salimkanoun / GaelO

src/scripts/validate_dicom_upload_tus.php

Indentation +13 added lines, -13 removed lines

@@ -59,7 +59,7 @@ 
 	ignore_user_abort(true);
 	//Set Visit as upload processing status
 	$visitObject->changeUploadStatus(Visit::UPLOAD_PROCESSING);
-    $start_time=microtime(true);
+	$start_time=microtime(true);
 	/**
 	 * Try block as each interruption of the proccess must make visit return as upload not done
 	 * To allow new upload
@@ -165,11 +165,11 @@ 
 			continue;
 		}
 		$files[]=$file->getPathname();
-    }
+	}
     
-    if(sizeof($files) != $nbOfInstances){
-        throw new Exception("Number Of Uploaded Files dosen't match expected instance number");
-    }
+	if(sizeof($files) != $nbOfInstances){
+		throw new Exception("Number Of Uploaded Files dosen't match expected instance number");
+	}
 	
 	$importedMap=null;
 	$importedInstances=0;
@@ -271,31 +271,31 @@ 
 
 function get_tus_file($fileName) {
     
-    $client = new Client([
-        // Base URI is used with relative requests
+	$client = new Client([
+		// Base URI is used with relative requests
 		'base_uri' => TUS_SERVER.'/tus/',
 		'headers' => ['Tus-Resumable' => '1.0.0']
-    ]);
+	]);
 	$downloadedFileName = tempnam(sys_get_temp_dir(), 'dicom');
 
 	$resource  = fopen( $downloadedFileName, 'r+');
 	
 	$client->request('GET', $fileName, ['sink' => $resource]);
 
-    return $downloadedFileName;
+	return $downloadedFileName;
 }
 
 function delete_tus_file($fileName){
 
-    $client = new Client([
-        // Base URI is used with relative requests
+	$client = new Client([
+		// Base URI is used with relative requests
 		'base_uri' => TUS_SERVER.'/tus/',
 		'headers' => ['Tus-Resumable' => '1.0.0']
-    ]);
+	]);
 
 	$client->request('DELETE', $fileName);
 	
-    //$code = $response->getStatusCode(); // 200
+	//$code = $response->getStatusCode(); // 200
 	//$reason = $response->getReasonPhrase(); // OK
 
 }

Spacing +13 added lines, -13 removed lines

@@ -37,16 +37,16 @@ 
 Session::checkSession();
 $linkpdo=Session::getLinkpdo();
 
-$timeStamp = time();
-$id_visit = $_POST['id_visit'];
-$nbOfInstances = $_POST['totalDicomFiles'];
+$timeStamp=time();
+$id_visit=$_POST['id_visit'];
+$nbOfInstances=$_POST['totalDicomFiles'];
 $anonFromOrthancId=$_POST['originalOrthancStudyID'];
 $username=$_SESSION['username'];
 $study=$_SESSION['study'];
 $role=$_SESSION['role'];
-$tusFilesID = $_POST['sucessIDsUploaded'];
+$tusFilesID=$_POST['sucessIDsUploaded'];
 
-$unzipedPath = $_SERVER['DOCUMENT_ROOT'].'/data/upload/temp/'.$timeStamp.'_'.$id_visit;
+$unzipedPath=$_SERVER['DOCUMENT_ROOT'].'/data/upload/temp/'.$timeStamp.'_'.$id_visit;
 
 $visitObject=new Visit($id_visit, $linkpdo);
 $userObject=new User($username, $linkpdo);
@@ -71,8 +71,8 @@ 
 		}
 
 		//Unzip each uploaded file and remove them from tus
-		foreach($tusFilesID as $fileName){
-			$tempZipPath = get_tus_file($fileName);
+		foreach ($tusFilesID as $fileName) {
+			$tempZipPath=get_tus_file($fileName);
 
 			$zipSize=filesize($tempZipPath);
 			$uncompressedzipSize=get_zip_originalsize($tempZipPath);
@@ -168,7 +168,7 @@ 
 		$files[]=$file->getPathname();
     }
     
-    if(sizeof($files) != $nbOfInstances){
+    if (sizeof($files) != $nbOfInstances) {
         throw new Exception("Number Of Uploaded Files dosen't match expected instance number");
     }
 	
@@ -271,23 +271,23 @@ 
 
 function get_tus_file($fileName) {
     
-    $client = new Client([
+    $client=new Client([
         // Base URI is used with relative requests
 		'base_uri' => TUS_SERVER.'/tus/',
 		'headers' => ['Tus-Resumable' => '1.0.0']
     ]);
-	$downloadedFileName = tempnam(sys_get_temp_dir(), 'dicom');
+	$downloadedFileName=tempnam(sys_get_temp_dir(), 'dicom');
 
-	$resource  = fopen( $downloadedFileName, 'r+');
+	$resource=fopen($downloadedFileName, 'r+');
 	
 	$client->request('GET', $fileName, ['sink' => $resource]);
 
     return $downloadedFileName;
 }
 
-function delete_tus_file($fileName){
+function delete_tus_file($fileName) {
 
-    $client = new Client([
+    $client=new Client([
         // Base URI is used with relative requests
 		'base_uri' => TUS_SERVER.'/tus/',
 		'headers' => ['Tus-Resumable' => '1.0.0']

Braces +9 added lines, -6 removed lines

@@ -133,7 +133,7 @@ 
 		//Log import
 		Tracker::logActivity($username, $role, $study, $visitObject->id_visit, "Upload Series", $logDetails);
 	
-	}catch (Throwable $e1) {
+	} catch (Throwable $e1) {
 		$logDetails['patientNumber']=$visitObject->patientCode;
 		$logDetails['visitType']=$visitObject->visitType;
 		$logDetails['modality_visit']=$visitObject->visitGroupObject->groupModality;
@@ -145,7 +145,7 @@ 
 	}
 		
 
-}else {
+} else {
 	header('HTTP/1.0 403 Forbidden');
 	die('You are not allowed to access this file.');
 }
@@ -200,11 +200,11 @@ 
 	
 	if (count($importedMap) == 1 && $importedInstances == $nbOfInstances) {
 		return $importedMap;
-	}else {
+	} else {
 		//These error shall never occur
 		if (count($importedMap) > 1) {
 			throw new Exception("More than one study in Zip");
-		}else if ($importedInstances != $nbOfInstances) {
+		} else if ($importedInstances != $nbOfInstances) {
 			throw new Exception("Imported DICOM not matching announced number of Instances");
 			
 		}
@@ -220,8 +220,11 @@ 
 	$it=new RecursiveDirectoryIterator($directory, FilesystemIterator::SKIP_DOTS);
 	$it=new RecursiveIteratorIterator($it, RecursiveIteratorIterator::CHILD_FIRST);
 	foreach ($it as $file) {
-		if ($file->isDir()) rmdir($file->getPathname());
-		else unlink($file->getPathname());
+		if ($file->isDir()) {
+			rmdir($file->getPathname());
+		} else {
+			unlink($file->getPathname());
+		}
 	}
 	rmdir($directory);
 }

src/models/Orthanc.php

Spacing +14 added lines, -14 removed lines

@@ -38,20 +38,20 @@ 
 		//Set Time Limit at 3H as operation could be really long
 		set_time_limit(10800);
 
-		$this->client = new Client();
+		$this->client=new Client();
 		//Set address of Orthanc server
 		if ($exposed) {
 			$this->url=GAELO_ORTHANC_EXPOSED_INTERNAL_ADDRESS.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PORT;
-			$this->login = GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN;
-			$this->password = GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD;
+			$this->login=GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN;
+			$this->password=GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD;
 			$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->login = GAELO_ORTHANC_PACS_LOGIN;
-			$this->password = GAELO_ORTHANC_PACS_PASSWORD;
+			$this->login=GAELO_ORTHANC_PACS_LOGIN;
+			$this->password=GAELO_ORTHANC_PACS_PASSWORD;
 			$this->context=array(
 	   			'http' => array(
 	   				'header'  => "Authorization: Basic ".base64_encode(GAELO_ORTHANC_PACS_LOGIN.':'.GAELO_ORTHANC_PACS_PASSWORD)
@@ -138,8 +138,8 @@ 
 	    
 		$context=stream_context_create($opts);
 
-		$tempFile = tmpfile();
-		stream_copy_to_stream ( fopen($this->url.'/tools/create-archive', 'rb', false, $context) , $tempFile);
+		$tempFile=tmpfile();
+		stream_copy_to_stream(fopen($this->url.'/tools/create-archive', 'rb', false, $context), $tempFile);
 	    
 		return $tempFile;
 	}
@@ -359,18 +359,18 @@ 
 	/**
 	 * This method has the advantage to stream the content and avoid running out memory
 	 */
-	public function importFileGuzzle(string $file){
-		try{
-			$body = fopen($file, 'r');
+	public function importFileGuzzle(string $file) {
+		try {
+			$body=fopen($file, 'r');
 
-			$options = ['auth' => [$this->login, $this->password],
+			$options=['auth' => [$this->login, $this->password],
 			'headers'  => ['content-type' => 'application/dicom', 'Accept' => 'application/json'],
 			'body' => $body];
 
-			$response = $this->client->request('POST', $this->url.'/instances' , $options);
+			$response=$this->client->request('POST', $this->url.'/instances', $options);
 			
-			return (string) $response->getBody();
-		} catch (Exception $e1) {
+			return (string)$response->getBody();
+		}catch (Exception $e1) {
 			error_log("Error during import Dcm ".$e1->getMessage());
 		}
 	}

Braces +9 added lines, -5 removed lines

@@ -48,7 +48,7 @@ 
 				'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->login = GAELO_ORTHANC_PACS_LOGIN;
 			$this->password = GAELO_ORTHANC_PACS_PASSWORD;
@@ -304,7 +304,11 @@ 
 			return $answer;
 		}
 	    
-		if (!$gzip) $data['Compression']="none"; else $data['Compression']="gzip";
+		if (!$gzip) {
+			$data['Compression']="none";
+		} else {
+			$data['Compression']="gzip";
+		}
 	    
 		$data['Peer']=$peer;
 	    
@@ -349,7 +353,7 @@ 
 			$context=stream_context_create($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;
@@ -433,7 +437,7 @@ 
 			$tagsObjects[]=new TagAnon("0008,103E", TagAnon::KEEP); //series Description
            
     
-		}else if ($profile == "Full") {
+		} else if ($profile == "Full") {
 			$date=TagAnon::CLEAR;
 			$body=TagAnon::CLEAR;
             
@@ -497,7 +501,7 @@ 
     	    
 			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;
 			}
             

src/scripts/get_possible_import.php

Spacing +1 added lines, -1 removed lines

@@ -50,7 +50,7 @@
 		}
 	}
     
-} else {
+}else {
 	$availableVisits=[];
 }
 

src/scripts/is_new_study.php

Spacing +1 added lines, -1 removed lines

@@ -34,7 +34,7 @@
 	//Output results
 	echo(json_encode($answer));
     
-} else {
+}else {
 	header('HTTP/1.0 403 Forbidden');
 	die('You are not allowed to access this data.');
 }
\ No newline at end of file

src/views/supervisor/tracker/tracker_investigator.php

Braces +3 added lines, -1 removed lines

@@ -70,11 +70,13 @@
             	<tr>
 					<td><?=$investigatorEvent['date']?></td>
 					<td><?=htmlspecialchars($investigatorEvent['username'])?></td>
-					<td><?php if ($investigatorEvent['action_type'] == "Create Visit") echo('<pre><code>'.json_encode($eventDetails, JSON_PRETTY_PRINT|JSON_HEX_QUOT|JSON_HEX_TAG|JSON_HEX_AMP|JSON_HEX_APOS).'</code></pre>')?></td>
+					<td><?php if ($investigatorEvent['action_type'] == "Create Visit") {
+	echo('<pre><code>'.json_encode($eventDetails, JSON_PRETTY_PRINT|JSON_HEX_QUOT|JSON_HEX_TAG|JSON_HEX_AMP|JSON_HEX_APOS).'</code></pre>')?></td>
 					<td><?php if ($investigatorEvent['action_type'] == "Upload Series") echo('<pre><code>'.json_encode($eventDetails, JSON_PRETTY_PRINT|JSON_HEX_QUOT|JSON_HEX_TAG|JSON_HEX_AMP|JSON_HEX_APOS).'</code></pre>')?></td>
 					<td><?php if ($investigatorEvent['action_type'] == "Upload Failure") echo('<pre><code>'.json_encode($eventDetails, JSON_PRETTY_PRINT|JSON_HEX_QUOT|JSON_HEX_TAG|JSON_HEX_AMP|JSON_HEX_APOS).'</code></pre>')?></td>
 					<td><?php if ($investigatorEvent['action_type'] == "Save Form") {
 						$specificForm=$eventDetails['raw_data'];
+}
 						unset($eventDetails['raw_data']);
 						echo('<pre><code>'.json_encode($eventDetails, JSON_PRETTY_PRINT|JSON_HEX_QUOT|JSON_HEX_TAG|JSON_HEX_AMP|JSON_HEX_APOS).'</code></pre>');
 						?>

src/views/supervisor/change_patient_status_view.php

Spacing +1 added lines, -1 removed lines

@@ -120,7 +120,7 @@
 				</SELECT>
 				<input type="text" class="form-control" id="reason" placeholder="Reason" name="reason" maxlength="255" style="display:none">
 				<?php
-			}else{
+			}else {
 				?>
 					<input type="text" class="form-control" id="reason" placeholder="Reason" name="reason" maxlength="255">
 				<?php

Braces +2 added lines, -2 removed lines

@@ -96,7 +96,7 @@ 
 		?>
             <label class="control-label">Declare patient withdrawal from the study</label>
 		<?php 
-		}else {
+		} else {
 		?>
             <label class="control-label">Cancel Withdrawal (re-inclusion)</label>
 		<?php 
@@ -120,7 +120,7 @@ 
 				</SELECT>
 				<input type="text" class="form-control" id="reason" placeholder="Reason" name="reason" maxlength="255" style="display:none">
 				<?php
-			}else{
+			} else{
 				?>
 					<input type="text" class="form-control" id="reason" placeholder="Reason" name="reason" maxlength="255">
 				<?php

src/models/Import_Patient.php

Braces +19 added lines, -19 removed lines

@@ -61,7 +61,7 @@ 
 				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]);
 				}
@@ -73,41 +73,41 @@ 
 				//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;
 				}
 
 			//If conditions not met, add to the fail list with the respective error reason
-			}else {
+			} else {
 			    
 				if (!$isExistingCenter) {
 					if (empty($patientInvestigatorNumCenter)) {
 						$this->failList['Missing Num Center'][]=$patientNumber;
-					}else {
+					} else {
 						$this->failList['Unknown Center'][]=$patientNumber;
 					}
 
-				}else if (!$isCorrectPatientNumberLenght) {
+				} else if (!$isCorrectPatientNumberLenght) {
 					$this->failList['Wrong PatientNumber length'][]=$patientNumber;
 				    
-				}else if (!$isNewPatient) {
+				} else if (!$isNewPatient) {
 					if( !empty($patientRegistrationDate) ){
 						$updated = $this->tryUpdateRegistrationDate($patientNumber, $patientRegistrationDate->format('Y-m-d'));
 						if($updated){
 							$this->sucessList[]=$patientNumber.' - Updated Registration Date';
-						}else{
+						} else{
 							$this->failList['Patient already in Database'][]=$patientNumber;
 						}
-					}else{
+					} else{
 						$this->failList['Patient already in Database'][]=$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;
 				}
 				
@@ -141,7 +141,7 @@ 
 		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]);
 		}
@@ -154,7 +154,7 @@ 
 	    
 		try {
 			$dateResult=new DateTime($registrationYear.'-'.$registrationMonth.'-'.$registrationDay);
-		}catch (Exception $e) {
+		} catch (Exception $e) {
 			return null;
 		}
 		return $dateResult;
@@ -170,7 +170,7 @@ 
 	private function isNewPatient($patientCode) {
 		try {
 			new Patient($patientCode, $this->linkpdo);
-		}catch (Exception $e1) {
+		} catch (Exception $e1) {
 			return true;
 		}
 	    
@@ -187,7 +187,7 @@ 
 		
 		if ($lenghtImport == GAELO_PATIENT_CODE_LENGHT) {
 			return true;
-		}else {
+		} else {
 			return false;
 		}
 	}
@@ -221,7 +221,7 @@ 
 	    
 		try {
 			new Center($this->linkpdo, $patientNumCenter);
-		}catch (Exception $e1) {
+		} catch (Exception $e1) {
 			return false;
 		}
 	    
@@ -260,7 +260,7 @@ 
 													'center' => $patientInvestigatorNumCenter,
 													'study' => $this->study));
 			$success=true;
-		}catch (Exception $e) {
+		} catch (Exception $e) {
 			$success=false;
 		}
 
@@ -292,12 +292,12 @@ 
 					$failReport=$failReport.$key.':<br>';
 					if (is_array($value)) {
 						$failReport=$failReport.implode('<br>', $value).'<br>';
-					}else {
+					} else {
 						$failReport=$failReport.$value.'<br>';
 					}
 				}
 			}
-		}else {
+		} else {
 			$failReport=$failReport.' None <br>';
 		}
 	    
@@ -316,7 +316,7 @@ 
 				$success=$value;
 				$successReport=$successReport.$success.'<br>';
 			}
-		}else {
+		} else {
 			$successReport=$successReport.' None <br>';
 		}
 	    

Spacing +8 added lines, -8 removed lines

@@ -93,14 +93,14 @@ 
 					$this->failList['Wrong PatientNumber length'][]=$patientNumber;
 				    
 				}else if (!$isNewPatient) {
-					if( !empty($patientRegistrationDate) ){
-						$updated = $this->tryUpdateRegistrationDate($patientNumber, $patientRegistrationDate->format('Y-m-d'));
-						if($updated){
+					if (!empty($patientRegistrationDate)) {
+						$updated=$this->tryUpdateRegistrationDate($patientNumber, $patientRegistrationDate->format('Y-m-d'));
+						if ($updated) {
 							$this->sucessList[]=$patientNumber.' - Updated Registration Date';
-						}else{
+						}else {
 							$this->failList['Patient already in Database'][]=$patientNumber;
 						}
-					}else{
+					}else {
 						$this->failList['Patient already in Database'][]=$patientNumber;
 					}
 					
@@ -118,10 +118,10 @@ 
 
 	}
 
-	private function tryUpdateRegistrationDate($patientNumber, $patientRegistrationDate){
-		$patientObject = new Patient($patientNumber, $this->linkpdo);
+	private function tryUpdateRegistrationDate($patientNumber, $patientRegistrationDate) {
+		$patientObject=new Patient($patientNumber, $this->linkpdo);
 		//If patient with default registration date, update to the new one
-		if($patientObject->patientRegistrationDate == '1900-01-01' && $patientRegistrationDate !== $patientObject->patientRegistrationDate ) {
+		if ($patientObject->patientRegistrationDate == '1900-01-01' && $patientRegistrationDate !== $patientObject->patientRegistrationDate) {
 			$patientObject->editPatientRegistrationDate($patientRegistrationDate);
 			return true;
 		}

src/models/FTP_Reader.php

Braces +9 added lines, -9 removed lines

@@ -77,10 +77,10 @@ 
 			$isAvailable=$this->isSearchedFileAvailable($fileArray);
 			if ($isAvailable) {
 				return array($this->ftpFileName);
-			}else {
+			} else {
 				throw new Exception('Target File Not Found');
 			}
-		}else {
+		} else {
 			return $fileArray;
 		}
 	}
@@ -112,7 +112,7 @@ 
 		if ($this->ftpIsSftp) {
 
 			$filesArray=$this->getSftp();
-		}else {
+		} else {
 			$filesArray=$this->getFtp();
 			//$ftpConnect = ftp_ssl_connect ($this->ftpHost, $this->ftpPort) or die("Can't Connect to Server ".$this->ftpHost);
 
@@ -136,7 +136,7 @@ 
 
 			return $sftp;
 
-		}else {
+		} else {
 
 			if (!$ftpConnect=ftp_connect($this->ftpHost, $this->ftpPort)) {
 				throw new Exception('Cant Connect to Server'.$this->ftpHost);
@@ -169,7 +169,7 @@ 
 
 			return $result;
 
-		}else {      
+		} else {      
 
 			$ftp=$this->connectAndGoToFolder();
 
@@ -191,7 +191,7 @@ 
 		$fileArray=array_filter($fileArray, function($file) {
 			if ($file == '.' || $file == '..') {
 				return false;
-			}else {
+			} else {
 				return true;
 			}
 		});
@@ -230,7 +230,7 @@ 
 		$fileArray=array_filter($fileArray, function($file) {
 			if ($file == '.' || $file == '..') {
 				return false;
-			}else {
+			} else {
 				return true;
 			}
 		});
@@ -274,7 +274,7 @@ 
 			if ($i == 0) {
 				//First line is column definition
 				$titles=$columns;
-			}else {
+			} else {
 				$patient=[];
 				//For each column associate data into an associative array
 				for ($j=0; $j < sizeof($columns); $j++) {
@@ -295,7 +295,7 @@ 
 			$email->setSubject('FTP Process Failed');
 			$email->addAminEmails();
 			$email->sendEmail();
-		}catch (Exception $e) {
+		} catch (Exception $e) {
 			echo('sendEmailException');
 			echo($e->getMessage());
 		}