salimkanoun / GaelO

src/models/Visit_Group.php

Indentation +93 added lines, -93 removed lines

@@ -21,101 +21,101 @@
 class Visit_Group
 {
 
-    public $groupId;
-    public $studyName;
-    public $groupModality;
-
-    public $linkpdo;
-
-    const GROUP_MODALITY_PET = "PT";
-    const GROUP_MODALITY_CT = "CT";
-    const GROUP_MODALITY_MR = "MR";
-
-    public function __construct(PDO $linkpdo, int $groupId)
-    {
-
-        $this->linkpdo = $linkpdo;
-        $visitGroupQuery = $this->linkpdo->prepare('SELECT * FROM visit_group WHERE id = :groupId');
-        $visitGroupQuery->execute(array('groupId' => $groupId));
-
-        $visitGroupData = $visitGroupQuery->fetch(PDO::FETCH_ASSOC);
-
-        if (empty($visitGroupData)) {
-            throw new Exception('No Visit Group Found');
-        }
-
-        $this->groupId = $visitGroupData['id'];
-        $this->studyName = $visitGroupData['study'];
-        $this->groupModality = $visitGroupData['group_modality'];
-    }
-
-    /**
-     * Get Visit Type object from Visit Name in this group
-     */
-    public function getVisitType(String $visitName): Visit_Type
-    {
-        return Visit_Type::getVisitTypeByName($this->groupId, $visitName, $this->linkpdo);
-    }
-
-    /**
-     * Return all visit type of the current visit group
-     */
-    public function getAllVisitTypesOfGroup(): array
-    {
-
-        $allVisitsType = $this->linkpdo->prepare('SELECT id FROM visit_type WHERE group_id= :groupId ORDER BY visit_order');
-        $allVisitsType->execute(array('groupId' => $this->groupId));
-        $allVisits = $allVisitsType->fetchall(PDO::FETCH_COLUMN);
-
-        $visitTypeArray = [];
-        foreach ($allVisits as $visitTypeId) {
-            $visitTypeArray[] = new Visit_Type($this->linkpdo, $visitTypeId);
-        }
-
-        return $visitTypeArray;
-    }
-
-    /**
-     * Get iterator for Visit Type in this group
-     */
-    public function getAllVisitTypesOfGroupIterator(): Visit_Type_Iterator
-    {
-        return new Visit_Type_Iterator($this->getAllVisitTypesOfGroup());
-    }
-
-    /**
-     * Get Study Visit manager of this group
-     */
-    public function getStudyVisitManager(): Group_Visit_Manager
-    {
-        $studyObject = new Study($this->studyName, $this->linkpdo);
-        return new Group_Visit_Manager($studyObject, $this, $this->linkpdo);
-    }
-
-    /**
-     * Get study Object of this group
-     */
-    public function getStudy(): Study
-    {
-        return new Study($this->studyName, $this->linkpdo);
-    }
-
-    /**
-     * Create a new Visit Group
-     */
-    public static function createVisitGroup(String $studyName, String $groupModality, PDO $linkpdo): Visit_Group
-    {
-
-        $req = $linkpdo->prepare('INSERT INTO visit_group (study,  group_modality)
+	public $groupId;
+	public $studyName;
+	public $groupModality;
+
+	public $linkpdo;
+
+	const GROUP_MODALITY_PET = "PT";
+	const GROUP_MODALITY_CT = "CT";
+	const GROUP_MODALITY_MR = "MR";
+
+	public function __construct(PDO $linkpdo, int $groupId)
+	{
+
+		$this->linkpdo = $linkpdo;
+		$visitGroupQuery = $this->linkpdo->prepare('SELECT * FROM visit_group WHERE id = :groupId');
+		$visitGroupQuery->execute(array('groupId' => $groupId));
+
+		$visitGroupData = $visitGroupQuery->fetch(PDO::FETCH_ASSOC);
+
+		if (empty($visitGroupData)) {
+			throw new Exception('No Visit Group Found');
+		}
+
+		$this->groupId = $visitGroupData['id'];
+		$this->studyName = $visitGroupData['study'];
+		$this->groupModality = $visitGroupData['group_modality'];
+	}
+
+	/**
+	 * Get Visit Type object from Visit Name in this group
+	 */
+	public function getVisitType(String $visitName): Visit_Type
+	{
+		return Visit_Type::getVisitTypeByName($this->groupId, $visitName, $this->linkpdo);
+	}
+
+	/**
+	 * Return all visit type of the current visit group
+	 */
+	public function getAllVisitTypesOfGroup(): array
+	{
+
+		$allVisitsType = $this->linkpdo->prepare('SELECT id FROM visit_type WHERE group_id= :groupId ORDER BY visit_order');
+		$allVisitsType->execute(array('groupId' => $this->groupId));
+		$allVisits = $allVisitsType->fetchall(PDO::FETCH_COLUMN);
+
+		$visitTypeArray = [];
+		foreach ($allVisits as $visitTypeId) {
+			$visitTypeArray[] = new Visit_Type($this->linkpdo, $visitTypeId);
+		}
+
+		return $visitTypeArray;
+	}
+
+	/**
+	 * Get iterator for Visit Type in this group
+	 */
+	public function getAllVisitTypesOfGroupIterator(): Visit_Type_Iterator
+	{
+		return new Visit_Type_Iterator($this->getAllVisitTypesOfGroup());
+	}
+
+	/**
+	 * Get Study Visit manager of this group
+	 */
+	public function getStudyVisitManager(): Group_Visit_Manager
+	{
+		$studyObject = new Study($this->studyName, $this->linkpdo);
+		return new Group_Visit_Manager($studyObject, $this, $this->linkpdo);
+	}
+
+	/**
+	 * Get study Object of this group
+	 */
+	public function getStudy(): Study
+	{
+		return new Study($this->studyName, $this->linkpdo);
+	}
+
+	/**
+	 * Create a new Visit Group
+	 */
+	public static function createVisitGroup(String $studyName, String $groupModality, PDO $linkpdo): Visit_Group
+	{
+
+		$req = $linkpdo->prepare('INSERT INTO visit_group (study,  group_modality)
                                       VALUES(:studyName, :groupModality)');
 
-        $req->execute(array(
-            'studyName' => $studyName,
-            'groupModality' => $groupModality
-        ));
+		$req->execute(array(
+			'studyName' => $studyName,
+			'groupModality' => $groupModality
+		));
 
-        $idGroup = $linkpdo->lastInsertId();
+		$idGroup = $linkpdo->lastInsertId();
 
-        return new Visit_Group($linkpdo, $idGroup);
-    }
+		return new Visit_Group($linkpdo, $idGroup);
+	}
 }

Spacing +16 added lines, -16 removed lines

@@ -27,26 +27,26 @@ 
 
     public $linkpdo;
 
-    const GROUP_MODALITY_PET = "PT";
-    const GROUP_MODALITY_CT = "CT";
-    const GROUP_MODALITY_MR = "MR";
+    const GROUP_MODALITY_PET="PT";
+    const GROUP_MODALITY_CT="CT";
+    const GROUP_MODALITY_MR="MR";
 
     public function __construct(PDO $linkpdo, int $groupId)
     {
 
-        $this->linkpdo = $linkpdo;
-        $visitGroupQuery = $this->linkpdo->prepare('SELECT * FROM visit_group WHERE id = :groupId');
+        $this->linkpdo=$linkpdo;
+        $visitGroupQuery=$this->linkpdo->prepare('SELECT * FROM visit_group WHERE id = :groupId');
         $visitGroupQuery->execute(array('groupId' => $groupId));
 
-        $visitGroupData = $visitGroupQuery->fetch(PDO::FETCH_ASSOC);
+        $visitGroupData=$visitGroupQuery->fetch(PDO::FETCH_ASSOC);
 
         if (empty($visitGroupData)) {
             throw new Exception('No Visit Group Found');
         }
 
-        $this->groupId = $visitGroupData['id'];
-        $this->studyName = $visitGroupData['study'];
-        $this->groupModality = $visitGroupData['group_modality'];
+        $this->groupId=$visitGroupData['id'];
+        $this->studyName=$visitGroupData['study'];
+        $this->groupModality=$visitGroupData['group_modality'];
     }
 
     /**
@@ -63,13 +63,13 @@ 
     public function getAllVisitTypesOfGroup(): array
     {
 
-        $allVisitsType = $this->linkpdo->prepare('SELECT id FROM visit_type WHERE group_id= :groupId ORDER BY visit_order');
+        $allVisitsType=$this->linkpdo->prepare('SELECT id FROM visit_type WHERE group_id= :groupId ORDER BY visit_order');
         $allVisitsType->execute(array('groupId' => $this->groupId));
-        $allVisits = $allVisitsType->fetchall(PDO::FETCH_COLUMN);
+        $allVisits=$allVisitsType->fetchall(PDO::FETCH_COLUMN);
 
-        $visitTypeArray = [];
+        $visitTypeArray=[];
         foreach ($allVisits as $visitTypeId) {
-            $visitTypeArray[] = new Visit_Type($this->linkpdo, $visitTypeId);
+            $visitTypeArray[]=new Visit_Type($this->linkpdo, $visitTypeId);
         }
 
         return $visitTypeArray;
@@ -88,7 +88,7 @@ 
      */
     public function getStudyVisitManager(): Group_Visit_Manager
     {
-        $studyObject = new Study($this->studyName, $this->linkpdo);
+        $studyObject=new Study($this->studyName, $this->linkpdo);
         return new Group_Visit_Manager($studyObject, $this, $this->linkpdo);
     }
 
@@ -106,7 +106,7 @@ 
     public static function createVisitGroup(String $studyName, String $groupModality, PDO $linkpdo): Visit_Group
     {
 
-        $req = $linkpdo->prepare('INSERT INTO visit_group (study,  group_modality)
+        $req=$linkpdo->prepare('INSERT INTO visit_group (study,  group_modality)
                                       VALUES(:studyName, :groupModality)');
 
         $req->execute(array(
@@ -114,7 +114,7 @@ 
             'groupModality' => $groupModality
         ));
 
-        $idGroup = $linkpdo->lastInsertId();
+        $idGroup=$linkpdo->lastInsertId();
 
         return new Visit_Group($linkpdo, $idGroup);
     }

src/models/Visit_Builder.php

Spacing +26 added lines, -26 removed lines

@@ -38,35 +38,35 @@ 
 	 */
 	public static function isTableEmpty(Visit_Type $vt): bool
 	{
-		$linkpdo = Visit_Builder::getLinkpdo();
-		$table = $vt->tableReviewSpecificName;
-		$pdoSt = $linkpdo->query('SELECT * FROM ' . $table . ';');
+		$linkpdo=Visit_Builder::getLinkpdo();
+		$table=$vt->tableReviewSpecificName;
+		$pdoSt=$linkpdo->query('SELECT * FROM '.$table.';');
 		return count($pdoSt->fetchAll()) == 0;
 	}
 
 	public static function dropColumn(Visit_Type $vt, string $column) : PDOStatement
 	{
-		$linkpdo = Visit_Builder::getLinkpdo();
-		$table = $vt->tableReviewSpecificName;
-		$sql = 'ALTER TABLE `' . $table . '` DROP COLUMN `' . $column . '`;';
+		$linkpdo=Visit_Builder::getLinkpdo();
+		$table=$vt->tableReviewSpecificName;
+		$sql='ALTER TABLE `'.$table.'` DROP COLUMN `'.$column.'`;';
 		return $linkpdo->query($sql);
 	}
 
 
 	public static function alterColumn(Visit_Type $vt, $columnNameBefore, $columnNameAfter, $dataType) : PDOStatement
 	{ 
-		$linkpdo = Visit_Builder::getLinkpdo();
-		$table = $vt->tableReviewSpecificName;
-		$sql = 'ALTER TABLE `' . $table . '` CHANGE `' . $columnNameBefore . '` `' . $columnNameAfter . '` ' . $dataType . ';';
+		$linkpdo=Visit_Builder::getLinkpdo();
+		$table=$vt->tableReviewSpecificName;
+		$sql='ALTER TABLE `'.$table.'` CHANGE `'.$columnNameBefore.'` `'.$columnNameAfter.'` '.$dataType.';';
 		return $linkpdo->query($sql);
 	}
 
 
 	public static function addColumn(Visit_Type $vt, $columnName, $dataType) : PDOStatement
 	{
-		$linkpdo = Visit_Builder::getLinkpdo();
-		$table = $vt->tableReviewSpecificName;
-		$sql = 'ALTER TABLE `' . $table . '` ADD `' . $columnName . '` ' . $dataType . ';';
+		$linkpdo=Visit_Builder::getLinkpdo();
+		$table=$vt->tableReviewSpecificName;
+		$sql='ALTER TABLE `'.$table.'` ADD `'.$columnName.'` '.$dataType.';';
 		return $linkpdo->query($sql);
 	}
 
@@ -79,38 +79,38 @@ 
 	 */
 	public static function formatDataType(string $typeLabel, $typeParams): string
 	{
-		$res = '';
+		$res='';
 		switch ($typeLabel) {
 			case 'int':
-				$res = 'INT(11)';
+				$res='INT(11)';
 				break;
 			case 'tinyint':
-				$res = 'TINYINT(1)';
+				$res='TINYINT(1)';
 				break;
 			case 'tinytext':
-				$res = 'TINYTEXT';
+				$res='TINYTEXT';
 				break;
 			case 'date':
-				$res = 'DATE';
+				$res='DATE';
 				break;
 			case 'varchar':
-				$param = Visit_Builder::escape($typeParams[0]);
+				$param=Visit_Builder::escape($typeParams[0]);
 				// Format params array into string e.g. '(123)'
-				$res = 'VARCHAR(' . $param . ')';
+				$res='VARCHAR('.$param.')';
 				break;
 			case 'decimal':
-				$param1 = Visit_Builder::escape($typeParams[0]);
-				$param2 = Visit_Builder::escape($typeParams[1]);
+				$param1=Visit_Builder::escape($typeParams[0]);
+				$param2=Visit_Builder::escape($typeParams[1]);
 				// Format params array into string e.g. '(12,3)'
-				$res = 'DECIMAL(' . $param1 . ',' . $param2 . ')';
+				$res='DECIMAL('.$param1.','.$param2.')';
 				break;
 			case 'enum':
-				$params = [];
+				$params=[];
 				foreach ($typeParams as $tp) {
 					array_push($params, Visit_Builder::escape($tp));
 				}
 				// Format params array into string e.g. '("abc","def","ghi")'
-				$res = 'ENUM("' . implode('","', $params) . '")';
+				$res='ENUM("'.implode('","', $params).'")';
 				break;
 			default:
 				throw new Exception('Unknown datatype');
@@ -139,14 +139,14 @@ 
 	 */
 	public static function getColumnDataType(Visit_Type $vt, string $columnName): string
 	{
-		$columns = $vt->getSpecificTableInputType();
+		$columns=$vt->getSpecificTableInputType();
 		foreach ($columns as $c) {
 			// Retrieving original data type
 			if ($c['COLUMN_NAME'] == $columnName) {
 				return $c['COLUMN_TYPE'];
 			}
 		}
-		throw new Exception('Cannot find column ' . $columnName . ' for visit type ' . $vt);
+		throw new Exception('Cannot find column '.$columnName.' for visit type '.$vt);
 	}
 
 

src/models/Session.php

Indentation +131 added lines, -131 removed lines

@@ -26,147 +26,147 @@
  */
 Class Session{
     
-    public static function checkSession(bool $log=true, bool $writeSession=false){
-        
-        if(session_status() == PHP_SESSION_NONE) {
-        		session_start();
-        }
-        
-        //Write logs
-        if($log){
-            isset($_POST['id_visit']) ? $logIdVisit=$_POST['id_visit'] : $logIdVisit='N/A';
-            isset($_POST['patient_num']) ? $logPatientNum=$_POST['patient_num'] : $logPatientNum='N/A';
-            @self::logInfo('Username : '.$_SESSION['username'].
-                ' Role: '.$_SESSION ['role'].' Study: '.$_SESSION['study'].' Visit ID: '.$logIdVisit.' Patient Num: '.$logPatientNum);
+	public static function checkSession(bool $log=true, bool $writeSession=false){
+        
+		if(session_status() == PHP_SESSION_NONE) {
+				session_start();
+		}
+        
+		//Write logs
+		if($log){
+			isset($_POST['id_visit']) ? $logIdVisit=$_POST['id_visit'] : $logIdVisit='N/A';
+			isset($_POST['patient_num']) ? $logPatientNum=$_POST['patient_num'] : $logPatientNum='N/A';
+			@self::logInfo('Username : '.$_SESSION['username'].
+				' Role: '.$_SESSION ['role'].' Study: '.$_SESSION['study'].' Visit ID: '.$logIdVisit.' Patient Num: '.$logPatientNum);
             
-        }
+		}
 
-        //Check session availability
-        if (isset($_SESSION['LAST_ACTIVITY']) && (time() - $_SESSION['LAST_ACTIVITY'] > 1200)) {
-            // last request was more than 30 minutes ago or unexisting
-            session_unset();     // unset $_SESSION variable for the run-time
-            session_destroy();   // destroy session data in storage
-            self::redirectAndEndScript();
-        }else if(empty($_SESSION)){
-            //if session already empty
-            self::redirectAndEndScript();
-        }else{
-            $_SESSION['LAST_ACTIVITY'] = time(); // update last activity time stamp
-        }
-        
-        //If script dosen't need to write on session data, close write to free async ajax request
-        if(!$writeSession){
-        	session_write_close();
-        }
-        
-    }
+		//Check session availability
+		if (isset($_SESSION['LAST_ACTIVITY']) && (time() - $_SESSION['LAST_ACTIVITY'] > 1200)) {
+			// last request was more than 30 minutes ago or unexisting
+			session_unset();     // unset $_SESSION variable for the run-time
+			session_destroy();   // destroy session data in storage
+			self::redirectAndEndScript();
+		}else if(empty($_SESSION)){
+			//if session already empty
+			self::redirectAndEndScript();
+		}else{
+			$_SESSION['LAST_ACTIVITY'] = time(); // update last activity time stamp
+		}
+        
+		//If script dosen't need to write on session data, close write to free async ajax request
+		if(!$writeSession){
+			session_write_close();
+		}
+        
+	}
     
-    /**
-     * Redirect to index and end script execution
-     */
-    private static function redirectAndEndScript(){
-        echo '<meta http-equiv="Refresh" content="0;/index.php">';
-        exit("Session Lost");
-    }
+	/**
+	 * Redirect to index and end script execution
+	 */
+	private static function redirectAndEndScript(){
+		echo '<meta http-equiv="Refresh" content="0;/index.php">';
+		exit("Session Lost");
+	}
     
-    /**
-     * Instanciate a new PDO object for database connexion
-     * And Fill Php constant parameter
-     * @return PDO
-     */
-    public static function getLinkpdo(){
-        
-        //Load the config file defining constants
-        if(!defined('DATABASE_HOST')){
-            require_once($_SERVER["DOCUMENT_ROOT"].'/data/_config/config.inc.php');
-        }
-        
-        //Instanciate PDO connexion with SSL or not
-        if(DATABASE_SSL){
-            $linkpdo= new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'', self::getSSLPDOArrayOptions() );    
-        }else{
-            $linkpdo= new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'');   
-        }
+	/**
+	 * Instanciate a new PDO object for database connexion
+	 * And Fill Php constant parameter
+	 * @return PDO
+	 */
+	public static function getLinkpdo(){
+        
+		//Load the config file defining constants
+		if(!defined('DATABASE_HOST')){
+			require_once($_SERVER["DOCUMENT_ROOT"].'/data/_config/config.inc.php');
+		}
+        
+		//Instanciate PDO connexion with SSL or not
+		if(DATABASE_SSL){
+			$linkpdo= new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'', self::getSSLPDOArrayOptions() );    
+		}else{
+			$linkpdo= new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'');   
+		}
 
-        $linkpdo->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
+		$linkpdo->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
         
-        //Load preferences from the database
-        if(! defined('GAELO_PATIENT_CODE_LENGHT') ) Session::loadPreferencesInConstants($linkpdo);
+		//Load preferences from the database
+		if(! defined('GAELO_PATIENT_CODE_LENGHT') ) Session::loadPreferencesInConstants($linkpdo);
         
-        return $linkpdo;
-    }
+		return $linkpdo;
+	}
     
-    /**
-     * Options to use SSL connexion
-     * @return array
-     */
-    public static function getSSLPDOArrayOptions(){
-        $sslOptions = array(
-            PDO::MYSQL_ATTR_SSL_CA => '',
-            PDO::MYSQL_ATTR_SSL_VERIFY_SERVER_CERT => false
-        );
-        
-        return $sslOptions;
-    }
+	/**
+	 * Options to use SSL connexion
+	 * @return array
+	 */
+	public static function getSSLPDOArrayOptions(){
+		$sslOptions = array(
+			PDO::MYSQL_ATTR_SSL_CA => '',
+			PDO::MYSQL_ATTR_SSL_VERIFY_SERVER_CERT => false
+		);
+        
+		return $sslOptions;
+	}
     
-    /**
-     * Write log in a daily log file in log folder
-     * @param string $stringInfo
-     */
-    public static function logInfo(string $stringInfo){
-        
-        if(is_writable($_SERVER["DOCUMENT_ROOT"].'/data/logs/')){
-            // create a log channel
-            $log = new Logger('OpenTrialProcessor');
-            $log->pushHandler(new RotatingFileHandler($_SERVER["DOCUMENT_ROOT"].'/data/logs/gaelO.log', Logger::INFO));
-            $log->pushProcessor(new WebProcessor());
-            $log->info($stringInfo);
-        }else{
-            error_log("Can't write logs folder");
-        }
-    }
+	/**
+	 * Write log in a daily log file in log folder
+	 * @param string $stringInfo
+	 */
+	public static function logInfo(string $stringInfo){
+        
+		if(is_writable($_SERVER["DOCUMENT_ROOT"].'/data/logs/')){
+			// create a log channel
+			$log = new Logger('OpenTrialProcessor');
+			$log->pushHandler(new RotatingFileHandler($_SERVER["DOCUMENT_ROOT"].'/data/logs/gaelO.log', Logger::INFO));
+			$log->pushProcessor(new WebProcessor());
+			$log->info($stringInfo);
+		}else{
+			error_log("Can't write logs folder");
+		}
+	}
     
-    /**
-     * Store preference from the database in PHP constants
-     * @param PDO $linkpdo
-     */
-    public static function loadPreferencesInConstants(PDO $linkpdo){
-        
-        $connecter = $linkpdo->prepare('SELECT * FROM preferences');
-        $connecter->execute();
-        
-        $result = $connecter->fetch(PDO::FETCH_ASSOC);
-        
-        define('GAELO_PATIENT_CODE_LENGHT',$result['patient_code_length']);
-        define('GAELO_PLATEFORM_NAME', $result['name']);
-        define('GAELO_ADMIN_EMAIL', $result['admin_email']);
-        define('GAELO_REPLY_TO', $result['email_reply_to']);
-        define('GAELO_CORPORATION', $result['corporation']);
-        define('GAELO_WEB_ADDRESS', $result['address']);
-        define('GAELO_DATE_FORMAT', $result['parse_date_import']);
-        define('GAELO_COUNTRY_LANGUAGE', $result['parse_country_name']);
+	/**
+	 * Store preference from the database in PHP constants
+	 * @param PDO $linkpdo
+	 */
+	public static function loadPreferencesInConstants(PDO $linkpdo){
+        
+		$connecter = $linkpdo->prepare('SELECT * FROM preferences');
+		$connecter->execute();
+        
+		$result = $connecter->fetch(PDO::FETCH_ASSOC);
+        
+		define('GAELO_PATIENT_CODE_LENGHT',$result['patient_code_length']);
+		define('GAELO_PLATEFORM_NAME', $result['name']);
+		define('GAELO_ADMIN_EMAIL', $result['admin_email']);
+		define('GAELO_REPLY_TO', $result['email_reply_to']);
+		define('GAELO_CORPORATION', $result['corporation']);
+		define('GAELO_WEB_ADDRESS', $result['address']);
+		define('GAELO_DATE_FORMAT', $result['parse_date_import']);
+		define('GAELO_COUNTRY_LANGUAGE', $result['parse_country_name']);
 
-        define('GAELO_ORTHANC_EXPOSED_INTERNAL_ADDRESS', $result['orthanc_exposed_internal_address']);
-        define('GAELO_ORTHANC_EXPOSED_INTERNAL_PORT', $result['orthanc_exposed_internal_port']);
-        define('GAELO_ORTHANC_EXPOSED_EXTERNAL_ADDRESS', $result['orthanc_exposed_external_address']);
-        define('GAELO_ORTHANC_EXPOSED_EXTERNAL_PORT', $result['orthanc_exposed_external_port']);
-        define('GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN', $result['orthanc_exposed_internal_login']);
-        define('GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD', $result['orthanc_exposed_internal_password']);
-        define('GAELO_ORTHANC_EXPOSED_EXTERNAL_LOGIN', $result['orthanc_exposed_external_login']);
-        define('GAELO_ORTHANC_EXPOSED_EXTERNAL_PASSWORD', $result['orthanc_exposed_external_password']);
-        
-        define('GAELO_ORTHANC_PACS_ADDRESS', $result['orthanc_pacs_address']);
-        define('GAELO_ORTHANC_PACS_PORT', $result['orthanc_pacs_port']);
-        define('GAELO_ORTHANC_PACS_LOGIN', $result['orthanc_pacs_login']);
-        define('GAELO_ORTHANC_PACS_PASSWORD', $result['orthanc_pacs_password']);
-        
-        define('GAELO_USE_SMTP', $result['use_smtp']);
-        define('GAELO_SMTP_HOST', $result['smtp_host']);
-        define('GAELO_SMTP_PORT', $result['smtp_port']);
-        define('GAELO_SMTP_USER', $result['smtp_user']);
-        define('GAELO_SMTP_PASSWORD', $result['smtp_password']);
-        define('GAELO_SMTP_SECURE', $result['smtp_secure']);
-        
-    }
+		define('GAELO_ORTHANC_EXPOSED_INTERNAL_ADDRESS', $result['orthanc_exposed_internal_address']);
+		define('GAELO_ORTHANC_EXPOSED_INTERNAL_PORT', $result['orthanc_exposed_internal_port']);
+		define('GAELO_ORTHANC_EXPOSED_EXTERNAL_ADDRESS', $result['orthanc_exposed_external_address']);
+		define('GAELO_ORTHANC_EXPOSED_EXTERNAL_PORT', $result['orthanc_exposed_external_port']);
+		define('GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN', $result['orthanc_exposed_internal_login']);
+		define('GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD', $result['orthanc_exposed_internal_password']);
+		define('GAELO_ORTHANC_EXPOSED_EXTERNAL_LOGIN', $result['orthanc_exposed_external_login']);
+		define('GAELO_ORTHANC_EXPOSED_EXTERNAL_PASSWORD', $result['orthanc_exposed_external_password']);
+        
+		define('GAELO_ORTHANC_PACS_ADDRESS', $result['orthanc_pacs_address']);
+		define('GAELO_ORTHANC_PACS_PORT', $result['orthanc_pacs_port']);
+		define('GAELO_ORTHANC_PACS_LOGIN', $result['orthanc_pacs_login']);
+		define('GAELO_ORTHANC_PACS_PASSWORD', $result['orthanc_pacs_password']);
+        
+		define('GAELO_USE_SMTP', $result['use_smtp']);
+		define('GAELO_SMTP_HOST', $result['smtp_host']);
+		define('GAELO_SMTP_PORT', $result['smtp_port']);
+		define('GAELO_SMTP_USER', $result['smtp_user']);
+		define('GAELO_SMTP_PASSWORD', $result['smtp_password']);
+		define('GAELO_SMTP_SECURE', $result['smtp_secure']);
+        
+	}
 
 }
\ No newline at end of file

Spacing +29 added lines, -29 removed lines

@@ -24,16 +24,16 @@ 
 /**
  * Methods that are call by all scripts
  */
-Class Session{
+Class Session {
     
-    public static function checkSession(bool $log=true, bool $writeSession=false){
+    public static function checkSession(bool $log=true, bool $writeSession=false) {
         
-        if(session_status() == PHP_SESSION_NONE) {
+        if (session_status() == PHP_SESSION_NONE) {
         		session_start();
         }
         
         //Write logs
-        if($log){
+        if ($log) {
             isset($_POST['id_visit']) ? $logIdVisit=$_POST['id_visit'] : $logIdVisit='N/A';
             isset($_POST['patient_num']) ? $logPatientNum=$_POST['patient_num'] : $logPatientNum='N/A';
             @self::logInfo('Username : '.$_SESSION['username'].
@@ -42,20 +42,20 @@ 
         }
 
         //Check session availability
-        if (isset($_SESSION['LAST_ACTIVITY']) && (time() - $_SESSION['LAST_ACTIVITY'] > 1200)) {
+        if (isset($_SESSION['LAST_ACTIVITY']) && (time()-$_SESSION['LAST_ACTIVITY'] > 1200)) {
             // last request was more than 30 minutes ago or unexisting
-            session_unset();     // unset $_SESSION variable for the run-time
-            session_destroy();   // destroy session data in storage
+            session_unset(); // unset $_SESSION variable for the run-time
+            session_destroy(); // destroy session data in storage
             self::redirectAndEndScript();
-        }else if(empty($_SESSION)){
+        }else if (empty($_SESSION)) {
             //if session already empty
             self::redirectAndEndScript();
-        }else{
-            $_SESSION['LAST_ACTIVITY'] = time(); // update last activity time stamp
+        }else {
+            $_SESSION['LAST_ACTIVITY']=time(); // update last activity time stamp
         }
         
         //If script dosen't need to write on session data, close write to free async ajax request
-        if(!$writeSession){
+        if (!$writeSession) {
         	session_write_close();
         }
         
@@ -64,7 +64,7 @@ 
     /**
      * Redirect to index and end script execution
      */
-    private static function redirectAndEndScript(){
+    private static function redirectAndEndScript() {
         echo '<meta http-equiv="Refresh" content="0;/index.php">';
         exit("Session Lost");
     }
@@ -74,24 +74,24 @@ 
      * And Fill Php constant parameter
      * @return PDO
      */
-    public static function getLinkpdo(){
+    public static function getLinkpdo() {
         
         //Load the config file defining constants
-        if(!defined('DATABASE_HOST')){
+        if (!defined('DATABASE_HOST')) {
             require_once($_SERVER["DOCUMENT_ROOT"].'/data/_config/config.inc.php');
         }
         
         //Instanciate PDO connexion with SSL or not
-        if(DATABASE_SSL){
-            $linkpdo= new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'', self::getSSLPDOArrayOptions() );    
-        }else{
-            $linkpdo= new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'');   
+        if (DATABASE_SSL) {
+            $linkpdo=new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'', self::getSSLPDOArrayOptions());    
+        }else {
+            $linkpdo=new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'');   
         }
 
         $linkpdo->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
         
         //Load preferences from the database
-        if(! defined('GAELO_PATIENT_CODE_LENGHT') ) Session::loadPreferencesInConstants($linkpdo);
+        if (!defined('GAELO_PATIENT_CODE_LENGHT')) Session::loadPreferencesInConstants($linkpdo);
         
         return $linkpdo;
     }
@@ -100,8 +100,8 @@ 
      * Options to use SSL connexion
      * @return array
      */
-    public static function getSSLPDOArrayOptions(){
-        $sslOptions = array(
+    public static function getSSLPDOArrayOptions() {
+        $sslOptions=array(
             PDO::MYSQL_ATTR_SSL_CA => '',
             PDO::MYSQL_ATTR_SSL_VERIFY_SERVER_CERT => false
         );
@@ -113,15 +113,15 @@ 
      * Write log in a daily log file in log folder
      * @param string $stringInfo
      */
-    public static function logInfo(string $stringInfo){
+    public static function logInfo(string $stringInfo) {
         
-        if(is_writable($_SERVER["DOCUMENT_ROOT"].'/data/logs/')){
+        if (is_writable($_SERVER["DOCUMENT_ROOT"].'/data/logs/')) {
             // create a log channel
-            $log = new Logger('OpenTrialProcessor');
+            $log=new Logger('OpenTrialProcessor');
             $log->pushHandler(new RotatingFileHandler($_SERVER["DOCUMENT_ROOT"].'/data/logs/gaelO.log', Logger::INFO));
             $log->pushProcessor(new WebProcessor());
             $log->info($stringInfo);
-        }else{
+        }else {
             error_log("Can't write logs folder");
         }
     }
@@ -130,14 +130,14 @@ 
      * Store preference from the database in PHP constants
      * @param PDO $linkpdo
      */
-    public static function loadPreferencesInConstants(PDO $linkpdo){
+    public static function loadPreferencesInConstants(PDO $linkpdo) {
         
-        $connecter = $linkpdo->prepare('SELECT * FROM preferences');
+        $connecter=$linkpdo->prepare('SELECT * FROM preferences');
         $connecter->execute();
         
-        $result = $connecter->fetch(PDO::FETCH_ASSOC);
+        $result=$connecter->fetch(PDO::FETCH_ASSOC);
         
-        define('GAELO_PATIENT_CODE_LENGHT',$result['patient_code_length']);
+        define('GAELO_PATIENT_CODE_LENGHT', $result['patient_code_length']);
         define('GAELO_PLATEFORM_NAME', $result['name']);
         define('GAELO_ADMIN_EMAIL', $result['admin_email']);
         define('GAELO_REPLY_TO', $result['email_reply_to']);

Braces +7 added lines, -5 removed lines

@@ -47,10 +47,10 @@ 
             session_unset();     // unset $_SESSION variable for the run-time
             session_destroy();   // destroy session data in storage
             self::redirectAndEndScript();
-        }else if(empty($_SESSION)){
+        } else if(empty($_SESSION)){
             //if session already empty
             self::redirectAndEndScript();
-        }else{
+        } else{
             $_SESSION['LAST_ACTIVITY'] = time(); // update last activity time stamp
         }
         
@@ -84,14 +84,16 @@ 
         //Instanciate PDO connexion with SSL or not
         if(DATABASE_SSL){
             $linkpdo= new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'', self::getSSLPDOArrayOptions() );    
-        }else{
+        } else{
             $linkpdo= new PDO('mysql:host='.DATABASE_HOST.';dbname='.DATABASE_NAME.';charset=UTF8', ''.DATABASE_USERNAME.'', ''.DATABASE_PASSWORD.'');   
         }
 
         $linkpdo->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
         
         //Load preferences from the database
-        if(! defined('GAELO_PATIENT_CODE_LENGHT') ) Session::loadPreferencesInConstants($linkpdo);
+        if(! defined('GAELO_PATIENT_CODE_LENGHT') ) {
+        	Session::loadPreferencesInConstants($linkpdo);
+        }
         
         return $linkpdo;
     }
@@ -121,7 +123,7 @@ 
             $log->pushHandler(new RotatingFileHandler($_SERVER["DOCUMENT_ROOT"].'/data/logs/gaelO.log', Logger::INFO));
             $log->pushProcessor(new WebProcessor());
             $log->info($stringInfo);
-        }else{
+        } else{
             error_log("Can't write logs folder");
         }
     }

src/models/Visit_Type_Iterator.php

Spacing +6 added lines, -6 removed lines

@@ -6,21 +6,21 @@ 
 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;
+        $this->visitsTypeArray=$visitTypeArray;
     }
 
     public function setVisitPosition(String $visitName)
     {
-        $visitNameArray = array_map(function (Visit_Type $visitTypeObject) {
+        $visitNameArray=array_map(function(Visit_Type $visitTypeObject) {
             return $visitTypeObject->name;
         }, $this->visitsTypeArray);
 
-        $this->index = array_search($visitName, $visitNameArray);
+        $this->index=array_search($visitName, $visitNameArray);
     }
 
 
@@ -55,7 +55,7 @@ 
 
     public function rewind()
     {
-        $this->index = 0;
+        $this->index=0;
     }
 
     public function key(): int

Indentation +49 added lines, -49 removed lines

@@ -6,65 +6,65 @@
 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()]);
+	}
 }

Braces +10 added lines, -4 removed lines

@@ -37,8 +37,11 @@ 
     public function hasPrevious()
     {
         $this->previous();
-        if ($this->valid()) return $this->current();
-        else return false;
+        if ($this->valid()) {
+        	return $this->current();
+        } else {
+        	return false;
+        }
     }
 
     public function next()
@@ -49,8 +52,11 @@ 
     public function hasNext()
     {
         $this->next();
-        if ($this->valid()) return $this->current();
-        else return false;
+        if ($this->valid()) {
+        	return $this->current();
+        } else {
+        	return false;
+        }
     }
 
     public function rewind()

src/models/Tracker.php

Indentation +63 added lines, -63 removed lines

@@ -20,79 +20,79 @@
  */
 class Tracker{
     
-    /**
-     * Get tracker data by Role +- Study Filter
-     * @param string $role
-     * @param PDO $linkpdo
-     * @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');
-            $queryTracker->execute(array(
-                'role' => $role
-            ));
+	/**
+	 * Get tracker data by Role +- Study Filter
+	 * @param string $role
+	 * @param PDO $linkpdo
+	 * @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');
+			$queryTracker->execute(array(
+				'role' => $role
+			));
            
-        }else{
-            $queryTracker = $linkpdo->prepare('SELECT * FROM tracker WHERE study = :study AND role=:role');
-            $queryTracker->execute(array('study' => $study,
-                'role' => $role,
-            ));
+		}else{
+			$queryTracker = $linkpdo->prepare('SELECT * FROM tracker WHERE study = :study AND role=:role');
+			$queryTracker->execute(array('study' => $study,
+				'role' => $role,
+			));
             
-        }
-        $trackerResult=$queryTracker->fetchAll(PDO::FETCH_ASSOC);
+		}
+		$trackerResult=$queryTracker->fetchAll(PDO::FETCH_ASSOC);
 
-        return $trackerResult;
-    }
+		return $trackerResult;
+	}
     
-    /**
-     * Return logged users messages of a study
-     * @param string $study
-     * @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"');
-        $queryTracker->execute(array('study' => $study));
-        $trackerResult=$queryTracker->fetchAll(PDO::FETCH_ASSOC);
-        return $trackerResult;
-    }
+	/**
+	 * Return logged users messages of a study
+	 * @param string $study
+	 * @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"');
+		$queryTracker->execute(array('study' => $study));
+		$trackerResult=$queryTracker->fetchAll(PDO::FETCH_ASSOC);
+		return $trackerResult;
+	}
     
-    /**
-     * Get tracker data for a specific visit
-     * @param string $id_visit
-     * @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');
-        $queryTracker->execute(array('id_visit' => $id_visit));
-        $trackerResult=$queryTracker->fetchAll(PDO::FETCH_ASSOC);
-        return $trackerResult;    
-    }
+	/**
+	 * Get tracker data for a specific visit
+	 * @param string $id_visit
+	 * @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');
+		$queryTracker->execute(array('id_visit' => $id_visit));
+		$trackerResult=$queryTracker->fetchAll(PDO::FETCH_ASSOC);
+		return $trackerResult;    
+	}
     
-    /**
-     * 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, $actionDetails){
+	/**
+	 * Activity logger to log user activity in database
+	 * Activity should be an associative key, will be JSON encoded
+	 */
+	public static function logActivity($username, $role, $study, $id_visit, $actionType, $actionDetails){
         
-        $linkpdo=Session::getLinkpdo();
+		$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" => $role,
-            "date"=> date('Y-m-d H:i:s') . substr((string)microtime(), 1, 6),
-            "study"=>$study,
-            "id_visit"=>$id_visit,
-            "action_type"=>$actionType,
-            "action_details"=>json_encode($actionDetails)
-        ));
+		$connecter->execute(array(
+			"username" => $username,
+			"role" => $role,
+			"date"=> date('Y-m-d H:i:s') . substr((string)microtime(), 1, 6),
+			"study"=>$study,
+			"id_visit"=>$id_visit,
+			"action_type"=>$actionType,
+			"action_details"=>json_encode($actionDetails)
+		));
         
-    }
+	}
     
 }
\ No newline at end of file

Spacing +13 added lines, -13 removed lines

@@ -18,7 +18,7 @@ 
  * @author salim
  *
  */
-class Tracker{
+class Tracker {
     
     /**
      * Get tracker data by Role +- Study Filter
@@ -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/Import_Patient.php

Braces +15 added lines, -14 removed lines

@@ -58,8 +58,7 @@ 
 			    if(GAELO_DATE_FORMAT=='m.d.Y'){
 			    	$birthDay=intval($birthDateArray[1]);
 			    	$birthMonth=intval($birthDateArray[0]);
-			    }
-			    else if(GAELO_DATE_FORMAT=='d.m.Y'){
+			    } else if(GAELO_DATE_FORMAT=='d.m.Y'){
 			    	$birthDay=intval($birthDateArray[0]);
 			    	$birthMonth=intval($birthDateArray[1]);
 			    }
@@ -71,8 +70,7 @@ 
 				//Store the patient result import process in this object
 				if ($insertddb){
 						$this->sucessList[] = $patientNumber;
-				}
-				else{
+				} else{
 					$patientFailed['PatientNumber']=$patientNumber;
 					$patientFailed['Reason']="Can't write to DB, wrong date or other wrong input";
 					$this->failList[]=$patientFailed;
@@ -84,8 +82,7 @@ 
 				if(!$isExistingCenter) {
 				    if( empty($patientInvestigatorNumCenter) ){
 				        $this->failList['Missing Num Center'][]=$patientNumber;
-				    }
-				    else {
+				    } else {
 				        $this->failList['Unknown Center'][]=$patientNumber;
 				    }
 
@@ -117,8 +114,7 @@ 
 	    if(GAELO_DATE_FORMAT=='m.d.Y'){
 	        $registrationDay=intval($dateNbArray[1]);
 	        $registrationMonth=intval($dateNbArray[0]);
-	    }
-	    else if(GAELO_DATE_FORMAT=='d.m.Y'){
+	    } else if(GAELO_DATE_FORMAT=='d.m.Y'){
 	        $registrationDay=intval($dateNbArray[0]);
 	        $registrationMonth=intval($dateNbArray[1]);
 	    }
@@ -148,7 +144,7 @@ 
 	private function isNewPatient($patientCode){
 	    try{
 	        new Patient($patientCode, $this->linkpdo);
-	    }catch(Exception $e1){
+	    } catch(Exception $e1){
 	        return true;
 	    }
 	    
@@ -176,11 +172,13 @@ 
      * @return boolean
      */
 	private function isExistingCenter($patientNumCenter){
-	    if(is_null($patientNumCenter) || strlen($patientNumCenter)==0) return false;
+	    if(is_null($patientNumCenter) || strlen($patientNumCenter)==0) {
+	    	return false;
+	    }
 	    
 	    try{
 	        new Center($this->linkpdo, $patientNumCenter);
-	    }catch(Exception $e1){
+	    } catch(Exception $e1){
 	        return false;
 	    }
 	    
@@ -250,11 +248,14 @@ 
 	        foreach ($this->failList as $key=>$value){
 	            if(! empty($value)){
 	                $failReport=$failReport.$key.':<br>';
-	                if(is_array($value)) $failReport=$failReport.implode('<br>',$value).'<br>';
-	                else $failReport=$failReport.$value.'<br>';
+	                if(is_array($value)) {
+	                	$failReport=$failReport.implode('<br>',$value).'<br>';
+	                } else {
+	                	$failReport=$failReport.$value.'<br>';
+	                }
 	            }
 	        }
-	    }else{
+	    } else{
 	        $failReport=$failReport.' None <br>' ;
 	    }
 	    

Indentation +102 added lines, -102 removed lines

@@ -27,9 +27,9 @@ 
 	private $studyObject;
 	
 	public function __construct($originalJson, $study, $linkpdo){
-	    $this->linkpdo= $linkpdo;
+		$this->linkpdo= $linkpdo;
 		//Store the JSON file and the target study
-	    $this->originalJson=$originalJson;
+		$this->originalJson=$originalJson;
 		$this->study = $study;
 		$this->studyObject = new Study($study, $linkpdo);
 	}
@@ -37,17 +37,17 @@ 
 	public function readJson(){
 		$jsonImport=json_decode($this->originalJson, true);
 		
-        //For each patient from the array list
+		//For each patient from the array list
 		foreach ($jsonImport as $patient){
 			//Get patient info
-		    $patientNumber=$patient['patientNumber'];
-		    $patientLastName=$patient['lastName'];
-		    $patientFirstName=$patient['firstName'];
-		    $patientGender=$patient['gender'];
-		    $patientInvestigatorNumCenter=$patient['investigatorNumCenter'];
-		    $patientDateOfBirth=$patient['dateOfBirth'];
-		    $patientInvestigatorName=$patient['investigatorName'];
-		    $patientRegistrationDate= $this->parseRegistrationDate($patient['registrationDate']);
+			$patientNumber=$patient['patientNumber'];
+			$patientLastName=$patient['lastName'];
+			$patientFirstName=$patient['firstName'];
+			$patientGender=$patient['gender'];
+			$patientInvestigatorNumCenter=$patient['investigatorNumCenter'];
+			$patientDateOfBirth=$patient['dateOfBirth'];
+			$patientInvestigatorName=$patient['investigatorName'];
+			$patientRegistrationDate= $this->parseRegistrationDate($patient['registrationDate']);
 		    
 			//Check condition before import
 			$isNewPatient=$this->isNewPatient($patientNumber);
@@ -56,20 +56,20 @@ 
 			$isPrefixCorrect = $this->isCorrectPrefix($patientNumber);
 			
 			if ($isNewPatient && $isCorrectPatientNumberLenght && $isPrefixCorrect && $isExistingCenter && !empty($patientRegistrationDate) ){
-			    //Store in DB
-			    $birthDateArray=explode("/", $patientDateOfBirth);
-			    if(GAELO_DATE_FORMAT=='m.d.Y'){
-			    	$birthDay=intval($birthDateArray[1]);
-			    	$birthMonth=intval($birthDateArray[0]);
-			    }
-			    else if(GAELO_DATE_FORMAT=='d.m.Y'){
-			    	$birthDay=intval($birthDateArray[0]);
-			    	$birthMonth=intval($birthDateArray[1]);
-			    }
-			    $birthYear=intval($birthDateArray[2]);
+				//Store in DB
+				$birthDateArray=explode("/", $patientDateOfBirth);
+				if(GAELO_DATE_FORMAT=='m.d.Y'){
+					$birthDay=intval($birthDateArray[1]);
+					$birthMonth=intval($birthDateArray[0]);
+				}
+				else if(GAELO_DATE_FORMAT=='d.m.Y'){
+					$birthDay=intval($birthDateArray[0]);
+					$birthMonth=intval($birthDateArray[1]);
+				}
+				$birthYear=intval($birthDateArray[2]);
 			    
 				$insertddb=$this->addPatientToDatabase($patientNumber, $patientLastName, $patientFirstName, $patientGender,
-				    $patientInvestigatorNumCenter, $patientRegistrationDate, $birthDay,$birthMonth, $birthYear, $patientInvestigatorName);
+					$patientInvestigatorNumCenter, $patientRegistrationDate, $birthDay,$birthMonth, $birthYear, $patientInvestigatorName);
 				
 				//Store the patient result import process in this object
 				if ($insertddb){
@@ -85,21 +85,21 @@ 
 			} else{
 			    
 				if(!$isExistingCenter) {
-				    if( empty($patientInvestigatorNumCenter) ){
-				        $this->failList['Missing Num Center'][]=$patientNumber;
-				    }
-				    else {
-				        $this->failList['Unknown Center'][]=$patientNumber;
-				    }
+					if( empty($patientInvestigatorNumCenter) ){
+						$this->failList['Missing Num Center'][]=$patientNumber;
+					}
+					else {
+						$this->failList['Unknown Center'][]=$patientNumber;
+					}
 
 				} else if(! $isCorrectPatientNumberLenght){
-				    $this->failList['Wrong PatientNumber length'][]=$patientNumber;
+					$this->failList['Wrong PatientNumber length'][]=$patientNumber;
 				    
 				} else if(!$isNewPatient ){
-				    $this->failList['Patient already in Database'][]=$patientNumber;
+					$this->failList['Patient already in Database'][]=$patientNumber;
 				    
 				} else if(empty($patientRegistrationDate)){
-				    $this->failList['Empty Registration Date'][]=$patientNumber;
+					$this->failList['Empty Registration Date'][]=$patientNumber;
 				} else if( ! $isPrefixCorrect){
 					$this->failList['Wrong Patient Code Prefix'][]=$patientNumber;
 				}
@@ -117,30 +117,30 @@ 
 	 * @return NULL|DateTime
 	 */
 	private function parseRegistrationDate(?string $registrationDate){
-	    $dateNbArray=explode('/', $registrationDate);
+		$dateNbArray=explode('/', $registrationDate);
 	    
-	    if(GAELO_DATE_FORMAT=='m.d.Y'){
-	        $registrationDay=intval($dateNbArray[1]);
-	        $registrationMonth=intval($dateNbArray[0]);
-	    }
-	    else if(GAELO_DATE_FORMAT=='d.m.Y'){
-	        $registrationDay=intval($dateNbArray[0]);
-	        $registrationMonth=intval($dateNbArray[1]);
-	    }
+		if(GAELO_DATE_FORMAT=='m.d.Y'){
+			$registrationDay=intval($dateNbArray[1]);
+			$registrationMonth=intval($dateNbArray[0]);
+		}
+		else if(GAELO_DATE_FORMAT=='d.m.Y'){
+			$registrationDay=intval($dateNbArray[0]);
+			$registrationMonth=intval($dateNbArray[1]);
+		}
 	    
-	    $registrationYear=intval($dateNbArray[2]);
+		$registrationYear=intval($dateNbArray[2]);
 	    
-	    if($registrationDay==0 || $registrationMonth==0 ||$registrationYear==0){
-	        return null;
-	    }
+		if($registrationDay==0 || $registrationMonth==0 ||$registrationYear==0){
+			return null;
+		}
 	    
-	    try {
-	        $dateResult = new DateTime($registrationYear.'-'.$registrationMonth.'-'.$registrationDay);
-	    } catch (Exception $e) {
-	        error_log( $e->getMessage());
-	        return null;
-	    }
-	    return $dateResult;
+		try {
+			$dateResult = new DateTime($registrationYear.'-'.$registrationMonth.'-'.$registrationDay);
+		} catch (Exception $e) {
+			error_log( $e->getMessage());
+			return null;
+		}
+		return $dateResult;
 	   
 	}
 
@@ -151,13 +151,13 @@ 
 	 * @return boolean
 	 */
 	private function isNewPatient($patientCode){
-	    try{
-	        new Patient($patientCode, $this->linkpdo);
-	    }catch(Exception $e1){
-	        return true;
-	    }
+		try{
+			new Patient($patientCode, $this->linkpdo);
+		}catch(Exception $e1){
+			return true;
+		}
 	    
-	    return false;
+		return false;
 	}
 
 	/**
@@ -192,21 +192,21 @@ 
 		return (substr($string, 0, $len) === $startString); 
 	} 
 
-    /**
-     * Check that patient's center is one of known center in the plateform
-     * @param $patientNumCenter
-     * @return boolean
-     */
+	/**
+	 * Check that patient's center is one of known center in the plateform
+	 * @param $patientNumCenter
+	 * @return boolean
+	 */
 	private function isExistingCenter($patientNumCenter){
-	    if(is_null($patientNumCenter) || strlen($patientNumCenter)==0) return false;
+		if(is_null($patientNumCenter) || strlen($patientNumCenter)==0) return false;
 	    
-	    try{
-	        new Center($this->linkpdo, $patientNumCenter);
-	    }catch(Exception $e1){
-	        return false;
-	    }
+		try{
+			new Center($this->linkpdo, $patientNumCenter);
+		}catch(Exception $e1){
+			return false;
+		}
 	    
-	    return true;
+		return true;
 	}
 
 	/**
@@ -223,7 +223,7 @@ 
 	 * @return boolean
 	 */
 	private function addPatientToDatabase($patientNumber, string $patientLastName, string $patientFirstName, string $patientGender
-	    , $patientInvestigatorNumCenter, $dateRegistration, $patientBirthDay, $patientBirthMonth, $patientBirthYear, string $patientInvestigatorName){
+		, $patientInvestigatorNumCenter, $dateRegistration, $patientBirthDay, $patientBirthMonth, $patientBirthYear, string $patientInvestigatorName){
 		
 		try {
 			$insert_bdd = $this->linkpdo->prepare('INSERT INTO patients(study, code, first_name, last_name, gender, birth_day, birth_month, birth_year, registration_date, investigator_name, center)
@@ -232,7 +232,7 @@ 
 			$insert_bdd->execute(array('code' => $patientNumber,
 													'first_name' => @strtoupper($patientFirstName[0]),
 													'last_name' => @strtoupper($patientLastName[0]),
-                                                    'gender' => @strtoupper($patientGender[0]),
+													'gender' => @strtoupper($patientGender[0]),
 													'birth_day' => $patientBirthDay,
 													'birth_month' => $patientBirthMonth,
 													'birth_year' => $patientBirthYear,
@@ -242,7 +242,7 @@ 
 													'study' => $this->study));
 			$success=true;
 		} catch (Exception $e) {
-		    $success=false;
+			$success=false;
 			error_log($e);
 		}
 
@@ -251,13 +251,13 @@ 
 	}
 	
 	public function getHTMLImportAnswer(){
-	    return $this->buildSuccessAnswer().$this->buildErrorAnswer();
+		return $this->buildSuccessAnswer().$this->buildErrorAnswer();
 	}
 	
 	public function getTextImportAnswer(){
-	    //Prepare Html2PlainText for email validity (both version to enhance spam validation)
-	    $htmlMessageObject = new \Html2Text\Html2Text($this->getHTMLImportAnswer());
-	    return $htmlMessageObject->getText();
+		//Prepare Html2PlainText for email validity (both version to enhance spam validation)
+		$htmlMessageObject = new \Html2Text\Html2Text($this->getHTMLImportAnswer());
+		return $htmlMessageObject->getText();
 	    
 	}
 	
@@ -266,21 +266,21 @@ 
 	 * @return string
 	 */
 	private function buildErrorAnswer(){
-	    //List of failed patients
-	    $failReport='Failed Patients: <br>';
-	    if ( !empty($this->failList) ){
-	        foreach ($this->failList as $key=>$value){
-	            if(! empty($value)){
-	                $failReport=$failReport.$key.':<br>';
-	                if(is_array($value)) $failReport=$failReport.implode('<br>',$value).'<br>';
-	                else $failReport=$failReport.$value.'<br>';
-	            }
-	        }
-	    }else{
-	        $failReport=$failReport.' None <br>' ;
-	    }
+		//List of failed patients
+		$failReport='Failed Patients: <br>';
+		if ( !empty($this->failList) ){
+			foreach ($this->failList as $key=>$value){
+				if(! empty($value)){
+					$failReport=$failReport.$key.':<br>';
+					if(is_array($value)) $failReport=$failReport.implode('<br>',$value).'<br>';
+					else $failReport=$failReport.$value.'<br>';
+				}
+			}
+		}else{
+			$failReport=$failReport.' None <br>' ;
+		}
 	    
-	    return $failReport;
+		return $failReport;
 	}
 	
 	/**
@@ -288,18 +288,18 @@ 
 	 * @return string
 	 */
 	private function buildSuccessAnswer(){
-	    //List of succeded patients
-	    $successReport='Success Patients: <br>';
-	    if ( !empty($this->sucessList) ){
-	        foreach ($this->sucessList as $value) {
-	            $success=$value;
-	            $successReport=$successReport.$success.'<br>';
-	        }
-	    } else {
-	        $successReport=$successReport.' None <br>';
-	    }
+		//List of succeded patients
+		$successReport='Success Patients: <br>';
+		if ( !empty($this->sucessList) ){
+			foreach ($this->sucessList as $value) {
+				$success=$value;
+				$successReport=$successReport.$success.'<br>';
+			}
+		} else {
+			$successReport=$successReport.' None <br>';
+		}
 	    
-	    return $successReport;
+		return $successReport;
 	}
 
 }

Spacing +63 added lines, -63 removed lines

@@ -17,7 +17,7 @@ 
  * Import patient in study (import data from Json structured file)
  */
 
-class Import_Patient{
+class Import_Patient {
 
 	private $originalJson;
 	private $linkpdo;
@@ -26,19 +26,19 @@ 
 	private $study;
 	private $studyObject;
 	
-	public function __construct($originalJson, $study, $linkpdo){
-	    $this->linkpdo= $linkpdo;
+	public function __construct($originalJson, $study, $linkpdo) {
+	    $this->linkpdo=$linkpdo;
 		//Store the JSON file and the target study
 	    $this->originalJson=$originalJson;
-		$this->study = $study;
-		$this->studyObject = new Study($study, $linkpdo);
+		$this->study=$study;
+		$this->studyObject=new Study($study, $linkpdo);
 	}
 
-	public function readJson(){
+	public function readJson() {
 		$jsonImport=json_decode($this->originalJson, true);
 		
         //For each patient from the array list
-		foreach ($jsonImport as $patient){
+		foreach ($jsonImport as $patient) {
 			//Get patient info
 		    $patientNumber=$patient['patientNumber'];
 		    $patientLastName=$patient['lastName'];
@@ -47,60 +47,60 @@ 
 		    $patientInvestigatorNumCenter=$patient['investigatorNumCenter'];
 		    $patientDateOfBirth=$patient['dateOfBirth'];
 		    $patientInvestigatorName=$patient['investigatorName'];
-		    $patientRegistrationDate= $this->parseRegistrationDate($patient['registrationDate']);
+		    $patientRegistrationDate=$this->parseRegistrationDate($patient['registrationDate']);
 		    
 			//Check condition before import
 			$isNewPatient=$this->isNewPatient($patientNumber);
 			$isCorrectPatientNumberLenght=$this->isCorrectPatientNumberLenght($patientNumber);
 			$isExistingCenter=$this->isExistingCenter($patientInvestigatorNumCenter);
-			$isPrefixCorrect = $this->isCorrectPrefix($patientNumber);
+			$isPrefixCorrect=$this->isCorrectPrefix($patientNumber);
 			
-			if ($isNewPatient && $isCorrectPatientNumberLenght && $isPrefixCorrect && $isExistingCenter && !empty($patientRegistrationDate) ){
+			if ($isNewPatient && $isCorrectPatientNumberLenght && $isPrefixCorrect && $isExistingCenter && !empty($patientRegistrationDate)) {
 			    //Store in DB
 			    $birthDateArray=explode("/", $patientDateOfBirth);
-			    if(GAELO_DATE_FORMAT=='m.d.Y'){
+			    if (GAELO_DATE_FORMAT == 'm.d.Y') {
 			    	$birthDay=intval($birthDateArray[1]);
 			    	$birthMonth=intval($birthDateArray[0]);
 			    }
-			    else if(GAELO_DATE_FORMAT=='d.m.Y'){
+			    else if (GAELO_DATE_FORMAT == 'd.m.Y') {
 			    	$birthDay=intval($birthDateArray[0]);
 			    	$birthMonth=intval($birthDateArray[1]);
 			    }
 			    $birthYear=intval($birthDateArray[2]);
 			    
 				$insertddb=$this->addPatientToDatabase($patientNumber, $patientLastName, $patientFirstName, $patientGender,
-				    $patientInvestigatorNumCenter, $patientRegistrationDate, $birthDay,$birthMonth, $birthYear, $patientInvestigatorName);
+				    $patientInvestigatorNumCenter, $patientRegistrationDate, $birthDay, $birthMonth, $birthYear, $patientInvestigatorName);
 				
 				//Store the patient result import process in this object
-				if ($insertddb){
-						$this->sucessList[] = $patientNumber;
+				if ($insertddb) {
+						$this->sucessList[]=$patientNumber;
 				}
-				else{
+				else {
 					$patientFailed['PatientNumber']=$patientNumber;
 					$patientFailed['Reason']="Can't write to DB, wrong date or other wrong input";
 					$this->failList[]=$patientFailed;
 				}
 
 			//If conditions not met, add to the fail list with the respective error reason
-			} else{
+			}else {
 			    
-				if(!$isExistingCenter) {
-				    if( empty($patientInvestigatorNumCenter) ){
+				if (!$isExistingCenter) {
+				    if (empty($patientInvestigatorNumCenter)) {
 				        $this->failList['Missing Num Center'][]=$patientNumber;
 				    }
 				    else {
 				        $this->failList['Unknown Center'][]=$patientNumber;
 				    }
 
-				} else if(! $isCorrectPatientNumberLenght){
+				}else if (!$isCorrectPatientNumberLenght) {
 				    $this->failList['Wrong PatientNumber length'][]=$patientNumber;
 				    
-				} else if(!$isNewPatient ){
+				}else if (!$isNewPatient) {
 				    $this->failList['Patient already in Database'][]=$patientNumber;
 				    
-				} else if(empty($patientRegistrationDate)){
+				}else if (empty($patientRegistrationDate)) {
 				    $this->failList['Empty Registration Date'][]=$patientNumber;
-				} else if( ! $isPrefixCorrect){
+				}else if (!$isPrefixCorrect) {
 					$this->failList['Wrong Patient Code Prefix'][]=$patientNumber;
 				}
 				
@@ -116,28 +116,28 @@ 
 	 * @param string $registrationDate
 	 * @return NULL|DateTime
 	 */
-	private function parseRegistrationDate(?string $registrationDate){
+	private function parseRegistrationDate(?string $registrationDate) {
 	    $dateNbArray=explode('/', $registrationDate);
 	    
-	    if(GAELO_DATE_FORMAT=='m.d.Y'){
+	    if (GAELO_DATE_FORMAT == 'm.d.Y') {
 	        $registrationDay=intval($dateNbArray[1]);
 	        $registrationMonth=intval($dateNbArray[0]);
 	    }
-	    else if(GAELO_DATE_FORMAT=='d.m.Y'){
+	    else if (GAELO_DATE_FORMAT == 'd.m.Y') {
 	        $registrationDay=intval($dateNbArray[0]);
 	        $registrationMonth=intval($dateNbArray[1]);
 	    }
 	    
 	    $registrationYear=intval($dateNbArray[2]);
 	    
-	    if($registrationDay==0 || $registrationMonth==0 ||$registrationYear==0){
+	    if ($registrationDay == 0 || $registrationMonth == 0 || $registrationYear == 0) {
 	        return null;
 	    }
 	    
 	    try {
-	        $dateResult = new DateTime($registrationYear.'-'.$registrationMonth.'-'.$registrationDay);
-	    } catch (Exception $e) {
-	        error_log( $e->getMessage());
+	        $dateResult=new DateTime($registrationYear.'-'.$registrationMonth.'-'.$registrationDay);
+	    }catch (Exception $e) {
+	        error_log($e->getMessage());
 	        return null;
 	    }
 	    return $dateResult;
@@ -150,10 +150,10 @@ 
 	 * @param $patientCode
 	 * @return boolean
 	 */
-	private function isNewPatient($patientCode){
-	    try{
+	private function isNewPatient($patientCode) {
+	    try {
 	        new Patient($patientCode, $this->linkpdo);
-	    }catch(Exception $e1){
+	    }catch (Exception $e1) {
 	        return true;
 	    }
 	    
@@ -165,30 +165,30 @@ 
 	 * @param $patientNumber
 	 * @return boolean
 	 */
-	private function isCorrectPatientNumberLenght($patientNumber){
+	private function isCorrectPatientNumberLenght($patientNumber) {
 		$lenghtImport=strlen($patientNumber);
 		
-		if($lenghtImport == GAELO_PATIENT_CODE_LENGHT){
+		if ($lenghtImport == GAELO_PATIENT_CODE_LENGHT) {
 			return true;
-		} else{
+		}else {
 			return false;
 		}
 	}
 
-	private function isCorrectPrefix($patientNumber){
+	private function isCorrectPrefix($patientNumber) {
 		//If no prefix return true
-		if(empty($this->studyObject->patientCodePrefix)){
+		if (empty($this->studyObject->patientCodePrefix)) {
 			return true;
 		}
 		//test that patient code start with study prefix
-		$patientNumberString = strval($patientNumber);
-		$studyPrefixString = strval($this->studyObject->patientCodePrefix);
-		return $this->startsWith( $patientNumberString, $studyPrefixString );
+		$patientNumberString=strval($patientNumber);
+		$studyPrefixString=strval($this->studyObject->patientCodePrefix);
+		return $this->startsWith($patientNumberString, $studyPrefixString);
 
 	}
 
-	private function startsWith (string $string, string $startString) { 
-		$len = strlen($startString); 
+	private function startsWith(string $string, string $startString) { 
+		$len=strlen($startString); 
 		return (substr($string, 0, $len) === $startString); 
 	} 
 
@@ -197,12 +197,12 @@ 
      * @param $patientNumCenter
      * @return boolean
      */
-	private function isExistingCenter($patientNumCenter){
-	    if(is_null($patientNumCenter) || strlen($patientNumCenter)==0) return false;
+	private function isExistingCenter($patientNumCenter) {
+	    if (is_null($patientNumCenter) || strlen($patientNumCenter) == 0) return false;
 	    
-	    try{
+	    try {
 	        new Center($this->linkpdo, $patientNumCenter);
-	    }catch(Exception $e1){
+	    }catch (Exception $e1) {
 	        return false;
 	    }
 	    
@@ -223,10 +223,10 @@ 
 	 * @return boolean
 	 */
 	private function addPatientToDatabase($patientNumber, string $patientLastName, string $patientFirstName, string $patientGender
-	    , $patientInvestigatorNumCenter, $dateRegistration, $patientBirthDay, $patientBirthMonth, $patientBirthYear, string $patientInvestigatorName){
+	    , $patientInvestigatorNumCenter, $dateRegistration, $patientBirthDay, $patientBirthMonth, $patientBirthYear, string $patientInvestigatorName) {
 		
 		try {
-			$insert_bdd = $this->linkpdo->prepare('INSERT INTO patients(study, code, first_name, last_name, gender, birth_day, birth_month, birth_year, registration_date, investigator_name, center)
+			$insert_bdd=$this->linkpdo->prepare('INSERT INTO patients(study, code, first_name, last_name, gender, birth_day, birth_month, birth_year, registration_date, investigator_name, center)
 			VALUES(:study, :code, :first_name, :last_name, :gender, :birth_day, :birth_month, :birth_year, :registration_date, :investigator_name, :center)');
 			
 			$insert_bdd->execute(array('code' => $patientNumber,
@@ -241,7 +241,7 @@ 
 													'center' => $patientInvestigatorNumCenter,
 													'study' => $this->study));
 			$success=true;
-		} catch (Exception $e) {
+		}catch (Exception $e) {
 		    $success=false;
 			error_log($e);
 		}
@@ -250,13 +250,13 @@ 
 
 	}
 	
-	public function getHTMLImportAnswer(){
+	public function getHTMLImportAnswer() {
 	    return $this->buildSuccessAnswer().$this->buildErrorAnswer();
 	}
 	
-	public function getTextImportAnswer(){
+	public function getTextImportAnswer() {
 	    //Prepare Html2PlainText for email validity (both version to enhance spam validation)
-	    $htmlMessageObject = new \Html2Text\Html2Text($this->getHTMLImportAnswer());
+	    $htmlMessageObject=new \Html2Text\Html2Text($this->getHTMLImportAnswer());
 	    return $htmlMessageObject->getText();
 	    
 	}
@@ -265,19 +265,19 @@ 
 	 * Build HTML for error answer
 	 * @return string
 	 */
-	private function buildErrorAnswer(){
+	private function buildErrorAnswer() {
 	    //List of failed patients
 	    $failReport='Failed Patients: <br>';
-	    if ( !empty($this->failList) ){
-	        foreach ($this->failList as $key=>$value){
-	            if(! empty($value)){
+	    if (!empty($this->failList)) {
+	        foreach ($this->failList as $key=>$value) {
+	            if (!empty($value)) {
 	                $failReport=$failReport.$key.':<br>';
-	                if(is_array($value)) $failReport=$failReport.implode('<br>',$value).'<br>';
+	                if (is_array($value)) $failReport=$failReport.implode('<br>', $value).'<br>';
 	                else $failReport=$failReport.$value.'<br>';
 	            }
 	        }
-	    }else{
-	        $failReport=$failReport.' None <br>' ;
+	    }else {
+	        $failReport=$failReport.' None <br>';
 	    }
 	    
 	    return $failReport;
@@ -287,15 +287,15 @@ 
 	 * Generate HTML for sucess answer
 	 * @return string
 	 */
-	private function buildSuccessAnswer(){
+	private function buildSuccessAnswer() {
 	    //List of succeded patients
 	    $successReport='Success Patients: <br>';
-	    if ( !empty($this->sucessList) ){
+	    if (!empty($this->sucessList)) {
 	        foreach ($this->sucessList as $value) {
 	            $success=$value;
 	            $successReport=$successReport.$success.'<br>';
 	        }
-	    } else {
+	    }else {
 	        $successReport=$successReport.' None <br>';
 	    }
 	    

src/models/Fill_Orthanc_Table.php

Indentation +142 added lines, -142 removed lines

@@ -20,71 +20,71 @@ 
 
 class Fill_Orthanc_Table {
     
-    private $linkpdo;
-    private $username;
-    private $studyOrthancObject;
-    private $visitObject;
+	private $linkpdo;
+	private $username;
+	private $studyOrthancObject;
+	private $visitObject;
 
     
-    public function __construct($id_visit, String $username, PDO $linkpdo){
-        $this->username= $username;
-        $this->linkpdo=$linkpdo;
-        $this->visitObject=new Visit($id_visit, $linkpdo);
-    }
+	public function __construct($id_visit, String $username, PDO $linkpdo){
+		$this->username= $username;
+		$this->linkpdo=$linkpdo;
+		$this->visitObject=new Visit($id_visit, $linkpdo);
+	}
     
-    /**
-     * return study details of a study stored in Orthanc
-     * @param String $studyID
-     * @return array
-     */
-    public function parseData(String $studyID){
-        $studyData=new Orthanc_Study($studyID,null,null);
-        $studyData->retrieveStudyData();
-        $this->studyOrthancObject=$studyData;
-        $studyDetails=get_object_vars($studyData);
-        return $studyDetails;
-    }
+	/**
+	 * return study details of a study stored in Orthanc
+	 * @param String $studyID
+	 * @return array
+	 */
+	public function parseData(String $studyID){
+		$studyData=new Orthanc_Study($studyID,null,null);
+		$studyData->retrieveStudyData();
+		$this->studyOrthancObject=$studyData;
+		$studyDetails=get_object_vars($studyData);
+		return $studyDetails;
+	}
     
-    /**
-     * Fill data in the database, write data for study and for each series
-     * Once done trigger the change upload status of visit to update upload status and eventually skip 
-     * local form and/or QC
-     */
-    public function fillDB($anonFromOrthancStudyId){
+	/**
+	 * Fill data in the database, write data for study and for each series
+	 * Once done trigger the change upload status of visit to update upload status and eventually skip 
+	 * local form and/or QC
+	 */
+	public function fillDB($anonFromOrthancStudyId){
         
-        //Check that original OrthancID is unknown for this study
-        if($this->visitObject->getParentStudyObject()->isOriginalOrthancNeverKnown($anonFromOrthancStudyId) ){
-            try{
-                //Fill la database
-                $this->addToDbStudy($anonFromOrthancStudyId, $this->username);
+		//Check that original OrthancID is unknown for this study
+		if($this->visitObject->getParentStudyObject()->isOriginalOrthancNeverKnown($anonFromOrthancStudyId) ){
+			try{
+				//Fill la database
+				$this->addToDbStudy($anonFromOrthancStudyId, $this->username);
                 
-                foreach ($this->studyOrthancObject->orthancSeries as $serie){
-                    //Fill series database
-                    $this->addtoDbSerie($serie);
-                }
-                $this->visitObject->changeUploadStatus(Visit::DONE, $this->username);
+				foreach ($this->studyOrthancObject->orthancSeries as $serie){
+					//Fill series database
+					$this->addtoDbSerie($serie);
+				}
+				$this->visitObject->changeUploadStatus(Visit::DONE, $this->username);
                 
-            }catch(Exception $e1){
-                throw new Exception("Error during import ".$e1->getMessage());
-            }
-        }else{
-            throw new Exception("Error during import Study Already Known");
-        }
-    }
+			}catch(Exception $e1){
+				throw new Exception("Error during import ".$e1->getMessage());
+			}
+		}else{
+			throw new Exception("Error during import Study Already Known");
+		}
+	}
     
-    /**
-     * Private function to write into Orthanc_Studies DB
-     * @param string $anonFromOrthancStudyId
-     */
-    private function addToDbStudy(string $anonFromOrthancStudyId){
-            $studyAcquisitionDate2=$this->parseDateTime($this->studyOrthancObject->studyDate, 1);
-            $studyAcquisitionTime2=$this->parseDateTime($this->studyOrthancObject->studyTime, 2);
+	/**
+	 * Private function to write into Orthanc_Studies DB
+	 * @param string $anonFromOrthancStudyId
+	 */
+	private function addToDbStudy(string $anonFromOrthancStudyId){
+			$studyAcquisitionDate2=$this->parseDateTime($this->studyOrthancObject->studyDate, 1);
+			$studyAcquisitionTime2=$this->parseDateTime($this->studyOrthancObject->studyTime, 2);
             
-            if($studyAcquisitionDate2!=null && $studyAcquisitionTime2!=null){
-                $acquisitionDateTime=$studyAcquisitionDate2." ".$studyAcquisitionTime2;
-            }
+			if($studyAcquisitionDate2!=null && $studyAcquisitionTime2!=null){
+				$acquisitionDateTime=$studyAcquisitionDate2." ".$studyAcquisitionTime2;
+			}
                         
-            $addBdd=$this->linkpdo->prepare('INSERT INTO orthanc_studies (id_visit, 
+			$addBdd=$this->linkpdo->prepare('INSERT INTO orthanc_studies (id_visit, 
                                             uploader, 
                                             upload_date, 
                                             acquisition_date, 
@@ -136,42 +136,42 @@ 
                                     uncompressed_disk_size=:uncompressed_disk_size, 
                                     deleted=0 ');
            
-            $addBdd->execute(array(
-                'id_visit'=>$this->visitObject->id_visit,  
-                'uploader'=>$this->username,
-                'upload_date'=>date("Y-m-d H:i:s"),  
-                'acquisition_date'=>$this->studyOrthancObject->studyDate, 
-                'acquisition_time'=>$this->studyOrthancObject->studyTime,
-                'acquisition_datetime'=> isset($acquisitionDateTime) ? $acquisitionDateTime : null,
-                'study_orthanc_id'=>$this->studyOrthancObject->studyOrthancID,
-            	'anon_from_orthanc_id'=>$anonFromOrthancStudyId,
-                'study_uid'=>$this->studyOrthancObject->studyInstanceUID, 
-                'study_description'=>$this->studyOrthancObject->studyDescription, 
-                'patient_orthanc_id'=>$this->studyOrthancObject->parentPartientOrthancID,
-                'patient_name'=>$this->studyOrthancObject->parentPatientName, 
-                'patient_id'=>$this->studyOrthancObject->parentPatientID, 
-                'number_of_series'=>$this->studyOrthancObject->numberOfSeriesInStudy,
-                'number_of_instances'=>$this->studyOrthancObject->countInstances,
-                'disk_size'=>$this->studyOrthancObject->diskSizeMb,
-                'uncompressed_disk_size'=>$this->studyOrthancObject->uncompressedSizeMb
-            ));
+			$addBdd->execute(array(
+				'id_visit'=>$this->visitObject->id_visit,  
+				'uploader'=>$this->username,
+				'upload_date'=>date("Y-m-d H:i:s"),  
+				'acquisition_date'=>$this->studyOrthancObject->studyDate, 
+				'acquisition_time'=>$this->studyOrthancObject->studyTime,
+				'acquisition_datetime'=> isset($acquisitionDateTime) ? $acquisitionDateTime : null,
+				'study_orthanc_id'=>$this->studyOrthancObject->studyOrthancID,
+				'anon_from_orthanc_id'=>$anonFromOrthancStudyId,
+				'study_uid'=>$this->studyOrthancObject->studyInstanceUID, 
+				'study_description'=>$this->studyOrthancObject->studyDescription, 
+				'patient_orthanc_id'=>$this->studyOrthancObject->parentPartientOrthancID,
+				'patient_name'=>$this->studyOrthancObject->parentPatientName, 
+				'patient_id'=>$this->studyOrthancObject->parentPatientID, 
+				'number_of_series'=>$this->studyOrthancObject->numberOfSeriesInStudy,
+				'number_of_instances'=>$this->studyOrthancObject->countInstances,
+				'disk_size'=>$this->studyOrthancObject->diskSizeMb,
+				'uncompressed_disk_size'=>$this->studyOrthancObject->uncompressedSizeMb
+			));
 
-    }
+	}
     
-    /**
-     * Private function to write into the Orthanc_Series DB
-     * @param Orthanc_Serie $serie
-     */
-    private function addtoDbSerie(Orthanc_Serie $serie){
+	/**
+	 * Private function to write into the Orthanc_Series DB
+	 * @param Orthanc_Serie $serie
+	 */
+	private function addtoDbSerie(Orthanc_Serie $serie){
         
-        $serieAcquisitionDate2=$this->parseDateTime($serie->seriesDate, 1);
-        $serieAcquisitionTime2=$this->parseDateTime($serie->seriesTime, 2);
+		$serieAcquisitionDate2=$this->parseDateTime($serie->seriesDate, 1);
+		$serieAcquisitionTime2=$this->parseDateTime($serie->seriesTime, 2);
         
-        if($serieAcquisitionDate2!=null && $serieAcquisitionTime2!=null){
-            $acquisitionDateTime=$serieAcquisitionDate2." ".$serieAcquisitionTime2;
-        }
+		if($serieAcquisitionDate2!=null && $serieAcquisitionTime2!=null){
+			$acquisitionDateTime=$serieAcquisitionDate2." ".$serieAcquisitionTime2;
+		}
         
-        $addBddSeries=$this->linkpdo->prepare('INSERT INTO orthanc_series (
+		$addBddSeries=$this->linkpdo->prepare('INSERT INTO orthanc_series (
                                                 study_orthanc_id, 
                                                 modality, 
                                                 acquisition_date, 
@@ -217,71 +217,71 @@ 
 
 		$value = array(
 				'Study_Orthanc_ID'=>$this->studyOrthancObject->studyOrthancID,
-                'Modality'=>$serie->modality,
-                'Acquisition_Date'=>$serie->seriesDate,
-                'Acquisition_Time'=>$serie->seriesTime,
-                'Acquisition_DateTime'=> isset($acquisitionDateTime) ? $acquisitionDateTime : null,
-                'Series_Description'=> $serie->seriesDescription,
-		        'Injected_Dose'=> is_numeric($serie->injectedDose) ? $serie->injectedDose : null,
-                'Radiopharmaceutical'=> $serie->radiopharmaceutical,
-                'HalfLife'=> is_numeric($serie->halfLife) ? $serie->halfLife : null,
-                'Injected_Time'=> $serie->injectedTime,
-                'Injected_DateTime'=> $this->parseDateTime($serie->injectedDateTime, 0),
-                'Injected_Activity'=> is_numeric($serie->injectedActivity) ? $serie->injectedActivity: null,
-                'Series_Orthanc_ID'=> $serie->serieOrthancID,
-                'Number_Instances'=> $serie->numberOfInstanceInOrthanc,
-                'Serie_UID'=> $serie->seriesInstanceUID,
-                'Serie_Number'=> $serie->seriesNumber,
-                'Patient_Weight'=>is_numeric($serie->patientWeight) ? $serie->patientWeight:null,
-                'Serie_Disk_Size'=> $serie->diskSizeMb,
-                'Serie_Uncompressed_Disk_Size' => $serie->uncompressedSizeMb,
-                'Manufacturer'=> $serie->seriesManufacturer,
-            	'Model_Name'=>$serie->seriesModelName
-            );
+				'Modality'=>$serie->modality,
+				'Acquisition_Date'=>$serie->seriesDate,
+				'Acquisition_Time'=>$serie->seriesTime,
+				'Acquisition_DateTime'=> isset($acquisitionDateTime) ? $acquisitionDateTime : null,
+				'Series_Description'=> $serie->seriesDescription,
+				'Injected_Dose'=> is_numeric($serie->injectedDose) ? $serie->injectedDose : null,
+				'Radiopharmaceutical'=> $serie->radiopharmaceutical,
+				'HalfLife'=> is_numeric($serie->halfLife) ? $serie->halfLife : null,
+				'Injected_Time'=> $serie->injectedTime,
+				'Injected_DateTime'=> $this->parseDateTime($serie->injectedDateTime, 0),
+				'Injected_Activity'=> is_numeric($serie->injectedActivity) ? $serie->injectedActivity: null,
+				'Series_Orthanc_ID'=> $serie->serieOrthancID,
+				'Number_Instances'=> $serie->numberOfInstanceInOrthanc,
+				'Serie_UID'=> $serie->seriesInstanceUID,
+				'Serie_Number'=> $serie->seriesNumber,
+				'Patient_Weight'=>is_numeric($serie->patientWeight) ? $serie->patientWeight:null,
+				'Serie_Disk_Size'=> $serie->diskSizeMb,
+				'Serie_Uncompressed_Disk_Size' => $serie->uncompressedSizeMb,
+				'Manufacturer'=> $serie->seriesManufacturer,
+				'Model_Name'=>$serie->seriesModelName
+			);
             
 		$addBddSeries->execute($value);
 		
-    }
+	}
     
-    /**
-     * Parse a DICOM date or Time string and return a string ready to send to database
-     * Return null if non parsable
-     * @param string $string
-     * @param type 0=dateTime, 1=Date, 2=Time
-     * return formated date for db saving, null if parse failed
-     */
-    private function parseDateTime( $string, int $type){
-        $parsedDateTime=null;
+	/**
+	 * Parse a DICOM date or Time string and return a string ready to send to database
+	 * Return null if non parsable
+	 * @param string $string
+	 * @param type 0=dateTime, 1=Date, 2=Time
+	 * return formated date for db saving, null if parse failed
+	 */
+	private function parseDateTime( $string, int $type){
+		$parsedDateTime=null;
         
-        //If contain time split the ms (after.) which are not constant
-        if($type==0 || $type==2){
-            if(strpos($string, ".")) {
-                $timeWithoutms=explode(".", $string);
-                $string=$timeWithoutms[0];
-            }
+		//If contain time split the ms (after.) which are not constant
+		if($type==0 || $type==2){
+			if(strpos($string, ".")) {
+				$timeWithoutms=explode(".", $string);
+				$string=$timeWithoutms[0];
+			}
             
-        }
+		}
         
-        if($type==2){
-            $dateObject=DateTime::createFromFormat('His', $string);
-            if($dateObject!==false){
-                $parsedDateTime=$dateObject->format('H:i:s');
-            }
-        }else if($type==1){
-            $dateObject=DateTime::createFromFormat('Ymd', $string);
-            if($dateObject!==false){
-                $parsedDateTime=$dateObject->format('Y-m-d');
-            }
-        }else if($type==0){
-            $dateObject=DateTime::createFromFormat('YmdHis', $string);
-            if($dateObject!==false){
-                $parsedDateTime=$dateObject->format('Y-m-d H:i:s');
-            }
-        }
+		if($type==2){
+			$dateObject=DateTime::createFromFormat('His', $string);
+			if($dateObject!==false){
+				$parsedDateTime=$dateObject->format('H:i:s');
+			}
+		}else if($type==1){
+			$dateObject=DateTime::createFromFormat('Ymd', $string);
+			if($dateObject!==false){
+				$parsedDateTime=$dateObject->format('Y-m-d');
+			}
+		}else if($type==0){
+			$dateObject=DateTime::createFromFormat('YmdHis', $string);
+			if($dateObject!==false){
+				$parsedDateTime=$dateObject->format('Y-m-d H:i:s');
+			}
+		}
         
-        return $parsedDateTime;
+		return $parsedDateTime;
   
-    }
+	}
     
 }
 

Spacing +26 added lines, -26 removed lines

@@ -26,8 +26,8 @@ 
     private $visitObject;
 
     
-    public function __construct($id_visit, String $username, PDO $linkpdo){
-        $this->username= $username;
+    public function __construct($id_visit, String $username, PDO $linkpdo) {
+        $this->username=$username;
         $this->linkpdo=$linkpdo;
         $this->visitObject=new Visit($id_visit, $linkpdo);
     }
@@ -37,8 +37,8 @@ 
      * @param String $studyID
      * @return array
      */
-    public function parseData(String $studyID){
-        $studyData=new Orthanc_Study($studyID,null,null);
+    public function parseData(String $studyID) {
+        $studyData=new Orthanc_Study($studyID, null, null);
         $studyData->retrieveStudyData();
         $this->studyOrthancObject=$studyData;
         $studyDetails=get_object_vars($studyData);
@@ -50,24 +50,24 @@ 
      * Once done trigger the change upload status of visit to update upload status and eventually skip 
      * local form and/or QC
      */
-    public function fillDB($anonFromOrthancStudyId){
+    public function fillDB($anonFromOrthancStudyId) {
         
         //Check that original OrthancID is unknown for this study
-        if($this->visitObject->getParentStudyObject()->isOriginalOrthancNeverKnown($anonFromOrthancStudyId) ){
-            try{
+        if ($this->visitObject->getParentStudyObject()->isOriginalOrthancNeverKnown($anonFromOrthancStudyId)) {
+            try {
                 //Fill la database
                 $this->addToDbStudy($anonFromOrthancStudyId, $this->username);
                 
-                foreach ($this->studyOrthancObject->orthancSeries as $serie){
+                foreach ($this->studyOrthancObject->orthancSeries as $serie) {
                     //Fill series database
                     $this->addtoDbSerie($serie);
                 }
                 $this->visitObject->changeUploadStatus(Visit::DONE, $this->username);
                 
-            }catch(Exception $e1){
+            }catch (Exception $e1) {
                 throw new Exception("Error during import ".$e1->getMessage());
             }
-        }else{
+        }else {
             throw new Exception("Error during import Study Already Known");
         }
     }
@@ -76,11 +76,11 @@ 
      * Private function to write into Orthanc_Studies DB
      * @param string $anonFromOrthancStudyId
      */
-    private function addToDbStudy(string $anonFromOrthancStudyId){
+    private function addToDbStudy(string $anonFromOrthancStudyId) {
             $studyAcquisitionDate2=$this->parseDateTime($this->studyOrthancObject->studyDate, 1);
             $studyAcquisitionTime2=$this->parseDateTime($this->studyOrthancObject->studyTime, 2);
             
-            if($studyAcquisitionDate2!=null && $studyAcquisitionTime2!=null){
+            if ($studyAcquisitionDate2 != null && $studyAcquisitionTime2 != null) {
                 $acquisitionDateTime=$studyAcquisitionDate2." ".$studyAcquisitionTime2;
             }
                         
@@ -162,12 +162,12 @@ 
      * Private function to write into the Orthanc_Series DB
      * @param Orthanc_Serie $serie
      */
-    private function addtoDbSerie(Orthanc_Serie $serie){
+    private function addtoDbSerie(Orthanc_Serie $serie) {
         
         $serieAcquisitionDate2=$this->parseDateTime($serie->seriesDate, 1);
         $serieAcquisitionTime2=$this->parseDateTime($serie->seriesTime, 2);
         
-        if($serieAcquisitionDate2!=null && $serieAcquisitionTime2!=null){
+        if ($serieAcquisitionDate2 != null && $serieAcquisitionTime2 != null) {
             $acquisitionDateTime=$serieAcquisitionDate2." ".$serieAcquisitionTime2;
         }
         
@@ -215,7 +215,7 @@ 
                                                         :Model_Name, :Injected_DateTime)
         ON DUPLICATE KEY UPDATE study_orthanc_id=:Study_Orthanc_ID, modality=:Modality, acquisition_date=:Acquisition_Date, acquisition_time=:Acquisition_Time, acquisition_datetime=:Acquisition_DateTime, series_description=:Series_Description, injected_dose=:Injected_Dose, radiopharmaceutical=:Radiopharmaceutical, half_life=:HalfLife, injected_time=:Injected_Time, injected_activity=:Injected_Activity, number_of_instances=:Number_Instances, serie_number=:Serie_Number, patient_weight=:Patient_Weight, serie_disk_size=:Serie_Disk_Size, serie_uncompressed_disk_size=:Serie_Uncompressed_Disk_Size, manufacturer=:Manufacturer, model_name=:Model_Name, deleted=0, injected_datetime=:Injected_DateTime');
 
-		$value = array(
+		$value=array(
 				'Study_Orthanc_ID'=>$this->studyOrthancObject->studyOrthancID,
                 'Modality'=>$serie->modality,
                 'Acquisition_Date'=>$serie->seriesDate,
@@ -227,12 +227,12 @@ 
                 'HalfLife'=> is_numeric($serie->halfLife) ? $serie->halfLife : null,
                 'Injected_Time'=> $serie->injectedTime,
                 'Injected_DateTime'=> $this->parseDateTime($serie->injectedDateTime, 0),
-                'Injected_Activity'=> is_numeric($serie->injectedActivity) ? $serie->injectedActivity: null,
+                'Injected_Activity'=> is_numeric($serie->injectedActivity) ? $serie->injectedActivity : null,
                 'Series_Orthanc_ID'=> $serie->serieOrthancID,
                 'Number_Instances'=> $serie->numberOfInstanceInOrthanc,
                 'Serie_UID'=> $serie->seriesInstanceUID,
                 'Serie_Number'=> $serie->seriesNumber,
-                'Patient_Weight'=>is_numeric($serie->patientWeight) ? $serie->patientWeight:null,
+                'Patient_Weight'=>is_numeric($serie->patientWeight) ? $serie->patientWeight : null,
                 'Serie_Disk_Size'=> $serie->diskSizeMb,
                 'Serie_Uncompressed_Disk_Size' => $serie->uncompressedSizeMb,
                 'Manufacturer'=> $serie->seriesManufacturer,
@@ -250,31 +250,31 @@ 
      * @param type 0=dateTime, 1=Date, 2=Time
      * return formated date for db saving, null if parse failed
      */
-    private function parseDateTime( $string, int $type){
+    private function parseDateTime($string, int $type) {
         $parsedDateTime=null;
         
         //If contain time split the ms (after.) which are not constant
-        if($type==0 || $type==2){
-            if(strpos($string, ".")) {
+        if ($type == 0 || $type == 2) {
+            if (strpos($string, ".")) {
                 $timeWithoutms=explode(".", $string);
                 $string=$timeWithoutms[0];
             }
             
         }
         
-        if($type==2){
+        if ($type == 2) {
             $dateObject=DateTime::createFromFormat('His', $string);
-            if($dateObject!==false){
+            if ($dateObject !== false) {
                 $parsedDateTime=$dateObject->format('H:i:s');
             }
-        }else if($type==1){
+        }else if ($type == 1) {
             $dateObject=DateTime::createFromFormat('Ymd', $string);
-            if($dateObject!==false){
+            if ($dateObject !== false) {
                 $parsedDateTime=$dateObject->format('Y-m-d');
             }
-        }else if($type==0){
+        }else if ($type == 0) {
             $dateObject=DateTime::createFromFormat('YmdHis', $string);
-            if($dateObject!==false){
+            if ($dateObject !== false) {
                 $parsedDateTime=$dateObject->format('Y-m-d H:i:s');
             }
         }

Braces +4 added lines, -4 removed lines

@@ -64,10 +64,10 @@ 
                 }
                 $this->visitObject->changeUploadStatus(Visit::DONE, $this->username);
                 
-            }catch(Exception $e1){
+            } catch(Exception $e1){
                 throw new Exception("Error during import ".$e1->getMessage());
             }
-        }else{
+        } else{
             throw new Exception("Error during import Study Already Known");
         }
     }
@@ -267,12 +267,12 @@ 
             if($dateObject!==false){
                 $parsedDateTime=$dateObject->format('H:i:s');
             }
-        }else if($type==1){
+        } else if($type==1){
             $dateObject=DateTime::createFromFormat('Ymd', $string);
             if($dateObject!==false){
                 $parsedDateTime=$dateObject->format('Y-m-d');
             }
-        }else if($type==0){
+        } else if($type==0){
             $dateObject=DateTime::createFromFormat('YmdHis', $string);
             if($dateObject!==false){
                 $parsedDateTime=$dateObject->format('Y-m-d H:i:s');

src/models/Orthanc_Study.php

Indentation +22 added lines, -22 removed lines

@@ -44,21 +44,21 @@ 
 	private $context;
 	
 	public function __construct($studyOrthancId, $url, $context){
-	    //Set http adress of orthanc
-	    if($url==null && $context==null){
-	        $linkpdo=Session::getLinkpdo();
+		//Set http adress of orthanc
+		if($url==null && $context==null){
+			$linkpdo=Session::getLinkpdo();
 	        
-	        $this->url=GAELO_ORTHANC_PACS_ADDRESS.':'.GAELO_ORTHANC_PACS_PORT;
-	    	$this->context = array(
-	    			'http' => array(
-	    			    'header'  => "Authorization: Basic " . base64_encode( GAELO_ORTHANC_PACS_LOGIN.':'.GAELO_ORTHANC_PACS_PASSWORD )
-	    			)
-	    	);
+			$this->url=GAELO_ORTHANC_PACS_ADDRESS.':'.GAELO_ORTHANC_PACS_PORT;
+			$this->context = array(
+					'http' => array(
+						'header'  => "Authorization: Basic " . base64_encode( GAELO_ORTHANC_PACS_LOGIN.':'.GAELO_ORTHANC_PACS_PASSWORD )
+					)
+			);
 	    	
-	    }else{
-	    	$this->url=$url;
-	    	$this->context = $context;	
-	    }
+		}else{
+			$this->url=$url;
+			$this->context = $context;	
+		}
 	    
 		//put current study orthanc ID in memory
 		$this->studyOrthancID=$studyOrthancId;
@@ -69,8 +69,8 @@ 
 	 *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);
+		$context  = stream_context_create($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
@@ -96,13 +96,13 @@ 
 	 *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);
-	    //On le decode
-	    $statisticsJson=json_decode($json, true);
-	    $this->countInstances=$statisticsJson['CountInstances'];
-	    $this->diskSizeMb=$statisticsJson['DiskSizeMB'];
-	    $this->uncompressedSizeMb=$statisticsJson['UncompressedSizeMB'];
+		$context  = stream_context_create($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'];
+		$this->diskSizeMb=$statisticsJson['DiskSizeMB'];
+		$this->uncompressedSizeMb=$statisticsJson['UncompressedSizeMB'];
 	    
 	}
 	

Spacing +17 added lines, -17 removed lines

@@ -17,7 +17,7 @@ 
  * Collect study's data from Orthanc Server
  */
 
- class Orthanc_Study{
+ class Orthanc_Study {
 	public $studyOrthancID;
 	public $studyIsStable;
 	public $studyDate;
@@ -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
@@ -79,9 +79,9 @@ 
 		$this->studyDescription=$studiesJson['MainDicomTags']['StudyDescription'];
 		$this->studyInstanceUID=$studiesJson['MainDicomTags']['StudyInstanceUID'];
 		$this->studyLastUpdate=$studiesJson['LastUpdate'];
-		$this->seriesInStudy= $studiesJson['Series'];
+		$this->seriesInStudy=$studiesJson['Series'];
 		$this->numberOfSeriesInStudy=sizeof($studiesJson['Series']);
-		$this->studyIsStable= $studiesJson['IsStable'];
+		$this->studyIsStable=$studiesJson['IsStable'];
 		$this->parentPatientName=$studiesJson['PatientMainDicomTags']['PatientName'];
 		$this->parentPatientID=$studiesJson['PatientMainDicomTags']['PatientID'];
 		$this->parentPartientOrthancID=$studiesJson['ParentPatient'];
@@ -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'];
@@ -109,8 +109,8 @@ 
 	/**
 	 * Create a series object with series data for each series and store them in this object
 	 */
-	private function getSeriesMainTag(){
-		foreach ($this->seriesInStudy as $seriesID){
+	private function getSeriesMainTag() {
+		foreach ($this->seriesInStudy as $seriesID) {
 			$series=new Orthanc_Serie($seriesID, $this->url, $this->context);
 			@$series->retrieveSeriesData();
 			$this->orthancSeries[]=$series;

Braces +1 added lines, -1 removed lines

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

src/models/Orthanc.php

Indentation +238 added lines, -238 removed lines

@@ -33,20 +33,20 @@ 
 	 * @param boolean $exposed
 	 */
 	public function __construct(bool $exposed=false){
-	    //Set Time Limit at 3H as operation could be really long
-	    set_time_limit(10800);
-        //Set address of Orthanc server
-        if($exposed){
-            $this->url=GAELO_ORTHANC_EXPOSED_INTERNAL_ADDRESS.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PORT;
-            $this->context = array(
-                'http' => array(
-                    'header'  => "Authorization: Basic " . base64_encode(GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD)
+		//Set Time Limit at 3H as operation could be really long
+		set_time_limit(10800);
+		//Set address of Orthanc server
+		if($exposed){
+			$this->url=GAELO_ORTHANC_EXPOSED_INTERNAL_ADDRESS.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PORT;
+			$this->context = array(
+				'http' => array(
+					'header'  => "Authorization: Basic " . base64_encode(GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD)
 	   			));
-        }else{
-            $this->url=GAELO_ORTHANC_PACS_ADDRESS.':'.GAELO_ORTHANC_PACS_PORT;
-            $this->context = array(
+		}else{
+			$this->url=GAELO_ORTHANC_PACS_ADDRESS.':'.GAELO_ORTHANC_PACS_PORT;
+			$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)
 	   			) );
 	   }
 
@@ -57,10 +57,10 @@ 
 	 * @return mixed
 	 */
 	public function getPeers(){
-	    $context =stream_context_create($this->context);
-	    $json = file_get_contents($this->url.'/peers/',false, $context);
-	    $peers=json_decode($json, true);
-	    return $peers;
+		$context =stream_context_create($this->context);
+		$json = file_get_contents($this->url.'/peers/',false, $context);
+		$peers=json_decode($json, true);
+		return $peers;
 	}
 	
 	/**
@@ -80,7 +80,7 @@ 
 				'PatientID' => $patientID,
 				'PatientName' => $patientName,
 				'StudyDate' => $studyDate,
-		        'StudyInstanceUID' => $studyUID,
+				'StudyInstanceUID' => $studyUID,
 				'AccessionNumber'=> $accessionNumber,
 				'StudyDescription'=> $studyDescription,
 		);
@@ -97,7 +97,7 @@ 
 				array(
 						'method'  => 'POST',
 						'content' => json_encode($query),
-				        'header'=>  ['Content-Type: application/json Accept: application/json ',$this->context['http']['header']]
+						'header'=>  ['Content-Type: application/json Accept: application/json ',$this->context['http']['header']]
 				)
 		);
 
@@ -115,26 +115,26 @@ 
 	 */
 	public function getZipTempFile(array $uidList){
 	   
-	    if( !is_array($uidList)){
-	        $uidList=array($uidList);
-	    }
+		if( !is_array($uidList)){
+			$uidList=array($uidList);
+		}
 	    
-	    $opts = array('http' =>
-	        array(
-	            'method'  => 'POST',
-	            'content' => json_encode($uidList),
-	            'timeout' => 3600,
-	            'header'=>  ['Content-Type: application/json', 'Accept: application/zip',$this->context['http']['header'] ]
-	        )
-	    );
+		$opts = array('http' =>
+			array(
+				'method'  => 'POST',
+				'content' => json_encode($uidList),
+				'timeout' => 3600,
+				'header'=>  ['Content-Type: application/json', 'Accept: application/zip',$this->context['http']['header'] ]
+			)
+		);
 	    
-	    $context = stream_context_create($opts);
+		$context = stream_context_create($opts);
 	    
- 	    $temp = tempnam(ini_get('upload_tmp_dir'), 'TMP_');
+ 		$temp = tempnam(ini_get('upload_tmp_dir'), 'TMP_');
 	    
-	    $nbbytes=file_put_contents($temp , fopen($this->url.'/tools/create-archive','rb', false, $context));
+		$nbbytes=file_put_contents($temp , fopen($this->url.'/tools/create-archive','rb', false, $context));
 	    
-	    return $temp;
+		return $temp;
 	}
 	
 	
@@ -145,15 +145,15 @@ 
 	 */
 	public function deleteFromOrthanc(string $level, string $uid){
 	    
-	    $opts = array('http' =>
-	        array(
-	            'method'  => 'DELETE',
-	            'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
-	        )
-	    );
+		$opts = array('http' =>
+			array(
+				'method'  => 'DELETE',
+				'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
+			)
+		);
 	    
-	    $context  = stream_context_create($opts);
-	    $result = file_get_contents($this->url.'/'.$level.'/'.$uid, false, $context);
+		$context  = stream_context_create($opts);
+		$result = file_get_contents($this->url.'/'.$level.'/'.$uid, false, $context);
 	    
 	}
 	
@@ -167,22 +167,22 @@ 
 	 */
 	public function addPeer(string $name , string $url, string $username, string $password){
 	    
-	    $peerValues['Username']=$username;
-	    $peerValues['Password']=$password;
-	    $peerValues['Url']=$url;
-	    $opts = array('http' =>
-	        array(
-	            'method'  => 'PUT',
-	            'content' => json_encode($peerValues),
-	            'header'=>  ['Content-Type: application/json Accept: application/json ',$this->context['http']['header']]
-	        )
-	    );
+		$peerValues['Username']=$username;
+		$peerValues['Password']=$password;
+		$peerValues['Url']=$url;
+		$opts = array('http' =>
+			array(
+				'method'  => 'PUT',
+				'content' => json_encode($peerValues),
+				'header'=>  ['Content-Type: application/json Accept: application/json ',$this->context['http']['header']]
+			)
+		);
 	    
-	    $context  = stream_context_create($opts);
-	    $resultJson = file_get_contents($this->url.'/peers/'.$name, false, $context);
+		$context  = stream_context_create($opts);
+		$resultJson = file_get_contents($this->url.'/peers/'.$name, false, $context);
 	    
-	    $result=json_decode($resultJson);
-	    return $result;
+		$result=json_decode($resultJson);
+		return $result;
 	    
 	}
 	
@@ -192,19 +192,19 @@ 
 	 */
 	public function removePeer(string $name){
 	    
-	    $opts = array('http' =>
-	        array(
-	            'method'  => 'DELETE',
-	            'header'=>  ['Content-Type: application/json Accept: application/json ',$this->context['http']['header']]
-	        )
-	    );
+		$opts = array('http' =>
+			array(
+				'method'  => 'DELETE',
+				'header'=>  ['Content-Type: application/json Accept: application/json ',$this->context['http']['header']]
+			)
+		);
 	    
-	    $context  = stream_context_create($opts);
-	    $resultJson = file_get_contents($this->url.'/peers/'.$name, false, $context);
+		$context  = stream_context_create($opts);
+		$resultJson = file_get_contents($this->url.'/peers/'.$name, false, $context);
 	    
-	    $result=json_decode($resultJson);
+		$result=json_decode($resultJson);
 	    
-	    return $result;
+		return $result;
 	}
 	
 	/**
@@ -212,11 +212,11 @@ 
 	 */
 	public function removeAllPeers(){
 	    
-	    $peers=$this->getPeers();
+		$peers=$this->getPeers();
 	    
-	    foreach ($peers as $peer){
-	        $this->removePeer($peer);
-	    }
+		foreach ($peers as $peer){
+			$this->removePeer($peer);
+		}
 	    
 	}
 	
@@ -226,15 +226,15 @@ 
 	 * @return boolean
 	 */
 	public function isPeerAccelerated(string $peer){
-	    $context =stream_context_create($this->context);
-	    $json = file_get_contents($this->url.'/transfers/peers/',false, $context);
-	    $peersTest=json_decode($json, true);
+		$context =stream_context_create($this->context);
+		$json = file_get_contents($this->url.'/transfers/peers/',false, $context);
+		$peersTest=json_decode($json, true);
 	    
-	    if($peersTest[$peer]=="installed"){
-	        return true;
-	    }
+		if($peersTest[$peer]=="installed"){
+			return true;
+		}
 	    
-	    return false;
+		return false;
 	}
 	
 	/**
@@ -247,7 +247,7 @@ 
 		$opts = array('http' =>
 				array(
 						'method'  => 'POST',
-                        "timeout" => 300, 
+						"timeout" => 300, 
 						'content' => json_encode($ids),
 						'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
 				)
@@ -266,20 +266,20 @@ 
 	 * @return string
 	 */
 	public function sendToPeerAsync(string $peer, array $ids){
-	    $data['Synchronous']=false;
-	    $data['Resources']=$ids;
-	    
-	    $opts = array('http' =>
-	        array(
-	            'method'  => 'POST',
-	            'content' => json_encode($data),
-	            'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
-	        )
-	    );
-	    
-	    $context = stream_context_create($opts);
-	    $result = file_get_contents($this->url.'/peers/'.$peer.'/store', false, $context);
-	    return $result;
+		$data['Synchronous']=false;
+		$data['Resources']=$ids;
+	    
+		$opts = array('http' =>
+			array(
+				'method'  => 'POST',
+				'content' => json_encode($data),
+				'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
+			)
+		);
+	    
+		$context = stream_context_create($opts);
+		$result = file_get_contents($this->url.'/peers/'.$peer.'/store', false, $context);
+		return $result;
 	}
 	
 	/**
@@ -291,35 +291,35 @@ 
 	 */
 	public function sendToPeerAsyncWithAccelerator(string $peer, array $ids, bool $gzip){
 	    
-	    //If Peer dosen't have accelerated transfers fall back to regular orthanc peer transfers
-	    if( ! $this->isPeerAccelerated($peer)){
-	        $answer=$this->sendToPeerAsync($peer, $ids);
-	        return $answer;
-	    }
+		//If Peer dosen't have accelerated transfers fall back to regular orthanc peer transfers
+		if( ! $this->isPeerAccelerated($peer)){
+			$answer=$this->sendToPeerAsync($peer, $ids);
+			return $answer;
+		}
 	    
-	    if(!$gzip) $data['Compression']="none" ; else $data['Compression']="gzip";
+		if(!$gzip) $data['Compression']="none" ; else $data['Compression']="gzip";
 	    
-	    $data['Peer']=$peer;
+		$data['Peer']=$peer;
 	    
 	    
-	    foreach ($ids as $serieID){
-	        $resourceSeries['Level']="Series";
-	        $resourceSeries['ID']=$serieID;
-	        $data['Resources'][]=$resourceSeries;
-	    }
+		foreach ($ids as $serieID){
+			$resourceSeries['Level']="Series";
+			$resourceSeries['ID']=$serieID;
+			$data['Resources'][]=$resourceSeries;
+		}
 	    
-	    $opts = array('http' =>
-	        array(
-	            'method'  => 'POST',
-	            'content' => json_encode($data),
-	            'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
-	        )
-	    );
+		$opts = array('http' =>
+			array(
+				'method'  => 'POST',
+				'content' => json_encode($data),
+				'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
+			)
+		);
 	    
-	    $context = stream_context_create($opts);
-	    $result = file_get_contents($this->url.'/transfers/send', false, $context);
+		$context = stream_context_create($opts);
+		$result = file_get_contents($this->url.'/transfers/send', false, $context);
 	    
-	    return $result;
+		return $result;
 	    
 	}
 	
@@ -330,22 +330,22 @@ 
 	 */
 	public function importFile(string $file){
 	    
-	    try{
-    	    $opts = array('http' =>
-    	        array(
-    	            'method'  => 'POST',
-    	            'content' => file_get_contents($file),
-    	            'header'=>  ['Content-Type: application/dicom Accept: application/json',"content-length: ".filesize($file),$this->context['http']['header']]
-    	        )
-    	    );
+		try{
+			$opts = array('http' =>
+				array(
+					'method'  => 'POST',
+					'content' => file_get_contents($file),
+					'header'=>  ['Content-Type: application/dicom Accept: application/json',"content-length: ".filesize($file),$this->context['http']['header']]
+				)
+			);
     	    
-    	    $context = stream_context_create($opts);
-    	    $result = file_get_contents($this->url.'/instances', false, $context);
+			$context = stream_context_create($opts);
+			$result = file_get_contents($this->url.'/instances', false, $context);
     	    
-	    }catch(Exception $e1){
-	        error_log("Error during import Dcm ".$e1->getMessage());
-	    }
-	    return $result;
+		}catch(Exception $e1){
+			error_log("Error during import Dcm ".$e1->getMessage());
+		}
+		return $result;
 
 	}
 
@@ -361,29 +361,29 @@ 
 	 */
 	public function Anonymize(string $studyID, string $profile, string $patientCode, string $visitType, string $studyName){
 	    
-	    $jsonAnonQuery=$this->buildAnonQuery($profile, $patientCode, $patientCode, $visitType, $studyName);
+		$jsonAnonQuery=$this->buildAnonQuery($profile, $patientCode, $patientCode, $visitType, $studyName);
 	    
-	    $opts = array('http' =>
-	        array(
-	            'method'  => 'POST',
-	            "timeout" => 300,
-	            'content' => json_encode($jsonAnonQuery),
-	            'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
-	        )
-	    );
+		$opts = array('http' =>
+			array(
+				'method'  => 'POST',
+				"timeout" => 300,
+				'content' => json_encode($jsonAnonQuery),
+				'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
+			)
+		);
 	    
-	    $context = stream_context_create($opts);
+		$context = stream_context_create($opts);
 
-        $result = file_get_contents($this->url."/studies/".$studyID."/anonymize", false, $context);
+		$result = file_get_contents($this->url."/studies/".$studyID."/anonymize", false, $context);
         
-	    //get the resulting Anonymized study Orthanc ID
-	    $anonAnswer=json_decode($result, true);
-	    $anonymizedID=$anonAnswer['ID'];
+		//get the resulting Anonymized study Orthanc ID
+		$anonAnswer=json_decode($result, true);
+		$anonymizedID=$anonAnswer['ID'];
 	    
-	    //Remove SC if any in the anonymized study
-	    $this->removeSC($anonymizedID);
+		//Remove SC if any in the anonymized study
+		$this->removeSC($anonymizedID);
 	    
-	    return $anonymizedID;
+		return $anonymizedID;
 	    
 	}
 	
@@ -397,121 +397,121 @@ 
 	 */
 	private function buildAnonQuery(string $profile, string $newPatientName, string $newPatientID, string $newStudyDescription, string $clinicalStudy){
     	    
-        $tagsObjects=[];
-        if($profile=="Default"){
-            $date=TagAnon::KEEP;
-            $body=TagAnon::KEEP;
+		$tagsObjects=[];
+		if($profile=="Default"){
+			$date=TagAnon::KEEP;
+			$body=TagAnon::KEEP;
             
-            $tagsObjects[]=new TagAnon("0010,0030", TagAnon::REPLACE, "19000101"); // BirthDay
-            $tagsObjects[]=new TagAnon("0008,1030", TagAnon::REPLACE, $newStudyDescription); //studyDescription
-            $tagsObjects[]=new TagAnon("0008,103E", TagAnon::KEEP); //series Description
+			$tagsObjects[]=new TagAnon("0010,0030", TagAnon::REPLACE, "19000101"); // BirthDay
+			$tagsObjects[]=new TagAnon("0008,1030", TagAnon::REPLACE, $newStudyDescription); //studyDescription
+			$tagsObjects[]=new TagAnon("0008,103E", TagAnon::KEEP); //series Description
            
     
-        }else if($profile=="Full"){
-            $date=TagAnon::CLEAR;
-            $body=TagAnon::CLEAR;
+		}else if($profile=="Full"){
+			$date=TagAnon::CLEAR;
+			$body=TagAnon::CLEAR;
             
-            $tagsObjects[]=new TagAnon("0010,0030", TagAnon::REPLACE, "19000101"); // BirthDay
-            $tagsObjects[]=new TagAnon("0008,1030", TagAnon::CLEAR); // studyDescription
-            $tagsObjects[]=new TagAnon("0008,103E", TagAnon::CLEAR); //series Description
-        }
+			$tagsObjects[]=new TagAnon("0010,0030", TagAnon::REPLACE, "19000101"); // BirthDay
+			$tagsObjects[]=new TagAnon("0008,1030", TagAnon::CLEAR); // studyDescription
+			$tagsObjects[]=new TagAnon("0008,103E", TagAnon::CLEAR); //series Description
+		}
         
-    	//List tags releted to Date
-    	$tagsObjects[]=new TagAnon("0008,0022", $date); // Acquisition Date
-    	$tagsObjects[]=new TagAnon("0008,002A", $date); // Acquisition DateTime
-    	$tagsObjects[]=new TagAnon("0008,0032", $date); // Acquisition Time
-    	$tagsObjects[]=new TagAnon("0038,0020", $date); // Admitting Date
-    	$tagsObjects[]=new TagAnon("0038,0021", $date); // Admitting Time
-    	$tagsObjects[]=new TagAnon("0008,0035", $date); // Curve Time
-    	$tagsObjects[]=new TagAnon("0008,0025", $date); // Curve Date
-    	$tagsObjects[]=new TagAnon("0008,0023", $date); // Content Date
-    	$tagsObjects[]=new TagAnon("0008,0033", $date); // Content Time
-    	$tagsObjects[]=new TagAnon("0008,0024", $date); // Overlay Date
-    	$tagsObjects[]=new TagAnon("0008,0034", $date); // Overlay Time
-    	$tagsObjects[]=new TagAnon("0040,0244", $date); // ...Start Date
-    	$tagsObjects[]=new TagAnon("0040,0245", $date); // ...Start Time
-    	$tagsObjects[]=new TagAnon("0008,0021", $date); // Series Date
-    	$tagsObjects[]=new TagAnon("0008,0031", $date); // Series Time
-    	$tagsObjects[]=new TagAnon("0008,0020", $date); // Study Date
-    	$tagsObjects[]=new TagAnon("0008,0030", $date); // Study Time
-    	$tagsObjects[]=new TagAnon("0010,21D0", $date); // Last menstrual date
-    	$tagsObjects[]=new TagAnon("0008,0201", $date); // Timezone offset from UTC
-    	$tagsObjects[]=new TagAnon("0040,0002", $date); // Scheduled procedure step start date
-    	$tagsObjects[]=new TagAnon("0040,0003", $date); // Scheduled procedure step start time
-    	$tagsObjects[]=new TagAnon("0040,0004", $date); // Scheduled procedure step end date
-    	$tagsObjects[]=new TagAnon("0040,0005", $date); // Scheduled procedure step end time
+		//List tags releted to Date
+		$tagsObjects[]=new TagAnon("0008,0022", $date); // Acquisition Date
+		$tagsObjects[]=new TagAnon("0008,002A", $date); // Acquisition DateTime
+		$tagsObjects[]=new TagAnon("0008,0032", $date); // Acquisition Time
+		$tagsObjects[]=new TagAnon("0038,0020", $date); // Admitting Date
+		$tagsObjects[]=new TagAnon("0038,0021", $date); // Admitting Time
+		$tagsObjects[]=new TagAnon("0008,0035", $date); // Curve Time
+		$tagsObjects[]=new TagAnon("0008,0025", $date); // Curve Date
+		$tagsObjects[]=new TagAnon("0008,0023", $date); // Content Date
+		$tagsObjects[]=new TagAnon("0008,0033", $date); // Content Time
+		$tagsObjects[]=new TagAnon("0008,0024", $date); // Overlay Date
+		$tagsObjects[]=new TagAnon("0008,0034", $date); // Overlay Time
+		$tagsObjects[]=new TagAnon("0040,0244", $date); // ...Start Date
+		$tagsObjects[]=new TagAnon("0040,0245", $date); // ...Start Time
+		$tagsObjects[]=new TagAnon("0008,0021", $date); // Series Date
+		$tagsObjects[]=new TagAnon("0008,0031", $date); // Series Time
+		$tagsObjects[]=new TagAnon("0008,0020", $date); // Study Date
+		$tagsObjects[]=new TagAnon("0008,0030", $date); // Study Time
+		$tagsObjects[]=new TagAnon("0010,21D0", $date); // Last menstrual date
+		$tagsObjects[]=new TagAnon("0008,0201", $date); // Timezone offset from UTC
+		$tagsObjects[]=new TagAnon("0040,0002", $date); // Scheduled procedure step start date
+		$tagsObjects[]=new TagAnon("0040,0003", $date); // Scheduled procedure step start time
+		$tagsObjects[]=new TagAnon("0040,0004", $date); // Scheduled procedure step end date
+		$tagsObjects[]=new TagAnon("0040,0005", $date); // Scheduled procedure step end time
     	
-    	// same for Body characteristics
-    	$tagsObjects[]=new TagAnon("0010,2160", $body); // Patient's ethnic group
-    	$tagsObjects[]=new TagAnon("0010,21A0", $body); // Patient's smoking status
-    	$tagsObjects[]=new TagAnon("0010,0040", $body); // Patient's sex
-    	$tagsObjects[]=new TagAnon("0010,2203", $body); // Patient's sex neutered
-    	$tagsObjects[]=new TagAnon("0010,1010", $body); // Patient's age
-    	$tagsObjects[]=new TagAnon("0010,21C0", $body); // Patient's pregnancy status
-    	$tagsObjects[]=new TagAnon("0010,1020", $body); // Patient's size
-    	$tagsObjects[]=new TagAnon("0010,1030", $body); // Patient's weight
+		// same for Body characteristics
+		$tagsObjects[]=new TagAnon("0010,2160", $body); // Patient's ethnic group
+		$tagsObjects[]=new TagAnon("0010,21A0", $body); // Patient's smoking status
+		$tagsObjects[]=new TagAnon("0010,0040", $body); // Patient's sex
+		$tagsObjects[]=new TagAnon("0010,2203", $body); // Patient's sex neutered
+		$tagsObjects[]=new TagAnon("0010,1010", $body); // Patient's age
+		$tagsObjects[]=new TagAnon("0010,21C0", $body); // Patient's pregnancy status
+		$tagsObjects[]=new TagAnon("0010,1020", $body); // Patient's size
+		$tagsObjects[]=new TagAnon("0010,1030", $body); // Patient's weight
     
-    	//Others
-    	$tagsObjects[]=new TagAnon("0008,0050", TagAnon::REPLACE, $clinicalStudy);  // Accession Number contains study name
-    	$tagsObjects[]=new TagAnon("0010,0020", TagAnon::REPLACE, $newPatientID); //new Patient Name
-    	$tagsObjects[]=new TagAnon("0010,0010", TagAnon::REPLACE, $newPatientName); //new Patient Name
+		//Others
+		$tagsObjects[]=new TagAnon("0008,0050", TagAnon::REPLACE, $clinicalStudy);  // Accession Number contains study name
+		$tagsObjects[]=new TagAnon("0010,0020", TagAnon::REPLACE, $newPatientID); //new Patient Name
+		$tagsObjects[]=new TagAnon("0010,0010", TagAnon::REPLACE, $newPatientName); //new Patient Name
     	
-    	// Keep some Private tags usefull for PET/CT or Scintigraphy
-    	$tagsObjects[]=new TagAnon("7053,1000", TagAnon::KEEP); //Phillips
-    	$tagsObjects[]=new TagAnon("7053,1009", TagAnon::KEEP); //Phillips
-    	$tagsObjects[]=new TagAnon("0009,103B", TagAnon::KEEP); //GE
-    	$tagsObjects[]=new TagAnon("0009,100D", TagAnon::KEEP); //GE
-    	$tagsObjects[]=new TagAnon("0011,1012", TagAnon::KEEP); //Other
+		// Keep some Private tags usefull for PET/CT or Scintigraphy
+		$tagsObjects[]=new TagAnon("7053,1000", TagAnon::KEEP); //Phillips
+		$tagsObjects[]=new TagAnon("7053,1009", TagAnon::KEEP); //Phillips
+		$tagsObjects[]=new TagAnon("0009,103B", TagAnon::KEEP); //GE
+		$tagsObjects[]=new TagAnon("0009,100D", TagAnon::KEEP); //GE
+		$tagsObjects[]=new TagAnon("0011,1012", TagAnon::KEEP); //Other
     	
-    	$jsonArrayAnon=[];
-    	$jsonArrayAnon['KeepPrivateTags']=false;
-    	$jsonArrayAnon['Force']=true;
+		$jsonArrayAnon=[];
+		$jsonArrayAnon['KeepPrivateTags']=false;
+		$jsonArrayAnon['Force']=true;
     	
-    	foreach($tagsObjects as $tag) {
+		foreach($tagsObjects as $tag) {
     	    
-    	    if($tag->choice==TagAnon::REPLACE){
-    	        $jsonArrayAnon['Replace'][$tag->tag]=$tag->newValue;
-    	    }else if($tag->choice==TagAnon::KEEP){
-    	        $jsonArrayAnon['Keep'][]=$tag->tag;
-            }
+			if($tag->choice==TagAnon::REPLACE){
+				$jsonArrayAnon['Replace'][$tag->tag]=$tag->newValue;
+			}else if($tag->choice==TagAnon::KEEP){
+				$jsonArrayAnon['Keep'][]=$tag->tag;
+			}
             
-    	}
+		}
     	
-    	return $jsonArrayAnon;
+		return $jsonArrayAnon;
     	
-    }
+	}
     
-    /**
-     * Remove secondary captures in the study
-     * @param string $orthancStudyID
-     */
-    private function removeSC(string $orthancStudyID){
+	/**
+	 * Remove secondary captures in the study
+	 * @param string $orthancStudyID
+	 */
+	private function removeSC(string $orthancStudyID){
     	
-    	$studyOrthanc=new Orthanc_Study($orthancStudyID, $this->url, $this->context);
-    	$studyOrthanc->retrieveStudyData();
-    	$seriesObjects=$studyOrthanc->orthancSeries;
-    	foreach ($studyOrthanc->orthancSeries as $serie){
-    		if($serie->isSecondaryCapture() ){
-    			$this->deleteFromOrthanc("series", $serie->serieOrthancID);
-    			error_log("Deleted SC");
-    		}
-    	}
+		$studyOrthanc=new Orthanc_Study($orthancStudyID, $this->url, $this->context);
+		$studyOrthanc->retrieveStudyData();
+		$seriesObjects=$studyOrthanc->orthancSeries;
+		foreach ($studyOrthanc->orthancSeries as $serie){
+			if($serie->isSecondaryCapture() ){
+				$this->deleteFromOrthanc("series", $serie->serieOrthancID);
+				error_log("Deleted SC");
+			}
+		}
     	
-    }
+	}
     
     
-    /**
-     * Return JobId details (get request in Orthanc)
-     * @param String $jobId
-     * @return mixed
-     */
-    public function getJobDetails(String $jobId){
+	/**
+	 * Return JobId details (get request in Orthanc)
+	 * @param String $jobId
+	 * @return mixed
+	 */
+	public function getJobDetails(String $jobId){
         
-        $context =stream_context_create($this->context);
-        $json = file_get_contents($this->url.'/jobs/'.$jobId, false, $context);
+		$context =stream_context_create($this->context);
+		$json = file_get_contents($this->url.'/jobs/'.$jobId, false, $context);
         
-        return json_decode($json, true);
+		return json_decode($json, true);
         
-    }
+	}
 
 }
\ No newline at end of file

Spacing +86 added lines, -86 removed lines

@@ -32,21 +32,21 @@ 
 	 * Build connexion string in Orthanc, boolean to connect with Orthanc Exposed or Orthanc PACS
 	 * @param boolean $exposed
 	 */
-	public function __construct(bool $exposed=false){
+	public function __construct(bool $exposed=false) {
 	    //Set Time Limit at 3H as operation could be really long
 	    set_time_limit(10800);
         //Set address of Orthanc server
-        if($exposed){
+        if ($exposed) {
             $this->url=GAELO_ORTHANC_EXPOSED_INTERNAL_ADDRESS.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PORT;
-            $this->context = array(
+            $this->context=array(
                 'http' => array(
-                    'header'  => "Authorization: Basic " . base64_encode(GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD)
+                    'header'  => "Authorization: Basic ".base64_encode(GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD)
 	   			));
-        }else{
+        }else {
             $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)
 	   			) );
 	   }
 
@@ -56,9 +56,9 @@ 
 	 * Return list of Peers declared in Orthanc
 	 * @return mixed
 	 */
-	public function getPeers(){
-	    $context =stream_context_create($this->context);
-	    $json = file_get_contents($this->url.'/peers/',false, $context);
+	public function getPeers() {
+	    $context=stream_context_create($this->context);
+	    $json=file_get_contents($this->url.'/peers/', false, $context);
 	    $peers=json_decode($json, true);
 	    return $peers;
 	}
@@ -74,7 +74,7 @@ 
 	 * @param string $studyDescription
 	 * @return string json
 	 */
-	public function searchInOrthanc(string $level, string $patientID, string $patientName, string $studyDate, string $studyUID, string $accessionNumber, string $studyDescription){
+	public function searchInOrthanc(string $level, string $patientID, string $patientName, string $studyDate, string $studyUID, string $accessionNumber, string $studyDescription) {
 		
 		$queryDetails=array(
 				'PatientID' => $patientID,
@@ -93,16 +93,16 @@ 
 				
 		);
 		
-		$opts = array('http' =>
+		$opts=array('http' =>
 				array(
 						'method'  => 'POST',
 						'content' => json_encode($query),
-				        'header'=>  ['Content-Type: application/json Accept: application/json ',$this->context['http']['header']]
+				        'header'=>  ['Content-Type: application/json Accept: application/json ', $this->context['http']['header']]
 				)
 		);
 
-		$context  = stream_context_create($opts);
-		$resultJson = file_get_contents($this->url.'/tools/find', false, $context);
+		$context=stream_context_create($opts);
+		$resultJson=file_get_contents($this->url.'/tools/find', false, $context);
 		$result=json_decode($resultJson);
 		
 		return $result;
@@ -113,26 +113,26 @@ 
 	 * @param array $uidList
 	 * @return string temporary file path
 	 */
-	public function getZipTempFile(array $uidList){
+	public function getZipTempFile(array $uidList) {
 	   
-	    if( !is_array($uidList)){
+	    if (!is_array($uidList)) {
 	        $uidList=array($uidList);
 	    }
 	    
-	    $opts = array('http' =>
+	    $opts=array('http' =>
 	        array(
 	            'method'  => 'POST',
 	            'content' => json_encode($uidList),
 	            'timeout' => 3600,
-	            'header'=>  ['Content-Type: application/json', 'Accept: application/zip',$this->context['http']['header'] ]
+	            'header'=>  ['Content-Type: application/json', 'Accept: application/zip', $this->context['http']['header']]
 	        )
 	    );
 	    
-	    $context = stream_context_create($opts);
+	    $context=stream_context_create($opts);
 	    
- 	    $temp = tempnam(ini_get('upload_tmp_dir'), 'TMP_');
+ 	    $temp=tempnam(ini_get('upload_tmp_dir'), 'TMP_');
 	    
-	    $nbbytes=file_put_contents($temp , fopen($this->url.'/tools/create-archive','rb', false, $context));
+	    $nbbytes=file_put_contents($temp, fopen($this->url.'/tools/create-archive', 'rb', false, $context));
 	    
 	    return $temp;
 	}
@@ -143,17 +143,17 @@ 
 	 * @param  $level
 	 * @param  $uidList
 	 */
-	public function deleteFromOrthanc(string $level, string $uid){
+	public function deleteFromOrthanc(string $level, string $uid) {
 	    
-	    $opts = array('http' =>
+	    $opts=array('http' =>
 	        array(
 	            'method'  => 'DELETE',
-	            'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
+	            'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
 	        )
 	    );
 	    
-	    $context  = stream_context_create($opts);
-	    $result = file_get_contents($this->url.'/'.$level.'/'.$uid, false, $context);
+	    $context=stream_context_create($opts);
+	    $result=file_get_contents($this->url.'/'.$level.'/'.$uid, false, $context);
 	    
 	}
 	
@@ -165,21 +165,21 @@ 
 	 * @param string $password
 	 * @return mixed
 	 */
-	public function addPeer(string $name , string $url, string $username, string $password){
+	public function addPeer(string $name, string $url, string $username, string $password) {
 	    
 	    $peerValues['Username']=$username;
 	    $peerValues['Password']=$password;
 	    $peerValues['Url']=$url;
-	    $opts = array('http' =>
+	    $opts=array('http' =>
 	        array(
 	            'method'  => 'PUT',
 	            'content' => json_encode($peerValues),
-	            'header'=>  ['Content-Type: application/json Accept: application/json ',$this->context['http']['header']]
+	            'header'=>  ['Content-Type: application/json Accept: application/json ', $this->context['http']['header']]
 	        )
 	    );
 	    
-	    $context  = stream_context_create($opts);
-	    $resultJson = file_get_contents($this->url.'/peers/'.$name, false, $context);
+	    $context=stream_context_create($opts);
+	    $resultJson=file_get_contents($this->url.'/peers/'.$name, false, $context);
 	    
 	    $result=json_decode($resultJson);
 	    return $result;
@@ -190,17 +190,17 @@ 
 	 * Remove Peer declaration from Orthanc
 	 * @param string $name
 	 */
-	public function removePeer(string $name){
+	public function removePeer(string $name) {
 	    
-	    $opts = array('http' =>
+	    $opts=array('http' =>
 	        array(
 	            'method'  => 'DELETE',
-	            'header'=>  ['Content-Type: application/json Accept: application/json ',$this->context['http']['header']]
+	            'header'=>  ['Content-Type: application/json Accept: application/json ', $this->context['http']['header']]
 	        )
 	    );
 	    
-	    $context  = stream_context_create($opts);
-	    $resultJson = file_get_contents($this->url.'/peers/'.$name, false, $context);
+	    $context=stream_context_create($opts);
+	    $resultJson=file_get_contents($this->url.'/peers/'.$name, false, $context);
 	    
 	    $result=json_decode($resultJson);
 	    
@@ -210,11 +210,11 @@ 
 	/**
 	 * Remove all peers from orthanc
 	 */
-	public function removeAllPeers(){
+	public function removeAllPeers() {
 	    
 	    $peers=$this->getPeers();
 	    
-	    foreach ($peers as $peer){
+	    foreach ($peers as $peer) {
 	        $this->removePeer($peer);
 	    }
 	    
@@ -225,12 +225,12 @@ 
 	 * @param string $peer
 	 * @return boolean
 	 */
-	public function isPeerAccelerated(string $peer){
-	    $context =stream_context_create($this->context);
-	    $json = file_get_contents($this->url.'/transfers/peers/',false, $context);
+	public function isPeerAccelerated(string $peer) {
+	    $context=stream_context_create($this->context);
+	    $json=file_get_contents($this->url.'/transfers/peers/', false, $context);
 	    $peersTest=json_decode($json, true);
 	    
-	    if($peersTest[$peer]=="installed"){
+	    if ($peersTest[$peer] == "installed") {
 	        return true;
 	    }
 	    
@@ -242,19 +242,19 @@ 
 	 * @param string $peer
 	 * @param array $ids
 	 */
-	public function sendToPeer(string $peer, array $ids){
+	public function sendToPeer(string $peer, array $ids) {
 		
-		$opts = array('http' =>
+		$opts=array('http' =>
 				array(
 						'method'  => 'POST',
                         "timeout" => 300, 
 						'content' => json_encode($ids),
-						'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
+						'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
 				)
 		);
 		
-		$context = stream_context_create($opts);
-		$result = file_get_contents($this->url.'/peers/'.$peer.'/store', false, $context);
+		$context=stream_context_create($opts);
+		$result=file_get_contents($this->url.'/peers/'.$peer.'/store', false, $context);
 		return $result;
 	    
 	}
@@ -265,20 +265,20 @@ 
 	 * @param array $ids
 	 * @return string
 	 */
-	public function sendToPeerAsync(string $peer, array $ids){
+	public function sendToPeerAsync(string $peer, array $ids) {
 	    $data['Synchronous']=false;
 	    $data['Resources']=$ids;
 	    
-	    $opts = array('http' =>
+	    $opts=array('http' =>
 	        array(
 	            'method'  => 'POST',
 	            'content' => json_encode($data),
-	            'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
+	            'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
 	        )
 	    );
 	    
-	    $context = stream_context_create($opts);
-	    $result = file_get_contents($this->url.'/peers/'.$peer.'/store', false, $context);
+	    $context=stream_context_create($opts);
+	    $result=file_get_contents($this->url.'/peers/'.$peer.'/store', false, $context);
 	    return $result;
 	}
 	
@@ -289,35 +289,35 @@ 
 	 * @param bool $gzip
 	 * @return string
 	 */
-	public function sendToPeerAsyncWithAccelerator(string $peer, array $ids, bool $gzip){
+	public function sendToPeerAsyncWithAccelerator(string $peer, array $ids, bool $gzip) {
 	    
 	    //If Peer dosen't have accelerated transfers fall back to regular orthanc peer transfers
-	    if( ! $this->isPeerAccelerated($peer)){
+	    if (!$this->isPeerAccelerated($peer)) {
 	        $answer=$this->sendToPeerAsync($peer, $ids);
 	        return $answer;
 	    }
 	    
-	    if(!$gzip) $data['Compression']="none" ; else $data['Compression']="gzip";
+	    if (!$gzip) $data['Compression']="none"; else $data['Compression']="gzip";
 	    
 	    $data['Peer']=$peer;
 	    
 	    
-	    foreach ($ids as $serieID){
+	    foreach ($ids as $serieID) {
 	        $resourceSeries['Level']="Series";
 	        $resourceSeries['ID']=$serieID;
 	        $data['Resources'][]=$resourceSeries;
 	    }
 	    
-	    $opts = array('http' =>
+	    $opts=array('http' =>
 	        array(
 	            'method'  => 'POST',
 	            'content' => json_encode($data),
-	            'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
+	            'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
 	        )
 	    );
 	    
-	    $context = stream_context_create($opts);
-	    $result = file_get_contents($this->url.'/transfers/send', false, $context);
+	    $context=stream_context_create($opts);
+	    $result=file_get_contents($this->url.'/transfers/send', false, $context);
 	    
 	    return $result;
 	    
@@ -328,21 +328,21 @@ 
 	 * @param string $file (path)
 	 * @return string
 	 */
-	public function importFile(string $file){
+	public function importFile(string $file) {
 	    
-	    try{
-    	    $opts = array('http' =>
+	    try {
+    	    $opts=array('http' =>
     	        array(
     	            'method'  => 'POST',
     	            'content' => file_get_contents($file),
-    	            'header'=>  ['Content-Type: application/dicom Accept: application/json',"content-length: ".filesize($file),$this->context['http']['header']]
+    	            'header'=>  ['Content-Type: application/dicom Accept: application/json', "content-length: ".filesize($file), $this->context['http']['header']]
     	        )
     	    );
     	    
-    	    $context = stream_context_create($opts);
-    	    $result = file_get_contents($this->url.'/instances', false, $context);
+    	    $context=stream_context_create($opts);
+    	    $result=file_get_contents($this->url.'/instances', false, $context);
     	    
-	    }catch(Exception $e1){
+	    }catch (Exception $e1) {
 	        error_log("Error during import Dcm ".$e1->getMessage());
 	    }
 	    return $result;
@@ -359,22 +359,22 @@ 
 	 * @param string $studyName
 	 * @return string
 	 */
-	public function Anonymize(string $studyID, string $profile, string $patientCode, string $visitType, string $studyName){
+	public function Anonymize(string $studyID, string $profile, string $patientCode, string $visitType, string $studyName) {
 	    
 	    $jsonAnonQuery=$this->buildAnonQuery($profile, $patientCode, $patientCode, $visitType, $studyName);
 	    
-	    $opts = array('http' =>
+	    $opts=array('http' =>
 	        array(
 	            'method'  => 'POST',
 	            "timeout" => 300,
 	            'content' => json_encode($jsonAnonQuery),
-	            'header'=>  ['Content-Type: application/json Accept: application/json',$this->context['http']['header']]
+	            'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
 	        )
 	    );
 	    
-	    $context = stream_context_create($opts);
+	    $context=stream_context_create($opts);
 
-        $result = file_get_contents($this->url."/studies/".$studyID."/anonymize", false, $context);
+        $result=file_get_contents($this->url."/studies/".$studyID."/anonymize", false, $context);
         
 	    //get the resulting Anonymized study Orthanc ID
 	    $anonAnswer=json_decode($result, true);
@@ -395,10 +395,10 @@ 
 	 * @param string $newStudyDescription
 	 * @return string
 	 */
-	private function buildAnonQuery(string $profile, string $newPatientName, string $newPatientID, string $newStudyDescription, string $clinicalStudy){
+	private function buildAnonQuery(string $profile, string $newPatientName, string $newPatientID, string $newStudyDescription, string $clinicalStudy) {
     	    
         $tagsObjects=[];
-        if($profile=="Default"){
+        if ($profile == "Default") {
             $date=TagAnon::KEEP;
             $body=TagAnon::KEEP;
             
@@ -407,7 +407,7 @@ 
             $tagsObjects[]=new TagAnon("0008,103E", TagAnon::KEEP); //series Description
            
     
-        }else if($profile=="Full"){
+        }else if ($profile == "Full") {
             $date=TagAnon::CLEAR;
             $body=TagAnon::CLEAR;
             
@@ -452,7 +452,7 @@ 
     	$tagsObjects[]=new TagAnon("0010,1030", $body); // Patient's weight
     
     	//Others
-    	$tagsObjects[]=new TagAnon("0008,0050", TagAnon::REPLACE, $clinicalStudy);  // Accession Number contains study name
+    	$tagsObjects[]=new TagAnon("0008,0050", TagAnon::REPLACE, $clinicalStudy); // Accession Number contains study name
     	$tagsObjects[]=new TagAnon("0010,0020", TagAnon::REPLACE, $newPatientID); //new Patient Name
     	$tagsObjects[]=new TagAnon("0010,0010", TagAnon::REPLACE, $newPatientName); //new Patient Name
     	
@@ -467,11 +467,11 @@ 
     	$jsonArrayAnon['KeepPrivateTags']=false;
     	$jsonArrayAnon['Force']=true;
     	
-    	foreach($tagsObjects as $tag) {
+    	foreach ($tagsObjects as $tag) {
     	    
-    	    if($tag->choice==TagAnon::REPLACE){
+    	    if ($tag->choice == TagAnon::REPLACE) {
     	        $jsonArrayAnon['Replace'][$tag->tag]=$tag->newValue;
-    	    }else if($tag->choice==TagAnon::KEEP){
+    	    }else if ($tag->choice == TagAnon::KEEP) {
     	        $jsonArrayAnon['Keep'][]=$tag->tag;
             }
             
@@ -485,13 +485,13 @@ 
      * Remove secondary captures in the study
      * @param string $orthancStudyID
      */
-    private function removeSC(string $orthancStudyID){
+    private function removeSC(string $orthancStudyID) {
     	
     	$studyOrthanc=new Orthanc_Study($orthancStudyID, $this->url, $this->context);
     	$studyOrthanc->retrieveStudyData();
     	$seriesObjects=$studyOrthanc->orthancSeries;
-    	foreach ($studyOrthanc->orthancSeries as $serie){
-    		if($serie->isSecondaryCapture() ){
+    	foreach ($studyOrthanc->orthancSeries as $serie) {
+    		if ($serie->isSecondaryCapture()) {
     			$this->deleteFromOrthanc("series", $serie->serieOrthancID);
     			error_log("Deleted SC");
     		}
@@ -505,10 +505,10 @@ 
      * @param String $jobId
      * @return mixed
      */
-    public function getJobDetails(String $jobId){
+    public function getJobDetails(String $jobId) {
         
-        $context =stream_context_create($this->context);
-        $json = file_get_contents($this->url.'/jobs/'.$jobId, false, $context);
+        $context=stream_context_create($this->context);
+        $json=file_get_contents($this->url.'/jobs/'.$jobId, false, $context);
         
         return json_decode($json, true);
         

Braces +9 added lines, -5 removed lines

@@ -42,7 +42,7 @@ 
                 'http' => array(
                     'header'  => "Authorization: Basic " . base64_encode(GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD)
 	   			));
-        }else{
+        } else{
             $this->url=GAELO_ORTHANC_PACS_ADDRESS.':'.GAELO_ORTHANC_PACS_PORT;
             $this->context = array(
 	   			'http' => array(
@@ -297,7 +297,11 @@ 
 	        return $answer;
 	    }
 	    
-	    if(!$gzip) $data['Compression']="none" ; else $data['Compression']="gzip";
+	    if(!$gzip) {
+	    	$data['Compression']="none" ;
+	    } else {
+	    	$data['Compression']="gzip";
+	    }
 	    
 	    $data['Peer']=$peer;
 	    
@@ -342,7 +346,7 @@ 
     	    $context = stream_context_create($opts);
     	    $result = file_get_contents($this->url.'/instances', false, $context);
     	    
-	    }catch(Exception $e1){
+	    } catch(Exception $e1){
 	        error_log("Error during import Dcm ".$e1->getMessage());
 	    }
 	    return $result;
@@ -407,7 +411,7 @@ 
             $tagsObjects[]=new TagAnon("0008,103E", TagAnon::KEEP); //series Description
            
     
-        }else if($profile=="Full"){
+        } else if($profile=="Full"){
             $date=TagAnon::CLEAR;
             $body=TagAnon::CLEAR;
             
@@ -471,7 +475,7 @@ 
     	    
     	    if($tag->choice==TagAnon::REPLACE){
     	        $jsonArrayAnon['Replace'][$tag->tag]=$tag->newValue;
-    	    }else if($tag->choice==TagAnon::KEEP){
+    	    } else if($tag->choice==TagAnon::KEEP){
     	        $jsonArrayAnon['Keep'][]=$tag->tag;
             }