salimkanoun / GaelO

src/scripts/add_review_attached_file.php

Spacing +4 added lines, -4 removed lines

@@ -44,11 +44,11 @@
 	$fileMime=$_FILES['files']['type'][0];
 	$tempFileLocation=$_FILES['files']['tmp_name'][0];
 	$fileSize=$_FILES['files']['size'][0];
-	try{
+	try {
 		$formProcessor->storeAssociatedFile($fileKey, $fileMime, $fileSize, $tempFileLocation);
-		echo( json_encode((true)) );
-	}catch (Throwable $t){
-		echo (json_encode((false)) );
+		echo(json_encode((true)));
+	}catch (Throwable $t) {
+		echo (json_encode((false)));
 	}
 
 }else {

Braces +2 added lines, -2 removed lines

@@ -47,11 +47,11 @@
 	try{
 		$formProcessor->storeAssociatedFile($fileKey, $fileMime, $fileSize, $tempFileLocation);
 		echo( json_encode((true)) );
-	}catch (Throwable $t){
+	} catch (Throwable $t){
 		echo (json_encode((false)) );
 	}
 
-}else {
+} else {
 	header('HTTP/1.0 403 Forbidden');
 	die('You are not allowed to access this file.');
 }
\ No newline at end of file

src/scripts/is_review_attached_file.php

Braces +7 added lines, -4 removed lines

@@ -31,17 +31,20 @@
 if ($accessCheck && in_array($_SESSION['role'], array(User::INVESTIGATOR, User::REVIEWER))) {
 
 	try {
-		if ($_SESSION['role'] == User::INVESTIGATOR) $reviewObject=$visitObject->getReviewsObject(true);
-		else $reviewObject=$visitObject->queryExistingReviewForReviewer($_SESSION['username']);
+		if ($_SESSION['role'] == User::INVESTIGATOR) {
+			$reviewObject=$visitObject->getReviewsObject(true);
+		} else {
+			$reviewObject=$visitObject->queryExistingReviewForReviewer($_SESSION['username']);
+		}
 		$filePath=$reviewObject->getAssociatedFilePath($fileKey);
 		$answer=is_file($filePath);
-	}catch (Exception $e) {
+	} catch (Exception $e) {
 		$answer=false;
 	}
 
 	echo(json_encode($answer));
 
-}else {
+} else {
 	header('HTTP/1.0 403 Forbidden');
 	die('You are not allowed to access this file.');
 }
\ No newline at end of file

src/models/Review.php

Spacing +6 added lines, -6 removed lines

@@ -40,7 +40,7 @@ 
 		));
 		$reviewData=$dataFetcher->fetch(PDO::FETCH_ASSOC);
 
-		if(empty($reviewData)) throw new Exception('No Review '.$id_review.' found');
+		if (empty($reviewData)) throw new Exception('No Review '.$id_review.' found');
         
 		$this->id_visit=$reviewData['id_visit'];
 		$this->username=$reviewData['username'];
@@ -183,9 +183,9 @@ 
 	 */
 	public function getAssociatedFilePath(string $fileKey) : String {
 		$fileArray=$this->associatedFiles;
-		if(array_key_exists($fileKey, $fileArray)){
+		if (array_key_exists($fileKey, $fileArray)) {
 			return $this->getAssociatedFileRootPath().'/'.$fileArray[$fileKey];
-		} else {
+		}else {
 			throw new Exception('Non Existing Key');
 		}
 		
@@ -194,9 +194,9 @@ 
 	public function deleteAssociatedFile($fileKey) {
 
 		if (!$this->validated) {
-			$filePath = $this->getAssociatedFilePath($fileKey);
-			if( ! is_file( $filePath ) ) throw new Exception('No File To Delete');
-			unlink( $filePath );
+			$filePath=$this->getAssociatedFilePath($fileKey);
+			if (!is_file($filePath)) throw new Exception('No File To Delete');
+			unlink($filePath);
 			unset($this->associatedFiles[$fileKey]);
 			$this->updateAssociatedFiles($this->associatedFiles);
 

Braces +10 added lines, -6 removed lines

@@ -40,7 +40,9 @@ 
 		));
 		$reviewData=$dataFetcher->fetch(PDO::FETCH_ASSOC);
 
-		if(empty($reviewData)) throw new Exception('No Review '.$id_review.' found');
+		if(empty($reviewData)) {
+			throw new Exception('No Review '.$id_review.' found');
+		}
         
 		$this->id_visit=$reviewData['id_visit'];
 		$this->username=$reviewData['username'];
@@ -109,7 +111,7 @@ 
 		if ($this->isLocal) {
 			$visitObject->resetQC();
 			$visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_NOT_DONE);
-		}else {
+		} else {
 			$formProcessor=$visitObject->getFromProcessor($this->isLocal, $this->username);
 			$formProcessor->setVisitValidation();
 		}
@@ -162,7 +164,7 @@ 
         
 		if ($result) {
 			return $finalFilename;
-		}else {
+		} else {
 			throw New Exception('Error writing associated File');
 		}
         
@@ -195,12 +197,14 @@ 
 
 		if (!$this->validated) {
 			$filePath = $this->getAssociatedFilePath($fileKey);
-			if( ! is_file( $filePath ) ) throw new Exception('No File To Delete');
+			if( ! is_file( $filePath ) ) {
+				throw new Exception('No File To Delete');
+			}
 			unlink( $filePath );
 			unset($this->associatedFiles[$fileKey]);
 			$this->updateAssociatedFiles($this->associatedFiles);
 
-		}else {
+		} else {
 			throw new Exception('Validated Review, can\'t remove file');
 		}
 
@@ -233,7 +237,7 @@ 
         
 		if ($this->isLocal) {
 			$visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_DRAFT);
-		}else {
+		} else {
 			$formProcessor=$visitObject->getFromProcessor($this->isLocal, $this->username);
 			$formProcessor->setVisitValidation();
 		}

src/models/Export_Study_Data.php

Spacing +4 added lines, -4 removed lines

@@ -83,7 +83,7 @@ 
 			foreach ($reviewsObjects as $reviewObject) {
 
 				foreach ($reviewObject->associatedFiles as $associatedFileKey => $associatedFilePath) {
-					$associatedFileLocation = $reviewObject->getAssociatedFilePath($associatedFileKey);
+					$associatedFileLocation=$reviewObject->getAssociatedFilePath($associatedFileKey);
 					$zip->addFile($associatedFileLocation);
 
 				};
@@ -256,9 +256,9 @@ 
 		$reviewDatas=$this->getGenericData($review);
 		$specificData=$review->getSpecificData();
 		unset($specificData["id_review"]);
-		$specificDataArray = [];
-		if( !empty($specificData) ){
-			$specificDataArray = array_values($specificData);
+		$specificDataArray=[];
+		if (!empty($specificData)) {
+			$specificDataArray=array_values($specificData);
 		}
 		$reviewLine=[...$reviewDatas, ...$specificDataArray];
 

Braces +14 added lines, -14 removed lines

@@ -39,7 +39,7 @@ 
 				$modalityCreatedVisits=$this->studyObject->getStudySpecificGroupManager($visitGroup->groupModality)->getCreatedVisits();
 				$modalityDeletedVisits=$this->studyObject->getStudySpecificGroupManager($visitGroup->groupModality)->getCreatedVisits(true);
 				array_push($this->allcreatedVisits, ...$modalityCreatedVisits, ...$modalityDeletedVisits);
-			}catch (Exception $e) { }
+			} catch (Exception $e) { }
 		}
 	}
 
@@ -216,12 +216,12 @@ 
 		$localReviews=[];
 		try {
 			$localReviews[]=$visitObject->getReviewsObject(true);
-		}catch (Exception $e) { }
+		} catch (Exception $e) { }
 
 		$expertReviews=[];
 		try {
 			$expertReviews=$visitObject->getReviewsObject(false, true);
-		}catch (Exception $e) { }
+		} catch (Exception $e) { }
 
 		//Merge all reviews in an array
 		$reviewObjects=array_merge($localReviews, $expertReviews);
@@ -320,29 +320,29 @@ 
 
 		if ($visitObject->statusDone == Visit::NOT_DONE) {
 			return 0;
-		}else if ($visitObject->uploadStatus == Visit::NOT_DONE || $visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
+		} else if ($visitObject->uploadStatus == Visit::NOT_DONE || $visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
 			if ($visitObject->uploadStatus == Visit::NOT_DONE && $visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
 				return 1;
-			}else if ($visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
+			} else if ($visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
 				return 3;
-			}else if ($visitObject->uploadStatus == Visit::NOT_DONE) {
+			} else if ($visitObject->uploadStatus == Visit::NOT_DONE) {
 				return 2;
 			}
-		}else if ($visitObject->qcStatus == Visit::QC_NOT_DONE) {
+		} else if ($visitObject->qcStatus == Visit::QC_NOT_DONE) {
 			return 4;
-		}else if ($visitObject->qcStatus == Visit::QC_CORRECTIVE_ACTION_ASKED) {
+		} else if ($visitObject->qcStatus == Visit::QC_CORRECTIVE_ACTION_ASKED) {
 			return 5;
-		}else if ($visitObject->qcStatus == Visit::QC_REFUSED) {
+		} else if ($visitObject->qcStatus == Visit::QC_REFUSED) {
 			return 6;
-		}else if ($visitObject->reviewStatus == Visit::NOT_DONE) {
+		} else if ($visitObject->reviewStatus == Visit::NOT_DONE) {
 			return 7;
-		}else if ($visitObject->reviewStatus == Visit::REVIEW_ONGOING) {
+		} else if ($visitObject->reviewStatus == Visit::REVIEW_ONGOING) {
 			return 8;
-		}else if ($visitObject->reviewStatus == Visit::REVIEW_WAIT_ADJUDICATION) {
+		} else if ($visitObject->reviewStatus == Visit::REVIEW_WAIT_ADJUDICATION) {
 			return 9;
-		}else if ($visitObject->reviewStatus == Visit::REVIEW_DONE) {
+		} else if ($visitObject->reviewStatus == Visit::REVIEW_DONE) {
 			return 10;
-		}else {
+		} else {
 			//If none of these case return -1, should not happen
 			return -1;
 		}

src/models/Form_Processor_File.php

Spacing +2 added lines, -2 removed lines

@@ -48,8 +48,8 @@
 		return 5;
 	}
 
-	private function createEmptySpecificForm(){
-		$insertion = $this->linkpdo->prepare('INSERT INTO '.$this->specificTable.' (id_review) VALUES (:id_review)');
+	private function createEmptySpecificForm() {
+		$insertion=$this->linkpdo->prepare('INSERT INTO '.$this->specificTable.' (id_review) VALUES (:id_review)');
 		$insertion->execute(array(
 			'id_review' => $this->reviewObject->id_review )
 		);

Braces +10 added lines, -4 removed lines

@@ -64,7 +64,7 @@ 
 		if (empty($this->reviewObject)) {
 			$this->createReview();
 			$this->createEmptySpecificForm();
-		}else {
+		} else {
 			//If review exist but validated throw exception
 			if ($this->reviewObject->validated) {
 				throw new Exception('Validated Review, can\'t add File');
@@ -74,9 +74,15 @@ 
 		//Get extension of file and check extension is allowed
 		//Get filesize and check it matches limits
 		$sizeMb=$fileSize/1048576;
-		if ($sizeMb > $this->getMaxSizeMb()) throw new Exception('File over limits');
-		if (!$this->isInDeclaredKey($fileKey)) throw new Exception('Unhauthrized file key'); 
-		if (!$this->isInAllowedType($mime)) throw new Exception('Extension not allowed');
+		if ($sizeMb > $this->getMaxSizeMb()) {
+			throw new Exception('File over limits');
+		}
+		if (!$this->isInDeclaredKey($fileKey)) {
+			throw new Exception('Unhauthrized file key');
+		}
+		if (!$this->isInAllowedType($mime)) {
+			throw new Exception('Extension not allowed');
+		}
 
 		$mimes=new \Mimey\MimeTypes;
 		$extension=$mimes->getExtension($mime);

src/rest/download-dicom.php

Spacing +3 added lines, -3 removed lines

@@ -39,7 +39,7 @@ 
 	//Generate zip from orthanc and output it to the navigator
 	$orthanc=new Orthanc();
 	$zipStream=$orthanc->getZipStream($resultatsIDs);
-	$fstat = fstat($zipStream);
+	$fstat=fstat($zipStream);
 
 	header("Content-Type: application/zip");
 	header("Content-Transfer-Encoding: Binary");
@@ -51,7 +51,7 @@ 
 	header("Expires: 0");
 
 	rewind($zipStream);
-	if(!$zipStream) exit('no file to stream');
+	if (!$zipStream) exit('no file to stream');
 
 	while (!feof($zipStream)) {
 		print(@fread($zipStream, 1024*1024));
@@ -60,7 +60,7 @@ 
 	
 	fclose($zipStream);
 	
-} else {
+}else {
 	header('HTTP/1.0 403 Forbidden');
 	die('You are not allowed to access this file.'); 
 }
\ No newline at end of file

Braces +3 added lines, -1 removed lines

@@ -51,7 +51,9 @@
 	header("Expires: 0");
 
 	rewind($zipStream);
-	if(!$zipStream) exit('no file to stream');
+	if(!$zipStream) {
+		exit('no file to stream');
+	}
 
 	while (!feof($zipStream)) {
 		print(@fread($zipStream, 1024*1024));

src/scripts/download_dicom.php

Spacing +2 added lines, -2 removed lines

@@ -66,7 +66,7 @@ 
 	$orthanc=new Orthanc();
 	
 	$zipStream=$orthanc->getZipStream($ids);
-	$fstat = fstat($zipStream);
+	$fstat=fstat($zipStream);
 	
 	header("Content-Type: application/zip");
 	header("Content-Transfer-Encoding: Binary");
@@ -89,7 +89,7 @@ 
 	header("Expires: 0");
 	
 	rewind($zipStream);
-	if(!$zipStream) exit('no file to stream');
+	if (!$zipStream) exit('no file to stream');
 
 	while (!feof($zipStream)) {
 		print(@fread($zipStream, 1024*1024));

Braces +8 added lines, -7 removed lines

@@ -39,19 +39,18 @@ 
 	$json=json_decode($postdata, true);
 	//SK ICI VERIFIER QUE LES id SONT BIEN DE L ETUDE AVEC LES DROITS ? Securite
 	$ids=$json['json'];
-}
-else if ($_SESSION['role'] == User::REVIEWER) {
+} else if ($_SESSION['role'] == User::REVIEWER) {
 	$permissionCheck=$userObject->isVisitAllowed($_POST['id_visit'], $_SESSION['role']);
 	$visitObject=new Visit($_POST['id_visit'], $linkpdo);
 	$ids=$visitObject->getSeriesOrthancID();
     
-}else if ($_SESSION['role'] == User::CONTROLLER) {
+} else if ($_SESSION['role'] == User::CONTROLLER) {
 	$permissionCheck=$userObject->isVisitAllowed($_POST['id_visit'], $_SESSION['role']);
 	$visitObject=new Visit($_POST['id_visit'], $linkpdo);
 	if (in_array($visitObject->qcStatus, array(Visit::QC_NOT_DONE, Visit::QC_WAIT_DEFINITVE_CONCLUSION))) {
 		$ids=$visitObject->getSeriesOrthancID();
 	}
-}else if ($_SESSION['role'] == User::INVESTIGATOR) {
+} else if ($_SESSION['role'] == User::INVESTIGATOR) {
 	$permissionCheck=$userObject->isVisitAllowed($_POST['id_visit'], $_SESSION['role']);
 	$visitObject=new Visit($_POST['id_visit'], $linkpdo);
 	if ($visitObject->uploadStatus == Visit::DONE) {
@@ -78,7 +77,7 @@ 
 		$date=Date('Ymd_his');
 		header('Content-Disposition: attachment; filename="Dicom-'.$_SESSION['study'].'_'.$date.'.zip"');
 	//For reviewer file name is identified by study_visit
-	}else {
+	} else {
 		$name=$_SESSION['study'].$visitObject->visitType;
 		header('Content-Disposition: attachment; filename="Dicom'.$name.'.zip"');
 	}
@@ -89,7 +88,9 @@ 
 	header("Expires: 0");
 	
 	rewind($zipStream);
-	if(!$zipStream) exit('no file to stream');
+	if(!$zipStream) {
+		exit('no file to stream');
+	}
 
 	while (!feof($zipStream)) {
 		print(@fread($zipStream, 1024*1024));
@@ -98,7 +99,7 @@ 
 	
 	fclose($zipStream);
 
-}else {
+} else {
 	header('HTTP/1.0 403 Forbidden');
 	die('You are not allowed to access this file.'); 
 }
\ No newline at end of file

src/rest/get-existing-form.php

Spacing +4 added lines, -4 removed lines

@@ -35,17 +35,17 @@
 	$visitObject=new Visit($id_visit, $linkpdo);
 	
 	try {
-		$formProcessor = $visitObject->getFromProcessor(false, $username);
-		$reviewData = $formProcessor->getExistingFormData();
+		$formProcessor=$visitObject->getFromProcessor(false, $username);
+		$reviewData=$formProcessor->getExistingFormData();
 		echo(json_encode($reviewData));
 
-	} catch (Exception $e) {
+	}catch (Exception $e) {
 		error_log($e->getMessage());
 		header('HTTP/1.0 404 Not Found');
 	}
 
     
-} else {
+}else {
 	header('HTTP/1.0 403 Forbidden');
 	die('You are not allowed to access this file.'); 
     

src/models/Form_Processor.php

Spacing +3 added lines, -3 removed lines

@@ -122,7 +122,7 @@ 
 			throw new Exception("Error during save");
 		}
 
-		if($update){
+		if ($update) {
 			$this->reviewObject->updateReviewDate();
 		}
 		
@@ -254,9 +254,9 @@ 
 	 * can be overrided to add additional data such as investigator form data
 	 */
 	public function getExistingFormData() {
-		if( ! empty($this->reviewObject)){
+		if (!empty($this->reviewObject)) {
 			return ($this->reviewObject->getSpecificData());
-		}else{
+		}else {
 			return [];
 		}
 		

Braces +9 added lines, -9 removed lines

@@ -102,7 +102,7 @@ 
 		if (empty($this->reviewObject)) {
 			$this->createReview();
 			$update=false;       
-		}else {
+		} else {
 			$update=true;
 			//If already existing validated review, exit without modifying anything
 			if ($this->reviewObject->validated) {
@@ -114,7 +114,7 @@ 
 		//Call the child redifined save specific form to save the specific data of the form
 		try {
 			$this->saveSpecificForm($data, $this->reviewObject->id_review, $update);
-		}catch (Exception $e) {
+		} catch (Exception $e) {
 			error_log($e->getMessage());
 			if (!$update) {
 				$this->reviewObject->hardDeleteReview();
@@ -133,7 +133,7 @@ 
 		if ($this->local) {
 			if ($validate) {
 				$this->visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_DONE);
-			}else {
+			} else {
 				$this->visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_DRAFT);
 			}
 		}
@@ -141,7 +141,7 @@ 
 		//Log Activity
 		if ($this->local) {
 			$role="Investigator";
-		}else {
+		} else {
 			$role="Reviewer";
 		}
 		$actionDetails['patient_code']=$this->visitObject->patientCode;
@@ -184,7 +184,7 @@ 
 					->addGroupEmails($this->visitObject->study, User::SUPERVISOR);
 			$email->sendAwaitingAdjudicationMessage($this->visitObject->study, $this->visitObject->patientCode, $this->visitObject->visitType);
 
-		}else if ($reviewStatus == Visit::REVIEW_DONE) {
+		} else if ($reviewStatus == Visit::REVIEW_DONE) {
 
 			$email=new Send_Email($this->linkpdo);
 			$uploaderUserObject=new User($this->visitObject->uploaderUsername, $this->linkpdo);
@@ -206,11 +206,11 @@ 
 		try {
 			if ($this->local) {
 				$this->reviewObject=$this->visitObject->getReviewsObject(true);
-			}else {
+			} else {
 				$this->reviewObject=$this->visitObject->queryExistingReviewForReviewer($this->username);
 			}
 
-		}catch (Exception $e) { }
+		} catch (Exception $e) { }
 	    
 		return $this->reviewObject;
 		
@@ -239,7 +239,7 @@ 
 		$validatedReviewObjects=array_filter($reviewsObject, function($review) {
 			if ($review->validated) {
 				return true;
-			}else {
+			} else {
 				return false;
 			}
 		});
@@ -256,7 +256,7 @@ 
 	public function getExistingFormData() {
 		if( ! empty($this->reviewObject)){
 			return ($this->reviewObject->getSpecificData());
-		}else{
+		} else{
 			return [];
 		}