add sequencing tab

2026-03-30 11:04:03 +07:00
parent 34358e3ee7
commit f0a5079b15
12 changed files with 125979 additions and 271 deletions
--- a/case_lab_results.sql
+++ b/case_lab_results.sql
--- a/dashboard/app/Http/Controllers/Api/DashboardController.php
+++ b/dashboard/app/Http/Controllers/Api/DashboardController.php
@@ -155,19 +155,49 @@ class DashboardController extends Controller
    //         return response()->json(['error' => 'Missing epiweek range'], 400);
    //     }

-        return response()->json($data);
-    }
+    //     return response()->json($data);
+    // }

-    public function fetchSourceData(){
-        try{
+    public function fetchSourceData()
+    {
+        try {
            $this->dataRetrievalService->getSurveillanceData();
            return response()->json(['message' => 'Data loaded successfully!'], 200);
-        }
-        catch (\Exception $e)
-        {
+        } catch (\Exception $e) {
            return response()->json(['error' => 'Data loaded unsuccessfully!'], 400);
        }
    }

+    /*
+    |--------------------------------------------------------------------------
+    | Sequencing Dashboard
+    |--------------------------------------------------------------------------
+    */
+
+    public function sequencing(Request $request)
+    {
+        $surveillanceId = (int) $request->query('surveillance_id');
+        $range = $this->getEpiRange($request);
+
+        if (!$surveillanceId || !$range) {
+            return response()->json(['error' => 'Missing parameters'], 400);
+        }
+
+        return response()->json([
+            'trend' => $this->service->sequencingTrend(
+                $surveillanceId,
+                $range['startYear'],
+                $range['startWeek'],
+                $range['endYear'],
+                $range['endWeek']
+            ),'distribution' => $this->service->subtypeDistribution(
+                $surveillanceId,
+                $range['startYear'],
+                $range['startWeek'],
+                $range['endYear'],
+                $range['endWeek']
+            )
+        ]);
+    }

 }
--- a/dashboard/app/Services/DashboardService.php
+++ b/dashboard/app/Services/DashboardService.php
@@ -727,28 +727,20 @@ class DashboardService
                $q->select('lab_code')
                    ->from('surveillance_cases')
                    ->where('surveillance_id', $surveillanceId)
-                    ->whereRaw(
-                        "(year_data > ? OR (year_data = ? AND week_data >= ?))",
-                        [$startYear, $startYear, $startWeek]
-                    )
-                    ->whereRaw(
-                        "(year_data < ? OR (year_data = ? AND week_data <= ?))",
-                        [$endYear, $endYear, $endWeek]
-                    );
+                    ->whereRaw("(year_data > ? OR (year_data = ? AND week_data >= ?))", [$startYear, $startYear, $startWeek])
+                    ->whereRaw("(year_data < ? OR (year_data = ? AND week_data <= ?))", [$endYear, $endYear, $endWeek]);
            })

            ->where('case_lab_results.is_positive', 1)

            ->selectRaw("
-                case_lab_results.subtype,
+                COALESCE(NULLIF(case_lab_results.subtype, ''), 'Unsubtyped') as subtype,
                COUNT(DISTINCT case_lab_results.lab_code) as total
            ")

-            ->whereNotNull('case_lab_results.subtype')
-            ->where('case_lab_results.subtype', '!=', '')
            ->where('case_lab_results.subtype', '!=', 'Positive')

-            ->groupBy('case_lab_results.subtype')
+            ->groupBy('subtype') 
            ->orderByDesc('total')
            ->get();

@@ -846,5 +838,40 @@ class DashboardService
            ->get();

    }
+    /*
+    |--------------------------------------------------------------------------
+    | sequencing trend
+    |--------------------------------------------------------------------------
+    */

+
+    public function sequencingTrend($surveillanceId, $startYear, $startWeek, $endYear, $endWeek)
+    {
+        return CaseLabResult::join(
+            'surveillance_cases',
+            'case_lab_results.lab_code',
+            '=',
+            'surveillance_cases.lab_code'
+        )
+            ->where('surveillance_cases.surveillance_id', $surveillanceId)
+
+            ->where('case_lab_results.is_positive', 1)
+
+            ->whereNotNull('subtype')
+
+            ->where(function ($q) use ($startYear, $startWeek, $endYear, $endWeek) {
+                $q->whereRaw("(year_data > ? OR (year_data = ? AND week_data >= ?))", [$startYear, $startYear, $startWeek])
+                    ->whereRaw("(year_data < ? OR (year_data = ? AND week_data <= ?))", [$endYear, $endYear, $endWeek]);
+            })
+
+            ->selectRaw("
+                surveillance_cases.week_data as period,
+                subtype,
+                COUNT(DISTINCT surveillance_cases.lab_code) as total
+            ")
+
+            ->groupBy('period', 'subtype')
+            ->orderBy('period')
+            ->get();
+    }
 }
--- a/dashboard/public/js/program.js
+++ b/dashboard/public/js/program.js
@@ -481,3 +481,5 @@ function renderSubtypeChart(rows) {
        rows.map(r => r.total)
    );
 }
+
+//Seq
--- a/dashboard/public/js/sequencing.js
+++ b/dashboard/public/js/sequencing.js
@@ -0,0 +1,238 @@
+let sequencingChart;
+document.addEventListener("DOMContentLoaded", () => {
+      const canvas = document.getElementById('sequencingChart');
+    if (!canvas) return; 
+    new DashboardFilter((startYear, startWeek, endYear, endWeek) => {
+
+        fetch(`/api/dashboard/sequencing?surveillance_id=${window.SURVEILLANCE_ID}&start_year=${startYear}&start_week=${startWeek}&end_year=${endYear}&end_week=${endWeek}`)
+            .then(res => res.json())
+            .then(data => {
+                renderSequencingChart(data.trend || []);
+                renderSequencingCountChart(data.trend || []);
+                renderSequencingPieChart(data.distribution || []);
+                renderSequencingTotalChart(data.trend || []);
+            });
+
+    });
+
+});
+
+function renderSequencingCountChart(rows) {
+
+    const ctx = document.getElementById('sequencingCountChart');
+
+    Chart.getChart('sequencingCountChart')?.destroy();
+
+    rows = processTopSubtypes(rows);
+
+    const weeks = [...new Set(rows.map(r => r.period))];
+    const subtypes = [...new Set(rows.map(r => r.subtype))];
+
+    const colors = [
+        '#2563eb', '#10b981', '#f59e0b', '#ef4444',
+        '#8b5cf6', '#14b8a6', '#f97316', '#84cc16'
+    ];
+
+    const datasets = subtypes.map((sub, i) => ({
+        label: sub,
+        data: weeks.map(w => {
+            const found = rows.find(r => r.period === w && r.subtype === sub);
+            return found ? found.total : 0;
+        }),
+        backgroundColor: colors[i % colors.length]
+    }));
+
+    new Chart(ctx, {
+        type: 'bar',
+        data: {
+            labels: weeks.map(w => `W${w}`),
+            datasets
+        },
+        options: {
+            maintainAspectRatio: false,
+            scales: {
+                x: { stacked: true },
+                y: { stacked: true }
+            },
+            plugins: {
+                legend: {
+                    display: true,
+                    position: 'bottom',
+                    align: 'center'
+                }
+            }
+
+        }
+    });
+}
+function renderSequencingPieChart(rows) {
+
+    const ctx = document.getElementById('sequencingPieChart');
+
+    Chart.getChart('sequencingPieChart')?.destroy();
+
+    const top = rows.slice(0, 8);
+
+    const labels = top.map(r => r.subtype);
+    const values = top.map(r => r.total);
+
+    new Chart(ctx, {
+        type: 'doughnut',
+        data: {
+            labels,
+            datasets: [{
+                data: values
+            }]
+        },
+        options: {
+            maintainAspectRatio: false,
+            plugins: {
+                legend: {
+                    position: 'bottom'
+                },
+            }
+
+        }
+    });
+}
+function renderSequencingTotalChart(rows) {
+
+    const ctx = document.getElementById('sequencingTotalChart');
+
+    Chart.getChart('sequencingTotalChart')?.destroy();
+
+    const totals = {};
+
+    rows.forEach(r => {
+        totals[r.period] = (totals[r.period] || 0) + Number(r.total);
+    });
+
+    const weeks = Object.keys(totals);
+    const values = Object.values(totals);
+
+    new Chart(ctx, {
+        type: 'bar',
+        data: {
+            labels: weeks.map(w => `W${w}`),
+            datasets: [{
+                label: 'Total Samples',
+                data: values,
+                backgroundColor: '#0B8F3C'
+            }]
+        },
+        options: {
+            maintainAspectRatio: false,
+            plugins: {
+                legend: { display: false }
+            },
+
+        }
+    });
+}
+function processTopSubtypes(rows) {
+
+    const totals = {};
+
+    rows.forEach(r => {
+        totals[r.subtype] = (totals[r.subtype] || 0) + Number(r.total);
+    });
+
+    const sorted = Object.entries(totals)
+        .sort((a, b) => b[1] - a[1]);
+
+    const top = sorted.slice(0, 8).map(([k]) => k);
+
+    return rows.map(r => {
+        if (!top.includes(r.subtype)) {
+            return { ...r, subtype: 'Others' };
+        }
+        return r;
+    });
+}
+function renderSequencingChart(rows) {
+
+    rows = processTopSubtypes(rows);
+
+    const ctx = document.getElementById('sequencingChart');
+
+    if (sequencingChart) {
+        sequencingChart.destroy();
+    }
+
+    const colors = [
+        '#2563eb', '#10b981', '#f59e0b', '#ef4444',
+        '#8b5cf6', '#14b8a6', '#f97316', '#84cc16',
+        '#6b7280'
+    ];
+
+    const aggregated = {};
+
+    rows.forEach(r => {
+        const key = `${r.period}_${r.subtype}`;
+        if (!aggregated[key]) {
+            aggregated[key] = { ...r };
+        } else {
+            aggregated[key].total += Number(r.total);
+        }
+    });
+
+    const cleanRows = Object.values(aggregated);
+
+    const weeks = [...new Set(cleanRows.map(r => r.period))];
+    const subtypes = [...new Set(cleanRows.map(r => r.subtype))]
+        .sort((a, b) => {
+            const sum = s => cleanRows
+                .filter(r => r.subtype === s)
+                .reduce((t, r) => t + r.total, 0);
+            return sum(b) - sum(a);
+        });
+
+    const datasets = subtypes.map((sub, i) => {
+        return {
+            label: sub,
+            data: weeks.map(w => {
+                const weekRows = cleanRows.filter(r => r.period === w);
+                const total = weekRows.reduce((s, r) => s + Number(r.total), 0);
+
+                const found = weekRows.find(r => r.subtype === sub);
+                return total ? ((found?.total || 0) / total) * 100 : 0;
+            }),
+            fill: true,
+            tension: 0.3,
+            backgroundColor: colors[i % colors.length],
+            borderColor: colors[i % colors.length]
+        };
+    });
+
+    sequencingChart = new Chart(ctx, {
+        type: 'line',
+        data: {
+            labels: weeks.map(w => `W${w}`),
+            datasets: datasets
+        },
+        options: {
+            responsive: true,
+            maintainAspectRatio: false,
+            plugins: {
+                legend: {
+                    display: true,
+                    position: 'bottom',
+                    align: 'center'
+                },
+                datalabels: {
+                    display: false
+                }
+            },
+            scales: {
+                x: { stacked: true },
+                y: {
+                    stacked: true,
+                    max: 100,
+                    ticks: {
+                        callback: v => v + '%'
+                    }
+                }
+            }
+        }
+    });
+}
--- a/dashboard/resources/views/dashboard/detail.blade.php
+++ b/dashboard/resources/views/dashboard/detail.blade.php
@@ -21,29 +21,14 @@
                </select>

                <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_week" class="form-select"></select>
-
                    <span class="mx-1">to</span>
-
                    <select id="end_year" class="form-select"></select>
                    <select id="end_week" class="form-select"></select>
-
                </div>
-
            </div>
-
        </div>
-
-
-        <!-- STATUS -->
-        <div class="alert alert-info mb-4">
-            <b>Current {{ $selected->code }} Status:</b>
-            <span id="activityStatus">Loading...</span>
-        </div>
-
-
        <!-- SUMMARY CARDS -->
        <div class="row g-3 mb-4">

--- a/dashboard/resources/views/dashboard/index.blade.php
+++ b/dashboard/resources/views/dashboard/index.blade.php
@@ -1,223 +0,0 @@
-<!DOCTYPE html>
-<html>
-<head>
-    <title>NRML Surveillance Dashboard</title>
-
-    <!-- Bootstrap 5 -->
-    <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet">
-
-    <!-- Chart.js -->
-    <script src="https://cdn.jsdelivr.net/npm/chart.js"></script>
-</head>
-<body class="bg-light">
-
-<div class="container-fluid py-4">
-
-    <h3 class="mb-4">NRML Surveillance Dashboard</h3>
-
-    <!-- Filters -->
-    <div class="card mb-4">
-        <div class="card-body row g-3 align-items-end">
-
-            <div class="col-md-3">
-                <label class="form-label">Surveillance Program</label>
-                <select id="surveillance_id" class="form-select">
-                    @foreach($programs as $program)
-                        <option value="{{ $program->id }}">
-                            {{ $program->code }} - {{ $program->name_en }}
-                        </option>
-                    @endforeach
-                </select>
-            </div>
-
-            <div class="col-md-2">
-                <label class="form-label">Period</label>
-                <select id="period_type" class="form-select">
-                    <option value="week">Epiweek</option>
-                    <option value="month">Month</option>
-                    <option value="year">Year</option>
-                </select>
-            </div>
-
-            <div class="col-md-2">
-                <label class="form-label">Date From</label>
-                <input type="date" id="date_from" class="form-control">
-            </div>
-
-            <div class="col-md-2">
-                <label class="form-label">Date To</label>
-                <input type="date" id="date_to" class="form-control">
-            </div>
-
-            <div class="col-md-2">
-                <button onclick="loadDashboard()" class="btn btn-primary w-100">
-                    Apply
-                </button>
-            </div>
-
-        </div>
-    </div>
-
-    <!-- Summary Cards -->
-    <div class="row" id="summary_cards"></div>
-
-    <!-- Trend Chart -->
-    <div class="card mt-4">
-        <div class="card-body">
-            <h5>Epidemic Trend</h5>
-            <canvas id="trendChart"></canvas>
-        </div>
-    </div>
-
-    <!-- Province Table -->
-    <div class="card mt-4">
-        <div class="card-body">
-            <h5>Cases by Province</h5>
-            <table class="table table-bordered" id="provinceTable">
-                <thead>
-                    <tr>
-                        <th>Province</th>
-                        <th>Total Cases</th>
-                    </tr>
-                </thead>
-                <tbody></tbody>
-            </table>
-        </div>
-    </div>
-
-</div>
-
-<script>
-
-let trendChart;
-
-function loadDashboard() {
-
-    const surveillanceId = document.getElementById('surveillance_id').value;
-    const periodType = document.getElementById('period_type').value;
-    const dateFrom = document.getElementById('date_from').value;
-    const dateTo = document.getElementById('date_to').value;
-
-    loadSummary(dateFrom, dateTo);
-    loadTrend(periodType, dateFrom, dateTo);
-    loadProvince(surveillanceId, dateFrom, dateTo);
-}
-
-function loadSummary(dateFrom, dateTo) {
-
-    fetch(`/api/dashboard/summary?date_from=${dateFrom}&date_to=${dateTo}`)
-        .then(res => res.json())
-        .then(data => {
-
-            let html = '';
-
-            data.forEach(item => {
-                html += `
-                    <div class="col-md-3 mb-3">
-                        <div class="card shadow-sm">
-                            <div class="card-body">
-                                <h6>${item.code}</h6>
-                                <h4>${item.current_total}</h4>
-                                <small class="${item.percent_change >= 0 ? 'text-success' : 'text-danger'}">
-                                    ${item.percent_change}%
-                                </small>
-                            </div>
-                        </div>
-                    </div>
-                `;
-            });
-
-            document.getElementById('summary_cards').innerHTML = html;
-        });
-}
-
-function loadTrend(periodType, dateFrom, dateTo) {
-
-    fetch(`/api/dashboard/trend?period_type=${periodType}&date_from=${dateFrom}&date_to=${dateTo}`)
-        .then(res => res.json())
-        .then(data => {
-
-            if (trendChart) trendChart.destroy();
-
-            const labelsSet = new Set();
-
-            Object.values(data).forEach(program => {
-                program.forEach(row => {
-                    labelsSet.add(`${row.year ?? ''}-${row.period}`);
-                });
-            });
-
-            const labels = Array.from(labelsSet).sort();
-
-            const datasets = [];
-
-            const colors = {
-                SARI: 'red',
-                ILI: 'blue',
-                LBM: 'green'
-            };
-
-            Object.keys(data).forEach(code => {
-
-                const values = labels.map(label => {
-                    const found = data[code].find(row =>
-                        `${row.year ?? ''}-${row.period}` === label
-                    );
-                    return found ? found.total : 0;
-                });
-
-                datasets.push({
-                    label: code,
-                    data: values,
-                    borderColor: colors[code] || 'black',
-                    fill: false
-                });
-            });
-
-            trendChart = new Chart(document.getElementById('trendChart'), {
-                type: 'line',
-                data: {
-                    labels: labels,
-                    datasets: datasets
-                }
-            });
-        });
-}
-
-function loadProvince(surveillanceId, dateFrom, dateTo) {
-
-    fetch(`/api/dashboard/province?surveillance_id=${surveillanceId}&date_from=${dateFrom}&date_to=${dateTo}`)
-        .then(res => res.json())
-        .then(data => {
-
-            let html = '';
-
-            data.forEach(item => {
-                html += `
-                    <tr>
-                        <td>${item.site_province_name}</td>
-                        <td>${item.total}</td>
-                    </tr>
-                `;
-            });
-
-            document.querySelector('#provinceTable tbody').innerHTML = html;
-        });
-}
-
-document.addEventListener('DOMContentLoaded', function() {
-
-    const today = new Date().toISOString().split('T')[0];
-    const past = new Date();
-    past.setDate(past.getDate() - 30);
-
-    document.getElementById('date_from').value = past.toISOString().split('T')[0];
-    document.getElementById('date_to').value = today;
-
-    loadDashboard();
-});
-
-</script>
-
-</body>
-</html>
--- a/dashboard/resources/views/dashboard/sequencing.blade.php
+++ b/dashboard/resources/views/dashboard/sequencing.blade.php
@@ -0,0 +1,69 @@
+@extends('layouts.app')
+
+@section('content')
+
+    <div class="container-fluid">
+
+        <div class="d-flex justify-content-between mb-3">
+
+            <h4 class="fw-bold">Sequencing Analysis</h4>
+
+            <div class="d-flex align-items-center gap-2">
+
+                <select id="trend_range" class="form-select w-auto">
+                    <option value="8" selected>Last 8 weeks</option>
+                    <option value="12">Last 12 weeks</option>
+                    <option value="26">Last 26 weeks</option>
+                    <option value="custom">Custom range</option>
+                </select>
+
+                <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_week" class="form-select"></select>
+                    <span class="mx-1">to</span>
+                    <select id="end_year" class="form-select"></select>
+                    <select id="end_week" class="form-select"></select>
+                </div>
+            </div>
+        </div>
+
+        <div class="card">
+            <div class="card-body" style="height:600px;">
+                <canvas id="sequencingChart"></canvas>
+            </div>
+        </div>
+        <div class="row mt-3">
+
+            <!-- Counts -->
+            <div class="col-md-6">
+                <div class="card">
+                    <div class="card-body" style="height:600px;">
+                        <h6 class="fw-bold">Lineage Counts Over Time</h6>
+                        <canvas id="sequencingCountChart"></canvas>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Distribution -->
+            <div class="col-md-6">
+                <div class="card">
+                    <div class="card-body" style="height:600px;">
+                        <h6 class="fw-bold">Total Sequenced Samples Over Time</h6>
+                        <canvas id="sequencingTotalChart" style="height: 550px;"></canvas>
+                    </div>
+                </div>
+            </div>
+
+        </div>
+
+    </div>
+
+@endsection
+
+@section('scripts')
+    <script>
+        window.SURVEILLANCE_ID = 6; 
+    </script>
+
+    <script src="/js/sequencing.js"></script>
+@endsection
--- a/dashboard/resources/views/layouts/app.blade.php
+++ b/dashboard/resources/views/layouts/app.blade.php
@@ -40,7 +40,7 @@
            display: flex;
            background: white;
            border-bottom: 1px solid #dcdcdc;
-            padding-left: 15px;
+            padding: 0 20px;
            position: sticky;
            top: 0;
            z-index: 1000;
@@ -49,6 +49,17 @@
        }

        /* NAV ITEMS */
+        .btn-theme-outline {
+            background-color: #fff;
+            color: #0B8F3C;
+            border: 1px solid #0B8F3C;
+        }
+
+        .btn-theme-outline:hover {
+            background-color: #cce0d4;
+            color: #0B8F3C;
+        }
+
        .nav-item {
            padding: 12px 18px;
            text-decoration: none;
@@ -92,7 +103,7 @@
        }

        .card {
-            border-radius: 10px;
+            border-radius: 0px !important;
            border: 1px solid #E5E7EB;
        }

@@ -112,9 +123,7 @@
        </div>

        <div class="ms-auto small">
-            Last update: 12:05 |
-            Data latency: 5–10 min |
-            User: National - Read Only
+            Last update: 12:05 | 2026-03-15
        </div>

    </div>
@@ -126,16 +135,34 @@
            Overview
        </a>

-        @foreach($programs as $program)
+        <!-- @foreach($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->where('code', '!=', 'NDS') as $program)
+
+            @if($program->code === 'SEQ')
+                        
+                <a href="/dashboard/seq"
+                    class="nav-item {{ request()->is('dashboard/seq') ? 'active-tab' : '' }}">
+                    SEQ
+                </a>
+            @else
+                <a href="/dashboard/{{ strtolower($program->code) }}"
+                    class="nav-item {{ request()->is('dashboard/' . strtolower($program->code)) ? 'active-tab' : '' }}">
+                    {{ $program->code }}
+                </a>
+            @endif
+
        @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 class="ms-auto d-flex align-items-center gap-4 pe-3">
+            <button type="button" onclick="reloadDataSource()" class="btn btn-sm btn-theme-outline">
+                Refresh Data
+            </button>
+        </div>

    </div>

--- a/dashboard/routes/api.php
+++ b/dashboard/routes/api.php
@@ -9,3 +9,4 @@ 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']);
+Route::get('/dashboard/sequencing', [DashboardController::class, 'sequencing']);
--- a/dashboard/routes/web.php
+++ b/dashboard/routes/web.php
@@ -9,9 +9,9 @@ Route::get('/', function () {
 });


-
+Route::get('/dashboard/seq', function () {
+    return view('dashboard.sequencing');
+});
 Route::get('/dashboard', [DashboardController::class, 'overview']);
 Route::get('/dashboard/{code}', [DashboardController::class, 'detail']);
-Route::get('/test-change', function () {
-    return "TEST_CHANGE_WORKING";
-});
+
--- a/surveillance_cases.sql
+++ b/surveillance_cases.sql