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REVERSE_LC.php
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<?php
namespace Vanderbilt\REVERSE_LC;
use stdClass;
use UserRights;
class REVERSE_LC extends \ExternalModules\AbstractExternalModule {
public $edc_data;
public $uad_data;
private $access_tier_by_role = [
'1042' => '1', // Safety Reviewer/DSMB
'1045' => '1', // Medical Monitor
'1028' => '3', // Principal Investigator (National)
'1039' => '2', // Principal Investigator (Site)
'1046' => '3', // Study Manager (National)
'1044' => '2', // Study Manager (Site)
'1043' => '3', // Statistical Team
'1041' => '2', // Site Study Team
'1040' => '2', // Sub-Investigator (Site)
'1047' => '3', // Financial Team/Administration
'1048' => '3', // Study Leadership/Steering Committee
'1049' => '1', // IDS
'1050' => '1', // Blood Bank
'1051' => '1', // Lab Personnel
'1030' => '1' // Other
];
public $record_fields = [
'screening_id',
'redcap_data_access_group',
'dag',
'dag_name',
'dm_sex',
'dm_race',
'transfusion_datetime',
'randomization_dttm',
'elig_app',
'randomization',
'append_d_calc',
'append_e_calc',
'append_f_calc',
'append_g_calc',
'randomization_arm',
'sda_a1d1',
'sda_a1d2',
'sda_a1d3',
'sda_a1d4',
'sda_a1d5',
'sda_a3d1',
'sda_given_a3d1',
'sda_given_a3d2',
'sda_given_a3d3',
'sda_given_a3d4',
'sda_given_a3d5',
'sda_given_a3d6',
'sda_given_a3d7',
'sda_given_a3d8',
'sda_given_a3d9',
'sda_given_a3d10',
'sda_given_a3d11',
'sda_given_a3d12',
'sda_given_a3d13',
'sda_given_a3d14',
'sda_given_a3d15',
'sda_given_a3d16',
'sda_given_a3d17',
'sda_given_a3d18',
'sda_given_a3d19',
'sda_given_a3d20',
'sda_given_a3d21',
'sda_given_a3d22',
'sda_given_a3d23',
'sda_given_a3d24',
'sda_given_a3d25',
'sda_given_a3d26',
'sda_given_a3d27',
'sda_given_a3d28',
'sda_a4d1',
'sda_a4d2',
'sda_a4d3',
'sda_a4d4',
'sda_a4d5',
'sda_a4d6',
'sda_a4d7',
'sda_a4d8',
'sda_a4d9',
'sda_a4d10',
'enroll_yn'
];
public $personnel_roles = [
'PI',
'Primary Coordinator',
'Primary dispensing pharmacist'
];
public $document_signoff_fields = [
'cv' => 'cv_review_vcc',
'doa' => 'doa_vcc_review',
'license' => 'license_review_vcc',
'fdf' => 'fin_dis_review_vcc',
'hand_prof' => 'handwrite_review_vcc',
'gcp' => 'gcp_review_vcc',
'hsp' => 'citi_review_vcc',
'training' => 'train_review_vcc'
];
public $personnel_form_complete_fields = [
'cv_complete',
'license_complete',
'study_training_complete',
'human_subjects_training_complete',
'gcp_training_complete',
'delegation_of_authority_doa_complete',
'financial_disclosure_complete',
'iata_training_complete',
'handwriting_profile_complete'
];
public $filteredSiteFields = [
"template_sent",
"contract_pe",
"contract_fe",
"vcc_survey_sent",
"vcc_survey_received",
"vcc_survey_accepted",
"vcc_survey_accepted",
"vcc_pt2_received",
"vcc_pt2_reviewed",
"vcc_pt2_approved",
"institutional_profile_complete",
"hrp_agreement",
"pi_survey",
"site_add_ready",
"site_add"
];
private const MAX_FOLDER_NAME_LEN = 60; // folder names truncated after n characters
public function __construct() {
parent::__construct();
define("CSS_PATH_1",$this->getUrl("css/style.css"));
define("CSS_MAIN_ACTIVE", $this->getUrl("css/mainActive.css"));
define("JS_PATH_1",$this->getUrl("js/dashboard.js"));
define("LOGO_LINK", $this->getUrl("images/main_logo.png"));
require_once(__DIR__."/vendor/autoload.php");
$id_field_name = "record_id";
$this->id_field_name = $id_field_name;
$this->record_fields[] = $id_field_name;
}
// LOW LEVEL methods
public function getEventIDs() {
if (!isset($this->event_ids)) {
$event_ids = new \stdClass();
$event_ids->demographics = $this->getProjectSetting('demographics_event');
$event_ids->transfusion = $this->getProjectSetting('transfusion_event');
$event_ids->screening = $this->getProjectSetting('screening_event');
$this->event_ids = $event_ids;
}
return $this->event_ids;
}
public function getDAGs($project_id = false) {
if (!isset($this->dags)) {
if(!$project_id) {
$edcProjectId = $this->getProjectSetting('edc_project');
$project_id = $edcProjectId;
}
// create global $Proj that REDCap class uses to generate DAG info
$EDCProject = new \Project($project_id);
$dags_unique = $EDCProject->getUniqueGroupNames();
$dags_display = $EDCProject->getGroups();
$dags = new \stdClass();
foreach ($dags_unique as $group_id => $unique_name) {
// get display name
if (empty($display_name = $dags_display[$group_id]))
$display_name = "";
// add entry with unique and display name with group_id as key
$dags->$group_id = new \stdClass();
$dags->$group_id->unique = $unique_name;
$dags->$group_id->display = $display_name;
unset($display_name);
}
$this->dags = $dags;
}
return $this->dags;
}
public function getFieldLabelMapping($fieldName = false) {
$edcProjectId = $this->getProjectSetting('edc_project');
$Proj = new \Project($edcProjectId);
if ($Proj->metadata[$fieldName]['element_type'] == 'calc') {
return false;
}
if(!isset($this->mappings)) {
$this->mappings = [];
foreach($this->record_fields as $thisField) {
$choices = $this->getChoiceLabels($thisField,$edcProjectId);
if($choices && (count($choices) > 1 || reset($choices)) != "") {
$this->mappings[$thisField] = $choices;
}
}
}
if($fieldName) {
if(isset($this->mappings[$fieldName])) {
return $this->mappings[$fieldName];
}
else {
return false;
}
}
else {
return $this->mappings;
}
}
public function getUADData($project_id = false) {
if (!isset($this->uad_data)) {
$this->uad_data = false;
if(!$project_id) {
$edcProjectId = $this->getProjectSetting('edc_project');
$project_id = $edcProjectId;
}
//User Access is defined in Regulatory Database
$uadProject = $this->getProjectSetting("site_regulation_project",$project_id);
$thisUser = $this->getUser();
$username = $thisUser->getUsername();
$rolField = $this->getProjectSetting("role_field",$project_id);
$params = [
'project_id' => $uadProject,
'return_format' => 'json',
'fields' => [
'dashboard',
$rolField,
'pref_name'
],
'filterLogic' => '[user_name] = "'.$username.'"'
];
$uad_data = json_decode(\REDCap::getData($params));
if(!empty($uad_data)) {
$rights = $thisUser->getRights();
$this->uad_data = $uad_data[0];
$this->uad_data->role = $this->uad_data->$rolField;
if(!empty($rights['group_id'])) {
$DAGs = (array)$this->getDAGs($uadProject);
$this->uad_data->dag_group_name = $DAGs[$rights['group_id']]->unique;
}
}
}
return $this->uad_data;
}
public function getEDCData($project_id = false)
{
if (!isset($this->edc_data) || !$this->edc_data) {
if(!$project_id) {
$edcProjectId = $this->getProjectSetting('edc_project');
$project_id = $edcProjectId;
}
$this->getEventIDs();
$params = [
'project_id' => $project_id,
'return_format' => 'json',
'fields' => $this->record_fields,
'exportDataAccessGroups' => true
];
$edc_data = json_decode(\REDCap::getData($params));
$projectDags = $this->getDAGs($project_id);
// add dag and dag_name property to each record
foreach ($edc_data as $record) {
foreach($projectDags as $groupId => $thisDag) {
if($thisDag->unique == $record->redcap_data_access_group) {
$record->dag = $groupId;
$record->dag_name = $thisDag->display;
break;
}
}
}
$this->edc_data = $edc_data;
}
return $this->edc_data;
}
public function getScreeningData($projectId = false)
{
if(!$this->screening_data) {
if(!$projectId) {
$edcProjectId = $this->getProjectSetting('edc_project');
$projectId = $edcProjectId;
}
$screeningProjectId = $this->getProjectSetting("screening_project", $projectId);
$this->screening_data = json_decode(\REDCap::getData([
"project_id" => $screeningProjectId,
"return_format" => "json",
'exportDataAccessGroups' => true
]));
$screeningProject = new \Project($screeningProjectId);
preg_match_all("/<li>(.+)$/m", $screeningProject->metadata['excl_desc_4']['element_label'], $labels);
$this->excl_desc_labels = $labels[1];
}
return $this->screening_data;
}
public function getInclusionData()
{
if (!$this->screening_data) {
$this->getScreeningData();
}
$inclusionData = [];
$total = 0;
foreach ($this->screening_data as $screening_rid => $screening_record) {
$dag = $screening_record->redcap_data_access_group;
if (!isset($inclusionData[$dag])) {
$inclusionData[$dag] = 0;
}
if ($screening_record->continue_yn == '1' || $screening_record->continue_yn == '99') {
$total++;
$inclusionData[$dag]++;
}
}
$inclusionData["_total"] = $total;
return $inclusionData;
}
public function getConsentedData()
{
if (!$this->screening_data) {
$this->getScreeningData();
}
$consentedData = [];
$total = 0;
foreach ($this->screening_data as $screening_rid => $screening_record) {
$dag = $screening_record->redcap_data_access_group;
if (!isset($consentedData[$dag])) {
$consentedData[$dag] = 0;
}
if ($screening_record->enroll_yn == '1') {
$total++;
$consentedData[$dag]++;
}
}
$consentedData["_total"] = $total;
return $consentedData;
}
private function getRegulatoryData($projectId = false)
{
if (!$this->regulatory_data) {
if(!$projectId) {
$edcProjectId = $this->getProjectSetting('edc_project');
$projectId = $edcProjectId;
}
$regulatoryProjectId = $this->getProjectSetting("site_regulation_project", $projectId);
$this->regulatory_data = json_decode(\REDCap::getData([
"project_id" => $regulatoryProjectId,
"return_format" => "json",
'exportDataAccessGroups' => true,
"fields" => ["record_id", "edc_dag_id", "site_international"]
]));
$this->regulatory_data['domestic_sites'] = [];
$this->regulatory_data['international_sites'] = [];
$this->regulatory_data['domestic_dag_ids'] = [];
$this->regulatory_data['international_dag_ids'] = [];
foreach ($this->regulatory_data as $reg_record) {
if ($reg_record->site_international == '1') {
$this->regulatory_data['international_sites'][] = $reg_record->record_id;
if (!empty($reg_record->edc_dag_id)) {
$this->regulatory_data['international_dag_ids'][] = $reg_record->edc_dag_id;
}
} elseif ($reg_record->site_international == '0') {
$this->regulatory_data['domestic_sites'][] = $reg_record->record_id;
if (!empty($reg_record->edc_dag_id)) {
$this->regulatory_data['domestic_dag_ids'][] = $reg_record->edc_dag_id;
}
}
}
}
return $this->regulatory_data;
}
public function getDashboardUser()
{
if (!isset($this->user)) {
$this->user = $this->getUADData();
define("PIO_USER_DISPLAY_NAME", $this->user->pref_name);
}
return $this->user;
}
// HIGHER LEVEL methods
public function authorizeUser()
{
$this->getDashboardUser();
//The access level 1, 2, or 3 is assigned to a specific role using the module settings.
/*
user->authorized == '1'
user can access dashboard
user can see all sites data
user cannot see my site data
user->authorized == '2'
user can access dashboard
user can see all sites data
user can my site data -- results limited to records with DAG that matches user's DAG
user->authorized == '3'
user can access dashboard
user can see all sites data
user can see my site data -- including all patient rows from all sites
*/
if ($this->user === false) {
$this->user = new stdClass();
//VCC staff won’t be entered as records in the Regulatory Database
//So we need to look at the system role
$uadProject = $this->getProjectSetting("site_regulation_project",$this->getProjectId());
$thisUser = $this->getUser();
$username = $thisUser->getUsername();
$userRights = UserRights::getPrivileges($uadProject,$username);
$userRights = $userRights[$uadProject][$username]['role_name'];
// If role starts with "VCC" give total access
if (strpos($userRights, "VCC") === 0) {
$this->user->authorized = 3; //
$this->user->dashboard = 1;
return;
} else {
$this->user->authorized = false;
}
return;
} elseif ($this->user->dashboard == 0) {
$this->user = new stdClass();
$this->user->authorized = false;
return;
} elseif (empty($this->user->authorized)) { //If this user has not been authorized yet.
$userRole = $this->user->role;
$accessLevel = $this->getAccessLevelByRole($userRole);
$this->user->authorized = $accessLevel;
}
}
public function getRecords($project_id = false)
{
if (!isset($this->records)) {
if($_GET['TESTING']) {
$this->records = json_decode(file_get_contents(__DIR__."/tests/test_data/records.json"),true);
return $this->records;
}
if(!$project_id) {
$edcProjectId = $this->getProjectSetting('edc_project');
$project_id = $edcProjectId;
}
$this->getEDCData($project_id);
// iterate over edc_data, collating data into record objects
$temp_records_obj = new \stdClass();
foreach ($this->edc_data as $record_event) {
// establish $record and $rid
$id_field_name = $this->id_field_name;
$rid = $record_event->$id_field_name;
if (!$record = $temp_records_obj->$rid) {
$record = new \stdClass();
// set empty fields
foreach ($this->record_fields as $field) {
$record->$field = "";
}
$record->$id_field_name = $rid;
$temp_records_obj->$rid = $record;
}
// set non-empty fields
foreach ($this->record_fields as $field) {
if (!empty($record_event->$field)) {
$labels = $this->getFieldLabelMapping($field);
if($labels != false) {
$record->$field = $labels[$record_event->$field];
} else {
$record->$field = $record_event->$field;
}
## Special shortening for certain fields
if($field == "dm_sex") {
$record->$field = substr($record->$field, 0, 1);
}
}
}
}
$records = [];
foreach ($temp_records_obj as $record) {
if (!empty($record->redcap_data_access_group))
$records[] = $record;
}
$this->records = $records;
}
return $this->records;
}
public function getAccessLevelByRole($userRole)
{
$project_id = $this->getProjectId();
$roles = $this->getProjectSetting("access_level_field_value",$project_id);
$level = $this->getProjectSetting("access_level",$project_id);
$accessLevel = [];
foreach($roles as $seq => $role) {
$accessLevel[$role] = $level[$seq];
}
return $accessLevel[$userRole];
}
public function getMySiteData()
{
if($_GET['TESTING']) {
return json_decode(file_get_contents(__DIR__."/tests/test_data/site_a_data.json"),true);
}
$this->getDAGs();
$this->getDashboardUser();
$this->getRecords();
$this->authorizeUser();
//Access level pending
if ($this->user->authorized == false or $this->user->authorized == '1') {
$this->my_site_data = false;
return $this->my_site_data;
}
$site_data = new \stdClass();
$site_data->site_name = "";
$site_data->rows = [];
$site_data->site_name = $this->user->dag_group_name;
// add record rows
foreach ($this->records as $record) {
if (($this->user->authorized == '2' and $record->dag_name == $this->user->dag_group_name) or $this->user->authorized == '3') {
$row = new \stdClass();
$id_field_name = $this->id_field_name;
$row->id = $record->$id_field_name;
if ($this->user->authorized == '3') {
$row->site = $record->dag_name;
}
$row->dm_sex = $record->dm_sex;
$row->race = $record->dm_race;
$row->enrolled = $record->randomization_dttm;
$row->treated = "";
// convert transfusion_datetime from Y-m-d H:m to Y-m-d
if (!empty($record->transfusion_datetime))
$row->treated = date("Y-m-d", strtotime($record->transfusion_datetime));
$site_data->rows[] = $row;
}
}
// sort site level data
if (!function_exists(__NAMESPACE__ . '\sortSiteData')) {
function sortSiteData($a, $b) {
if ($a->enrolled == $b->enrolled)
return 0;
return $a->enrolled > $b->enrolled ? -1 : 1;
}
}
uasort($site_data->rows, __NAMESPACE__ . '\sortSiteData');
// return
$this->my_site_data = $site_data;
return json_decode(json_encode($this->my_site_data), true);
}
public function getAllSitesData()
{
if($_GET['TESTING']) {
return json_decode(file_get_contents(__DIR__."/tests/test_data/all_sites_data.json"),true);
}
$this->getDAGs();
$this->getRecords();
$inclusionData = $this->getInclusionData();
$consentedData = $this->getConsentedData();
$reg_data = $this->getRegulatoryData();
$data = new \stdClass();
$data->totals = json_decode('[
{
"name": "Target",
"fpe": "-",
"lpe": "-",
"screened": "-",
"eligible": "-",
"randomized": 550,
"baricitinib": "0",
"treated": 1600,
"enroll_yn":"0"
},
{
"name": "Cumulative across all sites",
"fpe": "-",
"lpe": "-",
"screened": ' . $inclusionData['_total'] . ',
"eligible": "0",
"randomized": "0",
"baricitinib": "0",
"treated": "0",
"enroll_yn":' . $consentedData['_total'] . '
}
]');
// create temporary sites container
$sites = new \stdClass();
foreach ($this->records as $record) {
//Ignore the record if doesn't have a DAG
if (!$patient_dag = $record->dag)
continue;
// get or make site object
if (!$site = $sites->$patient_dag) {
$sites->$patient_dag = new \stdClass();
$site = $sites->$patient_dag;
$site->name = $record->dag_name;
$site->dag = $record->redcap_data_access_group;
$site->group_id = $record->dag;
$site->fpe = '-';
$site->lpe = '-';
$site->screened = 0;
if (isset($inclusionData[$site->dag])) {
$site->screened = $inclusionData[$site->dag];
}
$site->enroll_yn = 0;
if (isset($consentedData[$site->dag])) {
$site->enroll_yn = $consentedData[$site->dag];
}
$site->eligible = 0;
$site->randomized = 0;
$site->baricitinib = 0;
$site->treated = 0;
}
// // update columns using patient data
// FPE and LPE
$enroll_date = $record->randomization_dttm;
if (!empty($enroll_date)) {
if ($site->fpe == '-') {
$site->fpe = $enroll_date;
} else {
if (strtotime($site->fpe) > strtotime($enroll_date))
$site->fpe = $enroll_date;
}
if ($site->lpe == '-') {
$site->lpe = $enroll_date;
} else {
if (strtotime($site->lpe) < strtotime($enroll_date))
$site->lpe = $enroll_date;
}
}
// Eligible
if ($record->elig_app == 1) {
$data->totals[1]->eligible++;
$site->eligible++;
}
// Randomized
if ($record->randomization != '') {
$data->totals[1]->randomized++;
$site->randomized++;
if ($record->randomization_arm === "Baricitinib") {
$data->totals[1]->baricitinib++;
$site->baricitinib++;
}
}
// Treated
if (
$record->sda_a1d1 == '1' ||
$record->sda_a1d2 == '1' ||
$record->sda_a1d3 == '1' ||
$record->sda_a1d4 == '1' ||
$record->sda_a1d5 == '1' ||
$record->sda_a3d1 == '1' ||
$record->sda_given_a3d1 == '1' ||
$record->sda_given_a3d2 == '1' ||
$record->sda_given_a3d3 == '1' ||
$record->sda_given_a3d4 == '1' ||
$record->sda_given_a3d5 == '1' ||
$record->sda_given_a3d6 == '1' ||
$record->sda_given_a3d7 == '1' ||
$record->sda_given_a3d8 == '1' ||
$record->sda_given_a3d9 == '1' ||
$record->sda_given_a3d10 == '1' ||
$record->sda_given_a3d11 == '1' ||
$record->sda_given_a3d12 == '1' ||
$record->sda_given_a3d13 == '1' ||
$record->sda_given_a3d14 == '1' ||
$record->sda_given_a3d15 == '1' ||
$record->sda_given_a3d16 == '1' ||
$record->sda_given_a3d17 == '1' ||
$record->sda_given_a3d18 == '1' ||
$record->sda_given_a3d19 == '1' ||
$record->sda_given_a3d20 == '1' ||
$record->sda_given_a3d21 == '1' ||
$record->sda_given_a3d22 == '1' ||
$record->sda_given_a3d23 == '1' ||
$record->sda_given_a3d24 == '1' ||
$record->sda_given_a3d25 == '1' ||
$record->sda_given_a3d26 == '1' ||
$record->sda_given_a3d27 == '1' ||
$record->sda_given_a3d28 == '1' ||
$record->sda_a4d1 == '1' ||
$record->sda_a4d2 == '1' ||
$record->sda_a4d3 == '1' ||
$record->sda_a4d4 == '1' ||
$record->sda_a4d5 == '1' ||
$record->sda_a4d6 == '1' ||
$record->sda_a4d7 == '1' ||
$record->sda_a4d8 == '1' ||
$record->sda_a4d9 == '1' ||
$record->sda_a4d10 == '1'
) {
$data->totals[1]->treated++;
$site->treated++;
}
}
// site objects updated with patient data, dump into $data->sites
// effectively removing keys and keeping values in array
foreach ($sites as $site) {
$data->sites[] = $site;
}
// sort all sites, randomized descending
if (!function_exists(__NAMESPACE__ . '\sortAllSitesData')) {
function sortAllSitesData($a, $b) {
if ($a->randomized == $b->randomized)
return 0;
return $a->randomized < $b->randomized ? 1 : -1;
}
}
// return
$this->all_sites_data = $data;
return json_decode(json_encode($this->all_sites_data), true);
}
public function updateAllSitesData(&$sites, $startup)
{
foreach ($sites as &$site) {
// Site Activation (date)
foreach ($startup->sites as $site_i => $siteData) {
$site_number = $siteData->site_number;
if ($site_number == substr($site['name'], 0, strlen($site_number))) {
$site['open_date'] = $siteData->open_date;
break;
}
}
}
}
public function getScreeningLogData($site = null, $first_day_of_week = 0) {
// determine earliest screened date (upon which weeks array will be based)
$screening_data = $this->getScreeningData();
$first_date = date("Y-m-d");
$last_date = date("Y-m-d", 0);
foreach ($screening_data as $record) {
$site_match_or_null = $site === null ? true : $record->redcap_data_access_group == $site;
if (!empty($record->dos) and $site_match_or_null) {
if (strtotime($record->dos) < strtotime($first_date))
$first_date = date("Y-m-d", strtotime($record->dos));
if (strtotime($record->dos) > strtotime($last_date))
$last_date = date("Y-m-d", strtotime($record->dos));
}
}
if (strtotime($last_date) == 0)
$last_date = $first_date;
// Determine first day of the week based on $first_day_of_week
$day_of_week = date("w", strtotime($first_date)); // 0 = Sunday, 1 = Monday, ..., 6 = Saturday
$rewind_x_days = $day_of_week - 1;
$rewind_x_days = $day_of_week >= $first_day_of_week
? $day_of_week - $first_day_of_week
: $day_of_week + (7 - $first_day_of_week);
$first_week_start = date("Y-m-d", strtotime("-$rewind_x_days days", strtotime($first_date)));
// make report data object and rows
$screening_log_data = new \stdClass();
$screening_log_data->rows = [];
$total_screened = 0;
$iterations = 0;
while (true) {
$screened_this_week = 0;
// determine week boundary dates
$day_offset1 = ($iterations) * 7;
$day_offset2 = $day_offset1 + 6;
$date1 = date("Y-m-d", strtotime("+$day_offset1 days", strtotime($first_week_start)));
$date2 = date("Y-m-d", strtotime("+$day_offset2 days", strtotime($first_week_start)));
$row = [];
$row[0] = date("n/j/y", strtotime($date1)) . "-" . date("n/j/y", strtotime($date2));
$row[0] = str_replace("\\", "", $row[0]);
// count records that were screened this week
$ts_a = strtotime($date1);
$ts_b = strtotime("+24 hours", strtotime($date2));
// echo "\$date1, \$date2, \$ts_a, \$ts_b: $date1, $date2, $ts_a, $ts_b\n";
foreach ($screening_data as $record) {
$ts_x = strtotime($record->dos);
$site_match_or_null = $site === null ? true : $record->redcap_data_access_group == $site;
if ($ts_a <= $ts_x and $ts_x <= $ts_b and $site_match_or_null)
$screened_this_week++;
}
$total_screened += $screened_this_week;
$row[1] = $screened_this_week;
$row[2] = $total_screened;
$screening_log_data->rows[] = $row;
$iterations++;
// see if the week row just created captures the last screened date
// if so, break here
$cutoff_timestamp = strtotime("+1 days", $ts_b);
if ($cutoff_timestamp > strtotime($last_date) or $iterations > 999)
break;
}
$screening_log_data->rows[] = ["Grand Total", $total_screened, $total_screened];
return $screening_log_data;
}
public function getEnrollmentChartData($options = null)
{
// determine earliest screened date (upon which weeks array will be based)
// 2021-08-05 we're changing to count "Randomized" instead of "Enrolled"
if (isset($options['site_dag'])) {
$site = $options['site_dag'];
}
if (isset($options['site_locality'])) {
$site_locality = $options['site_locality'];
}
$all_enroll_data = $this->getEDCData();
$randArmlabels = $this->getFieldLabelMapping('randomization_arm');
if(is_bool($randArmlabels)){
$randArmlabels = [];
}
$enroll_data_to_consider = [];
$first_date = date("Y-m-d");
$last_date = date("Y-m-d", 0);
foreach ($all_enroll_data as $record) {
if ($site_locality == "Domestic" and $this->isSiteDomestic($record->dag) === false) {
continue;
} elseif ($site_locality == "International" and $this->isSiteInternational($record->dag) === false) {
continue;
}
$site_match_or_null = $site === null ? true : $record->redcap_data_access_group == $site;
if (!empty($record->randomization_dttm) and $site_match_or_null) {
if (strtotime($record->randomization_dttm) < strtotime($first_date))
$first_date = date("Y-m-d", strtotime($record->randomization_dttm));
if (strtotime($record->randomization_dttm) > strtotime($last_date))
$last_date = date("Y-m-d", strtotime($record->randomization_dttm));
}
$enroll_data_to_consider[] = $record;
}
if (strtotime($last_date) == 0)
$last_date = $first_date;
// determine date of sunday on or before first_date found
$day_of_week = date("N", strtotime($first_date));
$rewind_x_days = $day_of_week;
$first_sunday = date("Y-m-d", strtotime("-$rewind_x_days days", strtotime($first_date)));
// make report data object and rows
$enrollment_chart_data = new \stdClass();
$enrollment_chart_data->rows = [];
$cumulative_randomized = 0;
$cumulative_arms = array_fill_keys($randArmlabels, 0);
$iterations = 0;
while (true) {
$randomized_this_week = 0;
$arms_this_week = array_fill_keys($randArmlabels, 0);
// determine week boundary dates
$day_offset1 = ($iterations) * 7;
$day_offset2 = $day_offset1 + 6;
$date1 = date("Y-m-d", strtotime("+$day_offset1 days", strtotime($first_sunday)));
$date2 = date("Y-m-d", strtotime("+$day_offset2 days", strtotime($first_sunday)));
$row = [];
$row[0] = date("n/j/y", strtotime($date1)) . "-" . date("n/j/y", strtotime($date2));
$row[0] = str_replace("\\", "", $row[0]);
// count records that were screened this week
$ts_a = strtotime($date1);
$ts_b = strtotime($date2);
foreach ($enroll_data_to_consider as $record) {
// making sure the H:m part of the d-m-Y H:m field doesn't cause us to miscount
$ts_x = strtotime(date("Y-m-d", strtotime($record->randomization_dttm)));
$site_match_or_null = $site === null ? true : $record->redcap_data_access_group == $site;
if ($ts_a <= $ts_x and $ts_x <= $ts_b and $site_match_or_null) {
$randomized_this_week++;
$arms_this_week[$randArmlabels[$record->randomization_arm]]++;
}
}
foreach ($cumulative_arms as $arm => $total) {
$cumulative_arms[$arm] += $arms_this_week[$arm];
if ($cumulative_arms[$arm] === 0) {
$cumulative_arms[$arm] = null;
}
}
$cumulative_randomized += $randomized_this_week;
$row[1] = $randomized_this_week;
$row[2] = $cumulative_randomized;
$row[3] = $cumulative_arms;
$enrollment_chart_data->rows[] = $row;
$iterations++;
// see if the week row just created captures the last screened date
// if so, break here
$cutoff_timestamp = strtotime("+1 days", $ts_b);
if ($cutoff_timestamp > strtotime($last_date) or $iterations > 999)
break;
}
$cumulative_arms = array_filter($cumulative_arms);
$enrollment_chart_data->rows[] = ["Grand Total", $cumulative_randomized, $cumulative_randomized, $cumulative_arms];
return $enrollment_chart_data;
}
public function getExclusionReportData() {
if (!isset($this->exclusion_data)) {
// create data object
$exclusion_data = new \stdClass();
$exclusion_data->rows = [];
// get labels, init exclusion counts
$screening_pid = $this->getProjectSetting('screening_project');
$labels = $this->excl_desc_labels;
$exclusion_counts = [];
foreach ($labels as $i => $label) {
$exclusion_counts[$i] = 0;
}
// iterate through screening records, summing exclusion reasons from [exclude_primary_reason]
$screening_data = $this->getScreeningData();
foreach ($screening_data as $record) {
// // use below if exclude_primary_reason is a dropdown field type
// if (!empty($record->exclude_primary_reason) and isset($exclusion_counts[$record->exclude_primary_reason]))
// $exclusion_counts[$record->exclude_primary_reason]++;
// use below if exclude_primary_reason is a checkbox field type // can't think of a smarter way to do this
foreach($record as $field_name => $value) {
preg_match("/exclude_primary_reason___(\d*)/", $field_name, $match);
$exclusion_index = intval($match[1]);
unset($report_table_index);
if ($value && $exclusion_index > 0) {
switch ($exclusion_index) {
case 2:
$report_table_index = 0;
break;
case 3:
$report_table_index = 1;
break;
case 5:
$report_table_index = 2;
break;
case 6:
$report_table_index = 3;
break;
case 7:
$report_table_index = 4;
break;
case 8:
$report_table_index = 5;
break;
case 9:
$report_table_index = 6;