Fix all PhanUnusedVariable errors (aces#7389)

Fix all PhanUnusedVariable class errors.

.phan/config.php

@@ -13,8 +13,6 @@
     // suppressed rules, we should consider reducing this value to detect more
     // suspicious code.
     "minimum_severity" => 1,
-    // FIXME: allow_missing_properties should be false, but there's
-    // too many other things to fix first.
     "allow_missing_properties" => false,
     "null_casts_as_any_type" => false,
     "scalar_implicit_cast" => false,
@@ -29,11 +27,8 @@
     "ignore_undeclared_variables_in_global_scope" => true,
     // FIXME: We should add this.
     "dead_code_detection" => false,
-    // FIXME: We should add this. Note that dead_code_detection also covers
-    // unused_variable_detection. It might be a good idea to enable this first.
     "unused_variable_detection" => true,
     "suppress_issue_types" => [
-        "PhanUnusedVariable",
         "PhanUnusedPublicNoOverrideMethodParameter",
         "PhanTypePossiblyInvalidDimOffset",
     ],

modules/candidate_list/php/candidate_list.class.inc

@@ -88,29 +88,29 @@ class Candidate_List extends \DataFrameworkMenu
             $list_of_sites = $user->getStudySites();
         }
         $site_options = [];
-        foreach ($list_of_sites as $id => $name) {
+        foreach (array_values($list_of_sites) as $name) {
             $site_options[$name] = $name;
         }
 
         // get the list of projects
         $list_of_projects = \Utility::getProjectList();
         $project_options  = [];
-        foreach ($list_of_projects as $id => $name) {
+        foreach (array_values($list_of_projects) as $name) {
             $project_options[$name] = $name;
         }
 
         // get the list of subprojects
         $list_of_subprojects = \Utility::getSubprojectList();
         $subproject_options  = [];
-        foreach ($list_of_subprojects as $id => $name) {
+        foreach (array_values($list_of_subprojects) as $name) {
             $subproject_options[$name] = $name;
         }
 
         // get the list participant status options
         $list_of_participant_status
             = \Candidate::getParticipantStatusOptions();
         $participant_status_options = [];
-        foreach ($list_of_participant_status as $id => $name) {
+        foreach (array_values($list_of_participant_status) as $name) {
             $participant_status_options[$name] = $name;
         }
 

modules/candidate_parameters/ajax/getData.php

@@ -254,7 +254,7 @@ function getFamilyInfoFields()
     );
 
     $siblings = [];
-    foreach ($siblingsList as $key => $siblingArray) {
+    foreach (array_values($siblingsList) as $siblingArray) {
         foreach ($siblingArray as $ID) {
             array_push($siblings, $ID);
         }

modules/conflict_resolver/php/conflict_resolver.class.inc

@@ -317,7 +317,7 @@ class Conflict_Resolver extends \NDB_Menu_Filter_Form
         // Project list, if applicable
         $list_of_projects = [];
         $projectList      = \Utility::getProjectList();
-        foreach ($projectList as $key => $value) {
+        foreach (array_values($projectList) as $value) {
             $list_of_projects[$value] = $value;
         }
         $this->addSelect('project', 'Project: ', $list_of_projects);

modules/conflict_resolver/php/resolved_conflicts.class.inc

@@ -171,7 +171,7 @@ class Resolved_Conflicts extends \NDB_Menu_Filter
         // Project list, if applicable
         $list_of_projects = [];
         $projectList      = \Utility::getProjectList();
-        foreach ($projectList as $key => $value) {
+        foreach (array_values($projectList) as $value) {
             $list_of_projects[$value] = $value;
         }
         $this->addSelect('project', 'Project: ', $list_of_projects);

modules/dashboard/php/module.class.inc

@@ -100,7 +100,6 @@ class Module extends \Module
             );
         }
 
-        $logindatestring = "";
         if ($last_login === null) {
             $logindatestring = "...never. Welcome!";
         } else {
@@ -109,6 +108,7 @@ class Module extends \Module
             // a \DateTime object.
             $logindatestring = $last_login->format('Y-m-d H:i:s');
         }
+
         return new Widget(
             new WidgetContent(
                 "",

modules/dicom_archive/test/dicom_archiveTest.php

@@ -215,7 +215,6 @@ function testLinksViewImages()
             "document.querySelector('$location').click()"
         );
         sleep(1);
-        $text = $this->webDriver->getPageSource();
         $text = $this->webDriver->executescript(
             "return document.querySelector('#bc2>a:nth-child(3)>div').textContent"
         );

modules/document_repository/php/files.class.inc

@@ -334,9 +334,7 @@ class Files extends \NDB_Page
 
         $targetdir = new \SplFileInfo($path);
 
-        $fileSize = $uploadedFile->getSize();
-        $fileName = $uploadedFile->getClientFileName();
-        $fileType = pathinfo($fileName, PATHINFO_EXTENSION);
+        $filename = $uploadedFile->getClientFileName();
         try{
             $uploader = (new \LORIS\FilesUploadHandler($targetdir))
                 ->withPermittedMIMETypes(

modules/genomic_browser/php/methylation.class.inc

@@ -90,18 +90,6 @@ class Methylation extends \NDB_Page implements ETagCalculator
             : $user->getStudySites();
         $list_of_sites = array_combine($list_of_sites, $list_of_sites);
 
-        // Platform
-        $DB = \Database::singleton();
-        $platform_results = $DB->pselect(
-            "SELECT distinct Name FROM genotyping_platform",
-            []
-        );
-        $platform_options = [];
-        foreach ($platform_results as $row) {
-            $name = $row['Name'];
-            $platform_options[$name] = $name;
-        }
-
         return (new \LORIS\genomic_browser\Views\Methylation(
             $list_of_sites,
             \Utility::getSubprojectList()

modules/help_editor/php/edit_help_content.class.inc

@@ -45,9 +45,6 @@ class Edit_Help_Content extends \NDB_Form
       */
     function _getDefaults()
     {
-        //Get the default values
-        $defaults = [];
-
         // Sanitize user input
         $safeSection    = isset($_REQUEST['section']) ?
             htmlspecialchars($_REQUEST['section']) : '';

modules/imaging_browser/php/imaging_session_controlpanel.class.inc

@@ -112,7 +112,6 @@ class Imaging_Session_ControlPanel
         * any way by any user.
          */
         $params     = [];
-        $ID         = 'NULL';
         $EntityType = $candidate->getEntityType();
         if ($EntityType == 'Scanner') {
             $ID            = ":PVL";

modules/imaging_browser/php/viewsession.class.inc

@@ -235,7 +235,6 @@ class ViewSession extends \NDB_Form
             $FileInsertDate      = $FileObj->getParameter('InsertTime');
             $SeriesDescription   = $FileObj->getParameter('series_description');
             $SeriesNumber        = $FileObj->getParameter('series_number');
-            $SeriesUID           = $FileObj->getParameter('series_instance_uid');
             $EchoTime            = number_format(
                 (float)$FileObj->getParameter('echo_time') * 1000,
                 2

modules/imaging_qc/php/imaging_qc.class.inc

@@ -208,12 +208,12 @@ class Imaging_QC extends \NDB_Menu_Filter
 
         $projectList  = \Utility::getProjectList();
         $projectList2 = [];
-        foreach ($projectList as $key => $value) {
+        foreach (array_values($projectList) as $value) {
             $projectList2[$value] = $value;
         }
         $subprojectList  = \Utility::getSubprojectList();
         $subprojectList2 = [];
-        foreach ($subprojectList as $key => $value) {
+        foreach (array_values($subprojectList) as $value) {
             $subprojectList2[$value] = $value;
         }
         //print_r($subprojectList2);

modules/imaging_uploader/php/file_decompress.class.inc

@@ -89,7 +89,6 @@ class File_Decompress
      */
     function tgzDecompres()
     {
-        $decompressed_folder = null;
         $p = new \PharData($this->file_name);
         $decompressed_folder = $p->decompress(); // creates /path/to/my.tar
         $p->extractTo(
@@ -107,8 +106,7 @@ class File_Decompress
      */
     function gzipDecompress()
     {
-        $return_value = false;
-        $decomp_file  = new \PharData($this->file_name);
+        $decomp_file = new \PharData($this->file_name);
         // creates /path/to/my.tar
         $return_value = $decomp_file->decompress();
         return $return_value;
@@ -122,7 +120,6 @@ class File_Decompress
      */
     function untar()
     {
-        $return_value = false;
         $p            = new \PharData($this->file_name);
         $return_value = $p->extractTo($this->dest_path);
            //could remove the folder later once completed...
@@ -140,7 +137,6 @@ class File_Decompress
      */
     function unzip()
     {
-        $result = false;
         $zip    = new \ZipArchive();
         $result = $zip->open($this->file_name);
         if ($result === true) {

modules/instrument_list/php/instrument_list_controlpanel.class.inc

@@ -136,7 +136,7 @@ class Instrument_List_ControlPanel extends \TimePoint
             }
             $this->startStage($nextStage);
 
-            if ($nextStage = 'Recycling Bin') {
+            if ($nextStage == 'Recycling Bin') {
 
                 $battery = new \NDB_BVL_Battery();
 

modules/issue_tracker/ajax/EditIssue.php

@@ -606,7 +606,6 @@ function getIssueFields()
     $factory = \NDB_Factory::singleton();
     $db      = $factory->database();
     $user    = $factory->user();
-    $sites   = [];
 
     // get field options
     $sites = Issue_Tracker::getSites(false, true);

modules/issue_tracker/php/issue_tracker.class.inc

@@ -81,8 +81,7 @@ class Issue_Tracker extends \NDB_Menu_Filter_Form
         bool $study_site = true,
         bool $DCC = true
     ): array {
-        $user  = \User::singleton();
-        $sites = [];
+        $user = \User::singleton();
         if ($user->hasPermission('access_all_profiles')) {
             // get the list of study sites - to be replaced by the Site object
             $sites = \Utility::getSiteList($study_site, $DCC);
@@ -106,7 +105,6 @@ class Issue_Tracker extends \NDB_Menu_Filter_Form
         $db      = $factory->database();
 
         //sites
-        $sites = [];
         if ($user->hasPermission('access_all_profiles')) {
             $sites = \Utility::getSiteList();
         } else {

modules/login/php/requestaccount.class.inc

@@ -198,8 +198,6 @@ class RequestAccount extends \NDB_Form
             ['VEmail' => $from]
         );
 
-        $user_id = null;
-
         if ($result == 0) {
             // insert into DB only if email address doesn't exist
             $DB->insert('users', $vals);

modules/media/ajax/FileUpload.php

@@ -261,8 +261,6 @@ function getUploadFields()
     $languageList    = Utility::getLanguageList();
     $startYear       = $config->getSetting('startYear');
     $endYear         = $config->getSetting('endYear');
-    $visit           = '';
-    $pscid           = '';
 
     // Build array of session data to be used in upload media dropdowns
     $sessionData = [];

modules/my_preferences/php/my_preferences.class.inc

@@ -21,8 +21,6 @@ class My_Preferences extends \NDB_Form
      */
     function _getDefaults()
     {
-        $defaults = [];
-
         $user = \User::factory($this->identifier);
         // get the user defaults
         $defaults = $user->getData();

modules/statistics/php/statistics_mri_site.class.inc

@@ -97,8 +97,8 @@ class Statistics_Mri_Site extends Statistics_Site
         $scan_types = $DB->pselect("SELECT Scan_type from mri_scan_type", []);
         $where      = "WHERE (";
         $counter    = 1;
-        foreach ($scan_types as $index=>$scan) {
-            foreach ($scan as $type=>$label) {
+        foreach (array_values($scan_types) as $scan) {
+            foreach (array_values($scan) as $label) {
                 if ($counter < sizeof($scan_types)) {
                     $where .= "m.$label <> 'No' OR m.$label IS NULL OR ";
                 } else {
@@ -132,8 +132,8 @@ class Statistics_Mri_Site extends Statistics_Site
         case 'Files_Missing':
             $where   = "WHERE (";
             $counter = 1;
-            foreach ($scan_types as $index=>$scan) {
-                foreach ($scan as $type=>$label) {
+            foreach (array_values($scan_types) as $scan) {
+                foreach (array_values($scan) as $label) {
                     if ($counter < sizeof($scan_types)) {
                         $where .= "m.$label <> 'No' OR ";
                     } else {

modules/statistics/php/statistics_site.class.inc

@@ -108,8 +108,6 @@ class Statistics_Site extends \NDB_Menu
             $this->query_criteria   .= " AND s.CenterID =:cid ";
             $this->query_vars['cid'] = $centerID;
         } else {
-            $list_of_permitted_sites = [];
-
             if ($user->hasPermission('access_all_profiles')) {
                 $list_of_permitted_sites = array_keys(\Utility::getSiteList());
             } else {

modules/statistics/php/stats_behavioural.class.inc

@@ -99,7 +99,6 @@ class Stats_Behavioural extends \NDB_Form
         $allProjectList = \Utility::getProjectList();
         $projects       = [];
         $projects['']   = 'All Projects';
-        $Param_Project  = '';
 
         $userProjectsIDs = $user->getProjectIDs();
         foreach ($userProjectsIDs as $ProjectID) {
@@ -166,7 +165,6 @@ class Stats_Behavioural extends \NDB_Form
 
         //SITES
 
-        $Param_Centers = '';
         if ($user->hasPermission('access_all_profiles')) {
             $list_of_sites = \Utility::getSiteList();
         } else {

modules/statistics/php/stats_mri.class.inc

@@ -324,7 +324,7 @@ class Stats_MRI extends \NDB_Form
         if (empty($scans_selected_input)) {
             $scans_selected = $scan_types ?? [];
         } else {
-            foreach ($scans_selected_input as $key => $scid) {
+            foreach ($scans_selected_input as $scid) {
                 $scans_selected[$scid] =$scan_types[$scid];
             }
         }

modules/timepoint_list/php/timepoint_list.class.inc

@@ -76,9 +76,8 @@ class Timepoint_List extends \NDB_Menu
         // create candidate object
         $candidate = \Candidate::singleton($this->candID);
 
-        $numberOfVisits           = 0;
-        $this->tpl_data['candID'] = $this->candID;
-        $this->tpl_data['PSCID']  = $candidate->getPSCID();
+        $this->tpl_data['candID']    = $this->candID;
+        $this->tpl_data['PSCID']     = $candidate->getPSCID();
         $this->tpl_data['candidate'] = $candidate->getData();
 
         $listOfSessionIDs = $candidate->getListOfTimePoints();
@@ -121,7 +120,6 @@ class Timepoint_List extends \NDB_Menu
                 if (empty($firstDateOfVisit)) {
                     $firstDateOfVisit = $dateOfVisit;
                 }
-                $numberOfVisits++;
             }
 
             // get timepoint data

modules/user_accounts/php/edit_user.class.inc

@@ -784,7 +784,7 @@ class Edit_User extends \NDB_Form
         $editorProjects = $editor->getProjectIDs();
         $projects       = \Utility::getProjectList();
         $projectOptions = [];
-        foreach ($editorProjects as $key => $projectID) {
+        foreach (array_values($editorProjects) as $projectID) {
             $projectOptions[$projectID->__toString()]
                 = $projects[$projectID->__toString()];
         }

php/libraries/CandIDGenerator.php

@@ -53,7 +53,6 @@ public function __construct()
      */
     public function generate(): CandID
     {
-        $validID = false;
         do {
             $this->checkIDRangeFull();
             $id = new CandID(

php/libraries/Candidate.class.inc

@@ -303,7 +303,6 @@ class Candidate implements \LORIS\StudyEntities\AccessibleResource,
         // Generate a new CandID and insert it into the database.
         $generator = new \CandIDGenerator();
         // declare the variable to avoid static analysis warnings
-        $invalidID    = false;
         $attemptcount = 0;
         do {
             // Reset on each iteration