| " + title + " | |
|---|---|
| " + name + " | "; + text += "" + value + " | "; + text += "
+ The recruitment target ( + {data['recruitment_target']} + ) has been passed. +
+
+ {data['female_total']}
Females
+
+ {data['male_total']}
Males
+
+ Target: {data['recruitment_target']} +
+
+ {data['female_total']}
Females
+
+ {data['male_total']}
Males
+
+ Target: {data['recruitment_target']} +
+Project
+Cohort
+Site
+Visit
+Status
+There have been no candidates registered yet.
- ); - } - let projectBreakdownData = []; - for (const [key, value] of Object.entries(json['recruitment'])) { - if (key !== 'overall') { - projectBreakdownData.push( -- The recruitment target ( - {data['recruitment_target']} - ) has been passed. -
-
- {data['female_total']}
Females
-
- {data['male_total']}
Males
-
- Target: {data['recruitment_target']} -
-
- {data['female_total']}
Females
-
- {data['male_total']}
Males
-
- Target: {data['recruitment_target']} -
-There have been no candidates registered yet.
, + title: 'Recruitment - site breakdown', + }, + { + content: <> - {siteBreakdown} + {Object.entries(json['recruitment']).map(([key, value]) => { + if (key !== 'overall') { + returnThere have been no scans yet.
- ); - setSiteRecruitments( - json['studyprogression']['recruitment']['overall'] - ['total_recruitment'] > 0 - ?There have been no candidates registered yet.
- ); + setupCharts(false, chartDetails).then((data) => { + setChartDetails(data); + }); + json = props.data; setLoading(false); } }, [props.data]); - /** - * Renders the React component. - * - * @return {JSX.Element} - React markup for component. - */ + const updateFilters = (formDataObj, section) => { + props.updateFilters(formDataObj, section, + chartDetails, setChartDetails); + }; + return loading ?There have been no scans yet.
, + title: 'Study Progression - site scans', + }, + { + content: + json['studyprogression']['recruitment'] + ['overall']['total_recruitment'] + > 0 ? + <> +There have been no candidates registered yet.
, + title: 'Study Progression - site recruitment', + }, + ]} + /> + ); }; StudyProgression.propTypes = { data: PropTypes.object, + baseURL: PropTypes.string, + updateFilters: PropTypes.function, + showChart: PropTypes.function, }; StudyProgression.defaultProps = { data: {}, diff --git a/modules/statistics/php/charts.class.inc b/modules/statistics/php/charts.class.inc index 29bc3985de3..12e79759e92 100644 --- a/modules/statistics/php/charts.class.inc +++ b/modules/statistics/php/charts.class.inc @@ -85,9 +85,14 @@ class Charts extends \NDB_Page if (count($pathparts) != 2) { return new \LORIS\Http\Response\JSON\NotFound(); } + switch ($pathparts[1]) { case 'siterecruitment_pie': return $this->_handleSitePieData(); + case 'agerecruitment_pie': + return $this->_handleAgePieData(); + case 'ethnicity_pie': + return $this->_handleEthnicityPieData(); case 'siterecruitment_bysex': return $this->_handleSiteSexBreakdown(); case 'scans_bymonth': @@ -108,7 +113,11 @@ class Charts extends \NDB_Page { $DB = \NDB_Factory::singleton()->database(); + $params = $this->_parseGetParameters(); + $conditions = $this->_buildQueryConditions($params); + $recruitmentBySiteData = []; + $user = \NDB_Factory::singleton()->user(); $list_of_sites = $user->getStudySites(); @@ -116,7 +125,14 @@ class Charts extends \NDB_Page " SELECT COUNT(c.CandID), c.RegistrationCenterID as CenterID FROM candidate c + {$conditions['cohortJoin']} + {$conditions['participantStatusJoin']} WHERE c.Active='Y' AND c.Entity_type='Human' + {$conditions['projectQuery']} + {$conditions['cohortQuery']} + {$conditions['visitQuery']} + {$conditions['siteQuery']} + {$conditions['participantStatusQuery']} GROUP BY c.RegistrationCenterID ", [], @@ -140,8 +156,12 @@ class Charts extends \NDB_Page */ private function _handleSiteSexBreakdown() { - $DB = \NDB_Factory::singleton()->database(); - $sexData = []; + $DB = \NDB_Factory::singleton()->database(); + $sexData = []; + + $params = $this->_parseGetParameters(); + $conditions = $this->_buildQueryConditions($params); + $user = \NDB_Factory::singleton()->user(); $list_of_sites = $user->getStudySites(); @@ -151,7 +171,14 @@ class Charts extends \NDB_Page c.RegistrationCenterID as SiteID, c.Sex as Sex FROM candidate c + {$conditions['cohortJoin']} + {$conditions['participantStatusJoin']} WHERE c.Active='Y' AND c.Entity_type='Human' + {$conditions['projectQuery']} + {$conditions['cohortQuery']} + {$conditions['visitQuery']} + {$conditions['siteQuery']} + {$conditions['participantStatusQuery']} GROUP BY c.RegistrationCenterID, c.Sex", [] ); @@ -178,9 +205,134 @@ class Charts extends \NDB_Page $sexData['datasets']['male'][] = $processed_data[$siteID]['male'] ?? 0; } + return (new \LORIS\Http\Response\JsonResponse($sexData)); } + /** + * Handle an incoming request for age pie data. + * + * @return ResponseInterface + */ + private function _handleAgePieData() + { + $params = $this->_parseGetParameters(); + + $conditions = $this->_buildQueryConditions($params); + + $DB = \NDB_Factory::singleton()->database(); + + $dates = $DB->pselect( + "SELECT DISTINCT c.CandID, c.DoB, c.Date_registered + FROM candidate c + {$conditions['cohortJoin']} + {$conditions['participantStatusJoin']} + WHERE c.DoB IS NOT NULL + AND c.DoB <= c.date_registered + AND c.Active='Y' + AND c.Entity_type='Human' + {$conditions['projectQuery']} + {$conditions['cohortQuery']} + {$conditions['visitQuery']} + {$conditions['siteQuery']} + {$conditions['participantStatusQuery']}", + [] + ); + + // Initialize an array to store the dynamic age splits + $ageSplits = []; + + foreach ($dates as $_ => $value) { + // Note that age is calculated from date registered, not today + $ageOb = \Utility::calculateAge( + $value['DoB'], + $value['Date_registered'] + ); + $age = $ageOb['year']; + + // Determine the starting point of the age split (a multiple of 5) + $startOfSplit = intval(floor($age / 5) * 5); + + // Check if the age split already exists in the array + if (!isset($ageSplits[$startOfSplit])) { + // If not, create a new entry with the starting age as the key + $ageSplits[$startOfSplit] = 0; + } + + // Increment the count for the corresponding age split + ++$ageSplits[$startOfSplit]; + } + + // Convert the dynamic age splits into the desired format + $recruitmentByAgeData = []; + foreach ($ageSplits as $startOfSplit => $count) { + $endOfSplit = $startOfSplit + 4; // Adjust the age range as needed + $label = $startOfSplit . '-' . $endOfSplit; + $recruitmentByAgeData[] = ["label" => $label, "total" => $count]; + } + + return (new \LORIS\Http\Response\JsonResponse($recruitmentByAgeData)); + } + + /** + * Handle an incoming request for ethnicity pie data. + * + * @return ResponseInterface + */ + private function _handleEthnicityPieData() + { + $params = $this->_parseGetParameters(); + + $conditions = $this->_buildQueryConditions($params); + + $DB = \NDB_Factory::singleton()->database(); + + $candidates = $DB->pselect( + "SELECT DISTINCT c.CandID, c.Ethnicity + FROM candidate c + {$conditions['cohortJoin']} + {$conditions['participantStatusJoin']} + WHERE c.Active='Y' + AND c.Entity_type='Human' + {$conditions['projectQuery']} + {$conditions['cohortQuery']} + {$conditions['visitQuery']} + {$conditions['siteQuery']} + {$conditions['participantStatusQuery']}", + [] + ); + + // Initialize an array to store the ethnicities + $ethnicities = []; + + foreach ($candidates as $_ => $value) { + // Check if the ethnicity already exists in the array + if (!isset($ethnicities[$value["Ethnicity"]])) { + // If not, create a new entry with the ethnicity as the key + $ethnicities[$value["Ethnicity"]] = 0; + } + + // Increment the count for the corresponding ethnicity + ++$ethnicities[$value["Ethnicity"]]; + } + + // Convert into the desired format + $recruitmentByEthnicityData = []; + foreach ($ethnicities as $id => $count) { + $id = str_replace("_", " ", $id); + $id = strtolower($id); + $id = ucwords($id); + if ($id == null) { + $id = "Unknown"; + } + $label = $id; + $recruitmentByEthnicityData[] = ["label" => $label, "total" => $count]; + } + + return (new \LORIS\Http\Response\JsonResponse($recruitmentByEthnicityData)); + } + + /** * Handle an incoming request for monthly progression * @@ -190,6 +342,12 @@ class Charts extends \NDB_Page { $DB = \NDB_Factory::singleton()->database(); + $params = $this->_parseGetParameters(); + $conditions = $this->_buildQueryConditions($params, true); + + $user = \NDB_Factory::singleton()->user(); + $list_of_sites = $user->getStudySites(); + $scanData = []; // Run a query to get all the data. Order matters to ensure that the // labels are calculated in the correct order. @@ -201,14 +359,21 @@ class Charts extends \NDB_Page FROM files f LEFT JOIN parameter_file pf USING (FileID) LEFT JOIN session s ON (s.ID=f.SessionID) + {$conditions['participantStatusJoin']} JOIN parameter_type pt USING (ParameterTypeID) WHERE pt.Name='acquisition_date' + {$conditions['projectQuery']} + {$conditions['cohortQuery']} + {$conditions['visitQuery']} + {$conditions['siteQuery']} + {$conditions['participantStatusQuery']} GROUP BY MONTH(pf.Value), YEAR(pf.Value), s.CenterID, datelabel ORDER BY YEAR(pf.Value), MONTH(pf.Value), s.CenterID", [] ) ); + // TODO: make this work as bar data // Create the labels. // // We want to ensure that every month label appear exactly once and @@ -225,8 +390,6 @@ class Charts extends \NDB_Page $scanData['labels'] = array_keys($labels); // Massage the data into the appropriate format per site. - $user = \NDB_Factory::singleton()->user(); - $list_of_sites = $user->getStudySites(); foreach ($list_of_sites as $siteID => $siteName) { $scanData['datasets'][] = [ "name" => $siteName, @@ -285,6 +448,9 @@ class Charts extends \NDB_Page { $DB = \NDB_Factory::singleton()->database(); + $params = $this->_parseGetParameters(); + $conditions = $this->_buildQueryConditions($params, true); + $recruitmentData = []; $recruitmentStartDate = $DB->pselectOne( "SELECT MIN(Date_registered) FROM candidate", @@ -313,7 +479,12 @@ class Charts extends \NDB_Page YEAR(c.Date_registered) as Year, c.RegistrationCenterID as SiteID FROM candidate c + {$conditions['participantStatusJoin']} + {$conditions['cohortJoin']} WHERE c.Entity_type='Human' + {$conditions['projectQuery']} + {$conditions['cohortQuery']} + {$conditions['participantStatusQuery']} GROUP BY MONTH(c.Date_registered), YEAR(c.Date_registered), c.RegistrationCenterID", @@ -353,6 +524,133 @@ class Charts extends \NDB_Page return new \LORIS\Http\Response\JsonResponse($recruitmentData); } + /** + * Helper to parse the GET parameters from the incoming request. + * + * @return array + */ + private function _parseGetParameters() + { + $selectedProjects = empty($_GET['selectedProjects']) + || $_GET['selectedProjects'] === 'null' + || $_GET['selectedProjects'] === 'undefined' + ? null : explode(",", $_GET['selectedProjects']); + $selectedCohorts = empty($_GET['selectedCohorts']) + || $_GET['selectedCohorts'] === 'null' + || $_GET['selectedCohorts'] === 'undefined' + ? null : explode(",", $_GET['selectedCohorts']); + $selectedSites = empty($_GET['selectedSites']) + || $_GET['selectedSites'] === 'null' + || $_GET['selectedSites'] === 'undefined' + ? null : explode(",", $_GET['selectedSites']); + $selectedVisits = empty($_GET['selectedVisits']) + || $_GET['selectedVisits'] === 'null' + || $_GET['selectedVisits'] === 'undefined' + ? null : explode(",", $_GET['selectedVisits']); + $selectedParticipantStatus = empty( + $_GET['selectedParticipantStatus'] + ) + || $_GET['selectedParticipantStatus'] === 'null' + || $_GET['selectedParticipantStatus'] === 'undefined' ? null + : explode( + ",", + $_GET['selectedParticipantStatus'] + ); + + return [ + 'selectedProjects' => $selectedProjects, + 'selectedCohorts' => $selectedCohorts, + 'selectedSites' => $selectedSites, + 'selectedVisits' => $selectedVisits, + 'selectedParticipantStatus' => $selectedParticipantStatus, + ]; + } + + /** + * Helper to generate query conditions for for incoming requests. + * + * @param array $params The parameters from the incoming request. + * @param bool $scansbymonth Whether or not the request is for scans by month. + * + * @return array + */ + private function _buildQueryConditions( + $params, + $scansbymonth = false + ) { + $user = \NDB_Factory::singleton()->user(); + + $projectQuery = ''; + $cohortQuery = ''; + $cohortJoin = ''; + $visitQuery = ''; + $PSJoin = ''; + $participantStatusQuery = ''; + + if (!is_null($params['selectedProjects'])) { + $projectString = "'" . implode("','", $params['selectedProjects']) . "'"; + $projectQuery = " AND c.RegistrationProjectID IN ({$projectString}) "; + } + + if (!is_null($params['selectedCohorts'])) { + $cohortString = "'" . implode("','", $params['selectedCohorts']) . "'"; + $cohortQuery = " AND s.CohortID IN ({$cohortString}) "; + $cohortJoin = "JOIN session s ON s.CandID=c.CandID"; + } + if (!is_null($params['selectedSites'])) { + // Set site query if selected + $siteString = "'" . implode("','", $params['selectedSites']) . "'"; + $siteQuery = " AND c.RegistrationCenterID IN ({$siteString}) "; + if ($scansbymonth === true) { + $siteQuery = " AND s.CenterID IN ({$siteString}) "; + } + } else { + // If not selected, only take user sites + $centerIDs = $user->getCenterIDs(); + $centerList = "'" . implode("','", $centerIDs) . "'"; + $siteQuery = " AND c.RegistrationCenterID IN ({$centerList}) "; + if ($scansbymonth === true) { + $siteQuery = " AND s.CenterID IN ({$centerList}) "; + } + } + if (!is_null($params['selectedVisits'])) { + // Set visit query if visits selected + $visitString = "'" . implode("','", $params['selectedVisits']) . "'"; + $visitQuery = " AND s.Visit_label IN ({$visitString}) "; + // since they are the same, if visits are selected, + // then the cohort string is overwritten + $cohortJoin = "JOIN session s ON s.CandID=c.CandID"; + } + if (!is_null($params['selectedParticipantStatus'])) { + $PSJoin = 'LEFT JOIN participant_status ps ON c.CandID=ps.CandID'; + $participantStatusString = "'" . implode( + "','", + $params['selectedParticipantStatus'] + ) . "'"; + // Null participant status counts as Active because + // sometimes users do not update the participant_status tab + if (in_array('1', $params['selectedParticipantStatus'])) { + $participantStatusQuery = " AND ( + ps.participant_status IN ({$participantStatusString}) + OR ps.participant_status IS NULL + )"; + } else { + $participantStatusQuery = " AND ps.participant_status + IN ({$participantStatusString}) "; + } + } + + return [ + 'projectQuery' => $projectQuery, + 'cohortQuery' => $cohortQuery, + 'cohortJoin' => $cohortJoin, + 'visitQuery' => $visitQuery, + 'siteQuery' => $siteQuery, + 'participantStatusJoin' => $PSJoin, + 'participantStatusQuery' => $participantStatusQuery, + ]; + } + /** * Helper to generate labels for every month between startDate and endDate. * diff --git a/modules/statistics/php/widgets.class.inc b/modules/statistics/php/widgets.class.inc index 131429cf200..cc24e9443d3 100644 --- a/modules/statistics/php/widgets.class.inc +++ b/modules/statistics/php/widgets.class.inc @@ -89,38 +89,221 @@ class Widgets extends \NDB_Page implements ETagCalculator ) ]; - $projects = \Utility::getProjectList(); - foreach (array_keys($projects) as $projectID) { - $projectInfo = $config->getProjectSettings($projectID); + $user = $factory->user(); + $projects = $user->getProjectIDs(); + + $projectOptions = []; + $cohortOptions = []; + $visitOptions = []; + $recruitmentCohorts = []; + foreach ($projects as $projectID) { + // Set project recruitment data + $projectInfo = $config->getProjectSettings(intval(strval($projectID))); if (is_null($projectInfo)) { throw new \LorisException( 'No project settings exist in the Database for ' . - 'project ID ' . intval($projectID) + 'project ID ' . intval(strval($projectID)) ); } - $recruitment[$projectID] = $this->_createProjectProgressBar( - $projectID, - $projectInfo['Name'], - $projectInfo['recruitmentTarget'], - $this->getTotalRecruitmentByProject($recruitmentRaw, $projectID), - $recruitmentRaw - ); + $recruitment[intval(strval($projectID))] + = $this->_createProjectProgressBar( + strval($projectID), + $projectInfo['Name'], + $projectInfo['recruitmentTarget'], + $this->getTotalRecruitmentByProject( + $recruitmentRaw, + $projectID + ), + $recruitmentRaw + ); + + // Set cohort recruitment data + $project = \Project::getProjectFromID($projectID); + $cohorts = $project->getCohorts(); + + $projectOptions[strval($projectID)] = $project->getName(); + foreach ($cohorts AS $sp) { + $cohortOptions[$sp["cohortId"]] = $sp["title"]; + $recruitmentCohorts[$sp["cohortId"]] + = $this->_createCohortProgressBar( + $sp["cohortId"], + $sp["title"], + $sp["recruitmentTarget"], + $db + ); + $cohortVisits = \Utility::getVisitsForCohort( + intval($sp["cohortId"]) + ); + foreach ($cohortVisits as $visit) { + $visitOptions[$visit] = $cohortVisits[$visit]; + } + } } - $values = []; + $sites = \Utility::getSiteList(); + $userCenters = $user->getCenterIDs(); + + $siteOptions = array_intersect_key($sites, $userCenters); + + $participantStatusOptions + = \Candidate::getParticipantStatusOptions(); + + $options = [ + 'projects' => $projectOptions, + 'cohorts' => $cohortOptions, + 'sites' => $siteOptions, + 'visits' => $visitOptions, + 'participantStatus' => $participantStatusOptions + ]; + $values = []; // Used for the react widget recruitment.js $values['recruitment'] = $recruitment; // Used for the react widget studyprogression.js - $values['studyprogression'] = [ + $values['studyprogression'] = [ 'total_scans' => $totalScans, 'recruitment' => $recruitment ]; + $values['options'] = $options; + $values['recruitmentcohorts'] = $recruitmentCohorts; $this->_cache = new \LORIS\Http\Response\JsonResponse($values); return $this->_cache; } + /** + * Generates the template data for a progress bar. + * + * @param $ID The name of the progress bar being + * created. + * @param $title The title to add to the template variables. + * @param $recruitmentTarget The target for this recruitment type. + * @param \Database $db The database connection to get data from. + * + * @return array Smarty template data + */ + private function _createCohortProgressBar( + $ID, + $title, + $recruitmentTarget, + \Database $db + ) { + + $user = \User::singleton(); + $projectIDs = $user->getProjectIDs(); + $projectList = "'" . implode("','", $projectIDs) . "'"; + $centerIDs = $user->getCenterIDs(); + $centerList = "'" . implode("','", $centerIDs) . "'"; + + $totalRecruitment = intval( + $db->pselectOne( + "SELECT COUNT(DISTINCT s.CandID) + FROM session s JOIN candidate c + WHERE s.CohortID=:sid + AND s.CenterID IN ({$centerList}) + AND s.ProjectID IN ({$projectList}) + AND c.RegistrationCenterID <> 1", + ['sid' => $ID] + ) + ); + + $rv = [ + 'total_recruitment' => $totalRecruitment, + 'title' => $title, + ]; + + if (empty($recruitmentTarget)) { + $recruitmentTarget = $totalRecruitment; + } + + $rv['recruitment_target'] = $recruitmentTarget; + $totalFemales = $this->getTotalSexByCohort( + $db, + "Female", + intval($ID) + ); + $rv['female_total'] = $totalFemales; + $rv['female_percent'] = $recruitmentTarget ? + round($totalFemales / $recruitmentTarget * 100) : + null; + $totalMales = $this->getTotalSexByCohort( + $db, + "Male", + intval($ID) + ); + $rv['male_total'] = $totalMales; + $rv['male_percent'] = $recruitmentTarget ? + round($totalMales / $recruitmentTarget * 100) : + null; + if ($totalRecruitment > $recruitmentTarget) { + $rv['surpassed_recruitment'] = "true"; + + $rv['female_full_percent'] = $totalRecruitment ? + round($totalFemales / $totalRecruitment * 100) : + null; + + $rv['male_full_percent'] = $totalRecruitment ? + round($totalMales / $totalRecruitment * 100) : + null; + } + return $rv; + } + + /** + * Gets the total count of candidates of a specific sex, + * associated with a specific project + * + * @param \Database $DB A database connection to retrieve information + * from. + * @param string $sex A biological sex (male or female) + * @param int $cohortID Cohort ID + * + * @return int|string + */ + function getTotalSexByCohort(\Database $DB, string $sex, int $cohortID) + { + + $user = \User::singleton(); + $projectIDs = $user->getProjectIDs(); + $projectList = "'" . implode("','", $projectIDs) . "'"; + $centerIDs = $user->getCenterIDs(); + $centerList = "'" . implode("','", $centerIDs) . "'"; + + return intval( + $DB->pselectOne( + "SELECT COUNT(DISTINCT s.CandID) + FROM session s + JOIN candidate c ON c.CandID=s.CandID + WHERE CohortID=:sid + AND CenterID IN ({$centerList}) + AND ProjectID IN ({$projectList}) + AND c.Sex=:sex + AND c.RegistrationCenterID <> 1", + [ + 'sex' => $sex, + 'sid' => $cohortID + ] + ) + ); + } + + /** + * Gets the total count of candidates associated with a specific project + * + * @param \Database $DB The database connection to get the count from. + * + * @return int + */ + private function _getTotalRecruitment(\Database $DB): int + { + return $DB->pselectOneInt( + "SELECT COUNT(*) FROM candidate c + WHERE c.Active='Y' AND c.Entity_type='Human' + AND c.RegistrationCenterID <> 1", + [] + ) ?? 0; + } + /** * Generates the template data for a progress bar. * @@ -157,7 +340,7 @@ class Widgets extends \NDB_Page implements ETagCalculator $totalFemales = $this->getTotalSexByProject( $rawData, "Female", - intval($ID) + intval(strval($ID)) ); } $rv['female_total'] = $totalFemales; @@ -166,7 +349,11 @@ class Widgets extends \NDB_Page implements ETagCalculator if ($ID == 'overall') { $totalMales = $this->_getTotalSex($rawData, "Male"); } else { - $totalMales = $this->getTotalSexByProject($rawData, "Male", intval($ID)); + $totalMales = $this->getTotalSexByProject( + $rawData, + "Male", + intval(strval($ID)) + ); } $rv['male_total'] = $totalMales; $rv['male_percent'] @@ -226,16 +413,16 @@ class Widgets extends \NDB_Page implements ETagCalculator /** * Gets the total count of candidates associated with a specific project. * - * @param array $data The raw data returned from the SQL query. - * @param int $projectID The Project ID to get recruitment for. + * @param array $data The raw data returned from the SQL query. + * @param \ProjectID $projectID The Project ID to get recruitment for. * * @return int */ - function getTotalRecruitmentByProject(array $data, int $projectID): int + function getTotalRecruitmentByProject(array $data, \ProjectID $projectID): int { $sum = 0; foreach ($data as $row) { - if (intval($row['ProjectID']) == $projectID) { + if ($row['ProjectID'] == strval($projectID)) { $sum += intval($row['Count']); } } From d3fc6ffded6456b651d476eb8b3e058d4ec3f9ab Mon Sep 17 00:00:00 2001 From: Dave MacFarlane