* 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 => $event) {
/**
* AE_AEDECOD
*/
code_pt($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;
}
/**
* @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($data);
break;
default:
break;
}
}
* plugin
*/
echo "<h3>$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;
}
$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 $timer_time seconds");
/** * DCV_AEDECOD */ code_pt($project_id, $subject_id, $event_id, fix_case($event['dcv_aemodify']), $event['dcv_aedecod'], 'dcv_aedecod', $debug, $recode_pt); /** * HVN_AEDECOD */ code_pt($project_id, $subject_id, $event_id, fix_case($event['hvn_aemodify']), $event['hvn_aedecod'], 'hvn_aedecod', $debug, $recode_pt); /** * VPK_AEDECOD */ code_pt($project_id, $subject_id, $event_id, fix_case($event['vpk_aemodify']), $event['vpk_aedecod'], 'vpk_aedecod', $debug, $recode_pt); /** * DBV_AEDECOD */ code_pt($project_id, $subject_id, $event_id, fix_case($event['dbv_aemodify']), $event['dbv_aedecod'], 'dbv_aedecod', $debug, $recode_pt); /** * AE_AEBODSYS */ code_bodsys($project_id, $subject_id, $event_id, $event['ae_aedecod'], $event['ae_aebodsys'], 'ae_aebodsys', $debug, $recode_soc); /** * MH_MHBODSYS */ code_bodsys($project_id, $subject_id, $event_id, $event['othca_mhdecod'], $event['othca_mhbodsys'], 'othca_mhbodsys', $debug, $recode_soc); /** * MH_MHBODSYS */ code_bodsys($project_id, $subject_id, $event_id, $event['othpsy_mhdecod'], $event['othpsy_mhbodsys'], 'othpsy_mhbodsys', $debug, $recode_soc); /** * IFN_AEBODSYS */
} else {
error_log(db_error() . ': ' . $flush_sql);
echo db_error() . "<br />" . $flush_sql;
}
} else {
show_var($flush_sql);
error_log("DEBUG: " . $flush_sql);
}
}
}
}
foreach ($data[$subject_id] AS $subject) {
foreach ($subject AS $event_id => $event) {
if ($event['cm_cmoccur'] == 'Y') {
code_pt($project_id, $subject_id, $event_id, $event['cm_suppcm_indcmodf'], $event['cm_suppcm_indcod'], 'cm_suppcm_indcod', $debug, $recode_pt, $message);
if ($debug) {
error_log("DEBUG: Coded INDC PT: subject=$subject_id, event=$event_id for INDICATION {$event['cm_suppcm_indcmodf']}");
}
code_bodsys($project_id, $subject_id, $event_id, $event['cm_suppcm_indcod'], $event['cm_suppcm_indcsys'], 'cm_suppcm_indcsys', $debug, $recode_soc, $message);
if ($debug) {
error_log("DEBUG: Coded INDCSYS: subject=$subject_id, event=$event_id for INDC {$event['cm_suppcm_indcod']}");
}
code_atc_soc($project_id, $subject_id, $event_id, $event['cm_cmdecod'], $event['cm_suppcm_atcname'], $event['cm_suppcm_atc2name'], $debug, $recode_atc, $update_message);
if ($debug) {
error_log("DEBUG: Coded ATCs: subject=$subject_id, event=$event_id for CONMED {$event['cm_cmdecod']}");
}
}
}
}
}
$recode_llt = false;
$recode_pt = true;
$recode_soc = true;
$recode_atc = false;
$recode_cm = true;
$tx_prefixes[] = 'eot';
/**
* PREFIX_AEDECOD
* uses $tx_prefixes preset array
*/
foreach ($tx_prefixes as $prefix) {
$fields = array($prefix . "_aemodify", $prefix . "_aedecod");
$data = REDCap::getData('array', $record, $fields, $redcap_event_name);
foreach ($data as $subject_id => $subject) {
foreach ($subject as $event_id => $event) {
code_pt($project_id, $subject_id, $event_id, $event[$prefix . "_aemodify"], $event[$prefix . "_aedecod"], $prefix . "_aedecod", $debug, $recode_pt);
if ($debug) {
error_log("DEBUG: Coded " . strtoupper($prefix) . "_AEDECOD {$event[$prefix . '_aedecod']}: subject={$subject_id}, event={$event_id} for AEMODIFY {$event[$prefix . '_aemodify']}");
}
}
}
}
/**
* PREFIX_AEBODSYS
* uses $tx_prefixes preset array
*/
foreach ($tx_prefixes as $prefix) {
$fields = array($prefix . "_aedecod", $prefix . "_aebodsys");
$data = REDCap::getData('array', $record, $fields, $redcap_event_name);
foreach ($data as $subject_id => $subject) {
foreach ($subject as $event_id => $event) {