[dataquery/dictionary] Remove instruments and visits that the user doesnt have access to (#9903)

- Created a function in the User class to getVisits that the user can
access based on the Projects they have access to

* Resolves #9894

Author: skarya22

modules/behavioural_qc/php/behavioural.class.inc

@@ -92,7 +92,7 @@ class Behavioural extends \NDB_Page implements ETagCalculator
         ServerRequestInterface $request
     ) : array {
         $user         = $request->getAttribute('user');
-        $visit_array  = \Utility::getVisitList();
+        $visit_array  = $user->getVisits();
         $userProjects = $user->getProjects();
         $projects     = [];
         foreach ($userProjects as $project) {

modules/candidate_list/php/candidate_list.class.inc

@@ -70,58 +70,9 @@ class Candidate_List extends \DataFrameworkMenu
      */
     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(),
-        ];
+        // To modify the field options,
+        // you must edit getFieldOptions in options.class.inc
+        return [];
     }
 
     /**

modules/candidate_list/php/options.class.inc

@@ -47,8 +47,8 @@ class Options extends \LORIS\Http\Endpoint
         $user    = $factory->user();
         $config  = $factory->config();
 
-        // get the list of visit labels
-        $visit_label_options = \Utility::getVisitList();
+        // get the list of visit labels that the user has access to
+        $visit_label_options = $user->getVisits();
 
         // get the list of sites available for the user
         if ($user->hasPermission('access_all_profiles')) {
@@ -62,7 +62,8 @@ class Options extends \LORIS\Http\Endpoint
         }
 
         // get the list of projects
-        $list_of_projects = \Utility::getProjectList();
+        // $list_of_projects = \Utility::getProjectList();
+        $list_of_projects = $user->getProjectNames();
         $project_options  = [];
         foreach (array_values($list_of_projects) as $name) {
             $project_options[$name] = $name;

modules/candidate_parameters/php/candidatequeryengine.class.inc

@@ -250,9 +250,10 @@ class CandidateQueryEngine extends \LORIS\Data\Query\SQLQueryEngine
         if ($item->getScope()->__toString() !== 'session') {
             return [];
         }
+        $user = \NDB_Factory::singleton()->user();
 
         // Session scoped variables: VisitLabel, project, site, cohort
-        return array_keys(\Utility::getVisitList());
+        return array_keys($user->getVisits());
     }
 
     /**

modules/dataquery/php/visitlist.class.inc

@@ -16,6 +16,7 @@ class VisitList extends \NDB_Page
     protected $itemmodule;
     protected $itemcategory;
     protected $dictionaryitem;
+    protected $user;
 
     /**
      * {@inheritDoc}
@@ -28,9 +29,7 @@ class VisitList extends \NDB_Page
     {
         if ($this->dictionaryitem === null) {
             return new \LORIS\Http\Response\JSON\OK(
-                [
-                    'Visits' => array_values(\Utility::getVisitList()),
-                ],
+                ['Visits' => array_values($this->user->getVisits())],
             );
         }
 
@@ -62,6 +61,7 @@ class VisitList extends \NDB_Page
         \User $user,
         ServerRequestInterface $request,
     ) : void {
+        $this->user  = $user;
         $queryparams = $request->getQueryParams();
         if (!isset($queryparams['module']) || !isset($queryparams['item'])) {
             return;

modules/dictionary/php/dictionary.class.inc

@@ -63,7 +63,7 @@ class Dictionary extends \DataFrameworkMenu
             $cohort_options[$name] = $name;
         }
         $visit_options = [];
-        foreach (\Utility::getVisitList() as $visit) {
+        foreach ($user->getVisits() as $visit) {
             $visit_options[$visit] = $visit;
         }
         return [

modules/dictionary/php/module.class.inc

@@ -88,6 +88,18 @@ class Module extends \Module
         $categories  = [];
 
         $categoryitems = [];
+
+        // Get the instruments that the user has access to based on their Projects
+        $userVisits  = $user->getVisits();
+        $instruments = [];
+        foreach ($userVisits as $visitLabel => $_) {
+            $visitInstruments = \Utility::getVisitInstruments($visitLabel);
+            foreach ($visitInstruments as $testName => $fullName) {
+                if (!isset($instruments[$testName])) {
+                    $instruments[$testName] = $fullName;
+                }
+            }
+        }
         foreach ($modules as $module) {
             if ($formodule !== null && $module->getName() !== $formodule) {
                 continue;
@@ -104,6 +116,11 @@ class Module extends \Module
                 $categories[$mname] = [];
 
                 foreach ($mdict as $cat) {
+                    if ($mname === 'instruments'
+                        && !isset($instruments[$cat->getName()])
+                    ) {
+                        continue;
+                    }
                     $categories[$mname][$cat->getName()] = $cat->getDescription();
                     $categoryitems[] = [
                         'Module'   => $module,

modules/electrophysiology_uploader/php/electrophysiology_uploader.class.inc

@@ -77,7 +77,7 @@ class Electrophysiology_Uploader extends \DataFrameworkMenu
 
         return [
             'sites'      => $site_options,
-            'visitLabel' => \Utility::getVisitList(),
+            'visitLabel' => $user->getVisits(),
         ];
     }
 

modules/imaging_browser/php/queryengine.class.inc

@@ -357,9 +357,11 @@ class QueryEngine extends \LORIS\Data\Query\SQLQueryEngine
             return $visits;
         }
 
-        // Fall back on all visits if something ends up getting
+        $user = \NDB_Factory::singleton()->user();
+
+        // Fall back on user visits if something ends up getting
         // added that we can't derive the modality of.
-        return array_keys(\Utility::getVisitList());
+        return array_keys($user->getVisits());
     }
 
     /**

modules/imaging_uploader/php/imaging_uploader.class.inc

@@ -160,7 +160,8 @@ class Imaging_Uploader extends \NDB_Menu_Filter_Form
             'N' => 'No',
             'Y' => 'Yes',
         ];
-        $visitlabels   = \Utility::getVisitList();
+        $user          = \NDB_Factory::singleton()->user();
+        $visitlabels   = $user->getVisits();
         // Fields used for selection filter and upload form
         $this->addSelect('IsPhantom', 'Phantom Scans', $phantomOtions);
         $this->addBasicText('candID', 'CandID');