/**
* @param $record
* @param $redcap_event_name
* @param $instrument
* @param $debug
*/
public static function code_terms($record, $redcap_event_name, $instrument, $debug)
{
global $Proj, $project_id, $tx_fragment_labels;
$this_event_id = $Proj->getEventIdUsingUniqueEventName($redcap_event_name);
switch ($instrument) {
case 'ae_coding':
$recode_llt = false;
$recode_pt = true;
$recode_soc = true;
$prefix = 'ae';
/**
* AE_AEMODIFY
*/
$fields = array("ae_aeterm", "ae_oth_aeterm", "ae_aemodify");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_llt($project_id, $record, $this_event_id, fix_case($data[$record][$this_event_id]['ae_aeterm']), fix_case($data[$record][$this_event_id]['ae_oth_aeterm']), $data[$record][$this_event_id]['ae_aemodify'], 'ae_aemodify', $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded AE_AEMODIFY {$data[$record][$this_event_id]['ae_aemodify']}: subject=$record, event=$this_event_id for AE {$data[$record][$this_event_id]['ae_aeterm']} - {$data[$record][$this_event_id]['ae_oth_aeterm']}");
}
/**
* PREFIX_AEDECOD
* uses $tx_prefixes preset array
*/
$fields = array($prefix . "_aemodify", $prefix . "_aedecod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_pt($project_id, $record, $this_event_id, $data[$record][$this_event_id][$prefix . "_aemodify"], $data[$record][$this_event_id][$prefix . "_aedecod"], $prefix . "_aedecod", $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded " . strtoupper($prefix) . "_AEDECOD {$data[$record][$this_event_id][$prefix . '_aedecod']}: subject=$record, event=$this_event_id for AEMODIFY {$data[$record][$this_event_id][$prefix . '_aemodify']}");
}
/**
* PREFIX_AEBODSYS
* uses $tx_prefixes preset array
*/
$fields = array($prefix . "_aedecod", $prefix . "_aebodsys");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_bodsys($project_id, $record, $this_event_id, $data[$record][$this_event_id][$prefix . "_aedecod"], $data[$record][$this_event_id][$prefix . "_aebodsys"], $prefix . "_aebodsys", $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded SOC: subject=$record, event=$this_event_id for AE {$data[$record][$this_event_id][$prefix . "_aedecod"]}");
}
unset($data);
break;
/**
* ADVERSE EVENTS
* ACTION: auto-code AE
*/
case 'adverse_events':
$recode_llt = true;
$recode_pt = true;
$recode_soc = true;
/**
* AE_AEDECOD
*/
$fields = array("ae_aeterm", "ae_oth_aeterm", "ae_aemodify");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_llt($project_id, $record, $this_event_id, fix_case($data[$record][$this_event_id]['ae_aeterm']), fix_case($data[$record][$this_event_id]['ae_oth_aeterm']), $data[$record][$this_event_id]['ae_aemodify'], 'ae_aemodify', $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded AE_AEMODIFY {$data[$record][$this_event_id]['ae_aemodify']}: subject=$record, event=$this_event_id for AE {$data[$record][$this_event_id]['ae_aeterm']} - {$data[$record][$this_event_id]['ae_oth_aeterm']}");
}
/**
* AE_AEDECOD
*/
$fields = array("ae_aemodify", "ae_aedecod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_pt($project_id, $record, $this_event_id, fix_case($data[$record][$this_event_id]['ae_aemodify']), $data[$record][$this_event_id]['ae_aedecod'], 'ae_aedecod', $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded AE_AEDECOD {$data[$record][$this_event_id]['ae_aedecod']}: subject=$record, event=$this_event_id for AE {$data[$record][$this_event_id]['ae_aemodify']}");
}
/**
* AE_AEBODSYS
*/
$fields = array("ae_aedecod", "ae_aebodsys");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_bodsys($project_id, $record, $this_event_id, $data[$record][$this_event_id]['ae_aedecod'], $data[$record][$this_event_id]['ae_aebodsys'], 'ae_aebodsys', $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded SOC: subject=$record, event=$this_event_id for AE {$data[$record][$this_event_id]['ae_aedecod']}");
}
unset($data);
break;
/**
* MEDICAL HISTORY
* ACTION: auto-code MH
*/
case 'key_medical_history':
$recode_llt = false;
$recode_pt = true;
$recode_soc = true;
$mh_prefixes = array('othpsy', 'othca');
/**
* MH_MHMODIFY
*/
foreach ($mh_prefixes AS $prefix) {
$fields = array($prefix . "_oth_mhterm", $prefix . "_mhmodify");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_llt($project_id, $record, $this_event_id, fix_case($data[$record][$this_event_id][$prefix . "_oth_mhterm"]), '', $data[$record][$this_event_id][$prefix . "_mhmodify"], $prefix . "_mhmodify", $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded " . strtoupper($prefix) . "_MHMODIFY {$data[$record][$this_event_id][$prefix . "_mhmodify"]}: subject=$record, event=$this_event_id for MH {$data[$record][$this_event_id][$prefix . "_oth_mhterm"]}");
}
/**
* PREFIX_MHDECOD
* uses $mh_prefixes preset array
*/
$fields = array($prefix . "_mhmodify", $prefix . "_mhdecod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_pt($project_id, $record, $this_event_id, $data[$record][$this_event_id][$prefix . "_mhmodify"], $data[$record][$this_event_id][$prefix . "_mhdecod"], $prefix . "_mhdecod", $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded " . strtoupper($prefix) . "_MHDECOD {$data[$record][$this_event_id][$prefix . '_mhdecod']}: subject=$record, event=$this_event_id for MHMODIFY {$data[$record][$this_event_id][$prefix . '_mhmodify']}");
}
/**
* PREFIX_mhBODSYS
* uses $mh_prefixes preset array
*/
$fields = array($prefix . "_mhdecod", $prefix . "_mhbodsys");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_bodsys($project_id, $record, $this_event_id, $data[$record][$this_event_id][$prefix . "_mhdecod"], $data[$record][$this_event_id][$prefix . "_mhbodsys"], $prefix . "_mhbodsys", $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded " . strtoupper($prefix) . "_MHBODSYS {$data[$record][$this_event_id][$prefix . "_mhbodsys"]}: subject=$record, event=$this_event_id for MHDECOD {$data[$record][$this_event_id][$prefix . "_mhdecod"]}");
}
}
unset($data);
break;
/**
* EOT
*/
case 'early_discontinuation_eot':
$recode_llt = true;
$recode_pt = true;
$recode_soc = true;
/**
* EOT_AEDECOD
*/
$data = REDCap::getData('array', $record, array("eot_suppds_ncmpae", "eot_oth_suppds_ncmpae", "eot_aemodify", "eot_dsterm"), $this_event_id);
$ptdata = REDCap::getData('array', $record, array("eot_aemodify", "eot_aedecod"), $this_event_id);
$soc_data = REDCap::getData('array', $record, array("eot_aedecod", "eot_aebodsys"), $this_event_id);
foreach ($data[$record][$this_event_id] AS $event) {
if ($event['eot_dsterm'] == 'ADVERSE_EVENT') {
code_llt($project_id, $record, $this_event_id, fix_case($event['eot_suppds_ncmpae']), fix_case($event['eot_oth_suppds_ncmpae']), $event['eot_aemodify'], 'eot_aemodify', $debug, $recode_llt);
if ($debug) {
error_log("INFO (TESTING EOT): Coded EOT_AEMODIFY {$event['eot_aemodify']}: subject=$record, event=$this_event_id for AE {$event['eot_suppds_ncmpae']} - {$event['eot_oth_suppds_ncmpae']}");
}
/**
* AE_AEDECOD
*/
foreach ($ptdata[$record][$this_event_id] AS $ptevent) {
code_pt($project_id, $record, $this_event_id, fix_case($ptevent['eot_aemodify']), $ptevent['eot_aedecod'], 'eot_aedecod', $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded EOT_AEDECOD {$ptevent['eot_aedecod']}: subject=$record, event=$this_event_id for AEMODIFY {$ptevent['eot_aemodify']}");
}
}
/**
* EOT_AEBODSYS
*/
foreach ($soc_data[$record][$this_event_id] AS $soc_event) {
code_bodsys($project_id, $record, $this_event_id, $soc_event['eot_aedecod'], $soc_event['eot_aebodsys'], 'eot_aebodsys', $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded SOC: subject=$record, event=$this_event_id for AE {$soc_event['eot_aedecod']}");
}
}
}
}
unset($data);
unset($ptdata);
unset($soc_data);
break;
/**
* TX stop AEs
*/
case 'ribavirin_administration':
case 'harvoni_administration':
case 'ombitasvir_paritaprevir':
case 'dasabuvir':
case 'zepatier_administration':
$recode_llt = true;
$recode_pt = true;
$recode_soc = true;
$tx_prefix = array_search(substr($instrument, 0, strpos($instrument, '_')), $tx_fragment_labels);
/**
* AE_AEMODIFY
*/
$fields = array($tx_prefix . '_suppcm_cmncmpae', $tx_prefix . '_oth_suppcm_cmncmpae', $tx_prefix . '_aemodify');
$data = REDCap::getData('array', $record, $fields, $this_event_id);
foreach ($data[$record][$this_event_id] AS $event) {
code_llt($project_id, $record, $this_event_id, fix_case($event[$tx_prefix . '_suppcm_cmncmpae']), fix_case($event[$tx_prefix . '_oth_suppcm_cmncmpae']), $event[$tx_prefix . '_aemodify'], $tx_prefix . '_aemodify', $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded AE_AEMODIFY {$event[$tx_prefix . '_aemodify']}: subject=$record, event=$this_event_id for AE {$event[$tx_prefix . '_suppcm_cmncmpae']} - {$event[$tx_prefix . '_oth_suppcm_cmncmpae']}");
}
}
/**
* AE_AEDECOD
*/
$fields = array($tx_prefix . '_aemodify', $tx_prefix . "_aedecod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
foreach ($data[$record][$this_event_id] AS $event) {
code_pt($project_id, $record, $this_event_id, fix_case($event[$tx_prefix . '_aemodify']), $event[$tx_prefix . '_aedecod'], $tx_prefix . '_aedecod', $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded AE_AEDECOD {$event[$tx_prefix . '_aedecod']}: subject=$record, event=$this_event_id for AE {$event[$tx_prefix . '_aemodify']}");
}
}
/**
* AE_AEBODSYS
*/
$fields = array($tx_prefix . '_aedecod', $tx_prefix . '_aebodsys');
$data = REDCap::getData('array', $record, $fields, $this_event_id);
foreach ($data[$record][$this_event_id] AS $event) {
code_bodsys($project_id, $record, $this_event_id, $event[$tx_prefix . '_aedecod'], $event[$tx_prefix . '_aebodsys'], $tx_prefix . '_aebodsys', $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded SOC: subject=$record, event=$this_event_id for AE {$event[$tx_prefix . '_aedecod']}");
}
}
unset($data);
break;
/**
* CONMEDS
* ACTION: auto-code CONMEDS
*/
case 'conmeds':
/**
* CM_CMDECOD
*/
$recode_cm = true;
$recode_llt = true;
$recode_pt = true;
$recode_soc = true;
$recode_atc = true;
$fields = array("cm_cmtrt", "cm_cmdecod", "cm_cmindc", "cm_oth_cmindc", "cm_suppcm_indcod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_cm($project_id, $record, $this_event_id, $data[$record][$this_event_id], $debug, $recode_cm);
/**
* cm_suppcm_mktstat
* PRESCRIPTION or OTC
*/
$fields = array("cm_cmdecod", "cm_suppcm_mktstat");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
foreach ($data as $subject_id => $subject) {
foreach ($subject as $event_id => $event) {
if (isset($event['cm_cmdecod']) && $event['cm_cmdecod'] != '') {
update_field_compare($subject_id, $project_id, $event_id, get_conmed_mktg_status($event['cm_cmdecod']), $event['cm_suppcm_mktstat'], 'cm_suppcm_mktstat', $debug);
if ($debug) {
error_log("DEBUG: $subject_id Marketing Status = " . get_conmed_mktg_status($event['cm_cmdecod']));
}
}
}
}
/**
* CM_SUPPCM_INDCOD
*/
$fields = array("cm_cmindc", "cm_oth_cmindc", "cm_suppcm_indcmodf");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
/**
* re-code all nutritional support to nutritional supplement
*/
if ($data[$record][$this_event_id]['cm_oth_cmindc'] == 'Nutritional support') {
$data[$record][$this_event_id]['cm_oth_cmindc'] = 'Nutritional supplement';
}
code_llt($project_id, $record, $this_event_id, fix_case($data[$record][$this_event_id]['cm_cmindc']), fix_case($data[$record][$this_event_id]['cm_oth_cmindc']), $data[$record][$this_event_id]['cm_suppcm_indcmodf'], 'cm_suppcm_indcmodf', $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded INDC LLT: {} subject=$record, event=$this_event_id for INDICATION {$data[$record][$this_event_id]['cm_cmindc']}");
}
/**
* CM_SUPPCM_INDCOD
*/
$fields = array("cm_suppcm_indcmodf", "cm_suppcm_indcod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_pt($project_id, $record, $this_event_id, $data[$record][$this_event_id]['cm_suppcm_indcmodf'], $data[$record][$this_event_id]['cm_suppcm_indcod'], 'cm_suppcm_indcod', $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded INDC PT: subject=$record, event=$this_event_id for INDICATION {$data[$record][$this_event_id]['cm_suppcm_indcod']}");
}
/**
* CM_SUPPCM_INDCSYS
*/
$fields = array("cm_suppcm_indcod", "cm_suppcm_indcsys");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_bodsys($project_id, $record, $this_event_id, $data[$record][$this_event_id]['cm_suppcm_indcod'], $data[$record][$this_event_id]['cm_suppcm_indcsys'], 'cm_suppcm_indcsys', $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded INDCSYS: subject=$record, event=$this_event_id for INDC {$data[$record][$this_event_id]['cm_suppcm_indcod']}");
}
/**
* CM_SUPPCM_ATCNAME
* CM_SUPPCM_ATC2NAME
*/
$fields = array("cm_cmdecod", "cm_suppcm_atcname", "cm_suppcm_atc2name");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_atc($project_id, $record, $this_event_id, $data[$record][$this_event_id]['cm_cmdecod'], $data[$record][$this_event_id]['cm_suppcm_atcname'], $data[$record][$this_event_id]['cm_suppcm_atc2name'], $debug, $recode_atc);
if ($debug) {
error_log("DEBUG: Coded ATCs: subject=$record, event=$this_event_id for CONMED {$data[$record][$this_event_id]['cm_cmdecod']}");
}
break;
case 'transfusions':
$recode_cm = true;
$recode_llt = true;
$recode_soc = true;
$recode_atc = true;
/**
* XFSN_CMDECOD
*/
$fields = array("xfsn_cmtrt", "xfsn_cmdecod", "xfsn_cmindc", "xfsn_suppcm_indcod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_cm($project_id, $record, $this_event_id, $data[$record][$this_event_id], $debug, $recode_cm);
/**
* XFSN_SUPPCM_INDCOD
*/
$fields = array("xfsn_cmindc", "xfsn_suppcm_indcod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_llt($project_id, $record, $this_event_id, fix_case($data[$record][$this_event_id]['xfsn_cmindc']), fix_case($data[$record][$this_event_id]['xfsn_oth_cmindc']), $data[$record][$this_event_id]['xfsn_suppcm_indcod'], 'xfsn_suppcm_indcod', $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded XFSN INDC: subject=$record, event=$this_event_id for CONMED {$data[$record][$this_event_id]['xfsn_cmdecod']}");
}
/**
* XFSN_SUPPCM_INDCSYS
*/
$fields = array("xfsn_suppcm_indcod", "xfsn_suppcm_indcsys");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_bodsys($project_id, $record, $this_event_id, $data[$record][$this_event_id]['xfsn_suppcm_indcod'], $data[$record][$this_event_id]['xfsn_suppcm_indcsys'], 'xfsn_suppcm_indcsys', $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded XFSN INDCSYS: subject=$record, event=$this_event_id for INDC {$data[$record][$this_event_id]['xfsn_suppcm_indcod']}");
}
/**
* XFSN_SUPPCM_ATCNAME
* XFSN_SUPPCM_ATC2NAME
*/
$fields = array("xfsn_cmdecod", "xfsn_suppcm_atcname", "xfsn_suppcm_atc2name");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_atc_xfsn($project_id, $record, $this_event_id, $data[$record][$this_event_id]['xfsn_cmdecod'], $data[$record][$this_event_id]['xfsn_suppcm_atcname'], $data[$record][$this_event_id]['xfsn_suppcm_atc2name'], $debug, $recode_atc);
if ($debug) {
error_log("DEBUG: Coded XFSN ATCs: subject=$record, event=$this_event_id for CONMED {$data[$record][$this_event_id]['xfsn_cmdecod']}");
}
unset($data);
break;
case 'mh_coding':
$recode_llt = false;
$recode_pt = true;
$recode_soc = true;
$mh_prefixes = array('othpsy', 'othca');
/**
* MH_MHMODIFY
*/
foreach ($mh_prefixes AS $prefix) {
$fields = array($prefix . "_oth_mhterm", $prefix . "_mhmodify");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_llt($project_id, $record, $this_event_id, fix_case($data[$record][$this_event_id][$prefix . "_oth_mhterm"]), '', $data[$record][$this_event_id][$prefix . "_mhmodify"], $prefix . "_mhmodify", $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded " . strtoupper($prefix) . "_MHMODIFY {$data[$record][$this_event_id][$prefix . "_mhmodify"]}: subject=$record, event=$this_event_id for MH {$data[$record][$this_event_id][$prefix . "_oth_mhterm"]}");
}
/**
* PREFIX_MHDECOD
* uses $mh_prefixes preset array
*/
$fields = array($prefix . "_mhmodify", $prefix . "_mhdecod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_pt($project_id, $record, $this_event_id, $data[$record][$this_event_id][$prefix . "_mhmodify"], $data[$record][$this_event_id][$prefix . "_mhdecod"], $prefix . "_mhdecod", $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded " . strtoupper($prefix) . "_MHDECOD {$data[$record][$this_event_id][$prefix . '_mhdecod']}: subject=$record, event=$this_event_id for MHMODIFY {$data[$record][$this_event_id][$prefix . '_mhmodify']}");
}
/**
* PREFIX_mhBODSYS
* uses $mh_prefixes preset array
*/
$fields = array($prefix . "_mhdecod", $prefix . "_mhbodsys");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_bodsys($project_id, $record, $this_event_id, $data[$record][$this_event_id][$prefix . "_mhdecod"], $data[$record][$this_event_id][$prefix . "_mhbodsys"], $prefix . "_mhbodsys", $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded " . strtoupper($prefix) . "_MHBODSYS {$data[$record][$this_event_id][$prefix . "_mhbodsys"]}: subject=$record, event=$this_event_id for MHDECOD {$data[$record][$this_event_id][$prefix . "_mhdecod"]}");
}
}
unset($data);
break;
case 'cm_coding':
$recode_llt = false;
$recode_pt = true;
$recode_soc = true;
$recode_atc = false;
$recode_cm = true;
/**
* CM_CMDECOD
*/
$fields = array("cm_cmtrt", "cm_cmdecod", "cm_cmindc", "cm_oth_cmindc", "cm_suppcm_indcod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_cm($project_id, $record, $this_event_id, $data[$record][$this_event_id], $debug, $recode_cm);
if ($debug) {
error_log("DEBUG: Coded CONMED: subject=$record, event=$this_event_id for CMTRT {$data[$record][$this_event_id]['cm_cmtrt']}");
}
/**
* cm_suppcm_mktstat
* PRESCRIPTION or OTC
*/
$fields = array("cm_cmdecod", "cm_suppcm_mktstat");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
foreach ($data as $subject_id => $subject) {
foreach ($subject as $event_id => $event) {
if (isset($event['cm_cmdecod']) && $event['cm_cmdecod'] != '') {
update_field_compare($subject_id, $project_id, $event_id, get_conmed_mktg_status($event['cm_cmdecod']), $event['cm_suppcm_mktstat'], 'cm_suppcm_mktstat', $debug);
if ($debug) {
error_log("DEBUG: $subject_id Marketing Status = " . get_conmed_mktg_status($event['cm_cmdecod']));
}
}
}
}
/**
* CM_SUPPCM_INDCOD
*/
$fields = array("cm_cmindc", "cm_oth_cmindc", "cm_suppcm_indcmodf");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
/**
* re-code all nutritional support to nutritional supplement
*/
if ($data[$record][$this_event_id]['cm_oth_cmindc'] == 'Nutritional support') {
$data[$record][$this_event_id]['cm_oth_cmindc'] = 'Nutritional supplement';
}
code_llt($project_id, $record, $this_event_id, fix_case($data[$record][$this_event_id]['cm_cmindc']), fix_case($data[$record][$this_event_id]['cm_oth_cmindc']), $data[$record][$this_event_id]['cm_suppcm_indcmodf'], 'cm_suppcm_indcmodf', $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded INDC LLT: {} subject=$record, event=$this_event_id for INDICATION {$data[$record][$this_event_id]['cm_cmindc']}");
}
/**
* CM_SUPPCM_INDCOD
*/
$fields = array("cm_suppcm_indcmodf", "cm_suppcm_indcod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_pt($project_id, $record, $this_event_id, $data[$record][$this_event_id]['cm_suppcm_indcmodf'], $data[$record][$this_event_id]['cm_suppcm_indcod'], 'cm_suppcm_indcod', $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded INDC PT: subject=$record, event=$this_event_id for INDICATION {$data[$record][$this_event_id]['cm_suppcm_indcod']}");
}
/**
* CM_SUPPCM_INDCSYS
*/
$fields = array("cm_suppcm_indcod", "cm_suppcm_indcsys");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_bodsys($project_id, $record, $this_event_id, $data[$record][$this_event_id]['cm_suppcm_indcod'], $data[$record][$this_event_id]['cm_suppcm_indcsys'], 'cm_suppcm_indcsys', $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded INDCSYS: subject=$record, event=$this_event_id for INDC {$data[$record][$this_event_id]['cm_suppcm_indcod']}");
}
/**
* CM_SUPPCM_ATCNAME
* CM_SUPPCM_ATC2NAME
*/
$fields = array("cm_cmdecod", "cm_suppcm_atcname", "cm_suppcm_atc2name");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_atc_soc($project_id, $record, $this_event_id, $data[$record][$this_event_id]['cm_cmdecod'], $data[$record][$this_event_id]['cm_suppcm_atcname'], $data[$record][$this_event_id]['cm_suppcm_atc2name'], $debug, $recode_atc);
if ($debug) {
error_log("DEBUG: Coded ATCs: subject=$record, event=$this_event_id for CONMED {$data[$record][$this_event_id]['cm_cmdecod']}");
}
/**
* XFSN_CMDECOD
*/
$fields = array("xfsn_cmtrt", "xfsn_cmdecod", "xfsn_cmindc", "xfsn_suppcm_indcod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
foreach ($data AS $subject_id => $subject) {
foreach ($subject AS $event_id => $event) {
if (isset($event['xfsn_cmtrt']) && $event['xfsn_cmtrt'] != '') {
$med = array();
$med_result = db_query("SELECT DISTINCT drug_coded FROM _target_xfsn_coding WHERE drug_name = '" . prep($event['xfsn_cmtrt']) . "'");
if ($med_result) {
$med = db_fetch_assoc($med_result);
if (isset($med['drug_coded']) && $med['drug_coded'] != '') {
update_field_compare($subject_id, $project_id, $event_id, $med['drug_coded'], $event['xfsn_cmdecod'], 'xfsn_cmdecod', $debug);
}
}
if ($debug) {
error_log("DEBUG: Coded Transfusion: subject=$subject_id, event=$event_id for CMTRT {$event['xfsn_cmtrt']}");
}
} else {
update_field_compare($subject_id, $project_id, $event_id, '', $event['xfsn_cmdecod'], 'xfsn_cmdecod', $debug);
}
}
}
/**
* XFSN_SUPPCM_INDCOD
*/
$fields = array("xfsn_cmindc", "xfsn_suppcm_indcod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_llt($project_id, $record, $this_event_id, fix_case($data[$record][$this_event_id]['xfsn_cmindc']), fix_case($data[$record][$this_event_id]['xfsn_oth_cmindc']), $data[$record][$this_event_id]['xfsn_suppcm_indcod'], 'xfsn_suppcm_indcod', $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded XFSN INDC: subject=$record, event=$this_event_id for CONMED {$data[$record][$this_event_id]['xfsn_cmdecod']}");
}
/**
* XFSN_SUPPCM_INDCSYS
*/
$fields = array("xfsn_suppcm_indcod", "xfsn_suppcm_indcsys");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_bodsys($project_id, $record, $this_event_id, $data[$record][$this_event_id]['xfsn_suppcm_indcod'], $data[$record][$this_event_id]['xfsn_suppcm_indcsys'], 'xfsn_suppcm_indcsys', $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded XFSN INDCSYS: subject=$record, event=$this_event_id for INDC {$data[$record][$this_event_id]['xfsn_suppcm_indcod']}");
}
/**
* XFSN_SUPPCM_ATCNAME
* XFSN_SUPPCM_ATC2NAME
*/
$fields = array("xfsn_cmdecod", "xfsn_suppcm_atcname", "xfsn_suppcm_atc2name");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_atc_xfsn($project_id, $record, $this_event_id, $data[$record][$this_event_id]['xfsn_cmdecod'], $data[$record][$this_event_id]['xfsn_suppcm_atcname'], $data[$record][$this_event_id]['xfsn_suppcm_atc2name'], $debug, $recode_atc);
if ($debug) {
error_log("DEBUG: Coded XFSN ATCs: subject=$record, event=$this_event_id for CONMED {$data[$record][$this_event_id]['xfsn_cmdecod']}");
}
unset($data);
break;
case 'ex_coding':
$recode_pt = true;
$recode_soc = true;
$prefix = 'eot';
/**
* PREFIX_AEDECOD
* uses $tx_prefixes preset array
*/
$fields = array($prefix . "_aemodify", $prefix . "_aedecod");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_pt($project_id, $record, $this_event_id, $data[$record][$this_event_id][$prefix . "_aemodify"], $data[$record][$this_event_id][$prefix . "_aedecod"], $prefix . "_aedecod", $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded " . strtoupper($prefix) . "_AEDECOD {$data[$record][$this_event_id][$prefix . '_aedecod']}: subject=$record, event=$this_event_id for AEMODIFY {$data[$record][$this_event_id][$prefix . '_aemodify']}");
}
/**
* PREFIX_AEBODSYS
* uses $tx_prefixes preset array
*/
$fields = array($prefix . "_aedecod", $prefix . "_aebodsys");
$data = REDCap::getData('array', $record, $fields, $this_event_id);
code_bodsys($project_id, $record, $this_event_id, $data[$record][$this_event_id][$prefix . "_aedecod"], $data[$record][$this_event_id][$prefix . "_aebodsys"], $prefix . "_aebodsys", $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded SOC: subject=$record, event=$this_event_id for AE {$data[$record][$this_event_id][$prefix . "_aedecod"]}");
}
unset($data);
break;
default:
break;
}
}
* 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 $init_time;
}
foreach ($subject AS $event_id => $event) {
if ($subjects != '') {
d($event);
}
$inner_vals = array();
if ($usubjid == '') {
$usubjid = $event['dm_usubjid'];
}
/**
* some COVAL values will be text and some checkboxes
* handle strings and arrays in same field
*/
if (is_array($event[$fields['coval']])) {
$event[$fields['coval']] = fix_case(array_search('1', $event[$fields['coval']]));
}
$event[$fields['coeval']] = fix_case($event[$fields['coeval']]);
/**
* build values array
*/
foreach ($fields AS $key => $field) {
if (!in_array($field, array($fields['dm_usubjid']))) {
$inner_vals[$key] = $event[$field];
}
}
$vals_array[$usubjid][] = $inner_vals;
}
}
}
db_free_result($fields_result);
}
if ($subjects != '') {
/**
* @param array $subject_regimen_data
* @param null|string $dsterm
* @param null|string $txstat
* @return array
*/
public static function getRegimen($subject_regimen_data, $dsterm = null, $txstat = null)
{
global $tx_to_arm, $intended_regimens;
$actarm_array = array();
$actarmcd_array = array();
$arm = NULL;
$armcd = NULL;
$actarm = NULL;
$actarmcd = NULL;
foreach ($subject_regimen_data AS $regimen_event) {
foreach ($regimen_event AS $reg_key => $reg_val) {
if ($reg_key != 'reg_suppcm_regimen') { // actual ARM
if ($reg_val != '') {
$this_regimen = strtoupper(substr($reg_key, 0, strpos($reg_key, '_')));
foreach ($tx_to_arm[$this_regimen] AS $arm_order => $arm_pair) {
foreach ($arm_pair as $actarmcd => $arm_name) {
$actarm_array[$arm_order] = $arm_name;
$actarmcd_array[$arm_order] = $actarmcd;
}
}
}
} else { // planned ARM
if ($reg_val != '') {
$planned_array = $intended_regimens[$reg_val];
foreach ($planned_array as $key => $val) {
$arm = $val;
$armcd = $key;
}
}
}
}
}
/**
* Viekira relabeling
*/
d('before', $actarmcd_array);
d($actarm_array);
if (array_search('VPK', $actarmcd_array) !== false) {
if (array_search('DBV', $actarmcd_array) !== false) {
unset($actarmcd_array[7], $actarm_array[7]);
$actarm_array = array_replace($actarm_array, array(array_search('Viekira', $actarm_array) => 'Viekira Pak'));
} else {
$actarmcd_array = array_replace($actarmcd_array, array(array_search('VPK', $actarmcd_array) => 'TCN'));
$actarm_array = array_replace($actarm_array, array(array_search('Viekira', $actarm_array) => 'Technivie'));
}
}
if (!empty($actarm_array)) {
ksort($actarm_array);
ksort($actarmcd_array);
$actarm = implode('/', array_unique($actarm_array));
//$actarm = strpos($actarm, 'Viekira/Dasabuvir') !== false ? str_replace('Viekira/Dasabuvir', 'Viekira Pak', $actarm) : $actarm;
$actarmcd = implode('/', array_unique($actarmcd_array));
//$actarmcd = strpos($actarmcd, 'VPK/DBV') !== false ? str_replace('VPK/DBV', 'VPK', $actarmcd) : $actarmcd;
/**
* undocumented in JMP Clinical:
* if subject ARM or ARMCD are missing, the subject will be SCREEN FAIL.
* Yeah. Sweeet.
*/
$arm = !isset($arm) ? $actarm : $arm;
$armcd = !isset($armcd) ? $actarmcd : $armcd;
} else {
if ($dsterm == 'SCREEN_FAILURE') {
$actarm = fix_case($dsterm);
$actarmcd = 'SCRNFAIL';
} elseif ($txstat == 'N') {
$actarm = 'Not Treated';
$actarmcd = 'NOTTRT';
}
}
$return_array['arm'] = $arm;
$return_array['armcd'] = $armcd;
$return_array['actarm'] = $actarm;
$return_array['actarmcd'] = $actarmcd;
return $return_array;
}
require_once $base_path . '/plugins/includes/functions.php';
require_once APP_PATH_DOCROOT . '/Config/init_project.php';
require_once APP_PATH_DOCROOT . '/ProjectGeneral/header.php';
require_once APP_PATH_DOCROOT . '/DataExport/functions.php';
/**
* restricted use
*/
$allowed_pids = array('38');
REDCap::allowProjects($allowed_pids);
global $Proj;
Kint::enabled($debug);
/**
* INIT VARS
*/
$export_filename = 'SDV_COMPLETION_REPORT';
$plugin_title = fix_case($export_filename) . ' ' . "<span class='yellow'>DEVELOPMENT</span>";
$first_event = $Proj->firstEventId;
$table_csv = "";
$subject_event_locks = array();
$fields = array();
$excluded_forms = array('coding', 'derived_values', 'derived_values_baseline', 'post_monitoring_source_upload', 'protocol_deviations', 'cbc_standard', 'chemistry_standard', 'hcv_rna_standard');
$all_forms = array_diff(array_keys($Proj->forms), $excluded_forms);
foreach ($all_forms AS $form) {
$fields[] = $form . '_complete';
}
$events_forms = $Proj->eventsForms;
/**
* MAIN
*/
echo "<h3>$plugin_title</h3>";
if ($debug) {
}
$seq = 1;
$constants['USUBJID'] = $constants['STUDYID'] . '-' . $subj_usubjid;
foreach ($subj_val_array AS $subj_array) {
if ($subj_array['faorres'] != '') {
$query[] = '(' .
fix_null($constants['STUDYID']) . ',' .
fix_null($constants['DOMAIN']) . ',' .
fix_null($constants['USUBJID']) . ',' .
fix_null($seq) . ',' .
fix_null($subj_array['fatestcd']) . ',' .
fix_null($subj_array['fatest']) . ',' .
fix_null($subj_array['faorres']) . ',' .
fix_null($subj_array['fastresc']) . ',' .
fix_null($subj_array['fastresn']) . ',' .
fix_null(fix_case($subj_array['facat'])) . ',' .
fix_null($subj_array['faobj']) . ',' .
fix_null($subj_array['fadtc']) .
')';
$seq++;
}
}
}
$timer['end_main'] = microtime(true);
/**
* end Main Loop
*/
$table_create_query = "CREATE TABLE IF NOT EXISTS `$table_name` (
`STUDYID` VARCHAR(8) COLLATE utf8_unicode_ci NOT NULL,
`DOMAIN` VARCHAR(2) COLLATE utf8_unicode_ci NOT NULL,
`USUBJID` VARCHAR(16) COLLATE utf8_unicode_ci NOT NULL,
foreach ($subject AS $event_id => $event) {
/**
* AE_AEDECOD
*/
code_pt($project_id, $subject_id, $event_id, fix_case($event['ae_aemodify']), $event['ae_aedecod'], 'ae_aedecod', $debug, $recode_pt);
if ($debug) {
error_log("INFO (TESTING): Coded AE_AEDECOD {$event['ae_aedecod']}: subject=$subject_id, event=$event_id for AEMODIFY {$event['ae_aemodify']}");
}
/**
* EOT_AEDECOD
*/
code_pt($project_id, $subject_id, $event_id, fix_case($event['eot_aemodify']), $event['eot_aedecod'], 'eot_aedecod', $debug, $recode_pt);
if ($debug) {
error_log("INFO (TESTING): Coded EOT_AEDECOD {$event['eot_aedecod']}: subject=$subject_id, event=$event_id for AEMODIFY {$event['eot_aemodify']}");
}
/**
* TXDRUG_AEDECOD
*/
foreach ($tx_prefixes as $tx_prefix) {
code_pt($project_id, $subject_id, $event_id, fix_case($event[$tx_prefix . '_aemodify']), $event[$tx_prefix . '_aedecod'], $tx_prefix . '_aedecod', $debug, $recode_pt);
if ($debug) {
error_log("INFO (TESTING): Coded " . strtoupper($tx_prefix) . "_AEDECOD {$event[$tx_prefix . '_aedecod']}: subject=$subject_id, event=$event_id for AEMODIFY {$event[$tx_prefix . '_aemodify']}");
}
}
}
}
if ($debug) {
$timer['main_end'] = microtime(true);
$init_time = benchmark_timing($timer);
echo $init_time;
}
function split_full_name($full_name)
{
$full_name = trim($full_name);
// split into words
$unfiltered_name_parts = explode(" ", $full_name);
// completely ignore any words in parentheses
foreach ($unfiltered_name_parts as $word) {
if ($word[0] != "(") {
$name_parts[] = $word;
}
}
$num_words = sizeof($name_parts);
// is the first word a title? (Mr. Mrs, etc)
$salutation = is_salutation($name_parts[0]);
$suffix = is_suffix($name_parts[sizeof($name_parts) - 1]);
// set the range for the middle part of the name (trim prefixes & suffixes)
$start = $salutation ? 1 : 0;
$end = $suffix ? $num_words - 1 : $num_words;
// concat the first name
for ($i = $start; $i < $end - 1; $i++) {
$word = $name_parts[$i];
// move on to parsing the last name if we find an indicator of a compound last name (Von, Van, etc)
// we use $i != $start to allow for rare cases where an indicator is actually the first name (like "Von Fabella")
if (is_compound_lname($word) && $i != $start) {
break;
}
// is it a middle initial or part of their first name?
// if we start off with an initial, we'll call it the first name
if (is_initial($word)) {
// is the initial the first word?
if ($i == $start) {
// if so, do a look-ahead to see if they go by their middle name
// for ex: "R. Jason Smith" => "Jason Smith" & "R." is stored as an initial
// but "R. J. Smith" => "R. Smith" and "J." is stored as an initial
if (is_initial($name_parts[$i + 1])) {
$fname .= " " . strtoupper($word);
} else {
$initials .= " " . strtoupper($word);
}
// otherwise, just go ahead and save the initial
} else {
$initials .= " " . strtoupper($word);
}
} else {
$fname .= " " . fix_case($word);
}
}
// check that we have more than 1 word in our string
if ($end - $start > 1) {
// concat the last name
for ($i; $i < $end; $i++) {
$lname .= " " . fix_case($name_parts[$i]);
}
} else {
// otherwise, single word strings are assumed to be first names
$fname = fix_case($name_parts[$i]);
}
// return the various parts in an array
$name['salutation'] = $salutation;
$name['fname'] = trim($fname);
$name['initials'] = trim($initials);
$name['lname'] = trim($lname);
$name['suffix'] = $suffix;
return $name;
}
$fields = array("dm_subjid", "ae_aeterm", "ae_oth_aeterm", "ae_aemodify", "ae_aedecod", "ae_aebodsys");
$data = REDCap::getData('array', $subjects, $fields);
foreach ($data AS $subject_id => $subject) {
foreach ($subject AS $event_id => $event) {
/**
* AE_AEDECOD
*/
code_llt($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 $timer_time seconds");
* plugin
*/
echo "<h3>$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 $init_time;
}
fix_null($meddra['aelltcd']) . ',' . fix_null($subj_array['aedecod']) . ',' . fix_null($meddra['aeptcd']) . ',' . fix_null($meddra['aehlt']) . ',' . fix_null($meddra['aehltcd']) . ',' . fix_null($meddra['aehlgt']) . ',' . fix_null($meddra['aehlgtcd']) . ',' . fix_null($subj_array['aebodsys']) . ',' . fix_null($meddra['aebdsycd']) . ',' . fix_null($meddra['aesoc']) . ',' . fix_null($meddra['aebdsycd']) . ',' . fix_null(fix_case($subj_array['aesev'])) . ',' . fix_null($subj_array['aeser']) . ',' . fix_null(fix_case($subj_array['aeacn'])) . ',' . fix_null(fix_case($subj_array['aerel'])) . ',' . fix_null(fix_case($subj_array['aeout'])) . ',' . fix_null($subj_array['aescong']) . ',' . fix_null($subj_array['aesdisab']) . ',' . fix_null($subj_array['aesdth']) . ',' . fix_null($subj_array['aeshosp']) . ',' . fix_null($subj_array['aeslife']) . ',' . fix_null($subj_array['aesmie']) . ',' . fix_null($subj_array['aecontrt']) . ',' . fix_null($subj_array['aetoxgr']) . ',' . fix_null($subj_array['aestdtc']) . ',' . fix_null($subj_array['aeendtc']) . ')'; $seq++; } } }
* HCVRNA Followup Eligibility
* subjects are ineligible for followup if:
*/
foreach ($ie_data[$subject_id] as $ie_event) {
if ($ie_event['ie_ietestcd'] != '') { // failed i/e criteria
$hcv_fu_eligible = false;
$hcv_fu_ineligible_reason[] = $ie_criteria_labels[$ie_event['ie_ietestcd']];
}
}
/**
* disposition-related ineligibility
*/
if (in_array($date_event['eot_dsterm'], array('LOST_TO_FOLLOWUP', 'LACK_OF_EFFICACY'))) { // disposition is lost to followup
$lost_to_followup = true;
$hcv_fu_eligible = false;
$hcv_fu_ineligible_reason[] = fix_case($date_event['eot_dsterm']);
}
/**
* Quantified HCVRNA after EOT
*/
if (count($post_tx_scores) > 1 && !$hcvrna_improved) {
if (in_array('1', $post_tx_scores)) { // had quantified HCV RNA after EOT
$hcv_fu_eligible = false;
$hcv_fu_ineligible_reason[] = 'Quantified post-TX HCVRNA';
}
} else {
if (in_array('1', $post_tx_scores)) { // had quantified HCV RNA after EOT
$hcv_fu_eligible = false;
$hcv_fu_ineligible_reason[] = 'Quantified post-TX HCVRNA';
}
}
if ($debug) {
error_log("DEBUG: Coded Transfusion: subject={$subject_id}, event={$event_id} for CMTRT {$event['xfsn_cmtrt']}");
}
} else {
update_field_compare($subject_id, $project_id, $event_id, '', $event['xfsn_cmdecod'], 'xfsn_cmdecod', $debug);
}
}
}
/**
* XFSN_SUPPCM_INDCOD
*/
$fields = array("xfsn_cmindc", "xfsn_suppcm_indcod");
$data = REDCap::getData('array', $record, $fields, $redcap_event_name);
foreach ($data as $subject_id => $subject) {
foreach ($subject as $event_id => $event) {
code_llt($project_id, $subject_id, $event_id, fix_case($event['xfsn_cmindc']), fix_case($event['xfsn_oth_cmindc']), $event['xfsn_suppcm_indcod'], 'xfsn_suppcm_indcod', $debug, $recode_llt);
if ($debug) {
error_log("DEBUG: Coded XFSN INDC: subject={$subject_id}, event={$event_id} for CONMED {$event['xfsn_cmdecod']}");
}
}
}
/**
* XFSN_SUPPCM_INDCSYS
*/
$fields = array("xfsn_suppcm_indcod", "xfsn_suppcm_indcsys");
$data = REDCap::getData('array', $record, $fields, $redcap_event_name);
foreach ($data as $subject_id => $subject) {
foreach ($subject as $event_id => $event) {
code_bodsys($project_id, $subject_id, $event_id, $event['xfsn_suppcm_indcod'], $event['xfsn_suppcm_indcsys'], 'xfsn_suppcm_indcsys', $debug, $recode_soc);
if ($debug) {
error_log("DEBUG: Coded XFSN INDCSYS: subject={$subject_id}, event={$event_id} for INDC {$event['xfsn_suppcm_indcod']}");
if ($event[$fields['cmtrt']] != '') {
/**
* transform: descriptive units handling
* where cmdosu is element_type=descriptive, use the label as the unit
* this is done where there is only one possible unit
*/
if ($fields['utype'] == 'descriptive') {
$event[$fields['cmdosu']] = $fields['ulabel'];
}
/**
* transform: eliminate OTHER indications and clean up radio button value case
*/
if ($event[$fields['cmindc']] == 'OTHER') {
$event[$fields['cmindc']] = $event[$fields['oth_cmindc']];
} else {
$event[$fields['cmindc']] = fix_case($event[$fields['cmindc']]);
}
/**
* transform: immunosuppressant dosages
*/
if ($event[$fields['cmimmuno']] == 'Y') {
$event[$fields['cmdose']] = $event[$fields['imm_cmdose']];
$event[$fields['cmdosu']] = $event[$fields['imm_cmdosu']];
$event[$fields['cmdosfrq']] = $event[$fields['imm_cmdosfrq']];
}
/**
* build values array
*/
foreach ($fields AS $key => $field) {
if (!in_array($field, array($fields['dm_usubjid'], $fields['utype'], $fields['ulabel'], $fields['oth_cmindc'], $fields['cmimmuno'], $fields['imm_cmdose'], $fields['imm_cmdosu'], $fields['imm_cmdosfrq']))) {
$inner_vals[$key] = $event[$field];
*/
$constants['COUNTRY'] = substr($subj_usubjid, 0, 3) == '049' ? 'CAN' : $countries[substr($subj_usubjid, 0, 1)];
foreach ($subj_val_array AS $subj_array) {
$query[] = '(' .
fix_null($constants['STUDYID']) . ',' .
fix_null($constants['DOMAIN']) . ',' .
fix_null($constants['USUBJID']) . ',' .
fix_null($subj_array['SUBJID']) . ',' .
fix_null($subj_array['RFSTDTC']) . ',' .
fix_null($subj_array['RFENDTC']) . ',' .
fix_null($constants['SITEID']) . ',' .
fix_null($subj_array['BRTHDTC']) . ',' .
fix_null($subj_array['AGE']) . ',' .
fix_null($subj_array['SEX']) . ',' .
fix_null(fix_case($subj_array['RACE'])) . ',' .
fix_null(fix_case($subj_array['ETHNIC'])) . ',' .
fix_null($subj_array['armcd']) . ',' .
fix_null($subj_array['arm']) . ',' .
fix_null($subj_array['actarmcd']) . ',' .
fix_null($subj_array['actarm']) . ',' .
fix_null($constants['COUNTRY']) .
')';
$seq++;
}
}
/**
* end Main Loop
*/
$timer['end_main'] = microtime(true);
/**
* if not exists, create your domain data table
