$raw_data_rows = explode('|||', strip_tags(str_replace('<br>', '|||', $result['data_display'])));
foreach ($raw_data_rows AS $raw_data_row) {
$this_row_array = explode(': ', $raw_data_row);
$data_array[$this_row_array[0]] = $this_row_array[1];
}
ksort($data_array);
d($data_array);
/**
* we don't want to duplicate queries
* if the result is excluded or has a query history, ignore it
*/
if (!$result['exclude']) {
d($history);
//$data_row['monitor'] = $result['record'] & 1 ? 'dianne_mattingly' : 'wendy_robertson';
$data_row['subjid'] = quote_wrap($result['record']);
$data_row['usubjid'] = quote_wrap(get_single_field($result['record'], PROJECT_ID, $Proj->firstEventId, 'dm_usubjid', ''));
$data_row['event'] = quote_wrap(REDCap::getEventNames(false, false, $result['event_id']));
//$data_row['field'] = quote_wrap($Proj->metadata[$field]['element_label']);
//$data_row['data'] = quote_wrap(strip_tags(str_replace('<br>', ', ', $result['data_display'])));
foreach ($data_array AS $key => $val) {
$data_row[quote_wrap($Proj->metadata[$key]['element_label'] . " [$key]")] = quote_wrap($val);
}
$data_row['description'] = quote_wrap($rule_info['name']);
$data_row["Queries on $field"] = quote_wrap(count($history));
$row_csv = implode(',', $data_row) . "\n";
$table_csv .= $row_csv;
}
}
}
$headers = implode(',', array_keys($data_row)) . "\n";
if (!$debug) {
$allowed_pids = array('38');
REDCap::allowProjects($allowed_pids);
/**
* do stuff
*/
if ($debug) {
if (!is_form_locked($record, $instrument, $redcap_event_name)) {
d(is_t_complete($record, $event_id), $redcap_event_name);
}
global $Proj, $project_id;
$today = date("Y-m-d");
$fields = array();
$arms = get_arms(array_keys($Proj->eventsForms));
d($arms);
$baseline_event_id = $Proj->firstEventId;
$tx_duration = get_single_field($record, $project_id, $baseline_event_id, 'trt_exdur', null);
$tx_duration = substr($tx_duration, strpos($tx_duration, 'P') + 1, strlen($tx_duration) - 2);
$tx_first_event = array_search_recursive($tx_duration . ' Weeks', $arms) !== false ? array_search_recursive($tx_duration . ' Weeks', $arms) : null;
$survey_event_ids = $Proj->getEventsByArmNum($arms[$tx_first_event]['arm_num']);
d($survey_event_ids);
foreach ($survey_event_ids as $survey_event_id) {
$survey_event_name = $Proj->getUniqueEventNames($survey_event_id);
$survey_prefix = substr($survey_event_name, 0, strpos($survey_event_name, '_'));
$fields[] = $survey_prefix . '_completed';
$fields[] = $survey_prefix . '_date';
$fields[] = $survey_prefix . '_startdate';
$fields[] = $survey_prefix . '_deadline';
$fields[] = $survey_prefix . '_missed';
}
d($fields);
$data = REDCap::getData('array', $record, $fields, $baseline_event_id);
/**
* @param $record
* @param $debug
* determine completeness of all survey-containing events
*/
function set_survey_completion($record, $debug)
{
if (isset($record)) {
global $Proj, $project_id;
$today = date("Y-m-d");
$fields = array();
$arms = get_arms(array_keys($Proj->eventsForms));
$baseline_event_id = $Proj->firstEventId;
$trt = Treatment::getTrtInfo($record);
/**
* use the selected duration ($trt['arm']) to set timings
*/
$tx_first_event = array_search_recursive($trt['arm'], $arms) !== false ? array_search_recursive($trt['arm'], $arms) : null;
$survey_event_ids = isset($tx_first_event) ? $Proj->getEventsByArmNum($arms[$tx_first_event]['arm_num']) : null;
foreach ($survey_event_ids AS $survey_event_id) {
$data_event_name = $Proj->getUniqueEventNames($survey_event_id);
$prefix = substr($data_event_name, 0, strpos($data_event_name, '_'));
/**
* derive inter-event timing variables
*/
$start_date_value = get_single_field($record, $project_id, $baseline_event_id, $prefix . '_startdate', null);
$deadline_value = get_single_field($record, $project_id, $baseline_event_id, $prefix . '_deadline', null);
/**
* for baseline surveys, reference date is randomization date. For all other survey events,
* reference date is dm_rfxstdtc, recorded treatment start date NOT dm_rfstdtc, the
* treatment start derived from the treatment med data
*/
$t_base_date = in_array($prefix, array('baseline', 'eot1year', 'eot3year')) ? $trt['rand_date'] : $trt['rfxstdtc'];
if (isset($t_base_date) && $t_base_date != '') {
$t_start_date = add_date($t_base_date, ($arms[$data_event_name]['day_offset'] - $arms[$data_event_name]['offset_min']));
update_field_compare($record, $project_id, $baseline_event_id, $t_start_date, $start_date_value, $prefix . '_startdate', $debug);
$t_deadline_date = add_date($t_base_date, ($arms[$data_event_name]['day_offset'] + $arms[$data_event_name]['offset_max']) - 1);
update_field_compare($record, $project_id, $baseline_event_id, $t_deadline_date, $deadline_value, $prefix . '_deadline', $debug);
}
}
foreach ($survey_event_ids AS $survey_event_id) {
$survey_event_name = $Proj->getUniqueEventNames($survey_event_id);
$survey_prefix = substr($survey_event_name, 0, strpos($survey_event_name, '_'));
$fields[] = $survey_prefix . '_completed';
$fields[] = $survey_prefix . '_date';
$fields[] = $survey_prefix . '_startdate';
$fields[] = $survey_prefix . '_deadline';
}
$data = REDCap::getData('array', $record, $fields, $baseline_event_id);
/**
* switch to the scheduled arm to determine completion
* this is done to avoid subjects switching arms and orphaning surveys completed
* prior to duration change. This should (almost) never happen, but we still need to handle if it does
*/
$tx_first_event = array_search_recursive($trt['timing_arm'], $arms) !== false ? array_search_recursive($trt['timing_arm'], $arms) : null;
$survey_event_ids = isset($tx_first_event) ? $Proj->getEventsByArmNum($arms[$tx_first_event]['arm_num']) : null;
foreach ($survey_event_ids AS $survey_event_id) {
$data_event_name = $Proj->getUniqueEventNames($survey_event_id);
$prefix = substr($data_event_name, 0, strpos($data_event_name, '_'));
$is_t_complete = is_t_complete($record, $survey_event_id);
$t_complete = $is_t_complete ? '1' : '0';
$complete_value = get_single_field($record, $project_id, $baseline_event_id, $prefix . '_completed', null);
$deadline_value = get_single_field($record, $project_id, $baseline_event_id, $prefix . '_deadline', null);
$t_missed = $complete_value == '0' && $today > $deadline_value && isset($deadline_value) && $deadline_value != '' ? '1' : '0';
foreach ($data[$record] AS $data_event_id => $data_event) {
foreach ($data_event AS $key => $value) {
/**
* derive completion variables
*/
switch ($key) {
case $prefix . '_completed':
update_field_compare($record, $project_id, $data_event_id, $t_complete, $value, $key, $debug);
break;
case $prefix . '_date':
if ($value == '' && $is_t_complete) {
update_field_compare($record, $project_id, $data_event_id, $today, $value, $key, $debug);
}
break;
case $prefix . '_missed':
update_field_compare($record, $project_id, $data_event_id, $t_missed, $value, $key, $debug);
break;
default:
break;
}
}
}
}
}
}
$sof_rbv_regimen = false;
$sof = array();
$rbv = array();
foreach ($due_data[$subject_id] AS $event_id => $event) {
if ($event['sof_cmstdtc'] != '') {
$sof[] = true;
}
if ($event['rib_cmstdtc'] != '') {
$rbv[] = true;
}
}
$sof_rbv_regimen = eval("return ((" . implode(' || ', $sof) . ") && (" . implode(' || ', $rbv) . "));");
/**
* get genotype
*/
$genotype = get_single_field($subject_id, $project_id, $first_event_id, 'hcvgt_lborres', '');
/**
* if regimen is SOF + RBV and Genotype 1 or 3
*/
if ($sof_rbv_regimen && ($genotype == '1' || $genotype == '3')) {
/**
* AND if TX start is 168 days ago, data is due
*/
if (date("Y-m-d") >= (add_date($tx_start_date, 168, 0, 0))) {
$hcv_data_due = true;
}
/**
* if regimen is SOF + RBV and Genotype 2
*/
} elseif ($sof_rbv_regimen && ($genotype == '2')) {
/**
foreach ($actions AS $subject_id => $subject) {
if ($debug) {
d($subject_id);
if ($subjects != '') {
d($subject);
d($data[$subject_id]);
}
}
/**
* pop the latest of these off the $subject array and set the ae_aeacn for the AE
*/
foreach (array_pop($subject) AS $ae_event_id => $ae_event) {
foreach ($ae_event AS $tx_prefix => $ae_acn) {
d($tx_prefix);
d($ae_acn);
$this_action = get_single_field($subject_id, $project_id, $ae_event_id, 'ae_aeacn', '');
d(array_search($ae_acn['txacn'], $action_priority));
d(array_search($this_action, $action_priority));
/**
* make sure we have priorities for both $this_action and $ae_acn['txacn']
*/
if (array_search($ae_acn['txacn'], $action_priority) !== false && array_search($this_action, $action_priority) !== false) {
/**
* determine priority of the current action. If its priority is higher than the one recorded, update.
*/
if (array_search($ae_acn['txacn'], $action_priority) > array_search($this_action, $action_priority)) {
update_field_compare($subject_id, $project_id, $ae_event_id, $ae_acn['txacn'], $this_action, 'ae_aeacn', $debug);
}
}
}
}
/**
* @param $record
* @param $debug
*/
function set_deltas($record, $debug)
{
global $Proj, $project_id;
$enable_kint = $debug && (isset($record) && $record != '') ? true : false;
Kint::enabled($enable_kint);
$baseline_event_id = $Proj->firstEventId;
$thresholds = array();
$fields = array();
$baselines = array();
$all_deltas = array();
$prefix_result = db_query("SELECT DISTINCT prefix, threshold FROM _target_lab_deltas WHERE project_id = '$project_id'");
if ($prefix_result) {
while ($prefixes = db_fetch_assoc($prefix_result)) {
$thresholds[$prefixes['prefix']]['threshold'] = $prefixes['threshold'];
}
db_free_result($prefix_result);
}
foreach ($thresholds AS $key => $value) {
$fields[] = $key . "_lbstresn";
$fields[] = $key . "_im_lbstresn";
$fields[] = $key . "_lbblfl";
$fields[] = $key . "_im_lbblfl";
}
$data = REDCap::getData('array', $record, $fields);
d($data);
foreach ($data AS $subject_id => $subject) {
foreach ($subject AS $event_id => $event) {
foreach (array_keys($thresholds) AS $lab_prefix) {
$all_deltas[$subject_id][$lab_prefix] = false;
if ($event[$lab_prefix . '_lbblfl'] == 'Y' && $event[$lab_prefix . '_lbstresn'] != '') {
$baselines[$subject_id][$lab_prefix] = $event[$lab_prefix . '_lbstresn'];
}
if ($event[$lab_prefix . '_im_lbblfl'] == 'Y' && $event[$lab_prefix . '_im_lbstresn'] != '') {
$baselines[$subject_id][$lab_prefix] = $event[$lab_prefix . '_im_lbstresn'];
}
}
}
d($baselines);
foreach ($subject AS $event_id => $event) {
foreach (array_keys($thresholds) AS $lab_prefix) {
$threshold = $thresholds[$lab_prefix]['threshold'];
$baseline = $baselines[$subject_id][$lab_prefix];
if (isset($baseline) && $baseline != '' && isset($threshold) && $threshold != '' && !$all_deltas[$subject_id][$lab_prefix]) {
if (isset($event[$lab_prefix . '_lbstresn']) && $event[$lab_prefix . '_lbstresn'] != '') {
if ($event[$lab_prefix . '_lbstresn'] - $baseline > $threshold) {
$all_deltas[$subject_id][$lab_prefix] = true;
}
}
if (isset($event[$lab_prefix . '_im_lbstresn']) && $event[$lab_prefix . '_im_lbstresn'] != '') {
if ($event[$lab_prefix . '_im_lbstresn'] - $baseline > $threshold) {
$all_deltas[$subject_id][$lab_prefix] = true;
}
}
}
}
}
}
d($thresholds);
d($all_deltas);
foreach ($all_deltas AS $subject_id => $lab_prefix) {
foreach ($lab_prefix AS $prefix => $had_delta) {
$delta = $had_delta ? 'Y' : 'N';
update_field_compare($subject_id, $project_id, $baseline_event_id, $delta, get_single_field($subject_id, $project_id, $baseline_event_id, $prefix . '_suppdm_gtdelta', ''), $prefix . '_suppdm_gtdelta', $debug);
}
}
}
$this_baseline_flag = 'Y';
} else {
/**
* Now reset all other flags that have changed
*/
foreach ($data[$subject_id] AS $flag_event_id => $flag_event) {
$reset[$flag_event_id] = $flag_event[$lab_prefix . '_im_lbblfl'];
}
foreach ($reset AS $reset_event_id => $reset_event) {
foreach ($reset_event as $reset_field => $reset_val) {
update_field_compare($subject_id, $project_id, $reset_event_id, '', $reset_val, $lab_prefix . "_im_lbblfl", $debug);
}
}
}
/**
* Baseline flag belongs in the event where the date occurs
*/
update_field_compare($subject_id, $project_id, $this_data['event_id'], $this_baseline_flag, $data[$subject_id][$this_data['event_id']][$lab_prefix . "_im_lbblfl"], $lab_prefix . "_im_lbblfl", $debug);
/**
* Baseline date belongs in Baseline event - one date for both abstracted and imported
*/
d($baseline_date);
update_field_compare($subject_id, $project_id, $initial_event, $baseline_date, get_single_field($subject_id, $project_id, $initial_event, $lab_prefix . "_supplb_lbdtbl", ''), $lab_prefix . "_supplb_lbdtbl", $debug);
}
}
}
}
}
$timer['main_end'] = microtime(true);
$init_time = benchmark_timing($timer);
echo $init_time;
*/
code_llt($project_id, $subject_id, $event_id, fix_case($event['ae_aeterm']), fix_case($event['ae_oth_aeterm']), $event['ae_aemodify'], 'ae_aemodify', $debug, $recode_llt, $recode_msg);
if ($debug) {
error_log("DEBUG: Coded AE_AEMODIFY {$event['ae_aemodify']}: subject=$subject_id, event=$event_id for AE {$event['ae_aeterm']} - {$event['ae_oth_aeterm']}");
}
/**
* AE_AEDECOD
*/
$aemodify = get_single_field($subject_id, $project_id, $event_id, 'ae_aemodify', '');
code_pt($project_id, $subject_id, $event_id, fix_case($aemodify), $event['ae_aedecod'], 'ae_aedecod', $debug, $recode_pt, $recode_msg);
if ($debug) {
error_log("DEBUG: Coded AE_AEDECOD {$event['ae_aedecod']}: subject=$subject_id, event=$event_id for AE {$aemodify}");
}
/**
* AE_AEBODSYS
*/
$aedecod = get_single_field($subject_id, $project_id, $event_id, 'ae_aedecod', '');
code_bodsys($project_id, $subject_id, $event_id, $aedecod, $event['ae_aebodsys'], 'ae_aebodsys', $debug, $recode_soc, $recode_msg);
if ($debug) {
error_log("DEBUG: Coded SOC: subject=$subject_id, event=$event_id for AE {$event['ae_aedecod']}");
}
$timer_stop = microtime(true);
$timer_time = number_format(($timer_stop - $timer_start), 2);
if ($debug) {
error_log("DEBUG: This DET action (Code AE) took $timer_time seconds");
}
}
}
$timer_stop = microtime(true);
$timer_time = number_format(($timer_stop - $timer_start), 2);
echo 'This page loaded in ', $timer_time / 60, ' minutes';
* plugin
*/
echo "<h3>$plugin_title</h3>";
/**
* MAIN
*/
if ($debug) {
$timer['main_start'] = microtime(true);
}
$fields = array();
foreach ($mh_prefixes AS $prefix) {
$fields[] = $prefix . "_oth_mhterm";
$fields[] = $prefix . "_mhmodify";
$fields[] = $prefix . "_mhdecod";
$fields[] = $prefix . "_mhbodsys";
}
$data = REDCap::getData('array', $subjects, $fields);
foreach ($data AS $subject_id => $subject) {
foreach ($subject AS $event_id => $event) {
foreach ($mh_prefixes AS $prefix) {
code_llt($project_id, $subject_id, $event_id, fix_case($event[$prefix . '_oth_mhterm']), '', $event[$prefix . '_mhmodify'], $prefix . '_mhmodify', $debug, $recode_llt);
code_pt($project_id, $subject_id, $event_id, get_single_field($subject_id, $project_id, $event_id, $prefix . "_mhmodify", ''), $event[$prefix . "_mhdecod"], $prefix . "_mhdecod", $debug, $recode_pt);
code_bodsys($project_id, $subject_id, $event_id, get_single_field($subject_id, $project_id, $event_id, $prefix . "_mhdecod", ''), $event[$prefix . "_mhbodsys"], $prefix . "_mhbodsys", $debug, $recode_soc);
}
}
}
if ($debug) {
$timer['main_end'] = microtime(true);
$init_time = benchmark_timing($timer);
echo $init_time;
}
/**
* @param $subject_id
* @param $debug
* determine completeness of all survey-containing events
*/
function events_completion($subject_id, $debug) {
if (isset($subject_id)) {
global $Proj, $project_id;
$today = date("Y-m-d");
$fields = array();
$arms = get_arms(array_keys($Proj->eventsForms));
$baseline_event_id = $Proj->firstEventId;
$enrollment_event_id = getNextEventId($baseline_event_id);
$tx_duration = get_single_field($subject_id, $project_id, $enrollment_event_id, 'dm_suppdm_actarmdur', null);
$tx_first_event = array_search_recursive($tx_duration . ' Weeks', $arms) !== false ? array_search_recursive($tx_duration . ' Weeks', $arms) : null;
$survey_event_ids = isset($tx_first_event) ? array_merge(array($baseline_event_id), $Proj->getEventsByArmNum($arms[$tx_first_event]['arm_num'])) : array($baseline_event_id);
foreach ($survey_event_ids AS $survey_event_id) {
$survey_event_name = $Proj->getUniqueEventNames($survey_event_id);
$survey_prefix = substr($survey_event_name, 0, strpos($survey_event_name, '_'));
$fields[] = $survey_prefix . '_completed';
$fields[] = $survey_prefix . '_date';
$fields[] = $survey_prefix . '_startdate';
$fields[] = $survey_prefix . '_deadline';
}
$data = REDCap::getData('array', $subject_id, $fields, $baseline_event_id);
foreach ($survey_event_ids AS $survey_event_id) {
$data_event_name = $Proj->getUniqueEventNames($survey_event_id);
$prefix = substr($data_event_name, 0, strpos($data_event_name, '_'));
$is_t_complete = is_t_complete($subject_id, $survey_event_id);
$t_complete = $is_t_complete ? '1' : '0';
foreach ($data[$subject_id] AS $data_event_id => $data_event) {
foreach ($data_event AS $key => $value) {
/**
* derive intra-event timing variables
*/
switch ($key) {
case $prefix . '_completed':
update_field_compare($subject_id, $project_id, $data_event_id, $t_complete, $value, $key, $debug);
break;
case $prefix . '_date':
if ($value == '' && $is_t_complete) {
update_field_compare($subject_id, $project_id, $data_event_id, $today, $value, $key, $debug);
}
break;
default:
break;
}
}
}
/**
* derive inter-event timing variables
*/
$complete_value = get_single_field($subject_id, $project_id, $baseline_event_id, $prefix . '_completed', null);
$start_date_value = get_single_field($subject_id, $project_id, $baseline_event_id, $prefix . '_startdate', null);
$deadline_value = get_single_field($subject_id, $project_id, $baseline_event_id, $prefix . '_deadline', null);
$missed_value = get_single_field($subject_id, $project_id, $baseline_event_id, $prefix . '_missed', null);
$t_missed = $complete_value == '0' && $today > $deadline_value && isset($deadline_value) && $deadline_value != '' ? '1' : '0';
switch ($prefix) {
case 't1':
$t_base_date = get_single_field($subject_id, $project_id, $baseline_event_id, $prefix . '_date', null);
$t_start_date = $t_base_date;
$t_deadline_date = add_date($t_base_date, 89);
break;
default:
$t_base_date = get_single_field($subject_id, $project_id, $enrollment_event_id, 'dm_rfstdtc', null);
$t_start_date = add_date($t_base_date, ($arms[$data_event_name]['day_offset'] - $arms[$data_event_name]['offset_min']));
$t_deadline_date = add_date($t_base_date, ($arms[$data_event_name]['day_offset'] + $arms[$data_event_name]['offset_max']) - 1);
break;
}
update_field_compare($subject_id, $project_id, $baseline_event_id, $t_complete, $complete_value, $prefix . '_completed', $debug);
update_field_compare($subject_id, $project_id, $baseline_event_id, $t_missed, $missed_value, $prefix . '_missed', $debug);
if (isset($t_base_date) && $t_base_date != '') {
update_field_compare($subject_id, $project_id, $baseline_event_id, $t_start_date, $start_date_value, $prefix . '_startdate', $debug);
update_field_compare($subject_id, $project_id, $baseline_event_id, $t_deadline_date, $deadline_value, $prefix . '_deadline', $debug);
}
}
}
}
$destination_form = $Proj->metadata[$field]['form_name'];
/**
* Execute this rule
*/
$dq->executeRule($rule_id);
// $results_table = $dq->displayResultsTable($rule_info);
// print $results_table[2];
// print $results_table[1];
/**
* cycle through rule results
*/
$rule_results = $dq->getLogicCheckResults();
foreach ($rule_results AS $results) {
foreach ($results AS $result) {
$dag_prefix = substr(get_single_field($result['record'], $project_id, $Proj->firstEventId, 'dm_usubjid', ''), 0, 3);
$dag_result = db_query("SELECT group_name FROM redcap_data_access_groups WHERE project_id = '$project_id' AND LEFT(group_name, 3) = '$dag_prefix'");
if ($dag_result) {
$dag_name = db_result($dag_result, 0, 'group_name');
$dag_name = prep($dag_name);
}
/**
* if the result is excluded ignore it
*/
if ($result['exclude'] != 1) {
$today = date('Y-m-d');
$redcap_event_name = $Proj->getUniqueEventNames($result['event_id']);
$check_table = array();
$check_table_result = db_query("SELECT * FROM _target_notifications WHERE project_id = '$project_id' AND record = '{$result['record']}' AND redcap_event_name = '$redcap_event_name' AND redcap_data_access_group = '$dag_name' AND form_name = '$destination_form' AND type = 'rule' AND type_id = '$rule_id' AND action_date = '$today'");
if ($check_table_result) {
$check_table = db_fetch_assoc($check_table_result);
/**
* restrict access to one or more pids
*/
$allowed_pids = array('26');
REDCap::allowProjects($allowed_pids);
/**
* set header so browser knows it's JSON
*/
header('Content-Type: application/json; charset=utf-8');
/**
* conmeds
*/
$fields = array('cm_cmstdtc', 'cm_cmtrt', 'cm_cmindc', 'cm_oth_cmindc', 'cm_suppcm_exacindc', 'cm_suppcm_prphindc');
$conmeds_data = REDCap::getData('array', $subjid, $fields);
foreach ($conmeds_data AS $subject_id => $subject) {
$rfstdtc = get_single_field($subject_id, $project_id, $baseline_event_id, 'dm_rfstdtc', '');
foreach ($subject AS $event_id => $event) {
$url = APP_PATH_WEBROOT_FULL . "redcap_v" . $redcap_version . "/DataEntry/index.php?pid=$project_id&page=conmeds&id=$subjid&event_id=$event_id";
$desc_array = array();
foreach ($event AS $field => $item) {
if ($item != '' && !in_array($field, array('cm_cmstdtc', 'cm_oth_cmindc', 'cm_cmtrt'))) {
if ($field == 'cm_cmindc' && $item == 'OTHER') {
$item = $event['cm_oth_cmindc'];
}
$desc_array[] = get_field_label($field, $project_id) . ': <strong>' . $item . "</strong>";
}
}
$event_start = $event['cm_cmstdtc'] != '' ? $event['cm_cmstdtc'] : $rfstdtc;
if ($event['cm_cmtrt'] != '') {
$eventAtts[] = get_event_array($event_start, '', '', implode("<br />", $desc_array), $event['cm_cmtrt'], '', '', $url);
}
if ($fields['utype'] == 'descriptive') {
$event[$fields['lborresu']] = $fields['ulabel'];
}
/**
* INR, HCVGT lbstresn
*/
if (count($lbstresn_array) > 0 && $subjects != '') {
d($lbstresn_array);
}
$fields['lbstresc'] = is_numeric($event[$fields['lborres']]) ? $fields['lbstresn'] : $fields['lborres'];
/**
* HCV Genotype transform
* @TODO: change LBSTRESN back to float and test cleaned values that wouldn't float...
*/
if ($fields['lbtestcd'] == 'HCVGT') {
$subtype = get_single_field($subject_id, $project_id, $Proj->firstEventId, 'hcvgt_s_lborres', '');
if ($subtype != '' && $subtype != 'NOT_AVAILABLE') {
$event[$fields['lborres']] = $event[$fields['lborres']] . $subtype;
}
$fields['lbstresc'] = $fields['lborres'];
$event[$fields['lbstresn']] = is_numeric($event[$fields['lborres']]) ? $event[$fields['lborres']] : null;
}
if (in_array($fields['lbtestcd'], $lbstresn_array)) {
$event[$fields['lbstresn']] = $event[$fields['lborres']];
}
/**
* iterate the fields and add to inner_vals array
*/
$fields['lbstnrlo'] = 'LBSTNRLO';
$fields['lbstnrhi'] = 'LBSTNRHI';
$fields['lbnrind'] = 'LBNRIND';
/**
* @param $record
* @param $redcap_event_name
* @param $instrument
* @param $type
* @param $debug
*/
public static function set_notification($record, $redcap_event_name, $instrument, $debug)
{
global $Proj, $project_id;
$group_id = self::getGroupID($record);
$group_name_result = db_query("SELECT group_name FROM redcap_data_access_groups WHERE project_id = '{$project_id}' AND group_id = '{$group_id}'");
if ($group_name_result) {
$today = date('Y-m-d');
$group_name_row = db_fetch_assoc($group_name_result);
$group_name = $group_name_row['group_name'];
$site_id = substr($group_name_row['group_name'], 0, 3);
$first_event_id = $Proj->firstEventId;
switch ($instrument) {
case 'site_source_upload_form':
if ($debug) {
error_log("DEBUG: {$instrument} notification for {$group_name}");
} else {
if (!db_query("INSERT INTO target_email_actions SET project_id = '{$project_id}', record = '{$record}', redcap_event_name = '{$redcap_event_name}', redcap_data_access_group = '" . prep($group_name) . "', form_name = '{$instrument}', action_date = '{$today}'")) {
error_log(db_error());
}
}
break;
case 'source_upload_form':
if ($debug) {
error_log("DEBUG: {$instrument} notification for {$group_name}");
} else {
if ($site_id >= '300') {
if (!db_query("INSERT INTO target_email_actions SET project_id = '{$project_id}', record = '{$record}', redcap_event_name = '{$redcap_event_name}', redcap_data_access_group = '" . prep($group_name) . "', form_name = '{$instrument}', action_date = '{$today}'")) {
error_log(db_error());
}
}
}
break;
case 'treatment_start':
$started_tx = get_single_field($record, $project_id, $first_event_id, 'trt_suppex_txstat', null);
if ($started_tx == 'Y') {
if ($debug) {
error_log("DEBUG: Subject# {$record} for {$group_name} has started treatment");
} else {
if (!db_query("INSERT INTO target_email_actions SET project_id = '{$project_id}', record = '{$record}', redcap_event_name = '{$redcap_event_name}', redcap_data_access_group = '" . prep($group_name) . "', form_name = '{$instrument}', action_date = '{$today}'")) {
error_log(db_error());
}
}
} else {
error_log("DEBUG: Subject# {$record} for {$group_name} has not started treatment");
}
break;
default:
break;
}
}
}
/**
* @param $record
* @param $debug
*/
public static function setTrtDuration($record, $debug)
{
/**
* derive treatment duration and therefore arm from randomized treatment and duration selected in this form
*/
global $Proj, $project_id;
$first_event_id = $Proj->firstEventId;
$trt = self::getTrtInfo($record);
if ($debug) {
error_log(print_r($trt, true));
}
$prescribed_duration = get_single_field($record, $project_id, $first_event_id, 'dm_suppex_trtdur', null);
if (!isset($prescribed_duration) || $prescribed_duration == '') {
update_field_compare($record, $project_id, $first_event_id, $trt['dur'], $prescribed_duration, 'dm_suppex_trtdur', $debug);
}
}
/**
* restrict access to one or more pids
*/
$allowed_pids = array('38');
REDCap::allowProjects($allowed_pids);
/**
* set header so browser knows it's JSON
*/
header('Content-Type: application/json; charset=utf-8');
/**
* conmeds
*/
$fields = array('cm_cmstdtc', 'cm_cmtrt', 'cm_cmindc', 'cm_oth_cmindc', 'cm_suppcm_exacindc', 'cm_suppcm_prphindc');
$conmeds_data = REDCap::getData('array', $subjid, $fields);
foreach ($conmeds_data AS $subject_id => $subject) {
$rfstdtc = get_single_field($subject_id, $project_id, $first_event_id, 'dm_rfstdtc', '');
foreach ($subject AS $event_id => $event) {
$url = APP_PATH_WEBROOT_FULL . "redcap_v" . $redcap_version . "/DataEntry/index.php?pid=$project_id&page=conmeds&id=$subjid&event_id=$event_id";
$desc_array = array();
foreach ($event AS $field => $item) {
if ($item != '' && !in_array($field, array('cm_cmstdtc', 'cm_oth_cmindc', 'cm_cmtrt'))) {
if ($field == 'cm_cmindc' && $item == 'OTHER') {
$item = $event['cm_oth_cmindc'];
}
$desc_array[] = get_field_label($field, $project_id) . ': <strong>' . $item . "</strong>";
}
}
$event_start = $event['cm_cmstdtc'] != '' ? $event['cm_cmstdtc'] : $rfstdtc;
if ($event['cm_cmtrt'] != '') {
$eventAtts[] = get_event_array($event_start, '', '', implode("<br />", $desc_array), $event['cm_cmtrt'], '', '', $url);
}
* project metadata
*/
$project = new Project();
$first_event_id = $project->firstEventId;
$plugin_title = "Derive INDCMODF, INDCOD and INDCSYS for all CMINDC";
/**
* plugin
*/
echo "<h3>$plugin_title</h3>";
/**
* MAIN
*/
if ($debug) {
$timer['main_start'] = microtime(true);
}
$fields = array('cm_cmindc', 'cm_oth_cmindc', 'cm_suppcm_indcmodf', 'cm_suppcm_indcod', 'cm_suppcm_indcsys');
$data = REDCap::getData('array', $subjects, $fields);
foreach ($data AS $subject_id => $subject) {
foreach ($subject AS $event_id => $event) {
if ($event['cm_cmindc'] != '') {
code_llt($project_id, $subject_id, $event_id, fix_case($event['cm_cmindc']), fix_case($event['cm_oth_cmindc']), $event['cm_suppcm_indcmodf'], 'cm_suppcm_indcmodf', $debug, $recode_llt);
code_pt($project_id, $subject_id, $event_id, get_single_field($subject_id, $project_id, $event_id, "cm_suppcm_indcmodf", ''), $event["cm_suppcm_indcod"], "cm_suppcm_indcod", $debug, $recode_pt);
code_bodsys($project_id, $subject_id, $event_id, get_single_field($subject_id, $project_id, $event_id, "cm_suppcm_indcod", ''), $event["cm_suppcm_indcsys"], "cm_suppcm_indcsys", $debug, $recode_soc);
}
}
}
if ($debug) {
$timer['main_end'] = microtime(true);
$init_time = benchmark_timing($timer);
echo $init_time;
}
$chem_fields = array('chem_lbdtc', 'creat_lbstresn');
$fields = array('dm_brthyr', 'weight_suppvs_wtkg', 'dm_sex');
$data = REDCap::getData('array', $record, $fields, $project->firstEventId);
foreach ($data as $vitals) {
foreach ($vitals as $vital) {
if ($vital['dm_brthyr'] != '' && $vital['weight_suppvs_wtkg'] != '' && $vital['dm_sex'] != '') {
$chem_data = REDCap::getData('array', $record, $chem_fields, $redcap_event_name);
foreach ($chem_data as $chem_values) {
foreach ($chem_values as $chem_event => $values) {
unset($creatinine_clearance);
if ($values['chem_lbdtc'] != '' && $values['creat_lbstresn'] != '') {
$sex = isset($vital['dm_sex']) ? $vital['dm_sex'] : 'F';
$chem_age = (substr($values['chem_lbdtc'], 0, 4)) - $vital['dm_brthyr'];
$sex_factor = $sex == 'F' ? .85 : 1;
$creatinine_clearance = round(((140 - $chem_age) * $vital['weight_suppvs_wtkg'] * $sex_factor) / (72 * $values['creat_lbstresn']));
update_field_compare($record, $project_id, $chem_event, $creatinine_clearance, get_single_field($record, $project_id, $chem_event, 'crcl_lborres', ''), 'crcl_lborres', $debug);
}
}
}
}
}
}
$timer_stop = microtime(true);
$timer_time = number_format(($timer_stop - $timer_start), 2);
if ($debug) {
error_log("DEBUG: This DET action (Standardize $instrument) took $timer_time seconds");
}
break;
/**
* all other forms do nothing
*/
