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small_base.php
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<?php
namespace Vanderbilt\FlightTrackerExternalModule;
use PhpParser\Node\Expr\AssignOp\BitwiseOr;
use \Vanderbilt\CareerDevLibrary\Citation;
use \Vanderbilt\CareerDevLibrary\CohortConfig;
use \Vanderbilt\CareerDevLibrary\Cohorts;
use \Vanderbilt\CareerDevLibrary\Consortium;
use \Vanderbilt\CareerDevLibrary\CronManager;
use \Vanderbilt\CareerDevLibrary\Definitions;
use \Vanderbilt\CareerDevLibrary\Download;
use \Vanderbilt\CareerDevLibrary\EmailManager;
use \Vanderbilt\CareerDevLibrary\Filter;
use \Vanderbilt\CareerDevLibrary\Grant;
use \Vanderbilt\CareerDevLibrary\GrantFactory;
use \Vanderbilt\CareerDevLibrary\GrantLexicalTranslator;
use \Vanderbilt\CareerDevLibrary\Grants;
use \Vanderbilt\CareerDevLibrary\LDAP;
use \Vanderbilt\CareerDevLibrary\Links;
use \Vanderbilt\CareerDevLibrary\NameMatcher;
use \Vanderbilt\CareerDevLibrary\NavigationBar;
use \Vanderbilt\CareerDevLibrary\NIHExPORTER;
use \Vanderbilt\CareerDevLibrary\OracleConnection;
use \Vanderbilt\CareerDevLibrary\Publications;
use \Vanderbilt\CareerDevLibrary\REDCapManagement;
use \Vanderbilt\CareerDevLibrary\Scholar;
use \Vanderbilt\CareerDevLibrary\Upload;
use \Vanderbilt\CareerDevLibrary\iCite;
use \Vanderbilt\CareerDevLibrary\Application;
use \Vanderbilt\CareerDevLibrary\ConnectionStatus;
use \Vanderbilt\CareerDevLibrary\DataDictionaryManagement;
use \Vanderbilt\CareerDevLibrary\FeatureSwitches;
use \Vanderbilt\CareerDevLibrary\DateManagement;
use \Vanderbilt\CareerDevLibrary\Sanitizer;
use \Vanderbilt\CareerDevLibrary\URLManagement;
use \Vanderbilt\CareerDevLibrary\FileManagement;
use \Vanderbilt\CareerDevLibrary\Dashboard;
use \Vanderbilt\CareerDevLibrary\ReactNIHTables;
use \Vanderbilt\CareerDevLibrary\NIHTables;
require_once(__DIR__."/autoload.php");
ini_set("memory_limit", "4096M");
ini_set("auto_detect_line_endings", true);
if (!Application::isWebBrowser() && CareerDev::getPid()) {
date_default_timezone_set(CareerDev::getTimezone());
}
$pid = Sanitizer::sanitize(isset($module) ? $module->getProjectId($_GET['pid'] ?? "") : Sanitizer::sanitizePid($_GET['pid'] ?? ""));
if (!$pid && !Application::isWebBrowser() && is_array($argv) && (count($argv) >= 2) && in_array($argv[1], Application::getPids())) {
$pid = $argv[1];
$_GET['pid'] = $pid;
}
if (!$pid) {
if (isset($_GET['project_id']) && $_GET['project_id']) {
$pid = CareerDev::getSetting("pid", $_GET['project_id']);
} else {
$pid = CareerDev::getSetting("pid");
}
$_GET['pid'] = $pid;
}
define('INSTITUTION', CareerDev::getInstitution($pid));
define('PROGRAM_NAME', CareerDev::getProgramName());
define("ENVIRONMENT", "prod"); // for Oracle database connectivity
if (!isset($module) || !$module) {
$module = Application::getModule();
}
if (!$module) {
throw new \Exception("The base class has no module!");
}
$token = Application::getSetting("token", $pid);
try {
$token = Application::checkOrResetToken($token, $pid);
} catch (\Exception $e) {
if (!$token && USERID && $module->canRedirectToInstall()) {
header("Location: ".CareerDev::link("install.php"));
} else if (Sanitizer::sanitize($_GET['page'] ?? "") != "install") {
throw $e;
}
}
$server = Application::getSetting("server", $pid);
$event_id = Application::getSetting("event_id", $pid);
$tokenName = Application::getSetting("tokenName", $pid);
$adminEmail = Application::getSetting("admin_email", $pid);
$grantClass = Application::getSetting("grant_class", $pid);
$GLOBALS['pid'] = $pid;
$GLOBALS['server'] = $server;
$GLOBALS['token'] = $token;
$GLOBALS['tokenName'] = $tokenName;
$GLOBALS['event_id'] = $event_id;
$GLOBALS['module'] = $module;
$GLOBALS['adminEmail'] = $adminEmail;
$GLOBALS['grantClass'] = $grantClass;
set_exception_handler('\Vanderbilt\FlightTrackerExternalModule\displayException');
// set_error_handler('\Vanderbilt\FlightTrackerExternalModule\displayError');
############# FUNCTIONS ################
function displayException($exception) {
global $pid;
$header = "Flight Tracker Error!";
Application::log("Exception: ".$exception->getMessage(), $pid);
echo "<div class='red padded max-width' style='text-align: center;'><strong>".$header."</strong><br/>".$exception->getMessage()."<br/>File: ".$exception->getFile()."; Line: ".$exception->getLine()."<br/><code class='alignLeft'>".$exception->getTraceAsString()."</code></div>";
}
function displayError($error) {
# unimplemented
}
function getBaseAwardNumber($num) {
return Grant::translateToBaseAwardNumber($num);
}
function getDepartmentChoices() {
$choices2 = [];
$choices2[104300] = "Anesthesiology [104300]";
$choices2[104250] = "Biochemistry [104250]";
$choices2[120450] = "Biological Sciences [120450]";
$choices2[104785] = "Biomedical Informatics [104785]";
$choices2[104286] = "Cancer Biology [104286]";
$choices2[104280] = "Cell and Developmental Biology [104280]";
$choices2[104226] = "Center for Human Genetics Research [104226]";
$choices2[120430] = "Chemistry [120430]";
$choices2[104791] = "Emergency Medicine/Administration [104791]";
$choices2[104625] = "Health Policy [104625]";
$choices2[104782] = "Hearing And Speech Sciences [104782]";
$choices2[104216] = "Institute for Global Health [104216]";
$choices2[130100] = "Kennedy Center Institute (MC) [130100]";
$choices2[122450] = "Mechanical Engineering [122450]";
$choices2[104368] = "Medicine [104368]";
$choices2[104383] = "Medicine/Allergy Pulmonary & Critical Care [104383]";
$choices2[104333] = "Medicine/Cardiovascular Medicine [104333]";
$choices2[104342] = "Medicine/Clinical Pharmacology [104342]";
$choices2[104348] = "Medicine/Dermatology [104348]";
$choices2[104351] = "Medicine/Diabetes Endocrinology [104351]";
$choices2[104370] = "Medicine/Epidemiology [104370]";
$choices2[104355] = "Medicine/Gastroenterology [104355]";
$choices2[104366] = "Medicine/General Internal Medicine [104366]";
$choices2[104353] = "Medicine/Genetic Medicine [104353]";
$choices2[104379] = "Medicine/Hematology Oncology [104379]";
$choices2[104362] = "Medicine/Infectious Disease [104362]";
$choices2[104375] = "Medicine/Nephrology [104375]";
$choices2[104386] = "Medicine/Rheumatology [104386]";
$choices2[104336] = "Medicine/Stahlman Cardio Research [104336]";
$choices2[104270] = "Molecular Physiology & Biophysics [104270]";
$choices2[104400] = "Neurology [104400]";
$choices2[104407] = "Neurology/Cognitive Disorders [104407]";
$choices2[104403] = "Neurology/Epilepsy [104403]";
$choices2[104412] = "Neurology/Immunology [104412]";
$choices2[104409] = "Neurology/Movement Disorders [104409]";
$choices2[104415] = "Neurology/Neuromuscular [104415]";
$choices2[104418] = "Neurology/Oncology [104418]";
$choices2[104410] = "Neurology/Sleep Disorders [104410]";
$choices2[104425] = "Obstetrics and Gynecology [104425]";
$choices2[104450] = "Ophthalmology [104450]";
$choices2[104481] = "Ortho - Oncology [104481]";
$choices2[104475] = "Orthopaedics and Rehabilitation [104475]";
$choices2[999999] = "Other (999999)";
$choices2[104781] = "Otolaryngology [104781]";
$choices2[104500] = "Pathology [104500]";
$choices2[104555] = "Pediatrics/Adolescent Medicine [104555]";
$choices2[104565] = "Pediatrics/Cardiology [104565]";
$choices2[104570] = "Pediatrics/Child Development [104570]";
$choices2[104568] = "Pediatrics/Clinical Research Office [104568]";
$choices2[104582] = "Pediatrics/Emergency Medicine [104582]";
$choices2[104580] = "Pediatrics/Endocrinology [104580]";
$choices2[104585] = "Pediatrics/Gastroenterology [104585]";
$choices2[104595] = "Pediatrics/General Pediatrics [104595]";
$choices2[104590] = "Pediatrics/Genetics [104590]";
$choices2[104598] = "Pediatrics/Hematology [104598]";
$choices2[104623] = "Pediatrics/Hospital Medicine [104623]";
$choices2[104606] = "Pediatrics/Infectious Disease [104606]";
$choices2[104610] = "Pediatrics/Neonatology [104610]";
$choices2[104600] = "Pediatrics/Neurology [104600]";
$choices2[104621] = "Pediatrics/Pulmonary [104621]";
$choices2[104592] = "Pediatrics/Vanderbilt-Meharry Center in Sickle Cell [104592]";
$choices2[104290] = "Pharmacology [104290]";
$choices2[104291] = "Pharmacology/Clin Pharm [104291]";
$choices2[104795] = "Physical Medicine and Rehabilitation [104795]";
$choices2[104529] = "Psychiatry/Adult Psychiatry [104529]";
$choices2[104535] = "Psychiatry/Child & Adolescent Psychiatry [104535]";
$choices2[120660] = "Psychology [120660]";
$choices2[104675] = "Radiation Oncology [104675]";
$choices2[104650] = "Radiology and Radiological Science [104650]";
$choices2[106052] = "School of Nursing - Research Faculty [106052]";
$choices2[104703] = "Section of Surgical Science [104703]";
$choices2["SFS"] = "Service Free Stipends [SFS]";
$choices2[126230] = "Special Education [126230]";
$choices2[104477] = "Sports Medicine [104477]";
$choices2[104705] = "Surgery [104705]";
$choices2[104714] = "Surgery/Liver Transplant [104714]";
$choices2[104760] = "Surgery/Pediatric Surgery [104760]";
$choices2[104709] = "Surgery/Surgical Oncology [104709]";
$choices2[104726] = "Surgery/Thoracic Surgery [104726]";
$choices2[104717] = "Surgery/Trauma [104717]";
$choices2[104775] = "Urologic Surgery [104775]";
$choices2[104201] = "Vanderbilt Vaccine Center [104201]";
$choices2[104268] = "Biostatistics (104268)";
$choices2[104267] = "Biostatistics/Cancer Biostatistics (104267)";
$choices2[104202] = "Center for Biomedical Ethics and Society (104202)";
$choices2[104790] = "Emergency Medicine (104790)";
$choices2[104204] = "Institute of Medicine and Public Health (104204)";
$choices2[120727] = "Medicine, Health & Society (120727)";
}
function getReverseAwardTypes() {
return Grant::getReverseAwardTypes();
}
function getAwardTypes() {
return Grant::getAwardTypes();
}
# return boolean
function coeusNameMatch($n1, $n2) {
if (($n1 == "ho") || ($n2 == "ho") && (($n1 == "holden") || ($n2 == "holden"))) {
if ($n1 == $n2) {
return true;
}
} else {
if (preg_match("/^".$n1."/", $n2) || preg_match("/^".$n2."/", $n1)) {
return true;
}
}
if (preg_match("/[\(\-]".$n1."/", $n2) || preg_match("/[\(\-]".$n2."/", $n1)) {
return true;
}
return false;
}
# get rid of trailing initial
function coeusFixForMatch($n) {
$n = preg_replace("/\s+\w\.$/", "", $n);
$n = preg_replace("/\s+\w$/", "", $n);
$n = str_replace("???", "", $n);
return strtolower($n);
}
# returns true/false over whether the names "match"
function coeusMatch($fn1, $ln1, $fn2, $ln2) {
if (preg_match("/\s+\(.+\)/", $fn1)) {
$fn1 = preg_replace("/\s+\(.+\)/", "", $fn1);
}
$ln1s = array($ln1);
if (preg_match("/[\s\-]/", $ln1)) {
array_push($ln1s, preg_replace("/\-/", " ", $ln1), preg_replace("/\s/", "-", $ln1));
}
if (preg_match("/[a-z][A-Z]/", $ln1)) {
array_push($ln1s, preg_replace("/([a-z])([A-z])/", "$1 $2", $ln1));
}
if (preg_match("/[a-z] [A-Z]/", $ln1)) {
array_push($ln1s, preg_replace("/([a-z]) ([A-z])/", "$1$2", $ln1));
}
if (preg_match("/\s+\(.+\)/", $fn2)) {
$fn2 = preg_replace("/\s+\(.+\)/", "", $fn2);
}
$ln2s = array($ln2);
if (preg_match("/[\s\-]/", $ln2)) {
array_push($ln2s, preg_replace("/\-/", " ", $ln2), preg_replace("/\s/", "-", $ln2));
}
if (preg_match("/[a-z][A-Z]/", $ln2)) {
array_push($ln2s, preg_replace("/([a-z])([A-z])/", "$1 $2", $ln2));
}
if (preg_match("/[a-z] [A-Z]/", $ln2)) {
array_push($ln2s, preg_replace("/([a-z]) ([A-z])/", "$1$2", $ln2));
}
foreach ($ln1s as $ln1a) {
foreach ($ln2s as $ln2a) {
if ($fn1 && $ln1a && $fn2 && $ln2a) {
$fn1 = coeusFixForMatch($fn1);
$fn2 = coeusFixForMatch($fn2);
$ln1a = coeusFixForMatch($ln1a);
$ln2a = coeusFixForMatch($ln2a);
if (coeusNameMatch($fn1, $fn2) && coeusNameMatch($ln1a, $ln2a)) {
return true;
}
}
}
}
return false;
}
# returns recordId that matches
# returns "" if no match
function matchName($first, $last) {
global $token, $server;
return NameMatcher::matchName($first, $last, $token, $server);
}
# returns an array of recordId's that matches respective last, first
# returns "" if no match
function matchNames($firsts, $lasts) {
global $token, $server;
return NameMatcher::matchNames($firsts, $lasts, $token, $server);
}
function prettyMoney($n, $displayCents = TRUE) {
return REDCapManagement::prettyMoney($n, $displayCents);
}
function pretty($n, $numDecimalPlaces = 3) {
return REDCapManagement::pretty($n, $numDecimalPlaces);
}
function downloadURL($url) {
global $pid;
return REDCapManagement::downloadURL($url, $pid);
}
# given two timestamps (UNIX) $start, $end - let's call this duration.
# provide the timestamps of a larger period, $yearStart, $yearEnd
# figures the fraction of the year that is filled by the duration
# returns value | 0 <= value <= 1
function calculateFractionEffort($start, $end, $yearStart, $yearEnd) {
if ($start && $end) {
$grantDur = $end - $start;
$yearDur = $yearEnd - $yearStart;
$currDur = 0;
if (($start >= $yearStart) && ($start <= $yearEnd)) {
if ($end > $yearEnd) {
$currDur = $yearEnd - $start;
} else {
$currDur = $end - $start;
}
} else if (($end >= $yearStart) && ($end <= $yearEnd)) {
# currStart before yearStart
$currDur = $end - $yearStart;
} else if (($end > $yearEnd) && ($start < $yearStart)) {
$currDur = $yearDur;
}
return $currDur / $grantDur;
}
return 0;
}
# helper function to add to grant totals
# totals is the array with the totals (fields direct, vumc, nonvumc)
# row is the REDCap row with either COEUS or RePORTER/ExPORTER data
# instrument is coeus or exporter, or reporter, or custom
# fraction is the amount of the budget to be allocated for the current year. 0 <= value <= 1
# base award numbers are those base award numbers in reporter that do not need to be included from COEUS
function addToGrantTotals($totals, $row, $instrument, $fraction, $usedBaseAwardNumbers) {
if ($instrument == "coeus") {
$awardNo = $row['coeus_sponsor_award_number'];
$baseAwardNumber = getBaseAwardNumber($awardNo);
if ($row['coeus_direct_cost_budget_period']) {
$part = floor($fraction * $row['coeus_direct_cost_budget_period']);
$totals['direct'] += $part;
// echo "SUMMARY GRANTS A $fraction direct {$row['coeus_direct_cost_budget_period']} Adding $part = {$totals['direct']} $awardNo\n";
} else {
// echo "SUMMARY GRANTS B\n";
}
if (!in_array($baseAwardNumber, $usedBaseAwardNumbers) && $row['coeus_total_cost_budget_period']) {
$part = floor($fraction * $row['coeus_total_cost_budget_period']);
$totals['vumc'] += $part;
// echo "SUMMARY GRANTS C $fraction total {$row['coeus_total_cost_budget_period']} Adding $part = {$totals['vumc']} $awardNo\n";
} else {
// echo "SUMMARY GRANTS D '{$row['coeus_total_cost_budget_period']}' $baseAwardNumber: ".json_encode($usedBaseAwardNumbers)."\n";
}
} else if ($instrument == "exporter") {
$awardNo = $row['exporter_full_project_num'];
$baseAwardNumber = getBaseAwardNumber($awardNo);
if ($row['exporter_org_name'] && preg_match("/vanderbilt/", strtolower($row['exporter_org_name']))) {
if (!in_array($baseAwardNumber, $usedBaseAwardNumbers) && $row['exporter_total_cost']) {
$part = floor($fraction * $row['exporter_total_cost']);
$totals['vumc'] += $part;
// echo "SUMMARY GRANTS E $fraction total {$row['exporter_total_cost']} Adding $part = {$totals['vumc']} $awardNo\n";
} else {
// echo "SUMMARY GRANTS F $awardNo seen before\n";
}
} else {
$totals['nonvumc'] += floor($fraction * $row['exporter_total_cost']);
}
} else if ($instrument == "reporter") {
$awardNo = $row['reporter_projectnumber'];
$baseAwardNumber = getBaseAwardNumber($awardNo);
if ($row['reporter_orgname'] && preg_match("/vanderbilt/", strtolower($row['reporter_orgname']))) {
if (!in_array($baseAwardNumber, $usedBaseAwardNumbers) && $row['reporter_totalcostamount']) {
$part = floor($fraction * $row['reporter_totalcostamount']);
$totals['vumc'] += $part;
// echo "SUMMARY GRANTS G $fraction total {$row['reporter_totalcostamount']} Adding $part = {$totals['vumc']} $awardNo\n";
} else {
// echo "SUMMARY GRANTS H $awardNo seen before\n";
}
} else {
$totals['nonvumc'] += floor($fraction * $row['reporter_totalcostamount']);
}
} else if ($instrument == "custom_grant") {
$awardNo = $row['custom_number'];
$baseAwardNumber = getBaseAwardNumber($awardNo);
if (!in_array($baseAwardNumber, $usedBaseAwardNumbers) && $row['custom_costs']) {
$totals['direct'] += floor($fraction * $row['custom_costs']);
$totals['vumc'] += floor($fraction * $row['custom_costs']);
}
}
return $totals;
}
# gets the time from a RePORTER formatting (YYYY-MM-DDThh:mm:ss);
function getReporterTime($dt) {
if (!$dt) {
return "";
}
$nodes = preg_split("/T/", $dt);
if (count($nodes) != 2) {
return "";
}
return $nodes[1];
}
# gets the date from a RePORTER formatting (YYYY-MM-DDThh:mm:ss);
# returns YYYY-MM-DD
function getReporterDate($dt) {
return REDCapManagement::getReporterDateInYMD($dt);
}
function getCohorts($row) {
$ary = array();
$years = getCohort($row);
$ary[] = $years;
$KL2s = array("VCTRSKL2", "KL2", "VPSD", "VCTRS");
for ($i = 1; $i <= 15; $i++) {
# KL2 or Internal K
if (preg_match("/KL2/", $row['summary_award_sponsorno_'.$i]) || (in_array($row['summary_award_sponsorno_'.$i], $KL2s) && ($row['summary_award_type_'.$i] == 2)) || ($row['summary_award_type_'.$i] == 1)) {
if (!in_array("KL2s + Int_Ks", $ary)) {
$ary[] = "KL2s + Int_Ks";
}
}
}
return $ary;
}
function getCohort($row) {
$begins = array(1998, 2003, 2008, 2013);
$ends = array(2002, 2007, 2012, 2017);
for ($i = 1; $i <= 15; $i++) {
if ($row['summary_award_date_'.$i] && ($row['summary_award_type_'.$i] >= 1) && ($row['summary_award_type_'.$i] <= 4)) {
$nodes = preg_split("/-/", $row['summary_award_date_'.$i]);
for ($j = 0; $j < count($begins); $j++) {
if (($begins[$j] <= $nodes[0]) && ($ends[$j] >= $nodes[0])) {
return $begins[$j]."-".$ends[$j];
}
}
}
}
return "";
}
function json_encode_with_spaces($data) {
return REDCapManagement::json_encode_with_spaces($data);
}
function YMD2MDY($ymd) {
return REDCapManagement::YMD2MDY($ymd);
}
function MDY2YMD($mdy) {
return REDCapManagement::MDY2YMD($mdy);
}
function getLabels($metadata) {
return REDCapManagement::getLabels($metadata);
}
function getChoices($metadata) {
return REDCapManagement::getChoices($metadata);
}
function getAlphabetizedNames($token, $server) {
$names = Download::names($token, $server);
$lastNames = Download::lastnames($token, $server);
asort($lastNames);
$orderedNames = array();
foreach ($lastNames as $recordId => $lastName) {
$orderedNames[$recordId] = $names[$recordId];
}
return $orderedNames;
}
function getNamesForRow($row) {
$firstNamesPre = preg_split("/[\s\-]/", $row['identifier_first_name']);
$firstNames = array();
foreach ($firstNamesPre as $firstName) {
if (preg_match("/^\(.+\)$/", $firstName, $matches)) {
$match = preg_replace("/^\(/", "", $matches[0]);
$match = preg_replace("/\)$/", "", $match);
$firstNames[] = $match;
} else {
$firstNames[] = $firstName;
}
}
$lastNames = preg_split("/[\s\-]/", $row['identifier_last_name']);
$names = array($row['identifier_first_name']." ".$row['identifier_last_name']);
foreach ($firstNames as $firstName) {
foreach ($lastNames as $lastName) {
if (!in_array($firstName." ".$lastName, $names)) {
$names[] = $firstName." ".$lastName;
}
}
}
return $names;
}
# returns two-item array;
# first item: from array("Converted", "On Internal K", "On External K", "Left", "Not Converted")
# second item: the time the event has happened or will happen. NULL if Not Converted
function getConvertedStatus($normativeRow) {
if ($normativeRow['summary_first_r01']) {
return array("Converted", $normativeRow['summary_first_r01']);
}
if ($normativeRow['summary_left_vanderbilt']) {
return array("Left", $normativeRow['summary_left_vanderbilt']);
}
if ($normativeRow["summary_last_external_k"]) {
$today = time();
$start = strtotime($normativeRow['summary_last_external_k']);
$endDate = date("m-d", $start);
$endYear = date("Y", $start) + 5;
$end = strtotime($endYear."-".$endDate);
$extKs = array(3, 4);
for ($i = 1; $i <= 15; $i++) {
if (in_array($normativeRow['summary_award_type_'.$i], $extKs)) {
if ($normativeRow['summary_award_end_date_'.$i]) {
$currEndTs = strtotime($normativeRow['summary_award_end_date_'.$i]);
if ($currEndTs > $end) {
$end = $currEndTs;
}
}
}
}
if ($end > $today) {
return array("On External K", date("Y-m-d", $end));
}
}
if ($normativeRow["summary_last_any_k"]) {
$today = time();
$start = strtotime($normativeRow['summary_last_any_k']);
$endDate = date("m-d", $start);
$endYear = date("Y", $start) + 3;
$end = strtotime($endYear."-".$endDate);
$allKs = array(1, 2, 3, 4);
for ($i = 1; $i <= 15; $i++) {
if (in_array($normativeRow['summary_award_type_'.$i], $allKs)) {
if ($normativeRow['summary_award_end_date_'.$i]) {
$currEndTs = strtotime($normativeRow['summary_award_end_date_'.$i]);
if ($currEndTs) {
$end = $currEndTs;
}
}
}
}
if ($end > $today) {
return array("On Internal K", date("Y-m-d", $end));
}
}
return array("Not Converted", null);
}
function getNextRecord($record) {
global $token, $server;
$records = Download::recordIds($token, $server);
$i = 0;
foreach ($records as $rec) {
if ($rec == $record) {
if ($i + 1 < count($records)) {
return $records[$i + 1];
} else {
return $records[0];
}
}
$i++;
}
}
function decodeCitations($citationStr) {
$citationAry = array();
if ($citationStr) {
$citationAry = json_decode($citationStr, true);
}
return $citationAry;
}
function saveSetting($setting, $value) {
global $module;
$module->setProjectSetting($setting, $value);
}
function getSetting($setting) {
global $module;
return $module->getProjectSetting($setting);
}
function getSurveys() {
$emailSurveys = getSetting(getSurveySettingName());
if ($emailSurveys && !empty($emailSurveys)) {
return $emailSurveys;
} else {
$default = array(
"Initial Survey" => "check_date",
"Follow-Up Survey(s)" => "followup_date",
);
$json = json_encode($default);
saveEmailSetting(getSurveySettingName(), $default);
return $default;
}
}
function getSurveyTypes() {
return getSurveys();
}
function getAllEmailSettings() {
return getSurveySettings();
}
function getSurveySettings() {
return getAllSettings();
}
function saveEmailSetting($setting, $value) {
return saveSetting($setting, $value);
}
function getEmailSetting($setting) {
return getSetting($setting);
}
function dateSort(&$data) {
$newData = array();
foreach ($data as $key => $date) {
$newData[$key] = strtotime($date);
}
arsort($newData);
$returnData = array();
foreach ($newData as $key => $ts) {
$returnData[$key] = $data[$key];
}
return $returnData;
}
function getSurveySettingName() {
return "surveys";
}
function getAllSettings() {
global $module;
$data = $module->getProjectSetting(CareerDev::getGeneralSettingName());
if (is_array($data)) {
$isDate = TRUE;
foreach ($data as $key => $value) {
if (!preg_match("/^\d\d\d\d-\d+-\d+$/", $value)) {
$isDate = FALSE;
break;
}
}
if ($isDate) {
dateSort($data);
}
return $data;
}
return array();
}
function convertTo1DArray($ary) {
$ary2 = array();
foreach ($ary as $i => $id) {
array_push($ary2, $id);
}
return $ary2;
}
function indexREDCapData($redcapData) {
return REDCapManagement::indexREDCapData($redcapData);
}
function getIndexedRedcapData($token, $server, $fields, $cohort = "", $metadata = array()) {
if ($token && $server && $fields && !empty($fields)) {
if ($cohort) {
$records = Download::cohortRecordIds($token, $server, Application::getModule(), $cohort);
} else {
$records = Download::recordIds($token, $server);
}
$redcapData = Download::fieldsForRecords($token, $server, $fields, $records);
return indexREDCapData($redcapData);
}
return array();
}
function getCohortSelect($token, $server, $pid) {
$page = Sanitizer::sanitize($_GET['page'] ?? "");
$prefix = Sanitizer::sanitize($_GET['prefix'] ?? "");
$html = "<select onchange='var base = \"?page=".urlencode($page)."&prefix=".urlencode($prefix)."&pid=$pid\"; if ($(this).val()) { window.location.href = base+\"&cohort=\" + $(this).val(); } else { window.location.href = base; }'>\n";
$cohorts = new Cohorts($token, $server, CareerDev::getModule());
$cohortTitles = $cohorts->getCohortTitles();
$html .= "<option value=''>---ALL---</option>\n";
foreach ($cohortTitles as $title) {
$html .= "<option value='$title'";
if ($title == $_GET['cohort']) {
$html .= " selected";
}
$html .= ">$title</option>\n";
}
$html .= "</select>\n";
return $html;
}
function getCohortHeaderHTML() {
$html = "";
$html .= "<div class='subnav'>\n";
$html .= "<a class='yellow' href='".CareerDev::link("cohorts/addCohort.php")."'>Add a New Cohort</a>";
$html .= "<a class='yellow' href='".CareerDev::link("cohorts/viewCohorts.php")."'>View Existing Cohorts</a>";
$html .= "<a class='purple' href='".CareerDev::link("cohorts/manageCohorts.php")."'>Manage Cohorts</a>";
$html .= "<a class='purple' href='".CareerDev::link("cohorts/exportCohort.php")."'>Export a Cohort</a>";
$html .= "<a class='green' href='".CareerDev::link("cohorts/profile.php")."'>Cohort Profiles</a>";
$html .= "<a class='green' href='".CareerDev::link("cohorts/selectCohort.php")."'>View Cohort Metrics</a>";
# this CSS gives dropdowns enough space to stay above the footer
# I put it here so that it'd only apply to cohorts, not other pages, which seem not to have this problem
$html .= "<style>
#ui-id-1 { padding-bottom: 75px; }
.ui-dialog #ui-id-1 { padding-bottom: 0; }
</style>";
$html .= "</div>\n";
return $html;
}
function makeHTMLId($id) {
return REDCapManagement::makeHTMLId($id);
}
function makeSafe($htmlStr) {
$htmlStr = REDCapManagement::stripHTML($htmlStr);
$htmlStr = REDCapManagement::sanitize($htmlStr);
return $htmlStr;
}
function changeTextColorOfLink($str, $color) {
return Links::changeTextColorOfLink($str, $color);
}
function isAssoc($ary) {
if (empty($ary)) {
return FALSE;
}
return array_keys($ary) !== range(0, count($ary) - 1);
}
function avg($ary) {
return array_sum($ary) / count($ary);
}
function quartile($ary, $quartile) {
if (!is_int($quartile)) {
return FALSE;
}
if (($quartile < 0) || ($quartile > 4)) {
return FALSE;
}
if (isAssoc($ary)) {
return FALSE;
}
sort($ary);
$size = count($ary);
switch($quartile) {
case 0:
return $ary[0];
case 1:
$ary2 = array();
for ($i = 0; $i < $size / 2; $i++) {
array_push($ary2, $ary[$i]);
}
return getMedian($ary2);
case 2:
return getMedian($ary);
case 3:
$ary2 = array();
for ($i = (int) ceil($size / 2); $i < $size; $i++) {
array_push($ary2, $ary[$i]);
}
return getMedian($ary2);
case 4:
return $ary[$size - 1];
}
}
function getMedian($ary) {
sort($ary);
$size = count($ary);
if ($size % 2 == 0) {
$idx = (int) ($size / 2);
return ($ary[$idx - 1] + $ary[$idx]) / 2;
} else {
$idx = (int) (($size - 1) / 2);
return $ary[$idx];
}
}
function removeBrandLogo() {
global $module;
$module->removeProjectSetting(getBrandLogoName());
}
function saveBrandLogo($base64) {
global $module;
$module->setProjectSetting(getBrandLogoName(), $base64);
}
function getFieldForCurrentEmailSetting() {
return EmailManager::getFieldForCurrentEmailSetting();
}
function isEmailAddress($str) {
if (preg_match("/^\w+([\.-]?\w+)*@\w+([\.-]?\w+)*(\.\w{2,3})+$/", $str)) {
return TRUE;
}
return FALSE;
}
function getBrandLogoName($currModule = NULL) {
if ($currModule) {
return $currModule->getBrandLogoName();
}
global $module;
return $module->getBrandLogoName();
}
function getBrandLogo($currModule = NULL) {
if ($currModule) {
return $currModule->getBrandLogo();
}
global $module;
return $module->getBrandLogo();
}
function makeHeaders($module = NULL, $token = NULL, $server = NULL, $pid = NULL, $tokenName = NULL) {
if (!$module) { global $module; }
if (!$token) { global $token; }
if (!$server) { global $server; }
if (!$pid) { global $pid; }
if (!$tokenName) { global $tokenName; }
if ($module) {
return $module->makeHeaders($token, $server, $pid, $tokenName);
}
return "";
}
function isREDCap() {
return CareerDev::isREDCap();
}
function isFAQ() {
return CareerDev::isFAQ();
}
# eligibility determined by whether on K award (3 years for internal Ks; 5 years for external Ks)
# returns false if ineligible
# else returns index (1-15) of summary award
function findEligibleAward($row) {
if (isset($_GET['test'])) {
echo "findEligibleAward with ".$row['record_id']."<br>";
}
if ($row['redcap_repeat_instance'] !== "") {
return false;
}
$rs = array(5, 6);
$hasR = false;
for ($i = 1; $i <= Grants::$MAX_GRANTS; $i++) {
if (in_array($row['summary_award_type_'.$i], $rs)) {
$hasR = true;
}
}
if ($hasR) {
if (isset($_GET['test'])) {
echo $row['record_id']." has R<br>";
}
return false;
}
$extKs = array(3, 4);
for ($i = 1; $i <= Grants::$MAX_GRANTS; $i++) {
if (in_array($row['summary_award_type_'.$i], $extKs)) {
$diff = Grants::datediff(date("Y-m-d"), $row['summary_award_date_'.$i], "y");
$intendedYearSpan = Application::getIndividualKLength();
if ($row['summary_award_end_date_'.$i]) {
$intendedYearSpan = Grants::datediff($row['summary_award_end_date_'.$i], $row['summary_award_date_'.$i], "y");
}
if (isset($_GET['test'])) {
echo $row['record_id']." comparing $diff and $intendedYearSpan for $i<br>";
}
if ($diff <= $intendedYearSpan) {
return $i;
}
}
}
$intKs = array(1, 2);
for ($i = 1; $i <= Grants::$MAX_GRANTS; $i++) {
if (in_array($row['summary_award_type_'.$i], $intKs)) {
$diff = Grants::datediff(date("Y-m-d"), $row['summary_award_date_'.$i], "y");
$intendedYearSpan = 0;
if ($row['summary_award_type_'.$i] == 1) {
$intendedYearSpan = Application::getInternalKLength();
} else if ($row['summary_award_type_'.$i] == 2) {
$intendedYearSpan = Application::getK12KL2Length();
}
if ($row['summary_award_end_date_'.$i]) {
$intendedYearSpan = Grants::datediff($row['summary_award_end_date_'.$i], $row['summary_award_date_'.$i], "y");
}
if (isset($_GET['test'])) {
echo $row['record_id']." comparing $diff and $intendedYearSpan for $i<br>";
}
if ($diff <= $intendedYearSpan) {
return $i;
}
}
}
if (isset($_GET['test'])) {
echo $row['record_id']." returning FALSE<br>";
}
return false;
}
# $data is JSON or array structure from JSON in REDCap format
# returns a set of REDCap data sorted by last name
# if a record does not have a name, it is appended at the end
function alphabetizeREDCapData($data) {
if (!is_array($data)) {
$data = json_decode($data, true);
}
if ($data) {
$names = array();
$excluded = array();
if (!isAssoc($data)) {
foreach ($data as $row) {
if ($row['identifier_last_name'] && $row['identifier_first_name']) {
$names[$row['record_id']] = $row['identifier_last_name'].", ".$row['identifier_first_name'];
}
}
foreach ($data as $row) {
if (!in_array($row['record_id'], $excluded) && !isset($names[$row['record_id']])) {
$excluded[] = $row['record_id'];
}
}
} else {
foreach ($data as $recordId => $rows) {
foreach ($rows as $row) {
if ($row['identifier_last_name'] && $row['identifier_first_name']) {
$names[$row['record_id']] = $row['identifier_last_name'].", ".$row['identifier_first_name'];
}
}
}
foreach ($data as $recordId => $rows) {
foreach ($rows as $row) {
if (!in_array($row['record_id'], $excluded) && !isset($names[$row['record_id']])) {
$excluded[] = $row['record_id'];
}
}
}
}
asort($names);
$returnData = array();
foreach ($names as $recordId => $name) {
if (!isAssoc($data)) {
foreach ($data as $row) {
if ($recordId == $row['record_id']) {
$returnData[] = $row;
}
}
} else {
foreach ($data as $recordIdData => $rows) {
if ($recordId == $recordIdData) {
$returnData[$recordId] = $rows;
}
}
}
}
foreach ($excluded as $recordId) {
if (!isAssoc($data)) {
foreach ($data as $row) {