Merge pull request #721 from Pixilib/GaelO2-dev

Gael o2 dev
Pixilib · Apr 17, 2024 · 27802af · 27802af
2 parents e7dc0d6 + 3b21f4a
commit 27802af
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Showing 37 changed files with 1,249 additions and 2,274 deletions.
diff --git a/.github/workflows/clean-packages.yml b/.github/workflows/clean-packages.yml
@@ -3,7 +3,7 @@ name: 'clean-packages'
 on:
   push:
     branches:
-      - Gaelo2
+      - '*'
 
 jobs:
   build:
@@ -20,7 +20,7 @@ jobs:
           username: 'salimkanoun'
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: actions/delete-package-versions@v4
+      - uses: actions/delete-package-versions@v5
         with: 
           package-name: 'gaelo'
           package-type: 'container'

diff --git a/Dockerfile b/Dockerfile
@@ -22,6 +22,8 @@ RUN apt-get update -qy && \
     sqlite3 \
     supervisor \
     zip \
+    libc-client-dev \
+    libkrb5-dev \
     libpng-dev \
     libmemcached-dev \
     mariadb-client \
@@ -30,6 +32,10 @@ RUN apt-get update -qy && \
 
 RUN pecl install pcov redis memcached
 RUN docker-php-ext-install gd zip pdo pdo_mysql pdo_pgsql mbstring bcmath ctype fileinfo xml bz2 pcntl curl ftp
+
+RUN docker-php-ext-configure imap --with-kerberos --with-imap-ssl && \
+    docker-php-ext-install imap
+
 RUN docker-php-ext-configure opcache --enable-opcache \
     && docker-php-ext-install opcache
 

diff --git a/GaelO2/.env.example b/GaelO2/.env.example
@@ -42,6 +42,9 @@ AZURE_CONTAINER_NAME=''
 AZURE_BLOB_PREFIX=''
 AZURE_FILE_CACHE_CONTAINER_NAME=''
 FILE_CACHE_DRIVER='file'
+MONITORING_IMAP_CONNECTION_STRING=''
+MONITORING_IMAP_USERNAME=''
+MONITORING_IMAP_PASSWORD=''
 
 BROADCAST_DRIVER=log
 CACHE_DRIVER=file

diff --git a/GaelO2/app/Console/Commands/DeleteVisitsOlderThan.php b/GaelO2/app/Console/Commands/DeleteVisitsOlderThan.php
@@ -95,7 +95,7 @@ public function handle(
 
         $this->gaelODeleteRessourcesRepository->deleteReviews($visitIds, $studyName);
         $this->gaelODeleteRessourcesRepository->deleteReviewStatus($visitIds, $studyName);
-        $this->gaelODeleteRessourcesRepository->deleteTrackerOfVisits($visitIds, $studyEntity->name);
+        $this->gaelODeleteRessourcesRepository->deleteTrackerOfVisits($visitIds, $studyName);
 
         $dicomSeries = $this->getDicomSeriesOfVisits($visitIds);
         $orthancIdArray = array_map(function ($seriesId) {
@@ -119,10 +119,8 @@ public function handle(
             }
         }
 
-
         $this->info('The command was successful !');
 
-
         return 0;
     }
 

diff --git a/GaelO2/app/GaelO/Services/FormService/ReviewFormService.php b/GaelO2/app/GaelO/Services/FormService/ReviewFormService.php
@@ -2,7 +2,6 @@
 
 namespace App\GaelO\Services\FormService;
 
-use App\GaelO\Constants\Constants;
 use App\GaelO\Constants\Enums\ReviewStatusEnum;
 use App\GaelO\Exceptions\GaelOBadRequestException;
 use App\GaelO\Exceptions\GaelOException;

diff --git a/GaelO2/app/GaelO/Services/GaelOProcessingService/TmtvProcessingService.php b/GaelO2/app/GaelO/Services/GaelOProcessingService/TmtvProcessingService.php
@@ -38,7 +38,7 @@ public function runInference(): MaskProcessingService
         $this->orthancService->sendDicomToProcessing($this->ptOrthancSeriesId, $this->gaelOProcessingService);
         $this->addCreatedRessource('dicoms', $this->ptOrthancSeriesId);
         $this->orthancService->sendDicomToProcessing($this->ctOrthancSeriesId, $this->gaelOProcessingService);
-        $this->addCreatedRessource('dicoms', $this->ptOrthancSeriesId);
+        $this->addCreatedRessource('dicoms', $this->ctOrthancSeriesId);
 
         $idPT = $this->gaelOProcessingService->createSeriesFromOrthanc($this->ptOrthancSeriesId, true, true);
         $this->addCreatedRessource('series', $idPT);

diff --git a/GaelO2/app/GaelO/Services/GaelOStudiesService/AbstractVisitDecisions.php b/GaelO2/app/GaelO/Services/GaelOStudiesService/AbstractVisitDecisions.php
@@ -43,12 +43,16 @@ public function getPatientId()
         return $this->visitContext['patient_id'];
     }
 
-
     public function getPatientCode()
     {
         return $this->visitContext['patient']['code'];
     }
 
+    public function getVisitName(): string
+    {
+        return $this->visitContext['visit_type']['name'];
+    }
+
     /**
      * Must return the review status for each action on review (send, delete, unlock), 
      * needs to handle backward and forward

diff --git a/GaelO2/app/GaelO/Services/GaelOStudiesService/ExpectedPatient/ExpectedPatient.php b/GaelO2/app/GaelO/Services/GaelOStudiesService/ExpectedPatient/ExpectedPatient.php
@@ -5,10 +5,10 @@
 class ExpectedPatient
 {
     public string $code;
-    public int $centerCode;
+    public ?int $centerCode;
     public ?string $inclusionStatus;
 
-    public function __construct(string $code, int $centerCode = null, ?string $inclusionStatus = null)
+    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
@@ -390,7 +390,7 @@ public function sendUnlockedFormMessage(int $visitId, bool $investigatorForm, in
         $mailListBuilder = new MailListBuilder($this->userRepositoryInterface);
 
         $parameters = [
-            'name' => $this->getUserName($requestingUserId),
+            'supervisorName' => $this->getUserName($requestingUserId),
             'study' => $studyName,
             'patientId' => $patientId,
             'patientCode' => $patientCode,
@@ -624,7 +624,7 @@ public function sendRadiomicsReport(string $studyName, string $patientCode, stri
     }
 
 
-    public function sendJobFailure(string $jobType, array $details, string $errorMessage)
+    public function sendJobFailure(string $jobType, array $details, string $errorMessage, ?string $studyName = null, ?int $toUserId = null)
     {
         $parameters = [
             'jobType' => $jobType,
@@ -634,6 +634,12 @@ public function sendJobFailure(string $jobType, array $details, string $errorMes
 
         $mailListBuilder = new MailListBuilder($this->userRepositoryInterface, $this->studyRepositoryInterface);
         $mailListBuilder->withAdminsEmails();
+        if ($studyName) {
+            $mailListBuilder->withUsersEmailsByRolesInStudy($studyName, Constants::ROLE_SUPERVISOR);
+        }
+        if ($toUserId) {
+            $mailListBuilder->withUserEmail($toUserId);
+        }
         $this->mailInterface->setTo($mailListBuilder->get());
         $this->mailInterface->setParameters($parameters);
         $this->mailInterface->setBody(MailConstants::EMAIL_JOB_FAILURE);

diff --git a/GaelO2/app/GaelO/UseCases/GetStudyReviewProgression/GetStudyReviewProgression.php b/GaelO2/app/GaelO/UseCases/GetStudyReviewProgression/GetStudyReviewProgression.php
@@ -64,7 +64,7 @@ public function execute(GetStudyReviewProgressionRequest $getStudyReviewProgress
             $visits = $this->visitRepositoryInterface->getVisitsInStudy($originalStudyName, true, false, false, $studyName);
 
             //Get validated review for study
-            $validatedReview = $this->reviewRepositoryInterface->getStudyReviewsGroupedByUserIds($originalStudyName);
+            $validatedReview = $this->reviewRepositoryInterface->getStudyReviewsGroupedByUserIds($studyName);
 
             $answer = [];
 
@@ -74,18 +74,19 @@ public function execute(GetStudyReviewProgressionRequest $getStudyReviewProgress
                 //Listing users having done a review of this visit
                 if (key_exists($visitId, $validatedReview)) {
                     $userIdHavingReviewed = array_keys($validatedReview[$visitId]);
+                } else {
+                    $userIdHavingReviewed = [];
                 }
-                else $userIdHavingReviewed = [];
 
                 //Listing users not having done review of this visit
                 $userIdNotHavingReviewed = array_diff(array_keys($reviewersById), $userIdHavingReviewed);
 
                 $userDetailsHavingReviewed = [];
                 //Get reviewer details having reviewed from db answer (user may have been removed so won't be in the list of current reviewer in the study)
-                foreach($userIdHavingReviewed as $reviewerId){
+                foreach ($userIdHavingReviewed as $reviewerId) {
                     $userDetailsHavingReviewed[] = $validatedReview[(string) $visitId][(string) $reviewerId][0]['user'];
                 }
-               
+
                 $answer[] = [
                     'visitId' => $visitId,
                     'patientId' => $visit['patient_id'],

diff --git a/GaelO2/app/GaelO/views/mails/mail_unlocked_form.blade.php b/GaelO2/app/GaelO/views/mails/mail_unlocked_form.blade.php
@@ -4,6 +4,6 @@
     Your {{$formType}} form sent for study : {{$study}}<br>
     Patient Code : {{$patientCode}}<br>
     Visit  : {{$visitType}}<br>
-    Has been Unlocked.<br>
+    Has been unlocked by {{$supervisorName}}.<br>
     You can now resend a new version of this form.<br>
 @endsection
diff --git a/GaelO2/app/Models/Center.php b/GaelO2/app/Models/Center.php
@@ -12,12 +12,15 @@ class Center extends Model
     protected $primaryKey = 'code';
     public $incrementing = false;
 
-    protected $casts = [
-        'code' => 'integer',
-        'name' => 'string',
-        'country_code' => 'string'
-    ];
-
+    protected function casts(): array
+    {
+        return [
+            'code' => 'integer',
+            'name' => 'string',
+            'country_code' => 'string'
+        ];
+    }
+
     public function country()
     {
         return $this->belongsTo(Country::class, 'country_code', 'code');

diff --git a/GaelO2/app/Models/CenterUser.php b/GaelO2/app/Models/CenterUser.php
@@ -9,10 +9,13 @@ class CenterUser extends Model
 {
     use HasFactory;
 
-    protected $casts = [
-        'user_id' => 'integer',
-        'center_code' => 'integer'
-    ];
+    protected function casts(): array
+    {
+        return [
+            'user_id' => 'integer',
+            'center_code' => 'integer'
+        ];
+    }
 
     /**
      * The table associated with the model.

diff --git a/GaelO2/app/Models/Country.php b/GaelO2/app/Models/Country.php
@@ -9,10 +9,12 @@ class Country extends Model
     protected $primaryKey = 'code';
     public $incrementing = false;
 
-    protected $casts = [
-        'code' => 'string',
-        'country_us' => 'string',
-        'country_fr' => 'string'
-    ];
-
+    protected function casts(): array
+    {
+        return [
+            'code' => 'string',
+            'country_us' => 'string',
+            'country_fr' => 'string'
+        ];
+    }
 }
diff --git a/GaelO2/app/Models/DicomSeries.php b/GaelO2/app/Models/DicomSeries.php
@@ -15,27 +15,30 @@ class DicomSeries extends Model
     protected $keyType = 'string';
     public $incrementing = false;
 
-    protected $casts = [
-        'series_uid' => 'string',
-        'study_instance_uid' => 'string',
-        'orthanc_id' => 'string',
-        'acquisition_date' => 'date:Y-m-d',
-        'acquisition_time' => 'datetime:H:i:s',
-        'modality' => 'string',
-        'series_description' => 'string',
-        'injected_dose' => 'integer',
-        'radiopharmaceutical' => 'string',
-        'half_life' => 'integer',
-        'injected_time' => 'datetime:H:i:s',
-        'injected_datetime' => 'datetime',
-        'patient_weight' => 'integer',
-        'number_of_instances' => 'integer',
-        'series_number' => 'string',
-        'disk_size' => 'integer',
-        'uncompressed_disk_size' => 'integer',
-        'manufacturer' => 'string',
-        'model_name' => 'string'
-    ];
+    protected function casts(): array
+    {
+        return [
+            'series_uid' => 'string',
+            'study_instance_uid' => 'string',
+            'orthanc_id' => 'string',
+            'acquisition_date' => 'date:Y-m-d',
+            'acquisition_time' => 'datetime:H:i:s',
+            'modality' => 'string',
+            'series_description' => 'string',
+            'injected_dose' => 'integer',
+            'radiopharmaceutical' => 'string',
+            'half_life' => 'integer',
+            'injected_time' => 'datetime:H:i:s',
+            'injected_datetime' => 'datetime',
+            'patient_weight' => 'integer',
+            'number_of_instances' => 'integer',
+            'series_number' => 'string',
+            'disk_size' => 'integer',
+            'uncompressed_disk_size' => 'integer',
+            'manufacturer' => 'string',
+            'model_name' => 'string'
+        ];
+    }
 
     public function dicomStudy()
     {

diff --git a/GaelO2/app/Models/DicomStudy.php b/GaelO2/app/Models/DicomStudy.php
@@ -15,24 +15,27 @@ class DicomStudy extends Model
     protected $keyType = 'string';
     public $incrementing = false;
 
-    protected $casts = [
-        'study_uid' => 'string',
-        'orthanc_id' => 'string',
-        'visit_id' => 'integer',
-        'user_id' => 'integer',
-        'upload_date' => 'datetime',
-        'acquisition_date' => 'date:Y-m-d',
-        'acquisition_time' => 'datetime:H:i:s',
-        'anon_from_orthanc_id' => 'string',
-        'study_description' => 'string',
-        'patient_orthanc_id' => 'string',
-        'patient_name' => 'string',
-        'patient_id' => 'string',
-        'number_of_series' => 'integer',
-        'number_of_instances' => 'integer',
-        'disk_size' => 'integer',
-        'uncompressed_disk_size' => 'integer'
-    ];
+    protected function casts(): array
+    {
+        return [
+            'study_uid' => 'string',
+            'orthanc_id' => 'string',
+            'visit_id' => 'integer',
+            'user_id' => 'integer',
+            'upload_date' => 'datetime',
+            'acquisition_date' => 'date:Y-m-d',
+            'acquisition_time' => 'datetime:H:i:s',
+            'anon_from_orthanc_id' => 'string',
+            'study_description' => 'string',
+            'patient_orthanc_id' => 'string',
+            'patient_name' => 'string',
+            'patient_id' => 'string',
+            'number_of_series' => 'integer',
+            'number_of_instances' => 'integer',
+            'disk_size' => 'integer',
+            'uncompressed_disk_size' => 'integer'
+        ];
+    }
 
     public function dicomSeries()
     {

diff --git a/GaelO2/app/Models/Documentation.php b/GaelO2/app/Models/Documentation.php
@@ -10,18 +10,21 @@ class Documentation extends Model
 {
     use SoftDeletes, HasFactory;
 
-    protected $casts = [
-        'id' => 'integer',
-        'name' => 'string',
-        'document_date' => 'datetime',
-        'study_name' => 'string',
-        'version' => 'string',
-        'investigator' => 'boolean',
-        'controller' => 'boolean',
-        'monitor' => 'boolean',
-        'reviewer' => 'boolean',
-        'path' => 'string'
-    ];
+    protected function casts(): array
+    {
+        return [
+            'id' => 'integer',
+            'name' => 'string',
+            'document_date' => 'datetime',
+            'study_name' => 'string',
+            'version' => 'string',
+            'investigator' => 'boolean',
+            'controller' => 'boolean',
+            'monitor' => 'boolean',
+            'reviewer' => 'boolean',
+            'path' => 'string'
+        ];
+    }
 
     public function study()
     {