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

Study::getAllAwaitingReviewImagingVisit() A
last analyzed 2021-07-04 22:07 UTC

↳ Parent: Study

Complexity

Conditions	3
Paths	3

Size

Total Lines	15
Code Lines	7

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	7
nc	3
nop	1
dl	0
loc	15
c	0
b	0
f	0
cc	3
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
 */

/**
 * Access data for a study
 */

Class Study {
    
	private $linkpdo;
	public $study;
	public $patientCodePrefix;
    
	public function __construct(String $study, PDO $linkpdo) {

		$this->linkpdo=$linkpdo;
		$connecter=$this->linkpdo->prepare('SELECT * FROM studies WHERE name=:study');
		$connecter->execute(array(
				"study" => $study,
		));
		$result=$connecter->fetch(PDO::FETCH_ASSOC);

		$this->study=$result['name'];
		$this->patientCodePrefix=$result['patient_code_prefix'];
        
        
	}

	public function getPatientsLinkedToUserCenters($username)
	{
		$patients=$this->linkpdo->prepare(' SELECT patients.code
            FROM   patients
            WHERE  patients.center IN (SELECT affiliated_centers.center
                FROM   affiliated_centers
                WHERE  affiliated_centers.username = :username
                UNION
                SELECT users.center
                FROM   users
                WHERE  users.username = :username)
                AND study = :study
                GROUP  BY patients.code');

		$patients->execute(array(
			'username' => $username,
			'study' => $this->study
		));

		$patientsCodes=$patients->fetchAll(PDO::FETCH_COLUMN);

		$patientObjectsArray=[];

		foreach ($patientsCodes as $patientCode) {
			$patientObjectsArray[]=new Patient($patientCode, $this->linkpdo);
		}

		return $patientObjectsArray;
	}

	public function getAllCreatedVisits(bool $deleted=false) {

		$possibleStudyGroups=$this->getAllPossibleVisitGroups();

		$visitsObjectArray=[];

		foreach ($possibleStudyGroups as $studyGroup) {
			$createdVisits=$studyGroup->getStudyVisitManager()->getCreatedVisits($deleted);
			array_push($visitsObjectArray, ...$createdVisits);
		}

		return $visitsObjectArray;

	}

	public function getAllAwaitingUploadImagingVisit() {

		$possibleStudyGroups=$this->getAllPossibleVisitGroups();
		$visitsObjectArray=[];

		foreach ($possibleStudyGroups as $studyGroup) {
			if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET, Visit_Group::GROUP_MODALITY_RTSTRUCT))) {
				$awaitingUploadVisits=$studyGroup->getStudyVisitManager()->getAwaitingUploadVisit();
				array_push($visitsObjectArray, ...$awaitingUploadVisits);
			}
            
            
		}
        
		return $visitsObjectArray;

	}

	public function getAllAwaitingReviewImagingVisit($username=null) {

		$possibleStudyGroups=$this->getAllPossibleVisitGroups();
		$visitsObjectArray=[];

		foreach ($possibleStudyGroups as $studyGroup) {
			if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET, Visit_Group::GROUP_MODALITY_RTSTRUCT))) {
				$awaitingReviewVisits=$studyGroup->getStudyVisitManager()->getAwaitingReviewVisit($username);
				array_push($visitsObjectArray, ...$awaitingReviewVisits);
			}
            
            
		}
        
		return $visitsObjectArray;

	}

	public function getAllUploadedImagingVisits() {

		$possibleStudyGroups=$this->getAllPossibleVisitGroups();
		$visitsObjectArray=[];

		foreach ($possibleStudyGroups as $studyGroup) {
			if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET, Visit_Group::GROUP_MODALITY_RTSTRUCT))) {
				$uploadedVisits=$studyGroup->getStudyVisitManager()->getUploadedVisits();
				array_push($visitsObjectArray, ...$uploadedVisits);
			}
            
            
		}
        
		return $visitsObjectArray;

	}

	public function isHavingAwaitingReviewImagingVisit($username=null) {
		$awaitingVisits=$this->getAllAwaitingReviewImagingVisit($username);
		$havingAwaitingReview=(sizeof($awaitingVisits) > 0);
		return $havingAwaitingReview;
	}



	public function getAllPossibleVisitGroups() {

		$allGroupsType=$this->linkpdo->prepare('SELECT id FROM visit_group WHERE study = :study');
		$allGroupsType->execute(array('study' => $this->study));
		$allGroupsIds=$allGroupsType->fetchall(PDO::FETCH_COLUMN);
        
		$visitGroupArray=[];
		foreach ($allGroupsIds as $groupId) {
			$visitGroupArray[]=new Visit_Group($this->linkpdo, $groupId);
		}
        
		return $visitGroupArray;

	}

	public function getSpecificGroup(String $groupModality) : Visit_Group {

		$groupQuery=$this->linkpdo->prepare('SELECT id FROM visit_group WHERE study = :study AND group_modality=:groupModality');
		$groupQuery->execute(array('study' => $this->study, 'groupModality'=> $groupModality));
		$groupId=$groupQuery->fetch(PDO::FETCH_COLUMN);
        
		return new Visit_Group($this->linkpdo, $groupId);

	}

	public function getStudySpecificGroupManager(String $groupModality) : Group_Visit_Manager {

		$visitGroup=$this->getSpecificGroup($groupModality);
        
		return new Group_Visit_Manager($this, $visitGroup, $this->linkpdo);

	}

	public function getReviewManager() : Study_Review_Manager {
		return new Study_Review_Manager($this);
	}

	public function getExportStudyData() : Export_Study_Data{
		return new Export_Study_Data($this);
	}
    
	public function getAllPatientsInStudy() {
		$allPatientQuery=$this->linkpdo->prepare('SELECT code FROM patients WHERE study = :study');
		$allPatientQuery->execute(array('study' => $this->study));
		$allPatients=$allPatientQuery->fetchall(PDO::FETCH_COLUMN);
        
		$patientObjectArray=[];
		foreach ($allPatients as $patient) {
			$patientObjectArray[]=new Patient($patient, $this->linkpdo);
		}
        
		return $patientObjectArray;
        
	}
    
	public function getDocumentation(String $role) {
		if ($role == User::SUPERVISOR) {
			$documentationQuery=$this->linkpdo->prepare("SELECT id_documentation FROM documentation
                                                    WHERE study = :study");
            
		}else {
			$documentationQuery=$this->linkpdo->prepare("SELECT id_documentation FROM documentation
                                                    WHERE study = :study
                                                    AND ".$role."= 1 AND deleted=0");
            
		}
        
		$documentationQuery->execute(array('study' => $this->study));
		$documentationAnswers=$documentationQuery->fetchAll(PDO::FETCH_COLUMN);
        
		$documentationObjects=[];
		foreach ($documentationAnswers as $documentationId) {
			$documentationObjects[]=new Documentation($this->linkpdo, $documentationId);
		}
		return $documentationObjects;
	}
    
	/**
	 * Return userObject array for all users having role in the study
	 * @return User[]
	 */
	public function getUsersWithRoleInStudy() {
		$req=$this->linkpdo->prepare('SELECT DISTINCT users.username FROM roles,users
                                  WHERE roles.username=users.username
                                  AND roles.study=:study');
		$req->execute(array('study' => $this->study));
		$answers=$req->fetchAll(PDO::FETCH_COLUMN);
        
		$usersObjects=[];
		foreach ($answers as $username) {
			$usersObjects[]=new User($username, $this->linkpdo);
		}
		return $usersObjects;
        
	}
    
	public function getUsersByRoleInStudy(String $role) {
		$req=$this->linkpdo->prepare('SELECT username FROM roles
									   WHERE study=:study AND name=:role ');
		$req->execute(array('study' => $this->study, 'role'=>$role));
		$answers=$req->fetchAll(PDO::FETCH_COLUMN);
        
		$usersObjects=[];
		foreach ($answers as $username) {
			$usersObjects[]=new User($username, $this->linkpdo);
		}
		return $usersObjects;
        
	}
    
	public function getAllRolesByUsers() {
		$roles_query=$this->linkpdo->prepare('SELECT * FROM roles WHERE study=:study');
		$roles_query->execute(array('study'=>$this->study));
		$definedRoles=$roles_query->fetchall(PDO::FETCH_ASSOC);
        
		foreach ($definedRoles as $role) {
			$rolesList[$role['username']][]=$role['name'];
		}
		return $rolesList;

	}

	public function getStatistics(String $modality) {
		return new Statistics($this, $modality);
	}
    
	public function changeStudyActivation(bool $activated) {
		$req=$this->linkpdo->prepare('UPDATE studies SET
    								active = :active
						        WHERE name = :study');
		$req->execute(array('study'=> $this->study, 'active'=>intval($activated)));
	}
    
	public function isOriginalOrthancNeverKnown($anonFromOrthancStudyId) {

		$connecter=$this->linkpdo->prepare('SELECT Study_Orthanc_ID FROM visits 
                                                INNER JOIN visit_type ON 
                                                (visit_type.id=visits.visit_type_id 
                                                AND visit_type.group_id IN (SELECT id FROM visit_group WHERE study = :study))
                                                INNER JOIN orthanc_studies ON (orthanc_studies.id_visit=visits.id_visit) 
                                            AND orthanc_studies.Anon_From_Orthanc_ID=:Anon_From_Orthanc_ID 
                                            AND orthanc_studies.deleted=0 
                                            AND visits.deleted=0'
											);
		$connecter->execute(array(
			"study" => $this->study,
			"Anon_From_Orthanc_ID"=>$anonFromOrthancStudyId
		));
		$result=$connecter->fetchAll(PDO::FETCH_COLUMN);
        
		if (count($result) > 0) return false; else return true;
        
	}
    
	public static function createStudy(string $studyName, $patientCodePrefix, PDO $linkpdo) {
        
		$req=$linkpdo->prepare('INSERT INTO studies (name, patient_code_prefix) VALUES(:studyName, :patientCodePrefix) ');
        
		$req->execute(array(
			'studyName' => $studyName,
			'patientCodePrefix' => $patientCodePrefix
		));
        
	}
    
}

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			* Access data for a study
18			*/
19
20			Class Study {
21
22			private $linkpdo;
23			public $study;
24			public $patientCodePrefix;
25
26			public function __construct(String $study, PDO $linkpdo) {
27
28			$this->linkpdo=$linkpdo;
29			$connecter=$this->linkpdo->prepare('SELECT * FROM studies WHERE name=:study');
30			$connecter->execute(array(
31			"study" => $study,
32			));
33			$result=$connecter->fetch(PDO::FETCH_ASSOC);
34
35			$this->study=$result['name'];
36			$this->patientCodePrefix=$result['patient_code_prefix'];
37
38
39			}
40
41			public function getPatientsLinkedToUserCenters($username)
42			{
43			$patients=$this->linkpdo->prepare(' SELECT patients.code
44			FROM patients
45			WHERE patients.center IN (SELECT affiliated_centers.center
46			FROM affiliated_centers
47			WHERE affiliated_centers.username = :username
48			UNION
49			SELECT users.center
50			FROM users
51			WHERE users.username = :username)
52			AND study = :study
53			GROUP BY patients.code');
54
55			$patients->execute(array(
56			'username' => $username,
57			'study' => $this->study
58			));
59
60			$patientsCodes=$patients->fetchAll(PDO::FETCH_COLUMN);
61
62			$patientObjectsArray=[];
63
64			foreach ($patientsCodes as $patientCode) {
65			$patientObjectsArray[]=new Patient($patientCode, $this->linkpdo);
66			}
67
68			return $patientObjectsArray;
69			}
70
71			public function getAllCreatedVisits(bool $deleted=false) {
72
73			$possibleStudyGroups=$this->getAllPossibleVisitGroups();
74
75			$visitsObjectArray=[];
76
77			foreach ($possibleStudyGroups as $studyGroup) {
78			$createdVisits=$studyGroup->getStudyVisitManager()->getCreatedVisits($deleted);
79			array_push($visitsObjectArray, ...$createdVisits);
80			}
81
82			return $visitsObjectArray;
83
84			}
85
86			public function getAllAwaitingUploadImagingVisit() {
87
88			$possibleStudyGroups=$this->getAllPossibleVisitGroups();
89			$visitsObjectArray=[];
90
91			foreach ($possibleStudyGroups as $studyGroup) {
92			if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET, Visit_Group::GROUP_MODALITY_RTSTRUCT))) {
93			$awaitingUploadVisits=$studyGroup->getStudyVisitManager()->getAwaitingUploadVisit();
94			array_push($visitsObjectArray, ...$awaitingUploadVisits);
95			}
96
97
98			}
99
100			return $visitsObjectArray;
101
102			}
103
104			public function getAllAwaitingReviewImagingVisit($username=null) {
105
106			$possibleStudyGroups=$this->getAllPossibleVisitGroups();
107			$visitsObjectArray=[];
108
109			foreach ($possibleStudyGroups as $studyGroup) {
110			if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET, Visit_Group::GROUP_MODALITY_RTSTRUCT))) {
111			$awaitingReviewVisits=$studyGroup->getStudyVisitManager()->getAwaitingReviewVisit($username);
112			array_push($visitsObjectArray, ...$awaitingReviewVisits);
113			}
114
115
116			}
117
118			return $visitsObjectArray;
119
120			}
121
122			public function getAllUploadedImagingVisits() {
123
124			$possibleStudyGroups=$this->getAllPossibleVisitGroups();
125			$visitsObjectArray=[];
126
127			foreach ($possibleStudyGroups as $studyGroup) {
128			if (in_array($studyGroup->groupModality, array(Visit_Group::GROUP_MODALITY_CT, Visit_Group::GROUP_MODALITY_MR, Visit_Group::GROUP_MODALITY_PET, Visit_Group::GROUP_MODALITY_RTSTRUCT))) {
129			$uploadedVisits=$studyGroup->getStudyVisitManager()->getUploadedVisits();
130			array_push($visitsObjectArray, ...$uploadedVisits);
131			}
132
133
134			}
135
136			return $visitsObjectArray;
137
138			}
139
140			public function isHavingAwaitingReviewImagingVisit($username=null) {
141			$awaitingVisits=$this->getAllAwaitingReviewImagingVisit($username);
142			$havingAwaitingReview=(sizeof($awaitingVisits) > 0);
143			return $havingAwaitingReview;
144			}
145
146
147
148			public function getAllPossibleVisitGroups() {
149
150			$allGroupsType=$this->linkpdo->prepare('SELECT id FROM visit_group WHERE study = :study');
151			$allGroupsType->execute(array('study' => $this->study));
152			$allGroupsIds=$allGroupsType->fetchall(PDO::FETCH_COLUMN);
153
154			$visitGroupArray=[];
155			foreach ($allGroupsIds as $groupId) {
156			$visitGroupArray[]=new Visit_Group($this->linkpdo, $groupId);
157			}
158
159			return $visitGroupArray;
160
161			}
162
163			public function getSpecificGroup(String $groupModality) : Visit_Group {
164
165			$groupQuery=$this->linkpdo->prepare('SELECT id FROM visit_group WHERE study = :study AND group_modality=:groupModality');
166			$groupQuery->execute(array('study' => $this->study, 'groupModality'=> $groupModality));
167			$groupId=$groupQuery->fetch(PDO::FETCH_COLUMN);
168
169			return new Visit_Group($this->linkpdo, $groupId);
170
171			}
172
173			public function getStudySpecificGroupManager(String $groupModality) : Group_Visit_Manager {
174
175			$visitGroup=$this->getSpecificGroup($groupModality);
176
177			return new Group_Visit_Manager($this, $visitGroup, $this->linkpdo);
178
179			}
180
181			public function getReviewManager() : Study_Review_Manager {
182			return new Study_Review_Manager($this);
183			}
184
185			public function getExportStudyData() : Export_Study_Data{
186			return new Export_Study_Data($this);
187			}
188
189			public function getAllPatientsInStudy() {
190			$allPatientQuery=$this->linkpdo->prepare('SELECT code FROM patients WHERE study = :study');
191			$allPatientQuery->execute(array('study' => $this->study));
192			$allPatients=$allPatientQuery->fetchall(PDO::FETCH_COLUMN);
193
194			$patientObjectArray=[];
195			foreach ($allPatients as $patient) {
196			$patientObjectArray[]=new Patient($patient, $this->linkpdo);
197			}
198
199			return $patientObjectArray;
200
201			}
202
203			public function getDocumentation(String $role) {
204			if ($role == User::SUPERVISOR) {
205			$documentationQuery=$this->linkpdo->prepare("SELECT id_documentation FROM documentation
206			WHERE study = :study");
207
208			}else {
209			$documentationQuery=$this->linkpdo->prepare("SELECT id_documentation FROM documentation
210			WHERE study = :study
211			AND ".$role."= 1 AND deleted=0");
212
213			}
214
215			$documentationQuery->execute(array('study' => $this->study));
216			$documentationAnswers=$documentationQuery->fetchAll(PDO::FETCH_COLUMN);
217
218			$documentationObjects=[];
219			foreach ($documentationAnswers as $documentationId) {
220			$documentationObjects[]=new Documentation($this->linkpdo, $documentationId);
221			}
222			return $documentationObjects;
223			}
224
225			/**
226			* Return userObject array for all users having role in the study
227			* @return User[]
228			*/
229			public function getUsersWithRoleInStudy() {
230			$req=$this->linkpdo->prepare('SELECT DISTINCT users.username FROM roles,users
231			WHERE roles.username=users.username
232			AND roles.study=:study');
233			$req->execute(array('study' => $this->study));
234			$answers=$req->fetchAll(PDO::FETCH_COLUMN);
235
236			$usersObjects=[];
237			foreach ($answers as $username) {
238			$usersObjects[]=new User($username, $this->linkpdo);
239			}
240			return $usersObjects;
241
242			}
243
244			public function getUsersByRoleInStudy(String $role) {
245			$req=$this->linkpdo->prepare('SELECT username FROM roles
246			WHERE study=:study AND name=:role ');
247			$req->execute(array('study' => $this->study, 'role'=>$role));
248			$answers=$req->fetchAll(PDO::FETCH_COLUMN);
249
250			$usersObjects=[];
251			foreach ($answers as $username) {
252			$usersObjects[]=new User($username, $this->linkpdo);
253			}
254			return $usersObjects;
255
256			}
257
258			public function getAllRolesByUsers() {
259			$roles_query=$this->linkpdo->prepare('SELECT * FROM roles WHERE study=:study');
260			$roles_query->execute(array('study'=>$this->study));
261			$definedRoles=$roles_query->fetchall(PDO::FETCH_ASSOC);
262
263			foreach ($definedRoles as $role) {
264			$rolesList[$role['username']][]=$role['name'];
265			}
266			return $rolesList;
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report The variable `$rolesList` seems to be defined by a `foreach` iteration on line `263`. Are you sure the iterator is never empty, otherwise this variable is not defined? Loading history...
267			}
268
269			public function getStatistics(String $modality) {
270			return new Statistics($this, $modality);
271			}
272
273			public function changeStudyActivation(bool $activated) {
274			$req=$this->linkpdo->prepare('UPDATE studies SET
275			active = :active
276			WHERE name = :study');
277			$req->execute(array('study'=> $this->study, 'active'=>intval($activated)));
278			}
279
280			public function isOriginalOrthancNeverKnown($anonFromOrthancStudyId) {
281
282			$connecter=$this->linkpdo->prepare('SELECT Study_Orthanc_ID FROM visits
283			INNER JOIN visit_type ON
284			(visit_type.id=visits.visit_type_id
285			AND visit_type.group_id IN (SELECT id FROM visit_group WHERE study = :study))
286			INNER JOIN orthanc_studies ON (orthanc_studies.id_visit=visits.id_visit)
287			AND orthanc_studies.Anon_From_Orthanc_ID=:Anon_From_Orthanc_ID
288			AND orthanc_studies.deleted=0
289			AND visits.deleted=0'
290			);
291			$connecter->execute(array(
292			"study" => $this->study,
293			"Anon_From_Orthanc_ID"=>$anonFromOrthancStudyId
294			));
295			$result=$connecter->fetchAll(PDO::FETCH_COLUMN);
296
297			if (count($result) > 0) return false; else return true;
298
299			}
300
301			public static function createStudy(string $studyName, $patientCodePrefix, PDO $linkpdo) {
302
303			$req=$linkpdo->prepare('INSERT INTO studies (name, patient_code_prefix) VALUES(:studyName, :patientCodePrefix) ');
304
305			$req->execute(array(
306			'studyName' => $studyName,
307			'patientCodePrefix' => $patientCodePrefix
308			));
309
310			}
311
312			}

salimkanoun / GaelO

Study::getAllAwaitingReviewImagingVisit() A last analyzed 2021-07-04 22:07 UTC

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Study::getAllAwaitingReviewImagingVisit() A
last analyzed 2021-07-04 22:07 UTC