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

Tree::makeTreeFromPatients() A
last analyzed 2021-07-04 22:07 UTC

↳ Parent: Tree

Complexity

Conditions	4
Paths	5

Size

Total Lines	15
Code Lines	8

Duplication

Lines	0
Ratio	0 %

Importance

Changes	1
Bugs	0	Features	0

Metric	Value
eloc	8
nc	5
nop	1
dl	0
loc	15
c	1
b	0
f	0
cc	4
rs	10

<?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 for JSTree with patient's / visit's data
 *
 */

class Tree
{
  private $role;
  private $username;
  private $studyObject;
  private $linkpdo;

  public function __construct(string $role, string $username, string $study, PDO $linkpdo)
  {
	$this->linkpdo=$linkpdo;
	$this->role=$role;
	$this->username=$username;
	$this->studyObject=new Study($study, $linkpdo);
  }

  /**
   * Determine class value of Investigator and Controller visit item
   * to make specific color decoration depending on status of visit
   */
  private function determineClassOfVisit(Visit $visitObject): String
  {

	if ($this->role == User::INVESTIGATOR) {

	  //Add upload status / user form in class 
	  if ($visitObject->statusDone == Visit::DONE && $visitObject->uploadStatus == Visit::NOT_DONE && $visitObject->stateInvestigatorForm != Visit::DONE) {
		$class="NotBoth";
	  }else if ($visitObject->statusDone == Visit::DONE && $visitObject->stateInvestigatorForm != Visit::DONE) {
		$class="NotForm";
	  }else if ($visitObject->statusDone == Visit::DONE && $visitObject->uploadStatus == Visit::NOT_DONE) {
		$class="NotUpload";
	  }else {
		$class="OK";
	  }
	}else if ($this->role == User::CONTROLLER) {
	  if ($visitObject->stateQualityControl == Visit::QC_ACCEPTED || $visitObject->stateQualityControl == Visit::QC_REFUSED) {
		$class="OK";
	  }else if ($visitObject->stateQualityControl == Visit::QC_NOT_DONE || $visitObject->stateQualityControl == Visit::QC_WAIT_DEFINITVE_CONCLUSION) {
		$class="NotBoth";
	  }
	}else if ($this->role == User::REVIEWER) {
	  //Add status of review process (need to remove space from status string)
	  $class=str_replace(" ", "", $visitObject->reviewStatus); ;
	}

	return $class;

  }

  /**
   * Create visit entry in Tree from a visit Object
   */
  private function visitObjectToTreeObject(Visit $visitObject)
  {

	$jsonVisitLevel['id']=$visitObject->id_visit;

	$jsonVisitLevel['parent']=$visitObject->patientCode.'_'.$visitObject->visitGroupObject->groupModality;
	$jsonVisitLevel['icon']='/assets/images/report-icon.png';
	$jsonVisitLevel['text']=$visitObject->visitType;
	$jsonVisitLevel['level']='visit';
	$jsonVisitLevel['state']['opened']=false;

	if ($this->role == User::INVESTIGATOR || $this->role == User::CONTROLLER || $this->role == User::REVIEWER) {
	  //NB SI BESOIN ON PEUT AJOUTER UN CUSTOM ATRRIBUT A LA PLACE DE class
	  $attr['class']=$this->determineClassOfVisit($visitObject);

	  $jsonVisitLevel['li_attr']=$attr;
	}

	return $jsonVisitLevel;
  }

  /**
   * Create a patient entry in Tree
   */
  private function patientObjectToTreeObject(String $patientCode)
  {

	$jsonPatientLevel['id']=$patientCode;

	$jsonPatientLevel['parent']='#';
	$jsonPatientLevel['icon']='/assets/images/person-icon.png';
	$jsonPatientLevel['text']=$patientCode;
	$jsonPatientLevel['level']='patient';
	$jsonPatientLevel['state']['opened']=false;

	return $jsonPatientLevel;
  }

  /**
   * Create a Visit group entry in tree
   */
  private function visitGroupToTreeObject($patientCode, $groupModality)
  {

	$jsonGroupLevel['id']=$patientCode.'_'.$groupModality;

	$jsonGroupLevel['parent']=$patientCode;
	$jsonGroupLevel['icon']='/assets/images/person-icon.png';
	$jsonGroupLevel['text']=$groupModality;
	$jsonGroupLevel['level']='visit_group';
	$jsonGroupLevel['state']['opened']=true;


	return $jsonGroupLevel;
  }

  /**
   * sort Visits in key by modality
   */
  private function processVisitsArray($visitsArray)
  {

	$sortedModalities=[];

	foreach ($visitsArray as $visitObject) {
	  $sortedModalities[$visitObject->visitGroupObject->groupModality][]=$visitObject;
	}

	return $sortedModalities;
  }

  /**
   * Select visit from patients for some roles 
   */
  private function makeTreeFromPatients($patientsArray)
  {

	$resultTree=[];
	foreach ($patientsArray as $patientObject) {
	  //If investigator display all created visits
	  if ($this->role == User::INVESTIGATOR) $visitsArray=$patientObject->getAllCreatedPatientsVisits();
	  //if Reviewer display all QC accepted visits
	  if ($this->role == User::REVIEWER) $visitsArray=$patientObject->getAllQcDonePatientsVisits();
	  $stortedVisits=$this->processVisitsArray($visitsArray);

	  $resultTree[$patientObject->patientCode]['patientObject']=$patientObject;
	  $resultTree[$patientObject->patientCode]['modalities']=$stortedVisits;
	}

	return $resultTree;
  }

  /**
   * Sort an array of Visits by patient code
   */
  private function makeTreeFromVisits($visitsArray)
  {

	$resultTree=[];

	foreach ($visitsArray as $visitObject) {
	  $resultTree[$visitObject->patientCode]['patientObject']=$visitObject->getPatient();
	  $resultTree[$visitObject->patientCode]['modalities'][$visitObject->visitGroupObject->groupModality][]=$visitObject;
	}

	return $resultTree;
  }

  /**
   * Generate the final JSON tree by adding patient, modality and visit items
   */
  private function treeStructuretoJsonTree($treeStructure)
  {
	$jsonTree=[];
	foreach ($treeStructure as $patientCode => $patientData) {
	  $jsonTree[]=$this->patientObjectToTreeObject($patientCode);
	  foreach ($patientData['modalities'] as $modality => $visitObjects) {
		$jsonTree[]=$this->visitGroupToTreeObject($patientCode, $modality);
		foreach ($visitObjects as $visitObject) {
		  $jsonTree[]=$this->visitObjectToTreeObject($visitObject);
		}
	  }
	}

	return $jsonTree;
  }

  /**
   * Return JSON for JSTree according to role  (patient + Visit)
   * @return array
   */
  public function buildTree()
  {

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

	if ($this->role == User::INVESTIGATOR) {
	  //retrieve from DB the patient's list of the requested study and included in user's center or affiliated centers

	  $patientObjectArray=$this->studyObject->getPatientsLinkedToUserCenters($this->username);

	  $treeStructure=$this->makeTreeFromPatients($patientObjectArray);
	}else if ($this->role == User::CONTROLLER) {

	  $controllerVisitsArray=[];

	  foreach ($possibleVisitGroups as $visitGroup) {
		$studyVisitManager=$visitGroup->getStudyVisitManager();
		$visitsArray=$studyVisitManager->getVisitForControllerAction();
		array_push($controllerVisitsArray, ...$visitsArray);
	  }

	  $treeStructure=$this->makeTreeFromVisits($controllerVisitsArray);
	}else if ($this->role == User::MONITOR) {

	  $monitorVisitsArray=[];

	  foreach ($possibleVisitGroups as $visitGroup) {
		$studyVisitManager=$visitGroup->getStudyVisitManager();
		$visitsArray=$studyVisitManager->getCreatedVisits();
		array_push($monitorVisitsArray, ...$visitsArray);
	  }

	  $treeStructure=$this->makeTreeFromVisits($monitorVisitsArray);
	}else if ($this->role == User::REVIEWER) {
	  //SK attention une review pending fait reafficher toutes les reviews du patient
	  //que soit la modalite
	  //peut etre jouer avec le job des users pour filtrer le group de visite

	  $patientsList=[];
	  //For each visit group list patient having a least on visit awaiting review
	  foreach ($possibleVisitGroups as $visitGroup) {
		$studyVisitManager=$visitGroup->getStudyVisitManager();
		$visits=$studyVisitManager->getAwaitingReviewVisit($this->username);
		if (!empty($visits)) {
		  foreach ($visits as $visitObject) {
			$patientsList[$visitObject->patientCode]=$visitObject->patientCode;
		  }
		}
	  }
	  //extract unique patient array
	  $patientCodeArray=array_keys($patientsList);
	  $patientObjectArray=[];
	  foreach ($patientCodeArray as $patientCode) {
		$patientObjectArray[]=new Patient($patientCode, $this->linkpdo);
	  }

	  $treeStructure=$this->makeTreeFromPatients($patientObjectArray);

	}

	$jsonTree=$this->treeStructuretoJsonTree($treeStructure);


	return  $jsonTree;
  }
}


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 for JSTree with patient's / visit's data
18			*
19			*/
20
21			class Tree
22			{
23			private $role;
24			private $username;
25			private $studyObject;
26			private $linkpdo;
27
28			public function __construct(string $role, string $username, string $study, PDO $linkpdo)
29			{
30			$this->linkpdo=$linkpdo;
31			$this->role=$role;
32			$this->username=$username;
33			$this->studyObject=new Study($study, $linkpdo);
34			}
35
36			/**
37			* Determine class value of Investigator and Controller visit item
38			* to make specific color decoration depending on status of visit
39			*/
40			private function determineClassOfVisit(Visit $visitObject): String
41			{
42
43			if ($this->role == User::INVESTIGATOR) {
44
45			//Add upload status / user form in class
46			if ($visitObject->statusDone == Visit::DONE && $visitObject->uploadStatus == Visit::NOT_DONE && $visitObject->stateInvestigatorForm != Visit::DONE) {
47			$class="NotBoth";
48			}else if ($visitObject->statusDone == Visit::DONE && $visitObject->stateInvestigatorForm != Visit::DONE) {
49			$class="NotForm";
50			}else if ($visitObject->statusDone == Visit::DONE && $visitObject->uploadStatus == Visit::NOT_DONE) {
51			$class="NotUpload";
52			}else {
53			$class="OK";
54			}
55			}else if ($this->role == User::CONTROLLER) {
56			if ($visitObject->stateQualityControl == Visit::QC_ACCEPTED \|\| $visitObject->stateQualityControl == Visit::QC_REFUSED) {
57			$class="OK";
58			}else if ($visitObject->stateQualityControl == Visit::QC_NOT_DONE \|\| $visitObject->stateQualityControl == Visit::QC_WAIT_DEFINITVE_CONCLUSION) {
59			$class="NotBoth";
60			}
61			}else if ($this->role == User::REVIEWER) {
62			//Add status of review process (need to remove space from status string)
63			$class=str_replace(" ", "", $visitObject->reviewStatus); ;
64			}
65
66			return $class;
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report The variable `$class` does not seem to be defined for all execution paths leading up to this point. Loading history...
67			}
68
69			/**
70			* Create visit entry in Tree from a visit Object
71			*/
72			private function visitObjectToTreeObject(Visit $visitObject)
73			{
74
75			$jsonVisitLevel['id']=$visitObject->id_visit;
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report `$jsonVisitLevel` was never initialized. Although not strictly required by PHP, it is generally a good practice to add `$jsonVisitLevel = array();` before regardless. Loading history...
76			$jsonVisitLevel['parent']=$visitObject->patientCode.'_'.$visitObject->visitGroupObject->groupModality;
77			$jsonVisitLevel['icon']='/assets/images/report-icon.png';
78			$jsonVisitLevel['text']=$visitObject->visitType;
79			$jsonVisitLevel['level']='visit';
80			$jsonVisitLevel['state']['opened']=false;
81
82			if ($this->role == User::INVESTIGATOR \|\| $this->role == User::CONTROLLER \|\| $this->role == User::REVIEWER) {
83			//NB SI BESOIN ON PEUT AJOUTER UN CUSTOM ATRRIBUT A LA PLACE DE class
84			$attr['class']=$this->determineClassOfVisit($visitObject);
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report `$attr` was never initialized. Although not strictly required by PHP, it is generally a good practice to add `$attr = array();` before regardless. Loading history...
85			$jsonVisitLevel['li_attr']=$attr;
86			}
87
88			return $jsonVisitLevel;
89			}
90
91			/**
92			* Create a patient entry in Tree
93			*/
94			private function patientObjectToTreeObject(String $patientCode)
95			{
96
97			$jsonPatientLevel['id']=$patientCode;
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report `$jsonPatientLevel` was never initialized. Although not strictly required by PHP, it is generally a good practice to add `$jsonPatientLevel = array();` before regardless. Loading history...
98			$jsonPatientLevel['parent']='#';
99			$jsonPatientLevel['icon']='/assets/images/person-icon.png';
100			$jsonPatientLevel['text']=$patientCode;
101			$jsonPatientLevel['level']='patient';
102			$jsonPatientLevel['state']['opened']=false;
103
104			return $jsonPatientLevel;
105			}
106
107			/**
108			* Create a Visit group entry in tree
109			*/
110			private function visitGroupToTreeObject($patientCode, $groupModality)
111			{
112
113			$jsonGroupLevel['id']=$patientCode.'_'.$groupModality;
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report `$jsonGroupLevel` was never initialized. Although not strictly required by PHP, it is generally a good practice to add `$jsonGroupLevel = array();` before regardless. Loading history...
114			$jsonGroupLevel['parent']=$patientCode;
115			$jsonGroupLevel['icon']='/assets/images/person-icon.png';
116			$jsonGroupLevel['text']=$groupModality;
117			$jsonGroupLevel['level']='visit_group';
118			$jsonGroupLevel['state']['opened']=true;
119
120
121			return $jsonGroupLevel;
122			}
123
124			/**
125			* sort Visits in key by modality
126			*/
127			private function processVisitsArray($visitsArray)
128			{
129
130			$sortedModalities=[];
131
132			foreach ($visitsArray as $visitObject) {
133			$sortedModalities[$visitObject->visitGroupObject->groupModality][]=$visitObject;
134			}
135
136			return $sortedModalities;
137			}
138
139			/**
140			* Select visit from patients for some roles
141			*/
142			private function makeTreeFromPatients($patientsArray)
143			{
144
145			$resultTree=[];
146			foreach ($patientsArray as $patientObject) {
147			//If investigator display all created visits
148			if ($this->role == User::INVESTIGATOR) $visitsArray=$patientObject->getAllCreatedPatientsVisits();
149			//if Reviewer display all QC accepted visits
150			if ($this->role == User::REVIEWER) $visitsArray=$patientObject->getAllQcDonePatientsVisits();
151			$stortedVisits=$this->processVisitsArray($visitsArray);
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report The variable `$visitsArray` does not seem to be defined for all execution paths leading up to this point. Loading history...
152			$resultTree[$patientObject->patientCode]['patientObject']=$patientObject;
153			$resultTree[$patientObject->patientCode]['modalities']=$stortedVisits;
154			}
155
156			return $resultTree;
157			}
158
159			/**
160			* Sort an array of Visits by patient code
161			*/
162			private function makeTreeFromVisits($visitsArray)
163			{
164
165			$resultTree=[];
166
167			foreach ($visitsArray as $visitObject) {
168			$resultTree[$visitObject->patientCode]['patientObject']=$visitObject->getPatient();
169			$resultTree[$visitObject->patientCode]['modalities'][$visitObject->visitGroupObject->groupModality][]=$visitObject;
170			}
171
172			return $resultTree;
173			}
174
175			/**
176			* Generate the final JSON tree by adding patient, modality and visit items
177			*/
178			private function treeStructuretoJsonTree($treeStructure)
179			{
180			$jsonTree=[];
181			foreach ($treeStructure as $patientCode => $patientData) {
182			$jsonTree[]=$this->patientObjectToTreeObject($patientCode);
183			foreach ($patientData['modalities'] as $modality => $visitObjects) {
184			$jsonTree[]=$this->visitGroupToTreeObject($patientCode, $modality);
185			foreach ($visitObjects as $visitObject) {
186			$jsonTree[]=$this->visitObjectToTreeObject($visitObject);
187			}
188			}
189			}
190
191			return $jsonTree;
192			}
193
194			/**
195			* Return JSON for JSTree according to role (patient + Visit)
196			* @return array
197			*/
198			public function buildTree()
199			{
200
201			$possibleVisitGroups=$this->studyObject->getAllPossibleVisitGroups();
202
203			if ($this->role == User::INVESTIGATOR) {
204			//retrieve from DB the patient's list of the requested study and included in user's center or affiliated centers
205
206			$patientObjectArray=$this->studyObject->getPatientsLinkedToUserCenters($this->username);
207
208			$treeStructure=$this->makeTreeFromPatients($patientObjectArray);
209			}else if ($this->role == User::CONTROLLER) {
210
211			$controllerVisitsArray=[];
212
213			foreach ($possibleVisitGroups as $visitGroup) {
214			$studyVisitManager=$visitGroup->getStudyVisitManager();
215			$visitsArray=$studyVisitManager->getVisitForControllerAction();
216			array_push($controllerVisitsArray, ...$visitsArray);
217			}
218
219			$treeStructure=$this->makeTreeFromVisits($controllerVisitsArray);
220			}else if ($this->role == User::MONITOR) {
221
222			$monitorVisitsArray=[];
223
224			foreach ($possibleVisitGroups as $visitGroup) {
225			$studyVisitManager=$visitGroup->getStudyVisitManager();
226			$visitsArray=$studyVisitManager->getCreatedVisits();
227			array_push($monitorVisitsArray, ...$visitsArray);
228			}
229
230			$treeStructure=$this->makeTreeFromVisits($monitorVisitsArray);
231			}else if ($this->role == User::REVIEWER) {
232			//SK attention une review pending fait reafficher toutes les reviews du patient
233			//que soit la modalite
234			//peut etre jouer avec le job des users pour filtrer le group de visite
235
236			$patientsList=[];
237			//For each visit group list patient having a least on visit awaiting review
238			foreach ($possibleVisitGroups as $visitGroup) {
239			$studyVisitManager=$visitGroup->getStudyVisitManager();
240			$visits=$studyVisitManager->getAwaitingReviewVisit($this->username);
241			if (!empty($visits)) {
242			foreach ($visits as $visitObject) {
243			$patientsList[$visitObject->patientCode]=$visitObject->patientCode;
244			}
245			}
246			}
247			//extract unique patient array
248			$patientCodeArray=array_keys($patientsList);
249			$patientObjectArray=[];
250			foreach ($patientCodeArray as $patientCode) {
251			$patientObjectArray[]=new Patient($patientCode, $this->linkpdo);
252			}
253
254			$treeStructure=$this->makeTreeFromPatients($patientObjectArray);
255
256			}
257
258			$jsonTree=$this->treeStructuretoJsonTree($treeStructure);
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report The variable `$treeStructure` does not seem to be defined for all execution paths leading up to this point. Loading history...
259
260			return $jsonTree;
261			}
262			}
263

salimkanoun / GaelO

Tree::makeTreeFromPatients() A last analyzed 2021-07-04 22:07 UTC

Complexity

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Duplication

Importance

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Tree::makeTreeFromPatients() A
last analyzed 2021-07-04 22:07 UTC