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modify feature nphl api integration

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This commit is contained in:
pcalengratha
2026-05-04 10:15:54 +07:00
parent 63ae7bacbf
commit b1b6c639b2
2 changed files with 11 additions and 772 deletions
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771
dashboard/app/Services/DataRetrievalService.php
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@@ -63,18 +63,12 @@ class DataRetrievalService
$surveillances = DB::connection('mysql')->select("select * from surveillances");
foreach ($surveillances as $surveillance){
$surveillance_data = $this->get('api/labsurveil.php?surveillance_id='.$surveillance->id.'&start_date='.now()->subDays($lookbackDays[$surveillance->code])->toDateString());
$data = json_decode(preg_replace('/^\xEF\xBB\xBF/', '', $surveillance_data));
$data = json_decode(preg_replace('/^\x{FEFF}+/u', '', $surveillance_data));
@$this->insert_surveillance_cases((array)$data->laboratory_cases);
@$this->insert_surveillance_case_lab_results((array)$data->laboratory_results);
}
//$this->getSARICases(now()->subDays(config('app.lookback_days.SARI'))->toDateString(), $toDate); // done
// $this->getILICases(now()->subDays(config('app.lookback_days.ILI'))->toDateString(), $toDate); // done
// $this->getLBMCases(now()->subDays(config('app.lookback_days.LBM'))->toDateString(), $toDate); // done
// $this->getAFICases(now()->subDays(config('app.lookback_days.AFI'))->toDateString(), $toDate); // done
// $this->getNSDCases(now()->subDays(config('app.lookback_days.NDS'))->toDateString(), $toDate);
// $this->getSEQCases(now()->subDays(config('app.lookback_days.SEQ'))->toDateString(), $toDate); // done
Log::channel('jobs')->info(now()->toDateString(). ' Service Reload Data Successfully Ran');
return true;
}
@@ -85,761 +79,6 @@ class DataRetrievalService
}
public function getSARICases($dateFrom, $dateTo=NULL)
{
$cond = "";
$cond .= " and patient.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
$cond .= (!empty($dateTo)) ? " and patient.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
$sari_cases = DB::connection('mysql_nphl')
->select("
SELECT
patient.labcode,
min(if(year(tps.collected)=0,patient.patdate, tps.collected)) as patdate,
patient.isnewcase,
l.labname_en,
l.labaddress_en,
1 as surveillance_id,
min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'Y')) as year_data,
min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'W')) as week_data,
patient.patage,
patient.patsex,
NULL as is_alive,
p.proname_en
FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.sari_patients sr_p on sr_p.patid = patient.patid
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid and tps.status = 1
inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
left join niphc0_nphl.province p on p.proid = patient.frompro
WHERE patient.patgroup =2
and patient.status = 1
".$cond . "
group by
patient.labcode,
patient.isnewcase,
l.labname_en,
l.labaddress_en,
patient.patage,
patient.patsex,
p.proname_en;"
);
$this->insert_surveillance_cases($sari_cases);
$sari_case_results = DB::connection('mysql_nphl')->select("
SELECT
patient.labcode,
1 as surveillance_id,
if(trs.rtitle='Negatives', 0, 1) as is_positive,
if(trs.rtitle !='Negatives', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
'Influenza' as indicator
FROM `labopatients` patient
inner join sari_patients sr_p on sr_p.patid = patient.patid
inner join test_patsample tps on tps.patientid = patient.patid
inner join test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
inner join test_pattestresult tptr on tptr.pstid = tpst.pstid
inner join test_resultselect trs on trs.rid = tptr.rsltid
WHERE patient.patgroup =2
and patient.status = 1
and tps.status = 1
and tpst.status = 1
and trs.status = 1
and tpst.labtestid in (775,216,239,238,212,220,340,381,382)
" .$cond. "
union
SELECT
patient.labcode,
1 as surveillance_id,
if(trs.rtitle='Negative', 0, 1) as is_positive,
if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
'' as subtype,
'Covid-19' as indicator
FROM `labopatients` patient
inner join sari_patients sr_p
on sr_p.patid = patient.patid
inner join test_patsample tps
on tps.patientid = patient.patid
inner join test_patsamtest tpst
on tpst.patsmid = tps.sampleid
and tpst.patid = tps.patientid
inner join test_pattestresult tptr on tptr.pstid = tpst.pstid
inner join test_resultselect trs on trs.rid = tptr.rsltid
WHERE patient.patgroup =2
and patient.status = 1
and tps.status = 1
and tpst.status = 1
and trs.status = 1
and tpst.labtestid in (651,652,653,654,650)
and trs.rtitle !='Pending'
" .$cond);
$this->insert_surveillance_case_lab_results($sari_case_results);
}
public function getILICases($dateFrom, $dateTo = NULL)
{
$cond = "";
$cond .= " and patient.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
$cond .= (!empty($dateTo)) ? " and patient.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
$ili_cases = DB::connection('mysql_nphl')
->select("
SELECT
patient.labcode,
min(if(year(tps.collected)=0,patient.patdate, tps.collected)) as patdate,
patient.isnewcase,
l.labname_en,
l.labaddress_en,
2 as surveillance_id,
min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'Y')) as year_data,
min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'W')) as week_data,
patient.patage,
patient.patsex,
NULL as is_alive,
p.proname_en
FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid and tps.status = 1
inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
left join niphc0_nphl.province p on p.proid = patient.frompro
WHERE patient.patgroup =3
and patient.status = 1
".$cond . "
group by
patient.labcode,
patient.isnewcase,
l.labname_en,
l.labaddress_en,
patient.patage,
patient.patsex,
p.proname_en;"
);
$this->insert_surveillance_cases($ili_cases);
$ili_case_results = DB::connection('mysql_nphl')
->select("
SELECT
distinct
patient.labcode,
2 as surveillance_id,
if(trs.rtitle='Negatives', 0, 1) as is_positive,
if(trs.rtitle !='Negatives', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
'Influenza' as indicator
FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
WHERE patient.patgroup = 3
and patient.status = 1
and tps.status = 1
and tpst.status = 1
and trs.status = 1
and tpst.labtestid in (775,216,239,238,212,220,340,381,382)
".$cond."
union
SELECT
DISTINCT
patient.labcode,
2 as surveillance_id,
if(trs.rtitle='Negative', 0, 1) as is_positive,
if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
'' as subtype,
'Covid-19' as indicator
FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
WHERE patient.patgroup = 3
and patient.status = 1
and tps.status = 1
and tpst.status = 1
and trs.status = 1
and tpst.labtestid in (651,652,653,654,650)
and trs.rtitle !='Pending'
".$cond);
$this->insert_surveillance_case_lab_results($ili_case_results);
}
public function getLBMCases($dateFrom, $dateTo = NULL)
{
$cond = "";
$cond .= " and patient.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
$cond .= (!empty($dateTo)) ? " and patient.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
$lbm_cases = DB::connection('mysql_nphl')
->select("
SELECT
patient.labcode,
min(if(year(tps.collected)=0,patient.patdate, tps.collected)) as patdate,
patient.isnewcase,
l.labname_en,
l.labaddress_en,
3 as surveillance_id,
min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'Y')) as year_data,
min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'W')) as week_data,
patient.patage,
patient.patsex,
NULL as is_alive,
p.proname_en
FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.lbms_patients on lbms_patients.patid = patient.patid
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid and tps.status = 1
left join niphc0_nphl.province p on p.proid = patient.frompro
inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
WHERE patient.patgroup = 17
and patient.status = 1
".$cond . "
group by
patient.labcode,
patient.isnewcase,
l.labname_en,
l.labaddress_en,
patient.patage,
patient.patsex,
p.proname_en;"
);
$this->insert_surveillance_cases($lbm_cases);
$lbm_case_results = DB::connection('mysql_nphl')
->select("
SELECT
distinct
patient.labcode,
3 as surveillance_id,
if(trs.rtitle='Negatives', 0, 1) as is_positive,
if(trs.rtitle !='Negatives', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
'Influenza' as indicator
FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.lbms_patients sr_p on sr_p.patid = patient.patid
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
WHERE patient.patgroup = 17
and patient.status = 1
and tps.status = 1
and tpst.status = 1
and trs.status = 1
and tpst.labtestid in (775,216,239,238,212,220,340,381,382)
".$cond."
union
SELECT
DISTINCT
patient.labcode,
3 as surveillance_id,
if(trs.rtitle='Negative', 0, 1) as is_positive,
if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
'' as subtype,
'Covid-19' as indicator
FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.lbms_patients sr_p on sr_p.patid = patient.patid
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
WHERE patient.patgroup = 17
and patient.status = 1
and tps.status = 1
and tpst.status = 1
and trs.status = 1
and tpst.labtestid in (651,652,653,654,650)
and trs.rtitle !='Pending'
".$cond);
$this->insert_surveillance_case_lab_results($lbm_case_results);
}
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){
$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 $chunk) {
DB::connection('mysql')->table('tmp_surveillance_cases')->upsert($chunk, [
DB::connection('mysql')->table('surveillance_cases')->upsert($chunk, [
'lab_code',
'surveillance_id'
], [
@@ -892,9 +131,9 @@ class DataRetrievalService
'indicator' => $lab_result->indicator
];
}
$result_chunks = array_chunk($result_data, 100);
$result_chunks = array_chunk($result_data, 500);
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',
'surveillance_id',