Merge branch 'feature/service_retrieve_data' into develop
# Conflicts: # dashboard/app/Http/Controllers/Api/DashboardController.php
This commit is contained in:
pcalengratha
39
dashboard/app/Console/Commands/fetchSourceData.php
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39
dashboard/app/Console/Commands/fetchSourceData.php
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@@ -0,0 +1,39 @@
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<?php
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namespace App\Console\Commands;
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use App\Services\DataRetrievalService;
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use Illuminate\Console\Command;
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class fetchSourceData extends Command
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{
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/**
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* The name and signature of the console command.
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*
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* @var string
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*/
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protected $signature = 'app:fetch-source-data';
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/**
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* The console command description.
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*
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* @var string
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*/
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protected $description = 'Retrieve surveillance data from source database';
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protected $dataRetrievalService;
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public function __construct()
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{
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$this->dataRetrievalService = new DataRetrievalService();
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parent::__construct();
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}
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/**
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* Execute the console command.
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*/
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public function handle()
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{
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$this->dataRetrievalService->getSurveillanceData();
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}
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}
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@@ -2,6 +2,7 @@
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namespace App\Http\Controllers\Api;
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use App\Services\DataRetrievalService;
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use Illuminate\Http\Request;
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use App\Http\Controllers\Controller;
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use App\Services\DashboardService;
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@@ -10,10 +11,12 @@ use Carbon\Carbon;
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class DashboardController extends Controller
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{
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protected $service;
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protected $dataRetrievalService;
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public function __construct(DashboardService $service)
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{
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$this->service = $service;
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$this->dataRetrievalService = new DataRetrievalService();
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}
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/*
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@@ -152,13 +155,19 @@ class DashboardController extends Controller
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// return response()->json(['error' => 'Missing epiweek range'], 400);
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// }
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// $data = $this->service->sentinelSites(
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// $range['startYear'],
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// $range['startWeek'],
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// $range['endYear'],
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// $range['endWeek']
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// );
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return response()->json($data);
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}
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public function fetchSourceData(){
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try{
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$this->dataRetrievalService->getSurveillanceData();
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return response()->json(['message' => 'Data loaded successfully!'], 200);
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}
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catch (\Exception $e)
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{
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return response()->json(['error' => 'Data loaded unsuccessfully!'], 400);
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}
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}
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// return response()->json($data);
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// }
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}
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693
dashboard/app/Services/DataRetrievalService.php
Normal file
693
dashboard/app/Services/DataRetrievalService.php
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@@ -0,0 +1,693 @@
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<?php
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namespace App\Services;
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use Carbon\Carbon;
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use App\Models\Surveillance;
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use App\Models\SurveillanceCase;
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use App\Models\CaseLabResult;
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use Illuminate\Support\Facades\DB;
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use Illuminate\Support\Facades\Log;
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class DataRetrievalService
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{
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public function getSurveillanceData()
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{
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try{
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$toDate = now();
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$this->getSARICases(now()->subDays(config('app.lookback_days.SARI'))->toDateString(), $toDate); // done
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$this->getILICases(now()->subDays(config('app.lookback_days.ILI'))->toDateString(), $toDate); // done
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$this->getLBMCases(now()->subDays(config('app.lookback_days.LBM'))->toDateString(), $toDate); // done
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$this->getAFICases(now()->subDays(config('app.lookback_days.AFI'))->toDateString(), $toDate); // done
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//$this->getNSDCases(now()->subDays(config('app.lookback_days.NDS'))->toDateString(), $toDate);
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$this->getSEQCases(now()->subDays(config('app.lookback_days.SEQ'))->toDateString(), $toDate); // done
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Log::channel('jobs')->info($toDate->toDateString(). ' Service Reload Data Successfully Ran');
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return true;
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}
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catch (\Exception $e){
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Log::channel('jobs')->error($e->getMessage());
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return false;
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}
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}
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public function getSARICases($dateFrom, $dateTo=NULL)
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{
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$cond = "";
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$cond .= " and patient.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
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$cond .= (!empty($dateTo)) ? " and patient.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
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$sari_cases = DB::connection('mysql_nphl')
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->select("
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SELECT
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patient.labcode,
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patient.patdate,
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patient.isnewcase,
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l.labname_en,
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l.labaddress_en,
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1 as surveillance_id,
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niphc0_nphl.get_epi_period(patient.patdate, 'Y') as year_data,
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niphc0_nphl.get_epi_period(patient.patdate, 'W') as week_data,
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patient.patage,
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patient.patsex,
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NULL as is_alive,
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p.proname_en
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.sari_patients sr_p on sr_p.patid = patient.patid
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inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
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left join niphc0_nphl.province p on p.proid = patient.frompro
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WHERE patient.patgroup =2
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and patient.status = 1
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".$cond);
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$this->insert_surveillance_cases($sari_cases);
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$sari_case_results = DB::connection('mysql_nphl')->select("
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SELECT
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patient.labcode,
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1 as surveillance_id,
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if(trs.rtitle='Negatives', 0, 1) as is_positive,
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if(trs.rtitle !='Negatives', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
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if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
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'SARI Influenza Test' as indicator
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FROM `labopatients` patient
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inner join sari_patients sr_p on sr_p.patid = patient.patid
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inner join test_patsample tps on tps.patientid = patient.patid
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inner join test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
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inner join test_pattestresult tptr on tptr.pstid = tpst.pstid
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inner join test_resultselect trs on trs.rid = tptr.rsltid
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WHERE patient.patgroup =2
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and patient.status = 1
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and tps.status = 1
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and tpst.status = 1
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and trs.status = 1
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and tpst.labtestid in (775,216,239,238,212,220,340,381,382)
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" .$cond. "
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union
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SELECT
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patient.labcode,
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1 as surveillance_id,
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if(trs.rtitle='Negative', 0, 1) as is_positive,
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if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
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'' as subtype,
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'SARI Covid Test' as indicator
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FROM `labopatients` patient
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inner join sari_patients sr_p
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on sr_p.patid = patient.patid
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inner join test_patsample tps
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on tps.patientid = patient.patid
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inner join test_patsamtest tpst
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on tpst.patsmid = tps.sampleid
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and tpst.patid = tps.patientid
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inner join test_pattestresult tptr on tptr.pstid = tpst.pstid
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inner join test_resultselect trs on trs.rid = tptr.rsltid
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WHERE patient.patgroup =2
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and patient.status = 1
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and tps.status = 1
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and tpst.status = 1
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and trs.status = 1
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and tpst.labtestid in (651,652,653,654,650)
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and trs.rtitle !='Pending'
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" .$cond);
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$this->insert_surveillance_case_lab_results($sari_case_results);
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}
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public function getILICases($dateFrom, $dateTo = NULL)
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{
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$cond = "";
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$cond .= " and patient.patdate >= '".date('Y-m-d', strtotime($dateFrom))."' ";
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$cond .= (!empty($dateTo)) ? " and patient.patdate <='".date('Y-m-d', strtotime($dateTo))."' ":"";
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$ili_cases = DB::connection('mysql_nphl')
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->select("
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SELECT
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patient.labcode,
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patient.patdate,
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patient.isnewcase,
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l.labname_en,
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l.labaddress_en,
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2 as surveillance_id,
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niphc0_nphl.get_epi_period(patient.patdate, 'Y') as year_data,
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niphc0_nphl.get_epi_period(patient.patdate, 'W') as week_data,
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patient.patage,
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patient.patsex,
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NULL as is_alive,
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p.proname_en
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid
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inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
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left join niphc0_nphl.province p on p.proid = patient.frompro
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WHERE patient.patgroup =3
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and patient.status = 1
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".$cond
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);
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$this->insert_surveillance_cases($ili_cases);
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$ili_case_results = DB::connection('mysql_nphl')
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->select("
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SELECT
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distinct
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patient.labcode,
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2 as surveillance_id,
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if(trs.rtitle='Negatives', 0, 1) as is_positive,
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if(trs.rtitle !='Negatives', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
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if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
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'ILI Influenza Test' as indicator
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FROM niphc0_nphl.`labopatients` patient
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inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid
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inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
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inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
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inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
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inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
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WHERE patient.patgroup = 3
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and patient.status = 1
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and tps.status = 1
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and tpst.status = 1
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and trs.status = 1
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and tpst.labtestid in (775,216,239,238,212,220,340,381,382)
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".$cond."
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union
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SELECT
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DISTINCT
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patient.labcode,
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2 as surveillance_id,
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if(trs.rtitle='Negative', 0, 1) as is_positive,
|
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if(trs.rtitle !='Negative', 'SARS-CoV-2', '') as pathogen_name,
|
||||
'' as subtype,
|
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'ILI Covid Test' as indicator
|
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FROM niphc0_nphl.`labopatients` patient
|
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inner join niphc0_nphl.ili_patients sr_p on sr_p.patid = patient.patid
|
||||
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
|
||||
inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
|
||||
inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
|
||||
inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
|
||||
WHERE patient.patgroup = 3
|
||||
and patient.status = 1
|
||||
and tps.status = 1
|
||||
and tpst.status = 1
|
||||
and trs.status = 1
|
||||
and tpst.labtestid in (651,652,653,654,650)
|
||||
and trs.rtitle !='Pending'
|
||||
".$cond);
|
||||
|
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$this->insert_surveillance_case_lab_results($ili_case_results);
|
||||
|
||||
}
|
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|
||||
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))."' ":"";
|
||||
$lbm_cases = DB::connection('mysql_nphl')
|
||||
->select("
|
||||
SELECT
|
||||
patient.labcode,
|
||||
patient.patdate,
|
||||
patient.isnewcase,
|
||||
l.labname_en,
|
||||
l.labaddress_en,
|
||||
3 as surveillance_id,
|
||||
niphc0_nphl.get_epi_period(patient.patdate, 'Y') year_data,
|
||||
niphc0_nphl.get_epi_period(patient.patdate, 'W') week_data,
|
||||
patient.patage,
|
||||
patient.patsex,
|
||||
NULL as is_alive,
|
||||
p.proname_en
|
||||
FROM niphc0_nphl.`labopatients` patient
|
||||
inner join niphc0_nphl.lbms_patients on lbms_patients.patid = patient.patid
|
||||
left join niphc0_nphl.province p on p.proid = patient.frompro
|
||||
inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
|
||||
WHERE patient.patgroup = 17
|
||||
and patient.status = 1
|
||||
".$cond);
|
||||
|
||||
$this->insert_surveillance_cases($lbm_cases);
|
||||
|
||||
$lbm_case_results = DB::connection('mysql_nphl')
|
||||
->select("
|
||||
SELECT
|
||||
distinct
|
||||
patient.labcode,
|
||||
3 as surveillance_id,
|
||||
if(trs.rtitle='Negatives', 0, 1) as is_positive,
|
||||
if(trs.rtitle !='Negatives', concat('Influenza ',LEFT(UPPER(trs.rtitle),1)),'') pathogen_name,
|
||||
if(trs.rtitle !='Negatives', trs.rtitle, '') as subtype,
|
||||
'LBM Influenza Test' as indicator
|
||||
FROM niphc0_nphl.`labopatients` patient
|
||||
inner join niphc0_nphl.lbms_patients sr_p on sr_p.patid = patient.patid
|
||||
inner join niphc0_nphl.test_patsample tps on tps.patientid = patient.patid
|
||||
inner join niphc0_nphl.test_patsamtest tpst on tpst.patsmid = tps.sampleid and tpst.patid = tps.patientid
|
||||
inner join niphc0_nphl.test_pattestresult tptr on tptr.pstid = tpst.pstid
|
||||
inner join niphc0_nphl.test_resultselect trs on trs.rid = tptr.rsltid
|
||||
WHERE patient.patgroup = 17
|
||||
and patient.status = 1
|
||||
and tps.status = 1
|
||||
and tpst.status = 1
|
||||
and trs.status = 1
|
||||
and tpst.labtestid in (775,216,239,238,212,220,340,381,382)
|
||||
".$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,
|
||||
'LBM Covid Test' 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 = "";
|
||||
$cond .= " and afi_lab_result.results_date >= '".date('Y-m-d', strtotime($dateFrom))."' ";
|
||||
$cond .= (!empty($dateTo)) ? " and afi_lab_result.results_date <='".date('Y-m-d', strtotime($dateTo))."' ":"";
|
||||
$afi_cases = DB::connection('mysql_afi')
|
||||
->select("
|
||||
SELECT
|
||||
afi_lab_result.sample_code as labcode,
|
||||
afi_lab_result.results_date as patdate,
|
||||
1 as isnewcase,
|
||||
afi_case.sentinel_site as labname_en,
|
||||
'' as labaddress_en,
|
||||
4 as surveillance_id,
|
||||
niphc0_nphl.get_epi_period(afi_lab_result.results_date, 'Y') as year_data,
|
||||
niphc0_nphl.get_epi_period(afi_lab_result.results_date, 'W') as week_data,
|
||||
ifnull(DATEDIFF(afi_case.date_of_interview, date_of_birth),180) as patage,
|
||||
if(afi_case.sex='Male','M','F') as patsex,
|
||||
NULL as is_alive,
|
||||
p.proname_en as proname_en
|
||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
||||
left join afi_db.afi_tbl_result afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
||||
left join niphc0_nphl.province p on p.proid = afi_case.residence_province
|
||||
where
|
||||
afi_case.afi_event is NOT null
|
||||
and afi_lab_result.results_date is not null " .$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, '$[0].id'))),'_','/'),'') as subtype,
|
||||
'AFI Influenza Test' as indicator
|
||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
||||
where afi_lab_result.sample_code is not null
|
||||
and afi_lab_result.influenza_result in('Negative', 'Positive')
|
||||
and afi_case.afi_event is NOT null
|
||||
and afi_lab_result.results_date is not null ".$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,
|
||||
'AFI Covid Test' 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_lab_result.results_date is not null ".$cond."
|
||||
|
||||
union
|
||||
|
||||
SELECT
|
||||
afi_lab_result.sample_code as labcode,
|
||||
4 as surveillance_id,
|
||||
if(afi_lab_result.dengue_pcr='Positive',1,0) as is_positive,
|
||||
if(afi_lab_result.dengue_pcr='Positive', 'Dengue','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Dengue PCR Test' as indicator
|
||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
||||
where afi_lab_result.sample_code is not null
|
||||
and afi_lab_result.dengue_pcr in('Negative', 'Positive')
|
||||
and afi_case.afi_event is NOT null
|
||||
and afi_lab_result.results_date is not null ".$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','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Chikungunya PCR Test' 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_lab_result.results_date is not null ".$cond."
|
||||
|
||||
union
|
||||
|
||||
SELECT
|
||||
afi_lab_result.sample_code as labcode,
|
||||
4 as surveillance_id,
|
||||
if(afi_lab_result.leptospira_pcr='Positive',1,0) as is_positive,
|
||||
if(afi_lab_result.leptospira_pcr='Positive', 'Leptospira','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Leptospira PCR Test' as indicator
|
||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
||||
where afi_lab_result.sample_code is not null
|
||||
and afi_lab_result.leptospira_pcr in('Negative', 'Positive')
|
||||
and afi_case.afi_event is NOT null
|
||||
and afi_lab_result.results_date is not null ".$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','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Plasmodium PCR Test' 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_lab_result.results_date is not null ".$cond."
|
||||
|
||||
UNION
|
||||
|
||||
SELECT
|
||||
afi_lab_result.sample_code as labcode,
|
||||
4 as surveillance_id,
|
||||
if(afi_lab_result.rickettsia_pcr='Positive',1,0) as is_positive,
|
||||
if(afi_lab_result.rickettsia_pcr='Positive', 'Rickettsia','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Rickettsia PCR Test' as indicator
|
||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
||||
where afi_lab_result.sample_code is not null
|
||||
and afi_lab_result.rickettsia_pcr in('Negative', 'Positive')
|
||||
and afi_case.afi_event is NOT null
|
||||
and afi_lab_result.results_date is not null ".$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','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Salmonella PCR Test' 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_lab_result.results_date is not null ".$cond."
|
||||
|
||||
UNION
|
||||
|
||||
SELECT
|
||||
afi_lab_result.sample_code as labcode,
|
||||
4 as surveillance_id,
|
||||
if(afi_lab_result.westnile_pcr='Positive',1,0) as is_positive,
|
||||
if(afi_lab_result.westnile_pcr='Positive', 'Westnile Nile','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Westnile PCR Test' as indicator
|
||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
||||
where afi_lab_result.sample_code is not null
|
||||
and afi_lab_result.westnile_pcr in('Negative', 'Positive')
|
||||
and afi_case.afi_event is NOT null
|
||||
and afi_lab_result.results_date is not null ".$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','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI ZIKA PCR Test' 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_lab_result.results_date is not null ".$cond."
|
||||
|
||||
UNION
|
||||
|
||||
# SERUM
|
||||
|
||||
SELECT
|
||||
afi_lab_result.sample_code as labcode,
|
||||
4 as surveillance_id,
|
||||
if(afi_lab_result.chikungunya_serum='Positive',1,0) as is_positive,
|
||||
if(afi_lab_result.chikungunya_serum='Positive', 'Chikungunya','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Chikungunya Serum Test' as indicator
|
||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
||||
where afi_lab_result.sample_code is not null
|
||||
and afi_lab_result.chikungunya_serum in('Negative', 'Positive')
|
||||
and afi_case.afi_event is NOT null
|
||||
and afi_lab_result.results_date is not null ".$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','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Dengue Serum Test' 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_lab_result.results_date is not null ".$cond."
|
||||
|
||||
UNION
|
||||
|
||||
SELECT
|
||||
afi_lab_result.sample_code as labcode,
|
||||
4 as surveillance_id,
|
||||
if(afi_lab_result.westnile_serum='Positive',1,0) as is_positive,
|
||||
if(afi_lab_result.westnile_serum='Positive', 'Westnile','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Westnile Serum Test' as indicator
|
||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
||||
where afi_lab_result.sample_code is not null
|
||||
and afi_lab_result.westnile_serum in('Negative', 'Positive')
|
||||
and afi_case.afi_event is NOT null
|
||||
and afi_lab_result.results_date is not null ".$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','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI ZIKA Serum Test' 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_lab_result.results_date is not null ".$cond."
|
||||
|
||||
UNION
|
||||
|
||||
SELECT
|
||||
afi_lab_result.sample_code as labcode,
|
||||
4 as surveillance_id,
|
||||
if(afi_lab_result.je_virus='Positive',1,0) as is_positive,
|
||||
if(afi_lab_result.je_virus='Positive', 'Japanese Encephalitis','') pathogen_name,
|
||||
'' as subtype,
|
||||
'AFI Japanese Encephalitis Test' as indicator
|
||||
FROM afi_db.`afi_tbl_afiform` as afi_case
|
||||
INNER join afi_db.afi_tbl_result as afi_lab_result on afi_lab_result.unique_afi_id = afi_case.unique_afi_id
|
||||
where afi_lab_result.sample_code is not null
|
||||
and afi_lab_result.je_virus in('Negative', 'Positive')
|
||||
and afi_case.afi_event is NOT null
|
||||
and afi_lab_result.results_date is not null ".$cond
|
||||
);
|
||||
|
||||
$this->insert_surveillance_case_lab_results($afi_lab_results);
|
||||
}
|
||||
|
||||
public function getNSDCases($dateFrom, $dateTo = NULL)
|
||||
{
|
||||
return [];
|
||||
}
|
||||
|
||||
public function getSEQCases($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))."' ":"";
|
||||
$seq_cases = DB::connection('mysql_nphl')
|
||||
->select("
|
||||
SELECT DISTINCT
|
||||
patient.labcode,
|
||||
patient.patdate,
|
||||
patient.isnewcase,
|
||||
l.labname_en,
|
||||
l.labaddress_en,
|
||||
6 as surveillance_id,
|
||||
niphc0_nphl.get_epi_period(patient.patdate, 'Y') as year_data,
|
||||
niphc0_nphl.get_epi_period(patient.patdate, 'W') as week_data,
|
||||
patient.patage,
|
||||
patient.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 patient on patient.patid = sqsb.patid
|
||||
inner join niphc0_nphl.laboratory l on l.labid = patient.patsource
|
||||
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
|
||||
left join niphc0_nphl.province pro on pro.proid = patient.frompro
|
||||
where patient.status = 1
|
||||
and tpst.labtestid IN ( 659, 662, 666, 667, 668 )
|
||||
" . $cond);
|
||||
|
||||
$this->insert_surveillance_cases($seq_cases);
|
||||
|
||||
$seq_lab_results = DB::connection('mysql_nphl')
|
||||
->select("
|
||||
SELECT DISTINCT
|
||||
patient.labcode,
|
||||
6 as surveillance_id,
|
||||
1 is_positive,
|
||||
ifnull(sqsb.seqlineage,'N/A') as pathogen_name,
|
||||
trs.rtitle 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
|
||||
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 patient on patient.patid = sqsb.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.status = 1
|
||||
and tpst.labtestid IN ( 659, 662, 666, 667, 668 )
|
||||
and trs.rtitle not in ('Inconclusive', 'In Progress')
|
||||
" . $cond);
|
||||
|
||||
$this->insert_surveillance_case_lab_results($seq_lab_results);
|
||||
|
||||
}
|
||||
|
||||
private function insert_surveillance_cases($cases){
|
||||
|
||||
$case_data = [];
|
||||
foreach ($cases as $case) {
|
||||
$case_data[] = [
|
||||
'lab_code' => $case->labcode,
|
||||
'case_date' => $case->patdate,
|
||||
'is_newcase' => $case->isnewcase,
|
||||
'sentinel_site_name' => $case->labname_en,
|
||||
'site_province_name' => $case->labaddress_en,
|
||||
'surveillance_id' => $case->surveillance_id,
|
||||
'year_data' => $case->year_data,
|
||||
'week_data' => $case->week_data,
|
||||
'patient_age_inday' => $case->patage,
|
||||
'patient_sex' => $case->patsex,
|
||||
'is_alive' => $case->is_alive,
|
||||
'patient_province' => $case->proname_en
|
||||
];
|
||||
}
|
||||
|
||||
$case_chunks = array_chunk($case_data, 100);
|
||||
foreach ($case_chunks as $chunk) {
|
||||
DB::connection('mysql')->table('tmp_surveillance_cases')->upsert($chunk, [
|
||||
'lab_code',
|
||||
'surveillance_id'
|
||||
], [
|
||||
'case_date',
|
||||
'is_newcase',
|
||||
'sentinel_site_name',
|
||||
'site_province_name',
|
||||
'year_data',
|
||||
'week_data',
|
||||
'patient_age_inday',
|
||||
'patient_sex',
|
||||
'is_alive',
|
||||
'patient_province'
|
||||
]);
|
||||
}
|
||||
}
|
||||
|
||||
private function insert_surveillance_case_lab_results($lab_results){
|
||||
$result_data = [];
|
||||
foreach ($lab_results as $lab_result) {
|
||||
$result_data[] = [
|
||||
'lab_code' => $lab_result->labcode,
|
||||
'surveillance_id' => $lab_result->surveillance_id,
|
||||
'is_positive' => $lab_result->is_positive,
|
||||
'pathogen_name' => $lab_result->pathogen_name,
|
||||
'subtype' => $lab_result->subtype,
|
||||
'indicator' => $lab_result->indicator
|
||||
];
|
||||
}
|
||||
$result_chunks = array_chunk($result_data, 100);
|
||||
foreach ($result_chunks as $chunk) {
|
||||
DB::connection('mysql')->table('tmp_case_lab_results')->upsert($chunk,
|
||||
[
|
||||
'lab_code',
|
||||
'surveillance_id',
|
||||
'indicator'
|
||||
],
|
||||
[
|
||||
'is_positive',
|
||||
'pathogen_name',
|
||||
'subtype'
|
||||
]);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -15,6 +15,15 @@ return [
|
||||
|
||||
'name' => env('APP_NAME', 'Laravel'),
|
||||
|
||||
'lookback_days' => [
|
||||
'SARI' => 777, //
|
||||
'ILI' => 777,
|
||||
'LBM' => 777,
|
||||
'AFI' => 777,
|
||||
'NDS' => 777,
|
||||
'SEQ' => 200
|
||||
],
|
||||
|
||||
/*
|
||||
|--------------------------------------------------------------------------
|
||||
| Application Environment
|
||||
|
||||
@@ -113,6 +113,33 @@ return [
|
||||
// 'trust_server_certificate' => env('DB_TRUST_SERVER_CERTIFICATE', 'false'),
|
||||
],
|
||||
|
||||
'mysql_nphl' => [
|
||||
'driver' => 'mariadb',
|
||||
'host' => env('NPHL_DB_HOST', '127.0.0.1'),
|
||||
'port' => env('NPHL_DB_PORT', '3306'),
|
||||
'database' => env('NPHL_DB_DATABASE', 'laravel'),
|
||||
'username' => env('NPHL_DB_USERNAME', 'root'),
|
||||
'password' => env('NPHL_DB_PASSWORD', '')
|
||||
],
|
||||
|
||||
'mysql_afi' => [
|
||||
'driver' => 'mysql',
|
||||
'host' => env('AFI_DB_HOST', '127.0.0.1'),
|
||||
'port' => env('AFI_DB_PORT', '3306'),
|
||||
'database' => env('AFI_DB_DATABASE', 'laravel'),
|
||||
'username' => env('AFI_DB_USERNAME', 'root'),
|
||||
'password' => env('AFI_DB_PASSWORD', '')
|
||||
],
|
||||
|
||||
'mysql_nds' => [
|
||||
'driver' => 'mysql',
|
||||
'host' => env('NDS_DB_HOST', '127.0.0.1'),
|
||||
'port' => env('NDS_DB_PORT', '3306'),
|
||||
'database' => env('NDS_DB_DATABASE', 'laravel'),
|
||||
'username' => env('NDS_DB_USERNAME', 'root'),
|
||||
'password' => env('NDS_DB_PASSWORD', '')
|
||||
],
|
||||
|
||||
],
|
||||
|
||||
/*
|
||||
|
||||
@@ -94,6 +94,13 @@ return [
|
||||
'processors' => [PsrLogMessageProcessor::class],
|
||||
],
|
||||
|
||||
'jobs' => [
|
||||
'driver' => 'daily',
|
||||
'path' => storage_path('logs/job_run.log'),
|
||||
'level' => 'debug',
|
||||
'days' => 60,
|
||||
],
|
||||
|
||||
'stderr' => [
|
||||
'driver' => 'monolog',
|
||||
'level' => env('LOG_LEVEL', 'debug'),
|
||||
|
||||
@@ -133,6 +133,10 @@
|
||||
</a>
|
||||
@endforeach
|
||||
|
||||
<button type="button" onclick="reloadDataSource()" class="btn btn-sm btn-warning" style="height: 27px; position: absolute; right: 40px; top: 70px;">
|
||||
Refresh Data
|
||||
</button>
|
||||
|
||||
</div>
|
||||
|
||||
<!-- Main Wrapper -->
|
||||
@@ -146,6 +150,17 @@
|
||||
</div>
|
||||
|
||||
@yield('scripts')
|
||||
|
||||
<script>
|
||||
function reloadDataSource() {
|
||||
fetch(`/api/dashboard/reload`)
|
||||
.then(res => res.json())
|
||||
.then(data => {
|
||||
location.reload()
|
||||
});
|
||||
}
|
||||
</script>
|
||||
|
||||
</body>
|
||||
|
||||
</html>
|
||||
@@ -8,3 +8,4 @@ Route::get('/dashboard/trend', [DashboardController::class, 'trend']);
|
||||
Route::get('/dashboard/program', [DashboardController::class, 'program']);
|
||||
Route::get('/dashboard/province-circles', [DashboardController::class, 'provinceCircles']);
|
||||
Route::get('/dashboard/sentinel-map', [DashboardController::class, 'sentinelMap']);
|
||||
Route::get('/dashboard/reload', [DashboardController::class, 'fetchSourceData']);
|
||||
|
||||
@@ -2,7 +2,10 @@
|
||||
|
||||
use Illuminate\Foundation\Inspiring;
|
||||
use Illuminate\Support\Facades\Artisan;
|
||||
use Illuminate\Support\Facades\Schedule;
|
||||
|
||||
Artisan::command('inspire', function () {
|
||||
$this->comment(Inspiring::quote());
|
||||
})->purpose('Display an inspiring quote');
|
||||
|
||||
Schedule::command('app:fetch-source-data')->everyTwoHours();
|
||||
|
||||
Reference in New Issue
Block a user