salimkanoun / GaelO

src/models/Orthanc_Serie.php

Spacing +14 added lines, -14 removed lines

@@ -52,7 +52,7 @@ 
 	public function __construct($seriesOrthancID, $url, $context) {
 		//Set Orthanc http address
 		$this->url=$url;
-		$this->context = $context;
+		$this->context=$context;
 	    
 		//Set the current serie's Orthanc ID
 		$this->serieOrthancID=$seriesOrthancID;
@@ -61,12 +61,12 @@ 
 	/**
 	 *Get Series related data and store them in this object
 	 */
-	public function retrieveSeriesData(){
-		$context  = stream_context_create($this->context);
+	public function retrieveSeriesData() {
+		$context=stream_context_create($this->context);
 		//Store all shared tags
-		$this->sharedTags = json_decode(file_get_contents($this->url.'/series/'.$this->serieOrthancID.'/shared-tags', false, $context));
+		$this->sharedTags=json_decode(file_get_contents($this->url.'/series/'.$this->serieOrthancID.'/shared-tags', false, $context));
 		//parse main series informations
-		$json = file_get_contents($this->url.'/series/'.$this->serieOrthancID, false, $context);
+		$json=file_get_contents($this->url.'/series/'.$this->serieOrthancID, false, $context);
 		$seriesJson=json_decode($json, true);
 		//add needed informations in the current object
 		$this->seriesManufacturer=$seriesJson['MainDicomTags']['Manufacturer'];
@@ -93,9 +93,9 @@ 
 	/**
 	 * Get statistics of the series (size in MB)
 	 */
-	private function retrieveSeriesStatistics(){
-		$context  = stream_context_create($this->context);
-		$json = file_get_contents($this->url.'/series/'.$this->serieOrthancID.'/statistics/', false, $context);
+	private function retrieveSeriesStatistics() {
+		$context=stream_context_create($this->context);
+		$json=file_get_contents($this->url.'/series/'.$this->serieOrthancID.'/statistics/', false, $context);
 		$statisticsJson=json_decode($json, true);
 		$this->diskSizeMb=$statisticsJson['DiskSizeMB'];
 		$this->uncompressedSizeMb=$statisticsJson['UncompressedSizeMB'];
@@ -106,16 +106,16 @@ 
 	 * Store some data only available in the Instance level 
 	 * @param $instanceID
 	 */
-	private function retrieveInstancesData($instanceID){
-		$context  = stream_context_create($this->context);
-		$json = file_get_contents($this->url.'/instances/'.$instanceID.'/tags/', false, $context);
+	private function retrieveInstancesData($instanceID) {
+		$context=stream_context_create($this->context);
+		$json=file_get_contents($this->url.'/instances/'.$instanceID.'/tags/', false, $context);
 		$instanceJson=json_decode($json, true);
 		$this->patientWeight=$instanceJson['0010,1030']['Value'];
 		$this->seriesModelName=$instanceJson['0008,1090']['Value'];
 		$this->injectedDose=$instanceJson['0054,0016']['Value'][0]['0018,1074']['Value'];
 		//SK InjectedTime est deprecie en faveur de DateTime, A surveiller pour la suite
-		$this->injectedTime=$instanceJson['0054,0016']['Value'][0]['0018,1072']['Value'] ;
-		$this->injectedDateTime=$instanceJson['0054,0016']['Value'][0]['0018,1078']['Value'] ;
+		$this->injectedTime=$instanceJson['0054,0016']['Value'][0]['0018,1072']['Value'];
+		$this->injectedDateTime=$instanceJson['0054,0016']['Value'][0]['0018,1078']['Value'];
 		$this->injectedActivity=$instanceJson['0054,0016']['Value'][0]['0018,1077']['Value'];
 		$this->radiopharmaceutical=$instanceJson['0054,0016']['Value'][0]['0018,0031']['Value'];
 		$this->halfLife=$instanceJson['0054,0016']['Value'][0]['0018,1075']['Value'];
@@ -143,7 +143,7 @@ 
 		
 		if (in_array($this->sopClassUid, $scUids)) {
 			return true;
-		} else {
+		}else {
 			return false;
 		}
 		

src/models/Send_Email.php

Spacing +115 added lines, -115 removed lines

@@ -33,8 +33,8 @@ 
 
 	public $replyTo;
     
-	public function __construct(PDO $linkpdo){
-		$this->linkpdo= $linkpdo;
+	public function __construct(PDO $linkpdo) {
+		$this->linkpdo=$linkpdo;
        
 		$this->smtp_config=array(
 			'useSMTP'=> GAELO_USE_SMTP,
@@ -57,11 +57,11 @@ 
 	/**
 	 * Set the message to send (will be included in the HTML template)
 	 */
-	public function setMessage(string $message){
+	public function setMessage(string $message) {
 		$this->message=$message;
 	}
 
-	public function setSubject(String $subject){
+	public function setSubject(String $subject) {
 		$this->subject=$subject;
 	}
 
@@ -73,28 +73,28 @@ 
 	 * @param string $replyTo , optional, to allow a direct response to the user sending email
 	 * @return string
 	 */
-	public function sendEmail(){
+	public function sendEmail() {
 
-		$mail = new PHPMailer(true); // Passing `true` enables exceptions
-		$mail->CharSet = 'UTF-8';
+		$mail=new PHPMailer(true); // Passing `true` enables exceptions
+		$mail->CharSet='UTF-8';
 
 		//Recipients
-		if($this->smtp_config['useSMTP']){
-			$mail->IsSMTP();    // Set mailer to use SMTP
-			$mail->Host = $this->smtp_config['host'];   // Specify main and backup server
-			$mail->Port = $this->smtp_config['port'];   // Set the SMTP port
-			$mail->SMTPAuth = true; // Enable SMTP authentication
-			$mail->Username = $this->smtp_config['user'];   // SMTP username
-			$mail->Password = $this->smtp_config['password'];   // SMTP password
-			$mail->SMTPSecure = $this->smtp_config['SMTPSecure'];
-		}else{
+		if ($this->smtp_config['useSMTP']) {
+			$mail->IsSMTP(); // Set mailer to use SMTP
+			$mail->Host=$this->smtp_config['host']; // Specify main and backup server
+			$mail->Port=$this->smtp_config['port']; // Set the SMTP port
+			$mail->SMTPAuth=true; // Enable SMTP authentication
+			$mail->Username=$this->smtp_config['user']; // SMTP username
+			$mail->Password=$this->smtp_config['password']; // SMTP password
+			$mail->SMTPSecure=$this->smtp_config['SMTPSecure'];
+		}else {
 			//Add DKIM private key if exist
-			if(file_exists($_SERVER['DOCUMENT_ROOT'].'/data/_config/dkim.private')){
-				$mail->DKIM_domain = GAELO_WEB_ADDRESS;
-				$mail->DKIM_private = $_SERVER['DOCUMENT_ROOT'].'/data/_config/dkim.private';
-				$mail->DKIM_selector = 'mail';
-				$mail->DKIM_passphrase = '';
-				$mail->DKIM_identity = $mail->From;
+			if (file_exists($_SERVER['DOCUMENT_ROOT'].'/data/_config/dkim.private')) {
+				$mail->DKIM_domain=GAELO_WEB_ADDRESS;
+				$mail->DKIM_private=$_SERVER['DOCUMENT_ROOT'].'/data/_config/dkim.private';
+				$mail->DKIM_selector='mail';
+				$mail->DKIM_passphrase='';
+				$mail->DKIM_identity=$mail->From;
 			}
 		}
 
@@ -102,31 +102,31 @@ 
 		$mail->setFrom($this->adminEmail, $this->corporation, true);
         
 		//Add Reply To
-		try{
+		try {
 			$mail->addReplyTo($this->replyTo); 
-		}catch (Exception $e){
+		}catch (Exception $e) {
 			error_log("Reply to email problem".$e->getMessage());
 			return false;
 		}
         
 		//Add destinators
-		if (sizeof($this->emailsDestinators)>1){
-			foreach ($this->emailsDestinators as $value){
-				try{
+		if (sizeof($this->emailsDestinators) > 1) {
+			foreach ($this->emailsDestinators as $value) {
+				try {
 					$mail->addBCC($value);
-				}catch (Exception $e){
+				}catch (Exception $e) {
 					error_log('error adding email'.$e->getMessage());
 				}
 			 }
 			//Add message to mail object
 			$this->buildMessage($mail); 
-		} else if(sizeof($this->emailsDestinators) == 1){
+		}else if (sizeof($this->emailsDestinators) == 1) {
 			//If only one add regular adress
-			try{
+			try {
 				$mail->addAddress($this->emailsDestinators[0]);
 				$userObject=User::getUserByEmail($this->emailsDestinators[0], $this->linkpdo);
 				$this->buildMessage($mail, $userObject->lastName, $userObject->firstName);
-			}catch (Exception $e){
+			}catch (Exception $e) {
 				error_log('error adding email'.$e->getMessage());
 				return false;
 			}
@@ -135,12 +135,12 @@ 
 		}
 
 		//Content
-		$mail->isHTML(true);                                  // Set email format to HTML
-		$mail->Subject = $this->corporation.' Imaging Platform -' . $this->subject;
-		try{
+		$mail->isHTML(true); // Set email format to HTML
+		$mail->Subject=$this->corporation.' Imaging Platform -'.$this->subject;
+		try {
 			$answer=$mail->send();
 			return $answer;
-		}catch (Exception $e){
+		}catch (Exception $e) {
 			error_log("Message could not be sent. Mailer Error: {$mail->ErrorInfo}");
 			return false;
 		}
@@ -148,15 +148,15 @@ 
         
 	}
     
-	private function buildMessage(PHPMailer $mail, $lastName=null, $firstName=null){
+	private function buildMessage(PHPMailer $mail, $lastName=null, $firstName=null) {
         
-		if($lastName==null && $firstName==null){
+		if ($lastName == null && $firstName == null) {
 			$nameString="user";
-		}else{
+		}else {
 			$nameString=$firstName.' '.$lastName;
 		}
                     
-		$messageToSend =
+		$messageToSend=
 		'<!doctype html> <html lang="en">
             <head>
                 <meta charset="utf-8">
@@ -207,9 +207,9 @@ 
 		$messageToSend=str_replace(array("\r", "\n"), '', $messageToSend);
         
 		//Prepare Html2PlainText for email validity (both version to enhance spam validation)
-		$htmlMessageObject = new \Html2Text\Html2Text($messageToSend);
-		$mail->Body    = $messageToSend;
-		$mail->AltBody = $htmlMessageObject->getText();
+		$htmlMessageObject=new \Html2Text\Html2Text($messageToSend);
+		$mail->Body=$messageToSend;
+		$mail->AltBody=$htmlMessageObject->getText();
 		$mail->AddEmbeddedImage($_SERVER['DOCUMENT_ROOT'].'/assets/images/gaelo-logo-square.png', 'logo_gaelo');
         
         
@@ -218,8 +218,8 @@ 
 	/**
 	 * Retrieve all emails of Admins users
 	 */
-	public function getAdminsEmails(){
-		$connecter = $this->linkpdo->prepare('SELECT email FROM users WHERE is_administrator=1 AND status!="Deactivated"');
+	public function getAdminsEmails() {
+		$connecter=$this->linkpdo->prepare('SELECT email FROM users WHERE is_administrator=1 AND status!="Deactivated"');
 		$connecter->execute();
 		$adminResult=$connecter->fetchAll(PDO::FETCH_COLUMN);
        
@@ -231,7 +231,7 @@ 
 	 * @param string $username
 	 * @return string email
 	 */
-	public function getUserEmails(string $username){
+	public function getUserEmails(string $username) {
 		$userObject=new User($username, $this->linkpdo);
 		return $userObject->userEmail;
 	}
@@ -243,15 +243,15 @@ 
 	 * @param string $study
 	 * @return array mails
 	 */
-	public function getRolesEmails( string $study, string $role){
-		$connecter = $this->linkpdo->prepare('SELECT users.email FROM roles, users 
+	public function getRolesEmails(string $study, string $role) {
+		$connecter=$this->linkpdo->prepare('SELECT users.email FROM roles, users 
                                                      WHERE roles.study=:study 
                                                         AND roles.username=users.username 
                                                         AND roles.name=:role
                                                         AND users.status!="Deactivated"');
 		$connecter->execute(array(
 				'study'=>$study,
-				'role'=>$role) );
+				'role'=>$role));
     	
 		$results=$connecter->fetchAll(PDO::FETCH_COLUMN);
 		return $results;
@@ -294,15 +294,15 @@ 
 	 */
 	public function selectInvestigatorsEmailsWithSameCenter(String $study, int $center, ?array $job=null) : Send_Email {
 		//Select All users that has a matching center
-		$users =$this->getUsersAffiliatedToCenter($center);
+		$users=$this->getUsersAffiliatedToCenter($center);
 		//For each user check that we match role requirement (array if investigator), string if monitor or supervisor
-		foreach ($users as $user){
+		foreach ($users as $user) {
             
-			if( is_array($job) && !in_array($user->userJob, $job)){
+			if (is_array($job) && !in_array($user->userJob, $job)) {
 				continue;
 			}
         
-			if($user->isRoleAllowed($study, User::INVESTIGATOR)){
+			if ($user->isRoleAllowed($study, User::INVESTIGATOR)) {
 				$this->addEmail($user->userEmail);
 			}
             
@@ -321,10 +321,10 @@ 
 
 	public function addEmails(Array $emails) : Send_Email{
 
-		foreach($emails as $email){
+		foreach ($emails as $email) {
 			if (!in_array($email, $this->emailsDestinators))
 			{
-				$this->emailsDestinators[] = $email; 
+				$this->emailsDestinators[]=$email; 
 			}
 
 		}
@@ -344,55 +344,55 @@ 
 
 		if (!in_array($email, $this->emailsDestinators))
 			{
-				$this->emailsDestinators[] = $email; 
+				$this->emailsDestinators[]=$email; 
 			}
         
 		return $this;
 	}
 
-	public function sendModifyUserMessage($username, $newPassword){
+	public function sendModifyUserMessage($username, $newPassword) {
 
-		$message = "Your account password is reset. Please log in at: ".$this->webAddress."<br>
+		$message="Your account password is reset. Please log in at: ".$this->webAddress."<br>
         Username : $username<br>
         Temporary password : $newPassword<br>
         You will be asked to change this password at your first log in attempt<br>
         on the platform.<br>";
         
 		$this->setMessage($message);
-		$this->subject= 'Reactivation';
+		$this->subject='Reactivation';
 		$this->sendEmail();
 
 	}
 
-	public function sendNewAccountMessage($username, $password)  {
+	public function sendNewAccountMessage($username, $password) {
 
-		$message = "Your account is created for the upload platform used to exchange
-                imaging data. Please log in at: " . $this->webAddress . " <br>
+		$message="Your account is created for the upload platform used to exchange
+                imaging data. Please log in at: " . $this->webAddress." <br>
                 Username : $username<br>
                 Temporary password : $password<br>
                 You will be asked to change this password at your first log in attempt
                 on the platform.<br><br>";
 
 		$this->setMessage($message);
-		$this->subject= 'New account';
+		$this->subject='New account';
 		$this->sendEmail();
 	}
 
-	public function sendNewPasswordEmail($username, $password){
+	public function sendNewPasswordEmail($username, $password) {
 
-		$message = "This automatic e-mail contains your new temporary password for your
+		$message="This automatic e-mail contains your new temporary password for your
           user account.<br>
           Username : ".$username." <br>
           Temporary password : ".$password." <br>
           You will be asked to change this password at your first connection.<br>";
         
 		$this->setMessage($message);
-		$this->subject= 'New Password';
+		$this->subject='New Password';
 		$this->sendEmail();
 
 	}
 
-	public function sendQCDesicionEmail(String $controlDecision, String $study, String $patientCode, String $visitType, $formDecision, $formComment, $imageDecision, $imageComment){
+	public function sendQCDesicionEmail(String $controlDecision, String $study, String $patientCode, String $visitType, $formDecision, $formComment, $imageDecision, $imageComment) {
 		$message="Quality Control of the following visit has been set to : ".$controlDecision."<br>
                 Study : ".$study."<br>
                 Patient Number : ".$patientCode."<br>
@@ -401,89 +401,89 @@ 
                 Image Series : ".$imageDecision." Comment :".$imageComment." <br>";
 
 		$this->setMessage($message);
-		$this->subject= 'Quality Control';
+		$this->subject='Quality Control';
 		$this->sendEmail();
 	}
 
-	public function sendBlockedAccountNoPasswordChangeEmail($username, $linkedStudy){
+	public function sendBlockedAccountNoPasswordChangeEmail($username, $linkedStudy) {
 
-		$message = "The password change request cannot be done because the account is Deactivated<br>
+		$message="The password change request cannot be done because the account is Deactivated<br>
           Username : ".$username."<br>
           The account is linked to the following studies:".implode(',', $linkedStudy)."<br>
           Please contact the ".$this->corporation." to activate your account:<br>
           ".$this->adminEmail."<br>";
 
 		$this->setMessage($message);
-		$this->subject= 'Blocked account';
+		$this->subject='Blocked account';
 		$this->sendEmail();
 
 	}
 
-	public function sendAdminLoggedAlertEmail($username, $remoteAdress){
+	public function sendAdminLoggedAlertEmail($username, $remoteAdress) {
 		$message='the Admin user '.$username.' logged in from '.$remoteAdress.'
         <br> Please review this activity';
 		$this->setMessage($message);
-		$this->subject= "Admin Logged In";
+		$this->subject="Admin Logged In";
 		$this->sendEmail();
         
 	}
 
-	public function sendUnlockRequestMessage(String $role, String $username, String $visitType, $patientNum, String $study, String $request){
-		$message = "An Unlock " . $role . " form Request was emitted by " . $username . 
-		" for the " . $visitType . 
-		" visit of patient " . $patientNum . 
-		" in Study " . $study . "<br>
-        Reason for request: " . $request . " <br>";
+	public function sendUnlockRequestMessage(String $role, String $username, String $visitType, $patientNum, String $study, String $request) {
+		$message="An Unlock ".$role." form Request was emitted by ".$username. 
+		" for the ".$visitType. 
+		" visit of patient ".$patientNum. 
+		" in Study ".$study."<br>
+        Reason for request: " . $request." <br>";
 		$this->setMessage($message);
-		$this->subject= 'Ask Unlock';
+		$this->subject='Ask Unlock';
 		$this->sendEmail();
         
 	}
 
-	public function sendReviewReadyMessage(String $study, int $patientCode, String $visitType){
+	public function sendReviewReadyMessage(String $study, int $patientCode, String $visitType) {
 		$message="The following visit is ready for review in the platform: <br>
         Study : ".$study."<br>
         Patient Number : ".$patientCode."<br>
         Visit : ".$visitType."<br>";
 		$this->setMessage($message);
-		$this->subject= "Awaiting Review";
+		$this->subject="Awaiting Review";
 		$this->sendEmail();
 	}
 
-	public function sendCorrectiveActionDoneMessage(bool $done, String $study, int $patientCode, String $visitType){
+	public function sendCorrectiveActionDoneMessage(bool $done, String $study, int $patientCode, String $visitType) {
 
-		if (! $done) {
-			$message = "No corrective action could be applied on the following visit: <br>
-                        Study : " . $study . "<br>
-			            Patient Number : " . $patientCode . "<br>
-			            Uploaded visit : " . $visitType . "<br>";
+		if (!$done) {
+			$message="No corrective action could be applied on the following visit: <br>
+                        Study : " . $study."<br>
+			            Patient Number : " . $patientCode."<br>
+			            Uploaded visit : " . $visitType."<br>";
 		} 
 		else {
-			$message = "A corrective action was applied on the following visit: <br>
-                        Study : " . $study . "<br>
-		          		Patient Number : " . $patientCode . "<br>
-		          		Uploaded visit : " . $visitType . "<br>";
+			$message="A corrective action was applied on the following visit: <br>
+                        Study : " . $study."<br>
+		          		Patient Number : " . $patientCode."<br>
+		          		Uploaded visit : " . $visitType."<br>";
 			
 		}
 		$this->setMessage($message);
-		$this->subject= "Corrective Action";
+		$this->subject="Corrective Action";
 		$this->sendEmail();
 
 	}
 
-	public function sendRequestMessage(String $name, String $email, String $center, String $request){
-		$message = "The following request was sent and will be processed as soon as possible:<br>
+	public function sendRequestMessage(String $name, String $email, String $center, String $request) {
+		$message="The following request was sent and will be processed as soon as possible:<br>
 		Name : ".$name."<br>
 		E-mail : ".$email."<br>
 		Investigational center : ".$center."<br>
         Request : ".$request."<br>";
         
 		$this->setMessage($message);
-		$this->subject= "Request";
+		$this->subject="Request";
 		$this->sendEmail();
 	}
 
-	public function sendAwaitingAdjudicationMessage(String $study, int $patientCode , String $visitType){
+	public function sendAwaitingAdjudicationMessage(String $study, int $patientCode, String $visitType) {
 		$message="Review of the following visit is awaiting adjudication <br>
         Study : ".$study."<br>
         Patient Number : ".$patientCode."<br>
@@ -491,47 +491,47 @@ 
         The visit is awaiting for your adjudication review";
 
 		$this->setMessage($message);
-		$this->subject= "Awaiting Adjudication";
+		$this->subject="Awaiting Adjudication";
 		$this->sendEmail();
 	}
 
-	public function sendVisitConcludedMessage(String $study, int $patientCode, String $visitType, $conclusionValue){
+	public function sendVisitConcludedMessage(String $study, int $patientCode, String $visitType, $conclusionValue) {
 		$message="Review of the following visit is concluded <br>
                 Study : ".$study."<br>
                 Patient Number : ".$patientCode."<br>
 				Visit : ".$visitType."<br>
-                Conclusion Value : ".$conclusionValue ;
+                Conclusion Value : ".$conclusionValue;
 
 		$this->setMessage($message);
-		$this->subject= "Visit Concluded";
+		$this->subject="Visit Concluded";
 		$this->sendEmail();
 	}
 
-	public function sendBlockedAccountNotification($username, $studies){
-		$message = 'The following user account is blocked after too many bad password
+	public function sendBlockedAccountNotification($username, $studies) {
+		$message='The following user account is blocked after too many bad password
                 attempts.<br>
                 Username : '.$username.'<br>
                 The account is linked to the following studies:<br>
                 '. implode('<br>', $studies).' </br>';
 
 		$this->setMessage($message);
-		$this->subject= "Account Blocked";
+		$this->subject="Account Blocked";
 		$this->sendEmail();
 	}
 
-	public function sendUploadedVisitMessage($study, $patientCode, $visitType){
-		$message = "The following visit has been uploaded on the platform: <br>
+	public function sendUploadedVisitMessage($study, $patientCode, $visitType) {
+		$message="The following visit has been uploaded on the platform: <br>
         Study : ".$study."<br>
         Patient Number : ".$patientCode."<br>
         Uploaded visit : ".$visitType."<br>";
 
 		$this->setMessage($message);
-		$this->subject= "New upload";
+		$this->subject="New upload";
 		$this->sendEmail();
 
 	}
 
-	public function sendDeletedFormMessage(String $study, String $patientCode, String $visitType){
+	public function sendDeletedFormMessage(String $study, String $patientCode, String $visitType) {
 		$message="Your form sent for study : ".$study."<br>
         Patient : ".$patientCode."<br>
         Visit  : ".$visitType." <br>
@@ -539,12 +539,12 @@ 
         You can now resend a new version of this form <br>";
 
 		$this->setMessage($message);
-		$this->subject= "Form Deleted";
+		$this->subject="Form Deleted";
 		$this->sendEmail();
 
 	}
 
-	public function sendUnlockedFormMessage(String $study, String $patientCode, String $visitType){
+	public function sendUnlockedFormMessage(String $study, String $patientCode, String $visitType) {
 		$message="Your form sent for study : ".$study."<br>
         Patient : ".$patientCode."<br>
         Visit  : ".$visitType." <br>
@@ -552,12 +552,12 @@ 
         You can now resend a new version of this form <br>";
 
 		$this->setMessage($message);
-		$this->subject= "Form Unlocked";
+		$this->subject="Form Unlocked";
 		$this->sendEmail();
 
 	}
 
-	public function sendUploadValidationFailure($idVisit, $patientCode, String $visitType, String $study, String $zipPath, String $username, String $errorMessage){
+	public function sendUploadValidationFailure($idVisit, $patientCode, String $visitType, String $study, String $zipPath, String $username, String $errorMessage) {
 		$message="An Import Error occured during validation of upload <br>
             Visit ID : ".$idVisit."<br>
             Patient Code : ".$patientCode."<br>
@@ -565,14 +565,14 @@ 
             Study : ".$study."<br>
             zipPath : ".$zipPath."<br>
             username: ".$username."<br>
-            error  : ".$errorMessage."<br>" ;
+            error  : ".$errorMessage."<br>";
 
 		$this->setMessage($message);
-		$this->subject= "Error During Import";
+		$this->subject="Error During Import";
 		$this->sendEmail();
 	}
 
-	public function sendCreatedNotDoneVisitNotification($patientCode, $study, $visitType, $creatorUser){
+	public function sendCreatedNotDoneVisitNotification($patientCode, $study, $visitType, $creatorUser) {
 		$message="A Not Done visit has been created <br>
         Patient Number : ".$patientCode."<br>
         Study : ".$study."<br> 
@@ -580,7 +580,7 @@ 
         Creating Username : ".$creatorUser."<br>";
 
 		$this->setMessage($message);
-		$this->subject= "Visit Not Done";
+		$this->subject="Visit Not Done";
 		$this->sendEmail();
 	}
 

Braces +7 added lines, -8 removed lines

@@ -87,7 +87,7 @@ 
 			$mail->Username = $this->smtp_config['user'];   // SMTP username
 			$mail->Password = $this->smtp_config['password'];   // SMTP password
 			$mail->SMTPSecure = $this->smtp_config['SMTPSecure'];
-		}else{
+		} else{
 			//Add DKIM private key if exist
 			if(file_exists($_SERVER['DOCUMENT_ROOT'].'/data/_config/dkim.private')){
 				$mail->DKIM_domain = GAELO_WEB_ADDRESS;
@@ -104,7 +104,7 @@ 
 		//Add Reply To
 		try{
 			$mail->addReplyTo($this->replyTo); 
-		}catch (Exception $e){
+		} catch (Exception $e){
 			error_log("Reply to email problem".$e->getMessage());
 			return false;
 		}
@@ -114,7 +114,7 @@ 
 			foreach ($this->emailsDestinators as $value){
 				try{
 					$mail->addBCC($value);
-				}catch (Exception $e){
+				} catch (Exception $e){
 					error_log('error adding email'.$e->getMessage());
 				}
 			 }
@@ -126,7 +126,7 @@ 
 				$mail->addAddress($this->emailsDestinators[0]);
 				$userObject=User::getUserByEmail($this->emailsDestinators[0], $this->linkpdo);
 				$this->buildMessage($mail, $userObject->lastName, $userObject->firstName);
-			}catch (Exception $e){
+			} catch (Exception $e){
 				error_log('error adding email'.$e->getMessage());
 				return false;
 			}
@@ -140,7 +140,7 @@ 
 		try{
 			$answer=$mail->send();
 			return $answer;
-		}catch (Exception $e){
+		} catch (Exception $e){
 			error_log("Message could not be sent. Mailer Error: {$mail->ErrorInfo}");
 			return false;
 		}
@@ -152,7 +152,7 @@ 
         
 		if($lastName==null && $firstName==null){
 			$nameString="user";
-		}else{
+		} else{
 			$nameString=$firstName.' '.$lastName;
 		}
                     
@@ -457,8 +457,7 @@ 
                         Study : " . $study . "<br>
 			            Patient Number : " . $patientCode . "<br>
 			            Uploaded visit : " . $visitType . "<br>";
-		} 
-		else {
+		} else {
 			$message = "A corrective action was applied on the following visit: <br>
                         Study : " . $study . "<br>
 		          		Patient Number : " . $patientCode . "<br>

src/models/Study.php

Indentation +170 added lines, -170 removed lines

@@ -52,234 +52,234 @@ 
                 AND study = :study
                 GROUP  BY patients.code');
 
-        $patients->execute(array(
-            'username' => $username,
-            'study' => $this->study
-        ));
+		$patients->execute(array(
+			'username' => $username,
+			'study' => $this->study
+		));
 
-        $patientsCodes=$patients->fetchAll(PDO::FETCH_COLUMN);
+		$patientsCodes=$patients->fetchAll(PDO::FETCH_COLUMN);
 
-        $patientObjectsArray=[];
+		$patientObjectsArray=[];
 
-        foreach ($patientsCodes as $patientCode) {
-            $patientObjectsArray[]=new Patient($patientCode, $this->linkpdo);
-        }
+		foreach ($patientsCodes as $patientCode) {
+			$patientObjectsArray[]=new Patient($patientCode, $this->linkpdo);
+		}
 
-        return $patientObjectsArray;
-    }
+		return $patientObjectsArray;
+	}
 
-    public function getAllCreatedVisits(bool $deleted=false) {
+	public function getAllCreatedVisits(bool $deleted=false) {
 
-        $possibleStudyGroups=$this->getAllPossibleVisitGroups();
+		$possibleStudyGroups=$this->getAllPossibleVisitGroups();
 
-        $visitsObjectArray=[];
+		$visitsObjectArray=[];
 
-        foreach ($possibleStudyGroups as $studyGroup) {
-            $createdVisits=$studyGroup->getStudyVisitManager()->getCreatedVisits($deleted);
-            array_push($visitsObjectArray, ...$createdVisits);
-        }
+		foreach ($possibleStudyGroups as $studyGroup) {
+			$createdVisits=$studyGroup->getStudyVisitManager()->getCreatedVisits($deleted);
+			array_push($visitsObjectArray, ...$createdVisits);
+		}
 
-        return $visitsObjectArray;
+		return $visitsObjectArray;
 
-    }
+	}
 
-    public function getAllAwaitingUploadImagingVisit() {
+	public function getAllAwaitingUploadImagingVisit() {
 
-        $possibleStudyGroups=$this->getAllPossibleVisitGroups();
-        $visitsObjectArray=[];
+		$possibleStudyGroups=$this->getAllPossibleVisitGroups();
+		$visitsObjectArray=[];
 
-        foreach ($possibleStudyGroups as $studyGroup) {
-            if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET))) {
-                $awaitingUploadVisits=$studyGroup->getStudyVisitManager()->getAwaitingUploadVisit();
-                array_push($visitsObjectArray, ...$awaitingUploadVisits);
-            }
+		foreach ($possibleStudyGroups as $studyGroup) {
+			if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET))) {
+				$awaitingUploadVisits=$studyGroup->getStudyVisitManager()->getAwaitingUploadVisit();
+				array_push($visitsObjectArray, ...$awaitingUploadVisits);
+			}
             
             
-        }
+		}
         
-        return $visitsObjectArray;
+		return $visitsObjectArray;
 
-    }
+	}
 
-    public function getAllAwaitingReviewImagingVisit($username=null) {
+	public function getAllAwaitingReviewImagingVisit($username=null) {
 
-        $possibleStudyGroups=$this->getAllPossibleVisitGroups();
-        $visitsObjectArray=[];
+		$possibleStudyGroups=$this->getAllPossibleVisitGroups();
+		$visitsObjectArray=[];
 
-        foreach ($possibleStudyGroups as $studyGroup) {
-            if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET))) {
-                $awaitingReviewVisits=$studyGroup->getStudyVisitManager()->getAwaitingReviewVisit($username);
-                array_push($visitsObjectArray, ...$awaitingReviewVisits);
-            }
+		foreach ($possibleStudyGroups as $studyGroup) {
+			if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET))) {
+				$awaitingReviewVisits=$studyGroup->getStudyVisitManager()->getAwaitingReviewVisit($username);
+				array_push($visitsObjectArray, ...$awaitingReviewVisits);
+			}
             
             
-        }
+		}
         
-        return $visitsObjectArray;
+		return $visitsObjectArray;
 
-    }
+	}
 
-    public function getAllUploadedImagingVisits() {
+	public function getAllUploadedImagingVisits() {
 
-        $possibleStudyGroups=$this->getAllPossibleVisitGroups();
-        $visitsObjectArray=[];
+		$possibleStudyGroups=$this->getAllPossibleVisitGroups();
+		$visitsObjectArray=[];
 
-        foreach ($possibleStudyGroups as $studyGroup) {
-            if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET))) {
-                $uploadedVisits=$studyGroup->getStudyVisitManager()->getUploadedVisits();
-                array_push($visitsObjectArray, ...$uploadedVisits);
-            }
+		foreach ($possibleStudyGroups as $studyGroup) {
+			if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET))) {
+				$uploadedVisits=$studyGroup->getStudyVisitManager()->getUploadedVisits();
+				array_push($visitsObjectArray, ...$uploadedVisits);
+			}
             
             
-        }
+		}
         
-        return $visitsObjectArray;
+		return $visitsObjectArray;
 
-    }
+	}
 
-    public function isHavingAwaitingReviewImagingVisit($username=null) {
-        $awaitingVisits=$this->getAllAwaitingReviewImagingVisit($username);
-        $havingAwaitingReview=(sizeof($awaitingVisits) > 0);
-        return $havingAwaitingReview;
-    }
+	public function isHavingAwaitingReviewImagingVisit($username=null) {
+		$awaitingVisits=$this->getAllAwaitingReviewImagingVisit($username);
+		$havingAwaitingReview=(sizeof($awaitingVisits) > 0);
+		return $havingAwaitingReview;
+	}
 
 
 
-    public function getAllPossibleVisitGroups() {
+	public function getAllPossibleVisitGroups() {
 
-        $allGroupsType=$this->linkpdo->prepare('SELECT id FROM visit_group WHERE study = :study');
-        $allGroupsType->execute(array('study' => $this->study));
-        $allGroupsIds=$allGroupsType->fetchall(PDO::FETCH_COLUMN);
+		$allGroupsType=$this->linkpdo->prepare('SELECT id FROM visit_group WHERE study = :study');
+		$allGroupsType->execute(array('study' => $this->study));
+		$allGroupsIds=$allGroupsType->fetchall(PDO::FETCH_COLUMN);
         
-        $visitGroupArray=[];
-        foreach ($allGroupsIds as $groupId) {
-            $visitGroupArray[]=new Visit_Group($this->linkpdo, $groupId);
-        }
+		$visitGroupArray=[];
+		foreach ($allGroupsIds as $groupId) {
+			$visitGroupArray[]=new Visit_Group($this->linkpdo, $groupId);
+		}
         
-        return $visitGroupArray;
+		return $visitGroupArray;
 
-    }
+	}
 
-    public function getSpecificGroup(String $groupModality) : Visit_Group {
+	public function getSpecificGroup(String $groupModality) : Visit_Group {
 
-        $groupQuery=$this->linkpdo->prepare('SELECT id FROM visit_group WHERE study = :study AND group_modality=:groupModality');
-        $groupQuery->execute(array('study' => $this->study, 'groupModality'=> $groupModality));
-        $groupId=$groupQuery->fetch(PDO::FETCH_COLUMN);
+		$groupQuery=$this->linkpdo->prepare('SELECT id FROM visit_group WHERE study = :study AND group_modality=:groupModality');
+		$groupQuery->execute(array('study' => $this->study, 'groupModality'=> $groupModality));
+		$groupId=$groupQuery->fetch(PDO::FETCH_COLUMN);
         
-        return new Visit_Group($this->linkpdo, $groupId);
+		return new Visit_Group($this->linkpdo, $groupId);
 
-    }
+	}
 
-    public function getStudySpecificGroupManager(String $groupModality) : Group_Visit_Manager {
+	public function getStudySpecificGroupManager(String $groupModality) : Group_Visit_Manager {
 
-        $visitGroup=$this->getSpecificGroup($groupModality);
+		$visitGroup=$this->getSpecificGroup($groupModality);
         
-        return new Group_Visit_Manager($this, $visitGroup, $this->linkpdo);
+		return new Group_Visit_Manager($this, $visitGroup, $this->linkpdo);
 
-    }
+	}
 
-    public function getReviewManager() : Study_Review_Manager {
-        return new Study_Review_Manager($this);
-    }
+	public function getReviewManager() : Study_Review_Manager {
+		return new Study_Review_Manager($this);
+	}
 
-    public function getExportStudyData() : Export_Study_Data{
-        return new Export_Study_Data($this);
-    }
+	public function getExportStudyData() : Export_Study_Data{
+		return new Export_Study_Data($this);
+	}
     
-    public function getAllPatientsInStudy() {
-        $allPatientQuery=$this->linkpdo->prepare('SELECT code FROM patients WHERE study = :study');
-        $allPatientQuery->execute(array('study' => $this->study));
-        $allPatients=$allPatientQuery->fetchall(PDO::FETCH_COLUMN);
+	public function getAllPatientsInStudy() {
+		$allPatientQuery=$this->linkpdo->prepare('SELECT code FROM patients WHERE study = :study');
+		$allPatientQuery->execute(array('study' => $this->study));
+		$allPatients=$allPatientQuery->fetchall(PDO::FETCH_COLUMN);
         
-        $patientObjectArray=[];
-        foreach ($allPatients as $patient) {
-            $patientObjectArray[]=new Patient($patient, $this->linkpdo);
-        }
+		$patientObjectArray=[];
+		foreach ($allPatients as $patient) {
+			$patientObjectArray[]=new Patient($patient, $this->linkpdo);
+		}
         
-        return $patientObjectArray;
+		return $patientObjectArray;
         
-    }
+	}
     
-    public function getDocumentation(String $role){
-        if($role==User::SUPERVISOR){
-            $documentationQuery = $this->linkpdo->prepare("SELECT id_documentation FROM documentation
+	public function getDocumentation(String $role){
+		if($role==User::SUPERVISOR){
+			$documentationQuery = $this->linkpdo->prepare("SELECT id_documentation FROM documentation
                                                     WHERE study = :study");
             
-        } else{
-            $documentationQuery = $this->linkpdo->prepare("SELECT id_documentation FROM documentation
+		} else{
+			$documentationQuery = $this->linkpdo->prepare("SELECT id_documentation FROM documentation
                                                     WHERE study = :study
                                                     AND ".$role."= 1 AND deleted=0");
             
-        }
+		}
         
-        $documentationQuery->execute(array('study' => $this->study));
-        $documentationAnswers=$documentationQuery->fetchAll(PDO::FETCH_COLUMN);
+		$documentationQuery->execute(array('study' => $this->study));
+		$documentationAnswers=$documentationQuery->fetchAll(PDO::FETCH_COLUMN);
         
-        $documentationObjects=[];
-        foreach ($documentationAnswers as $documentationId) {
-        	$documentationObjects[]=new Documentation($this->linkpdo, $documentationId);
-        }
-        return $documentationObjects;
-    }
+		$documentationObjects=[];
+		foreach ($documentationAnswers as $documentationId) {
+			$documentationObjects[]=new Documentation($this->linkpdo, $documentationId);
+		}
+		return $documentationObjects;
+	}
     
-    /**
-     * Return userObject array for all users having role in the study
-     * @return User[]
-     */
-    public function getUsersWithRoleInStudy() {
-        $req=$this->linkpdo->prepare('SELECT DISTINCT users.username FROM roles,users
+	/**
+	 * Return userObject array for all users having role in the study
+	 * @return User[]
+	 */
+	public function getUsersWithRoleInStudy() {
+		$req=$this->linkpdo->prepare('SELECT DISTINCT users.username FROM roles,users
                                   WHERE roles.username=users.username
                                   AND roles.study=:study');
-        $req->execute(array('study' => $this->study));
-        $answers=$req->fetchAll(PDO::FETCH_COLUMN);
+		$req->execute(array('study' => $this->study));
+		$answers=$req->fetchAll(PDO::FETCH_COLUMN);
         
-        $usersObjects=[];
-        foreach ($answers as $username) {
-            $usersObjects[]=new User($username, $this->linkpdo);
-        }
-        return $usersObjects;
+		$usersObjects=[];
+		foreach ($answers as $username) {
+			$usersObjects[]=new User($username, $this->linkpdo);
+		}
+		return $usersObjects;
         
-    }
+	}
     
-    public function getUsersByRoleInStudy(String $role) {
-        $req=$this->linkpdo->prepare('SELECT username FROM roles
+	public function getUsersByRoleInStudy(String $role) {
+		$req=$this->linkpdo->prepare('SELECT username FROM roles
 									   WHERE study=:study AND name=:role ');
-        $req->execute(array('study' => $this->study, 'role'=>$role));
-        $answers=$req->fetchAll(PDO::FETCH_COLUMN);
+		$req->execute(array('study' => $this->study, 'role'=>$role));
+		$answers=$req->fetchAll(PDO::FETCH_COLUMN);
         
-        $usersObjects=[];
-        foreach ($answers as $username) {
-            $usersObjects[]=new User($username, $this->linkpdo);
-        }
-        return $usersObjects;
+		$usersObjects=[];
+		foreach ($answers as $username) {
+			$usersObjects[]=new User($username, $this->linkpdo);
+		}
+		return $usersObjects;
         
-    }
+	}
     
-    public function getAllRolesByUsers() {
-        $roles_query=$this->linkpdo->prepare('SELECT * FROM roles WHERE study=:study');
-        $roles_query->execute(array('study'=>$this->study));
-        $definedRoles=$roles_query->fetchall(PDO::FETCH_ASSOC);
+	public function getAllRolesByUsers() {
+		$roles_query=$this->linkpdo->prepare('SELECT * FROM roles WHERE study=:study');
+		$roles_query->execute(array('study'=>$this->study));
+		$definedRoles=$roles_query->fetchall(PDO::FETCH_ASSOC);
         
-        foreach ($definedRoles as $role) {
-            $rolesList[$role['username']][]=$role['name'];
-        }
-        return $rolesList;
-    }
-
-    public function getStatistics(String $modality) {
-        return new Statistics($this, $modality);
-    }
+		foreach ($definedRoles as $role) {
+			$rolesList[$role['username']][]=$role['name'];
+		}
+		return $rolesList;
+	}
+
+	public function getStatistics(String $modality) {
+		return new Statistics($this, $modality);
+	}
     
-    public function changeStudyActivation(bool $activated) {
-        $req=$this->linkpdo->prepare('UPDATE studies SET
+	public function changeStudyActivation(bool $activated) {
+		$req=$this->linkpdo->prepare('UPDATE studies SET
     								active = :active
 						        WHERE name = :study');
-        $req->execute(array('study'=> $this->study, 'active'=>intval($activated)));
-    }
+		$req->execute(array('study'=> $this->study, 'active'=>intval($activated)));
+	}
     
-    public function isOriginalOrthancNeverKnown($anonFromOrthancStudyId) {
+	public function isOriginalOrthancNeverKnown($anonFromOrthancStudyId) {
 
-        $connecter=$this->linkpdo->prepare('SELECT Study_Orthanc_ID FROM visits 
+		$connecter=$this->linkpdo->prepare('SELECT Study_Orthanc_ID FROM visits 
                                                 INNER JOIN visit_type ON 
                                                 (visit_type.id=visits.visit_type_id 
                                                 AND visit_type.group_id IN (SELECT id FROM visit_group WHERE study = :study))
@@ -287,30 +287,30 @@ 
                                             AND orthanc_studies.Anon_From_Orthanc_ID=:Anon_From_Orthanc_ID 
                                             AND orthanc_studies.deleted=0 
                                             AND visits.deleted=0'
-                                            );
-        $connecter->execute(array(
-            "study" => $this->study,
-            "Anon_From_Orthanc_ID"=>$anonFromOrthancStudyId
-        ));
-        $result = $connecter->fetchAll(PDO::FETCH_COLUMN);
+											);
+		$connecter->execute(array(
+			"study" => $this->study,
+			"Anon_From_Orthanc_ID"=>$anonFromOrthancStudyId
+		));
+		$result = $connecter->fetchAll(PDO::FETCH_COLUMN);
         
-        if(count($result)>0) {
-        	return false;
-        } else {
-        	return true;
-        }
+		if(count($result)>0) {
+			return false;
+		} else {
+			return true;
+		}
         
-    }
+	}
     
-    public static function createStudy(string $studyName, $patientCodePrefix, PDO $linkpdo){
+	public static function createStudy(string $studyName, $patientCodePrefix, PDO $linkpdo){
         
-        $req = $linkpdo->prepare('INSERT INTO studies (name, patient_code_prefix) VALUES(:studyName, :patientCodePrefix) ');
+		$req = $linkpdo->prepare('INSERT INTO studies (name, patient_code_prefix) VALUES(:studyName, :patientCodePrefix) ');
         
-        $req->execute(array(
-            'studyName' => $studyName,
-            'patientCodePrefix' => $patientCodePrefix
-        ));
+		$req->execute(array(
+			'studyName' => $studyName,
+			'patientCodePrefix' => $patientCodePrefix
+		));
         
-    }
+	}
     
 }
\ No newline at end of file

Spacing +15 added lines, -15 removed lines

@@ -23,24 +23,24 @@ 
 	public $study;
 	public $patientCodePrefix;
     
-	public function __construct(String $study, PDO $linkpdo){
+	public function __construct(String $study, PDO $linkpdo) {
 
 		$this->linkpdo=$linkpdo;
-		$connecter = $this->linkpdo->prepare('SELECT * FROM studies WHERE name=:study');
+		$connecter=$this->linkpdo->prepare('SELECT * FROM studies WHERE name=:study');
 		$connecter->execute(array(
 				"study" => $study,
 		));
-		$result = $connecter->fetch(PDO::FETCH_ASSOC);
+		$result=$connecter->fetch(PDO::FETCH_ASSOC);
 
 		$this->study=$result['name'];
-		$this->patientCodePrefix = $result['patient_code_prefix'];
+		$this->patientCodePrefix=$result['patient_code_prefix'];
         
         
 	}
 
 	public function getPatientsLinkedToUserCenters($username)
 	{
-		$patients = $this->linkpdo->prepare(' SELECT patients.code
+		$patients=$this->linkpdo->prepare(' SELECT patients.code
             FROM   patients
             WHERE  patients.center IN (SELECT affiliated_centers.center
                 FROM   affiliated_centers
@@ -200,13 +200,13 @@ 
         
     }
     
-    public function getDocumentation(String $role){
-        if($role==User::SUPERVISOR){
-            $documentationQuery = $this->linkpdo->prepare("SELECT id_documentation FROM documentation
+    public function getDocumentation(String $role) {
+        if ($role == User::SUPERVISOR) {
+            $documentationQuery=$this->linkpdo->prepare("SELECT id_documentation FROM documentation
                                                     WHERE study = :study");
             
-        } else{
-            $documentationQuery = $this->linkpdo->prepare("SELECT id_documentation FROM documentation
+        }else {
+            $documentationQuery=$this->linkpdo->prepare("SELECT id_documentation FROM documentation
                                                     WHERE study = :study
                                                     AND ".$role."= 1 AND deleted=0");
             
@@ -292,19 +292,19 @@ 
             "study" => $this->study,
             "Anon_From_Orthanc_ID"=>$anonFromOrthancStudyId
         ));
-        $result = $connecter->fetchAll(PDO::FETCH_COLUMN);
+        $result=$connecter->fetchAll(PDO::FETCH_COLUMN);
         
-        if(count($result)>0) {
+        if (count($result) > 0) {
         	return false;
-        } else {
+        }else {
         	return true;
         }
         
     }
     
-    public static function createStudy(string $studyName, $patientCodePrefix, PDO $linkpdo){
+    public static function createStudy(string $studyName, $patientCodePrefix, PDO $linkpdo) {
         
-        $req = $linkpdo->prepare('INSERT INTO studies (name, patient_code_prefix) VALUES(:studyName, :patientCodePrefix) ');
+        $req=$linkpdo->prepare('INSERT INTO studies (name, patient_code_prefix) VALUES(:studyName, :patientCodePrefix) ');
         
         $req->execute(array(
             'studyName' => $studyName,

src/models/Visit_Type_Iterator.php

Indentation +55 added lines, -55 removed lines

@@ -6,71 +6,71 @@
 class Visit_Type_Iterator implements Iterator
 {
 
-    private array $visitsTypeArray=[];
-    private int $index=0;
+	private array $visitsTypeArray=[];
+	private int $index=0;
 
-    public function __construct(array $visitTypeArray)
-    {
-        $this->visitsTypeArray=$visitTypeArray;
-    }
+	public function __construct(array $visitTypeArray)
+	{
+		$this->visitsTypeArray=$visitTypeArray;
+	}
 
-    public function setVisitPosition(String $visitName)
-    {
-        $visitNameArray=array_map(function(Visit_Type $visitTypeObject) {
-            return $visitTypeObject->name;
-        }, $this->visitsTypeArray);
+	public function setVisitPosition(String $visitName)
+	{
+		$visitNameArray=array_map(function(Visit_Type $visitTypeObject) {
+			return $visitTypeObject->name;
+		}, $this->visitsTypeArray);
 
-        $this->index=array_search($visitName, $visitNameArray);
-    }
+		$this->index=array_search($visitName, $visitNameArray);
+	}
 
 
-    public function current(): Visit_Type
-    {
-        return $this->visitsTypeArray[$this->index];
-    }
+	public function current(): Visit_Type
+	{
+		return $this->visitsTypeArray[$this->index];
+	}
 
-    public function previous()
-    {
-        $this->index--;
-    }
+	public function previous()
+	{
+		$this->index--;
+	}
 
-    public function hasPrevious()
-    {
-        $this->previous();
-        if ($this->valid()) {
-        	return $this->current();
-        } else {
-        	return false;
-        }
-    }
+	public function hasPrevious()
+	{
+		$this->previous();
+		if ($this->valid()) {
+			return $this->current();
+		} else {
+			return false;
+		}
+	}
 
-    public function next()
-    {
-        $this->index++;
-    }
+	public function next()
+	{
+		$this->index++;
+	}
 
-    public function hasNext()
-    {
-        $this->next();
-        if ($this->valid()) {
-        	return $this->current();
-        } else {
-        	return false;
-        }
-    }
+	public function hasNext()
+	{
+		$this->next();
+		if ($this->valid()) {
+			return $this->current();
+		} else {
+			return false;
+		}
+	}
 
-    public function rewind()
-    {
-        $this->index=0;
-    }
+	public function rewind()
+	{
+		$this->index=0;
+	}
 
-    public function key(): int
-    {
-        return $this->index;
-    }
+	public function key(): int
+	{
+		return $this->index;
+	}
 
-    public function valid(): bool
-    {
-        return isset($this->visitsTypeArray[$this->key()]);
-    }
+	public function valid(): bool
+	{
+		return isset($this->visitsTypeArray[$this->key()]);
+	}
 }

Spacing +2 added lines, -2 removed lines

@@ -39,7 +39,7 @@ 
         $this->previous();
         if ($this->valid()) {
         	return $this->current();
-        } else {
+        }else {
         	return false;
         }
     }
@@ -54,7 +54,7 @@ 
         $this->next();
         if ($this->valid()) {
         	return $this->current();
-        } else {
+        }else {
         	return false;
         }
     }

src/models/Orthanc_Study.php

Spacing +12 added lines, -12 removed lines

@@ -43,21 +43,21 @@ 
 	private $url;
 	private $context;
 	
-	public function __construct($studyOrthancId, $url, $context){
+	public function __construct($studyOrthancId, $url, $context) {
 		//Set http adress of orthanc
-		if($url==null && $context==null){
+		if ($url == null && $context == null) {
 			$linkpdo=Session::getLinkpdo();
 	        
 			$this->url=GAELO_ORTHANC_PACS_ADDRESS.':'.GAELO_ORTHANC_PACS_PORT;
-			$this->context = array(
+			$this->context=array(
 					'http' => array(
-						'header'  => "Authorization: Basic " . base64_encode( GAELO_ORTHANC_PACS_LOGIN.':'.GAELO_ORTHANC_PACS_PASSWORD )
+						'header'  => "Authorization: Basic ".base64_encode(GAELO_ORTHANC_PACS_LOGIN.':'.GAELO_ORTHANC_PACS_PASSWORD)
 					)
 			);
 	    	
-		}else{
+		}else {
 			$this->url=$url;
-			$this->context = $context;	
+			$this->context=$context;	
 		}
 	    
 		//put current study orthanc ID in memory
@@ -68,9 +68,9 @@ 
 	/**
 	 *Get study related tags and store them in this object
 	 */
-	public function retrieveStudyData(){
-		$context  = stream_context_create($this->context);
-		$json = file_get_contents($this->url.'/studies/'.$this->studyOrthancID, false, $context);
+	public function retrieveStudyData() {
+		$context=stream_context_create($this->context);
+		$json=file_get_contents($this->url.'/studies/'.$this->studyOrthancID, false, $context);
 		//On le decode
 		$studiesJson=json_decode($json, true);
 		//On cree un object patient avec les information
@@ -95,9 +95,9 @@ 
 	/**
 	 *Get study statistics info (size in MB, number of instances) and store them in this object
 	 */
-	private function retrieveStudyStatistics(){
-		$context  = stream_context_create($this->context);
-		$json = file_get_contents($this->url.'/studies/'.$this->studyOrthancID.'/statistics/', false, $context);
+	private function retrieveStudyStatistics() {
+		$context=stream_context_create($this->context);
+		$json=file_get_contents($this->url.'/studies/'.$this->studyOrthancID.'/statistics/', false, $context);
 		//On le decode
 		$statisticsJson=json_decode($json, true);
 		$this->countInstances=$statisticsJson['CountInstances'];

Braces +1 added lines, -1 removed lines

@@ -55,7 +55,7 @@
 					)
 			);
 	    	
-		}else{
+		} else{
 			$this->url=$url;
 			$this->context = $context;	
 		}

src/models/Group_Visit_Manager.php

Indentation +24 added lines, -24 removed lines

@@ -112,37 +112,37 @@
                                                                 AND review_available=1 
                                                                 ORDER BY visit_type.visit_order ');
 
-        $idVisitsQuery->execute(array(
-            'visitGroupId' => $this->visitGroupObject->groupId
-        ));
+		$idVisitsQuery->execute(array(
+			'visitGroupId' => $this->visitGroupObject->groupId
+		));
 
-        $visitList = $idVisitsQuery->fetchAll(PDO::FETCH_COLUMN);
+		$visitList = $idVisitsQuery->fetchAll(PDO::FETCH_COLUMN);
 
-        $visitObjectArray = [];
+		$visitObjectArray = [];
 
-        foreach ($visitList as $visitId) {
-            $visitObject = new Visit($visitId, $this->linkpdo);
+		foreach ($visitList as $visitId) {
+			$visitObject = new Visit($visitId, $this->linkpdo);
 
-            if (!empty($username)) {
-                if ($visitObject->isAwaitingReviewForReviewerUser($username)) {
-                	$visitObjectArray[] = $visitObject;
-                }
-            } else {
-                $visitObjectArray[] = $visitObject;
-            }
-        }
+			if (!empty($username)) {
+				if ($visitObject->isAwaitingReviewForReviewerUser($username)) {
+					$visitObjectArray[] = $visitObject;
+				}
+			} else {
+				$visitObjectArray[] = $visitObject;
+			}
+		}
 
-        return $visitObjectArray;
-    }
+		return $visitObjectArray;
+	}
 
-    /**
-     * For controller tree
-     * List all visits that awaiting QC Action (QC not done or waiting definitive conclusion)
-     */
-    public function getVisitForControllerAction(): array
-    {
+	/**
+	 * For controller tree
+	 * List all visits that awaiting QC Action (QC not done or waiting definitive conclusion)
+	 */
+	public function getVisitForControllerAction(): array
+	{
 
-        $visitsQuery=$this->linkpdo->prepare('SELECT id_visit FROM visits 
+		$visitsQuery=$this->linkpdo->prepare('SELECT id_visit FROM visits 
                                                     INNER JOIN visit_type ON 
                                                         (visit_type.id=visits.visit_type_id 
                                                         AND visit_type.group_id = :visitGroupId)

Spacing +52 added lines, -52 removed lines

@@ -28,9 +28,9 @@ 
 
 	public function __construct(Study $studyObject, Visit_Group $visitGroupObject, PDO $linkpdo)
 	{
-		$this->linkpdo = $linkpdo;
-		$this->studyObject = $studyObject;
-		$this->visitGroupObject = $visitGroupObject;
+		$this->linkpdo=$linkpdo;
+		$this->studyObject=$studyObject;
+		$this->visitGroupObject=$visitGroupObject;
 	}
 
 	public function getVisitGroupObject(): Visit_Group
@@ -44,7 +44,7 @@ 
 	public function getUploadedVisits(): array
 	{
 
-		$uploadedVisitQuery = $this->linkpdo->prepare('SELECT id_visit FROM visits 
+		$uploadedVisitQuery=$this->linkpdo->prepare('SELECT id_visit FROM visits 
                                                                     INNER JOIN visit_type ON 
                                                                         (visit_type.id=visits.visit_type_id 
                                                                         AND visit_type.group_id = :visitGroupId)
@@ -55,11 +55,11 @@ 
 			'visitGroupId' => $this->visitGroupObject->groupId
 		));
 
-		$uploadedVisitIds = $uploadedVisitQuery->fetchall(PDO::FETCH_COLUMN);
+		$uploadedVisitIds=$uploadedVisitQuery->fetchall(PDO::FETCH_COLUMN);
 
-		$visitObjectArray = [];
+		$visitObjectArray=[];
 		foreach ($uploadedVisitIds as $id_visit) {
-			$visitObjectArray[] = new Visit($id_visit, $this->linkpdo);
+			$visitObjectArray[]=new Visit($id_visit, $this->linkpdo);
 		}
 
 		return $visitObjectArray;
@@ -71,7 +71,7 @@ 
 	public function getAwaitingUploadVisit(): array
 	{
 
-		$uploadedVisitQuery = $this->linkpdo->prepare("SELECT id_visit FROM visits 
+		$uploadedVisitQuery=$this->linkpdo->prepare("SELECT id_visit FROM visits 
                                                                     INNER JOIN visit_type ON 
                                                                          (visit_type.id=visits.visit_type_id 
                                                                             AND visit_type.group_id = :visitGroupId)
@@ -84,11 +84,11 @@ 
 				'visitGroupId' => $this->visitGroupObject->groupId
 			)
 		);
-		$uploadedVisitIds = $uploadedVisitQuery->fetchAll(PDO::FETCH_COLUMN);
+		$uploadedVisitIds=$uploadedVisitQuery->fetchAll(PDO::FETCH_COLUMN);
 
-		$visitObjectArray = [];
+		$visitObjectArray=[];
 		foreach ($uploadedVisitIds as $id_visit) {
-			$visitObjectArray[] = new Visit($id_visit, $this->linkpdo);
+			$visitObjectArray[]=new Visit($id_visit, $this->linkpdo);
 		}
 
 		return $visitObjectArray;
@@ -100,11 +100,11 @@ 
 	 * @param string $username
 	 * @return Visit[]
 	 */
-	public function getAwaitingReviewVisit(string $username = null): array
+	public function getAwaitingReviewVisit(string $username=null): array
 	{
 
 		//Query visit to analyze visit awaiting a review
-		$idVisitsQuery = $this->linkpdo->prepare('SELECT id_visit FROM visits 
+		$idVisitsQuery=$this->linkpdo->prepare('SELECT id_visit FROM visits 
                                                                     INNER JOIN visit_type ON 
                                                                         (visit_type.id=visits.visit_type_id 
                                                                         AND visit_type.group_id = :visitGroupId)
@@ -116,19 +116,19 @@ 
             'visitGroupId' => $this->visitGroupObject->groupId
         ));
 
-        $visitList = $idVisitsQuery->fetchAll(PDO::FETCH_COLUMN);
+        $visitList=$idVisitsQuery->fetchAll(PDO::FETCH_COLUMN);
 
-        $visitObjectArray = [];
+        $visitObjectArray=[];
 
         foreach ($visitList as $visitId) {
-            $visitObject = new Visit($visitId, $this->linkpdo);
+            $visitObject=new Visit($visitId, $this->linkpdo);
 
             if (!empty($username)) {
                 if ($visitObject->isAwaitingReviewForReviewerUser($username)) {
-                	$visitObjectArray[] = $visitObject;
+                	$visitObjectArray[]=$visitObject;
                 }
-            } else {
-                $visitObjectArray[] = $visitObject;
+            }else {
+                $visitObjectArray[]=$visitObject;
             }
         }
 
@@ -157,11 +157,11 @@ 
 			'visitGroupId' => $this->visitGroupObject->groupId
 		));
 
-		$visits = $visitsQuery->fetchAll(PDO::FETCH_COLUMN);
+		$visits=$visitsQuery->fetchAll(PDO::FETCH_COLUMN);
 
-		$visitObjectArray = [];
+		$visitObjectArray=[];
 		foreach ($visits as $visit) {
-			$visitObjectArray[] = new Visit($visit, $this->linkpdo);
+			$visitObjectArray[]=new Visit($visit, $this->linkpdo);
 		}
 
 		return $visitObjectArray;
@@ -173,7 +173,7 @@ 
 	public function getVisitWithQCStatus($qcStatus): array
 	{
 
-		$visitQuery = $this->linkpdo->prepare("SELECT id_visit FROM visits 
+		$visitQuery=$this->linkpdo->prepare("SELECT id_visit FROM visits 
                                                         INNER JOIN visit_type ON 
                                                             (visit_type.id=visits.visit_type_id 
                                                             AND visit_type.group_id = :visitGroupId)
@@ -185,11 +185,11 @@ 
 			'qcStatus' => $qcStatus,
 			'visitGroupId' => $this->visitGroupObject->groupId
 		));
-		$visitIds = $visitQuery->fetchall(PDO::FETCH_COLUMN);
+		$visitIds=$visitQuery->fetchall(PDO::FETCH_COLUMN);
 
-		$visitObjectArray = [];
+		$visitObjectArray=[];
 		foreach ($visitIds as $id_visit) {
-			$visitObjectArray[] = new Visit($id_visit, $this->linkpdo);
+			$visitObjectArray[]=new Visit($id_visit, $this->linkpdo);
 		}
 
 		return $visitObjectArray;
@@ -201,7 +201,7 @@ 
 	public function getVisitsMissingInvestigatorForm(): array
 	{
 
-		$visitQuery = $this->linkpdo->prepare("SELECT id_visit FROM visits 
+		$visitQuery=$this->linkpdo->prepare("SELECT id_visit FROM visits 
                                                             INNER JOIN visit_type ON 
                                                                 (visit_type.id=visits.visit_type_id 
                                                                 AND visit_type.group_id = :visitGroupId)
@@ -213,11 +213,11 @@ 
 			'visitGroupId' => $this->visitGroupObject->groupId
 		));
 
-		$visitIds = $visitQuery->fetchAll(PDO::FETCH_COLUMN);
+		$visitIds=$visitQuery->fetchAll(PDO::FETCH_COLUMN);
 
-		$visitObjectArray = [];
+		$visitObjectArray=[];
 		foreach ($visitIds as $id_visit) {
-			$visitObjectArray[] = new Visit($id_visit, $this->linkpdo);
+			$visitObjectArray[]=new Visit($id_visit, $this->linkpdo);
 		}
 
 		return $visitObjectArray;
@@ -226,10 +226,10 @@ 
 	/**
 	 * Return studie's created visits
 	 */
-	public function getCreatedVisits(bool $deleted = false): array
+	public function getCreatedVisits(bool $deleted=false): array
 	{
 
-		$uploadedVisitQuery = $this->linkpdo->prepare('SELECT id_visit FROM visits 
+		$uploadedVisitQuery=$this->linkpdo->prepare('SELECT id_visit FROM visits 
                                                     INNER JOIN visit_type ON 
                                                         (visit_type.id=visits.visit_type_id 
                                                         AND visit_type.group_id = :visitGroupId)
@@ -241,11 +241,11 @@ 
 			'visitGroupId' => $this->visitGroupObject->groupId
 		));
 
-		$uploadedVisitIds = $uploadedVisitQuery->fetchAll(PDO::FETCH_COLUMN);
+		$uploadedVisitIds=$uploadedVisitQuery->fetchAll(PDO::FETCH_COLUMN);
 
-		$visitObjectArray = [];
+		$visitObjectArray=[];
 		foreach ($uploadedVisitIds as $id_visit) {
-			$visitObjectArray[] = new Visit($id_visit, $this->linkpdo);
+			$visitObjectArray[]=new Visit($id_visit, $this->linkpdo);
 		}
 
 		return $visitObjectArray;
@@ -258,26 +258,26 @@ 
 	{
 
 		//Get patients list in this study
-		$allPatients = $this->studyObject->getAllPatientsInStudy();
+		$allPatients=$this->studyObject->getAllPatientsInStudy();
 
-		$results = [];
+		$results=[];
 
 		foreach ($allPatients as $patient) {
 
-			$patientCenter = $patient->getPatientCenter();
-			$visitManager = $patient->getPatientVisitManager($this->visitGroupObject);
+			$patientCenter=$patient->getPatientCenter();
+			$visitManager=$patient->getPatientVisitManager($this->visitGroupObject);
 
-			$patientData = [];
-			$patientData['center'] = $patientCenter->name;
-			$patientData['country'] = $patientCenter->countryName;
-			$patientData['firstname'] = $patient->patientFirstName;
-			$patientData['lastname'] = $patient->patientLastName;
-			$patientData['birthdate'] = $patient->patientBirthDate;
-			$patientData['registration_date'] = $patient->patientRegistrationDate;
+			$patientData=[];
+			$patientData['center']=$patientCenter->name;
+			$patientData['country']=$patientCenter->countryName;
+			$patientData['firstname']=$patient->patientFirstName;
+			$patientData['lastname']=$patient->patientLastName;
+			$patientData['birthdate']=$patient->patientBirthDate;
+			$patientData['registration_date']=$patient->patientRegistrationDate;
 
-			$visitStatus = $visitManager->determineVisitStatus($visitType->name);
+			$visitStatus=$visitManager->determineVisitStatus($visitType->name);
 
-			$results[$patient->patientCode] = array_merge($patientData, $visitStatus);
+			$results[$patient->patientCode]=array_merge($patientData, $visitStatus);
 		}
 
 		return $results;
@@ -290,15 +290,15 @@ 
 	{
 
 		//Get ordered list of possible visits in this study
-		$allVisitsType = $this->visitGroupObject->getAllVisitTypesOfGroup();
+		$allVisitsType=$this->visitGroupObject->getAllVisitTypesOfGroup();
 
-		$results = [];
+		$results=[];
 
 		foreach ($allVisitsType as $visitType) {
 
-			$allPatientStatus = $this->getPatientVisitStatusForVisitType($visitType);
+			$allPatientStatus=$this->getPatientVisitStatusForVisitType($visitType);
 
-			$results[$visitType->name] = $allPatientStatus;
+			$results[$visitType->name]=$allPatientStatus;
 			//array_push($results, ...$allPatientStatus);
 		}
 

src/models/Tracker.php

Spacing +12 added lines, -12 removed lines

@@ -27,15 +27,15 @@ 
 	 * @param string $study
 	 * @return array
 	 */
-	public static function getTrackerByRoleStudy(string $role, PDO $linkpdo, $study=null){
-		if($study==null){
-			$queryTracker = $linkpdo->prepare('SELECT * FROM tracker WHERE role=:role');
+	public static function getTrackerByRoleStudy(string $role, PDO $linkpdo, $study=null) {
+		if ($study == null) {
+			$queryTracker=$linkpdo->prepare('SELECT * FROM tracker WHERE role=:role');
 			$queryTracker->execute(array(
 				'role' => $role
 			));
            
-		}else{
-			$queryTracker = $linkpdo->prepare('SELECT * FROM tracker WHERE study = :study AND role=:role');
+		}else {
+			$queryTracker=$linkpdo->prepare('SELECT * FROM tracker WHERE study = :study AND role=:role');
 			$queryTracker->execute(array('study' => $study,
 				'role' => $role,
 			));
@@ -52,8 +52,8 @@ 
 	 * @param PDO $linkpdo
 	 * @return array
 	 */
-	public static function getMessageStudy(string $study, PDO $linkpdo){
-		$queryTracker = $linkpdo->prepare('SELECT * FROM tracker WHERE study = :study AND action_type="Send Message"');
+	public static function getMessageStudy(string $study, PDO $linkpdo) {
+		$queryTracker=$linkpdo->prepare('SELECT * FROM tracker WHERE study = :study AND action_type="Send Message"');
 		$queryTracker->execute(array('study' => $study));
 		$trackerResult=$queryTracker->fetchAll(PDO::FETCH_ASSOC);
 		return $trackerResult;
@@ -65,8 +65,8 @@ 
 	 * @param PDO $linkpdo
 	 * @return array
 	 */
-	public static function getTackerForVisit(string $id_visit, PDO $linkpdo){
-		$queryTracker = $linkpdo->prepare('SELECT * FROM tracker WHERE id_visit = :id_visit ORDER BY date');
+	public static function getTackerForVisit(string $id_visit, PDO $linkpdo) {
+		$queryTracker=$linkpdo->prepare('SELECT * FROM tracker WHERE id_visit = :id_visit ORDER BY date');
 		$queryTracker->execute(array('id_visit' => $id_visit));
 		$trackerResult=$queryTracker->fetchAll(PDO::FETCH_ASSOC);
 		return $trackerResult;    
@@ -76,17 +76,17 @@ 
 	 * Activity logger to log user activity in database
 	 * Activity should be an associative key, will be JSON encoded
 	 */
-	public static function logActivity($username, $role, $study, $id_visit, $actionType, $actionDetails){
+	public static function logActivity($username, $role, $study, $id_visit, $actionType, $actionDetails) {
         
 		$linkpdo=Session::getLinkpdo();
         
-		$connecter = $linkpdo->prepare('INSERT INTO tracker (date, username, role, study, id_visit, action_type, action_details)
+		$connecter=$linkpdo->prepare('INSERT INTO tracker (date, username, role, study, id_visit, action_type, action_details)
 								VALUES(:date, :username, :role, :study, :id_visit, :action_type, :action_details)' );
         
 		$connecter->execute(array(
 			"username" => $username,
 			"role" => $role,
-			"date"=> date('Y-m-d H:i:s') . substr((string)microtime(), 1, 6),
+			"date"=> date('Y-m-d H:i:s').substr((string)microtime(), 1, 6),
 			"study"=>$study,
 			"id_visit"=>$id_visit,
 			"action_type"=>$actionType,

Braces +1 added lines, -1 removed lines

@@ -34,7 +34,7 @@
 				'role' => $role
 			));
            
-		}else{
+		} else{
 			$queryTracker = $linkpdo->prepare('SELECT * FROM tracker WHERE study = :study AND role=:role');
 			$queryTracker->execute(array('study' => $study,
 				'role' => $role,

src/models/Patient_Visit_Manager.php

Spacing +94 added lines, -94 removed lines

@@ -26,24 +26,24 @@ 
 	protected $visitGroup;
 
 	//Constants visit status available
-	const DONE = "Done";
-	const NOT_DONE = "Not Done";
-	const SHOULD_BE_DONE = "Should be done";
-	const PENDING = "Pending";
-	const COMPLIANCY_YES = "Yes";
-	const COMPLIANCY_NO = "No";
-	const VISIT_WITHDRAWN = "Visit Withdrawn";
-	const VISIT_POSSIBLY_WITHDRAWN = "Possibly Withdrawn";
-	const OPTIONAL_VISIT = "Optional";
+	const DONE="Done";
+	const NOT_DONE="Not Done";
+	const SHOULD_BE_DONE="Should be done";
+	const PENDING="Pending";
+	const COMPLIANCY_YES="Yes";
+	const COMPLIANCY_NO="No";
+	const VISIT_WITHDRAWN="Visit Withdrawn";
+	const VISIT_POSSIBLY_WITHDRAWN="Possibly Withdrawn";
+	const OPTIONAL_VISIT="Optional";
 	//Not needed status is no make custom choice to deactivate upload reminder
 	const VISIT_NOT_NEEDED="Not Nedded";
 
 	public function __construct(Patient $patientObject, Visit_Group $visitGroup, $linkpdo)
 	{
-		$this->linkpdo = $linkpdo;
-		$this->patientCode = $patientObject->patientCode;
-		$this->patientObject = $patientObject;
-		$this->visitGroup = $visitGroup;
+		$this->linkpdo=$linkpdo;
+		$this->patientCode=$patientObject->patientCode;
+		$this->patientObject=$patientObject;
+		$this->visitGroup=$visitGroup;
 	}
 
 
@@ -52,10 +52,10 @@ 
 	 * @param bool $deletedVisits
 	 * @return Visit[]
 	 */
-	public function getCreatedPatientsVisits(bool $deletedVisits = false) : Array
+	public function getCreatedPatientsVisits(bool $deletedVisits=false) : Array
 	{
 
-		$visitQuery = $this->linkpdo->prepare('SELECT id_visit FROM visits
+		$visitQuery=$this->linkpdo->prepare('SELECT id_visit FROM visits
                                                                 INNER JOIN visit_type ON 
                                                                 (visit_type.id=visits.visit_type_id 
                                                                 AND visit_type.group_id = :visitGroupId)
@@ -70,11 +70,11 @@ 
 			'deleted' => $deletedVisits
 		));
 
-		$visitsResults = $visitQuery->fetchAll(PDO::FETCH_COLUMN);
+		$visitsResults=$visitQuery->fetchAll(PDO::FETCH_COLUMN);
 
-		$visitsObjectArray = [];
+		$visitsObjectArray=[];
 		foreach ($visitsResults as $idVisit) {
-			$visitsObjectArray[] = new Visit($idVisit, $this->linkpdo);
+			$visitsObjectArray[]=new Visit($idVisit, $this->linkpdo);
 		}
 
 		return $visitsObjectArray;
@@ -85,10 +85,10 @@ 
 	 * @param bool $deletedVisits
 	 * @return Visit[]
 	 */
-	public function getQcDonePatientsVisits(bool $deletedVisits = false) : Array
+	public function getQcDonePatientsVisits(bool $deletedVisits=false) : Array
 	{
 
-		$visitQuery = $this->linkpdo->prepare('SELECT id_visit FROM visits
+		$visitQuery=$this->linkpdo->prepare('SELECT id_visit FROM visits
 													            INNER JOIN visit_type ON 
                                                                 (visit_type.id=visits.visit_type_id 
                                                                 AND visit_type.group_id = :visitGroupId)
@@ -105,11 +105,11 @@ 
 			'deleted' => $deletedVisits
 		));
 
-		$visitsResults = $visitQuery->fetchAll(PDO::FETCH_COLUMN);
+		$visitsResults=$visitQuery->fetchAll(PDO::FETCH_COLUMN);
 
-		$visitsObjectArray = [];
+		$visitsObjectArray=[];
 		foreach ($visitsResults as $idVisit) {
-			$visitsObjectArray[] = new Visit($idVisit, $this->linkpdo);
+			$visitsObjectArray[]=new Visit($idVisit, $this->linkpdo);
 		}
 
 		return $visitsObjectArray;
@@ -122,7 +122,7 @@ 
 	 */
 	public function getAvailableVisitsToCreate() : Array
 	{
-		$availableVisitName = [];
+		$availableVisitName=[];
 
 		// if withdraw disallow visit creation
 		if ($this->patientObject->patientWithdraw) {
@@ -130,44 +130,44 @@ 
 		}
 
 		$allPossibleVisits=$this->visitGroup->getAllVisitTypesOfGroup();
-		$createdVisits = $this->getCreatedPatientsVisits();
-		$createdVisitsNameArray=array_map(function (Visit $visit) {
+		$createdVisits=$this->getCreatedPatientsVisits();
+		$createdVisitsNameArray=array_map(function(Visit $visit) {
 			return $visit->visitType;
 		},  $createdVisits);
 
-		$createdVisitOrder = array_map(function (Visit $visit) {
+		$createdVisitOrder=array_map(function(Visit $visit) {
 			return $visit->getVisitCharacteristics()->visitOrder;
 		},  $createdVisits);
 
-		if(empty($createdVisitOrder)){
-			$lastCreatedVisitOrder= -1;
-		}else{
-			$lastCreatedVisitOrder = max($createdVisitOrder);
+		if (empty($createdVisitOrder)) {
+			$lastCreatedVisitOrder=-1;
+		}else {
+			$lastCreatedVisitOrder=max($createdVisitOrder);
 		}
 
 		foreach ($allPossibleVisits as $possibleVisit) {
 
-			if(in_array($possibleVisit->name, $createdVisitsNameArray) ){
+			if (in_array($possibleVisit->name, $createdVisitsNameArray)) {
 				//Already created do not display it
 				continue;
 			}
 
-			if ($possibleVisit->visitOrder < $lastCreatedVisitOrder ) {
-				$availableVisitName[] = $possibleVisit->name;
-			} else if($possibleVisit->visitOrder > $lastCreatedVisitOrder) {
+			if ($possibleVisit->visitOrder < $lastCreatedVisitOrder) {
+				$availableVisitName[]=$possibleVisit->name;
+			}else if ($possibleVisit->visitOrder > $lastCreatedVisitOrder) {
 				if ($possibleVisit->optionalVisit) {
 					//If optional add optional visit and look for the next order
-					$availableVisitName[] = $possibleVisit->name;
+					$availableVisitName[]=$possibleVisit->name;
 					$lastCreatedVisitOrder++;
-				} else if ($possibleVisit->visitOrder > $lastCreatedVisitOrder) {
-					$availableVisitName[] = $possibleVisit->name;
+				}else if ($possibleVisit->visitOrder > $lastCreatedVisitOrder) {
+					$availableVisitName[]=$possibleVisit->name;
 					break;
 				}
 			}
 		}
 
 		//Reverse to sort for the more advanced visit to create
-		$availableVisitName = array_reverse($availableVisitName);
+		$availableVisitName=array_reverse($availableVisitName);
 
 		if (empty($availableVisitName)) {
 			throw new Exception('No possible visit');
@@ -182,8 +182,8 @@ 
 	 */
 	public function isMissingVisit() : bool
 	{
-		try{
-			if( ! empty( $this->getAvailableVisitsToCreate() ) ) {
+		try {
+			if (!empty($this->getAvailableVisitsToCreate())) {
 				return true;
 			}
 		}catch (Exception $e) {
@@ -200,62 +200,62 @@ 
 	public function determineVisitStatus(String $visitName)
 	{
 
-		$registrationDate = $this->patientObject->getImmutableRegistrationDate();
-		$visitType = Visit_Type::getVisitTypeByName($this->visitGroup->groupId, $visitName, $this->linkpdo);
+		$registrationDate=$this->patientObject->getImmutableRegistrationDate();
+		$visitType=Visit_Type::getVisitTypeByName($this->visitGroup->groupId, $visitName, $this->linkpdo);
 
-		$dateDownLimit = $registrationDate->modify($visitType->limitLowDays . 'day');
-		$dateUpLimit = $registrationDate->modify($visitType->limitUpDays . 'day');
+		$dateDownLimit=$registrationDate->modify($visitType->limitLowDays.'day');
+		$dateUpLimit=$registrationDate->modify($visitType->limitUpDays.'day');
 
-		$visitAnswer['status'] = null;
-		$visitAnswer['compliancy'] = null;
-		$visitAnswer['shouldBeDoneBefore'] = $dateUpLimit->format('Y-m-d');
-		$visitAnswer['shouldBeDoneAfter'] = $dateDownLimit->format('Y-m-d');
-		$visitAnswer['state_investigator_form'] = null;
-		$visitAnswer['state_quality_control'] = null;
-		$visitAnswer['acquisition_date'] = null;
-		$visitAnswer['upload_date'] = null;
-		$visitAnswer['upload_status'] = null;
-		$visitAnswer['id_visit'] = null;
+		$visitAnswer['status']=null;
+		$visitAnswer['compliancy']=null;
+		$visitAnswer['shouldBeDoneBefore']=$dateUpLimit->format('Y-m-d');
+		$visitAnswer['shouldBeDoneAfter']=$dateDownLimit->format('Y-m-d');
+		$visitAnswer['state_investigator_form']=null;
+		$visitAnswer['state_quality_control']=null;
+		$visitAnswer['acquisition_date']=null;
+		$visitAnswer['upload_date']=null;
+		$visitAnswer['upload_status']=null;
+		$visitAnswer['id_visit']=null;
 
 		try {
 			//Visit Created check compliancy
-			$visitObject = $this->getCreatedVisitForVisitTypeId($visitType->id);
-			$visitAnswer['state_investigator_form'] = $visitObject->stateInvestigatorForm;
-			$visitAnswer['state_quality_control'] = $visitObject->stateQualityControl;
-			$visitAnswer['acquisition_date'] = $visitObject->acquisitionDate;
-			$visitAnswer['upload_date'] = $visitObject->uploadDate;
-			$visitAnswer['upload_status'] = $visitObject->uploadStatus;
-			$visitAnswer['id_visit'] = $visitObject->id_visit;
-			$testedDate = $visitObject->acquisitionDate;
-			$visitAnswer['status'] = Patient_Visit_Manager::DONE;
+			$visitObject=$this->getCreatedVisitForVisitTypeId($visitType->id);
+			$visitAnswer['state_investigator_form']=$visitObject->stateInvestigatorForm;
+			$visitAnswer['state_quality_control']=$visitObject->stateQualityControl;
+			$visitAnswer['acquisition_date']=$visitObject->acquisitionDate;
+			$visitAnswer['upload_date']=$visitObject->uploadDate;
+			$visitAnswer['upload_status']=$visitObject->uploadStatus;
+			$visitAnswer['id_visit']=$visitObject->id_visit;
+			$testedDate=$visitObject->acquisitionDate;
+			$visitAnswer['status']=Patient_Visit_Manager::DONE;
 
 			if ($testedDate >= $dateDownLimit && $testedDate <= $dateDownLimit) {
-				$visitAnswer['compliancy'] = Patient_Visit_Manager::COMPLIANCY_YES;
-			} else {
-				$visitAnswer['compliancy'] = Patient_Visit_Manager::COMPLIANCY_NO;
+				$visitAnswer['compliancy']=Patient_Visit_Manager::COMPLIANCY_YES;
+			}else {
+				$visitAnswer['compliancy']=Patient_Visit_Manager::COMPLIANCY_NO;
 			}
-		} catch (Exception $e) {
+		}catch (Exception $e) {
 			//Visit Not Created
 			//If optional visit no status determination
 			if ($visitType->optionalVisit) {
-				$visitAnswer['status'] = Patient_Visit_Manager::OPTIONAL_VISIT;
-			} else {
+				$visitAnswer['status']=Patient_Visit_Manager::OPTIONAL_VISIT;
+			}else {
 				//Compare actual time with theorical date to determine status
-				$testedDate = new DateTime(date("Y-m-d"));
+				$testedDate=new DateTime(date("Y-m-d"));
 				if ($testedDate <= $dateUpLimit) {
-					$visitAnswer['status'] = Patient_Visit_Manager::PENDING;
-				} else {
-					$visitAnswer['status'] = Patient_Visit_Manager::SHOULD_BE_DONE;
+					$visitAnswer['status']=Patient_Visit_Manager::PENDING;
+				}else {
+					$visitAnswer['status']=Patient_Visit_Manager::SHOULD_BE_DONE;
 				}
 			}
 		}
 
 		//Take account of possible withdrawal if not created
-		if ($this->patientObject->patientWithdraw &&  $visitAnswer['acquisition_date'] == null) {
+		if ($this->patientObject->patientWithdraw && $visitAnswer['acquisition_date'] == null) {
 			if ($this->patientObject->patientWithdrawDate < $dateDownLimit) {
-				$visitAnswer['status'] = Patient_Visit_Manager::VISIT_WITHDRAWN;
-			} else if ($this->patientObject->patientWithdrawDate > $dateDownLimit) {
-				$visitAnswer['status'] = Patient_Visit_Manager::VISIT_POSSIBLY_WITHDRAWN;
+				$visitAnswer['status']=Patient_Visit_Manager::VISIT_WITHDRAWN;
+			}else if ($this->patientObject->patientWithdrawDate > $dateDownLimit) {
+				$visitAnswer['status']=Patient_Visit_Manager::VISIT_POSSIBLY_WITHDRAWN;
 			}
 		}
 
@@ -268,13 +268,13 @@ 
 	public function getAwaitingReviewVisits()
 	{
 
-		$createdVisits = $this->getCreatedPatientsVisits();
+		$createdVisits=$this->getCreatedPatientsVisits();
 
-		$availableVisitsForReview = [];
+		$availableVisitsForReview=[];
 
 		foreach ($createdVisits as $visit) {
 			if ($visit->reviewAvailable) {
-				$availableVisitsForReview[] = $visit;
+				$availableVisitsForReview[]=$visit;
 			}
 		}
 
@@ -283,34 +283,34 @@ 
 
 	public function isHavingAwaitingReviewVisit()
 	{
-		$awaitingReviews = $this->getAwaitingReviewVisits();
+		$awaitingReviews=$this->getAwaitingReviewVisits();
 		return (!empty($awaitingReviews));
 	}
 
-	public function getCreatedVisitForVisitTypeId($visitTypeId){
-		$visitQuery = $this->linkpdo->prepare ( 'SELECT id_visit FROM visits WHERE patient_code=:patientCode AND visit_type_id=:visitTypeId AND deleted=0 ' );
+	public function getCreatedVisitForVisitTypeId($visitTypeId) {
+		$visitQuery=$this->linkpdo->prepare('SELECT id_visit FROM visits WHERE patient_code=:patientCode AND visit_type_id=:visitTypeId AND deleted=0 ');
         
-		$visitQuery->execute ( array('patientCode' => $this->patientCode, 'visitTypeId'=>$visitTypeId) );
-		$visitId = $visitQuery->fetch(PDO::FETCH_COLUMN);
+		$visitQuery->execute(array('patientCode' => $this->patientCode, 'visitTypeId'=>$visitTypeId));
+		$visitId=$visitQuery->fetch(PDO::FETCH_COLUMN);
 
-		if(empty($visitId)){
+		if (empty($visitId)) {
 			throw new Exception("Visit Non Existing");
-		}else{
+		}else {
 			return new Visit($visitId, $this->linkpdo);
 		}
         
 	}
 
-	public function getCreatedVisitByVisitName($visitName){
+	public function getCreatedVisitByVisitName($visitName) {
 
-		$visitQuery = $this->linkpdo->prepare ( 'SELECT id_visit FROM visits, visit_type WHERE visits.visit_type_id = visit_type.id AND visits.patient_code=:patientCode AND visit_type.name=:visitName AND visits.deleted=0 ' );
+		$visitQuery=$this->linkpdo->prepare('SELECT id_visit FROM visits, visit_type WHERE visits.visit_type_id = visit_type.id AND visits.patient_code=:patientCode AND visit_type.name=:visitName AND visits.deleted=0 ');
         
-		$visitQuery->execute ( array('patientCode' => $this->patientCode, 'visitName'=>$visitName) );
-		$visitId = $visitQuery->fetch(PDO::FETCH_COLUMN);
+		$visitQuery->execute(array('patientCode' => $this->patientCode, 'visitName'=>$visitName));
+		$visitId=$visitQuery->fetch(PDO::FETCH_COLUMN);
 
-		if(empty($visitId)){
+		if (empty($visitId)) {
 			throw new Exception("Visit Non Existing");
-		}else{
+		}else {
 			return new Visit($visitId, $this->linkpdo);
 		}
 

Braces +4 added lines, -4 removed lines

@@ -141,7 +141,7 @@ 
 
 		if(empty($createdVisitOrder)){
 			$lastCreatedVisitOrder= -1;
-		}else{
+		} else{
 			$lastCreatedVisitOrder = max($createdVisitOrder);
 		}
 
@@ -186,7 +186,7 @@ 
 			if( ! empty( $this->getAvailableVisitsToCreate() ) ) {
 				return true;
 			}
-		}catch (Exception $e) {
+		} catch (Exception $e) {
 			//if exception happens no visits are missing
 			return false;
 		}
@@ -295,7 +295,7 @@ 
 
 		if(empty($visitId)){
 			throw new Exception("Visit Non Existing");
-		}else{
+		} else{
 			return new Visit($visitId, $this->linkpdo);
 		}
         
@@ -310,7 +310,7 @@ 
 
 		if(empty($visitId)){
 			throw new Exception("Visit Non Existing");
-		}else{
+		} else{
 			return new Visit($visitId, $this->linkpdo);
 		}
 

src/models/Form_Processor.php

Spacing +23 added lines, -23 removed lines

@@ -87,63 +87,63 @@ 
 	 * This methods is triggered by the system at form submission and call the save specific form
 	 * to define which value need to be written in the specific table
 	 */
-	public function saveForm($data, bool $validate){
+	public function saveForm($data, bool $validate) {
 	    
 		$this->rawDataForm=$data;
 	    
 		//If reviewer check that review is available before saving process
-		if( !$this->local && !$this->reviewAvailable){
-			return ;
+		if (!$this->local && !$this->reviewAvailable) {
+			return;
 		}
 		
 		//Get saved form, return either local form or reviewer's users form if exist
 		//or null if not existing
 		
-		if(empty($this->reviewObject)){
+		if (empty($this->reviewObject)) {
 			$this->createReview();
 			$update=false;       
-		}else{
+		}else {
 			$update=true;
 			//If already existing validated review, exit without modifying anything
-			if($this->reviewObject->validated){
+			if ($this->reviewObject->validated) {
 				return;
 			}
 	       
 		}
 	    
 		//Call the child redifined save specific form to save the specific data of the form
-		try{
+		try {
 			$this->saveSpecificForm($data, $this->reviewObject->id_review, $update);
-		}catch(Exception $e){
+		}catch (Exception $e) {
 			error_log($e->getMessage());
-			if(!$update){
+			if (!$update) {
 				$this->reviewObject->hardDeleteReview();
 			}
 			throw new Exception("Error during save");
 		}
 		
-		if($validate) $this->reviewObject->changeReviewValidationStatus($validate);
+		if ($validate) $this->reviewObject->changeReviewValidationStatus($validate);
 		//update the visit status if we are processing a local form
-		if($this->local){
+		if ($this->local) {
 			if ($validate) $this->visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_DONE);
 			else $this->visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_DRAFT);	
 		}
 		
 		//Log Activity
-		if($this->local) $role="Investigator"; else $role="Reviewer";
+		if ($this->local) $role="Investigator"; else $role="Reviewer";
 		$actionDetails['patient_code']=$this->visitObject->patientCode;
 		$actionDetails['type_visit']=$this->visitObject->visitType;
 		$actionDetails['modality_visit']=$this->visitObject->visitGroupObject->groupModality;
 		$actionDetails['id_review']=$this->reviewObject->id_review;
 		$actionDetails['local_review']=intval($this->local);
-		$actionDetails['adjudication']=intval($this->reviewStatus==Visit::REVIEW_WAIT_ADJUDICATION);
-		$actionDetails['create']= !$update;
-		$actionDetails['raw_data']= $data;
+		$actionDetails['adjudication']=intval($this->reviewStatus == Visit::REVIEW_WAIT_ADJUDICATION);
+		$actionDetails['create']=!$update;
+		$actionDetails['raw_data']=$data;
 		
-		Tracker::logActivity($this->username, $role, $this->study ,$this->id_visit, "Save Form", $actionDetails);
+		Tracker::logActivity($this->username, $role, $this->study, $this->id_visit, "Save Form", $actionDetails);
 		
 		//If central review still not at "Done" status Check if validation is reached
-		if ($validate && !$this->local &&  $this->reviewStatus != Visit::REVIEW_DONE ) {
+		if ($validate && !$this->local && $this->reviewStatus != Visit::REVIEW_DONE) {
 			$this->setVisitValidation();
 		}
 		
@@ -156,12 +156,12 @@ 
 	 * @param string $reviewStatus
 	 * @param $conclusionValue
 	 */
-	protected function changeVisitValidationStatus(string $reviewStatus, $conclusionValue="N/A"){
+	protected function changeVisitValidationStatus(string $reviewStatus, $conclusionValue="N/A") {
 		$this->visitObject->changeVisitValidationStatus($reviewStatus, $conclusionValue);
 		$this->reviewAvailabilityDecision($reviewStatus);
 
 		//Send Notification emails
-		if($reviewStatus == Visit::REVIEW_WAIT_ADJUDICATION){
+		if ($reviewStatus == Visit::REVIEW_WAIT_ADJUDICATION) {
 
 			$email=new Send_Email($this->linkpdo);
 			//SK A AMELIORER POUR EVITER DE MAILIER LES REVIEWER QUI ONT DEJA REPONDU
@@ -206,9 +206,9 @@ 
 	 * return all reviews (local and reviewer) of the current visit
 	 * Usefull to determine visit conclusion status
 	 */
-	public function getAllValidatedFormsOfVisit(){
+	public function getAllValidatedFormsOfVisit() {
 	    
-		$query = $this->linkpdo->prepare('SELECT * FROM reviews,'.$this->specificTable.' WHERE reviews.id_review='.$this->specificTable.'.id_review AND reviews.id_visit=:idVisit AND reviews.validated=1 AND reviews.deleted=0');
+		$query=$this->linkpdo->prepare('SELECT * FROM reviews,'.$this->specificTable.' WHERE reviews.id_review='.$this->specificTable.'.id_review AND reviews.id_visit=:idVisit AND reviews.validated=1 AND reviews.deleted=0');
 		$query->execute(array(
 			'idVisit'=>$this->id_visit
 		));
@@ -240,9 +240,9 @@ 
 	 * Can be overided if needed different condition
 	 * @param string $reviewConclusion
 	 */
-	protected function reviewAvailabilityDecision(string $reviewConclusion){
+	protected function reviewAvailabilityDecision(string $reviewConclusion) {
 		//If Done reached make the review unavailable for review
-		if($reviewConclusion== Visit::REVIEW_DONE){
+		if ($reviewConclusion == Visit::REVIEW_DONE) {
 			$this->visitObject->changeReviewAvailability(false);
 		}
 		//Needed in case of deletion of a review (even if true by default initialy, need to come back if deletion)

Braces +19 added lines, -10 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();
@@ -122,15 +122,24 @@ 
 			throw new Exception("Error during save");
 		}
 		
-		if($validate) $this->reviewObject->changeReviewValidationStatus($validate);
+		if($validate) {
+			$this->reviewObject->changeReviewValidationStatus($validate);
+		}
 		//update the visit status if we are processing a local form
 		if($this->local){
-			if ($validate) $this->visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_DONE);
-			else $this->visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_DRAFT);	
+			if ($validate) {
+				$this->visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_DONE);
+			} else {
+				$this->visitObject->changeVisitStateInvestigatorForm(Visit::LOCAL_FORM_DRAFT);
+			}
 		}
 		
 		//Log Activity
-		if($this->local) $role="Investigator"; else $role="Reviewer";
+		if($this->local) {
+			$role="Investigator";
+		} else {
+			$role="Reviewer";
+		}
 		$actionDetails['patient_code']=$this->visitObject->patientCode;
 		$actionDetails['type_visit']=$this->visitObject->visitType;
 		$actionDetails['modality_visit']=$this->visitObject->visitGroupObject->groupModality;
@@ -170,7 +179,7 @@ 
 					->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, $this->linkpdo);
@@ -192,11 +201,11 @@ 
 		try {
 			if ($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;
 		
@@ -225,7 +234,7 @@ 
 		$validatedReviewObjects=array_filter($reviewsObject, function($review) {
 			if ($review->validated) {
 				return true;
-			}else {
+			} else {
 				return false;
 			}
 		});