change charts corlor, update AFI

dashboard/app/Http/Controllers/Auth/AuthenticatedSessionController.php

@@ -0,0 +1,67 @@
+<?php
+
+namespace App\Http\Controllers\Auth;
+
+use App\Http\Controllers\Controller;
+use App\Http\Requests\Auth\LoginRequest;
+use Illuminate\Http\RedirectResponse;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Auth;
+use Illuminate\View\View;
+
+class AuthenticatedSessionController extends Controller
+{
+    /**
+     * Display the login view.
+     */
+    public function create(): View
+    {
+        return view('auth.login');
+    }
+
+    /**
+     * Handle an incoming authentication request.
+     */
+    public function store(LoginRequest $request): RedirectResponse
+    {
+        $request->authenticate();
+
+        $request->session()->regenerate();
+        if (!Auth::user()->is_active) {
+
+            Auth::logout();
+
+            return back()->withErrors([
+                'email' => 'Account is disabled.',
+            ]);
+
+        }
+        Auth::user()->update([
+            'last_login_at' => now()
+        ]);
+        activity_log(
+            'login',
+            'User logged in'
+        );
+
+        return redirect()->intended(route('dashboard', absolute: false));
+    }
+
+    /**
+     * Destroy an authenticated session.
+     */
+    public function destroy(Request $request): RedirectResponse
+    {
+        Auth::guard('web')->logout();
+
+        $request->session()->invalidate();
+
+        $request->session()->regenerateToken();
+        activity_log(
+            'logout',
+            'User logged out'
+        );
+
+        return redirect('/');
+    }
+}

dashboard/app/Http/Controllers/Auth/ConfirmablePasswordController.php

@@ -0,0 +1,40 @@
+<?php
+
+namespace App\Http\Controllers\Auth;
+
+use App\Http\Controllers\Controller;
+use Illuminate\Http\RedirectResponse;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Auth;
+use Illuminate\Validation\ValidationException;
+use Illuminate\View\View;
+
+class ConfirmablePasswordController extends Controller
+{
+    /**
+     * Show the confirm password view.
+     */
+    public function show(): View
+    {
+        return view('auth.confirm-password');
+    }
+
+    /**
+     * Confirm the user's password.
+     */
+    public function store(Request $request): RedirectResponse
+    {
+        if (! Auth::guard('web')->validate([
+            'email' => $request->user()->email,
+            'password' => $request->password,
+        ])) {
+            throw ValidationException::withMessages([
+                'password' => __('auth.password'),
+            ]);
+        }
+
+        $request->session()->put('auth.password_confirmed_at', time());
+
+        return redirect()->intended(route('dashboard', absolute: false));
+    }
+}

dashboard/app/Http/Controllers/Auth/EmailVerificationNotificationController.php

@@ -0,0 +1,24 @@
+<?php
+
+namespace App\Http\Controllers\Auth;
+
+use App\Http\Controllers\Controller;
+use Illuminate\Http\RedirectResponse;
+use Illuminate\Http\Request;
+
+class EmailVerificationNotificationController extends Controller
+{
+    /**
+     * Send a new email verification notification.
+     */
+    public function store(Request $request): RedirectResponse
+    {
+        if ($request->user()->hasVerifiedEmail()) {
+            return redirect()->intended(route('dashboard', absolute: false));
+        }
+
+        $request->user()->sendEmailVerificationNotification();
+
+        return back()->with('status', 'verification-link-sent');
+    }
+}

dashboard/app/Http/Controllers/Auth/EmailVerificationPromptController.php

@@ -0,0 +1,21 @@
+<?php
+
+namespace App\Http\Controllers\Auth;
+
+use App\Http\Controllers\Controller;
+use Illuminate\Http\RedirectResponse;
+use Illuminate\Http\Request;
+use Illuminate\View\View;
+
+class EmailVerificationPromptController extends Controller
+{
+    /**
+     * Display the email verification prompt.
+     */
+    public function __invoke(Request $request): RedirectResponse|View
+    {
+        return $request->user()->hasVerifiedEmail()
+                    ? redirect()->intended(route('dashboard', absolute: false))
+                    : view('auth.verify-email');
+    }
+}

dashboard/app/Http/Controllers/Auth/NewPasswordController.php

@@ -0,0 +1,63 @@
+<?php
+
+namespace App\Http\Controllers\Auth;
+
+use App\Http\Controllers\Controller;
+use App\Models\User;
+use Illuminate\Auth\Events\PasswordReset;
+use Illuminate\Http\RedirectResponse;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Hash;
+use Illuminate\Support\Facades\Password;
+use Illuminate\Support\Str;
+use Illuminate\Validation\Rules;
+use Illuminate\Validation\ValidationException;
+use Illuminate\View\View;
+
+class NewPasswordController extends Controller
+{
+    /**
+     * Display the password reset view.
+     */
+    public function create(Request $request): View
+    {
+        return view('auth.reset-password', ['request' => $request]);
+    }
+
+    /**
+     * Handle an incoming new password request.
+     *
+     * @throws ValidationException
+     */
+    public function store(Request $request): RedirectResponse
+    {
+        $request->validate([
+            'token' => ['required'],
+            'email' => ['required', 'email'],
+            'password' => ['required', 'confirmed', Rules\Password::defaults()],
+        ]);
+
+        // Here we will attempt to reset the user's password. If it is successful we
+        // will update the password on an actual user model and persist it to the
+        // database. Otherwise we will parse the error and return the response.
+        $status = Password::reset(
+            $request->only('email', 'password', 'password_confirmation', 'token'),
+            function (User $user) use ($request) {
+                $user->forceFill([
+                    'password' => Hash::make($request->password),
+                    'remember_token' => Str::random(60),
+                ])->save();
+
+                event(new PasswordReset($user));
+            }
+        );
+
+        // If the password was successfully reset, we will redirect the user back to
+        // the application's home authenticated view. If there is an error we can
+        // redirect them back to where they came from with their error message.
+        return $status == Password::PASSWORD_RESET
+                    ? redirect()->route('login')->with('status', __($status))
+                    : back()->withInput($request->only('email'))
+                        ->withErrors(['email' => __($status)]);
+    }
+}

dashboard/app/Http/Controllers/Auth/PasswordController.php

@@ -0,0 +1,29 @@
+<?php
+
+namespace App\Http\Controllers\Auth;
+
+use App\Http\Controllers\Controller;
+use Illuminate\Http\RedirectResponse;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Hash;
+use Illuminate\Validation\Rules\Password;
+
+class PasswordController extends Controller
+{
+    /**
+     * Update the user's password.
+     */
+    public function update(Request $request): RedirectResponse
+    {
+        $validated = $request->validateWithBag('updatePassword', [
+            'current_password' => ['required', 'current_password'],
+            'password' => ['required', Password::defaults(), 'confirmed'],
+        ]);
+
+        $request->user()->update([
+            'password' => Hash::make($validated['password']),
+        ]);
+
+        return back()->with('status', 'password-updated');
+    }
+}

dashboard/app/Http/Controllers/Auth/PasswordResetLinkController.php

@@ -0,0 +1,45 @@
+<?php
+
+namespace App\Http\Controllers\Auth;
+
+use App\Http\Controllers\Controller;
+use Illuminate\Http\RedirectResponse;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Password;
+use Illuminate\Validation\ValidationException;
+use Illuminate\View\View;
+
+class PasswordResetLinkController extends Controller
+{
+    /**
+     * Display the password reset link request view.
+     */
+    public function create(): View
+    {
+        return view('auth.forgot-password');
+    }
+
+    /**
+     * Handle an incoming password reset link request.
+     *
+     * @throws ValidationException
+     */
+    public function store(Request $request): RedirectResponse
+    {
+        $request->validate([
+            'email' => ['required', 'email'],
+        ]);
+
+        // We will send the password reset link to this user. Once we have attempted
+        // to send the link, we will examine the response then see the message we
+        // need to show to the user. Finally, we'll send out a proper response.
+        $status = Password::sendResetLink(
+            $request->only('email')
+        );
+
+        return $status == Password::RESET_LINK_SENT
+                    ? back()->with('status', __($status))
+                    : back()->withInput($request->only('email'))
+                        ->withErrors(['email' => __($status)]);
+    }
+}

dashboard/app/Http/Controllers/Auth/RegisteredUserController.php

@@ -0,0 +1,51 @@
+<?php
+
+namespace App\Http\Controllers\Auth;
+
+use App\Http\Controllers\Controller;
+use App\Models\User;
+use Illuminate\Auth\Events\Registered;
+use Illuminate\Http\RedirectResponse;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Auth;
+use Illuminate\Support\Facades\Hash;
+use Illuminate\Validation\Rules;
+use Illuminate\Validation\ValidationException;
+use Illuminate\View\View;
+
+class RegisteredUserController extends Controller
+{
+    /**
+     * Display the registration view.
+     */
+    public function create(): View
+    {
+        return view('auth.register');
+    }
+
+    /**
+     * Handle an incoming registration request.
+     *
+     * @throws ValidationException
+     */
+    public function store(Request $request): RedirectResponse
+    {
+        $request->validate([
+            'name' => ['required', 'string', 'max:255'],
+            'email' => ['required', 'string', 'lowercase', 'email', 'max:255', 'unique:'.User::class],
+            'password' => ['required', 'confirmed', Rules\Password::defaults()],
+        ]);
+
+        $user = User::create([
+            'name' => $request->name,
+            'email' => $request->email,
+            'password' => Hash::make($request->password),
+        ]);
+
+        event(new Registered($user));
+
+        Auth::login($user);
+
+        return redirect(route('dashboard', absolute: false));
+    }
+}

dashboard/app/Http/Controllers/Auth/VerifyEmailController.php

@@ -0,0 +1,27 @@
+<?php
+
+namespace App\Http\Controllers\Auth;
+
+use App\Http\Controllers\Controller;
+use Illuminate\Auth\Events\Verified;
+use Illuminate\Foundation\Auth\EmailVerificationRequest;
+use Illuminate\Http\RedirectResponse;
+
+class VerifyEmailController extends Controller
+{
+    /**
+     * Mark the authenticated user's email address as verified.
+     */
+    public function __invoke(EmailVerificationRequest $request): RedirectResponse
+    {
+        if ($request->user()->hasVerifiedEmail()) {
+            return redirect()->intended(route('dashboard', absolute: false).'?verified=1');
+        }
+
+        if ($request->user()->markEmailAsVerified()) {
+            event(new Verified($request->user()));
+        }
+
+        return redirect()->intended(route('dashboard', absolute: false).'?verified=1');
+    }
+}

dashboard/app/Http/Controllers/ProfileController.php

@@ -0,0 +1,60 @@
+<?php
+
+namespace App\Http\Controllers;
+
+use App\Http\Requests\ProfileUpdateRequest;
+use Illuminate\Http\RedirectResponse;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Auth;
+use Illuminate\Support\Facades\Redirect;
+use Illuminate\View\View;
+
+class ProfileController extends Controller
+{
+    /**
+     * Display the user's profile form.
+     */
+    public function edit(Request $request): View
+    {
+        return view('profile.edit', [
+            'user' => $request->user(),
+        ]);
+    }
+
+    /**
+     * Update the user's profile information.
+     */
+    public function update(ProfileUpdateRequest $request): RedirectResponse
+    {
+        $request->user()->fill($request->validated());
+
+        if ($request->user()->isDirty('email')) {
+            $request->user()->email_verified_at = null;
+        }
+
+        $request->user()->save();
+
+        return Redirect::route('profile.edit')->with('status', 'profile-updated');
+    }
+
+    /**
+     * Delete the user's account.
+     */
+    public function destroy(Request $request): RedirectResponse
+    {
+        $request->validateWithBag('userDeletion', [
+            'password' => ['required', 'current_password'],
+        ]);
+
+        $user = $request->user();
+
+        Auth::logout();
+
+        $user->delete();
+
+        $request->session()->invalidate();
+        $request->session()->regenerateToken();
+
+        return Redirect::to('/');
+    }
+}

dashboard/app/Http/Middleware/RoleMiddleware.php

@@ -0,0 +1,28 @@
+<?php
+
+namespace App\Http\Middleware;
+
+use Closure;
+use Illuminate\Http\Request;
+use Symfony\Component\HttpFoundation\Response;
+
+class RoleMiddleware
+{
+    /**
+     * Handle an incoming request.
+     *
+     * @param  \Closure(\Illuminate\Http\Request): (\Symfony\Component\HttpFoundation\Response)  $next
+     */
+    public function handle($request, Closure $next, $role)
+    {
+        if (!auth()->check()) {
+            return redirect('/login');
+        }
+
+        if (auth()->user()->role !== $role) {
+            abort(403);
+        }
+
+        return $next($request);
+    }
+}

dashboard/app/Http/Requests/Auth/LoginRequest.php

@@ -0,0 +1,86 @@
+<?php
+
+namespace App\Http\Requests\Auth;
+
+use Illuminate\Auth\Events\Lockout;
+use Illuminate\Contracts\Validation\ValidationRule;
+use Illuminate\Foundation\Http\FormRequest;
+use Illuminate\Support\Facades\Auth;
+use Illuminate\Support\Facades\RateLimiter;
+use Illuminate\Support\Str;
+use Illuminate\Validation\ValidationException;
+
+class LoginRequest extends FormRequest
+{
+    /**
+     * Determine if the user is authorized to make this request.
+     */
+    public function authorize(): bool
+    {
+        return true;
+    }
+
+    /**
+     * Get the validation rules that apply to the request.
+     *
+     * @return array<string, ValidationRule|array<mixed>|string>
+     */
+    public function rules(): array
+    {
+        return [
+            'email' => ['required', 'string', 'email'],
+            'password' => ['required', 'string'],
+        ];
+    }
+
+    /**
+     * Attempt to authenticate the request's credentials.
+     *
+     * @throws ValidationException
+     */
+    public function authenticate(): void
+    {
+        $this->ensureIsNotRateLimited();
+
+        if (! Auth::attempt($this->only('email', 'password'), $this->boolean('remember'))) {
+            RateLimiter::hit($this->throttleKey());
+
+            throw ValidationException::withMessages([
+                'email' => trans('auth.failed'),
+            ]);
+        }
+
+        RateLimiter::clear($this->throttleKey());
+    }
+
+    /**
+     * Ensure the login request is not rate limited.
+     *
+     * @throws ValidationException
+     */
+    public function ensureIsNotRateLimited(): void
+    {
+        if (! RateLimiter::tooManyAttempts($this->throttleKey(), 5)) {
+            return;
+        }
+
+        event(new Lockout($this));
+
+        $seconds = RateLimiter::availableIn($this->throttleKey());
+
+        throw ValidationException::withMessages([
+            'email' => trans('auth.throttle', [
+                'seconds' => $seconds,
+                'minutes' => ceil($seconds / 60),
+            ]),
+        ]);
+    }
+
+    /**
+     * Get the rate limiting throttle key for the request.
+     */
+    public function throttleKey(): string
+    {
+        return Str::transliterate(Str::lower($this->string('email')).'|'.$this->ip());
+    }
+}

dashboard/app/Http/Requests/ProfileUpdateRequest.php

@@ -0,0 +1,31 @@
+<?php
+
+namespace App\Http\Requests;
+
+use App\Models\User;
+use Illuminate\Contracts\Validation\ValidationRule;
+use Illuminate\Foundation\Http\FormRequest;
+use Illuminate\Validation\Rule;
+
+class ProfileUpdateRequest extends FormRequest
+{
+    /**
+     * Get the validation rules that apply to the request.
+     *
+     * @return array<string, ValidationRule|array<mixed>|string>
+     */
+    public function rules(): array
+    {
+        return [
+            'name' => ['required', 'string', 'max:255'],
+            'email' => [
+                'required',
+                'string',
+                'lowercase',
+                'email',
+                'max:255',
+                Rule::unique(User::class)->ignore($this->user()->id),
+            ],
+        ];
+    }
+}

dashboard/app/Models/ActivityLog.php

@@ -0,0 +1,18 @@
+<?php
+
+namespace App\Models;
+
+use Illuminate\Database\Eloquent\Model;
+
+class ActivityLog extends Model
+{
+    protected $fillable = [
+        'user_id',
+        'action',
+        'description',
+        'ip_address',
+        'user_agent',
+    ];
+
+    public $timestamps = false;
+}

dashboard/app/Services/DashboardService.php

@@ -5,6 +5,7 @@ namespace App\Services;
 use App\Models\Surveillance;
 use App\Models\SurveillanceCase;
 use App\Models\CaseLabResult;
+use SebastianBergmann\CodeCoverage\Report\Xml\Totals;
 
 class DashboardService
 {
@@ -71,78 +72,365 @@ class DashboardService
     |--------------------------------------------------------------------------
     */
 
-    public function afiTrend($surveillanceId, $startYear, $startWeek, $endYear, $endWeek)
-    {
-        return CaseLabResult::join(
+    public function afiTrend(
+        $surveillanceId,
+        $startYear,
+        $startWeek,
+        $endYear,
+        $endWeek
+    ) {
+
+        $rows = CaseLabResult::join(
             'surveillance_cases',
             'case_lab_results.lab_code',
             '=',
             'surveillance_cases.lab_code'
         )
 
-            ->where('surveillance_cases.surveillance_id', $surveillanceId)
+            ->where(
+                'surveillance_cases.surveillance_id',
+                $surveillanceId
+            )
 
             ->where(function ($q) use ($startYear, $startWeek, $endYear, $endWeek) {
+
                 $q->whereRaw(
-                    "(year_data > ? OR (year_data = ? AND week_data >= ?))",
+                    "(year_data > ?
+                OR (
+                    year_data = ?
+                    AND week_data >= ?
+                )
+            )",
                     [$startYear, $startYear, $startWeek]
                 )
+
                     ->whereRaw(
-                        "(year_data < ? OR (year_data = ? AND week_data <= ?))",
+                        "(year_data < ?
+                OR (
+                    year_data = ?
+                    AND week_data <= ?
+                )
+            )",
                         [$endYear, $endYear, $endWeek]
                     );
             })
 
-            ->where(function ($q) {
-                $q->whereNotNull('case_lab_results.pathogen_name')
-                    ->orWhereRaw("LOWER(case_lab_results.indicator) LIKE '%serum%'");
-            })
+            ->where('case_lab_results.is_positive', 1)
+
+            ->whereNotNull('case_lab_results.pathogen_name')
+
             ->selectRaw("
-                surveillance_cases.year_data as year,
-                surveillance_cases.week_data as period,
 
-                CASE
-                    WHEN LOWER(case_lab_results.pathogen_name) LIKE '%influenza%'
-                        THEN 'Influenza'
-                    ELSE case_lab_results.pathogen_name
-                END as pathogen,
+        surveillance_cases.year_data as year,
+        surveillance_cases.week_data as period,
 
-                CASE
-                    WHEN LOWER(case_lab_results.indicator) LIKE '%serum%' THEN 'Serum'
-                    ELSE 'PCR'
-                END as test_type,
-                COUNT(case_lab_results.id) as total_tests,
-                COUNT(DISTINCT surveillance_cases.lab_code) as total_tested,
+        case_lab_results.pathogen_name as pathogen,
+        case_lab_results.subtype,
 
-                COUNT(CASE
-                    WHEN case_lab_results.is_positive = 1
-                    THEN surveillance_cases.lab_code
-                END) as total_positive
-            ")
+        CASE
+
+            WHEN LOWER(case_lab_results.pathogen_name)
+                LIKE '%influenza%'
+
+                OR LOWER(case_lab_results.pathogen_name)
+                LIKE '%covid%'
+
+                OR LOWER(case_lab_results.pathogen_name)
+                LIKE '%sars-cov%'
+
+                THEN 'section_1'
+
+            WHEN LOWER(case_lab_results.indicator)
+                LIKE '%serum%'
+
+                THEN 'section_3'
+
+            ELSE 'section_2'
+
+        END as afi_section,
+
+        COUNT(DISTINCT surveillance_cases.lab_code)
+            as total_positive
+
+    ")
 
             ->groupBy(
                 'surveillance_cases.year_data',
                 'surveillance_cases.week_data',
                 'pathogen',
-                'test_type'
+                'subtype',
+                'afi_section'
             )
+
             ->orderBy('surveillance_cases.year_data')
             ->orderBy('surveillance_cases.week_data')
 
-            ->get()
-            ->map(function ($r) {
+            ->get();
+
+        return [
+
+            'section_1' => $rows
+                ->where('afi_section', 'section_1')
+                ->values(),
+
+            'section_2' => $rows
+                ->where('afi_section', 'section_2')
+                ->values(),
+
+            'section_3' => $rows
+                ->where('afi_section', 'section_3')
+                ->values()
+
+        ];
+    }
+
+    public function afiCaseTrend(
+        $surveillanceId,
+        $startYear,
+        $startWeek,
+        $endYear,
+        $endWeek
+    ) {
+
+        /*
+        |--------------------------------------------------------------------------
+        | TOTAL CASES BY SECTION
+        |--------------------------------------------------------------------------
+        |
+        | Count DISTINCT lab_code PER SECTION
+        |
+        | section_1 = Influenza / Covid
+        | section_2 = PCR
+        | section_3 = Serum
+        |
+        */
+
+        $totalCases = CaseLabResult::join(
+            'surveillance_cases',
+            'case_lab_results.lab_code',
+            '=',
+            'surveillance_cases.lab_code'
+        )
+
+            ->where(
+                'surveillance_cases.surveillance_id',
+                $surveillanceId
+            )
+
+            ->where(function ($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, $endWeek]
+                    );
+            })
+
+            ->selectRaw("
+
+            surveillance_cases.year_data as year,
+            surveillance_cases.week_data as period,
+
+            CASE
+
+                WHEN LOWER(case_lab_results.indicator)
+                    LIKE '%influenza%'
+
+                    OR LOWER(case_lab_results.indicator)
+                    LIKE '%covid%'
+
+                    THEN 'section_1'
+
+                WHEN LOWER(case_lab_results.indicator)
+                    LIKE '%serum%'
+
+                    THEN 'section_3'
+
+                ELSE 'section_2'
+
+            END as afi_section,
+
+            COUNT(DISTINCT case_lab_results.lab_code)
+                as total_cases
+
+        ")
+
+            ->groupBy(
+                'surveillance_cases.year_data',
+                'surveillance_cases.week_data',
+                'afi_section'
+            )
+
+            ->get()
+
+            ->keyBy(
+                fn($r) =>
+                $r->year .
+                '-' .
+                $r->period .
+                '-' .
+                $r->afi_section
+            );
+
+        /*
+        |--------------------------------------------------------------------------
+        | POSITIVE RESULTS
+        |--------------------------------------------------------------------------
+        */
+
+        $rows = CaseLabResult::join(
+            'surveillance_cases',
+            'case_lab_results.lab_code',
+            '=',
+            'surveillance_cases.lab_code'
+        )
+
+            ->where(
+                'surveillance_cases.surveillance_id',
+                $surveillanceId
+            )
+
+            ->where(function ($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, $endWeek]
+                    );
+            })
+
+            ->where('case_lab_results.is_positive', 1)
+
+            ->whereNotNull('case_lab_results.pathogen_name')
+
+            ->selectRaw("
+
+            surveillance_cases.year_data as year,
+            surveillance_cases.week_data as period,
+
+            CASE
+
+                WHEN LOWER(case_lab_results.pathogen_name)
+                    LIKE '%influenza%'
+                    THEN 'Influenza'
+
+                ELSE case_lab_results.pathogen_name
+
+            END as pathogen,
+
+            case_lab_results.subtype,
+
+            CASE
+
+                WHEN LOWER(case_lab_results.indicator)
+                    LIKE '%influenza%'
+
+                    OR LOWER(case_lab_results.indicator)
+                    LIKE '%covid%'
+
+                    THEN 'section_1'
+
+                WHEN LOWER(case_lab_results.indicator)
+                    LIKE '%serum%'
+
+                    THEN 'section_3'
+
+                ELSE 'section_2'
+
+            END as afi_section,
+
+            COUNT(DISTINCT case_lab_results.lab_code)
+                as total_positive
+
+        ")
+
+            ->groupBy(
+                'surveillance_cases.year_data',
+                'surveillance_cases.week_data',
+                'pathogen',
+                'subtype',
+                'afi_section'
+            )
+
+            ->orderBy('surveillance_cases.year_data')
+
+            ->orderBy('surveillance_cases.week_data')
+
+            ->get()
+
+            ->map(function ($r) use ($totalCases) {
+
+                $key =
+                    $r->year .
+                    '-' .
+                    $r->period .
+                    '-' .
+                    $r->afi_section;
+
+                $r->total_cases =
+                    $totalCases[$key]->total_cases ?? 0;
+
+                $r->positivity_rate =
+                    $r->total_cases > 0
+
+                    ? round(
+                        ($r->total_positive / $r->total_cases) * 100,
+                        1
+                    )
 
-                $r->positivity_rate = $r->total_tested > 0
-                    ? round(($r->total_positive / $r->total_tested) * 100, 1)
                     : 0;
 
                 return $r;
             });
+
+        return [
+
+            'section_1' => $rows
+                ->where('afi_section', 'section_1')
+                ->values(),
+
+            'section_2' => $rows
+                ->where('afi_section', 'section_2')
+                ->values(),
+
+            'section_3' => $rows
+                ->where('afi_section', 'section_3')
+                ->values()
+
+        ];
     }
     public function programSummaryFast($surveillanceId, $year = null, $week = null, $dateFrom = null, $dateTo = null)
     {
         $query = SurveillanceCase::leftJoin(
-            'case_lab_results', 
+            'case_lab_results',
             'surveillance_cases.lab_code',
             '=',
             'case_lab_results.lab_code'
@@ -309,90 +597,7 @@ class DashboardService
     |--------------------------------------------------------------------------
     */
 
-    public function programDashboardData($surveillanceId, $startYear, $startWeek, $endYear, $endWeek)
-    {
 
-        return [
-
-            'summary' => $this->programSummary(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-
-            'trend' => $this->trendSingleProgram(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-
-            'pathogen_distribution' => $this->pathogenDistribution(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-
-            'age_distribution' => $this->ageDistribution(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-
-            'sex_distribution' => $this->sexDistribution(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-            'afi_trend' => $this->afiTrend(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-
-            'province_distribution' => $this->provinceProgram(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-            'virus_trend' => $this->virusTrend(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-            'subtype_distribution' => $this->subtypeDistribution(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-            'sentinel_sites' => $this->sentinelSites(
-                $surveillanceId,
-                $startYear,
-                $startWeek,
-                $endYear,
-                $endWeek
-            ),
-
-        ];
-
-    }
 
 
 
@@ -610,7 +815,7 @@ class DashboardService
             ->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
                     ]
@@ -881,13 +1086,13 @@ class DashboardService
             })
 
             ->where('case_lab_results.is_positive', 1)
+            ->where('case_lab_results.indicator', 'Influenza')
 
             ->selectRaw("
-                COALESCE(NULLIF(case_lab_results.subtype, ''), 'Unsubtyped') as subtype,
+                case_lab_results.subtype as subtype,
                 COUNT(DISTINCT case_lab_results.lab_code) as total
             ")
 
-            ->where('case_lab_results.subtype', '!=', 'Positive')
 
             ->groupBy('subtype')
             ->orderByDesc('total')
@@ -1053,4 +1258,105 @@ class DashboardService
             ->get();
     }
 
+
+    public function programDashboardData($surveillanceId, $startYear, $startWeek, $endYear, $endWeek)
+    {
+
+        return [
+
+            'total_tested' => $this->totalTested(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+
+            'summary' => $this->programSummary(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+
+            'trend' => $this->trendSingleProgram(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+
+            'pathogen_distribution' => $this->pathogenDistribution(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+
+            'age_distribution' => $this->ageDistribution(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+
+            'sex_distribution' => $this->sexDistribution(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+            // 'afi_trend' => $this->afiTrend(
+            //     $surveillanceId,
+            //     $startYear,
+            //     $startWeek,
+            //     $endYear,
+            //     $endWeek
+            // ),
+            'afi_case_trend' => $this->afiCaseTrend(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+
+            'province_distribution' => $this->provinceProgram(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+            'virus_trend' => $this->virusTrend(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+            'subtype_distribution' => $this->subtypeDistribution(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+            'sentinel_sites' => $this->sentinelSites(
+                $surveillanceId,
+                $startYear,
+                $startWeek,
+                $endYear,
+                $endWeek
+            ),
+
+        ];
+
+    }
+
 }

dashboard/app/View/Components/AppLayout.php

@@ -0,0 +1,17 @@
+<?php
+
+namespace App\View\Components;
+
+use Illuminate\View\Component;
+use Illuminate\View\View;
+
+class AppLayout extends Component
+{
+    /**
+     * Get the view / contents that represents the component.
+     */
+    public function render(): View
+    {
+        return view('layouts.app');
+    }
+}

dashboard/app/View/Components/GuestLayout.php

@@ -0,0 +1,17 @@
+<?php
+
+namespace App\View\Components;
+
+use Illuminate\View\Component;
+use Illuminate\View\View;
+
+class GuestLayout extends Component
+{
+    /**
+     * Get the view / contents that represents the component.
+     */
+    public function render(): View
+    {
+        return view('layouts.guest');
+    }
+}

dashboard/app/helpers.php

@@ -0,0 +1,18 @@
+<?php
+
+use App\Models\ActivityLog;
+
+if (!function_exists('activity_log')) {
+
+    function activity_log($action, $description = null)
+    {
+        ActivityLog::create([
+            'user_id' => auth()->id(),
+            'action' => $action,
+            'description' => $description,
+            'ip_address' => request()->ip(),
+            'user_agent' => request()->userAgent(),
+        ]);
+    }
+
+}