Migration to slim v4 and refactoring

.env.dist

-AMQP_HOST=amqp_host
\ No newline at end of file

.gitignore

@@ -2,6 +2,7 @@ nbproject/
 .vscode/
 .idea/
 vendor/*
+phpunit-coverage/
 data/
 build/*
 logs/*
@@ -14,5 +15,4 @@ cache
 .project
 .settings
 .phpunit*
-anis_v3.sqlite
-.env
\ No newline at end of file
+.env

.gitlab-ci.yml

 stages:
-    - metrics
-    - metrics-build
-    - metrics-deploy
-    - install
-    - test
-    - sonar
-    - build
-    - deploy
+  - install
+  - test
+  - sonar
+  - build
 
 variables:
-    VERSION: "3.0"
+    VERSION: "3.1"
     SONARQUBE_URL: https://sonarqube.lam.fr
-    METRICS_IMAGE: portus.lam.fr/anis/anis-server-metrics
     CONTAINER_IMAGE: portus.lam.fr/anis/anis-server
 
-php-metrics:
-    image: jakzal/phpqa
-    stage: metrics
-    script: 
-        - phpmetrics --report-html=var/php-metrics .
-    allow_failure: true
-    cache:
-        paths:
-            - var
-        policy: push
-    only:
-        refs:
-            - develop
-
-php-metrics-build:
-    image: docker:stable
-    stage: metrics-build
-    script:
-        - echo "FROM nginx" > var/Dockerfile
-        - echo "COPY php-metrics /usr/share/nginx/html" >> var/Dockerfile
-        - docker login -u fagneray -p $PORTUS_TOKEN portus.lam.fr
-        - docker pull $METRICS_IMAGE:latest || true
-        - docker build --cache-from $METRICS_IMAGE:latest -t $METRICS_IMAGE:latest var
-        - docker push $METRICS_IMAGE:latest
-    allow_failure: true
-    cache:
-        paths:
-            - var
-        policy: pull
-    only:
-        refs:
-            - develop
-
-php-metrics-deploy:
-    image: alpine
-    stage: metrics-deploy
-    script:
-        - apk add --update curl
-        - curl -XPOST $METRICS_WEBHOOK
-    only:
-        refs:
-            - develop
-
 install:
     image: jakzal/phpqa
     stage: install
@@ -102,9 +54,9 @@ build:
     stage: build
     script:
         - docker login -u fagneray -p $PORTUS_TOKEN portus.lam.fr
-        - docker pull $CONTAINER_IMAGE:latest-dev || true
-        - docker build --cache-from $CONTAINER_IMAGE:latest-dev -t $CONTAINER_IMAGE:latest-dev .
-        - docker push $CONTAINER_IMAGE:latest-dev
+        - docker pull $CONTAINER_IMAGE:latest || true
+        - docker build --cache-from $CONTAINER_IMAGE:latest -t $CONTAINER_IMAGE:latest .
+        - docker push $CONTAINER_IMAGE:latest
     cache:
         paths:
             - vendor
@@ -112,13 +64,3 @@ build:
     only:
         refs:
             - develop
-
-deploy:
-    image: alpine
-    stage: deploy
-    script:
-        - apk add --update curl
-        - curl -XPOST $DEV_WEBHOOK
-    only:
-        refs:
-            - develop
\ No newline at end of file

CHANGELOG.md

-# Changelog
-All notable changes to this project will be documented in this file.
-
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-
-## [3.0.0] - yyyy-mm-dd
-### Added
-- Pour les nouvelles fonctionnalités.
-
-### Changed
-- Pour les changements au sein des fonctionnalités déjà existantes.
-
-### Deprecated
-- Pour les fonctionnalités qui seront supprimées dans la prochaine publication.
-
-### Removed
-- Pour les anciennes fonctionnalités Deprecated qui viennent d’être supprimées.
-
-### Fixed
-- Pour les corrections de bugs.
-
-### Security
-- Pour encourager les utilisateurs à mettre à niveau afin d’éviter des failles de sécurité.

Dockerfile

@@ -3,7 +3,7 @@ FROM php:7.3-apache
 # Install modules
 RUN apt-get update \ 
     && apt-get install -y zlib1g zlib1g-dev libpq-dev libpq5 libzip-dev zip unzip \
-    && docker-php-ext-install pgsql pdo_pgsql zip
+    && docker-php-ext-install pgsql pdo_pgsql zip bcmath
 
 RUN a2enmod rewrite
 
@@ -12,4 +12,4 @@ COPY ./conf-dev/vhost.conf /etc/apache2/sites-available/000-default.conf
 
 WORKDIR /srv/app
 
-CMD ["apache2-foreground"]
\ No newline at end of file
+CMD ["apache2-foreground"]

LICENSE

-
-AstroNomical Information System - Server API
+AstroNomical Information System - Server
   
-  Copyright: François Agneray & Chrystel Moreau 2012 - 2019
+  Copyright: CNRS - 2019
   Address:  Centre de donneeS Astrophysique de Marseille (CeSAM)              
             Laboratoire d'Astrophysique de Marseille                          
             Ple de l'Etoile, site de Chteau-Gombert                         
@@ -9,14 +8,12 @@ AstroNomical Information System - Server API
             13388 Marseille cedex 13 France                                   
             CNRS U.M.R 7326
 
-ANIS Server API is governed by the CeCILL  license under French law and
+Anis Server is governed by the CeCILL license under French law and
 abiding by the rules of distribution of free software.  You can  use, 
 modify and/ or redistribute the software under the terms of the CeCILL
 license as circulated by CEA, CNRS and INRIA at the following URL
 "http://www.cecill.info" and/or below.
 
-
-
                     CeCILL FREE SOFTWARE LICENSE AGREEMENT
                     ======================================
 

Makefile

-UID := $(id -u)
-GID := $(id -g)
+UID := 1000
+GID := 1000
 
 list:
 	@echo ""
 	@echo "Useful targets:"
 	@echo ""
 	@echo "  install       > install php composer dependancies"
-	@echo "  up            > build php image and start anis-server containers for dev only (php + mailer)"
-	@echo "  start         > start anis-server containers"
-	@echo "  restart       > restart anis-server containers"
-	@echo "  stop          > stop  and kill running anis-server containers"
-	@echo "  logs          > display anis-server containers logs"
-	@echo "  shell         > shell into php anis-server container"
+	@echo "  rebuild       > rebuild php image and start containers for dev only"
+	@echo "  start         > start containers"
+	@echo "  restart       > restart containers"
+	@echo "  stop          > stop and kill running containers"
+	@echo "  status        > display stack containers status"
+	@echo "  logs          > display containers logs"
+	@echo "  shell         > shell into php container"
 	@echo "  phpunit       > run php unit test suite"
 	@echo "  phpcs         > run php code sniffer test suite"
-	@echo "  anis-init     > generate a new anis admin database and a default metamodel database (anis-server containers running needed)"
-	@echo "  dev-init      > add metadata datasets for devlopment purpose"
+	@echo "  create-db     > create a database for dev only"
+	@echo "  dev-meta      > load metamodel information for testing application"
 	@echo "  remove-pgdata > remove the metadata database"
-	@echo "  gen-key       > generate a new encryption key that you can use to encrypt data (see anis server config file)"
 	@echo ""
 
 install:
@@ -26,7 +26,7 @@ install:
 	-v $(CURDIR):/project \
 	-w /project jakzal/phpqa composer install --ignore-platform-reqs
 
-up:
+rebuild:
 	@docker-compose up --build -d
 
 start:
@@ -38,6 +38,9 @@ stop:
 	@docker-compose kill
 	@docker-compose rm -v --force
 
+status:
+	@docker-compose ps
+
 logs:
 	@docker-compose logs -f -t
 
@@ -48,21 +51,18 @@ phpunit:
 	@docker run --init -it --rm --user $(UID):$(GID) \
 	-v $(CURDIR):/project \
 	-w /project jakzal/phpqa phpdbg -qrr ./vendor/bin/phpunit --bootstrap ./tests/bootstrap.php \
-	--whitelist src --coverage-text --colors=never ./tests
+	--whitelist src --colors --coverage-html ./phpunit-coverage ./tests
 
 phpcs:
 	@docker run --init -it --rm --user $(UID):$(GID) \
 	-v $(CURDIR):/project \
-	-w /project jakzal/phpqa phpcs --standard=PSR2 --extensions=php --colors src tests
+	-w /project jakzal/phpqa phpcs --standard=PSR12 --extensions=php --colors src tests
 
-anis-init:
-	@docker-compose exec php sh ./conf-dev/anis_init.sh
+create-db:
+	@docker-compose exec php ./vendor/bin/doctrine orm:schema-tool:create
 
-dev-init:
-	@docker-compose exec php sh ./conf-dev/dev-init.sh
+dev-meta:
+	@docker-compose exec php sh ./conf-dev/dev-meta.sh
 
 remove-pgdata:
-	@docker volume rm anis-server_pgdata
-
-gen-key:
-	@docker-compose exec php php ./conf-dev/generate_encryption_key.php
\ No newline at end of file
+	@docker volume rm anis-metamodel_pgdata

README.md

@@ -6,7 +6,7 @@ AstroNomical Information System is a generic web tool that aims to facilitate th
 
 This software allows you to control one or more databases related to astronomical projects and allows access to datasets via URLs.
 
-Anis is protected by the `CeCILL` licence (see LICENCE file at the software root).
+Anis is protected by the CeCILL licence (see LICENCE file at the software root).
 
 ## Authors
 
@@ -16,111 +16,36 @@ Here is the list of people involved in the development:
 * `Chrystel Moreau` : Laboratoire d'Astrophysique de Marseille (CNRS)
 * `Tifenn Guillas` : Laboratoire d'Astrophysique de Marseille (CNRS)
 
-# Installation guide
+## Functionalities
 
-## Prerequisites
+Anis Server allows : 
 
-Before to start to install the anis-server you must make sure that you have the following commands installed on your computer: 
+- Add project/database that will contain a set of datasets
+- Add and configure a dataset that references a table or view of a business database
+- The possibility to search in a referenced dataset with search criteria
 
-1. `make`
-2. `docker`
-3. `docker-compose`
+## Installing and starting the application
 
-You also need an Internet connection to download packages and dependancies.
+Anis Server contains a Makefile that helps the developer to install and start the application.
 
-## List of commands
+To list all operations availables just type `make` in your terminal at the root of this application.
 
-The `Makefile` at the root of the project provides a list of commands available to manage the application in a development mode.
+- To install all dependancies : `make install`
+- To start/stop/restart/status all services : `make start|stop|restart|status`
+- To display logs for all services : `make logs`
+- To open a shell command into php container : `make shell`
+- To execute tests suite : `make phpunit`
+- To execute php code sniffer : `make phpcs`
+- To create the metamodel database : `make create-db`
+- To load metamodel information for testing : `make dev-meta`
 
-To see the list of commands just open a terminal in the root of the project and type: 
+## Open API
 
-> make
+You can find an open api documentation into the `anis-server.yaml` file.
 
-**Warning**: The `docker-compose.yml` and the` Makefile` commands must be used only for development or testing but no in production mode.
+## Few examples with curl
 
-## Dependancies installation
-
-To start installing dependancies, use the following command at the software root: 
-
-> make install
-
-The `Composer.phar` software will be downloaded and it will automatically use the `composer.json` and `composer.lock` files to download all the dependancies and save them to the `vendor` directory at the root of the application.
-
-After that anis-server can work!
-
-## Start anis-server
-
-Anis server has been developed to be used with docker containers. If you open the `docker-compose.yml` file you can see all containers needed for the **development or test configuration** of anis server.
-
-`Makefile` provides a command to build install and run all the containers that you need for a fresh installation of anis-server software:
-
-> make up
-
-**Note:** This command use `docker-compose` to work. These operations may take a few minutes as it is necessary to download docker images
-
-If you want to list all anis stack containers running:
-
-> docker-compose ps
-
-And if you want to print anis stack logs:
-
-> make logs
-
-## Databases installation
-
-Anis server need at least two databases to work:
-
-1. An admin database to store users and the list of available metamodel databases.
-2. A default metamodel database to store information about business databases, projects and datasets availables.
-
-Our `Makefile` provides a command to generate these two databases:
-
-> make anis-init
-
-## Datasets for beginning to use
-
-Our `Makefile` also provides a command to add a business database and configure datasets into the default metamodel database to beginning to test or develop the anis-server. To install the test datasets type:
-
-> make dev-init
-
-## Anis server is now ready to use
-
-Open a browser and go => [http://localhost:8080/](http://localhost:8080/)
-
-Few examples: 
-
-* To list all datasets available in the default instance => [http://localhost:8080/metadata/default/dataset](http://localhost:8080/metadata/default/dataset)
-* To print all data for the obs_cat dataset with column 1, 2 and 3 => [http://localhost:8080/search/default/data/obs_cat?a=1;2;3](http://localhost:8080/search/default/data/obs_cat?a=1;2;3)
-* To print only 3 obs_cat data (search by id) => [http://localhost:8080/search/default/data/obs_cat?a=1;2;3&c=1::in::104600094|104600095|104600108](http://localhost:8080/search/default/data/obs_cat?a=1;2;3&c=1::in::104600094|104600095|104600108)
-
-# More about Anis-Server
-
-First of all, you will find the user manual at the root of the project: [MANUAL.md](MANUAL.md)
-
-## Software directories
-
-* `conf-dev`: Configuration files used by make commands and docker-compose to work
-* `public`: Web server root (index.php)
-* `src`: Source code of Anis Server
-* `test`: Anis Unit Tests `phpunit`
-
-## Key files
-
-* `public/index.php`: Bootstrap file for starting application (file used by an http web server like nginx or apache)
-* `src/settings.php`: Anis server configuration file
-* `src/routes.php`: Anis server configured routes (list all availables URL)
-
-## Technologies
-
-You can see here just a few direct links about softwares or dependancies used by anis-team for the devlopment of anis-server: 
-
-* `Slim` : [http://www.slimframework.com/](http://www.slimframework.com/)
-* `Doctrine 2` : [https://www.doctrine-project.org/](https://www.doctrine-project.org/)
-* `Swiftmailer` : [https://swiftmailer.symfony.com/](https://swiftmailer.symfony.com/)
-* `Monolog` : [https://seldaek.github.io/monolog/](https://seldaek.github.io/monolog/)
-* `Composer` : [https://getcomposer.org/](https://getcomposer.org/)
-* `PHP-FIG` : [http://www.php-fig.org/](http://www.php-fig.org/)
-* `PHP-Unit` : [http://phpunit.de/](http://phpunit.de/)
-* `Docker` : [https://www.docker.com/](https://www.docker.com/)
-* `GIT` : [http://git-scm.com/](http://git-scm.com/)
-* `CeCILL`: [http://www.cecill.info/index.en.html](http://www.cecill.info/index.en.html)
\ No newline at end of file
+* To list all datasets available in the default instance => http://localhost:8082/dataset
+* To print all data for the obs_cat dataset with column 1, 2 and 3 => http://localhost:8082/search/obs_cat?a=1;2;3
+* To count the number of data available for a request => http://localhost:8082/search/obs_cat?a=count
+* To print only 3 obs_cat data (search by id) => http://localhost:8082/search/obs_cat?a=1;2;3&c=1::in::104600094|104600095|104600108
\ No newline at end of file

VERSION

-3.0.3
\ No newline at end of file
+3.1
\ No newline at end of file

app/constants.php

+<?php
+
+/*
+ * This file is part of Anis Server.
+ *
+ * (c) Laboratoire d'Astrophysique de Marseille / CNRS
+ *
+ * For the full copyright and license information, please view the LICENSE
+ * file that was distributed with this source code.
+ */
+declare(strict_types=1);
+
+define('GET', 'GET');
+define('POST', 'POST');
+define('PUT', 'PUT');
+define('DELETE', 'DELETE');
+define('OPTIONS', 'OPTIONS');
+define('SETTINGS', 'settings');

app/dependencies.php

+<?php
+
+/*
+ * This file is part of Anis Server.
+ *
+ * (c) Laboratoire d'Astrophysique de Marseille / CNRS
+ *
+ * For the full copyright and license information, please view the LICENSE
+ * file that was distributed with this source code.
+ */
+declare(strict_types=1);
+
+use Psr\Container\ContainerInterface;
+
+// Load settings
+$container->set(SETTINGS, function () {
+    return include __DIR__ . '/../app/settings.php';
+});
+
+// Doctrine factory
+$container->set('em', function (ContainerInterface $c) {
+    $settings = $c->get(SETTINGS)['database'];
+    $dc = \Doctrine\ORM\Tools\Setup::createAnnotationMetadataConfiguration(
+        array('src/Entity'),
+        $settings['dev_mode']
+    );
+    $dc->setProxyDir($settings['path_proxy']);
+    if ($settings['dev_mode']) {
+        $dc->setAutoGenerateProxyClasses(true);
+    } else {
+        $dc->setAutoGenerateProxyClasses(false);
+    }
+    return \Doctrine\ORM\EntityManager::create($settings['connection_options'], $dc);
+});
+
+// Monolog factory
+$container->set('logger', function (ContainerInterface $c) {
+    $loggerSettings = $c->get('settings')['logger'];
+    $logger = new \Monolog\Logger($loggerSettings['name']);
+    $logger->pushProcessor(new \Monolog\Processor\UidProcessor());
+    $logger->pushHandler(new \Monolog\Handler\StreamHandler($loggerSettings['path'], $loggerSettings['level']));
+    return $logger;
+});
+
+// Actions
+$container->set('App\Action\RootAction', function () {
+    return new App\Action\RootAction();
+});
+
+$container->set('App\Action\DatabaseListAction', function (ContainerInterface $c) {
+    return new App\Action\DatabaseListAction($c->get('em'));
+});
+
+$container->set('App\Action\DatabaseAction', function (ContainerInterface $c) {
+    return new App\Action\DatabaseAction($c->get('em'));
+});
+
+$container->set('App\Action\TableListAction', function (ContainerInterface $c) {
+    return new App\Action\TableListAction($c->get('em'), new App\Utils\DBALConnectionFactory());
+});
+
+$container->set('App\Action\ProjectListAction', function (ContainerInterface $c) {
+    return new App\Action\ProjectListAction($c->get('em'));
+});
+
+$container->set('App\Action\ProjectAction', function (ContainerInterface $c) {
+    return new App\Action\ProjectAction($c->get('em'));
+});
+
+$container->set('App\Action\FamilyListAction', function (ContainerInterface $c) {
+    return new App\Action\FamilyListAction($c->get('em'));
+});
+
+$container->set('App\Action\FamilyAction', function (ContainerInterface $c) {
+    return new App\Action\FamilyAction($c->get('em'));
+});
+
+$container->set('App\Action\OutputCategoryListAction', function (ContainerInterface $c) {
+    return new App\Action\OutputCategoryListAction($c->get('em'));
+});
+
+$container->set('App\Action\OutputCategoryAction', function (ContainerInterface $c) {
+    return new App\Action\OutputCategoryAction($c->get('em'));
+});
+
+$container->set('App\Action\DatasetListAction', function (ContainerInterface $c) {
+    return new App\Action\DatasetListAction($c->get('em'), new App\Utils\DBALConnectionFactory());
+});
+
+$container->set('App\Action\DatasetAction', function (ContainerInterface $c) {
+    return new App\Action\DatasetAction($c->get('em'), new App\Utils\DBALConnectionFactory());
+});
+
+$container->set('App\Action\AttributeListAction', function (ContainerInterface $c) {
+    return new App\Action\AttributeListAction($c->get('em'));
+});
+
+$container->set('App\Action\AttributeAction', function (ContainerInterface $c) {
+    return new App\Action\AttributeAction($c->get('em'));
+});
+
+$container->set('App\Action\SearchAction', function (ContainerInterface $c) {
+    return new App\Action\SearchAction(
+        $c->get('em'),
+        new App\Utils\DBALConnectionFactory(),
+        new App\Utils\Operator\OperatorFactory()
+    );
+});
+
+// Middlewares
+$container->set('App\Middleware\AuthorizationMiddleware', function (ContainerInterface $c) {
+    return new App\Middleware\AuthorizationMiddleware($c->get('em'), $c->get(SETTINGS)['token_options']);
+});

src/middleware.php → app/middlewares.php

-<?php declare(strict_types=1);
+<?php
+
 /*
- * This file is part of ANIS SERVER API.
+ * This file is part of Anis Server.
  *
- * (c) François Agneray <francois.agneray@lam.fr>
- * (c) Chrystel Moreau <chrystel.moreau@lam.fr>
+ * (c) Laboratoire d'Astrophysique de Marseille / CNRS
  *
  * For the full copyright and license information, please view the LICENSE
  * file that was distributed with this source code.
  */
+declare(strict_types=1);
 
-$app->add(App\Middleware\CorsMiddleware::class);
+$app->add(new App\Middleware\JsonBodyParserMiddleware());
+$app->add(new App\Middleware\ContentTypeJsonMiddleware());

app/routes.php

+<?php
+
+/*
+ * This file is part of Anis Server.
+ *
+ * (c) Laboratoire d'Astrophysique de Marseille / CNRS
+ *
+ * For the full copyright and license information, please view the LICENSE
+ * file that was distributed with this source code.
+ */
+declare(strict_types=1);
+
+use Slim\Routing\RouteCollectorProxy;
+
+$app->get('/', App\Action\RootAction::class);
+$app->map([OPTIONS, GET, POST], '/database', App\Action\DatabaseListAction::class);
+$app->map([OPTIONS, GET, PUT, DELETE], '/database/{id}', App\Action\DatabaseAction::class);
+$app->map([OPTIONS, GET], '/database/{id}/table', App\Action\TableListAction::class);
+$app->map([OPTIONS, GET, POST], '/project', App\Action\ProjectListAction::class);
+$app->map([OPTIONS, GET, PUT, DELETE], '/project/{name}', App\Action\ProjectAction::class);
+$app->map([OPTIONS, GET, POST], '/family/{type}', App\Action\FamilyListAction::class);
+$app->map([OPTIONS, GET, PUT, DELETE], '/family/{type}/{id}', App\Action\FamilyAction::class);
+$app->map([OPTIONS, GET, POST], '/output-category', App\Action\OutputCategoryListAction::class);
+$app->map([OPTIONS, GET, PUT, DELETE], '/output-category/{id}', App\Action\OutputCategoryAction::class);
+$app->map([OPTIONS, GET, POST], '/dataset', App\Action\DatasetListAction::class);
+$app->map([OPTIONS, GET, PUT, DELETE], '/dataset/{name}', App\Action\DatasetAction::class);
+$app->map([OPTIONS, GET], '/dataset/{name}/attribute', App\Action\AttributeListAction::class);
+$app->map([OPTIONS, GET, PUT], '/dataset/{name}/attribute/{id}', App\Action\AttributeAction::class);
+$app->get('/search/{dname}', App\Action\SearchAction::class);

app/settings.php

+<?php
+
+/*
+ * This file is part of Anis Server.
+ *
+ * (c) Laboratoire d'Astrophysique de Marseille / CNRS
+ *
+ * For the full copyright and license information, please view the LICENSE
+ * file that was distributed with this source code.
+ */
+declare(strict_types=1);
+
+return [
+    'displayErrorDetails' => getenv('DISPLAY_ERROR_DETAILS'),
+    'database' => [
+        'path_proxy' => getenv('DATABASE_PATH_PROXY'),
+        'dev_mode' => getenv('DATABASE_DEV_MODE'),
+        'connection_options' => [
+            'driver' => getenv('DATABASE_CO_DRIVER'),
+            'path' => getenv('DATABASE_CO_PATH'),
+            'host' => getenv('DATABASE_CO_HOST'),
+            'port' => (int) getenv('DATABASE_CO_PORT'),
+            'dbname' => getenv('DATABASE_CO_DBNAME'),
+            'user' => getenv('DATABASE_CO_USER'),
+            'password' => getenv('DATABASE_CO_PASSWORD')
+        ],
+    ],
+    'logger' => [
+        'name' => getenv('LOGGER_NAME'),
+        'path' => getenv('LOGGER_PATH'),
+        'level' => getenv('LOGGER_LEVEL')
+    ]
+];

cli-config.php

@@ -2,17 +2,17 @@
 // File needed by doctrine cli
 require 'vendor/autoload.php';