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Merge pull request #8086 from ridz1208/PUSH_24.0-release_INTO_MAIN_AGAIN
Push 24.0 release into main again
2 parents b8d5a8a + 826575f commit 8fbc01a

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‎CHANGELOG.md‎

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@@ -8,7 +8,7 @@ core section.***
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- ***When possible please provide the number of the pull request(s) containing the
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changes in the following format: PR #1234***
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11-
## LORIS 24.0 (Release Date: ??)
11+
## LORIS 24.0 (Release Date: 2022-03-24)
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### Core
1313
#### Features
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- Data tables may now stream data as they're loading rather than waiting
@@ -75,7 +75,10 @@ scanner candidates. This prevents an error from being thrown in the candidate pa
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- Download CSV fix to remove duplicates and entries that partially match the filtering criteria (PR #7242)
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- Partially fix instrument escaping issues by reloading instrument and its data upon successful save (PR #7776)
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- Fix recognition of null sessionID in NDB_BVL_Instrument (PR #8031)
78-
78+
- Fix delete_candidate.php / delete_timepoint.php failing because of json instruments / instruments with different table name than test_name (PR #8070)
79+
- Fix bug where server_processes_manager had a timeout (PR #8071)
80+
- Candidate profile page loads with only the visits listed that a user has access to
81+
if a candidate has some visits that the user should not see. Fixes error where page was not loading for this use case (PR #8072)
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### Modules
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#### API

‎SQL/0000-00-05-ElectrophysiologyTables.sql‎

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@@ -265,7 +265,7 @@ CREATE TABLE `physiological_annotation_archive` (
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CREATE TABLE `physiological_annotation_parameter` (
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`AnnotationParameterID` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
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`AnnotationFileID` INT(10) UNSIGNED NOT NULL,
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`Description` TEXT NOT NULL,
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`Description` TEXT DEFAULT NULL,
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`Sources` VARCHAR(255),
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`Author` VARCHAR(255),
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PRIMARY KEY (`AnnotationParameterID`),

‎SQL/New_patches/2022-02-03-physiological_annotation_parameter_fix_description_default.sql‎

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@@ -0,0 +1,3 @@
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ALTER TABLE `physiological_annotation_parameter`
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MODIFY COLUMN `Description` text DEFAULT NULL
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;

‎jsx/Form.js‎

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@@ -1295,6 +1295,10 @@ class EmailElement extends Component {
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<div className={inputClass}>
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<input
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type="email"
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pattern={'/^[a-zA-Z0-9.!#$%&\'*+\\/=?^_`{|}~-]+@[a-zA-Z0-9](?:[' +
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'a-zA-Z0-9-]{0,61}[a-zA-Z0-9])?(?:\\.[a-zA-Z0-9](?:[a-zA-Z0-9-' +
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']{0,61}[a-zA-Z0-9])?)*$/'}
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title="Please provide a valid email address!"
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className="form-control"
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name={this.props.name}
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id={this.props.id}

‎modules/behavioural_qc/php/behavioural.class.inc‎

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Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@ namespace LORIS\behavioural_qc;
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55
use LORIS\behavioural_qc\Provisioners\BehaviouralProvisioner;
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use \LORIS\Data\Filters\HasAnyPermissionOrUserSiteMatch;
7+
use LORIS\Data\Filters\UserProjectMatch;
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use \Psr\Http\Message\ServerRequestInterface;
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use \Psr\Http\Message\ResponseInterface;
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use \LORIS\Middleware\ETagCalculator;
@@ -54,9 +55,11 @@ class Behavioural extends \NDB_Page implements ETagCalculator
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private function _handleGET(ServerRequestInterface $request) : ResponseInterface
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{
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$filter = new HasAnyPermissionOrUserSiteMatch(
57-
['access_all_profiles', 'behavioural_quality_control_view']
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['access_all_profiles']
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);
59-
$provisioner = (new BehaviouralProvisioner())->filter($filter);
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$provisioner = (new BehaviouralProvisioner())
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->filter($filter)
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->filter(new UserProjectMatch());
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$user = $request->getAttribute('user');
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$data = (new \LORIS\Data\Table())
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->withDataFrom($provisioner)
@@ -69,6 +72,16 @@ class Behavioural extends \NDB_Page implements ETagCalculator
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return new \LORIS\Http\Response\JsonResponse($body);
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}
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75+
/**
76+
* Use project for filtering projects.
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*
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* @return bool
79+
*/
80+
public function useProjectFilter() : bool
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{
82+
return true;
83+
}
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7285
/**
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* Provide the field options for the behavioural form.
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*
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private function _getFieldOptions(
8093
ServerRequestInterface $request
8194
) : array {
82-
$user = $request->getAttribute('user');
83-
$visit_array = \Utility::getVisitList();
95+
$user = $request->getAttribute('user');
96+
$visit_array = \Utility::getVisitList();
97+
$userProjects = $user->getProjects();
98+
$projects = [];
99+
foreach ($userProjects as $project) {
100+
$projects[$project->getId()->__toString()] = $project->getName();
101+
}
84102
// centerID
85103
$list_of_sites = $user->hasPermission('access_all_profiles')
86104
? \Utility::getSiteList()
87105
: $user->getStudySites();
88106
return (new \LORIS\behavioural_qc\Views\Behavioral(
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$visit_array,
90108
\Utility::getAllInstruments(),
91-
\Utility::getProjectList(),
109+
$projects,
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\Utility::getSubprojectList(),
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$list_of_sites
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))->toArray();

‎modules/behavioural_qc/php/conflicts.class.inc‎

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@@ -4,6 +4,7 @@ namespace LORIS\behavioural_qc;
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55
use LORIS\behavioural_qc\Provisioners\ConflictsProvisioner;
66
use LORIS\Data\Filters\HasAnyPermissionOrUserSiteMatch;
7+
use LORIS\Data\Filters\UserProjectMatch;
78
use \Psr\Http\Message\ServerRequestInterface;
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use \Psr\Http\Message\ResponseInterface;
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use \LORIS\Middleware\ETagCalculator;
@@ -54,9 +55,11 @@ class Conflicts extends \NDB_Page implements ETagCalculator
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private function _handleGET(ServerRequestInterface $request) : ResponseInterface
5556
{
5657
$filter = new HasAnyPermissionOrUserSiteMatch(
57-
['access_all_profiles', 'behavioural_quality_control_view']
58+
['access_all_profiles']
5859
);
59-
$provisioner = (new ConflictsProvisioner())->filter($filter);
60+
$provisioner = (new ConflictsProvisioner())
61+
->filter($filter)
62+
->filter(new UserProjectMatch());
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6164
$user = $request->getAttribute('user');
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@@ -71,6 +74,16 @@ class Conflicts extends \NDB_Page implements ETagCalculator
7174
return new \LORIS\Http\Response\JsonResponse($body);
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}
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77+
/**
78+
* Use project for filtering projects.
79+
*
80+
* @return bool
81+
*/
82+
public function useProjectFilter() : bool
83+
{
84+
return true;
85+
}
86+
7487
/**
7588
* Provide the field options for the Conflicts form.
7689
*
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8194
private function _getFieldOptions(
8295
ServerRequestInterface $request
8396
) : array {
84-
$user = $request->getAttribute('user');
85-
$visit_array = \Utility::getVisitList();
97+
$user = $request->getAttribute('user');
98+
$visit_array = \Utility::getVisitList();
99+
$userProjects = $user->getProjects();
100+
$projects = [];
101+
foreach ($userProjects as $project) {
102+
$projects[$project->getId()->__toString()] = $project->getName();
103+
}
86104
// centerID
87105
$list_of_sites = $user->hasPermission('access_all_profiles')
88106
? \Utility::getSiteList()
89107
: $user->getStudySites();
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return (new \LORIS\behavioural_qc\Views\Conflicts(
91109
$visit_array,
92110
\Utility::getAllInstruments(),
93-
\Utility::getProjectList(),
111+
$projects,
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\Utility::getSubprojectList(),
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$list_of_sites
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))->toArray();

‎modules/behavioural_qc/php/incomplete.class.inc‎

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@@ -4,6 +4,7 @@ namespace LORIS\behavioural_qc;
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use LORIS\behavioural_qc\Provisioners\IncompleteProvisioner;
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use LORIS\Data\Filters\HasAnyPermissionOrUserSiteMatch;
7+
use LORIS\Data\Filters\UserProjectMatch;
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use \Psr\Http\Message\ServerRequestInterface;
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use \Psr\Http\Message\ResponseInterface;
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use \LORIS\Middleware\ETagCalculator;
@@ -54,9 +55,11 @@ class Incomplete extends \NDB_Page implements ETagCalculator
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private function _handleGET(ServerRequestInterface $request) : ResponseInterface
5556
{
5657
$filter = new HasAnyPermissionOrUserSiteMatch(
57-
['access_all_profiles', 'behavioural_quality_control_view']
58+
['access_all_profiles']
5859
);
59-
$provisioner = (new IncompleteProvisioner())->filter($filter);
60+
$provisioner = (new IncompleteProvisioner())
61+
->filter($filter)
62+
->filter(new UserProjectMatch());
6063

6164
$user = $request->getAttribute('user');
6265

@@ -71,6 +74,16 @@ class Incomplete extends \NDB_Page implements ETagCalculator
7174
return new \LORIS\Http\Response\JsonResponse($body);
7275
}
7376

77+
/**
78+
* Use project for filtering projects.
79+
*
80+
* @return bool
81+
*/
82+
public function useProjectFilter() : bool
83+
{
84+
return true;
85+
}
86+
7487
/**
7588
* Provide the field options for the incomplete form.
7689
*
@@ -81,9 +94,13 @@ class Incomplete extends \NDB_Page implements ETagCalculator
8194
private function _getFieldOptions(
8295
ServerRequestInterface $request
8396
) : array {
84-
$user = $request->getAttribute('user');
85-
$visit_array = \Utility::getVisitList();
86-
$projects = \Utility::getProjectList();
97+
$user = $request->getAttribute('user');
98+
$visit_array = \Utility::getVisitList();
99+
$userProjects = $user->getProjects();
100+
$projects = [];
101+
foreach ($userProjects as $project) {
102+
$projects[$project->getId()->__toString()] = $project->getName();
103+
}
87104
// centerID
88105
$list_of_sites = $user->hasPermission('access_all_profiles')
89106
? \Utility::getSiteList()

‎modules/behavioural_qc/php/models/behaviouraldto.class.inc‎

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@@ -17,7 +17,8 @@ namespace LORIS\behavioural_qc\Models;
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* @license http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
1818
* @link https://github.com/aces/Loris-Trunk
1919
*/
20-
class BehaviouralDTO implements \LORIS\Data\DataInstance
20+
class BehaviouralDTO implements \LORIS\Data\DataInstance,
21+
\LORIS\StudyEntities\SiteHaver
2122
{
2223
/**
2324
* The instrument
@@ -117,6 +118,28 @@ class BehaviouralDTO implements \LORIS\Data\DataInstance
117118
*/
118119
private $_feedback_status = '';
119120

121+
/**
122+
* Returns the CenterID for this instance, for filters such as
123+
* \LORIS\Data\Filters\UserSiteMatch to match against.
124+
*
125+
* @return \CenterID
126+
*/
127+
public function getCenterID(): \CenterID
128+
{
129+
return new \CenterID($this->_site);
130+
}
131+
132+
/**
133+
* Returns the ProjectID for this row, for filters such as
134+
* \LORIS\Data\Filters\UserProjectMatch to match again.
135+
*
136+
* @return \ProjectID
137+
*/
138+
public function getProjectID(): \ProjectID
139+
{
140+
return new \ProjectID($this->_project);
141+
}
142+
120143
/**
121144
* Implements \LORIS\Data\DataInstance interface for this row.
122145
*

‎modules/behavioural_qc/php/models/conflictsdto.class.inc‎

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@@ -17,7 +17,8 @@ namespace LORIS\behavioural_qc\Models;
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* @license http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
1818
* @link https://github.com/aces/Loris-Trunk
1919
*/
20-
class ConflictsDTO implements \LORIS\Data\DataInstance
20+
class ConflictsDTO implements \LORIS\Data\DataInstance,
21+
\LORIS\StudyEntities\SiteHaver
2122
{
2223
/**
2324
* The instrument
@@ -103,6 +104,28 @@ class ConflictsDTO implements \LORIS\Data\DataInstance
103104
*/
104105
private $_commentID = '';
105106

107+
/**
108+
* Returns the CenterID for this instance, for filters such as
109+
* \LORIS\Data\Filters\UserSiteMatch to match against.
110+
*
111+
* @return \CenterID
112+
*/
113+
public function getCenterID(): \CenterID
114+
{
115+
return new \CenterID($this->_site);
116+
}
117+
118+
/**
119+
* Returns the ProjectID for this row, for filters such as
120+
* \LORIS\Data\Filters\UserProjectMatch to match again.
121+
*
122+
* @return \ProjectID
123+
*/
124+
public function getProjectID(): \ProjectID
125+
{
126+
return new \ProjectID($this->_project);
127+
}
128+
106129
/**
107130
* Implements \LORIS\Data\DataInstance interface for this row.
108131
*

‎modules/behavioural_qc/php/models/incompletedto.class.inc‎

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@@ -17,7 +17,8 @@ namespace LORIS\behavioural_qc\Models;
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* @license http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
1818
* @link https://github.com/aces/Loris-Trunk
1919
*/
20-
class IncompleteDTO implements \LORIS\Data\DataInstance
20+
class IncompleteDTO implements \LORIS\Data\DataInstance,
21+
\LORIS\StudyEntities\SiteHaver
2122
{
2223
/**
2324
* The instrument
@@ -103,6 +104,28 @@ class IncompleteDTO implements \LORIS\Data\DataInstance
103104
*/
104105
private $_commentID = '';
105106

107+
/**
108+
* Returns the CenterID for this instance, for filters such as
109+
* \LORIS\Data\Filters\UserSiteMatch to match against.
110+
*
111+
* @return \CenterID
112+
*/
113+
public function getCenterID(): \CenterID
114+
{
115+
return new \CenterID($this->_site);
116+
}
117+
118+
/**
119+
* Returns the ProjectID for this row, for filters such as
120+
* \LORIS\Data\Filters\UserProjectMatch to match again.
121+
*
122+
* @return \ProjectID
123+
*/
124+
public function getProjectID(): \ProjectID
125+
{
126+
return new \ProjectID($this->_project);
127+
}
128+
106129
/**
107130
* Implements \LORIS\Data\DataInstance interface for this row.
108131
*

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