role="presentation" style="width:600px;" width="600" ><tr><td style="line-height:0px;font-size:0px;mso-line-height-rule:exactly;"><![endif]-->
+    <div style="margin:0px auto;max-width:600px;">
+      <table align="center" border="0" cellpadding="0" cellspacing="0" role="presentation" style="width:100%;">
+        <tbody>
+          <tr>
+            <td style="direction:ltr;font-size:0px;padding:20px 0;text-align:center;">
+              <!--[if mso | IE]><table role="presentation" border="0" cellpadding="0" cellspacing="0"><tr><td class="" style="vertical-align:top;width:600px;" ><![endif]-->
+              <div class="mj-column-per-100 mj-outlook-group-fix" style="font-size:0px;text-align:left;direction:ltr;display:inline-block;vertical-align:top;width:100%;">
+                <table border="0" cellpadding="0" cellspacing="0" role="presentation" style="vertical-align:top;" width="100%">
+                  <tbody>
+                    <tr>
+                      <td align="center" style="font-size:0px;padding:10px 25px;word-break:break-word;">
+                        <div style="font-family:Ubuntu, Helvetica, Arial, sans-serif;font-size:13px;line-height:16px;text-align:center;color:#000000;">For Investigational use only<br> These automatic calculations shall be validated by a trained physician<br></div>
+                      </td>
+                    </tr>
+                  </tbody>
+                </table>
+              </div>
+              <!--[if mso | IE]></td></tr></table><![endif]-->
+            </td>
+          </tr>
+        </tbody>
+      </table>
+    </div>
+    <!--[if mso | IE]></td></tr></table><table align="center" border="0" cellpadding="0" cellspacing="0" class="" role="presentation" style="width:600px;" width="600" ><tr><td style="line-height:0px;font-size:0px;mso-line-height-rule:exactly;"><![endif]-->
     <div style="margin:0px auto;max-width:600px;">
       <table align="center" border="0" cellpadding="0" cellspacing="0" role="presentation" style="width:100%;">
         <tbody>

diff --git a/GaelO2/app/GaelO/views/mails/mjml/radiomics_report.mjml b/GaelO2/app/GaelO/views/mails/mjml/radiomics_report.mjml
@@ -52,6 +52,14 @@
         </mj-table>
       </mj-column>
     </mj-section>
+    <mj-section>
+      <mj-column>
+        <mj-text align="center" line-height="16px">
+          For Investigational use only<br>
+          These automatic calculations shall be validated by a trained physician<br>
+        </mj-text>
+      </mj-column>
+    </mj-section>
     <mj-section>
       <mj-column>
         <mj-divider border-width="1px" border-color="#616161"></mj-divider>

diff --git a/GaelO2/app/Http/Controllers/Controller.php b/GaelO2/app/Http/Controllers/Controller.php
@@ -11,9 +11,14 @@ class Controller extends BaseController
 {
     use AuthorizesRequests, DispatchesJobs, ValidatesRequests;
 
-    public function getJsonResponse($body, int $statusCode, string $statusText)
+    public function getJsonResponse($body, int $statusCode, string $statusText, bool $emptyArrayAsObject = false)
     {
         if ($body === null) return response()->noContent()->setStatusCode($statusCode, $statusText);
-        else return response()->json($body)->setStatusCode($statusCode, $statusText);
+        else {
+            if (is_array($body) && sizeof($body) === 0 && $emptyArrayAsObject) {
+                $body = (object) [];
+            }
+            return response()->json($body)->setStatusCode($statusCode, $statusText);
+        };
     }
 }
diff --git a/GaelO2/app/Http/Controllers/ReviewController.php b/GaelO2/app/Http/Controllers/ReviewController.php
@@ -300,7 +300,7 @@ public function getAssociatedDataOfVisitForReviewer(GetAssociatedDataForReview $
 
         $getAssociatedDataForReview->execute($getAssociatedDataForReviewRequest, $getAssociatedDataForReviewResponse);
 
-        return $this->getJsonResponse($getAssociatedDataForReviewResponse->body, $getAssociatedDataForReviewResponse->status, $getAssociatedDataForReviewResponse->statusText);
+        return $this->getJsonResponse($getAssociatedDataForReviewResponse->body, $getAssociatedDataForReviewResponse->status, $getAssociatedDataForReviewResponse->statusText, true);
     }
 
     public function getAssociatedDataOfVisitForInvestigator(Request $request, GetAssociatedDataForInvestigator $getAssociatedDataForInvestigator, GetAssociatedDataForInvestigatorRequest $getAssociatedDataForInvestigatorRequest, GetAssociatedDataForInvestigatorResponse $getAssociatedDataForInvestigatorResponse, int $visitId)
@@ -314,6 +314,6 @@ public function getAssociatedDataOfVisitForInvestigator(Request $request, GetAss
 
         $getAssociatedDataForInvestigator->execute($getAssociatedDataForInvestigatorRequest, $getAssociatedDataForInvestigatorResponse);
 
-        return $this->getJsonResponse($getAssociatedDataForInvestigatorResponse->body, $getAssociatedDataForInvestigatorResponse->status, $getAssociatedDataForInvestigatorResponse->statusText);
+        return $this->getJsonResponse($getAssociatedDataForInvestigatorResponse->body, $getAssociatedDataForInvestigatorResponse->status, $getAssociatedDataForInvestigatorResponse->statusText, true);
     }
 }
diff --git a/GaelO2/app/Jobs/JobQcReport.php b/GaelO2/app/Jobs/JobQcReport.php
@@ -163,5 +163,8 @@ public function failed(Throwable $exception)
     {
         $mailServices = App::make(MailServices::class);
         $mailServices->sendJobFailure('QcReport', ['visitId' => $this->visitId], $exception->getMessage());
+        if (app()->bound('sentry')) {
+            app('sentry')->captureException($exception);
+        }
     }
 }
diff --git a/GaelO2/app/Jobs/JobRadiomicsReport.php b/GaelO2/app/Jobs/JobRadiomicsReport.php
@@ -5,6 +5,7 @@
 use App\GaelO\Exceptions\GaelOException;
 use App\GaelO\Interfaces\Repositories\DicomStudyRepositoryInterface;
 use App\GaelO\Interfaces\Repositories\VisitRepositoryInterface;
+use App\GaelO\Repositories\StudyRepository;
 use App\GaelO\Services\GaelOClientService;
 use App\GaelO\Services\GaelOProcessingService\GaelOProcessingService;
 use App\GaelO\Services\MailServices;
@@ -19,7 +20,6 @@
 use Illuminate\Queue\InteractsWithQueue;
 use Illuminate\Queue\SerializesModels;
 use Illuminate\Support\Facades\App;
-use Illuminate\Support\Facades\Log;
 use DateTime;
 use Exception;
 use Throwable;
@@ -32,20 +32,23 @@ class JobRadiomicsReport implements ShouldQueue, ShouldBeUnique
     public $timeout = 1200;
     public $tries = 1;
     private int $visitId;
-    private int $behalfUserId;
+    private ?int $behalfUserId;
+    private ?array $destinatorEmails;
     private array $createdFiles = [];
     private GaelOProcessingService $gaelOProcessingService;
     private OrthancService $orthancService;
 
-    public function __construct(int $visitId, int $behalfUserId)
+    public function __construct(int $visitId, ?int $behalfUserId, ?array $destinatorEmails)
     {
         $this->onQueue('processing');
         $this->visitId = $visitId;
         $this->behalfUserId = $behalfUserId;
+        $this->destinatorEmails = $destinatorEmails;
     }
 
     public function handle(
         VisitRepositoryInterface $visitRepositoryInterface,
+        StudyRepository $studyRepository,
         DicomStudyRepositoryInterface $dicomStudyRepositoryInterface,
         OrthancService $orthancService,
         GaelOProcessingService $gaelOProcessingService,
@@ -112,18 +115,28 @@ public function handle(
         $maskdicom = $this->gaelOProcessingService->getMaskDicomOrientation($fragmentedMaskId, 'LPI', true);
 
         #get Stats
-        $stats = $this->gaelOProcessingService->getStatsMask($threshold41MaskId);
-        $statValue = ['tmtv 41%' => $stats['volume'], 'DmaxVox' => $stats['dMax']];
+        $stats = $this->gaelOProcessingService->getStatsMaskSeries($threshold41MaskId, $idPT);
+        $statValue = [
+            'TMTV 41%' => $stats['volume'],
+            'Dmax (voxel)' => $stats['dmax'],
+            'SUVmax' => $stats['suvmax'],
+            'SUVmean'=> $stats['suvmean'],
+            'SUVpeak' => $stats['suvpeak'],
+            'TLG' => $stats['tlg'],
+            'Dmax Bulk' => $stats['dmaxbulk'],
+        ];
 
-        $mailServices->sendRadiomicsReport(
-            $studyName,
-            $patientCode,
-            $visitType,
-            $formattedVisitDate,
-            $mipMask,
-            $statValue,
-            $creatorUserId
-        );
+        if($this->destinatorEmails){
+            $mailServices->sendRadiomicsReport(
+                $studyName,
+                $patientCode,
+                $visitType,
+                $formattedVisitDate,
+                $mipMask,
+                $statValue,
+                $this->destinatorEmails
+            );
+        }
 
         $pdfReport  = $pdfServices->saveRadiomicsPdf(
             $studyName,
@@ -134,7 +147,13 @@ public function handle(
         );
 
         //Send file to store using API as job worker may not access to the storage backend
-        $user = User::find($this->behalfUserId);
+        if ($this->behalfUserId) {
+            $user = User::find($this->behalfUserId);
+        } else {
+            $studyEntity = $studyRepository->find($studyName);
+            $user = User::where('email', $studyEntity->contactEmail)->sole();
+        }
+
         $tokenResult = $user->createToken('GaelO')->plainTextToken;
         $gaeloClientService->loadUrl();
         $gaeloClientService->setAuthorizationToken($tokenResult);
@@ -159,9 +178,7 @@ public function handle(
     private function sendDicomToProcessing(string $orthancSeriesIdPt)
     {
         $temporaryZipDicom  = tempnam(ini_get('upload_tmp_dir'), 'TMP_Inference_');
-        $temporaryZipDicomHandle = fopen($temporaryZipDicom, 'r+');
-
-        $this->orthancService->getZipStreamToFile([$orthancSeriesIdPt], $temporaryZipDicomHandle);
+        $this->orthancService->getZipStreamToFile([$orthancSeriesIdPt], $temporaryZipDicom);
         $this->gaelOProcessingService->createDicom($temporaryZipDicom);
         $this->addCreatedRessource('dicoms', $orthancSeriesIdPt);
 
@@ -183,6 +200,11 @@ private function getSeriesOrthancIds(array $dicomStudyEntity)
             }
         }
 
+        if (!$idPT || !$idCT) {
+            //Can happen in case of a study reactivation, at reactivation series are softdeleted so we won't run the inference
+            throw new GaelOException("Didn't found CT and PT Series to run the inference");
+        }
+
         return [
             'orthancSeriesIdPt' => $idPT,
             'orthancSeriesIdCt' => $idCT
@@ -208,5 +230,8 @@ public function failed(Throwable $exception)
     {
         $mailServices = App::make(MailServices::class);
         $mailServices->sendJobFailure('RadiomicsReport', ['visitId' => $this->visitId, 'behalfUserId' => $this->behalfUserId], $exception->getMessage());
+        if (app()->bound('sentry')) {
+            app('sentry')->captureException($exception);
+        }
     }
 }