2024 debug cm project filter

CHANGELOG.md

@@ -15,13 +15,15 @@ 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)
 - bvl_feedback updates in real-time (PR #8966)
 - 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

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
 

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,

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;

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 {

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'],

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 = (

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
 
 

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) ? <td>{cell.join(', ')}</td> : <td></td>;
+      let result = (cell) ? <td>{cell}</td> : <td></td>;
       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}
         <FilterableDataTable
           name="candidateList"
-          data={this.state.data.Data}
+          data={this.state.data}
           fields={fields}
           actions={actions}
           getFormattedCell={this.formatColumn}
@@ -394,7 +398,7 @@ window.addEventListener('load', () => {
     document.getElementById('lorisworkspace')
   ).render(
     <CandidateListIndex
-      dataURL={`${loris.BaseURL}/candidate_list/?format=json`}
+      dataURL={`${loris.BaseURL}/candidate_list/?format=binary`}
       hasPermission={loris.userHasPermission}
       baseURL={loris.BaseURL}
       betaProfileLink={args['betaprofile']}

modules/candidate_list/php/options.class.inc

@@ -0,0 +1,109 @@
+<?php declare(strict_types=1);
+namespace LORIS\candidate_list;
+use \Psr\Http\Message\ServerRequestInterface;
+use \Psr\Http\Message\ResponseInterface;
+
+/**
+ * Implements the candidate_list menu
+ *
+ * @category Main
+ * @package  Candidate_List
+ * @author   Loris Team <loris.mni@bic.mni.mcgill.ca>
+ * @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());
+    }
+}
+