Merge pull request #701 from Pixilib/GaelO2-dev

Gael o2 dev

.github/workflows/publish.yml

@@ -5,6 +5,7 @@ on:
     branches:
       - GaelO2
       - GaelO2-dev
+      - tmtv-inference
     tags:
       - '*'
 
@@ -22,6 +23,7 @@ jobs:
         with:
           images: ghcr.io/pixilib/gaelo
           tags: |
+            type=ref,event=branch
             type=ref,event=tag
             v2-latest
             

GaelO2/.env.example

@@ -15,22 +15,22 @@ DB_DATABASE=laravel
 DB_USERNAME=root
 DB_PASSWORD=
 
-TUS_URL = 'http://localhost:1080'
+TUS_URL='http://localhost:1080'
 
-ORTHANC_TEMPORARY_URL = 'http://localhost:8042'
-ORTHANC_TEMPORARY_LOGIN = 'login'
-ORTHANC_TEMPORARY_PASSWORD = 'password'
+ORTHANC_TEMPORARY_URL='http://localhost:8042'
+ORTHANC_TEMPORARY_LOGIN='login'
+ORTHANC_TEMPORARY_PASSWORD='password'
 
-ORTHANC_STORAGE_URL = 'http://localhost:8043'
-ORTHANC_STORAGE_LOGIN = 'login'
-ORTHANC_STORAGE_PASSWORD = 'password'
+ORTHANC_STORAGE_URL='http://localhost:8043'
+ORTHANC_STORAGE_LOGIN='login'
+ORTHANC_STORAGE_PASSWORD='password'
 
-GAELO_PROCESSING_PROTOCOL='http://'
-GAELO_PROCESSING_HOST = 'gaeloprocessing'
-GAELO_PROCESSING_PORT= '8000'
+GAELO_PROCESSING_URL='http://gaeloprocessing:8000'
+GAELO_PROCESSING_LOGIN='login'
+GAELO_PROCESSING_PASSWORD='password'
 
-AZURE_CLIENT_ID =''
-AZURE_DIRECTORY_ID =''
+AZURE_CLIENT_ID=''
+AZURE_DIRECTORY_ID=''
 AZURE_CLIENT_SECRET=''
 AZURE_SUBSCRIPTION_ID=''
 AZURE_CONTAINER_GROUP=''

GaelO2/app/GaelO/Adapters/FrameworkAdapter.php

@@ -59,7 +59,7 @@ public static function sendRegisteredEventForEmailVerification(int $userId): voi
     public static function sendResetPasswordLink(string $email): bool
     {
         $status = Password::sendResetLink(
-            ['email' => $email]
+            ['email' => strtolower($email)]
         );
 
         return $status === Password::RESET_LINK_SENT;

GaelO2/app/GaelO/Adapters/HttpClientAdapter.php

@@ -46,6 +46,19 @@ public function setBasicAuthentication(string $login, string $password): void
         $this->password = $password;
     }
 
+    public function uploadFile(string $method, string $uri, string $filename): Psr7ResponseInterface
+    {
+        $fileHandler = fopen($filename, 'rb');
+        $headers = [
+            'auth' => [$this->login, $this->password],
+            'content-type' => 'application/zip',
+            'body' => $fileHandler
+        ];
+
+        $response = $this->client->request($method, $this->address . $uri, $headers);
+        return new Psr7ResponseAdapter($response);
+    }
+
     public function requestUploadArrayDicom(string $method, string $uri, array $files): array
     {
 
@@ -71,15 +84,15 @@ public function requestUploadArrayDicom(string $method, string $uri, array $file
             },
             'rejected' => function (RequestException $exception, $index) {
                 $reason = "Error sending dicom to orthanc";
-                
+
                 if ($exception->hasResponse()) {
                     $reason = $exception->getResponse()->getStatusCode();
                     Log::error($exception->getResponse()->getBody()->getContents());
                 } else {
                     $reason = $exception->getMessage();
                 }
                 // this is delivered each failed request
-                Log::error('DICOM Import Failed in Orthanc Temporary: '.$reason. ' index: '.$index);
+                Log::error('DICOM Import Failed in Orthanc Temporary: ' . $reason . ' index: ' . $index);
             },
         ]);
 
@@ -95,7 +108,14 @@ public function requestUploadArrayDicom(string $method, string $uri, array $file
 
     public function requestJson(string $method, string $uri, array $body = []): Psr7ResponseInterface
     {
-        $authenticationOption = ['auth' => [$this->login, $this->password]];
+        if ($this->login !== '' && $this->password !== '') {
+            $authenticationOption['auth'] = [$this->login, $this->password];
+        }
+
+        if ($this->authorizationToken != null) {
+            $authenticationOption['headers']['Authorization'] = 'Bearer ' . $this->authorizationToken;
+        }
+
         $bodyOption = ['json' => $body];
         $options = array_merge($authenticationOption, $bodyOption);
         $response = $this->client->request($method, $this->address . $uri, $options);
@@ -135,7 +155,7 @@ public function requestStreamResponseToFile(string $method, string $uri, $ressou
         return new Psr7ResponseAdapter($response);
     }
 
-    public function rowRequest(string $method, string $uri, $body, ?array $headers, $ressourceDestination = null, $httpErrors = true): Psr7ResponseInterface
+    public function rawRequest(string $method, string $uri, $body, ?array $headers, $ressourceDestination = null, $httpErrors = true): Psr7ResponseInterface
     {
         $options = [];
 

GaelO2/app/GaelO/Adapters/JobAdapter.php

@@ -4,11 +4,17 @@
 
 use App\GaelO\Interfaces\Adapters\JobInterface;
 use App\Jobs\JobQcReport;
+use App\Jobs\JobRadiomicsReport;
 
 class JobAdapter implements JobInterface
 {
     public function sendQcReportJob(int $visitId): void
     {
         JobQcReport::dispatch($visitId);
     }
+
+    public function sendRadiomicsReport(int $visitId, int $behalfUserId): void
+    {
+        JobRadiomicsReport::dispatch($visitId, $behalfUserId);
+    }
 }

GaelO2/app/GaelO/Adapters/MailerAdapter.php

@@ -29,7 +29,9 @@
 use App\GaelO\Interfaces\Adapters\MailerInterface;
 use App\Mail\QcReport;
 use App\Mail\ImportPatient;
+use App\Mail\JobFailure;
 use App\Mail\MagicLink;
+use App\Mail\RadiomicsReport;
 use App\Mail\RequestPatientCreation;
 use App\Mail\UserCreated;
 use Illuminate\Mail\Mailable;
@@ -158,6 +160,12 @@ private function getModel(int $model): Mailable
             case MailConstants::EMAIL_REQUEST_PATIENT_CREATION:
                 $model = new RequestPatientCreation($this->parameters);
                 break;
+            case MailConstants::EMAIL_RADIOMICS_REPORT:
+                $model = new RadiomicsReport($this->parameters);
+                break;
+            case MailConstants::EMAIL_JOB_FAILURE:
+                $model = new JobFailure($this->parameters);
+                break;
             default:
                 throw new GaelOException("Unkown Mail Type");
                 break;

GaelO2/app/GaelO/Adapters/MimeAdapter.php

@@ -3,20 +3,22 @@
 namespace App\GaelO\Adapters;
 
 use App\GaelO\Interfaces\Adapters\MimeInterface;
-use Mimey\MimeTypes;
+use Illuminate\Support\Facades\Log;
+use League\MimeTypeDetection\ExtensionMimeTypeDetector;
+use League\MimeTypeDetection\GeneratedExtensionToMimeTypeMap;
 
 class MimeAdapter implements MimeInterface
 {
 
     public static function getExtensionsFromMime(string $mime): array
     {
-        $mimes = new MimeTypes();
-        return $mimes->getAllExtensions($mime);
+        $mimes = new ExtensionMimeTypeDetector();
+        return $mimes->lookupAllExtensions($mime);
     }
 
-    public static function getMimesFromExtension(string $extension): array
+    public static function getMimeFromExtension(string $extension): string
     {
-        $mimes = new MimeTypes();
-        return $mimes->getAllMimeTypes($extension);
+        $mimes = new GeneratedExtensionToMimeTypeMap();
+        return $mimes->lookupMimeType($extension);
     }
 }

GaelO2/app/GaelO/Adapters/PdfAdapter.php

@@ -0,0 +1,16 @@
+<?php
+
+namespace App\GaelO\Adapters;
+
+use App\GaelO\Interfaces\Adapters\PdfInterface;
+use Barryvdh\DomPDF\Facade\Pdf;
+
+class PdfAdapter implements PdfInterface
+{
+
+    public function saveViewToPdf(string $view, array $parameters, string $filename): void
+    {
+        $pdf = Pdf::loadView('mails.mail_radiomics_report', $parameters)->setOption('defaultFont', 'sans-serif');
+        $pdf->save($filename);
+    }
+}

GaelO2/app/GaelO/Adapters/Psr7ResponseAdapter.php

@@ -4,6 +4,7 @@
 
 use App\GaelO\Interfaces\Adapters\Psr7ResponseInterface;
 use Psr\Http\Message\ResponseInterface;
+use Psr\Http\Message\StreamInterface;
 
 class Psr7ResponseAdapter implements Psr7ResponseInterface
 {
@@ -20,6 +21,11 @@ public function getStatusCode(): int
         return $this->response->getStatusCode();
     }
 
+    public function getStream(): StreamInterface
+    {
+        return $this->response->getBody();
+    }
+
     public function getBody(): string
     {
         return $this->response->getBody()->getContents();

GaelO2/app/GaelO/Constants/Constants.php

@@ -23,6 +23,7 @@ class Constants
     const TRACKER_CREATE_VISIT = "Create Visit";
     const TRACKER_UPLOAD_SERIES = "Upload Series";
     const TRACKER_UPDATE_VISIT_DATE = "Update Visit Date";
+    const TRACKER_UPDATE_VISIT_FILE = "Update Visit File";
     const TRACKER_UPLOAD_VALIDATION_FAILED = "Upload Failed";
     const TRACKER_ASK_UNLOCK = "Ask Unlock Form";
     const TRACKER_UNLOCK_INVESTIGATOR_FORM = "Unlock Investigator Form";

GaelO2/app/GaelO/Constants/MailConstants.php

@@ -27,4 +27,6 @@ class MailConstants {
     const EMAIL_UNLOCK_QC_REQUEST=22;
     const EMAIL_QC_REPORT = 23;
     const EMAIL_REQUEST_PATIENT_CREATION = 24;
+    const EMAIL_RADIOMICS_REPORT = 25;
+    const EMAIL_JOB_FAILURE = 26;
 }

GaelO2/app/GaelO/Constants/SettingsConstants.php

@@ -20,9 +20,9 @@ class SettingsConstants {
     const ORTHANC_STORAGE_LOGIN = 'orthanc_storage_login';
     const ORTHANC_STORAGE_PASSWORD = 'orthanc_storage_password';
 
-    const GAELO_PROCESSING_PROTOCOL='gaelo_processing_protocol';
-    const GAELO_PROCESSING_HOST = 'gaelo_processing_host';
-    const GAELO_PROCESSING_PORT= 'gaelo_processing_port';
+    const GAELO_PROCESSING_URL='gaelo_processing_url';
+    const GAELO_PROCESSING_LOGIN='gaelo_processing_login';
+    const GAELO_PROCESSING_PASSWORD='gaelo_processing_password';
 
     const AZURE_CLIENT_ID ='azure_client_id';
     const AZURE_DIRECTORY_ID ='azure_directory_id';

GaelO2/app/GaelO/Entities/ReviewEntity.php

@@ -21,13 +21,13 @@ public static function fillFromDBReponseArray(array $array): ReviewEntity
         $reviewEntity  = new ReviewEntity();
         $reviewEntity->local = $array['local'];
         $reviewEntity->id = $array['id'];
-        $reviewEntity->study_name = $array['study_name'];
+        $reviewEntity->studyName = $array['study_name'];
         $reviewEntity->userId = $array['user_id'];
         $reviewEntity->date = $array['review_date'];
         $reviewEntity->visitId = $array['visit_id'];
         $reviewEntity->validated = $array['validated'];
         $reviewEntity->data = $array['review_data'];
-        $reviewEntity->files = $array['sent_files'];
+        $reviewEntity->files = $array['sent_files'] ?? [];
         $reviewEntity->adjudication = $array['adjudication'];
         return $reviewEntity;
     }

GaelO2/app/GaelO/Entities/StudyEntity.php

@@ -13,6 +13,7 @@ class StudyEntity
     public bool $monitorShowAll;
     public bool $documentationMandatory;
     public bool $deleted;
+    public bool $creatablePatientsInvestigator;
     public ?string $ancillaryOf;
 
     //Array of VisitGroupEntities
@@ -29,6 +30,7 @@ public static function fillFromDBReponseArray(array $array) : StudyEntity
         $studyEntity->monitorShowAll = $array['monitor_show_all'];
         $studyEntity->ancillaryOf = $array['ancillary_of'];
         $studyEntity->documentationMandatory = $array['documentation_mandatory'];
+        $studyEntity->creatablePatientsInvestigator = $array['creatable_patients_investigator'];
         $studyEntity->deleted = $array['deleted_at'] !== null;
 
         return $studyEntity;

GaelO2/app/GaelO/Entities/VisitEntity.php

@@ -30,6 +30,7 @@ class VisitEntity
     public ?bool $correctiveActionInvestigatorForm;
     public ?string $correctiveActionOther;
     public ?bool $correctiveActionDecision;
+    public array $files;
     public ?string $deletedAt;
 
     public VisitGroupEntity $visitGroup;
@@ -70,6 +71,7 @@ public static function fillFromDBReponseArray(array $array): VisitEntity
         $visitEntity->correctiveActionInvestigatorForm = $array['corrective_action_investigator_form'];
         $visitEntity->correctiveActionOther = $array['corrective_action_comment'];
         $visitEntity->correctiveActionDecision = $array['corrective_action_applied'];
+        $visitEntity->files = $array['sent_files'] ?? [];
         $visitEntity->deletedAt = $array['deleted_at'];
         return $visitEntity;
     }

GaelO2/app/GaelO/Interfaces/Adapters/HttpClientInterface.php

@@ -13,8 +13,9 @@ public function setAuthorizationToken(string $authorizationToken): void;
 
     public function setBasicAuthentication(string $login, string $password): void;
 
-    public function rowRequest(string $method, string $uri, $body, ?array $headers, $ressourceDestination = null, $httpErrors = true): Psr7ResponseInterface;
+    public function rawRequest(string $method, string $uri, $body, ?array $headers, $ressourceDestination = null, $httpErrors = true): Psr7ResponseInterface;
 
+    public function uploadFile(string $method, string $uri, string $filename) : Psr7ResponseInterface;
     /**
      * Return array of PSR7 response adapter of multiple request, used to sent multiple files to an endpoint
      */

GaelO2/app/GaelO/Interfaces/Adapters/JobInterface.php

@@ -5,4 +5,5 @@
 interface JobInterface
 {
     public function sendQcReportJob(int $visitId) : void;
+    public function sendRadiomicsReport(int $visitId, int $behalfUserId) :void;
 }

GaelO2/app/GaelO/Interfaces/Adapters/MimeInterface.php

@@ -4,5 +4,5 @@
 
 Interface MimeInterface{
     public static function getExtensionsFromMime(string $mime) : array;
-    public static function getMimesFromExtension(string $extension) : array;
+    public static function getMimeFromExtension(string $extension) : string;
 }

GaelO2/app/GaelO/Interfaces/Adapters/PdfInterface.php

@@ -0,0 +1,8 @@
+<?php
+
+namespace App\GaelO\Interfaces\Adapters;
+
+interface PdfInterface
+{
+    public function saveViewToPdf(string $view, array $parameters, string $filename): void;
+}

GaelO2/app/GaelO/Interfaces/Adapters/Psr7ResponseInterface.php

@@ -2,10 +2,14 @@
 
 namespace App\GaelO\Interfaces\Adapters;
 
-Interface Psr7ResponseInterface {
-    public function getStatusCode() : int ;
-    public function getBody() : string ;
-    public function getReasonPhrase() :string ;
-    public function getHeaders()  : array ;
-    public function getJsonBody() : array ;
+use Psr\Http\Message\StreamInterface;
+
+interface Psr7ResponseInterface
+{
+    public function getStatusCode(): int;
+    public function getBody(): string;
+    public function getStream(): StreamInterface;
+    public function getReasonPhrase(): string;
+    public function getHeaders(): array;
+    public function getJsonBody(): array;
 }

GaelO2/app/GaelO/Interfaces/Repositories/StudyRepositoryInterface.php

@@ -11,7 +11,7 @@ public function find($name): StudyEntity;
 
     public function delete($name): void;
 
-    public function addStudy(String $name, string $code, int $patientCodeLength, string $contactEmail, bool $controllerShowAll, bool $monitorShowAll, bool $documentationMandatory, ?string $ancillaryOf): void;
+    public function addStudy(String $name, string $code, int $patientCodeLength, string $contactEmail, bool $controllerShowAll, bool $monitorShowAll, bool $documentationMandatory, ?string $ancillaryOf, bool $creatablePatientsInvestigator): void;
 
     public function isExistingStudyName(string $name): bool;
 

GaelO2/app/GaelO/Interfaces/Repositories/VisitRepositoryInterface.php

@@ -70,4 +70,6 @@ public function getVisitsInVisitType(int $visitTypeId, bool $withReviewStatus =
 
     public function getVisitContextByVisitIdArray(array $visitIdArray): array;
 
+    public function updateVisitFile(int $visitId, array $associatedFile): void;
+
 }

GaelO2/app/GaelO/Repositories/StudyRepository.php

@@ -27,7 +27,7 @@ public function delete($name): void
         $this->studyModel->findOrFail($name)->delete();
     }
 
-    public function addStudy(String $name, string $code, int $patientCodeLength, string $contactEmail, bool $controllerShowAll, bool $monitorShowAll, bool $documentationMandatory, ?string $ancillaryOf): void
+    public function addStudy(String $name, string $code, int $patientCodeLength, string $contactEmail, bool $controllerShowAll, bool $monitorShowAll, bool $documentationMandatory, ?string $ancillaryOf, bool $creatablePatientsInvestigator): void
     {
         $study = new Study();
         $study->name = $name;
@@ -38,6 +38,7 @@ public function addStudy(String $name, string $code, int $patientCodeLength, str
         $study->monitor_show_all = $monitorShowAll;
         $study->documentation_mandatory = $documentationMandatory;
         $study->ancillary_of = $ancillaryOf;
+        $study->creatable_patients_investigator = $creatablePatientsInvestigator;
         $study->save();
     }