diff --git a/.gitignore b/.gitignore index e1db685..01f8967 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,5 @@ # R Ignores /r_app/*.Rhistory /r_app/*.Rdata + +.DS_Store diff --git a/Current - Pivots planting date and harevsting data.xlsx b/Current - Pivots planting date and harevsting data.xlsx new file mode 100644 index 0000000..88cc23e Binary files /dev/null and b/Current - Pivots planting date and harevsting data.xlsx differ diff --git a/Laravel_app/.editorconfig b/Laravel_app/.editorconfig new file mode 100644 index 0000000..8f0de65 --- /dev/null +++ b/Laravel_app/.editorconfig @@ -0,0 +1,18 @@ +root = true + +[*] +charset = utf-8 +end_of_line = lf +indent_size = 4 +indent_style = space +insert_final_newline = true +trim_trailing_whitespace = true + +[*.md] +trim_trailing_whitespace = false + +[*.{yml,yaml}] +indent_size = 2 + +[docker-compose.yml] +indent_size = 4 diff --git a/Laravel_app/.env.example b/Laravel_app/.env.example new file mode 100644 index 0000000..ea0665b --- /dev/null +++ b/Laravel_app/.env.example @@ -0,0 +1,59 @@ +APP_NAME=Laravel +APP_ENV=local +APP_KEY= +APP_DEBUG=true +APP_URL=http://localhost + +LOG_CHANNEL=stack +LOG_DEPRECATIONS_CHANNEL=null +LOG_LEVEL=debug + +DB_CONNECTION=mysql +DB_HOST=127.0.0.1 +DB_PORT=3306 +DB_DATABASE=laravel +DB_USERNAME=root +DB_PASSWORD= + +BROADCAST_DRIVER=log +CACHE_DRIVER=file +FILESYSTEM_DISK=local +QUEUE_CONNECTION=sync +SESSION_DRIVER=file +SESSION_LIFETIME=120 + +MEMCACHED_HOST=127.0.0.1 + +REDIS_HOST=127.0.0.1 +REDIS_PASSWORD=null +REDIS_PORT=6379 + +MAIL_MAILER=smtp +MAIL_HOST=mailpit +MAIL_PORT=1025 +MAIL_USERNAME=null +MAIL_PASSWORD=null +MAIL_ENCRYPTION=null +MAIL_FROM_ADDRESS="hello@example.com" +MAIL_FROM_NAME="${APP_NAME}" + +AWS_ACCESS_KEY_ID= +AWS_SECRET_ACCESS_KEY= +AWS_DEFAULT_REGION=us-east-1 +AWS_BUCKET= +AWS_USE_PATH_STYLE_ENDPOINT=false + +PUSHER_APP_ID= +PUSHER_APP_KEY= +PUSHER_APP_SECRET= +PUSHER_HOST= +PUSHER_PORT=443 +PUSHER_SCHEME=https +PUSHER_APP_CLUSTER=mt1 + +VITE_APP_NAME="${APP_NAME}" +VITE_PUSHER_APP_KEY="${PUSHER_APP_KEY}" +VITE_PUSHER_HOST="${PUSHER_HOST}" +VITE_PUSHER_PORT="${PUSHER_PORT}" +VITE_PUSHER_SCHEME="${PUSHER_SCHEME}" +VITE_PUSHER_APP_CLUSTER="${PUSHER_APP_CLUSTER}" diff --git a/Laravel_app/.gitattributes b/Laravel_app/.gitattributes new file mode 100644 index 0000000..fcb21d3 --- /dev/null +++ b/Laravel_app/.gitattributes @@ -0,0 +1,11 @@ +* text=auto eol=lf + +*.blade.php diff=html +*.css diff=css +*.html diff=html +*.md diff=markdown +*.php diff=php + +/.github export-ignore +CHANGELOG.md export-ignore +.styleci.yml export-ignore diff --git a/Laravel_app/.gitignore b/Laravel_app/.gitignore new file mode 100644 index 0000000..7fe978f --- /dev/null +++ b/Laravel_app/.gitignore @@ -0,0 +1,19 @@ +/.phpunit.cache +/node_modules +/public/build +/public/hot +/public/storage +/storage/*.key +/vendor +.env +.env.backup +.env.production +.phpunit.result.cache +Homestead.json +Homestead.yaml +auth.json +npm-debug.log +yarn-error.log +/.fleet +/.idea +/.vscode diff --git a/Laravel_app/README.md b/Laravel_app/README.md new file mode 100644 index 0000000..3ed385a --- /dev/null +++ b/Laravel_app/README.md @@ -0,0 +1,66 @@ +

Laravel Logo

+ +

+Build Status +Total Downloads +Latest Stable Version +License +

+ +## About Laravel + +Laravel is a web application framework with expressive, elegant syntax. We believe development must be an enjoyable and creative experience to be truly fulfilling. Laravel takes the pain out of development by easing common tasks used in many web projects, such as: + +- [Simple, fast routing engine](https://laravel.com/docs/routing). +- [Powerful dependency injection container](https://laravel.com/docs/container). +- Multiple back-ends for [session](https://laravel.com/docs/session) and [cache](https://laravel.com/docs/cache) storage. +- Expressive, intuitive [database ORM](https://laravel.com/docs/eloquent). +- Database agnostic [schema migrations](https://laravel.com/docs/migrations). +- [Robust background job processing](https://laravel.com/docs/queues). +- [Real-time event broadcasting](https://laravel.com/docs/broadcasting). + +Laravel is accessible, powerful, and provides tools required for large, robust applications. + +## Learning Laravel + +Laravel has the most extensive and thorough [documentation](https://laravel.com/docs) and video tutorial library of all modern web application frameworks, making it a breeze to get started with the framework. + +You may also try the [Laravel Bootcamp](https://bootcamp.laravel.com), where you will be guided through building a modern Laravel application from scratch. + +If you don't feel like reading, [Laracasts](https://laracasts.com) can help. Laracasts contains over 2000 video tutorials on a range of topics including Laravel, modern PHP, unit testing, and JavaScript. Boost your skills by digging into our comprehensive video library. + +## Laravel Sponsors + +We would like to extend our thanks to the following sponsors for funding Laravel development. If you are interested in becoming a sponsor, please visit the Laravel [Patreon page](https://patreon.com/taylorotwell). + +### Premium Partners + +- **[Vehikl](https://vehikl.com/)** +- **[Tighten Co.](https://tighten.co)** +- **[Kirschbaum Development Group](https://kirschbaumdevelopment.com)** +- **[64 Robots](https://64robots.com)** +- **[Cubet Techno Labs](https://cubettech.com)** +- **[Cyber-Duck](https://cyber-duck.co.uk)** +- **[Many](https://www.many.co.uk)** +- **[Webdock, Fast VPS Hosting](https://www.webdock.io/en)** +- **[DevSquad](https://devsquad.com)** +- **[Curotec](https://www.curotec.com/services/technologies/laravel/)** +- **[OP.GG](https://op.gg)** +- **[WebReinvent](https://webreinvent.com/?utm_source=laravel&utm_medium=github&utm_campaign=patreon-sponsors)** +- **[Lendio](https://lendio.com)** + +## Contributing + +Thank you for considering contributing to the Laravel framework! The contribution guide can be found in the [Laravel documentation](https://laravel.com/docs/contributions). + +## Code of Conduct + +In order to ensure that the Laravel community is welcoming to all, please review and abide by the [Code of Conduct](https://laravel.com/docs/contributions#code-of-conduct). + +## Security Vulnerabilities + +If you discover a security vulnerability within Laravel, please send an e-mail to Taylor Otwell via [taylor@laravel.com](mailto:taylor@laravel.com). All security vulnerabilities will be promptly addressed. + +## License + +The Laravel framework is open-sourced software licensed under the [MIT license](https://opensource.org/licenses/MIT). diff --git a/Laravel_app/app/Console/Kernel.php b/Laravel_app/app/Console/Kernel.php new file mode 100644 index 0000000..e6b9960 --- /dev/null +++ b/Laravel_app/app/Console/Kernel.php @@ -0,0 +1,27 @@ +command('inspire')->hourly(); + } + + /** + * Register the commands for the application. + */ + protected function commands(): void + { + $this->load(__DIR__.'/Commands'); + + require base_path('routes/console.php'); + } +} diff --git a/Laravel_app/app/Exceptions/Handler.php b/Laravel_app/app/Exceptions/Handler.php new file mode 100644 index 0000000..56af264 --- /dev/null +++ b/Laravel_app/app/Exceptions/Handler.php @@ -0,0 +1,30 @@ + + */ + protected $dontFlash = [ + 'current_password', + 'password', + 'password_confirmation', + ]; + + /** + * Register the exception handling callbacks for the application. + */ + public function register(): void + { + $this->reportable(function (Throwable $e) { + // + }); + } +} diff --git a/Laravel_app/app/Http/Controllers/Controller.php b/Laravel_app/app/Http/Controllers/Controller.php new file mode 100644 index 0000000..77ec359 --- /dev/null +++ b/Laravel_app/app/Http/Controllers/Controller.php @@ -0,0 +1,12 @@ + + */ + protected $middleware = [ + // \App\Http\Middleware\TrustHosts::class, + \App\Http\Middleware\TrustProxies::class, + \Illuminate\Http\Middleware\HandleCors::class, + \App\Http\Middleware\PreventRequestsDuringMaintenance::class, + \Illuminate\Foundation\Http\Middleware\ValidatePostSize::class, + \App\Http\Middleware\TrimStrings::class, + \Illuminate\Foundation\Http\Middleware\ConvertEmptyStringsToNull::class, + ]; + + /** + * The application's route middleware groups. + * + * @var array> + */ + protected $middlewareGroups = [ + 'web' => [ + \App\Http\Middleware\EncryptCookies::class, + \Illuminate\Cookie\Middleware\AddQueuedCookiesToResponse::class, + \Illuminate\Session\Middleware\StartSession::class, + \Illuminate\View\Middleware\ShareErrorsFromSession::class, + \App\Http\Middleware\VerifyCsrfToken::class, + \Illuminate\Routing\Middleware\SubstituteBindings::class, + ], + + 'api' => [ + // \Laravel\Sanctum\Http\Middleware\EnsureFrontendRequestsAreStateful::class, + \Illuminate\Routing\Middleware\ThrottleRequests::class.':api', + \Illuminate\Routing\Middleware\SubstituteBindings::class, + ], + ]; + + /** + * The application's middleware aliases. + * + * Aliases may be used instead of class names to conveniently assign middleware to routes and groups. + * + * @var array + */ + protected $middlewareAliases = [ + 'auth' => \App\Http\Middleware\Authenticate::class, + 'auth.basic' => \Illuminate\Auth\Middleware\AuthenticateWithBasicAuth::class, + 'auth.session' => \Illuminate\Session\Middleware\AuthenticateSession::class, + 'cache.headers' => \Illuminate\Http\Middleware\SetCacheHeaders::class, + 'can' => \Illuminate\Auth\Middleware\Authorize::class, + 'guest' => \App\Http\Middleware\RedirectIfAuthenticated::class, + 'password.confirm' => \Illuminate\Auth\Middleware\RequirePassword::class, + 'precognitive' => \Illuminate\Foundation\Http\Middleware\HandlePrecognitiveRequests::class, + 'signed' => \App\Http\Middleware\ValidateSignature::class, + 'throttle' => \Illuminate\Routing\Middleware\ThrottleRequests::class, + 'verified' => \Illuminate\Auth\Middleware\EnsureEmailIsVerified::class, + ]; +} diff --git a/Laravel_app/app/Http/Middleware/Authenticate.php b/Laravel_app/app/Http/Middleware/Authenticate.php new file mode 100644 index 0000000..d4ef644 --- /dev/null +++ b/Laravel_app/app/Http/Middleware/Authenticate.php @@ -0,0 +1,17 @@ +expectsJson() ? null : route('login'); + } +} diff --git a/Laravel_app/app/Http/Middleware/EncryptCookies.php b/Laravel_app/app/Http/Middleware/EncryptCookies.php new file mode 100644 index 0000000..867695b --- /dev/null +++ b/Laravel_app/app/Http/Middleware/EncryptCookies.php @@ -0,0 +1,17 @@ + + */ + protected $except = [ + // + ]; +} diff --git a/Laravel_app/app/Http/Middleware/PreventRequestsDuringMaintenance.php b/Laravel_app/app/Http/Middleware/PreventRequestsDuringMaintenance.php new file mode 100644 index 0000000..74cbd9a --- /dev/null +++ b/Laravel_app/app/Http/Middleware/PreventRequestsDuringMaintenance.php @@ -0,0 +1,17 @@ + + */ + protected $except = [ + // + ]; +} diff --git a/Laravel_app/app/Http/Middleware/RedirectIfAuthenticated.php b/Laravel_app/app/Http/Middleware/RedirectIfAuthenticated.php new file mode 100644 index 0000000..afc78c4 --- /dev/null +++ b/Laravel_app/app/Http/Middleware/RedirectIfAuthenticated.php @@ -0,0 +1,30 @@ +check()) { + return redirect(RouteServiceProvider::HOME); + } + } + + return $next($request); + } +} diff --git a/Laravel_app/app/Http/Middleware/TrimStrings.php b/Laravel_app/app/Http/Middleware/TrimStrings.php new file mode 100644 index 0000000..88cadca --- /dev/null +++ b/Laravel_app/app/Http/Middleware/TrimStrings.php @@ -0,0 +1,19 @@ + + */ + protected $except = [ + 'current_password', + 'password', + 'password_confirmation', + ]; +} diff --git a/Laravel_app/app/Http/Middleware/TrustHosts.php b/Laravel_app/app/Http/Middleware/TrustHosts.php new file mode 100644 index 0000000..c9c58bd --- /dev/null +++ b/Laravel_app/app/Http/Middleware/TrustHosts.php @@ -0,0 +1,20 @@ + + */ + public function hosts(): array + { + return [ + $this->allSubdomainsOfApplicationUrl(), + ]; + } +} diff --git a/Laravel_app/app/Http/Middleware/TrustProxies.php b/Laravel_app/app/Http/Middleware/TrustProxies.php new file mode 100644 index 0000000..3391630 --- /dev/null +++ b/Laravel_app/app/Http/Middleware/TrustProxies.php @@ -0,0 +1,28 @@ +|string|null + */ + protected $proxies; + + /** + * The headers that should be used to detect proxies. + * + * @var int + */ + protected $headers = + Request::HEADER_X_FORWARDED_FOR | + Request::HEADER_X_FORWARDED_HOST | + Request::HEADER_X_FORWARDED_PORT | + Request::HEADER_X_FORWARDED_PROTO | + Request::HEADER_X_FORWARDED_AWS_ELB; +} diff --git a/Laravel_app/app/Http/Middleware/ValidateSignature.php b/Laravel_app/app/Http/Middleware/ValidateSignature.php new file mode 100644 index 0000000..093bf64 --- /dev/null +++ b/Laravel_app/app/Http/Middleware/ValidateSignature.php @@ -0,0 +1,22 @@ + + */ + protected $except = [ + // 'fbclid', + // 'utm_campaign', + // 'utm_content', + // 'utm_medium', + // 'utm_source', + // 'utm_term', + ]; +} diff --git a/Laravel_app/app/Http/Middleware/VerifyCsrfToken.php b/Laravel_app/app/Http/Middleware/VerifyCsrfToken.php new file mode 100644 index 0000000..9e86521 --- /dev/null +++ b/Laravel_app/app/Http/Middleware/VerifyCsrfToken.php @@ -0,0 +1,17 @@ + + */ + protected $except = [ + // + ]; +} diff --git a/Laravel_app/app/Models/User.php b/Laravel_app/app/Models/User.php new file mode 100644 index 0000000..4d7f70f --- /dev/null +++ b/Laravel_app/app/Models/User.php @@ -0,0 +1,45 @@ + + */ + protected $fillable = [ + 'name', + 'email', + 'password', + ]; + + /** + * The attributes that should be hidden for serialization. + * + * @var array + */ + protected $hidden = [ + 'password', + 'remember_token', + ]; + + /** + * The attributes that should be cast. + * + * @var array + */ + protected $casts = [ + 'email_verified_at' => 'datetime', + 'password' => 'hashed', + ]; +} diff --git a/Laravel_app/app/Providers/AppServiceProvider.php b/Laravel_app/app/Providers/AppServiceProvider.php new file mode 100644 index 0000000..452e6b6 --- /dev/null +++ b/Laravel_app/app/Providers/AppServiceProvider.php @@ -0,0 +1,24 @@ + + */ + protected $policies = [ + // + ]; + + /** + * Register any authentication / authorization services. + */ + public function boot(): void + { + // + } +} diff --git a/Laravel_app/app/Providers/BroadcastServiceProvider.php b/Laravel_app/app/Providers/BroadcastServiceProvider.php new file mode 100644 index 0000000..2be04f5 --- /dev/null +++ b/Laravel_app/app/Providers/BroadcastServiceProvider.php @@ -0,0 +1,19 @@ +> + */ + protected $listen = [ + Registered::class => [ + SendEmailVerificationNotification::class, + ], + ]; + + /** + * Register any events for your application. + */ + public function boot(): void + { + // + } + + /** + * Determine if events and listeners should be automatically discovered. + */ + public function shouldDiscoverEvents(): bool + { + return false; + } +} diff --git a/Laravel_app/app/Providers/RouteServiceProvider.php b/Laravel_app/app/Providers/RouteServiceProvider.php new file mode 100644 index 0000000..1cf5f15 --- /dev/null +++ b/Laravel_app/app/Providers/RouteServiceProvider.php @@ -0,0 +1,40 @@ +by($request->user()?->id ?: $request->ip()); + }); + + $this->routes(function () { + Route::middleware('api') + ->prefix('api') + ->group(base_path('routes/api.php')); + + Route::middleware('web') + ->group(base_path('routes/web.php')); + }); + } +} diff --git a/Laravel_app/artisan b/Laravel_app/artisan new file mode 100755 index 0000000..67a3329 --- /dev/null +++ b/Laravel_app/artisan @@ -0,0 +1,53 @@ +#!/usr/bin/env php +make(Illuminate\Contracts\Console\Kernel::class); + +$status = $kernel->handle( + $input = new Symfony\Component\Console\Input\ArgvInput, + new Symfony\Component\Console\Output\ConsoleOutput +); + +/* +|-------------------------------------------------------------------------- +| Shutdown The Application +|-------------------------------------------------------------------------- +| +| Once Artisan has finished running, we will fire off the shutdown events +| so that any final work may be done by the application before we shut +| down the process. This is the last thing to happen to the request. +| +*/ + +$kernel->terminate($input, $status); + +exit($status); diff --git a/Laravel_app/bootstrap/app.php b/Laravel_app/bootstrap/app.php new file mode 100644 index 0000000..037e17d --- /dev/null +++ b/Laravel_app/bootstrap/app.php @@ -0,0 +1,55 @@ +singleton( + Illuminate\Contracts\Http\Kernel::class, + App\Http\Kernel::class +); + +$app->singleton( + Illuminate\Contracts\Console\Kernel::class, + App\Console\Kernel::class +); + +$app->singleton( + Illuminate\Contracts\Debug\ExceptionHandler::class, + App\Exceptions\Handler::class +); + +/* +|-------------------------------------------------------------------------- +| Return The Application +|-------------------------------------------------------------------------- +| +| This script returns the application instance. The instance is given to +| the calling script so we can separate the building of the instances +| from the actual running of the application and sending responses. +| +*/ + +return $app; diff --git a/Laravel_app/bootstrap/cache/.gitignore b/Laravel_app/bootstrap/cache/.gitignore new file mode 100644 index 0000000..d6b7ef3 --- /dev/null +++ b/Laravel_app/bootstrap/cache/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore diff --git a/Laravel_app/composer.json b/Laravel_app/composer.json new file mode 100644 index 0000000..e1fb449 --- /dev/null +++ b/Laravel_app/composer.json @@ -0,0 +1,66 @@ +{ + "name": "laravel/laravel", + "type": "project", + "description": "The skeleton application for the Laravel framework.", + "keywords": ["laravel", "framework"], + "license": "MIT", + "require": { + "php": "^8.1", + "guzzlehttp/guzzle": "^7.2", + "laravel/framework": "^10.10", + "laravel/sanctum": "^3.2", + "laravel/tinker": "^2.8" + }, + "require-dev": { + "fakerphp/faker": "^1.9.1", + "laravel/pint": "^1.0", + "laravel/sail": "^1.18", + "mockery/mockery": "^1.4.4", + "nunomaduro/collision": "^7.0", + "phpunit/phpunit": "^10.1", + "spatie/laravel-ignition": "^2.0" + }, + "autoload": { + "psr-4": { + "App\\": "app/", + "Database\\Factories\\": "database/factories/", + "Database\\Seeders\\": "database/seeders/" + } + }, + "autoload-dev": { + "psr-4": { + "Tests\\": "tests/" + } + }, + "scripts": { + "post-autoload-dump": [ + "Illuminate\\Foundation\\ComposerScripts::postAutoloadDump", + "@php artisan package:discover --ansi" + ], + "post-update-cmd": [ + "@php artisan vendor:publish --tag=laravel-assets --ansi --force" + ], + "post-root-package-install": [ + "@php -r \"file_exists('.env') || copy('.env.example', '.env');\"" + ], + "post-create-project-cmd": [ + "@php artisan key:generate --ansi" + ] + }, + "extra": { + "laravel": { + "dont-discover": [] + } + }, + "config": { + "optimize-autoloader": true, + "preferred-install": "dist", + "sort-packages": true, + "allow-plugins": { + "pestphp/pest-plugin": true, + "php-http/discovery": true + } + }, + "minimum-stability": "stable", + "prefer-stable": true +} diff --git a/Laravel_app/composer.lock b/Laravel_app/composer.lock new file mode 100644 index 0000000..b32e29c --- /dev/null +++ b/Laravel_app/composer.lock @@ -0,0 +1,8076 @@ +{ + "_readme": [ + "This file locks the dependencies of your project to a known state", + "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#installing-dependencies", + "This file is @generated automatically" + ], + "content-hash": "aa322c53454393ed775cfe4807d54a50", + "packages": [ + { + "name": "brick/math", + "version": "0.11.0", + "source": { + "type": "git", + "url": "https://github.com/brick/math.git", + "reference": "0ad82ce168c82ba30d1c01ec86116ab52f589478" + }, + "dist": { + "type": "zip", + "url": "https://api.github.com/repos/brick/math/zipball/0ad82ce168c82ba30d1c01ec86116ab52f589478", + "reference": "0ad82ce168c82ba30d1c01ec86116ab52f589478", + "shasum": "" + }, + "require": { + "php": "^8.0" + }, + "require-dev": { + "php-coveralls/php-coveralls": "^2.2", + "phpunit/phpunit": "^9.0", + "vimeo/psalm": "5.0.0" + }, + "type": "library", + "autoload": { + "psr-4": { + "Brick\\Math\\": "src/" + } + }, + "notification-url": "https://packagist.org/downloads/", + "license": [ + "MIT" + ], + "description": "Arbitrary-precision arithmetic library", + "keywords": [ + "Arbitrary-precision", + "BigInteger", + "BigRational", + "arithmetic", + "bigdecimal", + "bignum", + "brick", + "math" + ], + "support": { + "issues": "https://github.com/brick/math/issues", + "source": "https://github.com/brick/math/tree/0.11.0" + }, + "funding": [ + { + "url": "https://github.com/BenMorel", + "type": "github" + } + ], + "time": "2023-01-15T23:15:59+00:00" + }, + { + "name": "dflydev/dot-access-data", + "version": "v3.0.2", + "source": { + "type": "git", + "url": "https://github.com/dflydev/dflydev-dot-access-data.git", + "reference": 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"environment" your application is currently + | running in. This may determine how you prefer to configure various + | services the application utilizes. Set this in your ".env" file. + | + */ + + 'env' => env('APP_ENV', 'production'), + + /* + |-------------------------------------------------------------------------- + | Application Debug Mode + |-------------------------------------------------------------------------- + | + | When your application is in debug mode, detailed error messages with + | stack traces will be shown on every error that occurs within your + | application. If disabled, a simple generic error page is shown. + | + */ + + 'debug' => (bool) env('APP_DEBUG', false), + + /* + |-------------------------------------------------------------------------- + | Application URL + |-------------------------------------------------------------------------- + | + | This URL is used by the console to properly generate URLs when using + | the Artisan command line tool. You should set this to the root of + | your application so that it is used when running Artisan tasks. + | + */ + + 'url' => env('APP_URL', 'http://localhost'), + + 'asset_url' => env('ASSET_URL'), + + /* + |-------------------------------------------------------------------------- + | Application Timezone + |-------------------------------------------------------------------------- + | + | Here you may specify the default timezone for your application, which + | will be used by the PHP date and date-time functions. We have gone + | ahead and set this to a sensible default for you out of the box. + | + */ + + 'timezone' => 'UTC', + + /* + |-------------------------------------------------------------------------- + | Application Locale Configuration + |-------------------------------------------------------------------------- + | + | The application locale determines the default locale that will be used + | by the translation service provider. You are free to set this value + | to any of the locales which will be supported by the application. + | + */ + + 'locale' => 'en', + + /* + |-------------------------------------------------------------------------- + | Application Fallback Locale + |-------------------------------------------------------------------------- + | + | The fallback locale determines the locale to use when the current one + | is not available. You may change the value to correspond to any of + | the language folders that are provided through your application. + | + */ + + 'fallback_locale' => 'en', + + /* + |-------------------------------------------------------------------------- + | Faker Locale + |-------------------------------------------------------------------------- + | + | This locale will be used by the Faker PHP library when generating fake + | data for your database seeds. For example, this will be used to get + | localized telephone numbers, street address information and more. + | + */ + + 'faker_locale' => 'en_US', + + /* + |-------------------------------------------------------------------------- + | Encryption Key + |-------------------------------------------------------------------------- + | + | This key is used by the Illuminate encrypter service and should be set + | to a random, 32 character string, otherwise these encrypted strings + | will not be safe. Please do this before deploying an application! + | + */ + + 'key' => env('APP_KEY'), + + 'cipher' => 'AES-256-CBC', + + /* + |-------------------------------------------------------------------------- + | Maintenance Mode Driver + |-------------------------------------------------------------------------- + | + | These configuration options determine the driver used to determine and + | manage Laravel's "maintenance mode" status. The "cache" driver will + | allow maintenance mode to be controlled across multiple machines. + | + | Supported drivers: "file", "cache" + | + */ + + 'maintenance' => [ + 'driver' => 'file', + // 'store' => 'redis', + ], + + /* + |-------------------------------------------------------------------------- + | Autoloaded Service Providers + |-------------------------------------------------------------------------- + | + | The service providers listed here will be automatically loaded on the + | request to your application. Feel free to add your own services to + | this array to grant expanded functionality to your applications. + | + */ + + 'providers' => ServiceProvider::defaultProviders()->merge([ + /* + * Package Service Providers... + */ + + /* + * Application Service Providers... + */ + App\Providers\AppServiceProvider::class, + App\Providers\AuthServiceProvider::class, + // App\Providers\BroadcastServiceProvider::class, + App\Providers\EventServiceProvider::class, + App\Providers\RouteServiceProvider::class, + ])->toArray(), + + /* + |-------------------------------------------------------------------------- + | Class Aliases + |-------------------------------------------------------------------------- + | + | This array of class aliases will be registered when this application + | is started. However, feel free to register as many as you wish as + | the aliases are "lazy" loaded so they don't hinder performance. + | + */ + + 'aliases' => Facade::defaultAliases()->merge([ + // 'Example' => App\Facades\Example::class, + ])->toArray(), + +]; diff --git a/Laravel_app/config/auth.php b/Laravel_app/config/auth.php new file mode 100644 index 0000000..9548c15 --- /dev/null +++ b/Laravel_app/config/auth.php @@ -0,0 +1,115 @@ + [ + 'guard' => 'web', + 'passwords' => 'users', + ], + + /* + |-------------------------------------------------------------------------- + | Authentication Guards + |-------------------------------------------------------------------------- + | + | Next, you may define every authentication guard for your application. + | Of course, a great default configuration has been defined for you + | here which uses session storage and the Eloquent user provider. + | + | All authentication drivers have a user provider. This defines how the + | users are actually retrieved out of your database or other storage + | mechanisms used by this application to persist your user's data. + | + | Supported: "session" + | + */ + + 'guards' => [ + 'web' => [ + 'driver' => 'session', + 'provider' => 'users', + ], + ], + + /* + |-------------------------------------------------------------------------- + | User Providers + |-------------------------------------------------------------------------- + | + | All authentication drivers have a user provider. This defines how the + | users are actually retrieved out of your database or other storage + | mechanisms used by this application to persist your user's data. + | + | If you have multiple user tables or models you may configure multiple + | sources which represent each model / table. These sources may then + | be assigned to any extra authentication guards you have defined. + | + | Supported: "database", "eloquent" + | + */ + + 'providers' => [ + 'users' => [ + 'driver' => 'eloquent', + 'model' => App\Models\User::class, + ], + + // 'users' => [ + // 'driver' => 'database', + // 'table' => 'users', + // ], + ], + + /* + |-------------------------------------------------------------------------- + | Resetting Passwords + |-------------------------------------------------------------------------- + | + | You may specify multiple password reset configurations if you have more + | than one user table or model in the application and you want to have + | separate password reset settings based on the specific user types. + | + | The expiry time is the number of minutes that each reset token will be + | considered valid. This security feature keeps tokens short-lived so + | they have less time to be guessed. You may change this as needed. + | + | The throttle setting is the number of seconds a user must wait before + | generating more password reset tokens. This prevents the user from + | quickly generating a very large amount of password reset tokens. + | + */ + + 'passwords' => [ + 'users' => [ + 'provider' => 'users', + 'table' => 'password_reset_tokens', + 'expire' => 60, + 'throttle' => 60, + ], + ], + + /* + |-------------------------------------------------------------------------- + | Password Confirmation Timeout + |-------------------------------------------------------------------------- + | + | Here you may define the amount of seconds before a password confirmation + | times out and the user is prompted to re-enter their password via the + | confirmation screen. By default, the timeout lasts for three hours. + | + */ + + 'password_timeout' => 10800, + +]; diff --git a/Laravel_app/config/broadcasting.php b/Laravel_app/config/broadcasting.php new file mode 100644 index 0000000..2410485 --- /dev/null +++ b/Laravel_app/config/broadcasting.php @@ -0,0 +1,71 @@ + env('BROADCAST_DRIVER', 'null'), + + /* + |-------------------------------------------------------------------------- + | Broadcast Connections + |-------------------------------------------------------------------------- + | + | Here you may define all of the broadcast connections that will be used + | to broadcast events to other systems or over websockets. Samples of + | each available type of connection are provided inside this array. + | + */ + + 'connections' => [ + + 'pusher' => [ + 'driver' => 'pusher', + 'key' => env('PUSHER_APP_KEY'), + 'secret' => env('PUSHER_APP_SECRET'), + 'app_id' => env('PUSHER_APP_ID'), + 'options' => [ + 'cluster' => env('PUSHER_APP_CLUSTER'), + 'host' => env('PUSHER_HOST') ?: 'api-'.env('PUSHER_APP_CLUSTER', 'mt1').'.pusher.com', + 'port' => env('PUSHER_PORT', 443), + 'scheme' => env('PUSHER_SCHEME', 'https'), + 'encrypted' => true, + 'useTLS' => env('PUSHER_SCHEME', 'https') === 'https', + ], + 'client_options' => [ + // Guzzle client options: https://docs.guzzlephp.org/en/stable/request-options.html + ], + ], + + 'ably' => [ + 'driver' => 'ably', + 'key' => env('ABLY_KEY'), + ], + + 'redis' => [ + 'driver' => 'redis', + 'connection' => 'default', + ], + + 'log' => [ + 'driver' => 'log', + ], + + 'null' => [ + 'driver' => 'null', + ], + + ], + +]; diff --git a/Laravel_app/config/cache.php b/Laravel_app/config/cache.php new file mode 100644 index 0000000..d4171e2 --- /dev/null +++ b/Laravel_app/config/cache.php @@ -0,0 +1,111 @@ + env('CACHE_DRIVER', 'file'), + + /* + |-------------------------------------------------------------------------- + | Cache Stores + |-------------------------------------------------------------------------- + | + | Here you may define all of the cache "stores" for your application as + | well as their drivers. You may even define multiple stores for the + | same cache driver to group types of items stored in your caches. + | + | Supported drivers: "apc", "array", "database", "file", + | "memcached", "redis", "dynamodb", "octane", "null" + | + */ + + 'stores' => [ + + 'apc' => [ + 'driver' => 'apc', + ], + + 'array' => [ + 'driver' => 'array', + 'serialize' => false, + ], + + 'database' => [ + 'driver' => 'database', + 'table' => 'cache', + 'connection' => null, + 'lock_connection' => null, + ], + + 'file' => [ + 'driver' => 'file', + 'path' => storage_path('framework/cache/data'), + 'lock_path' => storage_path('framework/cache/data'), + ], + + 'memcached' => [ + 'driver' => 'memcached', + 'persistent_id' => env('MEMCACHED_PERSISTENT_ID'), + 'sasl' => [ + env('MEMCACHED_USERNAME'), + env('MEMCACHED_PASSWORD'), + ], + 'options' => [ + // Memcached::OPT_CONNECT_TIMEOUT => 2000, + ], + 'servers' => [ + [ + 'host' => env('MEMCACHED_HOST', '127.0.0.1'), + 'port' => env('MEMCACHED_PORT', 11211), + 'weight' => 100, + ], + ], + ], + + 'redis' => [ + 'driver' => 'redis', + 'connection' => 'cache', + 'lock_connection' => 'default', + ], + + 'dynamodb' => [ + 'driver' => 'dynamodb', + 'key' => env('AWS_ACCESS_KEY_ID'), + 'secret' => env('AWS_SECRET_ACCESS_KEY'), + 'region' => env('AWS_DEFAULT_REGION', 'us-east-1'), + 'table' => env('DYNAMODB_CACHE_TABLE', 'cache'), + 'endpoint' => env('DYNAMODB_ENDPOINT'), + ], + + 'octane' => [ + 'driver' => 'octane', + ], + + ], + + /* + |-------------------------------------------------------------------------- + | Cache Key Prefix + |-------------------------------------------------------------------------- + | + | When utilizing the APC, database, memcached, Redis, or DynamoDB cache + | stores there might be other applications using the same cache. For + | that reason, you may prefix every cache key to avoid collisions. + | + */ + + 'prefix' => env('CACHE_PREFIX', Str::slug(env('APP_NAME', 'laravel'), '_').'_cache_'), + +]; diff --git a/Laravel_app/config/cors.php b/Laravel_app/config/cors.php new file mode 100644 index 0000000..8a39e6d --- /dev/null +++ b/Laravel_app/config/cors.php @@ -0,0 +1,34 @@ + ['api/*', 'sanctum/csrf-cookie'], + + 'allowed_methods' => ['*'], + + 'allowed_origins' => ['*'], + + 'allowed_origins_patterns' => [], + + 'allowed_headers' => ['*'], + + 'exposed_headers' => [], + + 'max_age' => 0, + + 'supports_credentials' => false, + +]; diff --git a/Laravel_app/config/database.php b/Laravel_app/config/database.php new file mode 100644 index 0000000..137ad18 --- /dev/null +++ b/Laravel_app/config/database.php @@ -0,0 +1,151 @@ + env('DB_CONNECTION', 'mysql'), + + /* + |-------------------------------------------------------------------------- + | Database Connections + |-------------------------------------------------------------------------- + | + | Here are each of the database connections setup for your application. + | Of course, examples of configuring each database platform that is + | supported by Laravel is shown below to make development simple. + | + | + | All database work in Laravel is done through the PHP PDO facilities + | so make sure you have the driver for your particular database of + | choice installed on your machine before you begin development. + | + */ + + 'connections' => [ + + 'sqlite' => [ + 'driver' => 'sqlite', + 'url' => env('DATABASE_URL'), + 'database' => env('DB_DATABASE', database_path('database.sqlite')), + 'prefix' => '', + 'foreign_key_constraints' => env('DB_FOREIGN_KEYS', true), + ], + + 'mysql' => [ + 'driver' => 'mysql', + 'url' => env('DATABASE_URL'), + 'host' => env('DB_HOST', '127.0.0.1'), + 'port' => env('DB_PORT', '3306'), + 'database' => env('DB_DATABASE', 'forge'), + 'username' => env('DB_USERNAME', 'forge'), + 'password' => env('DB_PASSWORD', ''), + 'unix_socket' => env('DB_SOCKET', ''), + 'charset' => 'utf8mb4', + 'collation' => 'utf8mb4_unicode_ci', + 'prefix' => '', + 'prefix_indexes' => true, + 'strict' => true, + 'engine' => null, + 'options' => extension_loaded('pdo_mysql') ? array_filter([ + PDO::MYSQL_ATTR_SSL_CA => env('MYSQL_ATTR_SSL_CA'), + ]) : [], + ], + + 'pgsql' => [ + 'driver' => 'pgsql', + 'url' => env('DATABASE_URL'), + 'host' => env('DB_HOST', '127.0.0.1'), + 'port' => env('DB_PORT', '5432'), + 'database' => env('DB_DATABASE', 'forge'), + 'username' => env('DB_USERNAME', 'forge'), + 'password' => env('DB_PASSWORD', ''), + 'charset' => 'utf8', + 'prefix' => '', + 'prefix_indexes' => true, + 'search_path' => 'public', + 'sslmode' => 'prefer', + ], + + 'sqlsrv' => [ + 'driver' => 'sqlsrv', + 'url' => env('DATABASE_URL'), + 'host' => env('DB_HOST', 'localhost'), + 'port' => env('DB_PORT', '1433'), + 'database' => env('DB_DATABASE', 'forge'), + 'username' => env('DB_USERNAME', 'forge'), + 'password' => env('DB_PASSWORD', ''), + 'charset' => 'utf8', + 'prefix' => '', + 'prefix_indexes' => true, + // 'encrypt' => env('DB_ENCRYPT', 'yes'), + // 'trust_server_certificate' => env('DB_TRUST_SERVER_CERTIFICATE', 'false'), + ], + + ], + + /* + |-------------------------------------------------------------------------- + | Migration Repository Table + |-------------------------------------------------------------------------- + | + | This table keeps track of all the migrations that have already run for + | your application. Using this information, we can determine which of + | the migrations on disk haven't actually been run in the database. + | + */ + + 'migrations' => 'migrations', + + /* + |-------------------------------------------------------------------------- + | Redis Databases + |-------------------------------------------------------------------------- + | + | Redis is an open source, fast, and advanced key-value store that also + | provides a richer body of commands than a typical key-value system + | such as APC or Memcached. Laravel makes it easy to dig right in. + | + */ + + 'redis' => [ + + 'client' => env('REDIS_CLIENT', 'phpredis'), + + 'options' => [ + 'cluster' => env('REDIS_CLUSTER', 'redis'), + 'prefix' => env('REDIS_PREFIX', Str::slug(env('APP_NAME', 'laravel'), '_').'_database_'), + ], + + 'default' => [ + 'url' => env('REDIS_URL'), + 'host' => env('REDIS_HOST', '127.0.0.1'), + 'username' => env('REDIS_USERNAME'), + 'password' => env('REDIS_PASSWORD'), + 'port' => env('REDIS_PORT', '6379'), + 'database' => env('REDIS_DB', '0'), + ], + + 'cache' => [ + 'url' => env('REDIS_URL'), + 'host' => env('REDIS_HOST', '127.0.0.1'), + 'username' => env('REDIS_USERNAME'), + 'password' => env('REDIS_PASSWORD'), + 'port' => env('REDIS_PORT', '6379'), + 'database' => env('REDIS_CACHE_DB', '1'), + ], + + ], + +]; diff --git a/Laravel_app/config/filesystems.php b/Laravel_app/config/filesystems.php new file mode 100644 index 0000000..e9d9dbd --- /dev/null +++ b/Laravel_app/config/filesystems.php @@ -0,0 +1,76 @@ + env('FILESYSTEM_DISK', 'local'), + + /* + |-------------------------------------------------------------------------- + | Filesystem Disks + |-------------------------------------------------------------------------- + | + | Here you may configure as many filesystem "disks" as you wish, and you + | may even configure multiple disks of the same driver. Defaults have + | been set up for each driver as an example of the required values. + | + | Supported Drivers: "local", "ftp", "sftp", "s3" + | + */ + + 'disks' => [ + + 'local' => [ + 'driver' => 'local', + 'root' => storage_path('app'), + 'throw' => false, + ], + + 'public' => [ + 'driver' => 'local', + 'root' => storage_path('app/public'), + 'url' => env('APP_URL').'/storage', + 'visibility' => 'public', + 'throw' => false, + ], + + 's3' => [ + 'driver' => 's3', + 'key' => env('AWS_ACCESS_KEY_ID'), + 'secret' => env('AWS_SECRET_ACCESS_KEY'), + 'region' => env('AWS_DEFAULT_REGION'), + 'bucket' => env('AWS_BUCKET'), + 'url' => env('AWS_URL'), + 'endpoint' => env('AWS_ENDPOINT'), + 'use_path_style_endpoint' => env('AWS_USE_PATH_STYLE_ENDPOINT', false), + 'throw' => false, + ], + + ], + + /* + |-------------------------------------------------------------------------- + | Symbolic Links + |-------------------------------------------------------------------------- + | + | Here you may configure the symbolic links that will be created when the + | `storage:link` Artisan command is executed. The array keys should be + | the locations of the links and the values should be their targets. + | + */ + + 'links' => [ + public_path('storage') => storage_path('app/public'), + ], + +]; diff --git a/Laravel_app/config/hashing.php b/Laravel_app/config/hashing.php new file mode 100644 index 0000000..bcd3be4 --- /dev/null +++ b/Laravel_app/config/hashing.php @@ -0,0 +1,52 @@ + 'bcrypt', + + /* + |-------------------------------------------------------------------------- + | Bcrypt Options + |-------------------------------------------------------------------------- + | + | Here you may specify the configuration options that should be used when + | passwords are hashed using the Bcrypt algorithm. This will allow you + | to control the amount of time it takes to hash the given password. + | + */ + + 'bcrypt' => [ + 'rounds' => env('BCRYPT_ROUNDS', 10), + ], + + /* + |-------------------------------------------------------------------------- + | Argon Options + |-------------------------------------------------------------------------- + | + | Here you may specify the configuration options that should be used when + | passwords are hashed using the Argon algorithm. These will allow you + | to control the amount of time it takes to hash the given password. + | + */ + + 'argon' => [ + 'memory' => 65536, + 'threads' => 1, + 'time' => 4, + ], + +]; diff --git a/Laravel_app/config/logging.php b/Laravel_app/config/logging.php new file mode 100644 index 0000000..c44d276 --- /dev/null +++ b/Laravel_app/config/logging.php @@ -0,0 +1,131 @@ + env('LOG_CHANNEL', 'stack'), + + /* + |-------------------------------------------------------------------------- + | Deprecations Log Channel + |-------------------------------------------------------------------------- + | + | This option controls the log channel that should be used to log warnings + | regarding deprecated PHP and library features. This allows you to get + | your application ready for upcoming major versions of dependencies. + | + */ + + 'deprecations' => [ + 'channel' => env('LOG_DEPRECATIONS_CHANNEL', 'null'), + 'trace' => false, + ], + + /* + |-------------------------------------------------------------------------- + | Log Channels + |-------------------------------------------------------------------------- + | + | Here you may configure the log channels for your application. Out of + | the box, Laravel uses the Monolog PHP logging library. This gives + | you a variety of powerful log handlers / formatters to utilize. + | + | Available Drivers: "single", "daily", "slack", "syslog", + | "errorlog", "monolog", + | "custom", "stack" + | + */ + + 'channels' => [ + 'stack' => [ + 'driver' => 'stack', + 'channels' => ['single'], + 'ignore_exceptions' => false, + ], + + 'single' => [ + 'driver' => 'single', + 'path' => storage_path('logs/laravel.log'), + 'level' => env('LOG_LEVEL', 'debug'), + 'replace_placeholders' => true, + ], + + 'daily' => [ + 'driver' => 'daily', + 'path' => storage_path('logs/laravel.log'), + 'level' => env('LOG_LEVEL', 'debug'), + 'days' => 14, + 'replace_placeholders' => true, + ], + + 'slack' => [ + 'driver' => 'slack', + 'url' => env('LOG_SLACK_WEBHOOK_URL'), + 'username' => 'Laravel Log', + 'emoji' => ':boom:', + 'level' => env('LOG_LEVEL', 'critical'), + 'replace_placeholders' => true, + ], + + 'papertrail' => [ + 'driver' => 'monolog', + 'level' => env('LOG_LEVEL', 'debug'), + 'handler' => env('LOG_PAPERTRAIL_HANDLER', SyslogUdpHandler::class), + 'handler_with' => [ + 'host' => env('PAPERTRAIL_URL'), + 'port' => env('PAPERTRAIL_PORT'), + 'connectionString' => 'tls://'.env('PAPERTRAIL_URL').':'.env('PAPERTRAIL_PORT'), + ], + 'processors' => [PsrLogMessageProcessor::class], + ], + + 'stderr' => [ + 'driver' => 'monolog', + 'level' => env('LOG_LEVEL', 'debug'), + 'handler' => StreamHandler::class, + 'formatter' => env('LOG_STDERR_FORMATTER'), + 'with' => [ + 'stream' => 'php://stderr', + ], + 'processors' => [PsrLogMessageProcessor::class], + ], + + 'syslog' => [ + 'driver' => 'syslog', + 'level' => env('LOG_LEVEL', 'debug'), + 'facility' => LOG_USER, + 'replace_placeholders' => true, + ], + + 'errorlog' => [ + 'driver' => 'errorlog', + 'level' => env('LOG_LEVEL', 'debug'), + 'replace_placeholders' => true, + ], + + 'null' => [ + 'driver' => 'monolog', + 'handler' => NullHandler::class, + ], + + 'emergency' => [ + 'path' => storage_path('logs/laravel.log'), + ], + ], + +]; diff --git a/Laravel_app/config/mail.php b/Laravel_app/config/mail.php new file mode 100644 index 0000000..e652bd0 --- /dev/null +++ b/Laravel_app/config/mail.php @@ -0,0 +1,125 @@ + env('MAIL_MAILER', 'smtp'), + + /* + |-------------------------------------------------------------------------- + | Mailer Configurations + |-------------------------------------------------------------------------- + | + | Here you may configure all of the mailers used by your application plus + | their respective settings. Several examples have been configured for + | you and you are free to add your own as your application requires. + | + | Laravel supports a variety of mail "transport" drivers to be used while + | sending an e-mail. You will specify which one you are using for your + | mailers below. You are free to add additional mailers as required. + | + | Supported: "smtp", "sendmail", "mailgun", "ses", "ses-v2", + | "postmark", "log", "array", "failover" + | + */ + + 'mailers' => [ + 'smtp' => [ + 'transport' => 'smtp', + 'url' => env('MAIL_URL'), + 'host' => env('MAIL_HOST', 'smtp.mailgun.org'), + 'port' => env('MAIL_PORT', 587), + 'encryption' => env('MAIL_ENCRYPTION', 'tls'), + 'username' => env('MAIL_USERNAME'), + 'password' => env('MAIL_PASSWORD'), + 'timeout' => null, + 'local_domain' => env('MAIL_EHLO_DOMAIN'), + ], + + 'ses' => [ + 'transport' => 'ses', + ], + + 'mailgun' => [ + 'transport' => 'mailgun', + // 'client' => [ + // 'timeout' => 5, + // ], + ], + + 'postmark' => [ + 'transport' => 'postmark', + // 'client' => [ + // 'timeout' => 5, + // ], + ], + + 'sendmail' => [ + 'transport' => 'sendmail', + 'path' => env('MAIL_SENDMAIL_PATH', '/usr/sbin/sendmail -bs -i'), + ], + + 'log' => [ + 'transport' => 'log', + 'channel' => env('MAIL_LOG_CHANNEL'), + ], + + 'array' => [ + 'transport' => 'array', + ], + + 'failover' => [ + 'transport' => 'failover', + 'mailers' => [ + 'smtp', + 'log', + ], + ], + ], + + /* + |-------------------------------------------------------------------------- + | Global "From" Address + |-------------------------------------------------------------------------- + | + | You may wish for all e-mails sent by your application to be sent from + | the same address. Here, you may specify a name and address that is + | used globally for all e-mails that are sent by your application. + | + */ + + 'from' => [ + 'address' => env('MAIL_FROM_ADDRESS', 'hello@example.com'), + 'name' => env('MAIL_FROM_NAME', 'Example'), + ], + + /* + |-------------------------------------------------------------------------- + | Markdown Mail Settings + |-------------------------------------------------------------------------- + | + | If you are using Markdown based email rendering, you may configure your + | theme and component paths here, allowing you to customize the design + | of the emails. Or, you may simply stick with the Laravel defaults! + | + */ + + 'markdown' => [ + 'theme' => 'default', + + 'paths' => [ + resource_path('views/vendor/mail'), + ], + ], + +]; diff --git a/Laravel_app/config/queue.php b/Laravel_app/config/queue.php new file mode 100644 index 0000000..01c6b05 --- /dev/null +++ b/Laravel_app/config/queue.php @@ -0,0 +1,109 @@ + env('QUEUE_CONNECTION', 'sync'), + + /* + |-------------------------------------------------------------------------- + | Queue Connections + |-------------------------------------------------------------------------- + | + | Here you may configure the connection information for each server that + | is used by your application. A default configuration has been added + | for each back-end shipped with Laravel. You are free to add more. + | + | Drivers: "sync", "database", "beanstalkd", "sqs", "redis", "null" + | + */ + + 'connections' => [ + + 'sync' => [ + 'driver' => 'sync', + ], + + 'database' => [ + 'driver' => 'database', + 'table' => 'jobs', + 'queue' => 'default', + 'retry_after' => 90, + 'after_commit' => false, + ], + + 'beanstalkd' => [ + 'driver' => 'beanstalkd', + 'host' => 'localhost', + 'queue' => 'default', + 'retry_after' => 90, + 'block_for' => 0, + 'after_commit' => false, + ], + + 'sqs' => [ + 'driver' => 'sqs', + 'key' => env('AWS_ACCESS_KEY_ID'), + 'secret' => env('AWS_SECRET_ACCESS_KEY'), + 'prefix' => env('SQS_PREFIX', 'https://sqs.us-east-1.amazonaws.com/your-account-id'), + 'queue' => env('SQS_QUEUE', 'default'), + 'suffix' => env('SQS_SUFFIX'), + 'region' => env('AWS_DEFAULT_REGION', 'us-east-1'), + 'after_commit' => false, + ], + + 'redis' => [ + 'driver' => 'redis', + 'connection' => 'default', + 'queue' => env('REDIS_QUEUE', 'default'), + 'retry_after' => 90, + 'block_for' => null, + 'after_commit' => false, + ], + + ], + + /* + |-------------------------------------------------------------------------- + | Job Batching + |-------------------------------------------------------------------------- + | + | The following options configure the database and table that store job + | batching information. These options can be updated to any database + | connection and table which has been defined by your application. + | + */ + + 'batching' => [ + 'database' => env('DB_CONNECTION', 'mysql'), + 'table' => 'job_batches', + ], + + /* + |-------------------------------------------------------------------------- + | Failed Queue Jobs + |-------------------------------------------------------------------------- + | + | These options configure the behavior of failed queue job logging so you + | can control which database and table are used to store the jobs that + | have failed. You may change them to any database / table you wish. + | + */ + + 'failed' => [ + 'driver' => env('QUEUE_FAILED_DRIVER', 'database-uuids'), + 'database' => env('DB_CONNECTION', 'mysql'), + 'table' => 'failed_jobs', + ], + +]; diff --git a/Laravel_app/config/sanctum.php b/Laravel_app/config/sanctum.php new file mode 100644 index 0000000..529cfdc --- /dev/null +++ b/Laravel_app/config/sanctum.php @@ -0,0 +1,67 @@ + explode(',', env('SANCTUM_STATEFUL_DOMAINS', sprintf( + '%s%s', + 'localhost,localhost:3000,127.0.0.1,127.0.0.1:8000,::1', + Sanctum::currentApplicationUrlWithPort() + ))), + + /* + |-------------------------------------------------------------------------- + | Sanctum Guards + |-------------------------------------------------------------------------- + | + | This array contains the authentication guards that will be checked when + | Sanctum is trying to authenticate a request. If none of these guards + | are able to authenticate the request, Sanctum will use the bearer + | token that's present on an incoming request for authentication. + | + */ + + 'guard' => ['web'], + + /* + |-------------------------------------------------------------------------- + | Expiration Minutes + |-------------------------------------------------------------------------- + | + | This value controls the number of minutes until an issued token will be + | considered expired. If this value is null, personal access tokens do + | not expire. This won't tweak the lifetime of first-party sessions. + | + */ + + 'expiration' => null, + + /* + |-------------------------------------------------------------------------- + | Sanctum Middleware + |-------------------------------------------------------------------------- + | + | When authenticating your first-party SPA with Sanctum you may need to + | customize some of the middleware Sanctum uses while processing the + | request. You may change the middleware listed below as required. + | + */ + + 'middleware' => [ + 'verify_csrf_token' => App\Http\Middleware\VerifyCsrfToken::class, + 'encrypt_cookies' => App\Http\Middleware\EncryptCookies::class, + ], + +]; diff --git a/Laravel_app/config/services.php b/Laravel_app/config/services.php new file mode 100644 index 0000000..0ace530 --- /dev/null +++ b/Laravel_app/config/services.php @@ -0,0 +1,34 @@ + [ + 'domain' => env('MAILGUN_DOMAIN'), + 'secret' => env('MAILGUN_SECRET'), + 'endpoint' => env('MAILGUN_ENDPOINT', 'api.mailgun.net'), + 'scheme' => 'https', + ], + + 'postmark' => [ + 'token' => env('POSTMARK_TOKEN'), + ], + + 'ses' => [ + 'key' => env('AWS_ACCESS_KEY_ID'), + 'secret' => env('AWS_SECRET_ACCESS_KEY'), + 'region' => env('AWS_DEFAULT_REGION', 'us-east-1'), + ], + +]; diff --git a/Laravel_app/config/session.php b/Laravel_app/config/session.php new file mode 100644 index 0000000..8fed97c --- /dev/null +++ b/Laravel_app/config/session.php @@ -0,0 +1,201 @@ + env('SESSION_DRIVER', 'file'), + + /* + |-------------------------------------------------------------------------- + | Session Lifetime + |-------------------------------------------------------------------------- + | + | Here you may specify the number of minutes that you wish the session + | to be allowed to remain idle before it expires. If you want them + | to immediately expire on the browser closing, set that option. + | + */ + + 'lifetime' => env('SESSION_LIFETIME', 120), + + 'expire_on_close' => false, + + /* + |-------------------------------------------------------------------------- + | Session Encryption + |-------------------------------------------------------------------------- + | + | This option allows you to easily specify that all of your session data + | should be encrypted before it is stored. All encryption will be run + | automatically by Laravel and you can use the Session like normal. + | + */ + + 'encrypt' => false, + + /* + |-------------------------------------------------------------------------- + | Session File Location + |-------------------------------------------------------------------------- + | + | When using the native session driver, we need a location where session + | files may be stored. A default has been set for you but a different + | location may be specified. This is only needed for file sessions. + | + */ + + 'files' => storage_path('framework/sessions'), + + /* + |-------------------------------------------------------------------------- + | Session Database Connection + |-------------------------------------------------------------------------- + | + | When using the "database" or "redis" session drivers, you may specify a + | connection that should be used to manage these sessions. This should + | correspond to a connection in your database configuration options. + | + */ + + 'connection' => env('SESSION_CONNECTION'), + + /* + |-------------------------------------------------------------------------- + | Session Database Table + |-------------------------------------------------------------------------- + | + | When using the "database" session driver, you may specify the table we + | should use to manage the sessions. Of course, a sensible default is + | provided for you; however, you are free to change this as needed. + | + */ + + 'table' => 'sessions', + + /* + |-------------------------------------------------------------------------- + | Session Cache Store + |-------------------------------------------------------------------------- + | + | While using one of the framework's cache driven session backends you may + | list a cache store that should be used for these sessions. This value + | must match with one of the application's configured cache "stores". + | + | Affects: "apc", "dynamodb", "memcached", "redis" + | + */ + + 'store' => env('SESSION_STORE'), + + /* + |-------------------------------------------------------------------------- + | Session Sweeping Lottery + |-------------------------------------------------------------------------- + | + | Some session drivers must manually sweep their storage location to get + | rid of old sessions from storage. Here are the chances that it will + | happen on a given request. By default, the odds are 2 out of 100. + | + */ + + 'lottery' => [2, 100], + + /* + |-------------------------------------------------------------------------- + | Session Cookie Name + |-------------------------------------------------------------------------- + | + | Here you may change the name of the cookie used to identify a session + | instance by ID. The name specified here will get used every time a + | new session cookie is created by the framework for every driver. + | + */ + + 'cookie' => env( + 'SESSION_COOKIE', + Str::slug(env('APP_NAME', 'laravel'), '_').'_session' + ), + + /* + |-------------------------------------------------------------------------- + | Session Cookie Path + |-------------------------------------------------------------------------- + | + | The session cookie path determines the path for which the cookie will + | be regarded as available. Typically, this will be the root path of + | your application but you are free to change this when necessary. + | + */ + + 'path' => '/', + + /* + |-------------------------------------------------------------------------- + | Session Cookie Domain + |-------------------------------------------------------------------------- + | + | Here you may change the domain of the cookie used to identify a session + | in your application. This will determine which domains the cookie is + | available to in your application. A sensible default has been set. + | + */ + + 'domain' => env('SESSION_DOMAIN'), + + /* + |-------------------------------------------------------------------------- + | HTTPS Only Cookies + |-------------------------------------------------------------------------- + | + | By setting this option to true, session cookies will only be sent back + | to the server if the browser has a HTTPS connection. This will keep + | the cookie from being sent to you when it can't be done securely. + | + */ + + 'secure' => env('SESSION_SECURE_COOKIE'), + + /* + |-------------------------------------------------------------------------- + | HTTP Access Only + |-------------------------------------------------------------------------- + | + | Setting this value to true will prevent JavaScript from accessing the + | value of the cookie and the cookie will only be accessible through + | the HTTP protocol. You are free to modify this option if needed. + | + */ + + 'http_only' => true, + + /* + |-------------------------------------------------------------------------- + | Same-Site Cookies + |-------------------------------------------------------------------------- + | + | This option determines how your cookies behave when cross-site requests + | take place, and can be used to mitigate CSRF attacks. By default, we + | will set this value to "lax" since this is a secure default value. + | + | Supported: "lax", "strict", "none", null + | + */ + + 'same_site' => 'lax', + +]; diff --git a/Laravel_app/config/view.php b/Laravel_app/config/view.php new file mode 100644 index 0000000..22b8a18 --- /dev/null +++ b/Laravel_app/config/view.php @@ -0,0 +1,36 @@ + [ + resource_path('views'), + ], + + /* + |-------------------------------------------------------------------------- + | Compiled View Path + |-------------------------------------------------------------------------- + | + | This option determines where all the compiled Blade templates will be + | stored for your application. Typically, this is within the storage + | directory. However, as usual, you are free to change this value. + | + */ + + 'compiled' => env( + 'VIEW_COMPILED_PATH', + realpath(storage_path('framework/views')) + ), + +]; diff --git a/Laravel_app/database/.gitignore b/Laravel_app/database/.gitignore new file mode 100644 index 0000000..9b19b93 --- /dev/null +++ b/Laravel_app/database/.gitignore @@ -0,0 +1 @@ +*.sqlite* diff --git a/Laravel_app/database/factories/UserFactory.php b/Laravel_app/database/factories/UserFactory.php new file mode 100644 index 0000000..a6ecc0a --- /dev/null +++ b/Laravel_app/database/factories/UserFactory.php @@ -0,0 +1,38 @@ + + */ +class UserFactory extends Factory +{ + /** + * Define the model's default state. + * + * @return array + */ + public function definition(): array + { + return [ + 'name' => fake()->name(), + 'email' => fake()->unique()->safeEmail(), + 'email_verified_at' => now(), + 'password' => '$2y$10$92IXUNpkjO0rOQ5byMi.Ye4oKoEa3Ro9llC/.og/at2.uheWG/igi', // password + 'remember_token' => Str::random(10), + ]; + } + + /** + * Indicate that the model's email address should be unverified. + */ + public function unverified(): static + { + return $this->state(fn (array $attributes) => [ + 'email_verified_at' => null, + ]); + } +} diff --git a/Laravel_app/database/migrations/2014_10_12_000000_create_users_table.php b/Laravel_app/database/migrations/2014_10_12_000000_create_users_table.php new file mode 100644 index 0000000..444fafb --- /dev/null +++ b/Laravel_app/database/migrations/2014_10_12_000000_create_users_table.php @@ -0,0 +1,32 @@ +id(); + $table->string('name'); + $table->string('email')->unique(); + $table->timestamp('email_verified_at')->nullable(); + $table->string('password'); + $table->rememberToken(); + $table->timestamps(); + }); + } + + /** + * Reverse the migrations. + */ + public function down(): void + { + Schema::dropIfExists('users'); + } +}; diff --git a/Laravel_app/database/migrations/2014_10_12_100000_create_password_reset_tokens_table.php b/Laravel_app/database/migrations/2014_10_12_100000_create_password_reset_tokens_table.php new file mode 100644 index 0000000..81a7229 --- /dev/null +++ b/Laravel_app/database/migrations/2014_10_12_100000_create_password_reset_tokens_table.php @@ -0,0 +1,28 @@ +string('email')->primary(); + $table->string('token'); + $table->timestamp('created_at')->nullable(); + }); + } + + /** + * Reverse the migrations. + */ + public function down(): void + { + Schema::dropIfExists('password_reset_tokens'); + } +}; diff --git a/Laravel_app/database/migrations/2019_08_19_000000_create_failed_jobs_table.php b/Laravel_app/database/migrations/2019_08_19_000000_create_failed_jobs_table.php new file mode 100644 index 0000000..249da81 --- /dev/null +++ b/Laravel_app/database/migrations/2019_08_19_000000_create_failed_jobs_table.php @@ -0,0 +1,32 @@ +id(); + $table->string('uuid')->unique(); + $table->text('connection'); + $table->text('queue'); + $table->longText('payload'); + $table->longText('exception'); + $table->timestamp('failed_at')->useCurrent(); + }); + } + + /** + * Reverse the migrations. + */ + public function down(): void + { + Schema::dropIfExists('failed_jobs'); + } +}; diff --git a/Laravel_app/database/migrations/2019_12_14_000001_create_personal_access_tokens_table.php b/Laravel_app/database/migrations/2019_12_14_000001_create_personal_access_tokens_table.php new file mode 100644 index 0000000..e828ad8 --- /dev/null +++ b/Laravel_app/database/migrations/2019_12_14_000001_create_personal_access_tokens_table.php @@ -0,0 +1,33 @@ +id(); + $table->morphs('tokenable'); + $table->string('name'); + $table->string('token', 64)->unique(); + $table->text('abilities')->nullable(); + $table->timestamp('last_used_at')->nullable(); + $table->timestamp('expires_at')->nullable(); + $table->timestamps(); + }); + } + + /** + * Reverse the migrations. + */ + public function down(): void + { + Schema::dropIfExists('personal_access_tokens'); + } +}; diff --git a/Laravel_app/database/seeders/DatabaseSeeder.php b/Laravel_app/database/seeders/DatabaseSeeder.php new file mode 100644 index 0000000..a9f4519 --- /dev/null +++ b/Laravel_app/database/seeders/DatabaseSeeder.php @@ -0,0 +1,22 @@ +create(); + + // \App\Models\User::factory()->create([ + // 'name' => 'Test User', + // 'email' => 'test@example.com', + // ]); + } +} diff --git a/Laravel_app/package-lock.json b/Laravel_app/package-lock.json new file mode 100644 index 0000000..13a0438 --- /dev/null +++ b/Laravel_app/package-lock.json @@ -0,0 +1,1483 @@ +{ + "name": "Laravel_app", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "dependencies": { + "tailwindcss": "^3.3.3" + }, + "devDependencies": { + "axios": "^1.1.2", + "laravel-vite-plugin": "^0.8.0", + "vite": "^4.0.0" + } + }, + "node_modules/@alloc/quick-lru": { + "version": "5.2.0", + "resolved": "https://registry.npmjs.org/@alloc/quick-lru/-/quick-lru-5.2.0.tgz", + "integrity": 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}, + "less": { + "optional": true + }, + "lightningcss": { + "optional": true + }, + "sass": { + "optional": true + }, + "stylus": { + "optional": true + }, + "sugarss": { + "optional": true + }, + "terser": { + "optional": true + } + } + }, + "node_modules/vite-plugin-full-reload": { + "version": "1.0.5", + "resolved": "https://registry.npmjs.org/vite-plugin-full-reload/-/vite-plugin-full-reload-1.0.5.tgz", + "integrity": "sha512-kVZFDFWr0DxiHn6MuDVTQf7gnWIdETGlZh0hvTiMXzRN80vgF4PKbONSq8U1d0WtHsKaFODTQgJeakLacoPZEQ==", + "dev": true, + "dependencies": { + "picocolors": "^1.0.0", + "picomatch": "^2.3.1" + }, + "peerDependencies": { + "vite": "^2 || ^3 || ^4" + } + }, + "node_modules/wrappy": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", + "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==" + }, + "node_modules/yaml": { + "version": "2.3.2", + "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.3.2.tgz", + "integrity": "sha512-N/lyzTPaJasoDmfV7YTrYCI0G/3ivm/9wdG0aHuheKowWQwGTsK0Eoiw6utmzAnI6pkJa0DUVygvp3spqqEKXg==", + "engines": { + "node": ">= 14" + } + } + } +} diff --git a/Laravel_app/package.json b/Laravel_app/package.json new file mode 100644 index 0000000..f9f46d0 --- /dev/null +++ b/Laravel_app/package.json @@ -0,0 +1,16 @@ +{ + "private": true, + "type": "module", + "scripts": { + "dev": "vite", + "build": "vite build" + }, + "devDependencies": { + "axios": "^1.1.2", + "laravel-vite-plugin": "^0.8.0", + "vite": "^4.0.0" + }, + "dependencies": { + "tailwindcss": "^3.3.3" + } +} diff --git a/Laravel_app/phpunit.xml b/Laravel_app/phpunit.xml new file mode 100644 index 0000000..f112c0c --- /dev/null +++ b/Laravel_app/phpunit.xml @@ -0,0 +1,31 @@ + + + + + tests/Unit + + + tests/Feature + + + + + app + + + + + + + + + + + + + + diff --git a/Laravel_app/public/.htaccess b/Laravel_app/public/.htaccess new file mode 100644 index 0000000..3aec5e2 --- /dev/null +++ b/Laravel_app/public/.htaccess @@ -0,0 +1,21 @@ + + + Options -MultiViews -Indexes + + + RewriteEngine On + + # Handle Authorization Header + RewriteCond %{HTTP:Authorization} . + RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}] + + # Redirect Trailing Slashes If Not A Folder... + RewriteCond %{REQUEST_FILENAME} !-d + RewriteCond %{REQUEST_URI} (.+)/$ + RewriteRule ^ %1 [L,R=301] + + # Send Requests To Front Controller... + RewriteCond %{REQUEST_FILENAME} !-d + RewriteCond %{REQUEST_FILENAME} !-f + RewriteRule ^ index.php [L] + diff --git a/Laravel_app/public/favicon.ico b/Laravel_app/public/favicon.ico new file mode 100644 index 0000000..e69de29 diff --git a/Laravel_app/public/index.php b/Laravel_app/public/index.php new file mode 100644 index 0000000..1d69f3a --- /dev/null +++ b/Laravel_app/public/index.php @@ -0,0 +1,55 @@ +make(Kernel::class); + +$response = $kernel->handle( + $request = Request::capture() +)->send(); + +$kernel->terminate($request, $response); diff --git a/Laravel_app/public/robots.txt b/Laravel_app/public/robots.txt new file mode 100644 index 0000000..eb05362 --- /dev/null +++ b/Laravel_app/public/robots.txt @@ -0,0 +1,2 @@ +User-agent: * +Disallow: diff --git a/Laravel_app/resources/css/app.css b/Laravel_app/resources/css/app.css new file mode 100644 index 0000000..e69de29 diff --git a/Laravel_app/resources/js/app.js b/Laravel_app/resources/js/app.js new file mode 100644 index 0000000..e59d6a0 --- /dev/null +++ b/Laravel_app/resources/js/app.js @@ -0,0 +1 @@ +import './bootstrap'; diff --git a/Laravel_app/resources/js/bootstrap.js b/Laravel_app/resources/js/bootstrap.js new file mode 100644 index 0000000..846d350 --- /dev/null +++ b/Laravel_app/resources/js/bootstrap.js @@ -0,0 +1,32 @@ +/** + * We'll load the axios HTTP library which allows us to easily issue requests + * to our Laravel back-end. This library automatically handles sending the + * CSRF token as a header based on the value of the "XSRF" token cookie. + */ + +import axios from 'axios'; +window.axios = axios; + +window.axios.defaults.headers.common['X-Requested-With'] = 'XMLHttpRequest'; + +/** + * Echo exposes an expressive API for subscribing to channels and listening + * for events that are broadcast by Laravel. Echo and event broadcasting + * allows your team to easily build robust real-time web applications. + */ + +// import Echo from 'laravel-echo'; + +// import Pusher from 'pusher-js'; +// window.Pusher = Pusher; + +// window.Echo = new Echo({ +// broadcaster: 'pusher', +// key: import.meta.env.VITE_PUSHER_APP_KEY, +// cluster: import.meta.env.VITE_PUSHER_APP_CLUSTER ?? 'mt1', +// wsHost: import.meta.env.VITE_PUSHER_HOST ? import.meta.env.VITE_PUSHER_HOST : `ws-${import.meta.env.VITE_PUSHER_APP_CLUSTER}.pusher.com`, +// wsPort: import.meta.env.VITE_PUSHER_PORT ?? 80, +// wssPort: import.meta.env.VITE_PUSHER_PORT ?? 443, +// forceTLS: (import.meta.env.VITE_PUSHER_SCHEME ?? 'https') === 'https', +// enabledTransports: ['ws', 'wss'], +// }); diff --git a/Laravel_app/resources/views/welcome.blade.php b/Laravel_app/resources/views/welcome.blade.php new file mode 100644 index 0000000..638ec96 --- /dev/null +++ b/Laravel_app/resources/views/welcome.blade.php @@ -0,0 +1,140 @@ + + + + + + + Laravel + + + + + + + + + +
+ @if (Route::has('login')) +
+ @auth + Home + @else + Log in + + @if (Route::has('register')) + Register + @endif + @endauth +
+ @endif + +
+
+ + + +
+ +
+
+ +
+
+ + + +
+ +

Documentation

+ +

+ Laravel has wonderful documentation covering every aspect of the framework. Whether you are a newcomer or have prior experience with Laravel, we recommend reading our documentation from beginning to end. +

+
+ + + + + + + +
+
+ + + +
+ +

Laracasts

+ +

+ Laracasts offers thousands of video tutorials on Laravel, PHP, and JavaScript development. Check them out, see for yourself, and massively level up your development skills in the process. +

+
+ + + + + + + +
+
+ + + +
+ +

Laravel News

+ +

+ Laravel News is a community driven portal and newsletter aggregating all of the latest and most important news in the Laravel ecosystem, including new package releases and tutorials. +

+
+ + + + + + +
+
+
+ + + +
+ +

Vibrant Ecosystem

+ +

+ Laravel's robust library of first-party tools and libraries, such as Forge, Vapor, Nova, and Envoyer help you take your projects to the next level. Pair them with powerful open source libraries like Cashier, Dusk, Echo, Horizon, Sanctum, Telescope, and more. +

+
+
+
+
+ +
+
+
+ + + + + Sponsor + +
+
+ +
+ Laravel v{{ Illuminate\Foundation\Application::VERSION }} (PHP v{{ PHP_VERSION }}) +
+
+
+
+ + diff --git a/Laravel_app/routes/api.php b/Laravel_app/routes/api.php new file mode 100644 index 0000000..889937e --- /dev/null +++ b/Laravel_app/routes/api.php @@ -0,0 +1,19 @@ +get('/user', function (Request $request) { + return $request->user(); +}); diff --git a/Laravel_app/routes/channels.php b/Laravel_app/routes/channels.php new file mode 100644 index 0000000..5d451e1 --- /dev/null +++ b/Laravel_app/routes/channels.php @@ -0,0 +1,18 @@ +id === (int) $id; +}); diff --git a/Laravel_app/routes/console.php b/Laravel_app/routes/console.php new file mode 100644 index 0000000..e05f4c9 --- /dev/null +++ b/Laravel_app/routes/console.php @@ -0,0 +1,19 @@ +comment(Inspiring::quote()); +})->purpose('Display an inspiring quote'); diff --git a/Laravel_app/routes/web.php b/Laravel_app/routes/web.php new file mode 100644 index 0000000..d259f33 --- /dev/null +++ b/Laravel_app/routes/web.php @@ -0,0 +1,18 @@ +make(Kernel::class)->bootstrap(); + + return $app; + } +} diff --git a/Laravel_app/tests/Feature/ExampleTest.php b/Laravel_app/tests/Feature/ExampleTest.php new file mode 100644 index 0000000..8364a84 --- /dev/null +++ b/Laravel_app/tests/Feature/ExampleTest.php @@ -0,0 +1,19 @@ +get('/'); + + $response->assertStatus(200); + } +} diff --git a/Laravel_app/tests/TestCase.php b/Laravel_app/tests/TestCase.php new file mode 100644 index 0000000..2932d4a --- /dev/null +++ b/Laravel_app/tests/TestCase.php @@ -0,0 +1,10 @@ +assertTrue(true); + } +} diff --git a/Laravel_app/vite.config.js b/Laravel_app/vite.config.js new file mode 100644 index 0000000..421b569 --- /dev/null +++ b/Laravel_app/vite.config.js @@ -0,0 +1,11 @@ +import { defineConfig } from 'vite'; +import laravel from 'laravel-vite-plugin'; + +export default defineConfig({ + plugins: [ + laravel({ + input: ['resources/css/app.css', 'resources/js/app.js'], + refresh: true, + }), + ], +}); diff --git a/Rplots.pdf b/Rplots.pdf new file mode 100644 index 0000000..a68f07a Binary files /dev/null and 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Ignore VSCode directory +.vscode/ + +# Ignore JetBrains IDEs directory +.idea/ + +# Ignore MacOS directory +.DS_Store + +# Ignore other unwanted file +*.log +*.bak +*.swp +*.swo +*.swp + diff --git a/python_app/Chemba_download.ipynb b/python_app/Chemba_download.ipynb new file mode 100644 index 0000000..e86e00a --- /dev/null +++ b/python_app/Chemba_download.ipynb @@ -0,0 +1,1031 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "b7ca7102-5fd9-481f-90cd-3ba60e288649", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "# $ pip install sentinelhub\n", + "# pip install gdal\n", + "\n", + "import os\n", + "import datetime\n", + "import numpy as np\n", + "import matplotlib.pyplot as plt\n", + "from pathlib import Path\n", + "from osgeo import gdal\n", + "\n", + "from sentinelhub import MimeType, CRS, BBox, SentinelHubRequest, SentinelHubDownloadClient, \\\n", + " DataCollection, bbox_to_dimensions, DownloadRequest, SHConfig, BBoxSplitter, read_data\n", + "\n", + "config = SHConfig()\n", + "\n", + "import time" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "330c967c-2742-4a7a-9a61-28bfdaf8eeca", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "#pip install pipreqs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8f2ec814-76b2-47e6-b74b-a4ffddd908f1", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "49f8496a-a267-4b74-9500-a168e031ed68", + "metadata": {}, + "outputs": [], + "source": [ + "#import pipreqs\n", + "#pipreqs Resilience BV/4002 CMD App - General/4002 CMD Team/4002 TechnicalData/04 WP2 technical/python/Chemba_download.ipynb" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "5491a840-779c-4f0c-8164-c3de738b3298", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "config.sh_client_id = '6e542a89-b040-40ca-8352-8b979ee3067a'\n", + "config.sh_client_secret = 'PiNaFQfP<.)59]rS.*}OF+hlrrzf#k~uqlhy-_F%'" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "eb1fb662-0e25-4ca9-8317-c6953290842b", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "collection_id = 'c691479f-358c-46b1-b0f0-e12b70a9856c'\n", + "byoc = DataCollection.define_byoc(\n", + " collection_id,\n", + " name='planet_data2',\n", + " is_timeless=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "244b5752-4f02-4347-9278-f6a0a46b88f4", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "\"\"\"\n", + "Utilities used by example notebooks\n", + "\"\"\"\n", + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "\n", + "\n", + "def plot_image(image, factor=1.0, clip_range=None, **kwargs):\n", + " \"\"\"\n", + " Utility function for plotting RGB images.\n", + " \"\"\"\n", + " fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(15, 15))\n", + " if clip_range is not None:\n", + " ax.imshow(np.clip(image * factor, *clip_range), **kwargs)\n", + " else:\n", + " ax.imshow(image * factor, **kwargs)\n", + " ax.set_xticks([])\n", + " ax.set_yticks([]) \n", + "\n", + "\n", + "#evalscript_true_color = \"\"\"\n", + "# //VERSION=3\n", + "#\n", + "# function setup() {\n", + "# return {\n", + "# input: [{\n", + "# bands: [\"B1\", \"B2\", \"B3\", \"B4\", \"UDM\"]\n", + "# }],\n", + "# output: {\n", + "# bands: 5\n", + "# }\n", + "# };\n", + "# }\n", + "#\n", + "# function evaluatePixel(sample) {\n", + "# return [2.5 * sample.B1 / 10000, 2.5 * sample.B2 / 10000, 2.5 * sample.B3 / 10000, 2.5 * sample.B4 / 10000, sample.UDM];\n", + "# }\n", + "#\"\"\"\n", + "\n", + "evalscript_true_color = \"\"\"\n", + " //VERSION=3\n", + "\n", + " function setup() {\n", + " return {\n", + " input: [{\n", + " bands: [\"Blue\", \"Green\", \"Red\", \"NIR\", \"UDM\"]\n", + " }],\n", + " output: {\n", + " bands: 5\n", + " }\n", + " };\n", + " }\n", + "\n", + " function evaluatePixel(sample) {\n", + " return [2.5 * sample.Blue / 10000, 2.5 * sample.Green / 10000, 2.5 * sample.Red / 10000, 2.5 * sample.NIR / 10000, sample.UDM];\n", + " }\n", + "\"\"\"\n", + "BASE_PATH_SINGLE_IMAGES = Path('../laravel_app/storage/app/chemba/single_images')\n", + "BASE_PATH_WEEKLY = Path('../laravel_app/storage/app/chemba/weekly_img')\n", + "\n", + "def get_true_color_request(time_interval): \n", + " return SentinelHubRequest(\n", + " evalscript=evalscript_true_color,\n", + " input_data=[\n", + " SentinelHubRequest.input_data(\n", + " data_collection=DataCollection.planet_data2,\n", + " time_interval=time_interval\n", + " )\n", + " ],\n", + " responses=[\n", + " SentinelHubRequest.output_response('default', MimeType.TIFF)\n", + " ],\n", + " bbox=chemba_bbox,\n", + " size=chemba_size,\n", + " config=config,\n", + " data_folder=str(BASE_PATH_SINGLE_IMAGES / date),\n", + "\n", + " )\n", + "\n", + "def get_true_color_request_day_east(time_interval):\n", + " base_path = '../laravel_app/storage/app/chemba/single_images/'\n", + " \n", + " return SentinelHubRequest(\n", + " evalscript=evalscript_true_color,\n", + " input_data=[\n", + " SentinelHubRequest.input_data(\n", + " data_collection=DataCollection.planet_data2,\n", + " time_interval=(time_interval, time_interval)\n", + " )\n", + " ],\n", + " responses=[\n", + " SentinelHubRequest.output_response('default', MimeType.TIFF)\n", + " ],\n", + " bbox=chemba_bbox_east,\n", + " size=chemba_size_east,\n", + " config=config,\n", + " data_folder=str(BASE_PATH_SINGLE_IMAGES / time_interval),\n", + "\n", + " )\n", + "\n", + "def get_true_color_request_day_west(time_interval):\n", + " base_path = '../laravel_app/storage/app/chemba/single_images/'\n", + " return SentinelHubRequest(\n", + " evalscript=evalscript_true_color,\n", + " input_data=[\n", + " SentinelHubRequest.input_data(\n", + " data_collection=DataCollection.planet_data2,\n", + " time_interval=(time_interval, time_interval)\n", + " )\n", + " ],\n", + " responses=[\n", + " SentinelHubRequest.output_response('default', MimeType.TIFF)\n", + " ],\n", + " bbox=chemba_bbox_west,\n", + " size=chemba_size_west,\n", + " config=config,\n", + " data_folder=str(BASE_PATH_SINGLE_IMAGES / time_interval),\n", + "\n", + " )\n", + "\n", + "def get_true_color_request_week(time_interval):\n", + " base_path = '../laravel_app/storage/app/chemba/weekly_img/'\n", + " return SentinelHubRequest(\n", + " evalscript=evalscript_true_color,\n", + " input_data=[\n", + " SentinelHubRequest.input_data(\n", + " data_collection=DataCollection.planet_data2,\n", + " time_interval=time_interval\n", + " )\n", + " ],\n", + " responses=[\n", + " SentinelHubRequest.output_response('default', MimeType.TIFF)\n", + " ],\n", + " bbox=chemba_bbox,\n", + " size=chemba_size,\n", + " config=config,\n", + " data_folder=str(BASE_PATH_SINGLE_IMAGES / date),\n", + " )" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "5abb2cc0-5e2f-46cd-9676-3093d07b0624", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "\n", + "#end = datetime.date.today() - datetime.timedelta(days=1)\n", + "#start = end - datetime.timedelta(days=6)\n", + "\n", + "#end = datetime.date(2022, 7, 1)\n", + "#start = datetime.date(2022, 7, 21)\n", + "\n", + "#n_chunks = start - end\n", + "#n_chunks.days\n" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "a4937240-27f9-44c3-ad9c-cec6f2ffe4c8", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Monthly time windows:\n", + "\n", + "2023-09-30\n", + "2023-10-01\n", + "2023-10-02\n", + "2023-10-03\n", + "2023-10-04\n", + "2023-10-05\n", + "2023-10-06\n" + ] + } + ], + "source": [ + "#end = datetime.date(2022, 8, 4)\n", + "#start = datetime.date(2023, 3, 1)\n", + "days_needed = 6\n", + "\n", + "end = datetime.date.today() - datetime.timedelta(days=days_needed - 1)\n", + "start = end - datetime.timedelta(days=1)\n", + "\n", + "\n", + "n_chunks = days_needed + 1\n", + "tdelta = datetime.timedelta(days=1)\n", + "edges = [(start + i*tdelta).isoformat() for i in range(n_chunks)]\n", + "#slots = [(edges[i], edges[i]) for i in range(len(edges))]\n", + "slots = [(edges[i]) for i in range(len(edges))]\n", + "\n", + "#date = start.strftime(\"%Y-%m-%d\")\n", + "\n", + "print('Monthly time windows:\\n')\n", + "for slot in slots:\n", + " print(slot)" + ] + }, + { + "cell_type": "markdown", + "id": "0c18e312-8421-47d7-84f9-ed7d5e47e7ee", + "metadata": {}, + "source": [ + "### Chemba east side" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "2335139b-dfb1-4371-ae2c-c2b9c8cbf10c", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "chemba_east = [34.8830, -17.3516, 34.9380, -17.2917]\n", + "resolution = 3\n", + "chemba_bbox_east = BBox(bbox=chemba_east, crs=CRS.WGS84)\n", + "chemba_size_east = bbox_to_dimensions(chemba_bbox_east, resolution=resolution)\n", + "\n", + "chemba_west = [34.9460, -17.3500, 34.9839, -17.3110]\n", + "chemba_bbox_west = BBox(bbox=chemba_west, crs=CRS.WGS84)\n", + "chemba_size_west = bbox_to_dimensions(chemba_bbox_west, resolution=resolution)" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "77513576-2fed-4d17-a665-d11267b42390", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def download_function(slot):\n", + " ### Chemba east side\n", + " # create a list of requests \n", + " list_of_requests = [get_true_color_request_day_east(slot)]\n", + " list_of_requests = [request.download_list[0] for request in list_of_requests]\n", + "\n", + " # download data chemba east with multiple threads\n", + " data = SentinelHubDownloadClient(config=config).download(list_of_requests, max_threads=15)\n", + " print(f' East downloaded ' +slot)\n", + "\n", + " ### Chemba west side\n", + " # create a list of requests\n", + " list_of_requests = [get_true_color_request_day_west(slot)]\n", + " list_of_requests = [request.download_list[0] for request in list_of_requests]\n", + "\n", + " # download data chemba west with multiple threads\n", + " data = SentinelHubDownloadClient(config=config).download(list_of_requests, max_threads=15)\n", + " print(f' West downloaded ' +slot)\n", + " \n", + " time.sleep(.5)\n", + "\n", + "def merge_files(slot):\n", + " base_path = Path('../laravel_app/storage/app/chemba')\n", + " # List the downloaded Tiffs in the different subfolders with pathlib (native library)\n", + " file_list = [f\"{x}/response.tiff\" for x in Path(base_path / 'single_images' / slot).iterdir()]\n", + " print(file_list)\n", + "\n", + " folder_for_merged_tifs = str(base_path / 'merged_tif' / f\"{slot}.tif\")\n", + " folder_for_virtual_raster = str(base_path / 'merged_virtual' / f\"merged{slot}.vrt\")\n", + "\n", + " # Create a virtual raster\n", + " vrt_all = gdal.BuildVRT(folder_for_virtual_raster, file_list)\n", + " vrt_all = gdal.BuildVRT(folder_for_virtual_raster, file_list)\n", + "\n", + " # Convert to JPEG\n", + " gdal.Translate(folder_for_merged_tifs,folder_for_virtual_raster)" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "d5830b6e-da0a-416f-867e-cbca4bd434f5", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " East downloaded 2023-09-30\n", + " West downloaded 2023-09-30\n", + " East downloaded 2023-10-01\n", + " West downloaded 2023-10-01\n", + " East downloaded 2023-10-02\n", + " West downloaded 2023-10-02\n", + " East downloaded 2023-10-03\n", + " West downloaded 2023-10-03\n", + " East downloaded 2023-10-04\n", + " West downloaded 2023-10-04\n", + " East downloaded 2023-10-05\n", + " West downloaded 2023-10-05\n", + " East downloaded 2023-10-06\n", + " West downloaded 2023-10-06\n" + ] + } + ], + "source": [ + "for slot in slots:\n", + " download_function(slot)" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "68db3c15-6f94-432e-b315-c329e4251b21", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['chemba_single_images/2023-09-30/369e30117c87ea5a93d4b1fdc1e200f5/response.tiff', 'chemba_single_images/2023-09-30/19f952f0b4dc03e82b31ddda504eca37/response.tiff']\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning 1: chemba_single_images/2023-09-30/369e30117c87ea5a93d4b1fdc1e200f5/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-09-30/19f952f0b4dc03e82b31ddda504eca37/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-09-30/369e30117c87ea5a93d4b1fdc1e200f5/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-09-30/19f952f0b4dc03e82b31ddda504eca37/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-09-30/369e30117c87ea5a93d4b1fdc1e200f5/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-09-30/19f952f0b4dc03e82b31ddda504eca37/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['chemba_single_images/2023-10-01/52579ecea6e4c674f3f15a70692b2470/response.tiff', 'chemba_single_images/2023-10-01/199af70a0a9bdf56a6938888f8ad073c/response.tiff']\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning 1: chemba_single_images/2023-10-01/52579ecea6e4c674f3f15a70692b2470/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-01/199af70a0a9bdf56a6938888f8ad073c/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-01/52579ecea6e4c674f3f15a70692b2470/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-01/199af70a0a9bdf56a6938888f8ad073c/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-01/52579ecea6e4c674f3f15a70692b2470/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-01/199af70a0a9bdf56a6938888f8ad073c/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['chemba_single_images/2023-10-02/131056d1de92580e74203e14cda16072/response.tiff', 'chemba_single_images/2023-10-02/f16e88a64ddff761b1c5b534c18588c5/response.tiff']\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning 1: chemba_single_images/2023-10-02/131056d1de92580e74203e14cda16072/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-02/f16e88a64ddff761b1c5b534c18588c5/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-02/131056d1de92580e74203e14cda16072/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-02/f16e88a64ddff761b1c5b534c18588c5/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-02/131056d1de92580e74203e14cda16072/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-02/f16e88a64ddff761b1c5b534c18588c5/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['chemba_single_images/2023-10-03/7a15a778f1bef721f997fc4c7071a022/response.tiff', 'chemba_single_images/2023-10-03/0cf952e5d972cd1b001c3ca1e0f286fc/response.tiff']\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning 1: chemba_single_images/2023-10-03/7a15a778f1bef721f997fc4c7071a022/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-03/0cf952e5d972cd1b001c3ca1e0f286fc/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-03/7a15a778f1bef721f997fc4c7071a022/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-03/0cf952e5d972cd1b001c3ca1e0f286fc/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-03/7a15a778f1bef721f997fc4c7071a022/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-03/0cf952e5d972cd1b001c3ca1e0f286fc/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['chemba_single_images/2023-10-04/37292b2973437bbcd8164d4b0cb5ce09/response.tiff', 'chemba_single_images/2023-10-04/a3957aa1c1478fed498c3f1e94b8703a/response.tiff']\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning 1: chemba_single_images/2023-10-04/37292b2973437bbcd8164d4b0cb5ce09/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-04/a3957aa1c1478fed498c3f1e94b8703a/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-04/37292b2973437bbcd8164d4b0cb5ce09/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-04/a3957aa1c1478fed498c3f1e94b8703a/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-04/37292b2973437bbcd8164d4b0cb5ce09/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-04/a3957aa1c1478fed498c3f1e94b8703a/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['chemba_single_images/2023-10-05/1ab274c42d49578ad25c592bc16c5c17/response.tiff', 'chemba_single_images/2023-10-05/ca219fceac18e287d129aaca803998f0/response.tiff']\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning 1: chemba_single_images/2023-10-05/1ab274c42d49578ad25c592bc16c5c17/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-05/ca219fceac18e287d129aaca803998f0/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-05/1ab274c42d49578ad25c592bc16c5c17/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-05/ca219fceac18e287d129aaca803998f0/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-05/1ab274c42d49578ad25c592bc16c5c17/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-05/ca219fceac18e287d129aaca803998f0/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['chemba_single_images/2023-10-06/a1c4a82635c5b3379cac01c44428a46c/response.tiff', 'chemba_single_images/2023-10-06/cae35e70e26ce81aff15dcea89246b07/response.tiff']\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning 1: chemba_single_images/2023-10-06/a1c4a82635c5b3379cac01c44428a46c/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-06/cae35e70e26ce81aff15dcea89246b07/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-06/a1c4a82635c5b3379cac01c44428a46c/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-06/cae35e70e26ce81aff15dcea89246b07/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-06/a1c4a82635c5b3379cac01c44428a46c/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: chemba_single_images/2023-10-06/cae35e70e26ce81aff15dcea89246b07/response.tiff: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n", + "Warning 1: TIFFReadDirectory:Sum of Photometric type-related color channels and ExtraSamples doesn't match SamplesPerPixel. Defining non-color channels as ExtraSamples.\n" + ] + } + ], + "source": [ + "for slot in slots:\n", + " merge_files(slot)" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "4f80e84e-95b5-41dc-83d8-720cd699a79a", + "metadata": {}, + "outputs": [ + { + "ename": "SyntaxError", + "evalue": "invalid syntax (4067800170.py, line 1)", + "output_type": "error", + "traceback": [ + "\u001b[0;36m Cell \u001b[0;32mIn[13], line 1\u001b[0;36m\u001b[0m\n\u001b[0;31m stop here\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n" + ] + } + ], + "source": [ + "raise SystemExit(\"Stop right there!\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a8d367da-3eb5-419a-9a8a-d315f8ae8d89", + "metadata": {}, + "outputs": [], + "source": [ + "days = 1\n", + "start = datetime.datetime(2021,3,12)\n", + "end = start + datetime.timedelta(days=days)\n", + "n_chunks = 1\n", + "tdelta = (end - start) / n_chunks\n", + "edges = [(start + i*tdelta).date().isoformat() for i in range(n_chunks)]\n", + "#slots = [(edges[i], edges[i]) for i in range(len(edges))]\n", + "slots = [(edges[i], edges[i]) for i in range(len(edges))]\n", + "\n", + "date = start.strftime(\"%Y-%m-%d\")\n", + "\n", + "print('Monthly time windows:\\n')\n", + "for slot in slots:\n", + " print(slot)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "461cc3fa-4b7a-48aa-abee-25eb97689707", + "metadata": {}, + "outputs": [], + "source": [ + "days = 1\n", + "start = datetime.datetime(2022,4,27)\n", + "end = start + datetime.timedelta(days=days)\n", + "n_chunks = 1\n", + "tdelta = (end - start) / n_chunks\n", + "edges = [(start + i*tdelta).date().isoformat() for i in range(n_chunks)]\n", + "#slots = [(edges[i], edges[i]) for i in range(len(edges))]\n", + "slots = [(edges[i], edges[i]) for i in range(len(edges))]\n", + "\n", + "date = start.strftime(\"%Y-%m-%d\")\n", + "\n", + "### Chemba east side\n", + "chemba_east = [34.8830, -17.3516, 34.9380, -17.2917]\n", + "resolution = 3\n", + "chemba_bbox = BBox(bbox=chemba_east, crs=CRS.WGS84)\n", + "chemba_size = bbox_to_dimensions(chemba_bbox, resolution=resolution)\n", + "\n", + "# create a list of requests \n", + "list_of_requests = [get_true_color_request(slot) for slot in slots]\n", + "list_of_requests = [request.download_list[0] for request in list_of_requests]\n", + "\n", + "# download data with multiple threads\n", + "data = SentinelHubDownloadClient(config=config).download(list_of_requests, max_threads=15)\n", + "\n", + "\n", + "\n", + "### Chemba west side\n", + "chemba_west = [34.9460, -17.3500, 34.9839, -17.3110]\n", + "chemba_bbox = BBox(bbox=chemba_west, crs=CRS.WGS84)\n", + "chemba_size = bbox_to_dimensions(chemba_bbox, resolution=resolution)\n", + "\n", + "print(f'Image shape at {resolution} m resolution: {chemba_size} pixels')\n", + "\n", + "# create a list of requests\n", + "list_of_requests = [get_true_color_request(slot) for slot in slots]\n", + "list_of_requests = [request.download_list[0] for request in list_of_requests]\n", + "\n", + "# download data with multiple threads\n", + "data = SentinelHubDownloadClient(config=config).download(list_of_requests, max_threads=15)\n", + "print(f'data downloaded')\n", + "\n", + "\n" + ] + }, + { + "cell_type": "markdown", + "id": "52b5f742-3db0-4290-a467-688f8aec36d5", + "metadata": {}, + "source": [ + "### Chemba west side" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d14b7a1e-87a6-4344-859c-5e602bd2e006", + "metadata": {}, + "outputs": [], + "source": [ + "a" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e9daf5c9-39f6-44ea-92dd-dee355669b19", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b7f42def-21c2-439c-9e96-a24ca1eb2176", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6c5d6f71-e7af-450f-b6c2-151810220159", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5e6f8a1d-bb36-4e96-b06d-6967ea8f3d98", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4a3c9cc9-ad37-405a-b8bf-996fd474540e", + "metadata": {}, + "outputs": [], + "source": [ + "a " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d2c127e0-eaf6-46b8-af5d-6f8000bf3df3", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "id": "3432ffcf-606f-4c34-8f8c-a21bee6326b4", + "metadata": {}, + "source": [ + "## Visualise the image" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0d6b8db8-a33b-45bc-80a9-877ee1b8b80c", + "metadata": {}, + "outputs": [], + "source": [ + "evalscript_true_color_png = \"\"\"\n", + " //VERSION=3\n", + "\n", + " function setup() {\n", + " return {\n", + " input: [{\n", + " bands: [\"B1\", \"B2\", \"B3\", \"UDM\"]\n", + " }],\n", + " output: {\n", + " bands: 3\n", + " }\n", + " };\n", + " }\n", + "\n", + " function evaluatePixel(sample) {\n", + " return [2.5 * sample.B1 / 10000, 2.5 * sample.B2 / 10000, 2.5 * sample.B3 / 10000, sample.UDM];\n", + " }\n", + "\"\"\"" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e498acb8-8e14-41f4-84cd-54f4648c1716", + "metadata": {}, + "outputs": [], + "source": [ + "def get_true_color_request_png(time_interval):\n", + " return SentinelHubRequest(\n", + " evalscript=evalscript_true_color_png,\n", + " input_data=[\n", + " SentinelHubRequest.input_data(\n", + " data_collection=DataCollection.planet_data,\n", + " time_interval=('2022-02-10', '2022-02-17')\n", + " )\n", + " ],\n", + " responses=[\n", + " SentinelHubRequest.output_response('default', MimeType.PNG)\n", + " ],\n", + " bbox=chemba_bbox,\n", + " size=chemba_size,\n", + " config=config\n", + " )" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "19fd091a-dd67-484f-a1a7-3bce61bc9517", + "metadata": {}, + "outputs": [], + "source": [ + "# create a list of requests\n", + "list_of_requests_png = [get_true_color_request_png(slot) for slot in slots]\n", + "list_of_requests_png = [request.download_list[0] for request in list_of_requests_png]\n", + "\n", + "# download data with multiple threads\n", + "data_png = SentinelHubDownloadClient(config=config).download(list_of_requests_png, max_threads=5)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6d8abc2e-e245-490a-83eb-36f6a5ec0418", + "metadata": {}, + "outputs": [], + "source": [ + "# some stuff for pretty plots\n", + "ncols = 4\n", + "nrows = 7\n", + "aspect_ratio = chemba_size[0] / chemba_size[1]\n", + "subplot_kw = {'xticks': [], 'yticks': [], 'frame_on': False}\n", + "\n", + "fig, axs = plt.subplots(ncols=ncols, nrows=nrows, figsize=(5 * ncols * aspect_ratio, 5 * nrows),\n", + " subplot_kw=subplot_kw)\n", + "\n", + "for idx, image in enumerate(data_png):\n", + " ax = axs[idx // ncols][idx % ncols]\n", + " ax.imshow(np.clip(image * 2.5/255, 0, 1))\n", + " ax.set_title(f'{slots[idx][0]} ', fontsize=10)\n", + "\n", + "plt.tight_layout()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7803cfac-ce53-4461-8702-88b872ef64aa", + "metadata": {}, + "outputs": [], + "source": [ + "evalscript_true_color = \"\"\"\n", + " //VERSION=3\n", + "\n", + " function setup() {\n", + " return {\n", + " input: [{\n", + " bands: [\"B1\", \"B2\", \"B3\"]\n", + " }],\n", + " output: {\n", + " bands: 3\n", + " }\n", + " };\n", + " }\n", + "\n", + " function evaluatePixel(sample) {\n", + " return [sample.B04, sample.B03, sample.B02];\n", + " }\n", + "\"\"\"\n", + "\n", + "request_true_color = SentinelHubRequest(\n", + " evalscript=evalscript_true_color,\n", + " input_data=[\n", + " SentinelHubRequest.input_data(\n", + " data_collection=DataCollection.planet_data2,\n", + " time_interval=('2022-02-01', '2022-02-10'),\n", + " )\n", + " ],\n", + " responses=[\n", + " SentinelHubRequest.output_response('default', MimeType.PNG)\n", + " ],\n", + " bbox=chemba_bbox,\n", + " size=chemba_size,\n", + " config=config\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ab26df2a-f780-4f6b-8d09-0eead9d6db2b", + "metadata": {}, + "outputs": [], + "source": [ + "true_color_imgs = request_true_color.get_data()\n" + ] + }, + { + "cell_type": "markdown", + "id": "a51f41f5-f5e1-4fa7-aef2-53371d1386ce", + "metadata": {}, + "source": [ + "## change file name\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "49a52f5b-2626-4dd2-9e57-6b44691f9952", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import glob\n", + "import json\n", + "import datetime as dt\n", + "from urllib.parse import unquote\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b3720a99-2906-41d9-ac1b-9c9993cd8308", + "metadata": {}, + "outputs": [], + "source": [ + "def get_request_dt(request_file):\n", + " with open(request_file, 'r') as req:\n", + " request = json.load(req)\n", + " url = unquote(request['url'])\n", + " time_parameter = [t for t in url.split('&') if t.startswith('TIME=')][0]\n", + " time = time_parameter.split('TIME=')[1].split('/')[0]\n", + " return dt.datetime.strptime(time, \"%Y-%m-%dT%H:%M:%S\")\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1f4e5844-34bc-4cb9-9365-46356b1db552", + "metadata": {}, + "outputs": [], + "source": [ + "if __name__ == \"__main__\":\n", + " folders = glob.glob('.\\\\test_dir2\\\\*')\n", + " dates = [get_request_dt(f'{folder}/request.json') for folder in folders]\n", + " df = pd.DataFrame(zip(folders, dates), columns=['folder', 'datetime'])\n", + " df.sort_values(by='datetime', ascending=True, inplace=True)\n", + " print(df.head().to_markdown())" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4319580b-f0b7-4370-91f4-bc4fcf068bc3", + "metadata": {}, + "outputs": [], + "source": [ + "def get_request_dt(request_file):\n", + " with open(request_file, 'r') as req:\n", + " request = json.load(req)\n", + " url = unquote(request['url'])\n", + " return url.split('/')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "87580f26-0ccc-4061-a460-52d941a90b6a", + "metadata": {}, + "outputs": [], + "source": [ + "folders = glob.glob('.\\\\test_dir2\\\\*')\n", + "[get_request_dt(f'{folder}/request.json') for folder in folders]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6569956e-91c5-42c9-acfa-74fde22ee1ce", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "folders = glob.glob('.\\\\test_dir2\\\\*')\n", + "dates = [get_request_dt(f'{folder}/request.json') for folder in folders]\n", + "dates" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2608ac51-fa24-4fd6-8758-cf27bda8860e", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.4" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/python_app/chemba_single_images/2023-10-04/37292b2973437bbcd8164d4b0cb5ce09/request.json b/python_app/chemba_single_images/2023-10-04/37292b2973437bbcd8164d4b0cb5ce09/request.json new file mode 100644 index 0000000..2891121 --- /dev/null +++ b/python_app/chemba_single_images/2023-10-04/37292b2973437bbcd8164d4b0cb5ce09/request.json @@ -0,0 +1,65 @@ +{ + "request": { + "headers": { + "accept": "image/tiff", + "content-type": "application/json" + }, + "payload": { + "evalscript": "\n //VERSION=3\n\n function setup() {\n return {\n input: [{\n bands: [\"Blue\", \"Green\", \"Red\", \"NIR\", \"UDM\"]\n }],\n output: {\n bands: 5\n }\n };\n }\n\n function evaluatePixel(sample) {\n return [2.5 * sample.Blue / 10000, 2.5 * sample.Green / 10000, 2.5 * sample.Red / 10000, 2.5 * sample.NIR / 10000, sample.UDM];\n }\n", + "input": { + "bounds": { + "bbox": [ + 34.946, + -17.35, + 34.9839, + -17.311 + ], + "properties": { + "crs": "http://www.opengis.net/def/crs/EPSG/0/4326" + } + }, + "data": [ + { + "dataFilter": { + "timeRange": { + "from": "2023-10-04T00:00:00Z", + "to": "2023-10-04T23:59:59Z" + } + }, + "type": "byoc-c691479f-358c-46b1-b0f0-e12b70a9856c" + } + ] + }, + "output": { + "height": 1425, + "responses": [ + { + "format": { + "type": "image/tiff" + }, + "identifier": "default" + } + ], + "width": 1358 + } + }, + "timestamp": "2023-10-10T11:45:04.511299", + "url": "https://services.sentinel-hub.com/api/v1/process" + }, + "response": { + "elapsed": 3.275736, + "headers": { + "Connection": "keep-alive", + "Content-Type": "image/tiff", + "Date": "Tue, 10 Oct 2023 09:45:04 GMT", + "Transfer-Encoding": "chunked", + "access-control-allow-credentials": "true", + "access-control-allow-headers": "origin,content-type,accept,accept-crs,authorization,cache-control", + "access-control-allow-methods": "GET, POST, PUT, DELETE, OPTIONS, HEAD, PATCH", + "access-control-allow-origin": "*", + "access-control-max-age": "3600", + "x-processingunits-spent": "12.303352062622253" + }, + "status_code": 200 + } +} \ No newline at end of file diff --git a/python_app/chemba_single_images/2023-10-04/a3957aa1c1478fed498c3f1e94b8703a/request.json b/python_app/chemba_single_images/2023-10-04/a3957aa1c1478fed498c3f1e94b8703a/request.json new file mode 100644 index 0000000..94f717d --- /dev/null +++ b/python_app/chemba_single_images/2023-10-04/a3957aa1c1478fed498c3f1e94b8703a/request.json @@ -0,0 +1,65 @@ +{ + "request": { + "headers": { + "accept": "image/tiff", + "content-type": "application/json" + }, + "payload": { + "evalscript": "\n //VERSION=3\n\n function setup() {\n return {\n input: [{\n bands: [\"Blue\", \"Green\", \"Red\", \"NIR\", \"UDM\"]\n }],\n output: {\n bands: 5\n }\n };\n }\n\n function evaluatePixel(sample) {\n return [2.5 * sample.Blue / 10000, 2.5 * sample.Green / 10000, 2.5 * sample.Red / 10000, 2.5 * sample.NIR / 10000, sample.UDM];\n }\n", + "input": { + "bounds": { + "bbox": [ + 34.883, + -17.3516, + 34.938, + -17.2917 + ], + "properties": { + "crs": "http://www.opengis.net/def/crs/EPSG/0/4326" + } + }, + "data": [ + { + "dataFilter": { + "timeRange": { + "from": "2023-10-04T00:00:00Z", + "to": "2023-10-04T23:59:59Z" + } + }, + "type": "byoc-c691479f-358c-46b1-b0f0-e12b70a9856c" + } + ] + }, + "output": { + "height": 2191, + "responses": [ + { + "format": { + "type": "image/tiff" + }, + "identifier": "default" + } + ], + "width": 1971 + } + }, + "timestamp": "2023-10-10T11:45:01.042605", + "url": "https://services.sentinel-hub.com/api/v1/process" + }, + "response": { + "elapsed": 5.668425, + "headers": { + "Connection": "keep-alive", + "Content-Type": "image/tiff", + "Date": "Tue, 10 Oct 2023 09:45:00 GMT", + "Transfer-Encoding": "chunked", + "access-control-allow-credentials": "true", + "access-control-allow-headers": "origin,content-type,accept,accept-crs,authorization,cache-control", + "access-control-allow-methods": "GET, POST, PUT, DELETE, OPTIONS, HEAD, PATCH", + "access-control-allow-origin": "*", + "access-control-max-age": "3600", + "x-processingunits-spent": "27.456034959410772" + }, + "status_code": 200 + } +} \ No newline at end of file diff --git a/python_app/chemba_single_images/2023-10-05/1ab274c42d49578ad25c592bc16c5c17/request.json b/python_app/chemba_single_images/2023-10-05/1ab274c42d49578ad25c592bc16c5c17/request.json new file mode 100644 index 0000000..af9a1f6 --- /dev/null +++ b/python_app/chemba_single_images/2023-10-05/1ab274c42d49578ad25c592bc16c5c17/request.json @@ -0,0 +1,65 @@ +{ + "request": { + "headers": { + "accept": "image/tiff", + "content-type": "application/json" + }, + "payload": { + "evalscript": "\n //VERSION=3\n\n function setup() {\n return {\n input: [{\n bands: [\"Blue\", \"Green\", \"Red\", \"NIR\", \"UDM\"]\n }],\n output: {\n bands: 5\n }\n };\n }\n\n function evaluatePixel(sample) {\n return [2.5 * sample.Blue / 10000, 2.5 * sample.Green / 10000, 2.5 * sample.Red / 10000, 2.5 * sample.NIR / 10000, sample.UDM];\n }\n", + "input": { + "bounds": { + "bbox": [ + 34.946, + -17.35, + 34.9839, + -17.311 + ], + "properties": { + "crs": "http://www.opengis.net/def/crs/EPSG/0/4326" + } + }, + "data": [ + { + "dataFilter": { + "timeRange": { + "from": "2023-10-05T00:00:00Z", + "to": "2023-10-05T23:59:59Z" + } + }, + "type": "byoc-c691479f-358c-46b1-b0f0-e12b70a9856c" + } + ] + }, + "output": { + "height": 1425, + "responses": [ + { + "format": { + "type": "image/tiff" + }, + "identifier": "default" + } + ], + "width": 1358 + } + }, + "timestamp": "2023-10-10T11:45:13.161955", + "url": "https://services.sentinel-hub.com/api/v1/process" + }, + "response": { + "elapsed": 2.723803, + "headers": { + "Connection": "keep-alive", + "Content-Type": "image/tiff", + "Date": "Tue, 10 Oct 2023 09:45:13 GMT", + "Transfer-Encoding": "chunked", + "access-control-allow-credentials": "true", + "access-control-allow-headers": "origin,content-type,accept,accept-crs,authorization,cache-control", + "access-control-allow-methods": "GET, POST, PUT, DELETE, OPTIONS, HEAD, PATCH", + "access-control-allow-origin": "*", + "access-control-max-age": "3600", + "x-processingunits-spent": "12.303352062622253" + }, + "status_code": 200 + } +} \ No newline at end of file diff --git a/python_app/chemba_single_images/2023-10-05/ca219fceac18e287d129aaca803998f0/request.json b/python_app/chemba_single_images/2023-10-05/ca219fceac18e287d129aaca803998f0/request.json new file mode 100644 index 0000000..653cc8a --- /dev/null +++ b/python_app/chemba_single_images/2023-10-05/ca219fceac18e287d129aaca803998f0/request.json @@ -0,0 +1,65 @@ +{ + "request": { + "headers": { + "accept": "image/tiff", + "content-type": "application/json" + }, + "payload": { + "evalscript": "\n //VERSION=3\n\n function setup() {\n return {\n input: [{\n bands: [\"Blue\", \"Green\", \"Red\", \"NIR\", \"UDM\"]\n }],\n output: {\n bands: 5\n }\n };\n }\n\n function evaluatePixel(sample) {\n return [2.5 * sample.Blue / 10000, 2.5 * sample.Green / 10000, 2.5 * sample.Red / 10000, 2.5 * sample.NIR / 10000, sample.UDM];\n }\n", + "input": { + "bounds": { + "bbox": [ + 34.883, + -17.3516, + 34.938, + -17.2917 + ], + "properties": { + "crs": "http://www.opengis.net/def/crs/EPSG/0/4326" + } + }, + "data": [ + { + "dataFilter": { + "timeRange": { + "from": "2023-10-05T00:00:00Z", + "to": 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a/r_app/.gitignore b/r_app/.gitignore new file mode 100644 index 0000000..2241998 --- /dev/null +++ b/r_app/.gitignore @@ -0,0 +1,18 @@ +# .gitignore + +# Ignore renv binary cache +renv/cache/ + +# Ignore temporary files +*.tmp +*.swp +*.save + +# Ignore files related to Rproj +.Rproj.user/ +.Rhistory +.RData + +# Ignore OSX files +.DS_Store + diff --git a/r_app/1_harvest_data_EcoFarm_v2.R b/r_app/1_harvest_data_EcoFarm_v2.R new file mode 100644 index 0000000..80cb946 --- /dev/null +++ b/r_app/1_harvest_data_EcoFarm_v2.R @@ -0,0 +1,178 @@ +#download excel with planting dates +library(googledrive) +library(here) +library(tidyverse) +library(lubridate) +library(readxl) + +#create directory +storage_dir <- here("laravel_app/storage/app") +data_dir <- here(storage_dir, "Data") +harvest_dir <- here(data_dir, "HarvestData") + +dir.create(file.path(data_dir)) +dir.create(file.path(harvest_dir)) + + +week = ymd(Sys.Date()) +file_name <- here(harvest_dir, paste("Data", week, ".xlsx")) +# yield_file_path <- here("Data", "HarvestData", paste("Current - Pivots planting date and harvesting data.xlsx")) + +#Check its existence +if (file.exists(file_name)) { + #Delete file if it exists + file.remove(file_name) + print("File deleted") +} + +#options(gargle_oauth_email = "henkpoldergraaf@gmail.com") + +#folder_url <- "https://docs.google.com/spreadsheets/d/1KPOPHvlzTBDvgFCYQetss0yoafeZeoNW/edit?rtpof=true#gid=1683410275" +#folder <- drive_get(as_id(folder_url)) + +#drive_download(folder, file_name, overwrite = T) + +excel_file_name = here(storage_dir,"harvesting_data", "Current - Pivots planting date and harevsting data.xlsx") + +# library(googlesheets4) +# read_sheet(folder_url) +#get dates in same column + +dates <- read_excel(excel_file_name, + skip=1, + col_types = c("text", "numeric", "text", "date", "numeric", "numeric", "numeric", + "date", "numeric", "skip", "skip", "numeric", "numeric", "numeric","skip", #2020 harvesting data + "date", "numeric", "skip", "skip", "numeric", "numeric", "numeric","skip", #2021 harvesting data + "date", "numeric", "skip", "skip", "numeric", "skip", "numeric","skip", #2022 harvesting data + "date", "numeric", "skip", "skip", "skip", "skip", "skip", "skip", "skip", "skip", "skip", "numeric", "numeric","numeric","skip", #2023 + "skip", "skip", "skip", "skip", "skip", "skip","skip", "skip")) %>% #empty columns + rename(pivot_quadrant = PIVOT, + planting_date = `Date planted`, + Age = `Age (WEEK)`, + Year_replanted = `Year replanted`, + Harvesting_date_2020 = `2020 Harvest data`, + Harvesting_age_2020 = `...9`, + MT_weight_2020 = `...10`, + Tcha_2020 = `...11`, + Tchm_2020 = `...12`, + Harvesting_date_2021 = `2021/2022 Harvest data`, + Harvesting_age_2021 = `...14`, + MT_weight_2021 = `...15`, + Tcha_2021 = `...16`, + Tchm_2021 = `...17`, + Harvesting_date_2022 = `2022/2023 Harvest data`, + Harvesting_age_2022 = `...19`, + MT_weight_2022 = `...20`, + Tcha_2022 = `...21`) %>% + + slice(-1) %>% #select(-age) %>% + filter(pivot_quadrant != "Total") %>% #drop_na(pivot_quadrant) %>% + mutate(planting_date = ymd(planting_date ), + Harvesting_date_2020 = ymd(Harvesting_date_2020), + Harvesting_date_2021 = ymd(Harvesting_date_2021), + Harvesting_date_2022= ymd(Harvesting_date_2022), + Age = round(Age,0)) %>% filter(pivot_quadrant != "Total/Average") + +#copy each row and add ABCD +quadrants <- dates %>% slice(rep(1:n(), each=4)) %>% + group_by(pivot_quadrant) %>% + mutate(pivot_quadrant = paste0(pivot_quadrant, c("A", "B", "C", "D"))) %>% + filter(pivot_quadrant != "P1.8D" & pivot_quadrant != "P1.8 Q.DA"& pivot_quadrant != "P1.8 Q.DB"& pivot_quadrant != "P1.8 Q.DC") %>% + mutate(pivot_quadrant = case_when(pivot_quadrant == "P1.3 ABA" ~ "P1.3A", + pivot_quadrant == "P1.3 ABB" ~ "1.3B", + pivot_quadrant == "P1.3 ABC" ~ "1.3A", + pivot_quadrant == "P1.3 ABD" ~ "1.3A", + pivot_quadrant == "P1.3 CDA" ~ "1.3C", + pivot_quadrant == "P1.3 CDB" ~ "1.3D", + pivot_quadrant == "P1.3 CDC" ~ "1.3C", + pivot_quadrant == "P1.3 CDD" ~ "1.3C", + + pivot_quadrant == "P1.8 Q.DD" ~ "1.8D", + + pivot_quadrant == "P1.9.ABA" ~ "1.9A", + pivot_quadrant == "P1.9.ABB" ~ "1.9B", + pivot_quadrant == "P1.9.ABC" ~ "1.9A", + pivot_quadrant == "P1.9.ABD" ~ "1.9A", + pivot_quadrant == "P1.9.CDA" ~ "1.9C", + pivot_quadrant == "P1.9.CDB" ~ "1.9D", + pivot_quadrant == "P1.9.CDC" ~ "1.9C", + pivot_quadrant == "P1.9.CDD" ~ "1.9C", + + pivot_quadrant == "P2.3AA" ~ "2.3A", + pivot_quadrant == "P2.3AB" ~ "2.3A", + pivot_quadrant == "P2.3AC" ~ "2.3A", + pivot_quadrant == "P2.3AD" ~ "2.3A", + pivot_quadrant == "P2.3DA" ~ "2.3D", + pivot_quadrant == "P2.3DB" ~ "2.3D", + pivot_quadrant == "P2.3DC" ~ "2.3D", + pivot_quadrant == "P2.3DD" ~ "2.3D", + pivot_quadrant == "P2.3BCA" ~ "2.3B", + pivot_quadrant == "P2.3BCB" ~ "2.3B", + pivot_quadrant == "P2.3BCC" ~ "2.3C", + pivot_quadrant == "P2.3BCD" ~ "2.3C", + + pivot_quadrant == "P2.5 ABA" ~ "2.5A", + pivot_quadrant == "P2.5 ABB" ~ "2.5B", + pivot_quadrant == "P2.5 ABC" ~ "2.5A", + pivot_quadrant == "P2.5 ABD" ~ "2.5A", + pivot_quadrant == "P2.5 CDA" ~ "2.5C", + pivot_quadrant == "P2.5 CDB" ~ "2.5D", + pivot_quadrant == "P2.5 CDC" ~ "2.5C", + pivot_quadrant == "P2.5 CDD" ~ "2.5C", + + pivot_quadrant == "P3.1ABA" ~ "3.1A", + pivot_quadrant == "P3.1ABB" ~ "3.1B", + pivot_quadrant == "P3.1ABC" ~ "3.1A", + pivot_quadrant == "P3.1ABD" ~ "3.1A", + pivot_quadrant == "P3.1CDA" ~ "3.1C", + pivot_quadrant == "P3.1CDB" ~ "3.1D", + pivot_quadrant == "P3.1CDC" ~ "3.1C", + pivot_quadrant == "P3.1CDD" ~ "3.1C", + + pivot_quadrant == "P3.2 ABA" ~ "3.2A", + pivot_quadrant == "P3.2 ABB" ~ "3.2B", + pivot_quadrant == "P3.2 ABC" ~ "3.2A", + pivot_quadrant == "P3.2 ABD" ~ "3.2A", + pivot_quadrant == "P3.2 CDA" ~ "3.2C", + pivot_quadrant == "P3.2 CDB" ~ "3.2D", + pivot_quadrant == "P3.2 CDC" ~ "3.2C", + pivot_quadrant == "P3.2 CDD" ~ "3.2C", + + pivot_quadrant == "DL 1.3A" ~ "DL1.3", + pivot_quadrant == "DL 1.3B" ~ "DL1.3", + pivot_quadrant == "DL 1.3C" ~ "DL1.3", + pivot_quadrant == "DL 1.3D" ~ "DL1.3", + + pivot_quadrant == "DL 1.1A" ~ "DL1.1", + pivot_quadrant == "DL 1.1B" ~ "DL1.1", + pivot_quadrant == "DL 1.1C" ~ "DL1.1", + pivot_quadrant == "DL 1.1D" ~ "DL1.1", + + TRUE ~ pivot_quadrant) ) %>% unique() %>% + mutate_at("pivot_quadrant", str_replace, "P", "") %>% + mutate(pivot = pivot_quadrant) %>% + mutate_at("pivot",str_replace, "[ABCD]", "") %>% + mutate(pivot = case_when(pivot == "L1.1"~"DL1.1", + pivot == "L1.3" ~"DL1.3", + TRUE ~ pivot)) + +quadrants2 <- quadrants %>% + mutate( + season_start_2021 = case_when(!is.na(Harvesting_date_2021) ~ Harvesting_date_2021 - (Harvesting_age_2021 * 30)) , + season_end_2021 = case_when(!is.na(Harvesting_date_2021) ~ Harvesting_date_2021), + + season_start_2022 = case_when(is.na(Harvesting_date_2021) & !is.na(Harvesting_date_2022) ~ Harvesting_date_2022 - (Harvesting_age_2022 * 30), + !is.na(Harvesting_date_2021) & !is.na(Harvesting_date_2022) ~ Harvesting_date_2021 + ), + season_end_2022 = case_when(!is.na(Harvesting_date_2022) & !is.na(season_start_2022) ~ Harvesting_date_2022), + + season_start_2023 = case_when(Ratoons == 0 ~ planting_date, + TRUE ~ Harvesting_date_2022), + season_start_2023 = case_when(is.na(Harvesting_date_2022) ~ Harvesting_date_2021, + TRUE ~ season_start_2023), + season_end_2023 = case_when(!is.na(season_start_2023) ~ ymd(Sys.Date())) + + ) + +saveRDS(quadrants2, here(harvest_dir, "harvest_data_new")) + diff --git a/r_app/2_CI_data_prep.R b/r_app/2_CI_data_prep.R new file mode 100644 index 0000000..33975a3 --- /dev/null +++ b/r_app/2_CI_data_prep.R @@ -0,0 +1,218 @@ +library(here) +library(sf) +library(tidyverse) +library(lubridate) +library(terra) +library(exactextractr) + +library(CIprep) + + +laravel_storage_dir <- here("laravel_app/storage/app") +#preparing directories +planet_tif_folder <- here(laravel_storage_dir, "chemba/merged_tif") + +data_dir <- here(laravel_storage_dir, "Data") +extracted_CI_dir <- here(data_dir, "extracted_CI") +daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals") +cumulative_CI_vals_dir <- here(extracted_CI_dir, "cumulative_vals") + +weekly_CI_mosaic <- here(data_dir, "weekly_mosaic") +harvest_dir <- here(data_dir, "HarvestData") + +dir.create(here(extracted_CI_dir)) +dir.create(here(daily_CI_vals_dir)) +dir.create(here(cumulative_CI_vals_dir)) +dir.create(here(weekly_CI_mosaic)) + + + + +# Creating weekly mosaic +dates <- date_list(0) + +#load pivot geojson +pivot_sf_q <- st_read(here(geojson_dir, "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect() + +#load and filter raster files +raster_files <- list.files(planet_tif_folder,full.names = T, pattern = ".tif") #use pattern = '.tif$' or something else if you have multiple files in this folder +filtered_files <- map(dates$days_filter, ~ raster_files[grepl(pattern = .x, x = raster_files)]) %>% + compact() %>% + flatten_chr() + +rasters_masked <- map(filtered_files, mask_raster, fields = pivot_sf_q) %>% set_names(filtered_files) + +rasters_masked[sapply(rasters_masked, is.null)] <- NULL + +rasters_masked <- setNames(rasters_masked, map_chr(names(rasters_masked), date_extract)) + +total_pix_area <- rast(filtered_files[1]) %>% terra::subset(1) %>% + crop(pivot_sf_q, mask = TRUE) %>% + global(., fun="notNA") #%>% +# as.matrix() %>% +# `[`(1, 1) + +total_pix_area <- rast(filtered_files[1]) %>% subset(1) %>% crop(pivot_sf_q, mask = TRUE) %>% freq(., usenames = TRUE) + + + +layer_5_list <- purrr::map(rasters_masked, function(spatraster) { + spatraster[[5]] +}) %>% rast() + +cloud_perc_list <- freq(layer_5_list, usenames = TRUE) %>% + mutate(cloud_perc = (100 -((count/sum(total_pix_area$count))*100)), + cloud_thres_5perc = as.integer(cloud_perc < 5), + cloud_thres_40perc = as.integer(cloud_perc < 40)) %>% + rename(Date = layer) %>% select(-value, -count) + +cloud_index_5perc <- which(cloud_perc_list$cloud_thres_5perc == max(cloud_perc_list$cloud_thres_5perc)) +cloud_index_40perc <- which(cloud_perc_list$cloud_thres_40perc == max(cloud_perc_list$cloud_thres_40perc)) + +## Create mosaic + +if(sum(cloud_perc_list$cloud_thres_5perc)>1){ + message("More than 1 raster without clouds (<5%), max composite made") + + cloudy_rasters_list <- rasters_masked[cloud_index_5perc] + raster_list_subset <- lapply(cloudy_rasters_list, function(r) { + subset(r, 6)}) + + rsrc <- sprc(raster_list_subset) + x <- mosaic(rsrc, fun = "max") + + # x <- rast(rasters_masked[cloud_index_5perc[1]]) + names(x) <- "CI" + # writeRaster(x, here(weekly_CI_mosaic ,paste0("week_", dates$week, "_", dates$year, ".tif")), overwrite=TRUE) + # message("raster exported") + +}else if(sum(cloud_perc_list$cloud_thres_5perc)==1){ + message("Only 1 raster without clouds (<5%)") + + x <- rast(rasters_masked[cloud_index_5perc[1]]) + names(x) <- c("red", "green", "blue","nir", "cloud" ,"CI") + + rsrc <- sprc(raster_list_subset) + x <- mosaic(rsrc, fun = "max") + + # x <- rast(rasters_masked[cloud_index_5perc[1]]) + names(x) <- "CI" + # writeRaster(x, here(weekly_CI_mosaic ,paste0("week_", dates$week, "_", dates$year, ".tif")), overwrite=TRUE) + # message("raster exported") + +}else if(sum(cloud_perc_list$cloud_thres_40perc)>1){ + message("More than 1 image contains clouds, composite made of <40% cloud cover images") + + cloudy_rasters_list <- rasters_masked[cloud_index_40perc] + raster_list_subset <- lapply(cloudy_rasters_list, function(r) { + subset(r, 6) + }) + + rsrc <- sprc(raster_list_subset) + x <- mosaic(rsrc, fun = "max") + names(x) <- "CI" + # writeRaster(x, here(weekly_CI_mosaic ,paste0("week_", dates$week, "_", dates$year, ".tif")), overwrite=TRUE) + # message("raster exported") + +}else{ + message("No cloud free images available") + x <- rast(rasters_masked[1]) + x[x] <- NA + names(x) <- c("red", "green", "blue","nir", "cloud" ,"CI") + # writeRaster(x, here(weekly_CI_mosaic ,paste0("week_", dates$week, "_", dates$year, ".tif")), overwrite=TRUE) + # message("raster exported") + +} + +plot(x$CI, main = paste("CI map", dates$week)) +#plotRGB(x, main = paste("RGB image week", dates$week)) + +# writeRaster(x, here(weekly_CI_mosaic ,paste0("week_", dates$week, "_", dates$year, ".tif")), overwrite=TRUE) +writeRaster(x, here(weekly_CI_mosaic ,paste0("week_", dates$week, "_", dates$year, ".tif")), overwrite=TRUE) + + + +# Extracting CI + +# pivot_sf_q <- st_read(here("..", "Data", "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% vect() +pivot_sf <- st_read(here(data_dir, "pivot_20210625.geojson")) %>% dplyr::select(pivot, pivot_quadrant) %>% group_by(pivot) %>% summarise() %>% vect() + +walk(filtered_files, extract_rasters_daily, field_geojson= pivot_sf_q, quadrants = TRUE, daily_CI_vals_dir) + +pivots_dates0 <- readRDS(here(harvest_dir, "harvest_data_new")) %>% filter( + pivot %in% c("1.1", "1.2", "1.3", "1.4", "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", + "1.14" , "1.16" , "1.17" , "1.18" ,"2.1", "2.2", "2.3" , "2.4", "2.5", "3.1", "3.2", "3.3", + "4.1", "4.2", "4.3", "4.4", "4.5", "4.6", "5.1" ,"5.2", "5.3", "5.4", "6.1", "6.2", "DL1.1", "DL1.3") +) + +# pivots_dates_long <- pivots_dates0 %>% +# select(c("pivot_quadrant", "season_start_2021", "season_end_2021", "season_start_2022", "season_end_2022", "season_start_2023", "season_end_2023")) %>% +# pivot_longer(cols = c("season_start_2021", "season_end_2021", "season_start_2022", "season_end_2022", "season_start_2023", "season_end_2023")) %>% +# separate(pivot_quadrant, into = c("name", "Year"), sep = "\\.") + +harvesting_data <- pivots_dates0 %>% + select(c("pivot_quadrant", "season_start_2021", "season_end_2021", "season_start_2022", "season_end_2022", "season_start_2023", "season_end_2023")) %>% + pivot_longer(cols = starts_with("season"), names_to = "Year", values_to = "value") %>% + separate(Year, into = c("name", "Year"), sep = "(?<=season_start|season_end)\\_", remove = FALSE) %>% + mutate(name = str_to_title(name)) %>% + pivot_wider(names_from = name, values_from = value) %>% + rename(Field = pivot_quadrant) +# extracted_values <- list.files("C:\\Users\\timon\\Resilience BV\\4002 CMD App - General\\4002 CMD Team\\4002 TechnicalData\\04 WP2 technical\\DetectingSpotsR\\EcoFarm\\planet\\extracted", +# pattern ="_quadrant", full.names = TRUE) +extracted_values <- list.files(here(daily_CI_vals_dir), full.names = TRUE) + +head(extracted_values) + +pivot_stats <- extracted_values %>% + map_dfr(readRDS) %>% + group_by(pivot_quadrant) %>% + summarise(across(everything(), ~ first(na.omit(.)))) + +pivots_data_present <- unique(pivots_dates0$pivot_quadrant) +quadrant_list <- pivots_data_present + +# gather data into long format for easier calculation and visualisation +pivot_stats_long <- pivot_stats %>% + tidyr::gather("Date", value, -pivot_quadrant, -pivot ) %>% + mutate(Date = right(Date, 8), + Date = lubridate::ymd(Date) + ) %>% + drop_na(c("value","Date")) %>% + mutate(value = as.numeric(value))%>% + filter_all(all_vars(!is.infinite(.)))%>% + rename(Field = pivot_quadrant) + +# #2021 +pivots_dates_Data_2021 <- pivots_dates0 %>% filter(!is.na(season_start_2021)) +pivot_select_model_Data_2021 <- unique(pivots_dates_Data_2021$pivot_quadrant) + +# #2022 +pivots_dates_Data_2022 <- pivots_dates0 %>% filter(!is.na(season_end_2022)) +pivot_select_model_Data_2022 <- unique(pivots_dates_Data_2022$pivot_quadrant ) +# #2023 +pivots_dates_Data_2023 <- pivots_dates0 %>% filter(!is.na(season_start_2023)) +pivot_select_model_Data_2023 <- unique(pivots_dates_Data_2023$pivot_quadrant) +# #2024 +#pivots_dates_Data_2024 <- pivots_dates0 %>% filter(!is.na(season_start_2024)) +#pivot_select_model_Data_2024 <- unique(pivots_dates_Data_2024$pivot_quadrant) + + +## Extracting the correct CI values + +Data_2021 <- map_dfr(pivot_select_model_Data_2021, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2021)) +Data_2022 <- map_dfr(pivot_select_model_Data_2022, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2022)) +Data_2023 <- map_dfr(pivot_select_model_Data_2023, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2023)) +#Data_2024 <- map_dfr(pivot_select_model_Data_2024, ~ extract_CI_data(.x, harvesting_data = harvesting_data, field_CI_data = pivot_stats_long, season = 2024)) + + +CI_all <- rbind(Data_2021, Data_2022, Data_2023) + +CI_all <- CI_all %>% group_by(model) %>% mutate(CI_per_day = FitData - lag(FitData), + cumulative_CI = cumsum(FitData)) + +head(CI_all) + + +saveRDS(CI_all, here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds")) + + diff --git a/r_app/CI_report_dashboard_planet.Rmd b/r_app/CI_report_dashboard_planet.Rmd new file mode 100644 index 0000000..88b489a --- /dev/null +++ b/r_app/CI_report_dashboard_planet.Rmd @@ -0,0 +1,513 @@ +--- +# title: paste0("CI report week ", week, " - all pivots from ", last_tuesday, " to ", today) +output: + word_document: + reference_docx: word-styles-reference-03.docx + # toc: true +editor_options: + chunk_output_type: console +--- + + +```{r libraries, message=FALSE, warning=FALSE, include=FALSE} +library(here) +library(sf) +library(tidyverse) +library(tmap) +library(lubridate) +library(exactextractr) +library(zoo) +library(raster) + +library(rsample) +library(caret) +library(CAST) +``` + +```{r directories, message=FALSE, warning=FALSE, include=FALSE} +laravel_storage_dir <- here("laravel_app/storage/app") +data_dir <- here(laravel_storage_dir, "Data") +extracted_CI_dir <- here(data_dir, "extracted_CI") +daily_CI_vals_dir <- here(extracted_CI_dir, "daily_vals") +cumulative_CI_vals_dir <- here(extracted_CI_dir, "cumulative_vals") +harvest_dir <- here(data_dir, "HarvestData") + +weekly_CI_mosaic <- here(data_dir, "weekly_mosaic") + +s2_dir <- "C:/Users/timon/Resilience BV/4002 CMD App - General/4002 CMD Team/4002 TechnicalData/04 WP2 technical/python/chemba_S2/" +``` + + +```{r week, message=FALSE, warning=FALSE, include=FALSE} +# week <- 5 +# today = "2023-02-02" +# week <- week(today) +# today = "2022-08-18" +# +today = as.character(Sys.Date()) +week = lubridate::week(Sys.time()) +# week = 26 +title_var <- paste0("CI dashboard week ", week, " - all pivots dashboard using 3x3 meter resolution") +``` + +--- +title: `r title_var` +--- + +This PDF-dashboard shows the status of your fields on a weekly basis. We will show this in different ways: + +1) The first way is with a general overview of field heterogeneity using ‘variation’ – a higher number indicates more differences between plants in the same field. +2) The second map shows a normal image of the latest week in colour, of the demo fields. +3) Then come the maps per field, which show the status for three weeks ago, two weeks ago, last week, and this week, as well as a percentage difference map between last week and this week. The percentage difference maps shows the relative difference in growth over the last week, with positive numbers showing growth, and negative numbers showing decline. +4) Below the maps are graphs that show how each pivot quadrant is doing, measured through the chlorophyll index. + + + +```{r data, message=FALSE, warning=FALSE, include=FALSE} +# get latest CI index +week_minus_1 <- as.numeric(week) -1 +week_minus_2 <- as.numeric(week) -2 +week_minus_3 <- as.numeric(week) -3 + +today_minus_1 <- as.character(ymd(today) - 7) +today_minus_2 <- as.character(ymd(today) - 14) +today_minus_3 <- as.character(ymd(today) - 21) + +# remove_pivots <- c("1.1", "1.12", "1.8", "1.9", "1.11", "1.14") +CI_quadrant <- readRDS(here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds")) %>% + rename(pivot_quadrant = Field) + +message("STOP - check ci name in layer") +CI <- brick(here(weekly_CI_mosaic, paste0("week_",week, "_2023.tif"))) %>% subset("CI") +CI_m1 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_1, "_2023.tif"))) %>% subset("CI") #%>% subset("CI") +CI_m2 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_2, "_2023.tif"))) %>% subset(6) #%>% subset("CI") +CI_m3 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_3, "_2023.tif"))) %>% subset(6) #%>% subset("CI") + +last_week_dif_raster <- ((CI - CI_m1) / CI_m1) * 100 +last_week_dif_raster_abs <- (CI - CI_m1) +two_week_dif_raster_abs <- (CI - CI_m2) + + +AllPivots0 <-st_read(here(data_dir, "pivot_20210625.geojson")) +joined_spans <-st_read(here(data_dir, "spans2.geojson")) %>% st_transform(crs(AllPivots0)) + +pivots_dates <- readRDS(here(harvest_dir, "harvest_data_new")) %>% filter( + pivot %in% c("1.1", "1.2", "1.3", "1.4", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", + "1.14" , "1.16" , "1.17" , "1.18" ,"2.1", "2.2", "2.3" , "2.4", "2.5", "3.1", "3.2", "3.3", + "4.1", "4.2", "4.3", "4.4", "4.5", "4.6", "5.1" ,"5.2", "5.3", "5.4", "6.1", "6.2", "DL1.1", "DL1.3") #without 1.6 +) +AllPivots <- merge(AllPivots0, pivots_dates, by = "pivot_quadrant") %>% + rename(pivot = pivot.x) #%>% select(-pivot.y) + +AllPivots_merged <- AllPivots %>% + group_by(pivot) %>% summarise() + +AllPivots_merged <- st_transform(AllPivots_merged, crs = proj4string(CI)) + +AllPivots_merged$pivot <- as.factor(AllPivots_merged$pivot) +AllPivots_merged$pivot <- ordered(AllPivots_merged$pivot, levels = c("1.1", "1.2", "1.3", "1.4", "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14" , "1.16" , "1.17" , "1.18" ,"2.1", "2.2", "2.3" , "2.4", "2.5", "3.1", "3.2", "3.3", "4.1", "4.2", "4.3", "4.4", "4.5", "4.6", "5.1" ,"5.2", "5.3", "5.4", "6.1", "6.2", "DL1.1", "DL1.3")) + +pivot_names <- unique(CI_quadrant$pivot) + +``` + + +```{r eval=FALSE, include=FALSE} +pivot_stats_q <- cbind(AllPivots0, round(exact_extract(CI, AllPivots0, c("coefficient_of_variation", "mean"), default_value = -9999),2)) %>% + st_drop_geometry() %>% as_tibble() + +hetero_pivots0 <- merge(AllPivots, pivot_stats_q %>% dplyr::select(-hectares, -radius, -pivot), by = "pivot_quadrant") + +hetero_pivots <- hetero_pivots0 %>% #dplyr::filter(variable %in% "CV") %>% + mutate(class = case_when(coefficient_of_variation <= 0.001 ~ "Missing data", + coefficient_of_variation >= 0.002 & coefficient_of_variation < 0.1 ~ "Homogeneous", + coefficient_of_variation >= 0.1 & coefficient_of_variation < 0.2~ "Somewhat Homogeneous", + coefficient_of_variation >= 0.2 & coefficient_of_variation < 0.4 ~ "Somewhat Heterogeneous", + coefficient_of_variation >= 0.4 ~ "Heterogeneous")) %>% + mutate(class = as.factor(class)) +# hetero_pivots %>% filter(pivot == "1.3") +hetero_pivots$class <- factor(hetero_pivots$class, levels = c("Missing data", "Homogeneous","Somewhat Homogeneous", "Somewhat Heterogeneous", "Heterogeneous" )) +# hetero_pivots %>% select(pivot_quadrant, class, Age, coefficient_of_variation , mean) %>% view() + +# hetero_pivots %>% filter(class == "Somewhat Heterogeneous" ) %>% select(pivot_quadrant, class, Age, coefficient_of_variation , mean) + + + +Mypal <- c('#dcdcdc', '#008000','#8db600','#FFC300','#F22222') + +hetero_plot <- function(data){ + # map <- + tm_shape(data) + tm_polygons(col = "class", palette=Mypal) + + tm_text("pivot_quadrant", size = 1/2) + + tm_layout(main.title=paste0("Homogeneity of pivot quadrants, week ", week, " 2022"),main.title.position = "center")+ + tm_compass(position = c("center", "top")) + + tm_scale_bar(position = c("center", "top")) + + # print(map, width = 20, units = "cm") + +} + +``` +\newpage +```{r eval=FALSE, fig.height=7, fig.width=10, message=FALSE, warning=FALSE, include=FALSE} +hetero_plot(hetero_pivots) +``` + + +```{r function, message=FALSE, warning=FALSE, include=FALSE} + +subchunkify <- function(g, fig_height=7, fig_width=5) { + g_deparsed <- paste0(deparse( + function() {g} + ), collapse = '') + + sub_chunk <- paste0(" + `","``{r sub_chunk_", floor(runif(1) * 10000), ", fig.height=", fig_height, ", fig.width=", fig_width, ", echo=FALSE}", + "\n(", + g_deparsed + , ")()", + "\n`","`` + ") + + cat(knitr::knit(text = knitr::knit_expand(text = sub_chunk), quiet = TRUE)) +} + + + +ci_plot <- function(pivotName){ + # pivotName = "2.1" + pivotShape <- AllPivots_merged %>% terra::subset(pivot %in% pivotName) %>% st_transform(crs(CI)) + age <- AllPivots %>% dplyr::filter(pivot %in% pivotName) %>% st_drop_geometry() %>% dplyr::select(Age) %>% unique() + + AllPivots2 <- AllPivots %>% dplyr::filter(pivot %in% pivotName) + + singlePivot <- CI %>% crop(., pivotShape) %>% mask(., pivotShape) + + singlePivot_m1 <- CI_m1 %>% crop(., pivotShape) %>% mask(., pivotShape) + singlePivot_m2 <- CI_m2 %>% crop(., pivotShape) %>% mask(., pivotShape) + singlePivot_m3 <- CI_m3 %>% crop(., pivotShape) %>% mask(., pivotShape) + + abs_CI_last_week <- last_week_dif_raster_abs %>% crop(., pivotShape) %>% mask(., pivotShape) + abs_CI_two_week <- two_week_dif_raster_abs %>% crop(., pivotShape) %>% mask(., pivotShape) + + planting_date <- pivots_dates %>% dplyr::filter(pivot %in% pivotName) %>% ungroup() %>% dplyr::select(planting_date) %>% unique() + + joined_spans2 <- joined_spans %>% st_transform(crs(pivotShape)) %>% dplyr::filter(pivot %in% pivotName) %>% st_crop(., pivotShape) + + CImap_m2 <- create_CI_map(singlePivot_m2, AllPivots2, joined_spans2, show_legend= T, legend_is_portrait = T, week = week_minus_2, age = age -2) + CImap_m1 <- create_CI_map(singlePivot_m1, AllPivots2, joined_spans2, show_legend= F, legend_is_portrait = F, week = week_minus_1, age = age -1) + CImap <- create_CI_map(singlePivot_m1, AllPivots2, joined_spans2, show_legend= F, legend_is_portrait = F, week = week_minus_1, age = age ) + + + CI_max_abs_last_week <- create_CI_diff_map(abs_CI_last_week,AllPivots2, joined_spans2, show_legend = T, legend_is_portrait = T, week_1 = week, week_2 = week_minus_1, age = age) + CI_max_abs_two_week <- create_CI_diff_map(abs_CI_last_week, AllPivots2, joined_spans2, show_legend = T, legend_is_portrait = T, week_1 = week, week_2 = week_minus_2, age = age) + + tst <- tmap_arrange(CImap_m2, CImap_m1, CImap,CI_max_abs_last_week, CI_max_abs_two_week, nrow = 1) + + cat('

Pivot', pivotName, '- week', week, '-', age$Age, 'weeks after planting/harvest

') + + print(tst) + +} + + +create_CI_map <- function(pivot_raster, pivot_shape, pivot_spans, show_legend = F, legend_is_portrait = F, week, age){ + tm_shape(pivot_raster, unit = "m")+ + tm_raster(breaks = c(0,0.5,1,2,3,4,5,6,7,Inf), palette = "RdYlGn",legend.is.portrait = legend_is_portrait ,midpoint = NA) + + tm_layout(main.title = paste0("\nMax CI week ", week,"\n", age, " weeks old"), + main.title.size = 0.7, legend.show = show_legend) + + tm_shape(pivot_shape) + + tm_borders(lwd = 3) + tm_text("pivot_quadrant", size = 1/2) + + tm_shape(pivot_spans) + tm_borders(lwd = 0.5, alpha=0.5) +} + +create_CI_diff_map <- function(pivot_raster, pivot_shape, pivot_spans, show_legend = F, legend_is_portrait = F, week_1, week_2, age){ + tm_shape(pivot_raster, unit = "m")+ + tm_raster(breaks = c(-3,-2,-1,0,1,2, 3), palette = "RdYlGn",legend.is.portrait = legend_is_portrait ,midpoint = 0, title = "CI difference") + + tm_layout(main.title = paste0("CI change week ", week_1, "- week ",week_2, "\n", age," weeks old"), + main.title.size = 0.7, legend.show = show_legend) + + tm_shape(pivot_shape) + + tm_borders(lwd = 3) + tm_text("pivot_quadrant", size = 1/2) + + tm_shape(pivot_spans) + tm_borders(lwd = 0.5, alpha=0.5) +} + + +cum_ci_plot <- function(pivotName){ + + # pivotName = "1.17" + data_ci <- CI_quadrant %>% filter(pivot == pivotName) + data_ci2 <- data_ci %>% mutate(CI_rate = cumulative_CI/DOY, + week = week(Date))%>% group_by(pivot_quadrant) %>% + mutate(mean_rolling10 = rollapplyr(CI_rate , width = 10, FUN = mean, partial = TRUE)) #%>% + + date_preperation_perfect_pivot <- data_ci2 %>% group_by(season) %>% summarise(min_date = min(Date), + max_date = max(Date), + days = max_date - min_date) + + perfect_pivot_raw <- CI_quadrant %>% group_by(pivot) %>% filter(pivot == "5.1" & season == "2022") %>% + group_by(DOY) %>% summarise(cumulative_CI = mean(cumulative_CI)) %>% mutate(CI_rate = cumulative_CI/DOY) %>% + mutate(mean_rolling10 = rollapplyr(CI_rate , width = 10, FUN = mean, partial = TRUE)) + + unique_seasons <- unique(date_preperation_perfect_pivot$season) + + if(length(unique_seasons) == 3) { + unique_seasons <- unique_seasons[c(2,3)] + } else { + unique_seasons <- unique_seasons + } + + perfect_pivot <- perfect_pivot_raw + + for (s in unique_seasons) { + season_dates <- seq(from = date_preperation_perfect_pivot$min_date[date_preperation_perfect_pivot$season == s], + to = date_preperation_perfect_pivot$min_date[date_preperation_perfect_pivot$season == s] + nrow(perfect_pivot_raw) - 1, + by = "1 day") + col_name <- as.character(s) + perfect_pivot <- dplyr::bind_cols(perfect_pivot, tibble(!!col_name := season_dates)) + } + + perfect_pivot <- perfect_pivot %>% + pivot_longer(cols = -c("DOY", "cumulative_CI", "CI_rate", "mean_rolling10"), + names_to = "season", values_to = "Date") + + g <- ggplot() + + facet_wrap(~season, scales = "free_x") + + geom_line(data= data_ci2 %>% filter(season %in% unique_seasons), aes(Date, mean_rolling10, col = pivot_quadrant)) + + geom_line(data= perfect_pivot, aes(Date , mean_rolling10, col = "Model CI (p5.1 Data 2022, \n date x axis is fictive)"), lty="11",size=1) + + labs(title = paste("14 day rolling MEAN CI rate - Pivot ", pivotName))+ + # scale_y_continuous(limits=c(0.5,3), breaks = seq(0.5, 3, 0.5))+ + scale_x_date(date_breaks = "1 month", date_labels = "%m-%Y") + + theme(axis.text.x = element_text(angle = 60, hjust = 1)) + # options(repr.plot.width = 2, repr.plot.height = 2) + subchunkify(g, 3.2, 10) + +} + +``` + +```{r eval=FALSE, fig.height=7.2, fig.width=10, message=FALSE, warning=FALSE, include=FALSE} + RGB_raster <- list.files(paste0(s2_dir,week),full.names = T, pattern = ".tiff", recursive = TRUE)[1] #use pattern = '.tif$' or something else if you have multiple files in this folder + + +RGB_raster <- brick(RGB_raster) +# RGB_raster <- brick(here("planet", paste0("week_",week, ".tif"))) +tm_shape(RGB_raster, unit = "m") + tm_rgb(r=1, g=2, b=3, max.value = 255) + + tm_layout(main.title = paste0("RGB image of the fields - week ", week), + main.title.position = 'center') + + tm_scale_bar(position = c("right", "top"), text.color = "white") + + + tm_compass(position = c("right", "top"), text.color = "white") + + tm_shape(AllPivots)+ tm_borders( col = "white") + + tm_text("pivot_quadrant", size = .6, col = "white") + +``` +\newpage + +```{r eval=FALSE, fig.height=7.2, fig.width=10, message=FALSE, warning=FALSE, include=FALSE} +tm_shape(CI, unit = "m")+ + tm_raster(breaks = c(0,0.5,1,2,3,4,5,6,7,Inf), palette = "RdYlGn", midpoint = NA,legend.is.portrait = F) + + tm_layout(legend.outside = TRUE,legend.outside.position = "bottom",legend.show = T, main.title = "Overview all fields (CI)")+ + tm_scale_bar(position = c("right", "top"), text.color = "black") + + + tm_compass(position = c("right", "top"), text.color = "black") + + tm_shape(AllPivots)+ tm_borders( col = "black") + + tm_text("pivot_quadrant", size = .6, col = "black") + + + +tm_shape(last_week_dif_raster_abs, unit = "m")+ + tm_raster(breaks = c(-3,-2,-1,0,1,2, 3), palette = "RdYlGn", midpoint = NA,legend.is.portrait = F) + + tm_layout(legend.outside = TRUE,legend.outside.position = "bottom",legend.show = F, main.title = "Overview all fields - CI difference")+ + tm_scale_bar(position = c("right", "top"), text.color = "black") + + + tm_compass(position = c("right", "top"), text.color = "black") + + tm_shape(AllPivots)+ tm_borders( col = "black") + + tm_text("pivot_quadrant", size = .6, col = "black") + + + +tm_shape(last_week_dif_raster, unit = "m")+ + tm_raster(breaks = c(-Inf,-50,-25,-5,5,25, Inf), palette = "RdYlGn", midpoint = NA,legend.is.portrait = T) + + tm_layout(legend.outside = TRUE,legend.outside.position = "right",legend.show = F, main.title = "Overview all fields - CI difference %")+ + tm_scale_bar(position = c("right", "top"), text.color = "black") + + + tm_compass(position = c("right", "top"), text.color = "black") + + tm_shape(AllPivots)+ tm_borders( col = "black") + + tm_text("pivot_quadrant", size = .6, col = "black") +``` + + +```{r plots_ci, echo=FALSE, fig.height=3.7, fig.width=10, message=FALSE, warning=FALSE, results='asis'} + # ci_plot("1.17") +# cum_ci_plot("1.17") +# x = 1 +# for(j in x){ +# coops <- Chemba_pivot_owners %>% filter(`OWNER update 18/6/2022` %in% c("chapo", "Lambane", "Canhinbe" )) +pivots <- AllPivots_merged %>% filter(pivot != "1.17") + +#%>% filter(pivot %in% c( "2.1", "2.2", "2.3", "2.4", "3.1", "3.2", "3.3", "4.4", "4.6" , "4.3", "4.5", "4.2", "4.1", "5.1", "5.2", "5.3", "5.4", "7.1", "7.2", "7.3" , "7.4", "7.5", "7.6" )) + +for(i in pivots$pivot) { + ci_plot(i) + cum_ci_plot(i) + } + +# lapply(pivots, function(pivot) { +# ci_plot(pivot) +# cum_ci_plot(pivot) +# }) + + #cat("\\newpage") +# } +``` + +```{r eval=FALSE, fig.height=10, fig.width=14, include=FALSE} +CI_all2 <- readRDS(here(cumulative_CI_vals_dir, "All_pivots_Cumulative_CI_whole_pivot_year.rds")) %>% + mutate(#line = substr(pivot, 1 , 1), + season = as.factor(season)) + +pivots_dates <- readRDS(here(harvest_dir, "harvest_data_new")) #%>% + +pvt_age <- pivots_dates %>% ungroup() %>% select(pivot, Age) %>% unique() +CI_all2 <- left_join(CI_all2, pvt_age , by = "pivot") %>% mutate(month = plyr::round_any((Age/4),2)) %>% + mutate(month = case_when(month > 16 ~ 18, + TRUE ~month)) %>% + group_by(pivot) %>% filter(Age == max(Age)) %>% ungroup() + +CI_all2$season <- ordered(CI_all2$season, levels = c("Data_2021", "Data_2022")) +# CI_all2 <- CI_all2 %>% mutate(season_order = as.integer(season)) +latest_model <- CI_all2 %>% group_by(pivot) %>% filter(season =="Data_2022") +# latest_model <- CI_all2 %>% group_by(pivot) %>% arrange(season, desc(DOY)) %>% slice(1) + +# CI_all2 <- CI_all %>% group_by(pivot, DOY ) %>% mutate(pivot_cumulative_CI = mean(cumulative_CI)) +# label_data <- CI_all2 %>% group_by(pivot) %>% arrange(season, desc(cumulative_CI)) %>% slice(1) %>% mutate(label = paste(pivot, " - ", round(cumulative_CI))) +label_data <- latest_model %>% arrange(season, desc(cumulative_CI)) %>% slice(1) %>% mutate(label = paste(pivot, " - ", round(cumulative_CI))) + +max_day <- label_data %>% group_by(pivot) %>% summarise(max_day = max(DOY)) + +ggplot(data= CI_all2%>% filter(season =="Data_2022"), aes(DOY, cumulative_CI, col = pivot)) + + facet_wrap(~month) + + geom_line() + + # scale_y_continuous(breaks = seq(0, max(label_data$cumulative_CI) + 100, by = 100)) + + labs(title = "Cumulative CI values over the year per pivot, split per 2-month age (rounded down)", x = "Days after harvest/planting (scale is per 2 weeks)", y = "Cumulative CI value", + color = "Line") + + geom_label_repel(data = label_data %>% filter(model %in% latest_model$model), aes(DOY, cumulative_CI, label = label), box.padding = 1, + # ylim = c(1300, NA), + max.overlaps = Inf + # segment.linetype = 4, + + # segment.curvature = -1e-20, + # arrow = arrow(length = unit(0.015, "npc")) + ) + + theme(legend.position="right", legend.text = element_text(size=8), legend.title = element_text(size = 8), + plot.title = element_text(size=19)) + + # geom_smooth()+ + guides(fill = guide_legend(nrow=2,byrow=TRUE)) + + scale_y_continuous(breaks=seq(0,max(label_data$cumulative_CI),100)) + + scale_x_continuous(breaks=seq(0,max(max_day$max_day),30)) + theme(axis.text.x = element_text(angle = 90)) + + labs(x = "Weeks")+ + theme(legend.position = "none") + +``` + +The below table shows estimates of the biomass if you would harvest them now. +```{r eval=FALSE, message=FALSE, warning=FALSE, include=FALSE} +CI_quadrant <- readRDS(here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds")) %>% + rename( pivot_quadrant = Field)#All_pivots_Cumulative_CI.rds + +pivots_dates0 <- readRDS(here(harvest_dir, "harvest_data_new")) %>% ungroup() %>% unique() %>% + dplyr::select(pivot, pivot_quadrant, Tcha_2021, Tcha_2022 ) %>% + pivot_longer(cols = c("Tcha_2021", "Tcha_2022"), names_to = "Tcha_Year", values_to = "Tcha") %>% + filter(Tcha > 50) + +CI_and_yield <- left_join(CI_quadrant , pivots_dates0, by = c("pivot", "pivot_quadrant")) %>% filter(!is.na(Tcha)) %>% + group_by(pivot_quadrant) %>% slice(which.max(DOY)) %>% + dplyr::select(pivot, pivot_quadrant, Tcha_Year, Tcha, cumulative_CI, DOY) %>% + mutate(CI_per_day = cumulative_CI/ DOY) + +set.seed(20) +CI_and_yield_split <- initial_split(CI_and_yield, prop = 0.75, weight = pivot_quadrant) +CI_and_yield_test <- training(CI_and_yield_split) +CI_and_yield_validation <- testing(CI_and_yield_split) + + +predictors <- c( "cumulative_CI" , "DOY" ,"CI_per_day" ) +response <- "Tcha" +CI_and_yield_test <- as.data.frame(CI_and_yield_test) + +ctrl <- trainControl(method="cv", + savePredictions = TRUE, + allowParallel= TRUE, + number = 5, + verboseIter = TRUE) + +set.seed(202) +model_ffs_rf <- ffs( CI_and_yield_test[,predictors], + CI_and_yield_test[,response], + method="rf" , + trControl=ctrl, + importance=TRUE, + withinSE = TRUE, + tuneLength = 5, + na.rm = TRUE +) + +pred_ffs_rf <- + predict(model_ffs_rf, newdata = CI_and_yield_validation) %>% as.data.frame() %>% rename(predicted_Tcha = ".") %>% mutate( + pivot_quadrant = CI_and_yield_validation$pivot_quadrant, + pivot = CI_and_yield_validation$pivot, + Age_days = CI_and_yield_validation$DOY, + total_CI = round(CI_and_yield_validation$cumulative_CI, 0), + predicted_Tcha = round(predicted_Tcha, 0) + ) %>% dplyr::select(pivot , pivot_quadrant, Age_days, total_CI, predicted_Tcha) %>% + left_join(., CI_and_yield_validation, by = c("pivot", "pivot_quadrant")) %>% + filter(Age_days > 250) + +ggplot(pred_ffs_rf, aes(y = predicted_Tcha , x = Tcha , col = pivot )) + + geom_point() +geom_abline() + + scale_x_continuous(limits = c(50, 160))+ + scale_y_continuous(limits = c(50, 160)) + + labs(title = "Model trained and tested on historical results - RF") + +prediction_2023 <- CI_quadrant %>% filter(season == "Data_2023") %>% group_by(pivot_quadrant) %>% slice(which.max(DOY))%>% + mutate(CI_per_day = cumulative_CI/ DOY) + +pred_rf_2023 <- predict(model_ffs_rf, newdata=prediction_2023) %>% + as.data.frame() %>% rename(predicted_Tcha_2023 = ".") %>% mutate(pivot_quadrant = prediction_2023$pivot_quadrant, + pivot = prediction_2023$pivot, + Age_days = prediction_2023$DOY, + total_CI = round(prediction_2023$cumulative_CI,0), + predicted_Tcha_2023 = round(predicted_Tcha_2023, 0)) %>% + filter(Age_days > 300) %>% + dplyr::select(pivot ,pivot_quadrant, Age_days, total_CI, predicted_Tcha_2023)%>% + mutate(CI_per_day = round(total_CI/ Age_days, 1)) + +ggplot(pred_rf_2023, aes(total_CI , predicted_Tcha_2023 , col = pivot )) + + geom_point() + labs(title = "2023 data (still to be harvested) - Fields over 300 days old") +knitr::kable(pred_rf_2023) + +``` + +```{r eval=FALSE, include=FALSE} + +model_CI <-lm( + formula = cumulative_CI ~ DOY , + data = CI_and_yield_test +) +pivot_ = "4.4" +df4 = data.frame(pivot_, 365, NA) +names(df4)=c("pivot", "DOY", "cumulative_CI") +a <- CI_all %>% filter(season == "Data_2022", pivot == pivot_) %>% ungroup() %>% select(pivot, DOY, cumulative_CI) %>% + complete(DOY = seq.int(max(DOY), 365, 1), pivot = pivot_) %>% arrange(DOY) # complete(DOY = seq.int(max(DOY), 365, 1)) # rbind(.,df4) + +b <- predict(model_CI, a) %>% + as.data.frame() %>% slice(which.max(.)) %>% rename(cumulative_CI = ".") %>% mutate(DOY = 365) + +pred_CI_2022 <- predict(model, newdata=b ) %>% + as.data.frame() %>% rename(predicted_Tcha_365 = ".") %>% mutate(pivot = df4$pivot, + predicted_Tcha_365 = round(predicted_Tcha_365, 0), + Age_days = df4$DOY) + +pred_CI_2022 +``` + diff --git a/r_app/renv.lock b/r_app/renv.lock new file mode 100644 index 0000000..d93c94d --- /dev/null +++ b/r_app/renv.lock @@ -0,0 +1,2052 @@ +{ + "R": { + "Version": "4.1.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cran.rstudio.com" + } + ] + }, + "Packages": { + "DBI": { + "Package": "DBI", + "Version": "1.1.2", + "Source": "Repository", + "Repository": "CRAN", + 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start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + if (!enabled) + return(FALSE) + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) + args$headers <- renv_bootstrap_download_custom_headers(url) + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # retrieve package database + db <- tryCatch( + as.data.frame( + utils::available.packages(type = type, repos = repos), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + pat <- Sys.getenv("GITHUB_PAT") + if (nzchar(Sys.which("curl")) && nzchar(pat)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + remote <- if (!is.null(description[["RemoteSha"]])) { + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + } else { + paste("renv", description[["Version"]], sep = "@") + } + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = description[["RemoteSha"]] + ) + + fmt <- paste( + "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", + "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", + "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", + sep = "\n" + ) + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- catch(renv_json_read_jsonlite(file, text)) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- catch(renv_json_read_default(file, text)) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% read(file), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% read(file), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/smartcane.sh b/smartcane.sh new file mode 100755 index 0000000..0bddccf --- /dev/null +++ b/smartcane.sh @@ -0,0 +1,38 @@ +#!/bin/bash + + +# Definieer de directories die aangemaakt moeten worden +#declare -a dirs=( + #"laravel_app/storage/app/extracted_ci/cumulative_vals" + #"laravel_app/storage/app/chemba/merged_tif" + #"laravel_app/storage/app/chemba/merged_virtual" + #"laravel_app/storage/app/chemba/single_images" +#) +# +## Loop door de directories en maak ze aan als ze nog niet bestaan, +## of maak ze leeg als ze al bestaan +#for dir in "${dirs[@]}"; do + #if [ ! -d "$dir" ]; then + #mkdir -p "$dir" + #chmod -R 775 "$dir" + #echo "Directory $dir is aangemaakt en bijgewerkt." + #else + ## Verwijder alle inhoud binnen de bestaande directory + #find "$dir" -mindepth 1 -delete + #echo "Inhoud van directory $dir is verwijderd." + #fi +#done +## Runnen van Jupyter Notebook +#jupyter nbconvert --execute --to script --stdout python_app/Chemba_download.ipynb +## Runnen van R scripts +# Kopieer de excel file met harvesting data en maak directory aan indien nodig +#mkdir -p laravel_app/storage/app/harvesting_data +#cp "Current - Pivots planting date and harevsting data.xlsx" "laravel_app/storage/app/harvesting_data/" +#Rscript r_app/1_harvest_data_EcoFarm_v2.R +#cp "pivot_20210625.geojson" "laravel_app/storage/app/Data" +#Rscript r_app/2_CI_data_prep.R +# +## Runnen van Rmd bestand +# -e betekent "evalueren" en -i specificeert de input file +Rscript -e "rmarkdown::render('r_app/CI_Report_dashboard_planet.Rmd', 'all')" +