modify feature nphl api integration
This commit is contained in:
pcalengratha
@@ -63,18 +63,12 @@ class DataRetrievalService
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$surveillances = DB::connection('mysql')->select("select * from surveillances");
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$surveillances = DB::connection('mysql')->select("select * from surveillances");
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foreach ($surveillances as $surveillance){
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foreach ($surveillances as $surveillance){
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$surveillance_data = $this->get('api/labsurveil.php?surveillance_id='.$surveillance->id.'&start_date='.now()->subDays($lookbackDays[$surveillance->code])->toDateString());
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$surveillance_data = $this->get('api/labsurveil.php?surveillance_id='.$surveillance->id.'&start_date='.now()->subDays($lookbackDays[$surveillance->code])->toDateString());
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$data = json_decode(preg_replace('/^\xEF\xBB\xBF/', '', $surveillance_data));
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$data = json_decode(preg_replace('/^\x{FEFF}+/u', '', $surveillance_data));
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@$this->insert_surveillance_cases((array)$data->laboratory_cases);
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@$this->insert_surveillance_cases((array)$data->laboratory_cases);
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@$this->insert_surveillance_case_lab_results((array)$data->laboratory_results);
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@$this->insert_surveillance_case_lab_results((array)$data->laboratory_results);
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}
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}
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//$this->getSARICases(now()->subDays(config('app.lookback_days.SARI'))->toDateString(), $toDate); // done
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// $this->getILICases(now()->subDays(config('app.lookback_days.ILI'))->toDateString(), $toDate); // done
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// $this->getLBMCases(now()->subDays(config('app.lookback_days.LBM'))->toDateString(), $toDate); // done
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// $this->getAFICases(now()->subDays(config('app.lookback_days.AFI'))->toDateString(), $toDate); // done
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// $this->getNSDCases(now()->subDays(config('app.lookback_days.NDS'))->toDateString(), $toDate);
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// $this->getSEQCases(now()->subDays(config('app.lookback_days.SEQ'))->toDateString(), $toDate); // done
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Log::channel('jobs')->info(now()->toDateString(). ' Service Reload Data Successfully Ran');
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Log::channel('jobs')->info(now()->toDateString(). ' Service Reload Data Successfully Ran');
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return true;
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return true;
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}
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}
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@@ -85,761 +79,6 @@ class DataRetrievalService
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}
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}
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public function getSARICases($dateFrom, $dateTo=NULL)
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{
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$cond = "";
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$cond .= " and patient.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
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$cond .= (!empty($dateTo)) ? " and patient.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
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$sari_cases = DB::connection('mysql_nphl')
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->select("
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SELECT
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patient.labcode,
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min(if(year(tps.collected)=0,patient.patdate, tps.collected)) as patdate,
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patient.isnewcase,
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l.labname_en,
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l.labaddress_en,
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1 as surveillance_id,
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min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'Y')) as year_data,
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min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'W')) as week_data,
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patient.patage,
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patient.patsex,
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NULL as is_alive,
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p.proname_en
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.sari_patients sr_p on sr_p.patid = patient.patid
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inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid and tps.status = 1
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inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
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left join niphc0_nphl.province p on p.proid = patient.frompro
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WHERE patient.patgroup =2
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and patient.status = 1
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".$cond . "
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group by
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patient.labcode,
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patient.isnewcase,
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l.labname_en,
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l.labaddress_en,
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patient.patage,
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patient.patsex,
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p.proname_en;"
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);
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$this->insert_surveillance_cases($sari_cases);
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$sari_case_results = DB::connection('mysql_nphl')->select("
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SELECT
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patient.labcode,
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1 as surveillance_id,
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if(trs.rtitle='Negatives', 0, 1) as is_positive,
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if(trs.rtitle !='Negatives', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
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if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
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'Influenza' as indicator
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FROM `labopatients` patient
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inner join sari_patients sr_p on sr_p.patid = patient.patid
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inner join test_patsample tps on tps.patientid = patient.patid
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inner join test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
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inner join test_pattestresult tptr on tptr.pstid = tpst.pstid
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inner join test_resultselect trs on trs.rid = tptr.rsltid
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WHERE patient.patgroup =2
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and patient.status = 1
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and tps.status = 1
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and tpst.status = 1
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and trs.status = 1
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and tpst.labtestid in (775,216,239,238,212,220,340,381,382)
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" .$cond. "
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union
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SELECT
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patient.labcode,
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1 as surveillance_id,
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if(trs.rtitle='Negative', 0, 1) as is_positive,
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if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
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'' as subtype,
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'Covid-19' as indicator
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FROM `labopatients` patient
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inner join sari_patients sr_p
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on sr_p.patid = patient.patid
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inner join test_patsample tps
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on tps.patientid = patient.patid
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inner join test_patsamtest tpst
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on tpst.patsmid = tps.sampleid
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and tpst.patid = tps.patientid
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inner join test_pattestresult tptr on tptr.pstid = tpst.pstid
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inner join test_resultselect trs on trs.rid = tptr.rsltid
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WHERE patient.patgroup =2
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and patient.status = 1
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and tps.status = 1
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and tpst.status = 1
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and trs.status = 1
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and tpst.labtestid in (651,652,653,654,650)
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and trs.rtitle !='Pending'
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" .$cond);
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$this->insert_surveillance_case_lab_results($sari_case_results);
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}
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public function getILICases($dateFrom, $dateTo = NULL)
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{
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$cond = "";
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$cond .= " and patient.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
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$cond .= (!empty($dateTo)) ? " and patient.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
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$ili_cases = DB::connection('mysql_nphl')
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->select("
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SELECT
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patient.labcode,
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min(if(year(tps.collected)=0,patient.patdate, tps.collected)) as patdate,
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patient.isnewcase,
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l.labname_en,
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l.labaddress_en,
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2 as surveillance_id,
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min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'Y')) as year_data,
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min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'W')) as week_data,
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patient.patage,
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patient.patsex,
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NULL as is_alive,
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p.proname_en
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid
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inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid and tps.status = 1
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inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
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left join niphc0_nphl.province p on p.proid = patient.frompro
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WHERE patient.patgroup =3
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and patient.status = 1
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".$cond . "
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group by
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patient.labcode,
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patient.isnewcase,
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l.labname_en,
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l.labaddress_en,
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patient.patage,
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patient.patsex,
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p.proname_en;"
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);
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$this->insert_surveillance_cases($ili_cases);
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$ili_case_results = DB::connection('mysql_nphl')
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->select("
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SELECT
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distinct
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patient.labcode,
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2 as surveillance_id,
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if(trs.rtitle='Negatives', 0, 1) as is_positive,
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if(trs.rtitle !='Negatives', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
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if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
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'Influenza' as indicator
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid
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inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
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inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
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inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
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inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
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WHERE patient.patgroup = 3
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and patient.status = 1
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and tps.status = 1
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and tpst.status = 1
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and trs.status = 1
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and tpst.labtestid in (775,216,239,238,212,220,340,381,382)
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".$cond."
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union
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SELECT
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DISTINCT
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patient.labcode,
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2 as surveillance_id,
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if(trs.rtitle='Negative', 0, 1) as is_positive,
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if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
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'' as subtype,
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'Covid-19' as indicator
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid
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inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
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inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
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inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
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inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
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WHERE patient.patgroup = 3
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and patient.status = 1
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and tps.status = 1
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and tpst.status = 1
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and trs.status = 1
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and tpst.labtestid in (651,652,653,654,650)
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and trs.rtitle !='Pending'
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".$cond);
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$this->insert_surveillance_case_lab_results($ili_case_results);
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}
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public function getLBMCases($dateFrom, $dateTo = NULL)
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{
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$cond = "";
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$cond .= " and patient.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
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$cond .= (!empty($dateTo)) ? " and patient.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
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$lbm_cases = DB::connection('mysql_nphl')
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->select("
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SELECT
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patient.labcode,
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min(if(year(tps.collected)=0,patient.patdate, tps.collected)) as patdate,
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patient.isnewcase,
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l.labname_en,
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l.labaddress_en,
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3 as surveillance_id,
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min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'Y')) as year_data,
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min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'W')) as week_data,
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patient.patage,
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patient.patsex,
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NULL as is_alive,
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p.proname_en
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.lbms_patients on lbms_patients.patid = patient.patid
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inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid and tps.status = 1
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left join niphc0_nphl.province p on p.proid = patient.frompro
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inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
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WHERE patient.patgroup = 17
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and patient.status = 1
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".$cond . "
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group by
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patient.labcode,
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patient.isnewcase,
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l.labname_en,
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l.labaddress_en,
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patient.patage,
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patient.patsex,
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p.proname_en;"
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);
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$this->insert_surveillance_cases($lbm_cases);
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$lbm_case_results = DB::connection('mysql_nphl')
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->select("
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SELECT
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distinct
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patient.labcode,
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3 as surveillance_id,
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if(trs.rtitle='Negatives', 0, 1) as is_positive,
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if(trs.rtitle !='Negatives', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
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if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
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'Influenza' as indicator
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.lbms_patients sr_p on sr_p.patid = patient.patid
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inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
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inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
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inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
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inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
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WHERE patient.patgroup = 17
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and patient.status = 1
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and tps.status = 1
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and tpst.status = 1
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and trs.status = 1
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and tpst.labtestid in (775,216,239,238,212,220,340,381,382)
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".$cond."
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union
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SELECT
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DISTINCT
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patient.labcode,
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3 as surveillance_id,
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if(trs.rtitle='Negative', 0, 1) as is_positive,
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if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
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'' as subtype,
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'Covid-19' as indicator
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.lbms_patients sr_p on sr_p.patid = patient.patid
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inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
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inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
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inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
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inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
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WHERE patient.patgroup = 17
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and patient.status = 1
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and tps.status = 1
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and tpst.status = 1
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and trs.status = 1
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and tpst.labtestid in (651,652,653,654,650)
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and trs.rtitle !='Pending'
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".$cond);
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$this->insert_surveillance_case_lab_results($lbm_case_results);
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}
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|
|
||||||
public function getAFICases($dateFrom, $dateTo = NULL)
|
|
||||||
{
|
|
||||||
$cond = "";
|
|
||||||
$cond .= " and afi_case.date_of_interview >= '".date('Y-m-d', strtotime($dateFrom))."' ";
|
|
||||||
$cond .= (!empty($dateTo)) ? " and afi_case.date_of_interview <='".date('Y-m-d', strtotime($dateTo))."' ":"";
|
|
||||||
$afi_cases = DB::connection('mysql_afi')
|
|
||||||
->select("
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
afi_case.date_of_interview as patdate,
|
|
||||||
1 as isnewcase,
|
|
||||||
afi_case.sentinel_site as labname_en,
|
|
||||||
'' as labaddress_en,
|
|
||||||
4 as surveillance_id,
|
|
||||||
niphc0_nphl.get_epi_period(afi_case.date_of_interview, 'Y') as year_data,
|
|
||||||
niphc0_nphl.get_epi_period(afi_case.date_of_interview, 'W') as week_data,
|
|
||||||
ifnull(DATEDIFF(afi_case.date_of_interview, date_of_birth),180) as patage,
|
|
||||||
if(afi_case.sex='Male','M','F') as patsex,
|
|
||||||
NULL as is_alive,
|
|
||||||
p.proname_en as proname_en
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
left join afi_db.afi_tbl_result afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
left join niphc0_nphl.province p on p.proid = afi_case.residence_province
|
|
||||||
where
|
|
||||||
afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null " .$cond);
|
|
||||||
|
|
||||||
$this->insert_surveillance_cases($afi_cases);
|
|
||||||
|
|
||||||
$afi_lab_results = DB::connection('mysql_afi')
|
|
||||||
->select(
|
|
||||||
"SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.influenza_result='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.influenza_result='Positive', concat('Influenza ',LEFT(UPPER(JSON_UNQUOTE(JSON_EXTRACT(afi_lab_result.influenza_subtypes, '$[0].id'))),1)),'') pathogen_name,
|
|
||||||
if(afi_lab_result.influenza_result='Positive', REPLACE(UPPER(JSON_UNQUOTE(JSON_EXTRACT(afi_lab_result.influenza_subtypes, '$[0].id'))),'_','/'),'') as subtype,
|
|
||||||
'Influenza' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.influenza_result in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
union
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.sarscov2_result='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.sarscov2_result='Positive', 'SARS-CoV-2','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Covid-19' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.sarscov2_result in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null
|
|
||||||
".$cond."
|
|
||||||
|
|
||||||
union
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.dengue_pcr='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.dengue_pcr='Positive', 'Dengue Virus','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Dengue Virus|PCR' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.dengue_pcr in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
union
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.chikungunya_pcr='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.chikungunya_pcr='Positive', 'Chikungunya Virus','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Chikungunya Virus|PCR' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.chikungunya_pcr in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
union
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.leptospira_pcr='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.leptospira_pcr='Positive', 'Leptospira spp.','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Leptospira spp.|PCR' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.leptospira_pcr in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
union
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.plasmodium_pcr='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.plasmodium_pcr='Positive', 'Plasmodium spp.','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Plasmodium spp.|PCR' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.plasmodium_pcr in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
UNION
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.rickettsia_pcr='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.rickettsia_pcr='Positive', 'Rickettsia spp.','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Rickettsia spp.|PCR' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.rickettsia_pcr in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
UNION
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.salmonella_pcr='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.salmonella_pcr='Positive', 'Salmonella spp.','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Salmonella spp.|PCR' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.salmonella_pcr in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
UNION
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.westnile_pcr='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.westnile_pcr='Positive', 'West Nile Virus','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'West Nile Virus|PCR' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.westnile_pcr in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
UNION
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.zika_pcr='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.zika_pcr='Positive', 'ZIKA Virus','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'ZIKA Virus|PCR' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.zika_pcr in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
UNION
|
|
||||||
|
|
||||||
# SERUM
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.chikungunya_serum='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.chikungunya_serum='Positive', 'Chikungunya Virus','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Chikungunya Virus|Serum' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.chikungunya_serum in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
UNION
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.dengue_serum='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.dengue_serum='Positive', 'Dengue Virus','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Dengue Virus|Serum' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.dengue_serum in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
UNION
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.westnile_serum='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.westnile_serum='Positive', 'West Nile Virus','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'West Nile Virus|Serum' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.westnile_serum in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
UNION
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.zika_serum='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.zika_serum='Positive', 'ZIKA Virus','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'ZIKA Virus|Serum' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.zika_serum in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond."
|
|
||||||
|
|
||||||
UNION
|
|
||||||
|
|
||||||
SELECT
|
|
||||||
afi_lab_result.sample_code as labcode,
|
|
||||||
4 as surveillance_id,
|
|
||||||
if(afi_lab_result.je_virus='Positive',1,0) as is_positive,
|
|
||||||
if(afi_lab_result.je_virus='Positive', 'Japanese Encephalitis Virus','') pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
'Japanese Encephalitis Virus|Serum' as indicator
|
|
||||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
|
||||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
|
||||||
where afi_lab_result.sample_code is not null
|
|
||||||
and afi_lab_result.je_virus in('Negative', 'Positive')
|
|
||||||
and afi_case.afi_event is NOT null
|
|
||||||
and afi_case.date_of_interview is not null
|
|
||||||
and afi_lab_result.sample_code is not null ".$cond
|
|
||||||
);
|
|
||||||
|
|
||||||
$this->insert_surveillance_case_lab_results($afi_lab_results);
|
|
||||||
}
|
|
||||||
|
|
||||||
public function getNSDCases($dateFrom, $dateTo = NULL)
|
|
||||||
{
|
|
||||||
$cond = "";
|
|
||||||
$cond .= " and sc.sc_date >= '".date('Y-m-d', strtotime($dateFrom))."' ";
|
|
||||||
$cond .= (!empty($dateTo)) ? " and sc.sc_date <='".date('Y-m-d', strtotime($dateTo))."' ":"";
|
|
||||||
$nds_cases = DB::connection('mysql_nds')
|
|
||||||
->select("
|
|
||||||
SELECT
|
|
||||||
DISTINCT
|
|
||||||
sc.sc_sample_code as labcode,
|
|
||||||
sc.sc_date as patdate,
|
|
||||||
1 as isnewcase,
|
|
||||||
site_ad.sn_name as labname_en,
|
|
||||||
'' as labaddress_en,
|
|
||||||
5 as surveillance_id,
|
|
||||||
niphc0_nphl.get_epi_period(sc.sc_date, 'Y') as year_data,
|
|
||||||
niphc0_nphl.get_epi_period(sc.sc_date, 'W') as week_data,
|
|
||||||
ifnull(DATEDIFF(sc.sc_date, patient.pat_dob),180) as patage,
|
|
||||||
if(patient.pat_gender='Male','M','F') as patsex,
|
|
||||||
NULL as is_alive,
|
|
||||||
pro.pro_eng as proname_en
|
|
||||||
from nds_db.tbl_nds_site_invest case_inv
|
|
||||||
inner join nds_db.tbl_nds_siteinvet_patient inv_patient
|
|
||||||
on inv_patient.pksi_id = case_inv.pksi_id
|
|
||||||
inner join nds_db.tbl_nds_site_address site_ad
|
|
||||||
on site_ad.pksn_id = case_inv.fksn_id
|
|
||||||
inner join nds_db.tbl_nds_patient patient
|
|
||||||
on patient.pkpat_id = inv_patient.fkpat_id
|
|
||||||
inner join nds_db.tbl_nds_basic_sample bs
|
|
||||||
on bs.fkpat_id = inv_patient.fkpat_id
|
|
||||||
inner join nds_db.tbl_nds_sample_collection sc
|
|
||||||
on sc.fkbs_id = bs.pkbs_id
|
|
||||||
left join nds_db.tblprovince pro
|
|
||||||
on pro.pkpro_code = JSON_UNQUOTE(JSON_EXTRACT(patient.pat_address, '$[0].province'))
|
|
||||||
where
|
|
||||||
sc.sc_sample_code is not null
|
|
||||||
and length(sc_sample_code)>0 " .$cond);
|
|
||||||
|
|
||||||
$this->insert_surveillance_cases($nds_cases);
|
|
||||||
|
|
||||||
$nds_lab_results = DB::connection('mysql_nds')
|
|
||||||
->select("
|
|
||||||
SELECT
|
|
||||||
DISTINCT
|
|
||||||
sc.sc_sample_code as labcode,
|
|
||||||
5 as surveillance_id,
|
|
||||||
rt.rt_positive as is_positive,
|
|
||||||
trt.trt_name pathogen_name,
|
|
||||||
'' as subtype,
|
|
||||||
trt.trt_name as indicator
|
|
||||||
from nds_db.tbl_nds_site_invest case_inv
|
|
||||||
inner join nds_db.tbl_nds_siteinvet_patient inv_patient
|
|
||||||
on inv_patient.pksi_id = case_inv.pksi_id
|
|
||||||
inner join nds_db.tbl_nds_patient patient
|
|
||||||
on patient.pkpat_id = inv_patient.fkpat_id
|
|
||||||
inner join nds_db.tbl_nds_basic_sample bs
|
|
||||||
on bs.fkpat_id = inv_patient.fkpat_id
|
|
||||||
inner join nds_db.tbl_nds_sample_collection sc
|
|
||||||
on sc.fkbs_id = bs.pkbs_id
|
|
||||||
inner join nds_db.tbl_nds_result_test rt
|
|
||||||
on rt.fkpat_id = bs.fkpat_id
|
|
||||||
inner join nds_db.tbl_nds_test_result_type trt
|
|
||||||
on trt.pktrt_id = rt.fktrt_id
|
|
||||||
|
|
||||||
where
|
|
||||||
sc.sc_sample_code is not null
|
|
||||||
and length(sc_sample_code)>0 " .$cond);
|
|
||||||
|
|
||||||
$this->insert_surveillance_case_lab_results($nds_lab_results);
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
public function getSEQCases($dateFrom, $dateTo = NULL)
|
|
||||||
{
|
|
||||||
$cond = "";
|
|
||||||
$cond .= " and c.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
|
|
||||||
$cond .= (!empty($dateTo)) ? " and c.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
|
|
||||||
$seq_cases = DB::connection('mysql_nphl')
|
|
||||||
->select("
|
|
||||||
SELECT DISTINCT
|
|
||||||
c.labcode,
|
|
||||||
min(if(year(tps.collected)=0,c.patdate, tps.collected)) as patdate,
|
|
||||||
c.isnewcase,
|
|
||||||
l.labname_en,
|
|
||||||
l.labaddress_en,
|
|
||||||
6 as surveillance_id,
|
|
||||||
min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,c.patdate, tps.collected), 'Y')) as year_data,
|
|
||||||
min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,c.patdate, tps.collected), 'W')) as week_data,
|
|
||||||
c.patage,
|
|
||||||
c.patsex,
|
|
||||||
NULL as is_alive,
|
|
||||||
pro.proname_en
|
|
||||||
from niphc0_nphl.sq_batch sqb
|
|
||||||
inner join niphc0_nphl.sq_sub_batch sqsb on sqsb.bt_id = sqb.bt_id
|
|
||||||
inner join niphc0_nphl.labopatients c on c.patid = sqsb.patid
|
|
||||||
inner join niphc0_nphl.laboratory l on l.labid = p.patsource
|
|
||||||
inner join niphc0_nphl.test_patsample tps on tps.patientid = c.patid and tps.status = 1
|
|
||||||
inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
|
|
||||||
left join niphc0_nphl.province pro on pro.proid = c.frompro
|
|
||||||
where c.status = 1
|
|
||||||
and tpst.labtestid IN ( 659, 662, 666, 667, 668 )
|
|
||||||
" . $cond . "
|
|
||||||
group by
|
|
||||||
c.labcode,
|
|
||||||
c.isnewcase,
|
|
||||||
l.labname_en,
|
|
||||||
l.labaddress_en,
|
|
||||||
c.patage,
|
|
||||||
c.patsex,
|
|
||||||
pro.proname_en;"
|
|
||||||
);
|
|
||||||
|
|
||||||
$this->insert_surveillance_cases($seq_cases);
|
|
||||||
|
|
||||||
$seq_lab_results = DB::connection('mysql_nphl')
|
|
||||||
->select("
|
|
||||||
SELECT
|
|
||||||
labcode,
|
|
||||||
6 as surveillance_id,
|
|
||||||
1 is_positive,
|
|
||||||
ifnull(seqlineage,'N/A') as pathogen_name,
|
|
||||||
GROUP_CONCAT(seq_result SEPARATOR '') as subtype,
|
|
||||||
(case
|
|
||||||
when (Group_concat(influ_result SEPARATOR '')='Negatives' or Group_concat(influ_result SEPARATOR '')='') and Group_concat(covid_result SEPARATOR '')='Positive' then 'Covid-19'
|
|
||||||
when (Group_concat(influ_result SEPARATOR '') !='Negatives' and Group_concat(influ_result SEPARATOR '')!='') and Group_concat(covid_result SEPARATOR '')='Negative' then 'Influenza'
|
|
||||||
when (Group_concat(influ_result SEPARATOR '') !='Negatives' and Group_concat(influ_result SEPARATOR '')!='') and Group_concat(covid_result SEPARATOR '')='Positive' then 'Co-infection'
|
|
||||||
else 'N/A'
|
|
||||||
end) as indicator
|
|
||||||
FROM (SELECT
|
|
||||||
c.labcode,
|
|
||||||
( CASE
|
|
||||||
WHEN e1.labtestid IN ( 238, 340, 381 ) THEN e3.rtitle
|
|
||||||
ELSE ''
|
|
||||||
end ) influ_result,
|
|
||||||
( CASE
|
|
||||||
WHEN e1.labtestid IN ( 650, 651 ) THEN e3.rtitle
|
|
||||||
ELSE ''
|
|
||||||
end ) covid_result,
|
|
||||||
( CASE
|
|
||||||
WHEN e1.labtestid IN ( 668, 659, 666, 667, 662 ) THEN
|
|
||||||
e3.rtitle
|
|
||||||
ELSE ''
|
|
||||||
end ) seq_result,
|
|
||||||
b.seqlineage
|
|
||||||
FROM niphc0_nphl.sq_batch a
|
|
||||||
LEFT JOIN niphc0_nphl.sq_sub_batch b
|
|
||||||
ON a.bt_id = b.bt_id
|
|
||||||
LEFT JOIN niphc0_nphl.labopatients c
|
|
||||||
ON b.patid = c.patid
|
|
||||||
LEFT JOIN niphc0_nphl.laboratory d
|
|
||||||
ON c.patsource = d.labid
|
|
||||||
LEFT JOIN niphc0_nphl.test_patsamtest e1
|
|
||||||
ON c.patid = e1.patid
|
|
||||||
LEFT JOIN niphc0_nphl.test_pattestresult e2
|
|
||||||
ON e1.pstid = e2.pstid
|
|
||||||
LEFT JOIN niphc0_nphl.test_resultselect e3
|
|
||||||
ON e2.rsltid = e3.rid
|
|
||||||
LEFT JOIN niphc0_nphl.ncov_patients e4
|
|
||||||
ON c.patid = e4.patid
|
|
||||||
LEFT JOIN niphc0_nphl.test_patsample e5
|
|
||||||
ON c.patid = e5.patientid
|
|
||||||
AND e5.sampleid = e1.patsmid
|
|
||||||
LEFT JOIN niphc0_nphl.test_patsmpbyunit f
|
|
||||||
ON e5.sampleid = f.patsamid
|
|
||||||
AND c.patid = f.patid
|
|
||||||
WHERE e1.labtestid IN ( 238, 340, 381, 650,
|
|
||||||
651, 668, 659, 666,
|
|
||||||
667, 662 )
|
|
||||||
" . $cond . "
|
|
||||||
) tbl_a
|
|
||||||
GROUP BY labcode,
|
|
||||||
seqlineage
|
|
||||||
HAVING
|
|
||||||
GROUP_CONCAT(seq_result SEPARATOR '') not in ('','Inconclusive', 'In Progress')
|
|
||||||
");
|
|
||||||
|
|
||||||
$this->insert_surveillance_case_lab_results($seq_lab_results);
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
private function insert_surveillance_cases($cases){
|
private function insert_surveillance_cases($cases){
|
||||||
|
|
||||||
$case_data = [];
|
$case_data = [];
|
||||||
@@ -860,9 +99,9 @@ class DataRetrievalService
|
|||||||
];
|
];
|
||||||
}
|
}
|
||||||
|
|
||||||
$case_chunks = array_chunk($case_data, 100);
|
$case_chunks = array_chunk($case_data, 500);
|
||||||
foreach ($case_chunks as $chunk) {
|
foreach ($case_chunks as $chunk) {
|
||||||
DB::connection('mysql')->table('tmp_surveillance_cases')->upsert($chunk, [
|
DB::connection('mysql')->table('surveillance_cases')->upsert($chunk, [
|
||||||
'lab_code',
|
'lab_code',
|
||||||
'surveillance_id'
|
'surveillance_id'
|
||||||
], [
|
], [
|
||||||
@@ -892,9 +131,9 @@ class DataRetrievalService
|
|||||||
'indicator' => $lab_result->indicator
|
'indicator' => $lab_result->indicator
|
||||||
];
|
];
|
||||||
}
|
}
|
||||||
$result_chunks = array_chunk($result_data, 100);
|
$result_chunks = array_chunk($result_data, 500);
|
||||||
foreach ($result_chunks as $chunk) {
|
foreach ($result_chunks as $chunk) {
|
||||||
DB::connection('mysql')->table('tmp_case_lab_results')->upsert($chunk,
|
DB::connection('mysql')->table('case_lab_results')->upsert($chunk,
|
||||||
[
|
[
|
||||||
'lab_code',
|
'lab_code',
|
||||||
'surveillance_id',
|
'surveillance_id',
|
||||||
|
|||||||
@@ -16,12 +16,12 @@ return [
|
|||||||
'name' => env('APP_NAME', 'Laravel'),
|
'name' => env('APP_NAME', 'Laravel'),
|
||||||
|
|
||||||
'lookback_days' => [
|
'lookback_days' => [
|
||||||
'SARI' => 7, //
|
'SARI' => 150,
|
||||||
'ILI' => 7,
|
'ILI' => 150,
|
||||||
'LBM' => 7,
|
'LBM' => 150,
|
||||||
'AFI' => 7,
|
'AFI' => 150,
|
||||||
'NDS' => 7,
|
'NDS' => 150,
|
||||||
'SEQ' => 7
|
'SEQ' => 150
|
||||||
],
|
],
|
||||||
|
|
||||||
/*
|
/*
|
||||||
|
|||||||
Reference in New Issue
Block a user