Statistics::getAcquisitionPetDelay() - Code Metrics - salimkanoun/GaelO - Measure and Improve Code Quality continuously with Scrutinizer

Statistics::getAcquisitionPetDelay() B
last analyzed 2021-07-04 22:07 UTC

↳ Parent: Statistics

Complexity

Conditions	7
Paths	5

Size

Total Lines	33
Code Lines	22

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	22
nc	5
nop	0
dl	0
loc	33
c	0
b	0
f	0
cc	7
rs	8.6346

<?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);

		$results[1]=$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;

		
	}
	
	
	/**
	 * 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) { }


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



			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;

        
		return $reviewsJson;
	}
	   
	
}


1			<?php
2			/**
3			Copyright (C) 2018-2020 KANOUN Salim
4			This program is free software; you can redistribute it and/or modify
5			it under the terms of the Affero GNU General Public v.3 License as published by
6			the Free Software Foundation;
7			This program is distributed in the hope that it will be useful,
8			but WITHOUT ANY WARRANTY; without even the implied warranty of
9			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
10			Affero GNU General Public Public for more details.
11			You should have received a copy of the Affero GNU General Public Public along
12			with this program; if not, write to the Free Software Foundation, Inc.,
13			51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
14			*/
15
16			/**
17			* Build Json data for statistics pages
18			*/
19			class Statistics {
20
21			public $studyObject;
22			private $studyVisitManager;
23
24			public function __construct(Study $study, String $modalityType) {
25			$this->studyObject=$study;
26			$this->studyVisitManager=$this->studyObject->getStudySpecificGroupManager($modalityType);
27			}
28
29			/**
30			* List review one by one with user and date
31			* @return array
32			*/
33			public function getReviewsDate() {
34			$reviewdetailsMap=$this->studyObject->getReviewManager()->getReviewsDetailsByVisit();
35
36			$result=[];
37
38			foreach ($reviewdetailsMap as $visitType=>$details) {
39			$review=[];
40			foreach ($details['reviewDetailsArray'] as $detail) {
41			$review['username']=$detail['user'];
42			$review['date']=$detail['date'];
43			$result[]=$review;
44
45			}
46			}
47			return $result;
48			}
49
50			/**
51			* Provide uploadedFraction of patient in position 0 and upload delay in position 1
52			* @return array
53			*/
54			public function getUploadFractionAndDelay() {
55
56			$allPatientStatus=$this->studyVisitManager->getPatientsAllVisitsStatus();
57			$results[0]=$this->getUploadedFraction($allPatientStatus);
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report `$results` was never initialized. Although not strictly required by PHP, it is generally a good practice to add `$results = array();` before regardless. Loading history...
58			$results[1]=$this->getUploadDelay($allPatientStatus);
59
60			return $results;
61
62			}
63
64			/**
65			* Return the uploaded fraction of patients
66			* @param array $allPatientStatus
67			* @return array
68			*/
69			private function getUploadedFraction($allPatientStatus) {
70			$resultArray=[];
71
72
73			foreach ($allPatientStatus as $visitType => $patients) {
74
75			foreach ($patients as $patientCode=>$patientDetails) {
76
77			if ($patientDetails['status'] == Patient_Visit_Manager::DONE \|\| $patientDetails['status'] == Patient_Visit_Manager::SHOULD_BE_DONE) {
78			$visit['status']=$patientDetails['status'];
79			$visit['uploadStatus']=$patientDetails['upload_status'];
80			$visit['visitType']=$visitType;
81			$visit['country']=$patientDetails['country'];
82			$visit['center']=$patientDetails['center'];
83			$resultArray[]=$visit;
84			}
85			}
86			}
87
88			return $resultArray;
89
90			}
91
92			/**
93			* Calculate upload delay (from declared visit date and upload date)
94			* @param array $allPatientStatus
95			* @return array
96			*/
97			private function getUploadDelay($allPatientStatus) {
98
99			$resultArray=[];
100
101			foreach ($allPatientStatus as $visitType => $patients) {
102			foreach ($patients as $patientCode=>$patientDetails) {
103
104			if ($patientDetails['status'] == Patient_Visit_Manager::DONE && $patientDetails['state_investigator_form'] == Patient_Visit_Manager::DONE) {
105
106			$acquisitionDate=new DateTimeImmutable($patientDetails['acquisition_date']);
107			$uploadDate=new DateTimeImmutable($patientDetails['upload_date']);
108			$uploadDelay=($uploadDate->getTimestamp()-$acquisitionDate->getTimestamp())/(3600*24);
109			$visit['uploadDelay']=$uploadDelay;
110			$visit['acquisitionCompliancy']=$patientDetails['compliancy'];
111			$visit['visitType']=$visitType;
112			$visit['idVisit']=$patientDetails['id_visit'];
113			$visit['center']=$patientDetails['center'];
114			$visit['country']=$patientDetails['country'];
115			$resultArray[]=$visit;
116			}
117			}
118			}
119
120			return $resultArray;
121
122
123			}
124
125			/**
126			* Return QC time (in days) for each visit (from upload date to QC)
127			* @return array
128			*/
129			public function getQCTime() {
130
131			$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
132
133			$responseDelayArray=[];
134
135			foreach ($uploadedVisitArray as $visit) {
136			$responseQcArrayDetails=[];
137			if ($visit->qcStatus != Visit::QC_NOT_DONE) {
138			$uploadDate=new DateTimeImmutable($visit->uploadDate);
139			$qcDate=new DateTimeImmutable($visit->controlDate);
140			$qcDelay=($qcDate->getTimestamp()-$uploadDate->getTimestamp())/(3600*24);
141
142			if ($visit->correctiveActionDate == null) {
143			$hasCorrectiveAction=false;
144			}else {
145			$hasCorrectiveAction=true;
146			}
147
148			$responseQcArrayDetails['idVisit']=$visit->id_visit;
149			$responseQcArrayDetails['qcDelay']=$qcDelay;
150			$responseQcArrayDetails['hasCorrectiveAction']=$hasCorrectiveAction;
151			}
152			$responseDelayArray[]=$responseQcArrayDetails;
153			}
154
155			return $responseDelayArray;
156
157			}
158
159			/**
160			* Output the time to reach the review conclusion (from QC date to Review Done status)
161			* @return array[]
162			*/
163			public function getConclusionTime() {
164
165			$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
166
167			$responseDelayArray=[];
168
169			foreach ($uploadedVisitArray as $visit) {
170			if ($visit->reviewStatus == Visit::REVIEW_DONE) {
171			$qcDate=new DateTimeImmutable($visit->controlDate);
172			$conclusionDate=new DateTimeImmutable($visit->reviewConclusionDate);
173			$conclusionDelay=($conclusionDate->getTimestamp()-$qcDate->getTimestamp())/(3600*24);
174
175			$responseConclusionArrayDetails['idVisit']=$visit->id_visit;
176			$responseConclusionArrayDetails['conclusionDelay']=$conclusionDelay;
177
178			$responseDelayArray[]=$responseConclusionArrayDetails;
179			}
180			}
181
182			return $responseDelayArray;
183
184			}
185
186			/**
187			* Return all review status for each visit
188			* @return array
189			*/
190			public function getReviewStatus() {
191
192			$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
193
194			$responseReviewArray=[];
195
196			foreach ($uploadedVisitArray as $visit) {
197			$responseReviewArrayElement=[];
198			if ($visit->statusDone == Visit::DONE) {
199			$responseReviewArrayElement['status']=$visit->reviewStatus;
200			if ($visit->reviewStatus == Visit::DONE) {
201			$responseReviewArrayElement['visitType']=$visit->visitType;
202			$responseReviewArrayElement['conclusionValue']=$visit->reviewConclusion;
203			}
204			}
205			$responseReviewArray[]=$responseReviewArrayElement;
206			}
207
208			return $responseReviewArray;
209
210			}
211
212			/**
213			* Return array of each visit's QC status
214			* @return string
215			*/
216			public function getQcStatus() {
217
218			$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
219
220			$responseQcArray=[];
221
222			foreach ($uploadedVisitArray as $visit) {
223			$responseQcArrayDetails=[];
224			if ($visit->statusDone == Visit::DONE) {
225			$patientObject=$visit->getPatient();
226			$center=$patientObject->getPatientCenter();
227			if ($visit->correctiveActionDate == null) {
228			$hasCorrectiveAction=false;
229			}else {
230			$hasCorrectiveAction=true;
231			}
232			$responseQcArrayDetails['qcStatus']=$visit->qcStatus;
233			$responseQcArrayDetails['hasCorrectiveAction']=$hasCorrectiveAction;
234			$responseQcArrayDetails['center']=$center->name;
235			$responseQcArrayDetails['country']=$center->countryName;
236			}
237			$responseQcArray[]=$responseQcArrayDetails;
238			}
239
240			return $responseQcArray;
			0 ignored issues – show Bug Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report The expression `return $responseQcArray` returns the type `array\|array<mixed,array>` which is incompatible with the documented return type `string`. Loading history...
241
242			}
243
244
245			/**
246			* Return array of delay between injection time and acquisition time.
247			* Will only return the first PET series found for each visit
248			* @return array\|number
249			*/
250			public function getAcquisitionPetDelay() {
251
252			$uploadedVisitArray=$this->studyVisitManager->getUploadedVisits();
253
254			$delayArray=array();
255			foreach ($uploadedVisitArray as $visit) {
256			$uploadedSeries=$visit->getSeriesDetails();
257			foreach ($uploadedSeries as $serie) {
258
259			if ($serie->acquisitionDateTime == null \|\| $serie->injectedDateTime == null) {
260			continue;
261			}
262
263			$acquisitionTime=new DateTimeImmutable($serie->acquisitionDateTime);
264			$injectionTime=new DateTimeImmutable($serie->injectedDateTime);
265			if ($acquisitionTime != null && $injectionTime != null) {
266			$acquisitionDelay=($acquisitionTime->getTimestamp()-$injectionTime->getTimestamp())/60;
267			$relatedPatient=$visit->getPatient();
268			$patientCenter=$relatedPatient->getPatientCenter();
269			$delayDetails['country']=$patientCenter->countryName;
270			$delayDetails['idVisit']=$visit->id_visit;
271			$delayDetails['center']=$patientCenter->name;
272			$delayDetails['patientNumber']=$relatedPatient->patientCode;
273			$delayDetails['visitType']=$visit->visitType;
274			$delayDetails['delayAcquisition']=$acquisitionDelay;
275
276			$delayArray[]=$delayDetails;
277			break;
278			}
279			}
280			}
281
282			return $delayArray;
283
284			}
285
286			/**
287			* Return specific data of all reviews
288			* @return array[]
289			*/
290			public function getReviewData() {
291
292			$createdVisits=$this->studyVisitManager->getUploadedVisits();
293
294			$reviewsJson=[];
295			foreach ($createdVisits as $visit) {
296
297			$reviews=[];
298
299			try {
300			$reviews[]=$visit->getReviewsObject(true);
301			}catch (Exception $e) { }
			0 ignored issues – show Coding Style Comprehensibility introduced 2020-03-31 22:19 UTC by Report Bug Copy Issue Report Consider adding a comment why this CATCH block is empty. Loading history...
302
303			try {
304			$reviewsReviewers=$visit->getReviewsObject(false);
305			foreach ($reviewsReviewers as $expertReview) {
306			$reviews[]=$expertReview;
307			}
308			}catch (Exception $e) { }
			0 ignored issues – show Coding Style Comprehensibility introduced 2020-03-31 22:19 UTC by Report Bug Copy Issue Report Consider adding a comment why this CATCH block is empty. Loading history...
309
310
311			foreach ($reviews as $review) {
312
313			if ($review->validated) {
314			$specificData=$review->getSpecificData();
315			$parentVisit=$review->getParentVisitObject();
316			$visitType=$parentVisit->visitType;
317			$reviewResult=$specificData;
318			$reviewResult['_reviewDate']=$review->reviewDate;
319			$reviewResult['_localForm']=boolval($review->isLocal);
320			$reviewResult['_adjudicationForm']=boolval($review->isAdjudication);
321			$reviewResult['_username']=$review->username;
322			$reviewResult['_center']=$parentVisit->getPatient()->getPatientCenter()->name;
323			$reviewResult['_visitType']=$visitType;
324
325			$reviewsJson['data'][$visitType][]=$reviewResult;
326			}
327
328			}
329			}
330
331			$visitTypePossible=$this->studyVisitManager->getVisitGroupObject()->getAllVisitTypesOfGroup();
332			foreach ($visitTypePossible as $visitType) {
333			$inputType=$visitType->getSpecificTableInputType();
334			$dataDetails[$visitType->name]=$inputType;
335			}
336
337			$reviewsJson['structureDetails']=$dataDetails;
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report 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? Loading history...
338
339			return $reviewsJson;
340			}
341
342
343			}
344

salimkanoun / GaelO

Statistics::getAcquisitionPetDelay() B last analyzed 2021-07-04 22:07 UTC

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Statistics::getAcquisitionPetDelay() B
last analyzed 2021-07-04 22:07 UTC