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Merge branch 'master' of github.com:khantey1998/nrml-dashboard

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This commit is contained in:
Khantey Long
2026-04-15 15:58:08 +07:00
parent 840b93a651 4534f502e2
commit 6cefcccd10
8 changed files with 1357 additions and 345 deletions
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81
dashboard/app/Http/Controllers/Api/DashboardController.php
View File

@@ -139,6 +139,87 @@ class DashboardController extends Controller
return response()->json($data); return response()->json($data);
} }
/*
|--------------------------------------------------------------------------
| Influenza subtype distribution (Overview)
|--------------------------------------------------------------------------
*/
public function influenzaSubtypeDetected(Request $request)
{
$range = $this->getEpiRange($request);
if (!$range) {
return response()->json(['error' => 'Missing epiweek range'], 400);
}
$data = $this->service->influenzaSubtypeDetected(
$range['startYear'],
$range['startWeek'],
$range['endYear'],
$range['endWeek']
);
return response()->json($data);
}
public function covidDistributedByAgeGroup(Request $request)
{
$range = $this->getEpiRange($request);
if (!$range) {
return response()->json(['error' => 'Missing epiweek range'], 400);
}
$data = $this->service->covidDistributedByAgeGroup(
$range['startYear'],
$range['startWeek'],
$range['endYear'],
$range['endWeek']
);
return response()->json($data);
}
public function covidLineageRelativeOverTime(Request $request)
{
$range = $this->getEpiRange($request);
if (!$range) {
return response()->json(['error' => 'Missing epiweek range'], 400);
}
$data = $this->service->covidLineageRelativeOverTime(
$range['startYear'],
$range['startWeek'],
$range['endYear'],
$range['endWeek']
);
return response()->json($data);
}
public function influenzaRelativeOverTime(Request $request)
{
$range = $this->getEpiRange($request);
if (!$range) {
return response()->json(['error' => 'Missing epiweek range'], 400);
}
$data = $this->service->influenzaRelativeOverTime(
$range['startYear'],
$range['startWeek'],
$range['endYear'],
$range['endWeek']
);
return response()->json($data);
}
/* /*
|-------------------------------------------------------------------------- |--------------------------------------------------------------------------

173
dashboard/app/Services/DashboardService.php
View File

@@ -575,6 +575,33 @@ class DashboardService
*/ */
public function provinceCircles($startYear, $startWeek, $endYear, $endWeek) public function provinceCircles($startYear, $startWeek, $endYear, $endWeek)
{ {
return SurveillanceCase::join('case_lab_results', function ($join) {
$join->on('surveillance_cases.lab_code', '=', 'case_lab_results.lab_code')
->on('surveillance_cases.surveillance_id', '=', 'case_lab_results.surveillance_id');
})
->where(function ($q) use ($startYear, $startWeek, $endYear, $endWeek) {
$q->whereRaw(
"(surveillance_cases.year_data * 100 + surveillance_cases.week_data) BETWEEN ? AND ?",
[
$startYear * 100 + $startWeek,
$endYear * 100 + $endWeek
]
);
})
->whereRaw('case_lab_results.is_positive = 1 and surveillance_cases.surveillance_id not in(6) and case_lab_results.indicator="Influenza"')
->selectRaw("
surveillance_cases.patient_province,
case_lab_results.subtype as pathogen_name,
COUNT(DISTINCT surveillance_cases.lab_code) as total
")
->groupBy(
'surveillance_cases.patient_province',
'case_lab_results.subtype'
)
->get();
return SurveillanceCase::leftJoin( return SurveillanceCase::leftJoin(
'case_lab_results', 'case_lab_results',
'surveillance_cases.lab_code', 'surveillance_cases.lab_code',
@@ -590,28 +617,156 @@ class DashboardService
->whereRaw( ->whereRaw(
"(surveillance_cases.year_data < ? OR (surveillance_cases.year_data = ? AND surveillance_cases.week_data <= ?))", "(surveillance_cases.year_data < ? OR (surveillance_cases.year_data = ? AND surveillance_cases.week_data <= ?))",
[$endYear, $endYear, $endWeek] [$endYear, $endYear, $endWeek]
); )
->whereRaw('case_lab_results.is_positive = 1 and surveillance_cases.surveillance_id not in(6)');
}) })
->selectRaw(" ->selectRaw("
surveillance_cases.patient_province, surveillance_cases.patient_province,
surveillance_cases.surveillance_id, case_lab_results.pathogen_name,
COUNT(DISTINCT surveillance_cases.lab_code) as total, COUNT(DISTINCT surveillance_cases.lab_code) as total
COUNT(DISTINCT CASE
WHEN case_lab_results.is_positive = 1
THEN surveillance_cases.lab_code
END) as positive
") ")
->groupBy( ->groupBy(
'surveillance_cases.patient_province', 'surveillance_cases.patient_province',
'surveillance_cases.surveillance_id' 'case_lab_results.pathogen_name'
) )
->get(); ->get();
} }
/* Start Overview Section */
public function influenzaSubtypeDetected($startYear, $startWeek, $endYear, $endWeek)
{
return SurveillanceCase::join('case_lab_results', function ($join) {
$join->on('surveillance_cases.lab_code', '=', 'case_lab_results.lab_code')
->on('surveillance_cases.surveillance_id', '=', 'case_lab_results.surveillance_id');
})
->where(function ($q) use ($startYear, $startWeek, $endYear, $endWeek) {
$q->whereRaw(
"(surveillance_cases.year_data * 100 + surveillance_cases.week_data) BETWEEN ? AND ?",
[
$startYear * 100 + $startWeek,
$endYear * 100 + $endWeek
]
);
})
->whereRaw('case_lab_results.is_positive = 1 and surveillance_cases.surveillance_id not in(6) and case_lab_results.indicator="Influenza"')
->selectRaw("
case_lab_results.subtype,
COUNT(DISTINCT surveillance_cases.lab_code) as total
")
->groupBy(
'case_lab_results.subtype'
)
->get();
}
public function covidDistributedByAgeGroup($startYear, $startWeek, $endYear, $endWeek)
{
return SurveillanceCase::join('case_lab_results', function ($join) {
$join->on('surveillance_cases.lab_code', '=', 'case_lab_results.lab_code')
->on('surveillance_cases.surveillance_id', '=', 'case_lab_results.surveillance_id');
})
->where(function ($q) use ($startYear, $startWeek, $endYear, $endWeek) {
$q->whereRaw(
"(surveillance_cases.year_data * 100 + surveillance_cases.week_data) BETWEEN ? AND ?",
[
$startYear * 100 + $startWeek,
$endYear * 100 + $endWeek
]
);
})
->whereRaw('case_lab_results.is_positive = 1 and surveillance_cases.surveillance_id not in(6) and case_lab_results.indicator="Covid-19"')
->selectRaw("
CASE
WHEN patient_age_inday <= 28 THEN '0–28 days'
WHEN patient_age_inday <= 364 THEN '29 days–11 months'
WHEN patient_age_inday <= 1460 THEN '1–4 years'
WHEN patient_age_inday <= 5110 THEN '5–14 years'
WHEN patient_age_inday <= 8765 THEN '15–24 years'
WHEN patient_age_inday <= 18250 THEN '25–49 years'
WHEN patient_age_inday <= 23725 THEN '50–64 years'
ELSE '65+ years'
END as age_group,
CASE
WHEN patient_age_inday <= 28 THEN 1
WHEN patient_age_inday <= 364 THEN 2
WHEN patient_age_inday <= 1460 THEN 3
WHEN patient_age_inday <= 5110 THEN 4
WHEN patient_age_inday <= 8765 THEN 5
WHEN patient_age_inday <= 18250 THEN 6
WHEN patient_age_inday <= 23725 THEN 7
ELSE 8
END as age_order,
COUNT(*) as total
")
->groupBy('age_group', 'age_order')
->orderBy('age_order')
->get();
}
public function covidLineageRelativeOverTime($startYear, $startWeek, $endYear, $endWeek)
{
return SurveillanceCase::join('case_lab_results', function ($join) {
$join->on('surveillance_cases.lab_code', '=', 'case_lab_results.lab_code')
->on('surveillance_cases.surveillance_id', '=', 'case_lab_results.surveillance_id');
})
->where(function ($q) use ($startYear, $startWeek, $endYear, $endWeek) {
$q->whereRaw(
"(surveillance_cases.year_data * 100 + surveillance_cases.week_data) BETWEEN ? AND ?",
[
$startYear * 100 + $startWeek,
$endYear * 100 + $endWeek
]
);
})
->whereRaw('case_lab_results.is_positive = 1 and surveillance_cases.surveillance_id=6 and case_lab_results.indicator="Covid-19" and case_lab_results.pathogen_name not in("","unable to align","N/A","NA")')
->selectRaw("
case_lab_results.pathogen_name as lineage,
concat(surveillance_cases.year_data,'-',surveillance_cases.week_data) as week,
COUNT(DISTINCT surveillance_cases.lab_code) as total
")
->groupBy(
'case_lab_results.pathogen_name',
'week'
)
->get();
}
public function influenzaRelativeOverTime($startYear, $startWeek, $endYear, $endWeek)
{
return SurveillanceCase::join('case_lab_results', function ($join) {
$join->on('surveillance_cases.lab_code', '=', 'case_lab_results.lab_code')
->on('surveillance_cases.surveillance_id', '=', 'case_lab_results.surveillance_id');
})
->where(function ($q) use ($startYear, $startWeek, $endYear, $endWeek) {
$q->whereRaw(
"(surveillance_cases.year_data * 100 + surveillance_cases.week_data) BETWEEN ? AND ?",
[
$startYear * 100 + $startWeek,
$endYear * 100 + $endWeek
]
);
})
->whereRaw('case_lab_results.is_positive = 1 and surveillance_cases.surveillance_id not in(6) and case_lab_results.indicator="Influenza"')
->selectRaw("
case_lab_results.subtype as lineage,
concat(surveillance_cases.year_data,'-',surveillance_cases.week_data) as week,
COUNT(DISTINCT surveillance_cases.lab_code) as total
")
->groupBy(
'case_lab_results.subtype',
'week'
)
->get();
}
/* End Overview Section */
public function provinceProgram($surveillanceId, $startYear, $startWeek, $endYear, $endWeek) public function provinceProgram($surveillanceId, $startYear, $startWeek, $endYear, $endWeek)
{ {
return SurveillanceCase::selectRaw(" return SurveillanceCase::selectRaw("

364
dashboard/app/Services/DataRetrievalService.php
View File

@@ -20,7 +20,7 @@ class DataRetrievalService
$this->getILICases(now()->subDays(config('app.lookback_days.ILI'))->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->getLBMCases(now()->subDays(config('app.lookback_days.LBM'))->toDateString(), $toDate); // done
$this->getAFICases(now()->subDays(config('app.lookback_days.AFI'))->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->getNSDCases(now()->subDays(config('app.lookback_days.NDS'))->toDateString(), $toDate);
$this->getSEQCases(now()->subDays(config('app.lookback_days.SEQ'))->toDateString(), $toDate); // done $this->getSEQCases(now()->subDays(config('app.lookback_days.SEQ'))->toDateString(), $toDate); // done
Log::channel('jobs')->info($toDate->toDateString(). ' Service Reload Data Successfully Ran'); Log::channel('jobs')->info($toDate->toDateString(). ' Service Reload Data Successfully Ran');
return true; return true;
@@ -42,24 +42,35 @@ class DataRetrievalService
->select(" ->select("
SELECT SELECT
patient.labcode, patient.labcode,
patient.patdate, min(if(year(tps.collected)=0,patient.patdate, tps.collected)) as patdate,
patient.isnewcase, patient.isnewcase,
l.labname_en, l.labname_en,
l.labaddress_en, l.labaddress_en,
1 as surveillance_id, 1 as surveillance_id,
niphc0_nphl.get_epi_period(patient.patdate, 'Y') as year_data, min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'Y')) as year_data,
niphc0_nphl.get_epi_period(patient.patdate, 'W') as week_data, min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'W')) as week_data,
patient.patage, patient.patage,
patient.patsex, patient.patsex,
NULL as is_alive, NULL as is_alive,
p.proname_en p.proname_en
FROM niphc0_nphl.`labopatients` patient FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.sari_patients sr_p on sr_p.patid = patient.patid inner join niphc0_nphl.sari_patients sr_p on sr_p.patid = patient.patid
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid and tps.status = 1
inner join niphc0_nphl.laboratory l on l.labid = patient.patsource inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
left join niphc0_nphl.province p on p.proid = patient.frompro left join niphc0_nphl.province p on p.proid = patient.frompro
WHERE patient.patgroup =2 WHERE patient.patgroup =2
and patient.status = 1 and patient.status = 1
".$cond); ".$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); $this->insert_surveillance_cases($sari_cases);
@@ -71,7 +82,7 @@ class DataRetrievalService
if(trs.rtitle='Negatives', 0, 1) as is_positive, 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', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype, if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
'SARI Influenza Test' as indicator 'Influenza' as indicator
FROM `labopatients` patient FROM `labopatients` patient
inner join sari_patients sr_p on sr_p.patid = patient.patid 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_patsample tps on tps.patientid = patient.patid
@@ -93,7 +104,7 @@ class DataRetrievalService
if(trs.rtitle='Negative', 0, 1) as is_positive, if(trs.rtitle='Negative', 0, 1) as is_positive,
if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name, if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
'' as subtype, '' as subtype,
'SARI Covid Test' as indicator 'Covid-19' as indicator
FROM `labopatients` patient FROM `labopatients` patient
inner join sari_patients sr_p inner join sari_patients sr_p
on sr_p.patid = patient.patid on sr_p.patid = patient.patid
@@ -126,24 +137,33 @@ class DataRetrievalService
->select(" ->select("
SELECT SELECT
patient.labcode, patient.labcode,
patient.patdate, min(if(year(tps.collected)=0,patient.patdate, tps.collected)) as patdate,
patient.isnewcase, patient.isnewcase,
l.labname_en, l.labname_en,
l.labaddress_en, l.labaddress_en,
2 as surveillance_id, 2 as surveillance_id,
niphc0_nphl.get_epi_period(patient.patdate, 'Y') as year_data, min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'Y')) as year_data,
niphc0_nphl.get_epi_period(patient.patdate, 'W') as week_data, min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'W')) as week_data,
patient.patage, patient.patage,
patient.patsex, patient.patsex,
NULL as is_alive, NULL as is_alive,
p.proname_en p.proname_en
FROM niphc0_nphl.`labopatients` patient FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid 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 inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
left join niphc0_nphl.province p on p.proid = patient.frompro left join niphc0_nphl.province p on p.proid = patient.frompro
WHERE patient.patgroup =3 WHERE patient.patgroup =3
and patient.status = 1 and patient.status = 1
".$cond ".$cond . "
group by
patient.labcode,
patient.isnewcase,
l.labname_en,
l.labaddress_en,
patient.patage,
patient.patsex,
p.proname_en;"
); );
@@ -158,7 +178,7 @@ class DataRetrievalService
if(trs.rtitle='Negatives', 0, 1) as is_positive, 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', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype, if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
'ILI Influenza Test' as indicator 'Influenza' as indicator
FROM niphc0_nphl.`labopatients` patient FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid 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_patsample tps on tps.patientid = patient.patid
@@ -182,7 +202,7 @@ class DataRetrievalService
if(trs.rtitle='Negative', 0, 1) as is_positive, if(trs.rtitle='Negative', 0, 1) as is_positive,
if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name, if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
'' as subtype, '' as subtype,
'ILI Covid Test' as indicator 'Covid-19' as indicator
FROM niphc0_nphl.`labopatients` patient FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid 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_patsample tps on tps.patientid = patient.patid
@@ -211,24 +231,34 @@ class DataRetrievalService
->select(" ->select("
SELECT SELECT
patient.labcode, patient.labcode,
patient.patdate, min(if(year(tps.collected)=0,patient.patdate, tps.collected)) as patdate,
patient.isnewcase, patient.isnewcase,
l.labname_en, l.labname_en,
l.labaddress_en, l.labaddress_en,
3 as surveillance_id, 3 as surveillance_id,
niphc0_nphl.get_epi_period(patient.patdate, 'Y') year_data, min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'Y')) as year_data,
niphc0_nphl.get_epi_period(patient.patdate, 'W') week_data, min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,patient.patdate, tps.collected), 'W')) as week_data,
patient.patage, patient.patage,
patient.patsex, patient.patsex,
NULL as is_alive, NULL as is_alive,
p.proname_en p.proname_en
FROM niphc0_nphl.`labopatients` patient FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.lbms_patients on lbms_patients.patid = patient.patid 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 left join niphc0_nphl.province p on p.proid = patient.frompro
inner join niphc0_nphl.laboratory l on l.labid = patient.patsource inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
WHERE patient.patgroup = 17 WHERE patient.patgroup = 17
and patient.status = 1 and patient.status = 1
".$cond); ".$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); $this->insert_surveillance_cases($lbm_cases);
@@ -241,7 +271,7 @@ class DataRetrievalService
if(trs.rtitle='Negatives', 0, 1) as is_positive, 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', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype, if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
'LBM Influenza Test' as indicator 'Influenza' as indicator
FROM niphc0_nphl.`labopatients` patient FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.lbms_patients sr_p on sr_p.patid = patient.patid 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_patsample tps on tps.patientid = patient.patid
@@ -264,7 +294,7 @@ class DataRetrievalService
if(trs.rtitle='Negative', 0, 1) as is_positive, if(trs.rtitle='Negative', 0, 1) as is_positive,
if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name, if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
'' as subtype, '' as subtype,
'LBM Covid Test' as indicator 'Covid-19' as indicator
FROM niphc0_nphl.`labopatients` patient FROM niphc0_nphl.`labopatients` patient
inner join niphc0_nphl.lbms_patients sr_p on sr_p.patid = patient.patid 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_patsample tps on tps.patientid = patient.patid
@@ -287,19 +317,19 @@ class DataRetrievalService
public function getAFICases($dateFrom, $dateTo = NULL) public function getAFICases($dateFrom, $dateTo = NULL)
{ {
$cond = ""; $cond = "";
$cond .= " and afi_lab_result.results_date >= '".date('Y-m-d', strtotime($dateFrom))."' "; $cond .= " and afi_case.date_of_interview >= '".date('Y-m-d', strtotime($dateFrom))."' ";
$cond .= (!empty($dateTo)) ? " and afi_lab_result.results_date <='".date('Y-m-d', strtotime($dateTo))."' ":""; $cond .= (!empty($dateTo)) ? " and afi_case.date_of_interview <='".date('Y-m-d', strtotime($dateTo))."' ":"";
$afi_cases = DB::connection('mysql_afi') $afi_cases = DB::connection('mysql_afi')
->select(" ->select("
SELECT SELECT
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
afi_lab_result.results_date as patdate, afi_case.date_of_interview as patdate,
1 as isnewcase, 1 as isnewcase,
afi_case.sentinel_site as labname_en, afi_case.sentinel_site as labname_en,
'' as labaddress_en, '' as labaddress_en,
4 as surveillance_id, 4 as surveillance_id,
niphc0_nphl.get_epi_period(afi_lab_result.results_date, 'Y') as year_data, niphc0_nphl.get_epi_period(afi_case.date_of_interview, 'Y') as year_data,
niphc0_nphl.get_epi_period(afi_lab_result.results_date, 'W') as week_data, niphc0_nphl.get_epi_period(afi_case.date_of_interview, 'W') as week_data,
ifnull(DATEDIFF(afi_case.date_of_interview, date_of_birth),180) as patage, ifnull(DATEDIFF(afi_case.date_of_interview, date_of_birth),180) as patage,
if(afi_case.sex='Male','M','F') as patsex, if(afi_case.sex='Male','M','F') as patsex,
NULL as is_alive, NULL as is_alive,
@@ -309,7 +339,8 @@ class DataRetrievalService
left join niphc0_nphl.province p on p.proid = afi_case.residence_province left join niphc0_nphl.province p on p.proid = afi_case.residence_province
where where
afi_case.afi_event is NOT null afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null " .$cond); 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); $this->insert_surveillance_cases($afi_cases);
@@ -321,13 +352,14 @@ class DataRetrievalService
if(afi_lab_result.influenza_result='Positive',1,0) as is_positive, 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, '$[0].id'))),1)),'') pathogen_name, if(afi_lab_result.influenza_result='Positive', concat('Influenza ',LEFT(UPPER(JSON_UNQUOTE(JSON_EXTRACT(afi_lab_result.influenza_subtypes, '$[0].id'))),1)),'') pathogen_name,
if(afi_lab_result.influenza_result='Positive', REPLACE(UPPER(JSON_UNQUOTE(JSON_EXTRACT(afi_lab_result.influenza_subtypes, '$[0].id'))),'_','/'),'') as subtype, if(afi_lab_result.influenza_result='Positive', REPLACE(UPPER(JSON_UNQUOTE(JSON_EXTRACT(afi_lab_result.influenza_subtypes, '$[0].id'))),'_','/'),'') as subtype,
'AFI Influenza Test' as indicator 'Influenza' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.influenza_result in('Negative', 'Positive') and afi_lab_result.influenza_result in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
union union
@@ -337,13 +369,15 @@ class DataRetrievalService
if(afi_lab_result.sarscov2_result='Positive',1,0) as is_positive, if(afi_lab_result.sarscov2_result='Positive',1,0) as is_positive,
if(afi_lab_result.sarscov2_result='Positive', 'SARS-CoV-2','') pathogen_name, if(afi_lab_result.sarscov2_result='Positive', 'SARS-CoV-2','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Covid Test' as indicator 'Covid-19' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.sarscov2_result in('Negative', 'Positive') and afi_lab_result.sarscov2_result in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null
".$cond."
union union
@@ -351,15 +385,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.dengue_pcr='Positive',1,0) as is_positive, if(afi_lab_result.dengue_pcr='Positive',1,0) as is_positive,
if(afi_lab_result.dengue_pcr='Positive', 'Dengue','') pathogen_name, if(afi_lab_result.dengue_pcr='Positive', 'Dengue Virus','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Dengue PCR Test' as indicator 'Dengue Virus|PCR' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.dengue_pcr in('Negative', 'Positive') and afi_lab_result.dengue_pcr in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
union union
@@ -367,15 +402,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.chikungunya_pcr='Positive',1,0) as is_positive, if(afi_lab_result.chikungunya_pcr='Positive',1,0) as is_positive,
if(afi_lab_result.chikungunya_pcr='Positive', 'Chikungunya','') pathogen_name, if(afi_lab_result.chikungunya_pcr='Positive', 'Chikungunya Virus','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Chikungunya PCR Test' as indicator 'Chikungunya Virus|PCR' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.chikungunya_pcr in('Negative', 'Positive') and afi_lab_result.chikungunya_pcr in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
union union
@@ -383,15 +419,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.leptospira_pcr='Positive',1,0) as is_positive, if(afi_lab_result.leptospira_pcr='Positive',1,0) as is_positive,
if(afi_lab_result.leptospira_pcr='Positive', 'Leptospira','') pathogen_name, if(afi_lab_result.leptospira_pcr='Positive', 'Leptospira spp.','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Leptospira PCR Test' as indicator 'Leptospira spp.|PCR' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.leptospira_pcr in('Negative', 'Positive') and afi_lab_result.leptospira_pcr in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
union union
@@ -399,15 +436,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.plasmodium_pcr='Positive',1,0) as is_positive, if(afi_lab_result.plasmodium_pcr='Positive',1,0) as is_positive,
if(afi_lab_result.plasmodium_pcr='Positive', 'Plasmodium','') pathogen_name, if(afi_lab_result.plasmodium_pcr='Positive', 'Plasmodium spp.','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Plasmodium PCR Test' as indicator 'Plasmodium spp.|PCR' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.plasmodium_pcr in('Negative', 'Positive') and afi_lab_result.plasmodium_pcr in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
UNION UNION
@@ -415,15 +453,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.rickettsia_pcr='Positive',1,0) as is_positive, if(afi_lab_result.rickettsia_pcr='Positive',1,0) as is_positive,
if(afi_lab_result.rickettsia_pcr='Positive', 'Rickettsia','') pathogen_name, if(afi_lab_result.rickettsia_pcr='Positive', 'Rickettsia spp.','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Rickettsia PCR Test' as indicator 'Rickettsia spp.|PCR' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.rickettsia_pcr in('Negative', 'Positive') and afi_lab_result.rickettsia_pcr in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
UNION UNION
@@ -431,15 +470,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.salmonella_pcr='Positive',1,0) as is_positive, if(afi_lab_result.salmonella_pcr='Positive',1,0) as is_positive,
if(afi_lab_result.salmonella_pcr='Positive', 'Salmonella','') pathogen_name, if(afi_lab_result.salmonella_pcr='Positive', 'Salmonella spp.','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Salmonella PCR Test' as indicator 'Salmonella spp.|PCR' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.salmonella_pcr in('Negative', 'Positive') and afi_lab_result.salmonella_pcr in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
UNION UNION
@@ -447,15 +487,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.westnile_pcr='Positive',1,0) as is_positive, if(afi_lab_result.westnile_pcr='Positive',1,0) as is_positive,
if(afi_lab_result.westnile_pcr='Positive', 'Westnile Nile','') pathogen_name, if(afi_lab_result.westnile_pcr='Positive', 'West Nile Virus','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Westnile PCR Test' as indicator 'West Nile Virus|PCR' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.westnile_pcr in('Negative', 'Positive') and afi_lab_result.westnile_pcr in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
UNION UNION
@@ -463,15 +504,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.zika_pcr='Positive',1,0) as is_positive, if(afi_lab_result.zika_pcr='Positive',1,0) as is_positive,
if(afi_lab_result.zika_pcr='Positive', 'ZIKA','') pathogen_name, if(afi_lab_result.zika_pcr='Positive', 'ZIKA Virus','') pathogen_name,
'' as subtype, '' as subtype,
'AFI ZIKA PCR Test' as indicator 'ZIKA Virus|PCR' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.zika_pcr in('Negative', 'Positive') and afi_lab_result.zika_pcr in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
UNION UNION
@@ -481,15 +523,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.chikungunya_serum='Positive',1,0) as is_positive, if(afi_lab_result.chikungunya_serum='Positive',1,0) as is_positive,
if(afi_lab_result.chikungunya_serum='Positive', 'Chikungunya','') pathogen_name, if(afi_lab_result.chikungunya_serum='Positive', 'Chikungunya Virus','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Chikungunya Serum Test' as indicator 'Chikungunya Virus|Serum' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.chikungunya_serum in('Negative', 'Positive') and afi_lab_result.chikungunya_serum in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
UNION UNION
@@ -497,15 +540,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.dengue_serum='Positive',1,0) as is_positive, if(afi_lab_result.dengue_serum='Positive',1,0) as is_positive,
if(afi_lab_result.dengue_serum='Positive', 'Dengue','') pathogen_name, if(afi_lab_result.dengue_serum='Positive', 'Dengue Virus','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Dengue Serum Test' as indicator 'Dengue Virus|Serum' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.dengue_serum in('Negative', 'Positive') and afi_lab_result.dengue_serum in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
UNION UNION
@@ -513,15 +557,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.westnile_serum='Positive',1,0) as is_positive, if(afi_lab_result.westnile_serum='Positive',1,0) as is_positive,
if(afi_lab_result.westnile_serum='Positive', 'Westnile','') pathogen_name, if(afi_lab_result.westnile_serum='Positive', 'West Nile Virus','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Westnile Serum Test' as indicator 'West Nile Virus|Serum' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.westnile_serum in('Negative', 'Positive') and afi_lab_result.westnile_serum in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
UNION UNION
@@ -529,15 +574,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.zika_serum='Positive',1,0) as is_positive, if(afi_lab_result.zika_serum='Positive',1,0) as is_positive,
if(afi_lab_result.zika_serum='Positive', 'ZIKA','') pathogen_name, if(afi_lab_result.zika_serum='Positive', 'ZIKA Virus','') pathogen_name,
'' as subtype, '' as subtype,
'AFI ZIKA Serum Test' as indicator 'ZIKA Virus|Serum' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.zika_serum in('Negative', 'Positive') and afi_lab_result.zika_serum in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond." and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond."
UNION UNION
@@ -545,15 +591,16 @@ class DataRetrievalService
afi_lab_result.sample_code as labcode, afi_lab_result.sample_code as labcode,
4 as surveillance_id, 4 as surveillance_id,
if(afi_lab_result.je_virus='Positive',1,0) as is_positive, if(afi_lab_result.je_virus='Positive',1,0) as is_positive,
if(afi_lab_result.je_virus='Positive', 'Japanese Encephalitis','') pathogen_name, if(afi_lab_result.je_virus='Positive', 'Japanese Encephalitis Virus','') pathogen_name,
'' as subtype, '' as subtype,
'AFI Japanese Encephalitis Test' as indicator 'Japanese Encephalitis Virus|Serum' as indicator
FROM afi_db.`afi_tbl_afiform` as afi_case 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 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 where afi_lab_result.sample_code is not null
and afi_lab_result.je_virus in('Negative', 'Positive') and afi_lab_result.je_virus in('Negative', 'Positive')
and afi_case.afi_event is NOT null and afi_case.afi_event is NOT null
and afi_lab_result.results_date is not null ".$cond and afi_case.date_of_interview is not null
and afi_lab_result.sample_code is not null ".$cond
); );
$this->insert_surveillance_case_lab_results($afi_lab_results); $this->insert_surveillance_case_lab_results($afi_lab_results);
@@ -561,62 +608,179 @@ class DataRetrievalService
public function getNSDCases($dateFrom, $dateTo = NULL) public function getNSDCases($dateFrom, $dateTo = NULL)
{ {
return []; $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, $dateTo = NULL) public function getSEQCases($dateFrom, $dateTo = NULL)
{ {
$cond = ""; $cond = "";
$cond .= " and patient.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' "; $cond .= " and c.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
$cond .= (!empty($dateTo)) ? " and patient.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":""; $cond .= (!empty($dateTo)) ? " and c.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
$seq_cases = DB::connection('mysql_nphl') $seq_cases = DB::connection('mysql_nphl')
->select(" ->select("
SELECT DISTINCT SELECT DISTINCT
patient.labcode, c.labcode,
patient.patdate, min(if(year(tps.collected)=0,c.patdate, tps.collected)) as patdate,
patient.isnewcase, c.isnewcase,
l.labname_en, l.labname_en,
l.labaddress_en, l.labaddress_en,
6 as surveillance_id, 6 as surveillance_id,
niphc0_nphl.get_epi_period(patient.patdate, 'Y') as year_data, min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,c.patdate, tps.collected), 'Y')) as year_data,
niphc0_nphl.get_epi_period(patient.patdate, 'W') as week_data, min(niphc0_nphl.get_epi_period(if(year(tps.collected)=0,c.patdate, tps.collected), 'W')) as week_data,
patient.patage, c.patage,
patient.patsex, c.patsex,
NULL as is_alive, NULL as is_alive,
pro.proname_en pro.proname_en
from niphc0_nphl.sq_batch sqb 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.sq_sub_batch sqsb on sqsb.bt_id = sqb.bt_id
inner join niphc0_nphl.labopatients patient on patient.patid = sqsb.patid inner join niphc0_nphl.labopatients c on c.patid = sqsb.patid
inner join niphc0_nphl.laboratory l on l.labid = patient.patsource inner join niphc0_nphl.laboratory l on l.labid = p.patsource
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid 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 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 = patient.frompro left join niphc0_nphl.province pro on pro.proid = c.frompro
where patient.status = 1 where c.status = 1
and tpst.labtestid IN ( 659, 662, 666, 667, 668 ) and tpst.labtestid IN ( 659, 662, 666, 667, 668 )
" . $cond); " . $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); $this->insert_surveillance_cases($seq_cases);
$seq_lab_results = DB::connection('mysql_nphl') $seq_lab_results = DB::connection('mysql_nphl')
->select(" ->select("
SELECT DISTINCT SELECT
patient.labcode, labcode,
6 as surveillance_id, 6 as surveillance_id,
1 is_positive, 1 is_positive,
ifnull(sqsb.seqlineage,'N/A') as pathogen_name, ifnull(seqlineage,'N/A') as pathogen_name,
trs.rtitle as subtype, GROUP_CONCAT(seq_result SEPARATOR '') as subtype,
concat('Sequencing Test ', case when patgroup=2 then 'SARI' when patgroup=3 then 'ILI' when patgroup=19 then 'COVID-19' else '' end) as indicator (case
from niphc0_nphl.sq_batch sqb when (Group_concat(influ_result SEPARATOR '')='Negatives' or Group_concat(influ_result SEPARATOR '')='') and Group_concat(covid_result SEPARATOR '')='Positive' then 'Covid-19'
inner join niphc0_nphl.sq_sub_batch sqsb on sqsb.bt_id = sqb.bt_id when (Group_concat(influ_result SEPARATOR '') !='Negatives' and Group_concat(influ_result SEPARATOR '')!='') and Group_concat(covid_result SEPARATOR '')='Negative' then 'Influenza'
inner join niphc0_nphl.labopatients patient on patient.patid = sqsb.patid when (Group_concat(influ_result SEPARATOR '') !='Negatives' and Group_concat(influ_result SEPARATOR '')!='') and Group_concat(covid_result SEPARATOR '')='Positive' then 'Co-infection'
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid else 'N/A'
inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid end) as indicator
inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid FROM (SELECT
inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid c.labcode,
where patient.status = 1 ( CASE
and tpst.labtestid IN ( 659, 662, 666, 667, 668 ) WHEN e1.labtestid IN ( 238, 340, 381 ) THEN e3.rtitle
and trs.rtitle not in ('Inconclusive', 'In Progress') ELSE ''
" . $cond); 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); $this->insert_surveillance_case_lab_results($seq_lab_results);

12
dashboard/config/app.php
View File

@@ -16,12 +16,12 @@ return [
'name' => env('APP_NAME', 'Laravel'), 'name' => env('APP_NAME', 'Laravel'),
'lookback_days' => [ 'lookback_days' => [
'SARI' => 777, // 'SARI' => 7, //
'ILI' => 777, 'ILI' => 7,
'LBM' => 777, 'LBM' => 7,
'AFI' => 777, 'AFI' => 7,
'NDS' => 777, 'NDS' => 7,
'SEQ' => 200 'SEQ' => 7
], ],
/* /*

635
dashboard/public/js/overview.js
View File

@@ -1,4 +1,8 @@
let trendChart; let trendChart;
let influenzaSubtypeChart;
let covidDistributedByAgeChart;
let covidLineageFrequencyChart;
let influenzaSubtypeFrequencyChart;
let map; let map;
/* /*
@@ -30,7 +34,7 @@ function loadSummary() {
<div class="d-flex justify-content-between"> <div class="d-flex justify-content-between">
<div> <div>
<h6 class="fw-bold">${item.code}</h6> <h6 class="fw-bold">${item.code} Cases</h6>
<h3 class="mb-1">${item.current_total}</h3> <h3 class="mb-1">${item.current_total}</h3>
<small class="text-muted">Last 7 days</small> <small class="text-muted">Last 7 days</small>
</div> </div>
@@ -102,12 +106,15 @@ function loadTrend(periodType, startYear, startWeek, endYear, endWeek) {
const colors = { const colors = {
SARI: '#2563eb', SARI: '#2563eb',
ILI: '#10b981', ILI: '#10b981',
LBM: '#9333ea' LBM: '#9333ea',
AFI: '#fc5741',
NDS: '#d59d01',
SEQ: '#9ca3af'
}; };
const datasets = []; const datasets = [];
const allowedPrograms = ['SARI', 'ILI', 'LBM']; const allowedPrograms = ['SARI', 'ILI', 'LBM', 'AFI', 'NDS', 'SEQ'];
Object.keys(data).forEach(code => { Object.keys(data).forEach(code => {
@@ -145,7 +152,10 @@ function loadTrend(periodType, startYear, startWeek, endYear, endWeek) {
options: { options: {
responsive: true, responsive: true,
plugins: { plugins: {
legend: { position: 'bottom' } legend: { position: 'bottom' },
datalabels: {
display: false
}
}, },
interaction: { interaction: {
mode: 'index', mode: 'index',
@@ -154,15 +164,499 @@ function loadTrend(periodType, startYear, startWeek, endYear, endWeek) {
scales: { scales: {
y: { y: {
beginAtZero: true, beginAtZero: true,
ticks: { stepSize: 1 } ticks: {
stepSize: 1
}, },
x: { grid: { display: false } } title: {
display: true,
text: 'Number of Cases'
},
},
x: {
grid: {
display: false
},
title: {
display: true,
text: 'Surveillance'
},
}
} }
} }
}); });
}); });
} }
function loadInfluenzaSubtypeDistribution(periodType, startYear, startWeek, endYear, endWeek) {
fetch(`/api/dashboard/influenza-subtype-distribution?period_type=${periodType}&start_year=${startYear}&start_week=${startWeek}&end_year=${endYear}&end_week=${endWeek}`)
.then(res => res.json())
.then(data => {
let displayLabels = data.map(item => item.subtype);
let dataset = data.map(item => item.total);
const colors = [
'rgba(177,111,243,0.94)'
];
if (influenzaSubtypeChart) influenzaSubtypeChart.destroy();
influenzaSubtypeChart = new Chart(document.getElementById('influenzaSubtypeDistribution'), {
type: 'bar', // you can change to 'pie', 'doughnut', etc.
data: {
labels: displayLabels,
datasets: [{
data: dataset,
backgroundColor: colors,
}]
},
options: {
indexAxis: 'y',
responsive: true,
plugins: {
legend: {
display: false,
position:'right'
},
datalabels: {
color: '#ffffff',
backgroundColor: 'rgba(68,76,68,0.31)',
borderRadius: 6,
z: 1000,
padding: {
top: 6,
bottom: 6,
left: 10,
right: 10
},
font: {
weight: 'bold',
size: 12
},
formatter: (value) => value,
anchor: 'end',
align: 'end',
offset: 10,
clamp: false
}
},
scales: {
x: {
stacked: true,
beginAtZero: true,
title: {
display: true,
text: 'Number of Positive Influenza Subtypes'
}
},
y: {
stacked: true,
beginAtZero: true,
title: {
display: true,
text: 'Influenza Subtypes'
},
grid:{
display: false
}
}
}
},
plugins: [ChartDataLabels]
});
});
}
function loadCovidDistributedByAgeGroup(periodType, startYear, startWeek, endYear, endWeek) {
fetch(`/api/dashboard/covid-distributed-by-age-group?period_type=${periodType}&start_year=${startYear}&start_week=${startWeek}&end_year=${endYear}&end_week=${endWeek}`)
.then(res => res.json())
.then(data => {
let displayLabels = data.map(item => item.age_group);
let dataset = data.map(item => item.total);
const colors = [
'#84cc16'
];
if (covidDistributedByAgeChart) covidDistributedByAgeChart.destroy();
covidDistributedByAgeChart = new Chart(document.getElementById('covidDistributedByAgeGroup'), {
type: 'bar', // you can change to 'pie', 'doughnut', etc.
data: {
labels: displayLabels,
datasets: [{
label: 'Total Covid-19 Detected',
data: dataset,
backgroundColor: colors,
}]
},
options: {
responsive: true,
plugins: {
legend: {
display: false,
position:'bottom'
},
datalabels: {
color: '#fff',
backgroundColor: 'rgba(68,76,68,0.7)',
borderRadius: 6,
z: 1000,
padding: {
top: 6,
bottom: 6,
left: 10,
right: 10
},
font: {
weight: 'bold',
size: 12
},
formatter: (value) => value,
anchor: 'end',
align: 'end',
offset: 10,
clamp: false
}
},
scales: {
x: {
stacked: true,
beginAtZero: true,
title: {
display: true,
text: 'Patient Age Group'
},
grid:{
display: false
}
},
y: {
stacked: true,
beginAtZero: true,
title: {
display: true,
text: 'Number of Positive SARS-CoV-2'
}
}
}
}
});
});
}
function loadCovidLineageFrequency(periodType, startYear, startWeek, endYear, endWeek) {
fetch(`/api/dashboard/covid-lineage-frequency?period_type=${periodType}&start_year=${startYear}&start_week=${startWeek}&end_year=${endYear}&end_week=${endWeek}`)
.then(res => res.json())
.then(data => {
// Extract unique weeks (X-axis)
const weeks = [...new Set(data.map(item => item.week))].sort();
// Extract unique lineages
const lineages = [...new Set(data.map(item => item.lineage))];
// Color palette
const colors = [
'#84cc16','#22c55e','#06b6d4','#3b82f6',
'#6366f1','#a855f7','#ec4899','#ef4444',
'#f97316','#eab308'
];
// Build datasets
const datasets = lineages.map((lineage, index) => {
const lineageData = weeks.map(week => {
const found = data.find(
item => item.week === week && item.lineage === lineage
);
return found ? found.total : 0;
});
return {
label: lineage,
data: lineageData,
fill: true, // area fill
tension: 0.4, // smooth curve
borderColor: 'transparent', // hide the line
borderWidth: 0,
pointRadius: 0, // hide points
backgroundColor: hexToRGBA(colors[index % colors.length], 0.3),
stack: 'total'
};
});
// Destroy previous chart if exists
if (covidLineageFrequencyChart) covidLineageFrequencyChart.destroy();
const ctx = document.getElementById('covidLineageFrequency').getContext('2d');
covidLineageFrequencyChart = new Chart(ctx, {
type: 'line',
data: {
labels: weeks,
datasets: datasets
},
options: {
responsive: true,
maintainAspectRatio: false,
interaction: {
mode: 'index',
intersect: false
},
plugins: {
legend: {
display: false // hide default legend
},
tooltip: {
mode: 'index',
intersect: false
},
datalabels: {
display: false // hide labels
}
},
scales: {
x: {
stacked: true,
title: {
display: true,
text: 'Week'
},
grid:{
display: false
}
},
y: {
stacked: true,
beginAtZero: true,
title: {
display: true,
text: 'Relative Frequency'
},
}
}
}
});
// -------------------------
// Custom right-side scrollable legend
// -------------------------
const legendContainer = document.getElementById('legendContainer');
legendContainer.innerHTML = ''; // clear old legend
datasets.forEach((dataset, index) => {
const item = document.createElement('div');
item.style.display = 'flex';
item.style.alignItems = 'center';
item.style.marginBottom = '4px';
item.style.fontSize = '11px';
item.style.cursor = 'pointer';
item.innerHTML = `
<span style="width:15px;height:15px;background:${dataset.backgroundColor};display:inline-block;margin-right:8px;"></span>
${dataset.label}
`;
item.addEventListener('click', () => {
const meta = covidLineageFrequencyChart.getDatasetMeta(index);
// If the clicked dataset is already the only visible one, show all
const allHidden = datasets.every((d, i) => covidLineageFrequencyChart.getDatasetMeta(i).hidden || i === index);
if (!allHidden) {
// Hide all datasets
datasets.forEach((d, i) => {
covidLineageFrequencyChart.getDatasetMeta(i).hidden = true;
});
// Show only clicked
meta.hidden = false;
} else {
// Show all datasets
datasets.forEach((d, i) => {
covidLineageFrequencyChart.getDatasetMeta(i).hidden = false;
});
}
covidLineageFrequencyChart.update();
// Update legend opacity
Array.from(legendContainer.children).forEach((child, i) => {
const metaItem = covidLineageFrequencyChart.getDatasetMeta(i);
child.style.opacity = metaItem.hidden ? 0.5 : 1;
});
});
legendContainer.appendChild(item);
});
// Scrollable CSS (in case legend is long)
legendContainer.style.maxHeight = '375px';
legendContainer.style.overflowY = 'auto';
legendContainer.style.padding = '8px';
legendContainer.style.borderRadius = '0px';
});
}
function loadInfluenzaSubtypeFrequency(periodType, startYear, startWeek, endYear, endWeek) {
fetch(`/api/dashboard/influenza-relative-frequency?period_type=${periodType}&start_year=${startYear}&start_week=${startWeek}&end_year=${endYear}&end_week=${endWeek}`)
.then(res => res.json())
.then(data => {
// Extract unique weeks (X-axis)
const weeks = [...new Set(data.map(item => item.week))].sort();
const colors = [
'#84cc16','#22c55e','#06b6d4','#3b82f6',
'#6366f1','#a855f7','#ec4899','#ef4444',
'#f97316','#eab308'
];
// Extract unique lineages
const lineages = [...new Set(data.map(item => item.lineage))];
// Build datasets
const datasets = lineages.map((lineage, index) => {
const lineageData = weeks.map(week => {
const found = data.find(
item => item.week === week && item.lineage === lineage
);
return found ? found.total : 0;
});
return {
label: lineage,
data: lineageData,
fill: true, // area fill
tension: 0.4, // smooth curve
borderColor: 'transparent', // hide the line
borderWidth: 0,
pointRadius: 0, // hide points
backgroundColor: hexToRGBA(colors[index % colors.length], 0.3),
stack: 'total'
};
});
// Destroy previous chart if exists
if (influenzaSubtypeFrequencyChart) influenzaSubtypeFrequencyChart.destroy();
const ctx = document.getElementById('influenzaSubtypeFrequency').getContext('2d');
influenzaSubtypeFrequencyChart = new Chart(ctx, {
type: 'line',
data: {
labels: weeks,
datasets: datasets
},
options: {
responsive: true,
maintainAspectRatio: false,
interaction: {
mode: 'index',
intersect: false
},
plugins: {
legend: {
display: false // hide default legend
},
tooltip: {
mode: 'index',
intersect: false
},
datalabels: {
display: false // hide labels
}
},
scales: {
x: {
stacked: true,
title: {
display: true,
text: 'Week'
},
grid:{
display: false
}
},
y: {
stacked: true,
beginAtZero: true,
title: {
display: true,
text: 'Relative Frequency'
},
}
}
}
});
const legendContainer = document.getElementById('legendContainerInfluenzaSubtypeFrequency');
legendContainer.innerHTML = ''; // clear old legend
datasets.forEach((dataset, index) => {
const item = document.createElement('div');
item.style.display = 'flex';
item.style.alignItems = 'center';
item.style.marginBottom = '4px';
item.style.fontSize = '11px';
item.style.cursor = 'pointer';
item.innerHTML = `
<span style="width:15px;height:15px;background:${dataset.backgroundColor};display:inline-block;margin-right:8px;"></span>
${dataset.label}
`;
item.addEventListener('click', () => {
const meta = influenzaSubtypeFrequencyChart.getDatasetMeta(index);
// If the clicked dataset is already the only visible one, show all
const allHidden = datasets.every((d, i) => influenzaSubtypeFrequencyChart.getDatasetMeta(i).hidden || i === index);
if (!allHidden) {
// Hide all datasets
datasets.forEach((d, i) => {
influenzaSubtypeFrequencyChart.getDatasetMeta(i).hidden = true;
});
// Show only clicked
meta.hidden = false;
} else {
// Show all datasets
datasets.forEach((d, i) => {
influenzaSubtypeFrequencyChart.getDatasetMeta(i).hidden = false;
});
}
influenzaSubtypeFrequencyChart.update();
// Update legend opacity
Array.from(legendContainer.children).forEach((child, i) => {
const metaItem = influenzaSubtypeFrequencyChart.getDatasetMeta(i);
child.style.opacity = metaItem.hidden ? 0.5 : 1;
});
});
legendContainer.appendChild(item);
});
// Scrollable CSS (in case legend is long)
legendContainer.style.maxHeight = '375px';
legendContainer.style.overflowY = 'auto';
legendContainer.style.padding = '8px';
legendContainer.style.borderRadius = '0px';
});
}
// -------------------------
// Helper to convert hex to rgba
// -------------------------
function hexToRGBA(hex, alpha) {
const r = parseInt(hex.slice(1, 3), 16);
const g = parseInt(hex.slice(3, 5), 16);
const b = parseInt(hex.slice(5, 7), 16);
return `rgba(${r}, ${g}, ${b}, ${alpha})`;
}
function updateAlerts() { function updateAlerts() {
if (!window._summaryData || !window._provinceData) return; if (!window._summaryData || !window._provinceData) return;
@@ -380,10 +874,14 @@ function renderAlerts(alerts) {
|-------------------------------------------------------------------------- |--------------------------------------------------------------------------
*/ */
function getPositivityColor(p) { function getPositivityColor(p) {
if (p > 20) return "#b91c1c"; if (p == 'A/H1N1pdm') return "#2563eb";
if (p > 10) return "#ef4444"; if (p == 'A/H3N2') return "#11de9d";
if (p > 5) return "#f59e0b"; if (p == 'B/Yam') return "#9333ea";
if (p > 0) return "#84cc16"; if (p == 'B/Vic') return "#1021b9";
if (p == 'A/H9N2') return "#b91081";
if (p == 'A/H5N1') return "#ad850d";
if (p == 'A/Unsubtypable') return "#047393";
if (p == 'B/Unsubtypable') return "#890512";
return "#9ca3af"; return "#9ca3af";
} }
function normalizeProvince(name, validSet) { function normalizeProvince(name, validSet) {
@@ -432,13 +930,15 @@ function addPositivityLegend() {
div.innerHTML = ` div.innerHTML = `
<div style="background:white;padding:10px 12px;border-radius:6px; <div style="background:white;padding:10px 12px;border-radius:6px;
box-shadow:0 2px 6px rgba(0,0,0,0.2);font-size:12px;"> box-shadow:0 2px 6px rgba(0,0,0,0.2);font-size:12px;">
<div style="font-weight:600;margin-bottom:6px;">Positivity</div> <div style="font-weight:600;margin-bottom:6px;">Influenza Subtypes</div>
<div><span style="background: #2563eb; border: 2px solid #aa9d9d; width:12px;height:12px;display:inline-block;margin-right:6px; border-radius: 50%;"></span>A/H1N1pdm</div>
<div><span style="border:3px solid #b91c1c;width:12px;height:12px;display:inline-block;margin-right:6px;"></span>> 20%</div> <div><span style="background: #11de9d; border: 2px solid #aa9d9d; width:12px;height:12px;display:inline-block;margin-right:6px; border-radius: 50%;"></span>A/H3N2</div>
<div><span style="border:3px solid #ef4444;width:12px;height:12px;display:inline-block;margin-right:6px;"></span>10–20%</div> <div><span style="background: #b91081; border: 2px solid #aa9d9d; width:12px;height:12px;display:inline-block;margin-right:6px; border-radius: 50%;"></span>A/H9N2</div>
<div><span style="border:3px solid #f59e0b;width:12px;height:12px;display:inline-block;margin-right:6px;"></span>5–10%</div> <div><span style="background: #ad850d; border: 2px solid #aa9d9d; width:12px;height:12px;display:inline-block;margin-right:6px; border-radius: 50%;"></span>A/H5N1</div>
<div><span style="border:3px solid #84cc16;width:12px;height:12px;display:inline-block;margin-right:6px;"></span>0–5%</div> <div><span style="background: #047393; border: 2px solid #aa9d9d; width:12px;height:12px;display:inline-block;margin-right:6px; border-radius: 50%;"></span>A/Unsubtypable</div>
<div><span style="border:3px solid #9ca3af;width:12px;height:12px;display:inline-block;margin-right:6px;"></span>0%</div> <div><span style="background: #9333ea; border: 2px solid #aa9d9d; width:12px;height:12px;display:inline-block;margin-right:6px; border-radius: 50%;"></span>B/Yam</div>
<div><span style="background: #1021b9; border: 2px solid #aa9d9d; width:12px;height:12px;display:inline-block;margin-right:6px; border-radius: 50%;"></span>B/Vic</div>
<div><span style="background: #890512; border: 2px solid #aa9d9d; width:12px;height:12px;display:inline-block;margin-right:6px; border-radius: 50%;"></span>B/Unsubtypable</div>
</div> </div>
`; `;
@@ -490,52 +990,42 @@ function loadProvinceMap(startYear, startWeek, endYear, endWeek) {
const center = layer.getBounds().getCenter(); const center = layer.getBounds().getCenter();
const rows = data.filter(d => { const rows = data.filter(d => {
if (![1, 2, 3].includes(d.surveillance_id)) return false;
const name = normalizeProvince(d.patient_province, validProvinces); const name = normalizeProvince(d.patient_province, validProvinces);
return name === province; return name === province;
}); });
const offsets = { 1: -0.15, 2: 0, 3: 0.15 }; if (!rows.length) return;
const colors = { // 👉 group by pathogen_name
1: '#2563eb', const pathogens = [...new Set(rows.map(r => r.pathogen_name))];
2: '#10b981',
3: '#9333ea' const spacing = 1; //0.12; // adjust spacing between circles
};
rows.forEach(row => { rows.forEach(row => {
const percent = row.total // 👉 dynamic offset based on pathogen index
? ((row.positive / row.total) * 100).toFixed(1) const index = pathogens.indexOf(row.pathogen_name);
: 0; const offset = (index - (pathogens.length - 1) / 2) * spacing;
const offset = offsets[row.surveillance_id] ?? 0;
const lat = center.lat; const lat = center.lat;
const lng = center.lng + offset; const lng = center.lng + offset;
const programName =
row.surveillance_id === 1 ? 'SARI' :
row.surveillance_id === 2 ? 'ILI' : 'LBM';
L.circleMarker([lat, lng], { L.circleMarker([lat, lng], {
radius: getRadius(row.total), radius: getRadius(row.total),
fillColor: colors[row.surveillance_id], fillColor: getColorByPathogen(row.pathogen_name), // 👈 new function
color: getPositivityColor(percent), color: getPositivityColor(row.pathogen_nam),
weight: 2, weight: 2,
fillOpacity: 0.9 fillOpacity: 0.9
}) })
.bindTooltip(` .bindTooltip(`
<strong>${province}</strong><br> <strong>${province}</strong><br>
${programName}<br> ${row.pathogen_name}<br>
Cases: ${row.total}<br> Total Detected: ${row.total}<br>
Positivity: ${percent}%
`) `)
.addTo(map); .addTo(map);
}); });
} }
}).addTo(map); }).addTo(map);
@@ -544,6 +1034,21 @@ function loadProvinceMap(startYear, startWeek, endYear, endWeek) {
} }
function getColorByPathogen(name) {
const colors = {
"A/H1N1pdm": "#2563eb",
"A/H3N2": "#11de9d",
"B/Yam": "#9333ea",
"B/Vic" : "#1021b9",
"A/H9N2": "#b91081",
"A/H5N1": "#ad850d",
"A/Unsubtypable": "#047393",
"B/Unsubtypable": "#890512"
};
return colors[name] || "#000000"; // fallback color
}
/* /*
|-------------------------------------------------------------------------- |--------------------------------------------------------------------------
@@ -558,8 +1063,58 @@ document.addEventListener("DOMContentLoaded", () => {
new DashboardFilter((startYear, startWeek, endYear, endWeek) => { new DashboardFilter((startYear, startWeek, endYear, endWeek) => {
loadTrend('week', startYear, startWeek, endYear, endWeek); loadTrend('week', startYear, startWeek, endYear, endWeek);
loadInfluenzaSubtypeDistribution('week', startYear, startWeek, endYear, endWeek);
loadCovidDistributedByAgeGroup('week', startYear, startWeek, endYear, endWeek);
loadInfluenzaSubtypeFrequency('week', startYear, startWeek, endYear, endWeek);
loadCovidLineageFrequency('week', startYear, startWeek, endYear, endWeek);
loadProvinceMap(startYear, startWeek, endYear, endWeek); loadProvinceMap(startYear, startWeek, endYear, endWeek);
const elements = document.querySelectorAll(".report-period");
elements.forEach(el => {
el.textContent = 'Week ' + startWeek + ' of '+startYear+' to ' + 'Week ' + endWeek + ' of ' + endYear
});
}); });
}); });
document.addEventListener("DOMContentLoaded", function () {
let currentSlide = 0;
const slides = document.querySelectorAll('.slide');
const nextBtn = document.querySelector('.next-btn');
const prevBtn = document.querySelector('.prev-btn');
function showSlide(index) {
slides.forEach((slide, i) => {
slide.classList.remove('active', 'prev');
if (i === index) {
slide.classList.add('active');
} else if (i === index - 1) {
slide.classList.add('prev');
}
});
}
function nextSlide() {
currentSlide = (currentSlide + 1) % slides.length;
showSlide(currentSlide);
}
function prevSlide() {
currentSlide = (currentSlide - 1 + slides.length) % slides.length;
showSlide(currentSlide);
}
// Button events
nextBtn.addEventListener('click', nextSlide);
prevBtn.addEventListener('click', prevSlide);
// Auto slide every 1 minute
let slideInterval = 2 * (60 * 1000);
setInterval(nextSlide, slideInterval);
// Init
showSlide(currentSlide);
});

160
dashboard/resources/views/dashboard/overview.blade.php
View File

@@ -20,7 +20,6 @@
</select> </select>
<div id="custom_range_container" style="display:none;" class="align-items-center gap-1"> <div id="custom_range_container" style="display:none;" class="align-items-center gap-1">
<select id="start_year" class="form-select"></select> <select id="start_year" class="form-select"></select>
<select id="start_week" class="form-select"></select> <select id="start_week" class="form-select"></select>
@@ -28,88 +27,155 @@
<select id="end_year" class="form-select"></select> <select id="end_year" class="form-select"></select>
<select id="end_week" class="form-select"></select> <select id="end_week" class="form-select"></select>
</div> </div>
</div> </div>
</div> </div>
<!-- Summary Cards --> <!-- Summary Cards -->
<div class="row flex-grow-1" id="summary_cards"></div> <div class="row flex-grow-1 mb-2" id="summary_cards"></div>
<!-- SLIDESHOW -->
<div class="row">
<div class="col-8">
<div class="row flex-grow-1"> <div class="slide-wrapper">
<!-- LEFT COLUMN --> <!-- SLIDE 1 -->
<div class="col-lg-8 d-flex flex-column"> <div class="slide active">
<div class="row">
<div class="col-lg-12 d-flex flex-column">
<!-- Trend Chart --> <div class="card shadow-sm mb-3" style="height:60vh;">
<div class="card shadow-sm mb-3 flex-grow-1"> <div class="card-body" >
<div class="card-body">
<div class="mb-3"> <h5 class="fw-bold">Epidemic Trend</h5>
<h5 class="fw-bold mb-1">Epidemic Trend</h5> <p class="text-muted small report-period">
<p class="text-muted small mb-0">
(based on selected epiweek range) (based on selected epiweek range)
</p> </p>
</div>
<canvas id="trendChart" height="90"></canvas> <canvas id="trendChart" height="90"></canvas>
</div> </div>
</div> </div>
<!-- Alerts --> </div>
<div class="card shadow-sm flex-grow-1"> </div>
</div>
<!-- SLIDE 2 -->
<div class="slide">
<div class="row">
<div class="col-lg-12 d-flex flex-column">
<div class="card shadow-sm" style="height:60vh;">
<div class="card-body"> <div class="card-body">
<h5 class="fw-bold">Influenza Subtypes Distribution</h5>
<p class="text-muted small report-period">
(based on selected epiweek range)
</p>
<h5 class="fw-bold">Recent Alerts & Notifications</h5> <canvas id="influenzaSubtypeDistribution" style="max-width: 100%; max-height:40vh; float: left;"></canvas>
<ul id="alertsList" class="list-group list-group-flush mt-3"></ul>
</div> </div>
</div> </div>
</div> </div>
</div>
</div>
<!-- SLIDE 3 -->
<div class="slide">
<div class="row">
<div class="col-lg-12 d-flex flex-column">
<div class="card shadow-sm" style="height:60vh;">
<div class="card-body">
<h5 class="fw-bold">SARS-CoV-2 Detected Distribute by Age Group</h5>
<p class="text-muted small report-period">
(based on selected epiweek range)
</p>
<canvas id="covidDistributedByAgeGroup" style="max-width: 100%; max-height:40vh; float: left;"></canvas>
</div>
</div>
<!-- RIGHT COLUMN --> </div>
<div class="col-lg-4 d-flex flex-column"> </div>
</div>
<!-- SLIDE 3 -->
<div class="slide">
<div class="row">
<div class="col-lg-12 d-flex flex-column">
<div class="card shadow-sm" style="height:60vh; display: flex">
<div class="card-body" >
<h5 class="fw-bold">SARS-CoV-2 Lineage Relative Frequencies Over Time</h5>
<p class="text-muted small report-period">
(based on selected epiweek range)
</p>
<canvas id="covidLineageFrequency" style=" flex:1; max-width: 90%; max-height:45vh; float: left;"></canvas>
<div id="legendContainer" style="
width:10%;
margin-left:20px;
max-height:375px;
overflow-y:auto;
padding:8px;
"></div>
</div>
</div>
</div>
</div>
</div>
<!-- SLIDE 3 -->
<div class="slide">
<div class="row">
<div class="col-lg-12 d-flex flex-column">
<div class="card shadow-sm" style="height:60vh; display: flex">
<div class="card-body" >
<h5 class="fw-bold">Influenza Subtypes Relative Frequencies Over Time</h5>
<p class="text-muted small report-period">
(based on selected epiweek range)
</p>
<canvas id="influenzaSubtypeFrequency" style=" flex:1; max-width: 90%; max-height:45vh; float: left;"></canvas>
<div id="legendContainerInfluenzaSubtypeFrequency" style="
width:10%;
margin-left:20px;
max-height:375px;
overflow-y:auto;
padding:8px;
"></div>
</div>
</div>
</div>
</div>
</div>
<!-- CONTROLS -->
<button class="slide-btn prev-btn">❮</button>
<button class="slide-btn next-btn">❯</button>
</div>
</div>
<div class="col-4">
<div class="row">
<div class="col-lg-12 d-flex flex-column">
<div class="card shadow-sm"> <div class="card shadow-sm">
<div class="card-body"> <div class="card-body">
<h5 class="fw-bold">Total Cases by Provinces</h5> <h5 class="fw-bold">Influenza Subtypes Detected by Province</h5>
<p class="text-muted small">(based on selected epiweek range)</p> <p class="text-muted small report-period">(based on selected epiweek range)</p>
<div id="provinceMap" style="height:50vh;"></div> <div id="provinceMap" style="height:40vh;"></div>
<div class="d-flex justify-content-center align-items-center gap-4 mt-4 small">
<span>
<span
style="display:inline-block;width:10px;height:10px;background:#2563eb;border-radius:50%;margin-right:6px;"></span>
SARI
</span>
<span>
<span
style="display:inline-block;width:10px;height:10px;background:#10b981;border-radius:50%;margin-right:6px;"></span>
ILI
</span>
<span>
<span
style="display:inline-block;width:10px;height:10px;background:#9333ea;border-radius:50%;margin-right:6px;"></span>
LBM
</span>
</div>
</div> </div>
</div> </div>
</div> </div>
</div>
</div>
</div> </div>

151
dashboard/resources/views/layouts/app.blade.php
View File

@@ -4,11 +4,14 @@
<head> <head>
<title>NRML Dashboard</title> <title>NRML Dashboard</title>
<meta name="viewport" content="width=device-width, initial-scale=1"> <meta name="viewport" content="width=device-width, initial-scale=1">
<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet"> <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet">
<script src="https://cdn.jsdelivr.net/npm/chart.js@3.9.1"></script> <script src="https://cdn.jsdelivr.net/npm/chart.js@3.9.1"></script>
<script src="https://cdn.jsdelivr.net/npm/chartjs-plugin-datalabels@2.2.0"></script> <script src="https://cdn.jsdelivr.net/npm/chartjs-plugin-datalabels@2.2.0"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jspdf/2.5.1/jspdf.umd.min.js"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jspdf/2.5.1/jspdf.umd.min.js"></script>
<script src="https://html2canvas.hertzen.com/dist/html2canvas.min.js"></script> <script src="https://html2canvas.hertzen.com/dist/html2canvas.min.js"></script>
<link rel="stylesheet" href="https://unpkg.com/leaflet/dist/leaflet.css" /> <link rel="stylesheet" href="https://unpkg.com/leaflet/dist/leaflet.css" />
<script src="https://unpkg.com/leaflet/dist/leaflet.js"></script> <script src="https://unpkg.com/leaflet/dist/leaflet.js"></script>
@@ -16,11 +19,8 @@
<script src="/js/dashboard/charts.js"></script> <script src="/js/dashboard/charts.js"></script>
<script src="/js/dashboard/export.js"></script> <script src="/js/dashboard/export.js"></script>
<style> <style>
body { body { margin: 0; }
margin: 0;
}
.top-navbar { .top-navbar {
height: 60px; height: 60px;
@@ -34,6 +34,7 @@
.brand-title { .brand-title {
font-weight: 600; font-weight: 600;
font-size: 18px; font-size: 18px;
color: #f8f9fa;
} }
.nav-bar { .nav-bar {
@@ -44,8 +45,6 @@
position: sticky; position: sticky;
top: 0; top: 0;
z-index: 1000; z-index: 1000;
background: white;
border-bottom: 1px solid #dcdcdc;
} }
.btn-theme-outline { .btn-theme-outline {
@@ -56,7 +55,6 @@
.btn-theme-outline:hover { .btn-theme-outline:hover {
background-color: #cce0d4; background-color: #cce0d4;
color: #0B8F3C;
} }
.nav-item { .nav-item {
@@ -68,9 +66,7 @@
font-size: 14px; font-size: 14px;
} }
.nav-item:hover { .nav-item:hover { background: #cce0d4; }
background: #cce0d4;
}
.active-tab { .active-tab {
color: #0B8F3C; color: #0B8F3C;
@@ -78,27 +74,10 @@
background: #e5efe8; background: #e5efe8;
} }
.content-area {
padding: 25px;
}
.brand-title {
font-weight: 600;
font-size: 18px;
color: #f8f9fa;
}
.content-area { .content-area {
padding: 20px; padding: 20px;
background: #f8f9fa; background: #f8f9fa;
min-height: calc(100vh - 60px); min-height: calc(100vh - 110px);
}
.brand-logo {
width: 32px;
height: 32px;
object-fit: contain;
margin-right: 10px;
} }
.card { .card {
@@ -106,13 +85,13 @@
border: 1px solid #E5E7EB; border: 1px solid #E5E7EB;
} }
.card h3 { .form-select { border-radius: 0px !important; }
color: #0B8F3C; .shadow-sm { box-shadow: none !important; }
}
.export-control { .card h3 { color: #0B8F3C; }
position: relative;
} /* EXPORT */
.export-control { position: relative; }
#exportItems { #exportItems {
display: flex; display: flex;
@@ -132,12 +111,11 @@
width: auto; width: auto;
} }
.export-modal { .export-modal {
display: none; display: none;
position: fixed; position: fixed;
inset: 0; inset: 0;
background: rgba(0, 0, 0, 0.4); background: rgba(0,0,0,0.4);
z-index: 10000; z-index: 10000;
} }
@@ -149,53 +127,72 @@
border-radius: 10px; border-radius: 10px;
} }
/* SLIDE FEATURE (from master) */
.slide-wrapper {
position: relative;
overflow: hidden;
height: 100%;
min-height: 400px;
}
.slide {
position: absolute;
width: 100%;
top: 0;
left: 100%;
opacity: 0;
transition: all 0.5s ease-in-out;
}
.slide.active { left: 0; opacity: 1; z-index: 2; }
.slide.prev { left: -100%; opacity: 0; }
.slide-btn {
position: absolute;
top: 10%;
transform: translateY(-50%);
background: rgba(0,128,0,0.43);
color: white;
border: none;
padding: 8px 15px;
cursor: pointer;
z-index: 10;
}
.prev-btn { right: 75px; }
.next-btn { right: 25px; }
.slide-btn:hover {
background: rgba(7,120,24,0.8);
}
@media print { @media print {
#floatingExport { #floatingExport { display: none !important; }
display: none !important; .nav-bar, .top-navbar { display: none !important; }
} .card { page-break-inside: avoid; }
.nav-bar,
.top-navbar {
display: none !important;
}
.card {
page-break-inside: avoid;
}
} }
</style> </style>
</head> </head>
<body> <body>
<div class="top-navbar"> <div class="top-navbar">
<div class="brand-title"> <div class="brand-title">
National Reference Medical Laboratory Surveillance Dashboard National Reference Medical Laboratory Surveillance Dashboard
</div> </div>
<div class="ms-auto small"> <div class="ms-auto small">
Last update: 12:05 | 2026-03-15 Last update: 12:05 | 2026-03-15
</div> </div>
</div>
</div> <div class="nav-bar">
<div class="nav-bar">
<a href="/dashboard" class="nav-item {{ request()->is('dashboard') ? 'active-tab' : '' }}"> <a href="/dashboard" class="nav-item {{ request()->is('dashboard') ? 'active-tab' : '' }}">
Overview Overview
</a> </a>
<!-- @foreach($programs as $program)
<a href="/dashboard/{{ strtolower($program->code) }}"
class="nav-item {{ request()->is('dashboard/' . strtolower($program->code)) ? 'active-tab' : '' }}">
{{ $program->code }}
</a>
@endforeach -->
@foreach($programs as $program) @foreach($programs as $program)
@if($program->code === 'SEQ') @if($program->code === 'SEQ')
<a href="/dashboard/seq" class="nav-item {{ request()->is('dashboard/seq') ? 'active-tab' : '' }}"> <a href="/dashboard/seq" class="nav-item {{ request()->is('dashboard/seq') ? 'active-tab' : '' }}">
SEQ SEQ
</a> </a>
@@ -205,12 +202,11 @@
{{ $program->code }} {{ $program->code }}
</a> </a>
@endif @endif
@endforeach @endforeach
<div class="ms-auto d-flex align-items-center gap-2 pe-3"> <div class="ms-auto d-flex align-items-center gap-2 pe-3">
<button type="button" onclick="reloadDataSource()" class="btn btn-sm btn-theme-outline"> <button onclick="reloadDataSource()" class="btn btn-sm btn-theme-outline">
Refresh Data Refresh Data
</button> </button>
@@ -221,14 +217,12 @@
</button> </button>
<div id="exportItems" class="align-items-center gap-2"> <div id="exportItems" class="align-items-center gap-2">
<button class="btn btn-sm btn-light" onclick="openChartSelector()">Charts</button> <button class="btn btn-sm btn-light" onclick="openChartSelector()">Charts</button>
<button class="btn btn-sm btn-light" onclick="exportFullDashboard()">Screen</button> <button class="btn btn-sm btn-light" onclick="exportFullDashboard()">Screen</button>
<button class="btn btn-sm btn-light" onclick="window.print()">Print</button> <button class="btn btn-sm btn-light" onclick="window.print()">Print</button>
<button class="btn btn-sm btn-outline-secondary" id="exportClose">✕</button> <button class="btn btn-sm btn-outline-secondary" id="exportClose">✕</button>
</div> </div>
<div id="chartModal" class="export-modal"> <div id="chartModal" class="export-modal">
<div class="export-content"> <div class="export-content">
<h5>Select Charts</h5> <h5>Select Charts</h5>
@@ -245,35 +239,28 @@
</div> </div>
</div> </div>
<div class="main-wrapper">
<div class="main-wrapper">
<div class="content-area"> <div class="content-area">
@yield('content') @yield('content')
</div> </div>
</div>
</div> @yield('scripts')
<script>
@yield('scripts')
<script>
window.addEventListener("click", (e) => { window.addEventListener("click", (e) => {
const modal = document.getElementById("chartModal"); const modal = document.getElementById("chartModal");
if (e.target === modal) modal.style.display = "none";
if (e.target === modal) {
modal.style.display = "none";
}
}); });
function reloadDataSource() { function reloadDataSource() {
fetch(`/api/dashboard/reload`) fetch(`/api/dashboard/reload`)
.then(res => res.json()) .then(res => res.json())
.then(() => location.reload()); .then(() => location.reload());
} }
</script> </script>
</body> </body>
</html> </html>

4
dashboard/routes/api.php
View File

@@ -7,6 +7,10 @@ Route::get('/dashboard/summary', [DashboardController::class, 'summary']);
Route::get('/dashboard/trend', [DashboardController::class, 'trend']); Route::get('/dashboard/trend', [DashboardController::class, 'trend']);
Route::get('/dashboard/program', [DashboardController::class, 'program']); Route::get('/dashboard/program', [DashboardController::class, 'program']);
Route::get('/dashboard/province-circles', [DashboardController::class, 'provinceCircles']); Route::get('/dashboard/province-circles', [DashboardController::class, 'provinceCircles']);
Route::get('/dashboard/influenza-subtype-distribution', [DashboardController::class, 'influenzaSubtypeDetected']);
Route::get('/dashboard/covid-distributed-by-age-group', [DashboardController::class, 'covidDistributedByAgeGroup']);
Route::get('/dashboard/covid-lineage-frequency', [DashboardController::class, 'covidLineageRelativeOverTime']);
Route::get('/dashboard/influenza-relative-frequency', [DashboardController::class, 'influenzaRelativeOverTime']);
Route::get('/dashboard/sentinel-map', [DashboardController::class, 'sentinelMap']); Route::get('/dashboard/sentinel-map', [DashboardController::class, 'sentinelMap']);
Route::get('/dashboard/reload', [DashboardController::class, 'fetchSourceData']); Route::get('/dashboard/reload', [DashboardController::class, 'fetchSourceData']);
Route::get('/dashboard/sequencing', [DashboardController::class, 'sequencing']); Route::get('/dashboard/sequencing', [DashboardController::class, 'sequencing']);