public function parse()
{
// print_array($_FILES);
// $config['upload_path'] = './assets/files/';
// $config['allowed_types'] = '*';
// $config['max_size'] = '0';
// $config['remove_spaces'] = true;
//
//
// $this->load->library('upload', $config);
//
// if (!$this->upload->do_upload('file')) {
// $error = array('error' => $this->upload->display_errors());
// $this->session->set_flashdata('error', $error);
// redirect(base_url('parser'));
// }
// $fileInfo = $this->upload->data();
//
// $excelData = excel_parser($fileInfo['file_name']);
$excelData = excel_parser('ae.xlsx');
// print_array($excelData);exit;
// dataset name
$datasetName = end($excelData['header'][1]);
// dataset description
$search = 'Dataset Description:';
$result = $this->array_find_like($search, $excelData['values']);
$datasetDesc = end($result);
// study name
$search = 'Study Name:';
$result = $this->array_find($search, $excelData['values']);
$studyName = end($result);
// protocol id
$search = 'Protocol ID:';
$result = $this->array_find($search, $excelData['values']);
$protocolIdReal = end($result);
// Date
$search = 'Date:';
$result = $this->array_find($search, $excelData['values']);
$date = end($result);
// Number of subjects
$search = 'Subjects:';
$result = $this->array_find($search, $excelData['values']);
$numSubjects = end($result);
// Number of Study Event Definitions
$search = 'Study Event Definitions';
$result = $this->array_find($search, $excelData['values']);
$studyEventDef = end($result);
//CHECK IF THE FILE HASE BEEN UPLOADED ONCE
$checkData = array('dataset_name' => $datasetName, 'study_name' => $studyName, 'protocol_id' => $protocolIdReal, 'date' => $date);
$studyModel = load_basic_model('adverse_events');
$resultAE = $studyModel->get($checkData);
if (count($resultAE) > 0) {
$this->session->set_flashdata('error', 'File already uploaded.');
redirect(base_url('ae_parser'));
}
// Study Event Definition data
$search = 'Study Event Definition ';
$result = $this->array_find_like($search, $excelData['values']);
$studyEventDefData = $result;
$SED = $studyEventDefData['C'];
// CRF data
$search = 'CRF';
$result = $this->array_find_like($search, $excelData['values']);
$crfData = $result;
$CRF = end($crfData);
// re order array
$excelData['values'] = array_values($excelData['values']);
// get field names
foreach ($excelData['values'] as $index => $val) {
$key = array_search('Study Subject ID', $val);
if (is_string($key)) {
$fieldsNamesIndex = $index;
$fieldsNames = $excelData['values'][$index];
break;
}
}
$basicModel = load_basic_model('adverse_events');
//adverse_events table insertion
$data = array('dataset_name' => $datasetName, 'study_name' => $studyName, 'protocol_id' => $protocolIdReal, 'subjects' => $numSubjects, 'study_event_definitions' => $studyEventDef, 'date' => $date);
$studyProcessResult = $basicModel->insert($data);
if (count($studyProcessResult) < 1) {
$this->session->set_flashdata('error', 'Operation failed.');
redirect(base_url('ae_parser'));
}
$aeId = $this->db->insert_id();
// get field values
$fieldsValuesArr = array_slice($excelData['values'], $fieldsNamesIndex + 1);
$basicModel = load_basic_model('adverse_events_data');
$SEDCRF = '_' . $SED . '_' . $CRF;
foreach ($fieldsValuesArr as $fieldsValues) {
// Study Subject ID
$key = array_search('Study Subject ID', $fieldsNames);
$studySubId = $this->check_value($fieldsValues, $key);
// protocol id
$key = array_search('Protocol ID', $fieldsNames);
$protocolId = $this->check_value($fieldsValues, $key);
// Stie ID
$siteId = substr($studySubId, 0, 4);
// Sex
$key = array_search('Sex', $fieldsNames);
$sex = $this->check_value($fieldsValues, $key);
// count the number of AE for every client
$key = $this->array_like('StartDate', $fieldsNames);
$arr_split = explode('_', $key);
$countOfArr = end($arr_split);
for ($i = 1; $i <= $countOfArr; $i++) {
$SEDCRF = '_' . $SED . '_' . $i . '_' . $CRF;
// StartDate
$key = array_search('StartDate' . '_' . $SED . '_' . $i, $fieldsNames);
$startDate = $this->check_value($fieldsValues, $key);
// CRF Version Status
$key = $this->array_find_key('CRF Version Status' . $SEDCRF, $fieldsNames);
$crfVersionStatus = $this->check_value($fieldsValues, $key);
// Version Name
$key = $this->array_find_key('Version Name' . $SEDCRF, $fieldsNames);
$versionName = $this->check_value($fieldsValues, $key);
// advevent_desc
$key = $this->array_find_key('advevent_desc' . $SEDCRF, $fieldsNames);
$adveventDesc = $this->check_value($fieldsValues, $key);
// advevent_date
$key = $this->array_find_key('advevent_date' . $SEDCRF, $fieldsNames);
$adveventDate = $this->check_value($fieldsValues, $key);
// advevent_time
$key = $this->array_find_key('advevent_time' . $SEDCRF, $fieldsNames);
$advevent_time = $this->check_value($fieldsValues, $key);
// advevent_inter
$key = $this->array_find_key('advevent_inter' . $SEDCRF, $fieldsNames);
$advevent_inter = $this->check_value($fieldsValues, $key);
// advevent_severity
$key = $this->array_find_key('advevent_severity' . $SEDCRF, $fieldsNames);
$advevent_severity = $this->check_value($fieldsValues, $key);
// advevent_action
$key = $this->array_find_key('advevent_action' . $SEDCRF, $fieldsNames);
$advevent_action = $this->check_value($fieldsValues, $key);
// advevent_other
$key = $this->array_find_key('advevent_other' . $SEDCRF, $fieldsNames);
$advevent_other = $this->check_value($fieldsValues, $key);
// advevent_outcome
$key = $this->array_find_key('advevent_outcome' . $SEDCRF, $fieldsNames);
$advevent_outcome = $this->check_value($fieldsValues, $key);
// advevent_related
$key = $this->array_find_key('advevent_related' . $SEDCRF, $fieldsNames);
$advevent_related = $this->check_value($fieldsValues, $key);
// advevent_resdate
$key = $this->array_find_key('advevent_resdate' . $SEDCRF, $fieldsNames);
$advevent_resdate = $this->check_value($fieldsValues, $key);
// advevent_restime
$key = $this->array_find_key('advevent_restime' . $SEDCRF, $fieldsNames);
$advevent_restime = $this->check_value($fieldsValues, $key);
// advevent_SAE
$key = $this->array_find_key('advevent_SAE' . $SEDCRF, $fieldsNames);
$advevent_SAE = $this->check_value($fieldsValues, $key);
// advevent_reporter
$key = $this->array_find_key('advevent_reporter' . $SEDCRF, $fieldsNames);
$advevent_reporter = $this->check_value($fieldsValues, $key);
// advevent_lastdosedate
$key = $this->array_find_key('advevent_lastdosedate' . $SEDCRF, $fieldsNames);
$advevent_lastdosedate = $this->check_value($fieldsValues, $key);
if ($advevent_lastdosedate != '-') {
$advevent_lastdosedate = ($advevent_lastdosedate - 25569) * 86400;
//conversion from excel date to unix date
}
// advevent_lastdosetime
$key = $this->array_find_key('advevent_lastdosetime' . $SEDCRF, $fieldsNames);
$advevent_lastdosetime = $this->check_value($fieldsValues, $key);
$AEData = array('ae_id' => $aeId, 'study_subject_id' => $studySubId, 'protocol_id' => $protocolId, 'sex' => $sex, 'site_number' => $siteId, 'start_date' => $startDate, 'version_name' => $versionName, 'crf_version_status' => $crfVersionStatus, 'advevent_desc' => $adveventDesc, 'advevent_date' => $adveventDate, 'advevent_inter' => $advevent_inter, 'advevent_severity' => $advevent_severity, 'advevent_action' => $advevent_action, 'advevent_other' => $advevent_other, 'advevent_outcome' => $advevent_outcome, 'advevent_related' => $advevent_related, 'advevent_resdate' => $advevent_resdate, 'advevent_SAE' => $advevent_SAE, 'advevent_reporter' => $advevent_reporter, 'advevent_lastdosedate' => $advevent_lastdosedate, 'advevent_lastdosetime' => $advevent_lastdosetime, 'datetime' => date('Y-m-d', time()));
$this->db->trans_start();
$processResult = $basicModel->insert($AEData);
$this->db->trans_complete();
if ($this->db->trans_status() === TRUE) {
$this->session->set_flashdata('success', 'Operation successfully completedly.');
} else {
$this->session->set_flashdata('error', 'Operation failed.');
}
}
}
redirect(base_url('ae_parser'));
}
public function parse()
{
// print_array($_FILES);
$config['upload_path'] = './assets/files/';
$config['allowed_types'] = '*';
$config['max_size'] = '0';
$config['remove_spaces'] = true;
$this->load->library('upload', $config);
if (!$this->upload->do_upload('file')) {
$error = array('error' => $this->upload->display_errors());
$this->session->set_flashdata('error', $error);
redirect(base_url('parser'));
}
$fileInfo = $this->upload->data();
// print_array($fileInfo);
if ($fileInfo['file_ext'] == '.xlds') {
//load the excel library
$this->load->library('excel');
$path = './assets/files/' . $fileInfo['file_name'];
$inputFileType = PHPExcel_IOFactory::identify($path);
// echo $inputFileType;
$reader = PHPExcel_IOFactory::createReader("{$inputFileType}");
$reader->setReadDataOnly(false);
$excel = $reader->load($path);
$writer = PHPExcel_IOFactory::createWriter($excel, 'Excel5');
// $writer->setUseBOM(true);
$fileName = $fileInfo['raw_name'];
$writer->save('./assets/files/' . $fileName . '.xls');
// echo 'done';exit;
$inputFileType2 = PHPExcel_IOFactory::identify($path);
// echo $inputFileType;exit;
$reader = PHPExcel_IOFactory::createReader("{$inputFileType2}");
$reader->setReadDataOnly(false);
$excel2 = $reader->load($path);
$writer2 = PHPExcel_IOFactory::createWriter($excel2, 'Excel2007');
// $writer->setUseBOM(true);
$writer2->save('./assets/files/' . $fileName . '.xlsx');
$fileInfo['file_name'] = $fileName . '.xlsx';
}
// echo $fileInfo['file_name'];exit;
$excelData = excel_parser($fileInfo['file_name']);
// print_array($excelData);
// $excelData = excel_parser('testnew.xlsx');
// dataset name
$datasetName = end($excelData['header'][1]);
// dataset description
$search = 'Dataset Description:';
$result = $this->array_find_like($search, $excelData['values']);
$datasetDesc = end($result);
// study name
$search = 'Study Name:';
$result = $this->array_find($search, $excelData['values']);
$studyName = end($result);
// protocol id
$search = 'Protocol ID:';
$result = $this->array_find($search, $excelData['values']);
$protocolIdReal = end($result);
// Date
$search = 'Date:';
$result = $this->array_find($search, $excelData['values']);
$date = end($result);
// Number of subjects
$search = 'Subjects:';
$result = $this->array_find($search, $excelData['values']);
$numSubjects = end($result);
// Number of Study Event Definitions
$search = 'Study Event Definitions';
$result = $this->array_find($search, $excelData['values']);
$studyEventDef = end($result);
//CHECK IF THE FILE HASE BEEN UPLOADED ONCE
$checkData = array('dataset_name' => $datasetName, 'study_name' => $studyName, 'protocol_id' => $protocolIdReal, 'date' => $date);
$studyModel = load_basic_model('study');
$resultStudy = $studyModel->get($checkData);
if (count($resultStudy) > 0) {
$this->session->set_flashdata('error', 'File already uploaded.');
redirect(base_url('parser'));
}
// Study Event Definition data
$search = 'Study Event Definition ';
$result = $this->array_find_like($search, $excelData['values']);
$studyEventDefData = $result;
$SED = $studyEventDefData['C'];
// CRF data
$search = 'CRF';
$result = $this->array_find_like($search, $excelData['values']);
$crfData = $result;
$CRF = end($crfData);
$SEDCRF = '_' . $SED . '_' . $CRF;
// re order array
$excelData['values'] = array_values($excelData['values']);
// get field names
foreach ($excelData['values'] as $index => $val) {
$key = array_search('Study Subject ID', $val);
if (is_string($key)) {
$fieldsNamesIndex = $index;
$fieldsNames = $excelData['values'][$index];
break;
}
}
$basicModel = load_basic_model('study');
//study table insertion
$data = array('dataset_name' => $datasetName, 'study_name' => $studyName, 'protocol_id' => $protocolIdReal, 'subjects' => $numSubjects, 'study_event_definitions' => $studyEventDef, 'date' => $date);
$studyProcessResult = $basicModel->insert($data);
if (count($studyProcessResult) < 1) {
$this->session->set_flashdata('error', 'Operation failed.');
redirect(base_url('parser'));
}
$lastId = $this->db->insert_id();
// get field values
$fieldsValuesArr = array_slice($excelData['values'], $fieldsNamesIndex + 1);
$basicModel = load_basic_model('implant_administration');
foreach ($fieldsValuesArr as $fieldsValues) {
// Study Subject ID
$key = array_search('Study Subject ID', $fieldsNames);
$studySubId = $this->check_value($fieldsValues, $key);
//extract site id
$siteId = substr($studySubId, 0, -3);
// protocol id
$key = array_search('Protocol ID', $fieldsNames);
$protocolId = $this->check_value($fieldsValues, $key);
// Person ID
// $key = array_search('Person ID', $fieldsNames);
// $personId = $this->check_value($fieldsValues, $key);
$personId = substr($studySubId, -3);
// Sex
$key = array_search('Sex', $fieldsNames);
$sex = $this->check_value($fieldsValues, $key);
// Version Name
// $key = $this->array_find_key('Version Name' . $SEDCRF, $fieldsNames);
// $versionName = $this->check_value($fieldsValues, $key);
// epp_symptoms
$key = $this->array_find_key('Psympts' . $SEDCRF, $fieldsNames);
$eppSymptoms = $this->check_value($fieldsValues, $key);
// epp_pregnant
$key = $this->array_find_key('Ppregn' . $SEDCRF, $fieldsNames);
$eppPregnant = $this->check_value($fieldsValues, $key);
// implant_date
$key = $this->array_find_key('Padmind' . $SEDCRF, $fieldsNames);
$implantDate = $this->check_value($fieldsValues, $key);
$impUnixDate = ($implantDate - 25569) * 86400;
//conversion from excel date to unix date
// implant_time
$key = $this->array_find_key('Padmtm' . $SEDCRF, $fieldsNames);
$implantTime = $this->check_value($fieldsValues, $key);
// implant_min
// $key = $this->array_find_key('EPP_elig_scen_admin_min' . $SEDCRF, $fieldsNames);
// $implantMinCrf = $this->check_value($fieldsValues, $key);
// $implantMin = $implantMinCrf * 5;
// implant_batch
$key = $this->array_find_key('Pbatch' . $SEDCRF, $fieldsNames);
$implantBatch = $this->check_value($fieldsValues, $key);
// scen_admin_side
$key = $this->array_find_key('Padmsid' . $SEDCRF, $fieldsNames);
$implantSide = $this->check_value($fieldsValues, $key);
// implant_prob
$key = $this->array_find_key('Padmprb' . $SEDCRF, $fieldsNames);
$implantProb = $this->check_value($fieldsValues, $key);
// problem specifications : If yes, please comment and, if applicable, please also complete the adverse events page
// $key = $this->array_find_key('scen_admin_probspec' . $SEDCRF, $fieldsNames);
// $implantProbSpec = $this->check_value($fieldsValues, $key);
// scen_admin_suprail
$key = $this->array_find_key('Psupra' . $SEDCRF, $fieldsNames);
$implantSuprail = $this->check_value($fieldsValues, $key);
// suprail explanation
$key = $this->array_find_key('Psuprax' . $SEDCRF, $fieldsNames);
$implantSuprailExpl = $this->check_value($fieldsValues, $key);
$impAdminData = array('study_id' => $lastId, 'study_subject_id' => $studySubId, 'site_id' => $siteId, 'protocol_id' => $protocolId, 'person_id' => $personId, 'sex' => $sex, 'version_name' => NULL, 'epp_symptoms' => $eppSymptoms, 'implant_date' => $impUnixDate, 'implant_time' => $implantTime, 'implant_prob' => $implantProb, 'implant_batch' => $implantBatch, 'epp_pregnant' => $eppPregnant, 'implant_suprail' => $implantSuprail, 'implant_suprail_expl' => $implantSuprailExpl, 'date' => date('Y-m-d', time()));
$this->db->trans_start();
$processResult = $basicModel->insert($impAdminData);
$this->db->trans_complete();
if ($this->db->trans_status() === TRUE) {
$this->session->set_flashdata('success', 'Operation successfully completedly.');
} else {
$this->session->set_flashdata('error', 'Operation failed.');
}
}
redirect(base_url('parser'));
}
