CrayFits as part of Crayfish (#178)

Co-authored-by: Alan Stanley <astanley@upei.ca>
Co-authored-by: ajstanley <vagrant@claw>
Co-authored-by: Alan Stanley <alanjarlathstanley@gmail.com>
Co-authored-by: Nigel Banks <nigel.g.banks@gmail.com>
Co-authored-by: Alexander O'Neill <aloneill@gmail.com>

CrayFits/.env

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+# In all environments, the following files are loaded if they exist,
+# the later taking precedence over the former:
+#
+#  * .env                contains default values for the environment variables needed by the app
+#  * .env.local          uncommitted file with local overrides
+#  * .env.$APP_ENV       committed environment-specific defaults
+#  * .env.$APP_ENV.local uncommitted environment-specific overrides
+#
+# Real environment variables win over .env files.
+#
+# DO NOT DEFINE PRODUCTION SECRETS IN THIS FILE NOR IN ANY OTHER COMMITTED FILES.
+#
+# Run "composer dump-env prod" to compile .env files for production use (requires symfony/flex >=1.2).
+# https://symfony.com/doc/current/best_practices/configuration.html#infrastructure-related-configuration
+
+###> symfony/framework-bundle ###
+APP_ENV=dev
+APP_SECRET=5273c9fd27359cc05a2f653521d8add0
+#TRUSTED_PROXIES=127.0.0.1,127.0.0.2
+#TRUSTED_HOSTS='^localhost|example\.com$'
+###< symfony/framework-bundle ###
+
+###> doctrine/doctrine-bundle ###
+# Format described at http://docs.doctrine-project.org/projects/doctrine-dbal/en/latest/reference/configuration.html#connecting-using-a-url
+# For an SQLite database, use: "sqlite:///%kernel.project_dir%/var/data.db"
+# Configure your db driver and server_version in config/packages/doctrine.yaml
+DATABASE_URL=mysql://db_user:db_password@127.0.0.1:3306/db_name
+###< doctrine/doctrine-bundle ###
+FITS_WEBSERVICE_URI=http://localhost:8080/fits/
+
+
+###> nelmio/cors-bundle ###
+CORS_ALLOW_ORIGIN=^https?://localhost(:[0-9]+)?$
+###< nelmio/cors-bundle ###

CrayFits/README.md

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+# CrayFits
+
+## Introduction
+
+[FITS][1] as a microservice.
+
+## Requirements
+
+* Tomcat
+* [Composer][2]
+
+## Installation
+
+### Install FITS webservice
+
+* Download the latest `fits.zip` and `fits.war` from
+[https://projects.iq.harvard.edu/fits/downloads](https://projects.iq.harvard.edu/fits/downloads).
+You may need to install a zip library to unzip the file.
+* Copy the `.war` file to your Tomcat webapps directory and test.
+* Edit the Tomcat `conf/catalina.properties` file by adding the
+following two lines to the bottom of the file:
+```properties
+fits.home=/\<path-to-fits>/fits
+shared.loader=/\<path-to-fits>/fits/lib/*.jar
+```
+* Restart Tomcat.
+* Test the webservice with:
+```bash
+curl -k -F datafile="@/path/to/myfile.jpg" http://[tomcat_domain]:[tomcat_port]/fits/examine
+```
+(note: the ‘@’ is required.)
+
+### Install CrayFITS microservice
+
+* Clone this repository somewhere in your web root.
+* `$ cd /path/to/CrayFits` and run `$ composer install`
+* For production, configure your web server appropriately (e.g. add a VirtualHost for CrayFits in Apache)
+
+To run the microservice on the Symfony Console, enter:
+```bash
+php bin/console server:start *:8050
+```
+in the microservice root folder.
+
+The server is stopped with:
+```bash
+php bin/console server:stop
+```
+On a production machine you'd probably want to configure an additional
+port in Apache.
+
+Note: The location of the FITS webserver is stored in the `.env` file in the
+root dir of the Symfony app.  This will have to be reconfigured if the FITS
+server is anywhere other than `localhost:8080/fits`
+
+
+#### Optional: Configure Alpaca to accept derivative requests from Islandora.
+
+To use Alpaca as an interface to this microservice, configure
+an [`islandora-connector-derivative`](https://github.com/Islandora/Alpaca#islandora-connector-derivative)
+appropriate to your installation of CrayFits.
+
+[1]: https://projects.iq.harvard.edu/fits
+[2]: https://getcomposer.org/download/
+
+

CrayFits/bin/console

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+#!/usr/bin/env php
+<?php
+
+use App\Kernel;
+use Symfony\Bundle\FrameworkBundle\Console\Application;
+use Symfony\Component\Console\Input\ArgvInput;
+use Symfony\Component\Debug\Debug;
+
+if (false === in_array(\PHP_SAPI, ['cli', 'phpdbg', 'embed'], true)) {
+    echo 'Warning: The console should be invoked via the CLI version of PHP, not the '.\PHP_SAPI.' SAPI'.\PHP_EOL;
+}
+
+set_time_limit(0);
+
+require dirname(__DIR__).'/vendor/autoload.php';
+
+if (!class_exists(Application::class)) {
+    throw new RuntimeException('You need to add "symfony/framework-bundle" as a Composer dependency.');
+}
+
+$input = new ArgvInput();
+if (null !== $env = $input->getParameterOption(['--env', '-e'], null, true)) {
+    putenv('APP_ENV='.$_SERVER['APP_ENV'] = $_ENV['APP_ENV'] = $env);
+}
+
+if ($input->hasParameterOption('--no-debug', true)) {
+    putenv('APP_DEBUG='.$_SERVER['APP_DEBUG'] = $_ENV['APP_DEBUG'] = '0');
+}
+
+require dirname(__DIR__).'/config/bootstrap.php';
+
+if ($_SERVER['APP_DEBUG']) {
+    umask(0000);
+
+    if (class_exists(Debug::class)) {
+        Debug::enable();
+    }
+}
+
+$kernel = new Kernel($_SERVER['APP_ENV'], (bool) $_SERVER['APP_DEBUG']);
+$application = new Application($kernel);
+$application->run($input);

CrayFits/composer.json

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+{
+    "type": "project",
+    "license": "proprietary",
+    "require": {
+        "ext-ctype": "*",
+        "ext-iconv": "*",
+        "guzzlehttp/guzzle": "^6.3",
+        "monolog/monolog": "^1.24",
+        "symfony/console": "^4.4",
+        "symfony/dotenv": "^4.4",
+        "symfony/flex": "^1.1",
+        "symfony/framework-bundle": "^4.4",
+        "symfony/monolog-bundle": "^3.3",
+        "symfony/yaml": "^4.4"
+    },
+    "config": {
+        "preferred-install": {
+            "*": "dist"
+        },
+        "sort-packages": true,
+        "allow-plugins": {
+            "symfony/flex": true
+        }
+    },
+    "autoload": {
+        "psr-4": {
+            "App\\": "src/"
+        }
+    },
+    "autoload-dev": {
+        "psr-4": {
+            "App\\Tests\\": "tests/"
+        }
+    },
+    "replace": {
+        "paragonie/random_compat": "2.*",
+        "symfony/polyfill-ctype": "*",
+        "symfony/polyfill-iconv": "*",
+        "symfony/polyfill-php71": "*",
+        "symfony/polyfill-php70": "*",
+        "symfony/polyfill-php56": "*"
+    },
+    "scripts": {
+        "auto-scripts": {
+            "cache:clear": "symfony-cmd",
+            "assets:install %PUBLIC_DIR%": "symfony-cmd"
+        },
+        "post-install-cmd": [
+            "@auto-scripts"
+        ],
+        "post-update-cmd": [
+            "@auto-scripts"
+        ],
+        "test": [
+	    "@check"
+	]
+    },
+    "conflict": {
+        "symfony/symfony": "*"
+    },
+    "extra": {
+        "symfony": {
+            "allow-contrib": false,
+            "require": "^4.4"
+        }
+    }
+}

CrayFits/config/bootstrap.php

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+<?php
+
+use Symfony\Component\Dotenv\Dotenv;
+
+require dirname(__DIR__).'/vendor/autoload.php';
+
+// Load cached env vars if the .env.local.php file exists
+// Run "composer dump-env prod" to create it (requires symfony/flex >=1.2)
+if (is_array($env = @include dirname(__DIR__).'/.env.local.php')) {
+    $_ENV += $env;
+} elseif (!class_exists(Dotenv::class)) {
+    throw new RuntimeException('Please run "composer require symfony/dotenv" to load the ".env" files configuring the application.');
+} else {
+    // load all the .env files
+    (new Dotenv(false))->loadEnv(dirname(__DIR__).'/.env');
+}
+
+$_SERVER += $_ENV;
+$_SERVER['APP_ENV'] = $_ENV['APP_ENV'] = ($_SERVER['APP_ENV'] ?? $_ENV['APP_ENV'] ?? null) ?: 'dev';
+$_SERVER['APP_DEBUG'] = $_SERVER['APP_DEBUG'] ?? $_ENV['APP_DEBUG'] ?? 'prod' !== $_SERVER['APP_ENV'];
+$_SERVER['APP_DEBUG'] = $_ENV['APP_DEBUG'] = (int) $_SERVER['APP_DEBUG'] || filter_var($_SERVER['APP_DEBUG'], FILTER_VALIDATE_BOOLEAN) ? '1' : '0';

CrayFits/config/bundles.php

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+<?php
+
+return [
+    Symfony\Bundle\FrameworkBundle\FrameworkBundle::class => ['all' => true],
+    Symfony\Bundle\MonologBundle\MonologBundle::class => ['all' => true],
+];

CrayFits/config/packages/cache.yaml

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+framework:
+    cache:
+        # Put the unique name of your app here: the prefix seed
+        # is used to compute stable namespaces for cache keys.
+        #prefix_seed: your_vendor_name/app_name
+
+        # The app cache caches to the filesystem by default.
+        # Other options include:
+
+        # Redis
+        #app: cache.adapter.redis
+        #default_redis_provider: redis://localhost
+
+        # APCu (not recommended with heavy random-write workloads as memory fragmentation can cause perf issues)
+        #app: cache.adapter.apcu
+
+        # Namespaced pools use the above "app" backend by default
+        #pools:
+            #my.dedicated.cache: ~

CrayFits/config/packages/dev/routing.yaml

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+framework:
+    router:
+        strict_requirements: true

CrayFits/config/packages/framework.yaml

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+framework:
+    secret: '%env(APP_SECRET)%'
+    #default_locale: en
+    #csrf_protection: true
+    #http_method_override: true
+
+    # Enables session support. Note that the session will ONLY be started if you read or write from it.
+    # Remove or comment this section to explicitly disable session support.
+    session:
+        handler_id: ~
+        cookie_secure: auto
+        cookie_samesite: lax
+
+    #esi: true
+    #fragments: true
+    php_errors:
+        log: true

CrayFits/config/packages/routing.yaml

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+framework:
+    router:
+        strict_requirements: ~
+        utf8: true

CrayFits/config/packages/test/framework.yaml

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+framework:
+    test: true
+    session:
+        storage_id: session.storage.mock_file

CrayFits/config/packages/test/routing.yaml

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+framework:
+    router:
+        strict_requirements: true

CrayFits/config/routes.yaml

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+# config/routes.yaml
+
+app_fits_exec:
+  path: /
+  controller: App\Controller\FitsController::generate_fits

CrayFits/config/services.yaml

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+# This file is the entry point to configure your own services.
+# Files in the packages/ subdirectory configure your dependencies.
+
+# Put parameters here that don't need to change on each machine where the app is deployed
+# https://symfony.com/doc/current/best_practices/configuration.html#application-related-configuration
+parameters:
+
+services:
+    # default configuration for services in *this* file
+    _defaults:
+        autowire: true      # Automatically injects dependencies in your services.
+        autoconfigure: true # Automatically registers your services as commands, event subscribers, etc.
+
+    # makes classes in src/ available to be used as services
+    # this creates a service per class whose id is the fully-qualified class name
+    App\:
+        resource: '../src/*'
+        exclude: '../src/{DependencyInjection,Entity,Migrations,Tests,Kernel.php}'
+
+    # controllers are imported separately to make sure services can be injected
+    # as action arguments even if you don't extend any base controller class
+    App\Controller\:
+        resource: '../src/Controller'
+        tags: ['controller.service_arguments']
+
+    # add more service definitions when explicit configuration is needed
+    # please note that last definitions always *replace* previous ones