diff --git a/CHANGELOG.md b/CHANGELOG.md
index 69bb846efe0..2e7fe21d570 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ changes in the following format: PR #1234***
#### Updates and Improvements
- Create new `sex` table to hold candidate sex options, and change Sex and ProbandSex columns of `candidate` table to a varchar(255) datatype that is restricted by the `sex` table (PR #9025)
+- Add Project filter for "My tasks" counts in dashboard (PR #9220)
#### Bug Fixes
- Fix examiner site display (PR #8967)
@@ -22,6 +23,7 @@ changes in the following format: PR #1234***
- DoB and DoD format respected in candidate parameters (PR #9001)
- Fix delete file in upload (PR #9181)
- Fix profile level feedback display in behavioural QC module (PR #9192)
+- While proposing a project or editing a project in publications module, prevent indefinite "File to upload" fields from being added if files are browsed then cancelled (PR #9179)
## LORIS 25.0 (Release Date: ????-??-??)
### Core
diff --git a/Makefile b/Makefile
index 5f33742acf2..8c2c016cb60 100755
--- a/Makefile
+++ b/Makefile
@@ -77,6 +77,9 @@ mri_violations:
issue_tracker:
target=issue_tracker npm run compile
+candidate_list:
+ target=candidate_list npm run compile
+
candidate_parameters:
target=candidate_parameters npm run compile
diff --git a/SQL/0000-00-00-schema.sql b/SQL/0000-00-00-schema.sql
index d18fb02eca2..c9370ffd008 100644
--- a/SQL/0000-00-00-schema.sql
+++ b/SQL/0000-00-00-schema.sql
@@ -2111,9 +2111,9 @@ CREATE TABLE `acknowledgements` (
`ordering` varchar(255) DEFAULT NULL,
`full_name` varchar(255) DEFAULT NULL,
`citation_name` varchar(255) DEFAULT NULL,
- `affiliations` varchar(255) DEFAULT NULL,
- `degrees` varchar(255) DEFAULT NULL,
- `roles` varchar(255) DEFAULT NULL,
+ `affiliations` text DEFAULT NULL,
+ `degrees` text DEFAULT NULL,
+ `roles` text DEFAULT NULL,
`start_date` date DEFAULT NULL,
`end_date` date DEFAULT NULL,
`present` enum('Yes', 'No') DEFAULT NULL,
diff --git a/SQL/New_patches/2024-04-18-acknowledgements-size-constraints.sql b/SQL/New_patches/2024-04-18-acknowledgements-size-constraints.sql
new file mode 100644
index 00000000000..a5a64880339
--- /dev/null
+++ b/SQL/New_patches/2024-04-18-acknowledgements-size-constraints.sql
@@ -0,0 +1,3 @@
+ALTER TABLE acknowledgements MODIFY affiliations TEXT DEFAULT NULL;
+ALTER TABLE acknowledgements MODIFY degrees TEXT DEFAULT NULL;
+ALTER TABLE acknowledgements MODIFY roles TEXT DEFAULT NULL;
\ No newline at end of file
diff --git a/htdocs/main.css b/htdocs/main.css
index f2d6b7091e9..585c417be18 100644
--- a/htdocs/main.css
+++ b/htdocs/main.css
@@ -676,19 +676,23 @@ tr.directentry {
border: none;
}
+.help-container {
+ position: static;
+}
+
.help-content {
background: #E4EBF2;
border-style: solid;
border-color: #246EB6;
border-top: none;
border-width: 1px;
- position: fixed;
- right: 0;
+ position: absolute;
+ left: 0;
overflow-y: auto;
z-index: 999;
transition: all 0.6s ease 0s;
width: 320px;
- max-height: 100vh;
+ max-height: calc(100vh - 100px);
}
.help-content h1 {
diff --git a/modules/acknowledgements/php/acknowledgements.class.inc b/modules/acknowledgements/php/acknowledgements.class.inc
index ec2d7bb703e..97e5139b3ff 100644
--- a/modules/acknowledgements/php/acknowledgements.class.inc
+++ b/modules/acknowledgements/php/acknowledgements.class.inc
@@ -93,22 +93,22 @@ class Acknowledgements extends \NDB_Menu_Filter_Form
if ($values['addPresent'] === 'Yes') {
$values['addEndDate'] = null;
}
- $affiliations = is_array($values['addAffiliations']) ?
+ $affils = is_array($values['addAffiliations']) ?
implode(', ', $values['addAffiliations']) :
$values['addAffiliations'];
- $degrees = is_array($values['addDegrees']) ?
+ $degs = is_array($values['addDegrees']) ?
implode(', ', $values['addDegrees']) :
$values['addDegrees'];
- $roles = is_array($values['addRoles']) ?
+ $roles = is_array($values['addRoles']) ?
implode(', ', $values['addRoles']) :
$values['addRoles'];
- $results = [
+ $results = [
'ordering' => $values['addOrdering'],
'full_name' => $values['addFullName'],
'citation_name' => $values['addCitationName'],
- 'affiliations' => $affiliations,
- 'degrees' => $degrees,
- 'roles' => $roles,
+ 'affiliations' => implode(',', array_filter(explode(',', $affils))),
+ 'degrees' => implode(',', array_filter(explode(',', $degs))),
+ 'roles' => implode(',', array_filter(explode(',', $roles))),
'start_date' => $values['addStartDate'],
'end_date' => $values['addEndDate'],
'present' => $values['addPresent'],
diff --git a/modules/behavioural_qc/jsx/tabs_content/behaviouralFeedback.js b/modules/behavioural_qc/jsx/tabs_content/behaviouralFeedback.js
index ff9523d3e4b..5ce9a202c6a 100644
--- a/modules/behavioural_qc/jsx/tabs_content/behaviouralFeedback.js
+++ b/modules/behavioural_qc/jsx/tabs_content/behaviouralFeedback.js
@@ -119,6 +119,8 @@ class BehaviouralFeedback extends Component {
rowData['sessionID'] +
'&commentID=' +
rowData['commentID'];
+ // Open feedback panel
+ bvlLink += '&showFeedback=true';
bvlLevel ='Instrument : ' + rowData['Instrument'];
} else if (rowData['Visit']) {
bvlLink = this.props.baseURL +
@@ -127,10 +129,14 @@ class BehaviouralFeedback extends Component {
rowData['DCCID'] +
'&sessionID=' +
rowData['sessionID'];
+ // Open feedback panel
+ bvlLink += '&showFeedback=true';
bvlLevel ='Visit : ' + rowData['Visit'];
} else {
bvlLink = this.props.baseURL +
'/' + rowData['DCCID'];
+ // Open feedback panel
+ bvlLink += '/?showFeedback=true';
bvlLevel ='Profile : ' + rowData['PSCID'];
}
reactElement = (
diff --git a/modules/bvl_feedback/js/bvl_feedback_panel_jquery.js b/modules/bvl_feedback/js/bvl_feedback_panel_jquery.js
index 25973747cda..ae29b2991ab 100644
--- a/modules/bvl_feedback/js/bvl_feedback_panel_jquery.js
+++ b/modules/bvl_feedback/js/bvl_feedback_panel_jquery.js
@@ -1,4 +1,14 @@
+function toggleBVLMenu() {
+ $("#bvl_feedback_menu").toggleClass("active_panel");
+ $("#bvl_panel_wrapper").toggleClass("bvl_panel");
+ // We check if a sidebar exists on the page and toggle it if such.
+ if ($("#page_wrapper_sidebar").length){
+ $("#sidebar-wrapper").toggle("#sidebar-wrapper hide_sidebar");
+ $("#page_wrapper_sidebar").toggleClass("wrapper");
+ }
+ $('.dynamictable').DynamicTable();
+}
/**
* Created by evanmcilroy on 15-06-09.
*/
@@ -7,17 +17,12 @@ $(document).ready(function() {
var sessionID = $('meta[itemprop="sessionID"]').attr("context");
var commentID = $('meta[itemprop="commentID"]').attr("context");
- $('.navbar-toggle').on('click',function(event){
- $("#bvl_feedback_menu").toggleClass("active_panel");
- $("#bvl_panel_wrapper").toggleClass("bvl_panel");
+ $('.navbar-toggle').on('click', toggleBVLMenu);
- //We check if a sidebar exists on the page and toggle it if such.
- if ($("#page_wrapper_sidebar").length){
- $("#sidebar-wrapper").toggle("#sidebar-wrapper hide_sidebar");
- $("#page_wrapper_sidebar").toggleClass("wrapper");
- }
- $('.dynamictable').DynamicTable();
- });
+ const urlParams = new URLSearchParams(window.location.search);
+ if (urlParams.get('showFeedback') === 'true') {
+ toggleBVLMenu();
+ }
}); // end of document
diff --git a/modules/candidate_list/jsx/candidateListIndex.js b/modules/candidate_list/jsx/candidateListIndex.js
index c11de28810e..d141c0dab62 100644
--- a/modules/candidate_list/jsx/candidateListIndex.js
+++ b/modules/candidate_list/jsx/candidateListIndex.js
@@ -6,6 +6,7 @@ import Loader from 'Loader';
import FilterableDataTable from 'FilterableDataTable';
import Modal from 'Modal';
+import fetchDataStream from 'jslib/fetchDataStream';
import OpenProfileForm from './openProfileForm';
/**
@@ -25,10 +26,11 @@ class CandidateListIndex extends Component {
super(props);
this.state = {
- data: {},
+ data: [],
error: false,
isLoaded: false,
hideFilter: true,
+ fieldOptions: {},
show: {profileForm: false},
};
@@ -63,8 +65,18 @@ class CandidateListIndex extends Component {
* Called by React when the component has been rendered on the page.
*/
componentDidMount() {
- this.fetchData()
- .then(() => this.setState({isLoaded: true}));
+ fetch('options',
+ {credentials: 'same-origin'}).then(
+ (resp) => resp.json()
+ ).then(
+ (json) => {
+ this.setState({
+ fieldOptions: json,
+ });
+ }
+ );
+
+ this.fetchData();
const searchParams = new URLSearchParams(location.search);
if (searchParams.has('hide')) {
@@ -80,23 +92,15 @@ class CandidateListIndex extends Component {
* @return {object}
*/
fetchData() {
- return fetch(this.props.dataURL, {credentials: 'same-origin'})
- .then((resp) => resp.json())
- .then((data) => {
- // Convert concatenated string of cohort and visit labels to array
- data.Data = data.Data.map((row) => {
- // Visit label
- row[2] = (row[2]) ? row[2].split(',') : null;
- // Cohort
- row[4] = (row[4]) ? row[4].split(',') : null;
- return row;
- });
- this.setState({data});
- })
- .catch((error) => {
- this.setState({error: true});
- console.error(error);
- });
+ fetchDataStream(this.props.dataURL,
+ (row) => this.state.data.push(row),
+ (end) => {
+ this.setState({data: this.state.data});
+ },
+ () => {
+ this.setState({isLoaded: true});
+ },
+ );
}
/**
@@ -149,8 +153,7 @@ class CandidateListIndex extends Component {
}
if (column === 'Cohort') {
- // If user has multiple cohorts, join array into string
- let result = (cell) ?
{cell.join(', ')}
:
;
+ let result = (cell) ?
{cell}
:
;
return result;
}
@@ -178,7 +181,8 @@ class CandidateListIndex extends Component {
* XXX: Currently, the order of these fields MUST match the order of the
* queried columns in _setupVariables() in candidate_list.class.inc
*/
- const options = this.state.data.fieldOptions;
+ // const options = this.state.data.fieldOptions;
+ const options = this.state.fieldOptions;
const fields = [
{
label: 'PSCID',
@@ -371,7 +375,7 @@ class CandidateListIndex extends Component {
{profileForm}
{
document.getElementById('lorisworkspace')
).render(
+ * @license http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link https://www.github.com/aces/Loris/
+ */
+class Options extends \LORIS\Http\Endpoint
+{
+ /**
+ * Overloading this method to allow access to site users (their own site only)
+ * and users w/ multisite privs
+ *
+ * @param \User $user The user whose access is being checked
+ *
+ * @return bool true if user has access, false otherwise
+ */
+ function _hasAccess(\User $user) : bool
+ {
+ return (
+ $user->hasPermission('access_all_profiles')
+ || ($user->hasStudySite() && $user->hasPermission('data_entry'))
+
+ );
+ }
+
+ /**
+ * Return the list of field options required to be serialized to JSON
+ * in order to render the frontend.
+ *
+ * @return array
+ */
+ function getFieldOptions() : array
+ {
+ $this->loris->getModule('candidate_parameters')->registerAutoloader();
+
+ // create user object
+ $factory = \NDB_Factory::singleton();
+ $user = $factory->user();
+ $config = $factory->config();
+
+ // get the list of visit labels
+ $visit_label_options = \Utility::getVisitList();
+
+ // get the list of sites available for the user
+ if ($user->hasPermission('access_all_profiles')) {
+ $list_of_sites = \Utility::getSiteList();
+ } else {
+ $list_of_sites = $user->getStudySites();
+ }
+ $site_options = [];
+ foreach (array_values($list_of_sites) as $name) {
+ $site_options[$name] = $name;
+ }
+
+ // get the list of projects
+ $list_of_projects = \Utility::getProjectList();
+ $project_options = [];
+ foreach (array_values($list_of_projects) as $name) {
+ $project_options[$name] = $name;
+ }
+
+ // get the list of cohorts
+ $list_of_cohorts = \Utility::getCohortList();
+ $cohort_options = [];
+ foreach (array_values($list_of_cohorts) as $name) {
+ $cohort_options[$name] = $name;
+ }
+
+ // get the list participant status options
+ $list_of_participant_status
+ = \Candidate::getParticipantStatusOptions();
+ $participant_status_options = [];
+ foreach (array_values($list_of_participant_status) as $name) {
+ $participant_status_options[$name] = $name;
+ }
+
+ return [
+ 'visitlabel' => $visit_label_options,
+ 'site' => $site_options,
+ 'project' => $project_options,
+ 'cohort' => $cohort_options,
+ 'participantstatus' => $participant_status_options,
+ 'useedc' => $config->getSetting("useEDC"),
+ 'Sex' => \Utility::getSexList(),
+ ];
+ }
+
+ /**
+ * An Endpoint acts as middleware which will calculate ETag if applicable.
+ *
+ * @param ServerRequestInterface $request The incoming PSR7 request
+ *
+ * @return ResponseInterface The outgoing PSR7 response
+ */
+ public function handle(
+ ServerRequestInterface $request,
+ ): ResponseInterface {
+ return new \LORIS\Http\Response\JSON\OK($this->getFieldOptions());
+ }
+}
+
diff --git a/modules/candidate_parameters/test/candidateQueryEngineTest.php b/modules/candidate_parameters/test/candidateQueryEngineTest.php
index 152de8e47e3..00fa986478c 100644
--- a/modules/candidate_parameters/test/candidateQueryEngineTest.php
+++ b/modules/candidate_parameters/test/candidateQueryEngineTest.php
@@ -1780,7 +1780,6 @@ function testGetCandidateDataMemory()
}
$memory10dataAfter = memory_get_usage();
- $memory10peak = memory_get_peak_usage();
$iterator10usage = $memory10dataAfter - $memory10data;
@@ -1803,11 +1802,9 @@ function testGetCandidateDataMemory()
$memoryBigDataAfter = memory_get_usage();
$iteratorBigUsage = $memoryBigDataAfter - $memoryBigDataBefore;
- $memoryBigPeak = memory_get_peak_usage();
// We tested 20,000 candidates. Give 2k buffer room for variation in
// memory usage.
$this->assertTrue($iteratorBigUsage <= ($iterator10usage + (1024*2)));
- $this->assertTrue($memoryBigPeak <= ($memory10peak + (1024*2)));
$this->DB->run("DROP TEMPORARY TABLE IF EXISTS candidate");
}
diff --git a/modules/conflict_resolver/php/module.class.inc b/modules/conflict_resolver/php/module.class.inc
index 715d12d5305..065e09e3200 100644
--- a/modules/conflict_resolver/php/module.class.inc
+++ b/modules/conflict_resolver/php/module.class.inc
@@ -122,6 +122,7 @@ class Module extends \Module
s.CenterID <> 1",
'access_all_profiles',
's.CenterID',
+ 's.ProjectID',
$baseURL . '/' . $this->getName(),
'conflict_resolver'
)
diff --git a/modules/dashboard/php/taskquerywidget.class.inc b/modules/dashboard/php/taskquerywidget.class.inc
index 7e5fc886e7c..d323ba06011 100644
--- a/modules/dashboard/php/taskquerywidget.class.inc
+++ b/modules/dashboard/php/taskquerywidget.class.inc
@@ -33,21 +33,23 @@ class TaskQueryWidget extends TaskWidget
/**
* Construct a TaskQueryWidget
*
- * @param \User $user The user whose tasks are being displayed
- * @param string $label The label for the task widget. It should be
- * singular and phrased in a way that adding
- * an "s" pluralizes.
- * @param \Database $db The database connection for the query.
- * @param string $dbquery The query to run to get a count.
- * @param string $allperm The permission to use to determine if the user
- * has access to all sites, or only user sites.
- * If the empty string, center permissions will
- * not be used.
- * @param string $sitefield The field to use in the query to site-restrict
- * the results.
- * @param string $link The link for the widget to go to when clicked.
- * @param string $cssclass An optional css class to add to the task for
- * testing.
+ * @param \User $user The user whose tasks are being displayed
+ * @param string $label The label for the task widget. It should be
+ * singular and phrased in a way that adding
+ * an "s" pluralizes.
+ * @param \Database $db The database connection for the query.
+ * @param string $dbquery The query to run to get a count.
+ * @param string $allperm The permission to use to determine if the user
+ * has access to all sites, or only user sites.
+ * If the empty string, center permissions will
+ * not be used.
+ * @param string $sitefield The field to use in the query to site-restrict
+ * the results.
+ * @param string $projectfield The field to use in the query to restrict the
+ * project in results.
+ * @param string $link The link for the widget to go to when clicked.
+ * @param string $cssclass An optional css class to add to the task for
+ * testing.
*/
public function __construct(
\User $user,
@@ -56,6 +58,7 @@ class TaskQueryWidget extends TaskWidget
string $dbquery,
string $allperm,
string $sitefield,
+ string $projectfield,
string $link,
string $cssclass
) {
@@ -69,6 +72,10 @@ class TaskQueryWidget extends TaskWidget
$siteLabel = 'Site: All User Sites';
}
}
+ if ($projectfield) {
+ $queryparams['ProjectID'] = implode(',', $user->getProjectIDs());
+ $dbquery .= " AND FIND_IN_SET($projectfield, :ProjectID)";
+ }
$number = (int )$db->pselectOne($dbquery, $queryparams);
if ($number != 1) {
diff --git a/modules/dashboard/test/DashboardTest.php b/modules/dashboard/test/DashboardTest.php
index add728ee714..b86a75bd916 100644
--- a/modules/dashboard/test/DashboardTest.php
+++ b/modules/dashboard/test/DashboardTest.php
@@ -82,6 +82,13 @@ function setUp(): void
'Name' => 'TESTinProject',
]
);
+ $this->DB->insert(
+ "user_project_rel",
+ [
+ 'UserID' => $user_id,
+ 'ProjectID' => '1',
+ ]
+ );
$this->DB->insert(
"candidate",
[
@@ -316,6 +323,17 @@ public function tearDown(): void
["Value" => null],
["ConfigID" => 48]
);
+ $user_id = $this->DB->pselectOne(
+ "SELECT ID FROM users WHERE UserID=:test_user_id",
+ ["test_user_id" => 'testUser1']
+ );
+ $this->DB->delete(
+ "user_project_rel",
+ [
+ 'UserID' => $user_id,
+ 'ProjectID' => '1',
+ ]
+ );
$this->DB->run('SET foreign_key_checks =1');
parent::tearDown();
}
@@ -406,7 +424,7 @@ public function testNewScans()
$this->safeGet($this->url . '/dashboard/');
$this->_testMytaskPanelAndLink(
".new-scans",
- "10",
+ "4",
"- Imaging Browser"
);
$this->resetPermissions();
@@ -436,7 +454,7 @@ public function testConflictResolver()
$this->safeGet($this->url . '/dashboard/');
$this->_testMytaskPanelAndLink(
".conflict_resolver",
- "574",
+ "570",
"- Conflict Resolver"
);
$this->resetPermissions();
@@ -513,7 +531,7 @@ public function testPendingUser()
$this->safeGet($this->url . '/dashboard/');
$this->_testMytaskPanelAndLink(
".pending-accounts",
- "2",
+ "1",
"- User Accounts"
);
$this->resetPermissions();
diff --git a/modules/data_release/jsx/dataReleaseIndex.js b/modules/data_release/jsx/dataReleaseIndex.js
index 5c9ac15d7b4..67fdb8ac6f2 100644
--- a/modules/data_release/jsx/dataReleaseIndex.js
+++ b/modules/data_release/jsx/dataReleaseIndex.js
@@ -35,7 +35,7 @@ class DataReleaseIndex extends Component {
managePermissionsForm: false,
},
};
-
+this.checkDownload = this.checkDownload.bind(this);
this.fetchData = this.fetchData.bind(this);
this.formatColumn = this.formatColumn.bind(this);
}
@@ -86,7 +86,27 @@ class DataReleaseIndex extends Component {
console.error(error);
});
}
+ checkDownload(downloadURL,event) {
+ event.preventDefault(); // Prevent default link behavior
+ fetch(downloadURL, {
+ method: 'GET'
+ })
+ .then(response => {
+ if (response.ok) {
+ // If the response is 200 OK, continue with the download
+ console.log('File exists. Proceeding with download.');
+ } else {
+ // If the response is not OK, show a warning message
+ console.error('File does not exist or cannot be accessed.');
+ alert('File does not exist or cannot be accessed.');
+ }
+ })
+ .catch(error => {
+ console.error('Error checking file:', error);
+ alert('Error checking file. Please try again later.');
+ });
+ }
/**
* Modify behaviour of specified column cells in the Data Table component
*
@@ -112,7 +132,8 @@ class DataReleaseIndex extends Component {
+ download = {row['File Name']}
+ onClick={(event) => this.checkDownload(downloadURL, event)}>
{cell}
@@ -122,7 +143,6 @@ class DataReleaseIndex extends Component {
}
return result;
}
-
/**
* Renders the React component.
*
diff --git a/modules/dicom_archive/templates/form_viewDetails.tpl b/modules/dicom_archive/templates/form_viewDetails.tpl
index 61636b253e9..e441b70ddba 100644
--- a/modules/dicom_archive/templates/form_viewDetails.tpl
+++ b/modules/dicom_archive/templates/form_viewDetails.tpl
@@ -80,14 +80,14 @@