salimkanoun / GaelO

src/models/Statistics.php

<?php 
/**
 Copyright (C) 2018-2020 KANOUN Salim
 This program is free software; you can redistribute it and/or modify
 it under the terms of the Affero GNU General Public v.3 License as published by
 the Free Software Foundation;
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 Affero GNU General Public Public for more details.
 You should have received a copy of the Affero GNU General Public Public along
 with this program; if not, write to the Free Software Foundation, Inc.,
 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
 */

/**
 * Build Json data for statistics pages
 */
class Statistics {

	public $studyObject;
	private $studyVisitManager;

	public function __construct(Study $study, String $modalityType) {
		$this->studyObject=$study;
		$this->studyVisitManager=$this->studyObject->getStudySpecificGroupManager($modalityType);
	}

	/**
	 * List review one by one with user and date
	 * @return array
	 */
	public function getReviewsDate() {
		$reviewdetailsMap=$this->studyObject->getReviewManager()->getReviewsDetailsByVisit();

		$result=[];
		
		foreach ($reviewdetailsMap as $visitType=>$details) {
			$review=[];
			foreach ($details['reviewDetailsArray'] as $detail) {
				$review['username']=$detail['user'];
				$review['date']=$detail['date'];
				$result[]=$review;

			}
		}
		return $result;
	}

	/**
	 * Provide uploadedFraction of patient in position 0 and upload delay in position 1
	 * @return array
	 */
	public function getUploadFractionAndDelay() {

		$allPatientStatus=$this->studyVisitManager->getPatientsAllVisitsStatus();
		$results[0]=$this->getUploadedFraction($allPatientStatus);

$results was never initialized. Although not strictly required by PHP, it is generally a good practice to add $results = array(); before regardless.

		$results[1]=$this->getUploadDelay($allPatientStatus);

		return $results;
		
	}
	
	/**
	 * Return the uploaded fraction of patients
	 * @param array $allPatientStatus
	 * @return array
	 */
	private function getUploadedFraction($allPatientStatus) {
		$resultArray=[];
		
		
		foreach ($allPatientStatus as $visitType => $patients) {
			
			foreach ($patients as $patientCode=>$patientDetails) {
				
				if ($patientDetails['status'] == Patient_Visit_Manager::DONE || $patientDetails['status'] == Patient_Visit_Manager::SHOULD_BE_DONE) {
					$visit['status']=$patientDetails['status'];
					$visit['uploadStatus']=$patientDetails['upload_status'];
					$visit['visitType']=$visitType;
					$visit['country']=$patientDetails['country'];
					$visit['center']=$patientDetails['center'];
					$resultArray[]=$visit;
				}
			}
		}

		return $resultArray;
		
	}
	
	/**
	 * Calculate upload delay (from declared visit date and upload date)
	 * @param array $allPatientStatus
	 * @return array
	 */
	private function getUploadDelay($allPatientStatus) {

		$resultArray=[];
	    
		foreach ($allPatientStatus as $visitType => $patients) {
			foreach ($patients as $patientCode=>$patientDetails) {
	            
				if ($patientDetails['status'] == Patient_Visit_Manager::DONE && $patientDetails['state_investigator_form'] == Patient_Visit_Manager::DONE) {
	                
					$acquisitionDate=new DateTimeImmutable($patientDetails['acquisition_date']);
					$uploadDate=new DateTimeImmutable($patientDetails['upload_date']);
					$uploadDelay=($uploadDate->getTimestamp()-$acquisitionDate->getTimestamp())/(3600*24);
					$visit['uploadDelay']=$uploadDelay;
					$visit['acquisitionCompliancy']=$patientDetails['compliancy'];
					$visit['visitType']=$visitType;
					$visit['idVisit']=$patientDetails['id_visit'];
					$visit['center']=$patientDetails['center'];
					$visit['country']=$patientDetails['country'];
					$resultArray[]=$visit;
				}
			}
		}
	    
		return $resultArray;
		
	
	}
	
	/**
	 * Return QC time (in days) for each visit (from upload date to QC)
	 * @return array
	 */
	public function getQCTime() {
		
		$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
		
		$responseDelayArray=[];
		
		foreach ($uploadedVisitArray as $visit) {
			$responseQcArrayDetails=[];
			if ($visit->qcStatus != Visit::QC_NOT_DONE) {
				$uploadDate=new DateTimeImmutable($visit->uploadDate);
				$qcDate=new DateTimeImmutable($visit->controlDate);
				$qcDelay=($qcDate->getTimestamp()-$uploadDate->getTimestamp())/(3600*24);

				if ($visit->correctiveActionDate == null) {
					$hasCorrectiveAction=false;
				}else {
					$hasCorrectiveAction=true;
				}

				$responseQcArrayDetails['idVisit']=$visit->id_visit;
				$responseQcArrayDetails['qcDelay']=$qcDelay;
				$responseQcArrayDetails['hasCorrectiveAction']=$hasCorrectiveAction;
			}
			$responseDelayArray[]=$responseQcArrayDetails;
		}
		
		return $responseDelayArray;
		
	}
	
	/**
	 * Output the time to reach the review conclusion (from QC date to Review Done status)
	 * @return array[]
	 */
	public function getConclusionTime() {
		
		$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
		
		$responseDelayArray=[];
		
		foreach ($uploadedVisitArray as $visit) {
			if ($visit->reviewStatus == Visit::REVIEW_DONE) {
				$qcDate=new DateTimeImmutable($visit->controlDate);
				$conclusionDate=new DateTimeImmutable($visit->reviewConclusionDate);
				$conclusionDelay=($conclusionDate->getTimestamp()-$qcDate->getTimestamp())/(3600*24);
				
				$responseConclusionArrayDetails['idVisit']=$visit->id_visit;
				$responseConclusionArrayDetails['conclusionDelay']=$conclusionDelay;
				
				$responseDelayArray[]=$responseConclusionArrayDetails;
			}
		}
		
		return $responseDelayArray;
		
	}
	
	/**
	 * Return all review status for each visit
	 * @return array
	 */
	public function getReviewStatus() {
		
		$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
		
		$responseReviewArray=[];
		
		foreach ($uploadedVisitArray as $visit) {
			$responseReviewArrayElement=[];
			if ($visit->statusDone == Visit::DONE) {
				$responseReviewArrayElement['status']=$visit->reviewStatus;
				if ($visit->reviewStatus == Visit::DONE) {
					$responseReviewArrayElement['visitType']=$visit->visitType;
					$responseReviewArrayElement['conclusionValue']=$visit->reviewConclusion;
				}
			}
			$responseReviewArray[]=$responseReviewArrayElement;
		}
		
		return $responseReviewArray;
		
	}
	
	/**
	 * Return array of each visit's QC status
	 * @return string
	 */
	public function getQcStatus() {
		
		$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
		
		$responseQcArray=[];
		
		foreach ($uploadedVisitArray as $visit) {
			$responseQcArrayDetails=[];
			if ($visit->statusDone == Visit::DONE) {
				$patientObject=$visit->getPatient();
				$center=$patientObject->getPatientCenter();
				if ($visit->correctiveActionDate == null) {
					$hasCorrectiveAction=false;
				}else {
					$hasCorrectiveAction=true;
				}
				$responseQcArrayDetails['qcStatus']=$visit->qcStatus;
				$responseQcArrayDetails['hasCorrectiveAction']=$hasCorrectiveAction;
				$responseQcArrayDetails['center']=$center->name;
				$responseQcArrayDetails['country']=$center->countryName;
			}
			$responseQcArray[]=$responseQcArrayDetails;
		}
		
		return $responseQcArray;

The expression return $responseQcArray returns the type array|array<mixed,array> which is incompatible with the documented return type string.

		
	}
	
	
	/**
	 * Return array of delay between injection time and acquisition time.
	 * Will only return the first PET series found for each visit
	 * @return array|number
	 */
	public function getAcquisitionPetDelay() {
		
		$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
		
		$delayArray=array();
		foreach ($uploadedVisitArray as $visit) {
			$uploadedSeries=$visit->getSeriesDetails();
			foreach ($uploadedSeries as $serie) {

				if ($serie->acquisitionDateTime == null || $serie->injectedDateTime == null) {
					continue;
				}
				
				$acquisitionTime=new DateTimeImmutable($serie->acquisitionDateTime);
				$injectionTime=new DateTimeImmutable($serie->injectedDateTime);
				if ($acquisitionTime != null && $injectionTime != null) {
					$acquisitionDelay=($acquisitionTime->getTimestamp()-$injectionTime->getTimestamp())/60;
					$relatedPatient=$visit->getPatient();
					$patientCenter=$relatedPatient->getPatientCenter();
					$delayDetails['country']=$patientCenter->countryName;
					$delayDetails['idVisit']=$visit->id_visit;
					$delayDetails['center']=$patientCenter->name;
					$delayDetails['patientNumber']=$relatedPatient->patientCode;
					$delayDetails['visitType']=$visit->visitType;
					$delayDetails['delayAcquisition']=$acquisitionDelay;
					
					$delayArray[]=$delayDetails;
					break;
				}
			}
		}

		return $delayArray;
		
	}
	
	/**
	 * Return specific data of all reviews
	 * @return array[]
	 */
	public function getReviewData() {
	    
		$createdVisits=$this->studyVisitManager->getUploadedVisits();
        
		$reviewsJson=[];
		foreach ($createdVisits as $visit) {

					$reviews=[];

					try {
						$reviews[]=$visit->getReviewsObject(true);
					}catch (Exception $e) { }

Consider adding a comment why this CATCH block is empty.

					try {
						$reviewsReviewers=$visit->getReviewsObject(false);
						foreach ($reviewsReviewers as $expertReview) {
							$reviews[]=$expertReview;
						}
					}catch (Exception $e) { }

Consider adding a comment why this CATCH block is empty.

			foreach ($reviews as $review) {

						if ($review->validated) {
								$specificData=$review->getSpecificData();
								$parentVisit=$review->getParentVisitObject();
								$visitType=$parentVisit->visitType;
								$reviewResult=$specificData;
								$reviewResult['_reviewDate']=$review->reviewDate;
								$reviewResult['_localForm']=boolval($review->isLocal);
								$reviewResult['_adjudicationForm']=boolval($review->isAdjudication);
								$reviewResult['_username']=$review->username;
								$reviewResult['_center']=$parentVisit->getPatient()->getPatientCenter()->name;
								$reviewResult['_visitType']=$visitType;
								
								$reviewsJson['data'][$visitType][]=$reviewResult;
						}

			}
		}
		
		$visitTypePossible=$this->studyVisitManager->getVisitGroupObject()->getAllVisitTypesOfGroup();
		foreach ($visitTypePossible as $visitType) {
			$inputType=$visitType->getSpecificTableInputType();
			$dataDetails[$visitType->name]=$inputType;
		}
        
		$reviewsJson['structureDetails']=$dataDetails;

The variable $dataDetails seems to be defined by a foreach iteration on line 332. Are you sure the iterator is never empty, otherwise this variable is not defined?

        
		return $reviewsJson;
	}
	   
	
}