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

Export_Study_Data::exportAssociatedFiles() A
last analyzed 2021-07-04 22:07 UTC

↳ Parent: Export_Study_Data

Complexity

Conditions	4
Paths	4

Size

Total Lines	26
Code Lines	11

Duplication

Lines	0
Ratio	0 %

Importance

Changes	1
Bugs	0	Features	0

Metric	Value
cc	4
eloc	11
c	1
b	0
f	0
nc	4
nop	0
dl	0
loc	26
rs	9.9

<?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
 */
//SK faire evoluer vers generator pour eviter sortie memoire ?

/**
 * Export all data relative to a study
 */
class Export_Study_Data
{

	public $studyObject;
	private $allcreatedVisits;

	public function __construct(Study $studyObject)
	{

		$this->studyObject=$studyObject;

		$this->allcreatedVisits=[];

		$visitGroupArray=$this->studyObject->getAllPossibleVisitGroups();

		foreach ($visitGroupArray as $visitGroup) {

			try {
				$modalityCreatedVisits=$this->studyObject->getStudySpecificGroupManager($visitGroup->groupModality)->getCreatedVisits();
				$modalityDeletedVisits=$this->studyObject->getStudySpecificGroupManager($visitGroup->groupModality)->getCreatedVisits(true);
				array_push($this->allcreatedVisits, ...$modalityCreatedVisits, ...$modalityDeletedVisits);
			}catch (Exception $e) { }

		}
	}

	/**
	 * Generate and fill the patients CSV
	 */
	public function exportPatientTable(): String
	{

		$patientCsv[]=array('Patient Code', 'Initials', 'Gender', 'Birthdate', 'Registration Date', 'Investigator Name', 'Center Code', 'Center Name', 'Country', 'Withdraw', 'Withdraw Reason', 'Withdraw Date');


		$patientsInStudy=$this->studyObject->getAllPatientsInStudy();
		foreach ($patientsInStudy as $patient) {
			$patientCenter=$patient->getPatientCenter();
			$patientCsv[]=array(
				$patient->patientCode, $patient->patientLastName.$patient->patientFirstName, $patient->patientGender,
				$patient->patientBirthDate, $patient->patientRegistrationDate, $patient->patientInvestigatorName, $patientCenter->code, $patientCenter->name, $patientCenter->countryName,
				$patient->patientWithdraw, $patient->patientWithdrawReason, $patient->patientWithdrawDateString
			);
		}

		$patientCsvString=$this->writeCsv($patientCsv);

		return $patientCsvString;
	}


	/**
	 * 
	 */
	public function exportAssociatedFiles()
	{

		$zip=new ZipArchive;
		$tempZip=tempnam(ini_get('upload_tmp_dir'), 'TMPZIPAF_');
		$zip->open($tempZip, ZipArchive::CREATE);
        

		foreach ($this->allcreatedVisits as $visitObject) {
			$reviewsObjects=$this->getAllreviewObjects($visitObject);

			foreach ($reviewsObjects as $reviewObject) {

				foreach ($reviewObject->associatedFiles as $associatedFileKey => $associatedFilePath) {
					$associatedFileLocation = $reviewObject->getAssociatedFilePath($associatedFileKey);
					$zip->addFile($associatedFileLocation);

				};

			}

		}

		$zip->close();

		return $tempZip;

	}

	/**
	 * Export the visit table relative to this study
	 */
	public function exportVisitTable(): String
	{

		$visitCSV=[];

		//Prepare visit CSV
		$visitCSV[]=array(
			'Patient Code', 'Visit Group', 'ID Visit', 'Code Status', 'Creator Name', 'Creator Date',
			'Type', 'Status', 'Reason For Not Done', 'Acquisition Date', 'Upload Status', 'Uploader',
			'Upload Date', 'State Investigator Form', 'State QC', 'QC done by', 'QC date', 'Review Status', 'Review Date', 'Review Conclusion', 'visit deleted'
		);

		foreach ($this->allcreatedVisits as $visit) {
			$codeStatus=$this->dertermineVisitStatusCode($visit);
			$visitCSV[]=array(
				$visit->patientCode, $visit->visitGroupObject->groupModality, $visit->id_visit, $codeStatus, $visit->creatorName, $visit->creationDate,
				$visit->visitType, $visit->statusDone, $visit->reasonForNotDone, $visit->acquisitionDate, $visit->uploadStatus, $visit->uploaderUsername,
				$visit->uploadDate, $visit->stateInvestigatorForm, $visit->stateQualityControl, $visit->controllerUsername, $visit->controlDate,
				$visit->reviewStatus, $visit->reviewConclusionDate, $visit->reviewConclusion, $visit->deleted
			);
		}

		$visitCsvString=$this->writeCsv($visitCSV);

		return $visitCsvString;
	}

	/**
	 * Export Data relative to Imaging stored data (Orthanc Stored Data)
	 */
	public function getImagingData()
	{

		//Prepare Orthanc Series data CSV
		$orthancCSV[]=array(

			'ID Visit', 'Study Orthanc ID',
			'Study UID', 'Study Description', 'Dicom Patient Name', 'Dicom Patient ID', 'Serie Description', 'modality', 'Acquisition Date Time',
			'Serie Orthanc ID', 'Serie UID', 'Instance Number', 'Manufacturer', 'Disk Size', 'Serie Number', 'Patient Weight', 'Injected_Activity', 'Injected_Dose', 'Radiopharmaceutical', 'Half Life', 'Injected Time', 'Deleted'
		);

		$imagingVisit=array_filter($this->allcreatedVisits, function(Visit $visitObject) {
			$inArrayBool=in_array(
				$visitObject->visitGroupObject->groupModality,
				array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_PET, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_RTSTRUCT)
			);
			return ($inArrayBool);
		});

		foreach ($imagingVisit as $visit) {

			$allSeries=$visit->getSeriesDetails();

			foreach ($allSeries as $serieObject) {
				$studyDetailsObject=$serieObject->studyDetailsObject;
				$orthancCSV[]=array(
					$studyDetailsObject->idVisit, $studyDetailsObject->studyOrthancId, $studyDetailsObject->studyUID,
					$studyDetailsObject->studyDescription, $studyDetailsObject->patientName, $studyDetailsObject->patientId, $serieObject->seriesDescription, $serieObject->modality, $serieObject->acquisitionDateTime, $serieObject->seriesOrthancID,
					$serieObject->serieUID, $serieObject->numberInstances, $serieObject->manufacturer, $serieObject->serieUncompressedDiskSize, $serieObject->seriesNumber, $serieObject->patientWeight, $serieObject->injectedActivity, $serieObject->injectedDose, $serieObject->radiopharmaceutical, $serieObject->halfLife, $serieObject->injectedDateTime, $serieObject->deleted
				);
			}
		}

		$orthancCsvFile=$this->writeCsv($orthancCSV);

		return $orthancCsvFile;
	}

	/**
	 * Return an associative array in which each CSV file reference will be stored
	 */
	public function getReviewData()
	{

		$mappedVisitByGroup=[];

		foreach ($this->allcreatedVisits as $visitObject) {
			$modality=$visitObject->visitGroupObject->groupModality;
			$visitName=$visitObject->visitType;
			$mappedVisitByGroup[$modality][$visitName][]=$visitObject;
		};

		foreach ($mappedVisitByGroup as $modality => $visitTypes) {

			$groupObject=$this->studyObject->getSpecificGroup($modality);

			foreach ($visitTypes as $visitType => $visitArray) {
				$csv=[];

				//Export Reviews
				$genericHeader=array('Patient Code', 'Visit Type', 'ID Visit', 'ID review', 'Reviewer', 'Review Date', 'Validated', 'Local Form', 'Adjudcation form', 'Review Deleted');

				$visitTypeObject=$groupObject->getVisitType($visitType);
				$specificFormTable=$visitTypeObject->getSpecificFormColumn();
				unset($specificFormTable[0]);

				$csv[]=array_merge($genericHeader, $specificFormTable);

				foreach ($visitArray as $visitObject) {

					array_push($csv, ...$this->getReviews($visitObject));
				}

				$reviewCsvFiles[$modality.'_'.$visitType]=$this->writeCsv($csv);
			}
		}

		return $reviewCsvFiles;

	}

	private function getAllreviewObjects(Visit $visitObject) : array {

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


		$expertReviews=[];

		try {
			$expertReviews=$visitObject->getReviewsObject(false, true);
		}catch (Exception $e) { }


		//Merge all reviews in an array
		$reviewObjects=array_merge($localReviews, $expertReviews);

		return $reviewObjects;

	}

	/**
	 * Merge local and review form and call getReviewDatas function to build one line of the CSV array for each review
	 */
	private function getReviews(Visit $visitObject): array
	{

		$reviewObjects=$this->getAllreviewObjects($visitObject);

		$csv=[];
		foreach ($reviewObjects as $reviewObject) {
			$patientCode=$visitObject->patientCode;
			$visitType=$visitObject->visitType;
			$reviewData=$this->getReviewDatas($reviewObject);
			$csv[]=[$patientCode, $visitType, ...$reviewData];
		}

		return $csv;
	}

	/**
	 * Merge generic and specific column to build a CSV array
	 */
	private function getReviewDatas(Review $review): array
	{
		//Add to final map
		$reviewDatas=$this->getGenericData($review);
		$specificData=$review->getSpecificData();
		unset($specificData["id_review"]);
		$specificDataArray = [];
		if( !empty($specificData) ){
			$specificDataArray = array_values($specificData);
		}
		$reviewLine=[...$reviewDatas, ...$specificDataArray];

		return $reviewLine;
	}

	/**
	 * Build the generic part of the review array
	 */
	private function getGenericData(Review $review) : array
	{
		//Add to final map
		$reviewDatas=array(
			$review->id_visit, $review->id_review,
			$review->username, $review->reviewDate, $review->validated, $review->isLocal, $review->isAdjudication, $review->deleted
		);

		return $reviewDatas;
	}

	/**
	 * Write CSV Array to a temporary file
	 */
	private function writeCsv($csvArray) : String
	{

		$tempCsv=tempnam(ini_get('upload_tmp_dir'), 'TMPCSV_');
		$fichier_csv=fopen($tempCsv, 'w');
		foreach ($csvArray as $fields) {
			fputcsv($fichier_csv, $fields);
		}
		fclose($fichier_csv);

		return $tempCsv;
	}


	/**
	 * Return Code Status
	 * 0 Visit not Done
	 * 1 Done but DICOM and Form not sent
	 * 2 Done but upload not done (form sent)
	 * 3 done but investigator form not done (dicom sent)
	 * 4 QC not done
	 * 5 QC corrective action
	 * 6 QC refused
	 * 7 Review Not Done
	 * 8 Review ongoing
	 * 9 Review Wait adjudication
	 * 10 review done
	 * -1 If any of these case (should not happen)
	 * @param Visit $visitObject
	 * @return number
	 */
	private function dertermineVisitStatusCode(Visit $visitObject) : int
	{

		if ($visitObject->statusDone == Visit::NOT_DONE) {
			return 0;
		}else if ($visitObject->uploadStatus == Visit::NOT_DONE || $visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
			if ($visitObject->uploadStatus == Visit::NOT_DONE && $visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
				return 1;
			}else if ($visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
				return 3;
			}else if ($visitObject->uploadStatus == Visit::NOT_DONE) {
				return 2;
			}
interface ReturnsInt {
    public function returnsIntHinted(): int;
}

class MyClass implements ReturnsInt {
    public function returnsIntHinted(): int
    {
        if (foo()) {
            return 123;
        }
        // here: null is implicitly returned
    }
}
		}else if ($visitObject->qcStatus == Visit::QC_NOT_DONE) {
			return 4;
		}else if ($visitObject->qcStatus == Visit::QC_CORRECTIVE_ACTION_ASKED) {
			return 5;
		}else if ($visitObject->qcStatus == Visit::QC_REFUSED) {
			return 6;
		}else if ($visitObject->reviewStatus == Visit::NOT_DONE) {
			return 7;
		}else if ($visitObject->reviewStatus == Visit::REVIEW_ONGOING) {
			return 8;
		}else if ($visitObject->reviewStatus == Visit::REVIEW_WAIT_ADJUDICATION) {
			return 9;
		}else if ($visitObject->reviewStatus == Visit::REVIEW_DONE) {
			return 10;
		}else {
			//If none of these case return -1, should not happen
			return -1;
		}
	}

}


1			<?php
2
3			/**
4			Copyright (C) 2018-2020 KANOUN Salim
5			This program is free software; you can redistribute it and/or modify
6			it under the terms of the Affero GNU General Public v.3 License as published by
7			the Free Software Foundation;
8			This program is distributed in the hope that it will be useful,
9			but WITHOUT ANY WARRANTY; without even the implied warranty of
10			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11			Affero GNU General Public Public for more details.
12			You should have received a copy of the Affero GNU General Public Public along
13			with this program; if not, write to the Free Software Foundation, Inc.,
14			51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
15			*/
16			//SK faire evoluer vers generator pour eviter sortie memoire ?
17
18			/**
19			* Export all data relative to a study
20			*/
21			class Export_Study_Data
22			{
23
24			public $studyObject;
25			private $allcreatedVisits;
26
27			public function __construct(Study $studyObject)
28			{
29
30			$this->studyObject=$studyObject;
31
32			$this->allcreatedVisits=[];
33
34			$visitGroupArray=$this->studyObject->getAllPossibleVisitGroups();
35
36			foreach ($visitGroupArray as $visitGroup) {
37
38			try {
39			$modalityCreatedVisits=$this->studyObject->getStudySpecificGroupManager($visitGroup->groupModality)->getCreatedVisits();
40			$modalityDeletedVisits=$this->studyObject->getStudySpecificGroupManager($visitGroup->groupModality)->getCreatedVisits(true);
41			array_push($this->allcreatedVisits, ...$modalityCreatedVisits, ...$modalityDeletedVisits);
42			}catch (Exception $e) { }
			0 ignored issues – show Coding Style Comprehensibility introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report Consider adding a comment why this CATCH block is empty. Loading history...
43			}
44			}
45
46			/**
47			* Generate and fill the patients CSV
48			*/
49			public function exportPatientTable(): String
50			{
51
52			$patientCsv[]=array('Patient Code', 'Initials', 'Gender', 'Birthdate', 'Registration Date', 'Investigator Name', 'Center Code', 'Center Name', 'Country', 'Withdraw', 'Withdraw Reason', 'Withdraw Date');
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report `$patientCsv` was never initialized. Although not strictly required by PHP, it is generally a good practice to add `$patientCsv = array();` before regardless. Loading history...
53
54			$patientsInStudy=$this->studyObject->getAllPatientsInStudy();
55			foreach ($patientsInStudy as $patient) {
56			$patientCenter=$patient->getPatientCenter();
57			$patientCsv[]=array(
58			$patient->patientCode, $patient->patientLastName.$patient->patientFirstName, $patient->patientGender,
59			$patient->patientBirthDate, $patient->patientRegistrationDate, $patient->patientInvestigatorName, $patientCenter->code, $patientCenter->name, $patientCenter->countryName,
60			$patient->patientWithdraw, $patient->patientWithdrawReason, $patient->patientWithdrawDateString
61			);
62			}
63
64			$patientCsvString=$this->writeCsv($patientCsv);
65
66			return $patientCsvString;
67			}
68
69
70			/**
71			*
72			*/
73			public function exportAssociatedFiles()
74			{
75
76			$zip=new ZipArchive;
77			$tempZip=tempnam(ini_get('upload_tmp_dir'), 'TMPZIPAF_');
78			$zip->open($tempZip, ZipArchive::CREATE);
79
80
81			foreach ($this->allcreatedVisits as $visitObject) {
82			$reviewsObjects=$this->getAllreviewObjects($visitObject);
83
84			foreach ($reviewsObjects as $reviewObject) {
85
86			foreach ($reviewObject->associatedFiles as $associatedFileKey => $associatedFilePath) {
87			$associatedFileLocation = $reviewObject->getAssociatedFilePath($associatedFileKey);
88			$zip->addFile($associatedFileLocation);
89
90			};
91
92			}
93
94			}
95
96			$zip->close();
97
98			return $tempZip;
99
100			}
101
102			/**
103			* Export the visit table relative to this study
104			*/
105			public function exportVisitTable(): String
106			{
107
108			$visitCSV=[];
109
110			//Prepare visit CSV
111			$visitCSV[]=array(
112			'Patient Code', 'Visit Group', 'ID Visit', 'Code Status', 'Creator Name', 'Creator Date',
113			'Type', 'Status', 'Reason For Not Done', 'Acquisition Date', 'Upload Status', 'Uploader',
114			'Upload Date', 'State Investigator Form', 'State QC', 'QC done by', 'QC date', 'Review Status', 'Review Date', 'Review Conclusion', 'visit deleted'
115			);
116
117			foreach ($this->allcreatedVisits as $visit) {
118			$codeStatus=$this->dertermineVisitStatusCode($visit);
119			$visitCSV[]=array(
120			$visit->patientCode, $visit->visitGroupObject->groupModality, $visit->id_visit, $codeStatus, $visit->creatorName, $visit->creationDate,
121			$visit->visitType, $visit->statusDone, $visit->reasonForNotDone, $visit->acquisitionDate, $visit->uploadStatus, $visit->uploaderUsername,
122			$visit->uploadDate, $visit->stateInvestigatorForm, $visit->stateQualityControl, $visit->controllerUsername, $visit->controlDate,
123			$visit->reviewStatus, $visit->reviewConclusionDate, $visit->reviewConclusion, $visit->deleted
124			);
125			}
126
127			$visitCsvString=$this->writeCsv($visitCSV);
128
129			return $visitCsvString;
130			}
131
132			/**
133			* Export Data relative to Imaging stored data (Orthanc Stored Data)
134			*/
135			public function getImagingData()
136			{
137
138			//Prepare Orthanc Series data CSV
139			$orthancCSV[]=array(
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report `$orthancCSV` was never initialized. Although not strictly required by PHP, it is generally a good practice to add `$orthancCSV = array();` before regardless. Loading history...
140			'ID Visit', 'Study Orthanc ID',
141			'Study UID', 'Study Description', 'Dicom Patient Name', 'Dicom Patient ID', 'Serie Description', 'modality', 'Acquisition Date Time',
142			'Serie Orthanc ID', 'Serie UID', 'Instance Number', 'Manufacturer', 'Disk Size', 'Serie Number', 'Patient Weight', 'Injected_Activity', 'Injected_Dose', 'Radiopharmaceutical', 'Half Life', 'Injected Time', 'Deleted'
143			);
144
145			$imagingVisit=array_filter($this->allcreatedVisits, function(Visit $visitObject) {
146			$inArrayBool=in_array(
147			$visitObject->visitGroupObject->groupModality,
148			array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_PET, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_RTSTRUCT)
149			);
150			return ($inArrayBool);
151			});
152
153			foreach ($imagingVisit as $visit) {
154
155			$allSeries=$visit->getSeriesDetails();
156
157			foreach ($allSeries as $serieObject) {
158			$studyDetailsObject=$serieObject->studyDetailsObject;
159			$orthancCSV[]=array(
160			$studyDetailsObject->idVisit, $studyDetailsObject->studyOrthancId, $studyDetailsObject->studyUID,
161			$studyDetailsObject->studyDescription, $studyDetailsObject->patientName, $studyDetailsObject->patientId, $serieObject->seriesDescription, $serieObject->modality, $serieObject->acquisitionDateTime, $serieObject->seriesOrthancID,
162			$serieObject->serieUID, $serieObject->numberInstances, $serieObject->manufacturer, $serieObject->serieUncompressedDiskSize, $serieObject->seriesNumber, $serieObject->patientWeight, $serieObject->injectedActivity, $serieObject->injectedDose, $serieObject->radiopharmaceutical, $serieObject->halfLife, $serieObject->injectedDateTime, $serieObject->deleted
163			);
164			}
165			}
166
167			$orthancCsvFile=$this->writeCsv($orthancCSV);
168
169			return $orthancCsvFile;
170			}
171
172			/**
173			* Return an associative array in which each CSV file reference will be stored
174			*/
175			public function getReviewData()
176			{
177
178			$mappedVisitByGroup=[];
179
180			foreach ($this->allcreatedVisits as $visitObject) {
181			$modality=$visitObject->visitGroupObject->groupModality;
182			$visitName=$visitObject->visitType;
183			$mappedVisitByGroup[$modality][$visitName][]=$visitObject;
184			};
185
186			foreach ($mappedVisitByGroup as $modality => $visitTypes) {
187
188			$groupObject=$this->studyObject->getSpecificGroup($modality);
189
190			foreach ($visitTypes as $visitType => $visitArray) {
191			$csv=[];
192
193			//Export Reviews
194			$genericHeader=array('Patient Code', 'Visit Type', 'ID Visit', 'ID review', 'Reviewer', 'Review Date', 'Validated', 'Local Form', 'Adjudcation form', 'Review Deleted');
195
196			$visitTypeObject=$groupObject->getVisitType($visitType);
197			$specificFormTable=$visitTypeObject->getSpecificFormColumn();
198			unset($specificFormTable[0]);
199
200			$csv[]=array_merge($genericHeader, $specificFormTable);
201
202			foreach ($visitArray as $visitObject) {
203
204			array_push($csv, ...$this->getReviews($visitObject));
205			}
206
207			$reviewCsvFiles[$modality.'_'.$visitType]=$this->writeCsv($csv);
208			}
209			}
210
211			return $reviewCsvFiles;
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:19 UTC by Report Bug Copy Issue Report The variable `$reviewCsvFiles` does not seem to be defined for all execution paths leading up to this point. Loading history...
212			}
213
214			private function getAllreviewObjects(Visit $visitObject) : array {
215
216			$localReviews=[];
217			try {
218			$localReviews[]=$visitObject->getReviewsObject(true);
219			}catch (Exception $e) { }
			0 ignored issues – show Coding Style Comprehensibility introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report Consider adding a comment why this CATCH block is empty. Loading history...
220
221			$expertReviews=[];
			0 ignored issues – show Unused Code introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report The assignment to `$expertReviews` is dead and can be removed. Loading history...
222			try {
223			$expertReviews=$visitObject->getReviewsObject(false, true);
224			}catch (Exception $e) { }
			0 ignored issues – show Coding Style Comprehensibility introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report Consider adding a comment why this CATCH block is empty. Loading history...
225
226			//Merge all reviews in an array
227			$reviewObjects=array_merge($localReviews, $expertReviews);
228
229			return $reviewObjects;
230
231			}
232
233			/**
234			* Merge local and review form and call getReviewDatas function to build one line of the CSV array for each review
235			*/
236			private function getReviews(Visit $visitObject): array
237			{
238
239			$reviewObjects=$this->getAllreviewObjects($visitObject);
240
241			$csv=[];
242			foreach ($reviewObjects as $reviewObject) {
243			$patientCode=$visitObject->patientCode;
244			$visitType=$visitObject->visitType;
245			$reviewData=$this->getReviewDatas($reviewObject);
246			$csv[]=[$patientCode, $visitType, ...$reviewData];
247			}
248
249			return $csv;
250			}
251
252			/**
253			* Merge generic and specific column to build a CSV array
254			*/
255			private function getReviewDatas(Review $review): array
256			{
257			//Add to final map
258			$reviewDatas=$this->getGenericData($review);
259			$specificData=$review->getSpecificData();
260			unset($specificData["id_review"]);
261			$specificDataArray = [];
262			if( !empty($specificData) ){
263			$specificDataArray = array_values($specificData);
264			}
265			$reviewLine=[...$reviewDatas, ...$specificDataArray];
266
267			return $reviewLine;
268			}
269
270			/**
271			* Build the generic part of the review array
272			*/
273			private function getGenericData(Review $review) : array
274			{
275			//Add to final map
276			$reviewDatas=array(
277			$review->id_visit, $review->id_review,
278			$review->username, $review->reviewDate, $review->validated, $review->isLocal, $review->isAdjudication, $review->deleted
279			);
280
281			return $reviewDatas;
282			}
283
284			/**
285			* Write CSV Array to a temporary file
286			*/
287			private function writeCsv($csvArray) : String
288			{
289
290			$tempCsv=tempnam(ini_get('upload_tmp_dir'), 'TMPCSV_');
291			$fichier_csv=fopen($tempCsv, 'w');
292			foreach ($csvArray as $fields) {
293			fputcsv($fichier_csv, $fields);
294			}
295			fclose($fichier_csv);
296
297			return $tempCsv;
298			}
299
300
301			/**
302			* Return Code Status
303			* 0 Visit not Done
304			* 1 Done but DICOM and Form not sent
305			* 2 Done but upload not done (form sent)
306			* 3 done but investigator form not done (dicom sent)
307			* 4 QC not done
308			* 5 QC corrective action
309			* 6 QC refused
310			* 7 Review Not Done
311			* 8 Review ongoing
312			* 9 Review Wait adjudication
313			* 10 review done
314			* -1 If any of these case (should not happen)
315			* @param Visit $visitObject
316			* @return number
317			*/
318			private function dertermineVisitStatusCode(Visit $visitObject) : int
319			{
320
321			if ($visitObject->statusDone == Visit::NOT_DONE) {
322			return 0;
323			}else if ($visitObject->uploadStatus == Visit::NOT_DONE \|\| $visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
324			if ($visitObject->uploadStatus == Visit::NOT_DONE && $visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
325			return 1;
326			}else if ($visitObject->stateInvestigatorForm == Visit::NOT_DONE) {
327			return 3;
328			}else if ($visitObject->uploadStatus == Visit::NOT_DONE) {
329			return 2;
330			}
			0 ignored issues – show Bug Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report The function implicitly returns `null` when the `if` condition on line 328 is `false`. This is incompatible with the type-hinted return `integer`. Consider adding a return statement or allowing `null` as return value. For hinted functions/methods where all return statements with the correct type are only reachable via conditions, ?null? gets implicitly returned which may be incompatible with the hinted type. Let?s take a look at an example: interface ReturnsInt { public function returnsIntHinted(): int; } class MyClass implements ReturnsInt { public function returnsIntHinted(): int { if (foo()) { return 123; } // here: null is implicitly returned } } Loading history...
331			}else if ($visitObject->qcStatus == Visit::QC_NOT_DONE) {
332			return 4;
333			}else if ($visitObject->qcStatus == Visit::QC_CORRECTIVE_ACTION_ASKED) {
334			return 5;
335			}else if ($visitObject->qcStatus == Visit::QC_REFUSED) {
336			return 6;
337			}else if ($visitObject->reviewStatus == Visit::NOT_DONE) {
338			return 7;
339			}else if ($visitObject->reviewStatus == Visit::REVIEW_ONGOING) {
340			return 8;
341			}else if ($visitObject->reviewStatus == Visit::REVIEW_WAIT_ADJUDICATION) {
342			return 9;
343			}else if ($visitObject->reviewStatus == Visit::REVIEW_DONE) {
344			return 10;
345			}else {
346			//If none of these case return -1, should not happen
347			return -1;
348			}
349			}
350
351			}
352

salimkanoun / GaelO

Export_Study_Data::exportAssociatedFiles() A last analyzed 2021-07-04 22:07 UTC

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Export_Study_Data::exportAssociatedFiles() A
last analyzed 2021-07-04 22:07 UTC