Adding Instance into metamodel

Makefile

@@ -65,4 +65,4 @@ dev-meta:
 	@docker-compose exec php sh ./conf-dev/dev-meta.sh
 
 remove-pgdata:
-	@docker volume rm anis-metamodel_pgdata
+	@docker volume rm anis-server_pgdata

app/routes.php

@@ -22,6 +22,8 @@ $app->map([OPTIONS, GET, POST], '/family/{type}', App\Action\FamilyListAction::c
 $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], '/instance', App\Action\InstanceListAction::class);
+$app->map([OPTIONS, GET, PUT, DELETE], '/instance/{name}', App\Action\InstanceAction::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);

src/Action/DatasetListAction.php

@@ -19,6 +19,7 @@ use Doctrine\ORM\EntityManagerInterface;
 use App\Utils\DBALConnectionFactory;
 use App\Entity\Database;
 use App\Entity\Project;
+use App\Entity\Instance;
 use App\Entity\DatasetFamily;
 use App\Entity\Dataset;
 use App\Entity\Attribute;
@@ -75,6 +76,7 @@ final class DatasetListAction extends AbstractAction
                 'data_path',
                 'selectable_row',
                 'project_name',
+                'instance_name',
                 'id_dataset_family'
             );
             foreach ($fields as $a) {
@@ -95,6 +97,15 @@ final class DatasetListAction extends AbstractAction
                 );
             }
 
+            // Instance is mandatory to add a new dataset
+            $instance = $this->em->find('App\Entity\Instance', $parsedBody['instance_name']);
+            if (is_null($instance)) {
+                throw new HttpBadRequestException(
+                    $request,
+                    'Instance with name ' . $parsedBody['instance_name'] . ' is not found'
+                );
+            }
+
             $family = $this->em->find('App\Entity\DatasetFamily', $parsedBody['id_dataset_family']);
             if (is_null($family)) {
                 throw new HttpBadRequestException(
@@ -103,7 +114,7 @@ final class DatasetListAction extends AbstractAction
                 );
             }
 
-            $dataset = $this->postDataset($parsedBody, $project, $family);
+            $dataset = $this->postDataset($parsedBody, $project, $instance, $family);
             $payload = json_encode($dataset);
             $response = $response->withStatus(201);
         }
@@ -121,8 +132,12 @@ final class DatasetListAction extends AbstractAction
      *
      * @return Dataset
      */
-    private function postDataset(array $parsedBody, Project $project, DatasetFamily $family): Dataset
-    {
+    private function postDataset(
+        array $parsedBody,
+        Project $project,
+        Instance $instance,
+        DatasetFamily $family
+    ): Dataset {
         $dataset = new Dataset($parsedBody['name']);
         $dataset->setTableRef($parsedBody['table_ref']);
         $dataset->setLabel($parsedBody['label']);
@@ -133,6 +148,7 @@ final class DatasetListAction extends AbstractAction
         $dataset->setDataPath($parsedBody['data_path']);
         $dataset->setSelectableRow($parsedBody['selectable_row']);
         $dataset->setProject($project);
+        $dataset->setInstance($instance);
         $dataset->setDatasetFamily($family);
 
         $this->em->persist($dataset);

src/Action/InstanceAction.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);
+
+namespace App\Action;
+
+use Psr\Http\Message\ServerRequestInterface as Request;
+use Psr\Http\Message\ResponseInterface as Response;
+use Slim\Exception\HttpBadRequestException;
+use Slim\Exception\HttpNotFoundException;
+use App\Entity\Instance;
+
+final class InstanceAction extends AbstractAction
+{
+    /**
+     * `GET` Returns the instance found
+     * `PUT` Full update the instance and returns the new version
+     * `DELETE` Delete the instance found and return a confirmation message
+     *
+     * @param  ServerRequestInterface $request  PSR-7 This object represents the HTTP request
+     * @param  ResponseInterface      $response PSR-7 This object represents the HTTP response
+     * @param  string[]               $args     This table contains information transmitted in the URL (see routes.php)
+     *
+     * @return ResponseInterface
+     */
+    public function __invoke(Request $request, Response $response, array $args): Response
+    {
+        if ($request->getMethod() === OPTIONS) {
+            return $response->withHeader('Access-Control-Allow-Methods', 'GET, PUT, DELETE, OPTIONS');
+        }
+
+        // Search the correct instance with primary key
+        $instance = $this->em->find('App\Entity\Instance', $args['name']);
+
+        // If instance is not found 404
+        if (is_null($instance)) {
+            throw new HttpNotFoundException(
+                $request,
+                'Instance with name ' . $args['name'] . ' is not found'
+            );
+        }
+
+        if ($request->getMethod() === GET) {
+            $payload = json_encode($instance);
+        }
+
+        if ($request->getMethod() === PUT) {
+            $parsedBody = $request->getParsedBody();
+
+            // If mandatories empty fields 400
+            foreach (array('label', 'client_url') as $a) {
+                if ($this->isEmptyField($a, $parsedBody)) {
+                    throw new HttpBadRequestException(
+                        $request,
+                        'Param ' . $a . ' needed to edit the instance'
+                    );
+                }
+            }
+
+            $this->editInstance($instance, $parsedBody);
+            $payload = json_encode($instance);
+        }
+
+        if ($request->getMethod() === DELETE) {
+            $name = $instance->getName();
+            $this->em->remove($instance);
+            $this->em->flush();
+            $payload = json_encode(array('message' => 'Instance with name ' . $name . ' is removed!'));
+        }
+
+        $response->getBody()->write($payload);
+        return $response;
+    }
+
+    /**
+     * Update instance object with setters
+     *
+     * @param Instance $instance   The instance to update
+     * @param array    $parsedBody Contains the new values ​​of the instance sent by the user
+     */
+    private function editInstance(Instance $instance, array $parsedBody): void
+    {
+        $instance->setLabel($parsedBody['label']);
+        $instance->setClientUrl($parsedBody['client_url']);
+        $this->em->flush();
+    }
+}

src/Action/InstanceListAction.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);
+
+namespace App\Action;
+
+use Psr\Http\Message\ServerRequestInterface as Request;
+use Psr\Http\Message\ResponseInterface as Response;
+use Slim\Exception\HttpBadRequestException;
+use App\Entity\Instance;
+
+final class InstanceListAction extends AbstractAction
+{
+    /**
+     * `GET`  Returns a list of all instances listed in the metamodel
+     * `POST` Add a new instance
+     *
+     * @param  ServerRequestInterface $request  PSR-7 This object represents the HTTP request
+     * @param  ResponseInterface      $response PSR-7 This object represents the HTTP response
+     * @param  string[]               $args     This table contains information transmitted in the URL (see routes.php)
+     *
+     * @return ResponseInterface
+     */
+    public function __invoke(Request $request, Response $response, array $args): Response
+    {
+        if ($request->getMethod() === OPTIONS) {
+            return $response->withHeader('Access-Control-Allow-Methods', 'GET, POST, OPTIONS');
+        }
+
+        if ($request->getMethod() === GET) {
+            // Retrieve user with email adress
+            $instances = $this->em->getRepository('App\Entity\Instance')->findAll();
+            $payload = json_encode($instances);
+        }
+
+        if ($request->getMethod() === POST) {
+            $parsedBody = $request->getParsedBody();
+
+            // To work this action needs user information to update
+            foreach (array('name', 'label', 'client_url') as $a) {
+                if ($this->isEmptyField($a, $parsedBody)) {
+                    throw new HttpBadRequestException(
+                        $request,
+                        'Param ' . $a . ' needed to add a new instance'
+                    );
+                }
+            }
+
+            $instance = $this->postInstance($parsedBody);
+            $payload = json_encode($instance);
+            $response = $response->withStatus(201);
+        }
+
+        $response->getBody()->write($payload);
+        return $response;
+    }
+
+    /**
+     * Add a new instance into the metamodel
+     *
+     * @param array $parsedBody Contains the values ​​of the new instance sent by the user
+     */
+    private function postInstance(array $parsedBody): Instance
+    {
+        $instance = new Instance($parsedBody['name'], $parsedBody['label']);
+        $instance->setClientUrl($parsedBody['client_url']);
+
+        $this->em->persist($instance);
+        $this->em->flush();
+
+        return $instance;
+    }
+}

src/Entity/Dataset.php

@@ -92,6 +92,14 @@ class Dataset implements \JsonSerializable
      */
     protected $project;
 
+    /**
+     * @var Anis\Entity\Instance
+     *
+     * @ManyToOne(targetEntity="Instance")
+     * @JoinColumn(name="instance_name", referencedColumnName="name", nullable=false)
+     */
+    protected $instance;
+
     /**
      * @var Anis\Entity\Project
      *
@@ -222,6 +230,16 @@ class Dataset implements \JsonSerializable
         $this->project = $project;
     }
 
+    public function getInstance(): Instance
+    {
+        return $this->instance;
+    }
+
+    public function setInstance(Instance $instance): void
+    {
+        $this->instance = $instance;
+    }
+
     public function getDatasetFamily()
     {
         return $this->datasetFamily;
@@ -265,6 +283,7 @@ class Dataset implements \JsonSerializable
             'data_path' => $this->getDataPath(),
             'selectable_row' => $this->getSelectableRow(),
             'project_name' => $this->getProject()->getName(),
+            'instance_name' => $this->getInstance()->getName(),
             'id_dataset_family' => $this->getDatasetFamily()->getId()
         ];
     }

src/Entity/Instance.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);
+
+namespace App\Entity;
+
+/**
+ * @Entity
+ * @Table(name="instance")
+ */
+class Instance implements \JsonSerializable
+{
+    /**
+     * @var integer
+     *
+     * @Id
+     * @Column(type="string", nullable=false)
+     */
+    protected $name;
+
+    /**
+     * @var string
+     *
+     * @Column(type="string", nullable=false)
+     */
+    protected $label;
+
+    /**
+     * @var string
+     *
+     * @Column(type="string", nullable=true)
+     */
+    protected $clientUrl;
+
+    public function __construct(string $name, string $label)
+    {
+        $this->name = $name;
+        $this->label = $label;
+    }
+
+    public function getName(): string
+    {
+        return $this->name;
+    }
+
+    public function getLabel(): string
+    {
+        return $this->label;
+    }
+
+    public function setLabel(string $label): void
+    {
+        $this->label = $label;
+    }
+
+    public function getClientUrl(): string
+    {
+        return $this->clientUrl;
+    }
+
+    public function setClientUrl($clientUrl): void
+    {
+        $this->clientUrl = $clientUrl;
+    }
+
+    public function jsonSerialize()
+    {
+        return [
+            'name' => $this->getName(),
+            'label' => $this->getLabel(),
+            'client_url' => $this->getClientUrl()
+        ];
+    }
+}

tests/Action/AttributeActionTest.php

@@ -20,6 +20,7 @@ use Slim\Exception\HttpBadRequestException;
 use App\tests\EntityManagerBuilder;
 use App\Entity\Database;
 use App\Entity\Project;
+use App\Entity\Instance;
 use App\Entity\DatasetFamily;
 use App\Entity\CriteriaFamily;
 use App\Entity\OutputFamily;
@@ -161,6 +162,15 @@ final class AttributeActionTest extends TestCase
         return $project;
     }
 
+    private function addInstance(): Instance
+    {
+        $instance = new Instance('aspic', 'Aspic');
+        $instance->setClientUrl('http://cesam.lam.fr/aspic');
+        $this->entityManager->persist($instance);
+        $this->entityManager->flush();
+        return $instance;
+    }
+
     private function addDatasetFamily(): DatasetFamily
     {
         $family = new DatasetFamily();
@@ -208,6 +218,7 @@ final class AttributeActionTest extends TestCase
     private function addADataset(): Dataset
     {
         $project = $this->addProject();
+        $instance = $this->addInstance();
         $family = $this->addDatasetFamily();
 
         $dataset = new Dataset('obs_cat');
@@ -220,6 +231,7 @@ final class AttributeActionTest extends TestCase
         $dataset->setDataPath('/mnt/obs_cat');
         $dataset->setSelectableRow(false);
         $dataset->setProject($project);
+        $dataset->setInstance($instance);
         $dataset->setDatasetFamily($family);
         $this->entityManager->persist($dataset);
         $this->entityManager->flush();

tests/Action/AttributeListActionTest.php

@@ -20,6 +20,7 @@ use Slim\Exception\HttpNotFoundException;
 use App\tests\EntityManagerBuilder;
 use App\Entity\Database;
 use App\Entity\Project;
+use App\Entity\Instance;
 use App\Entity\DatasetFamily;
 use App\Entity\Dataset;
 use App\Entity\Attribute;
@@ -97,6 +98,15 @@ final class AttributeListActionTest extends TestCase
         return $project;
     }
 
+    private function addInstance(): Instance
+    {
+        $instance = new Instance('aspic', 'Aspic');
+        $instance->setClientUrl('http://cesam.lam.fr/aspic');
+        $this->entityManager->persist($instance);
+        $this->entityManager->flush();
+        return $instance;
+    }
+
     private function addDatasetFamily(): DatasetFamily
     {
         $family = new DatasetFamily();
@@ -110,6 +120,7 @@ final class AttributeListActionTest extends TestCase
     private function addADataset(): Dataset
     {
         $project = $this->addProject();
+        $instance = $this->addInstance();
         $family = $this->addDatasetFamily();
 
         $dataset = new Dataset('obs_cat');
@@ -122,6 +133,7 @@ final class AttributeListActionTest extends TestCase
         $dataset->setDataPath('/mnt/obs_cat');
         $dataset->setSelectableRow(false);
         $dataset->setProject($project);
+        $dataset->setInstance($instance);
         $dataset->setDatasetFamily($family);
         $this->entityManager->persist($dataset);
         $this->entityManager->flush();

tests/Action/DatasetActionTest.php

@@ -20,6 +20,7 @@ use Slim\Exception\HttpBadRequestException;
 use App\tests\EntityManagerBuilder;
 use App\Entity\Database;
 use App\Entity\Project;
+use App\Entity\Instance;
 use App\Entity\DatasetFamily;
 use App\Entity\Dataset;
 
@@ -92,7 +93,7 @@ final class DatasetActionTest extends TestCase
                 array_merge(
                     ['name' => 'obs_cat', 'table_ref' => 'v_obs_cat'],
                     $fields,
-                    ['project_name' => 'anis_project', 'id_dataset_family' => 1]
+                    ['project_name' => 'anis_project', 'instance_name' => 'aspic', 'id_dataset_family' => 1]
                 ),
                 JSON_UNESCAPED_SLASHES
             ),
@@ -101,7 +102,7 @@ final class DatasetActionTest extends TestCase
         $this->assertEquals(200, (int) $response->getStatusCode());
     }
 
-    public function testDeleteADatabase(): void
+    public function testDeleteADataset(): void
     {
         $this->addADataset();
         $request = $this->getRequest('DELETE');
@@ -162,6 +163,15 @@ final class DatasetActionTest extends TestCase
         return $project;
     }
 
+    private function addInstance(): Instance
+    {
+        $instance = new Instance('aspic', 'Aspic');
+        $instance->setClientUrl('http://cesam.lam.fr/aspic');
+        $this->entityManager->persist($instance);
+        $this->entityManager->flush();
+        return $instance;
+    }
+
     private function addDatasetFamily(): DatasetFamily
     {
         $family = new DatasetFamily();
@@ -176,6 +186,7 @@ final class DatasetActionTest extends TestCase
     private function addADataset(): Dataset
     {
         $project = $this->addProject();
+        $instance = $this->addInstance();
         $family = $this->addDatasetFamily();
 
         $dataset = new Dataset('obs_cat');
@@ -188,6 +199,7 @@ final class DatasetActionTest extends TestCase
         $dataset->setDataPath('/mnt/obs_cat');
         $dataset->setSelectableRow(false);
         $dataset->setProject($project);
+        $dataset->setInstance($instance);
         $dataset->setDatasetFamily($family);
         $this->entityManager->persist($dataset);
         $this->entityManager->flush();

tests/Action/DatasetListActionTest.php

@@ -24,6 +24,7 @@ use Doctrine\DBAL\Types\Type;
 use App\tests\EntityManagerBuilder;
 use App\Entity\Database;
 use App\Entity\Project;
+use App\Entity\Instance;
 use App\Entity\DatasetFamily;
 use App\Entity\Dataset;
 
@@ -78,6 +79,7 @@ final class DatasetListActionTest extends TestCase
     public function testAddANewDatasetFamilyNotFound(): void
     {
         $this->addProject();
+        $this->addInstance();
         $this->expectException(HttpBadRequestException::class);
         $this->expectExceptionMessage('Dataset family with id 1 is not found');
         $fields = $this->getNewDatasetFields();
@@ -86,9 +88,21 @@ final class DatasetListActionTest extends TestCase
         $this->assertEquals(400, (int) $response->getStatusCode());
     }
 
+    public function testAddANewDatasetInstanceNotFound(): void
+    {
+        $this->addProject();
+        $this->expectException(HttpBadRequestException::class);
+        $this->expectExceptionMessage('Instance with name aspic is not found');
+        $fields = $this->getNewDatasetFields();
+        $request = $this->getRequest('POST')->withParsedBody($fields);
+        $response = ($this->action)($request, new Response(), array());
+        $this->assertEquals(400, (int) $response->getStatusCode());
+    }
+
     public function testAddANewDataset(): void
     {
         $this->addProject();
+        $this->addInstance();
         $this->addDatasetFamily();
         $fields = $this->getNewDatasetFields();
         $request = $this->getRequest('POST')->withParsedBody($fields);
@@ -125,6 +139,7 @@ final class DatasetListActionTest extends TestCase
             'data_path' => '/mnt/dataset1',
             'selectable_row' => false,
             'project_name' => 'anis_project',
+            'instance_name' => 'aspic',
             'id_dataset_family' => 1
         );
     }
@@ -153,6 +168,15 @@ final class DatasetListActionTest extends TestCase
         return $project;
     }
 
+    private function addInstance(): Instance
+    {
+        $instance = new Instance('aspic', 'Aspic');
+        $instance->setClientUrl('http://cesam.lam.fr/aspic');
+        $this->entityManager->persist($instance);
+        $this->entityManager->flush();
+        return $instance;
+    }
+
     private function addDatasetFamily(): DatasetFamily
     {
         $family = new DatasetFamily();
@@ -167,6 +191,7 @@ final class DatasetListActionTest extends TestCase
     private function addDatasets(): array
     {
         $project = $this->addProject();
+        $instance = $this->addInstance();
         $family = $this->addDatasetFamily();
 
         $dataset1 = new Dataset('dataset1');
@@ -179,6 +204,7 @@ final class DatasetListActionTest extends TestCase
         $dataset1->setDataPath('/mnt/dataset1');
         $dataset1->setSelectableRow(false);
         $dataset1->setProject($project);
+        $dataset1->setInstance($instance);
         $dataset1->setDatasetFamily($family);
         $this->entityManager->persist($dataset1);
 
@@ -192,6 +218,7 @@ final class DatasetListActionTest extends TestCase
         $dataset2->setDataPath('/mnt/dataset2');
         $dataset2->setSelectableRow(false);
         $dataset2->setProject($project);
+        $dataset2->setInstance($instance);
         $dataset2->setDatasetFamily($family);
         $this->entityManager->persist($dataset2);
 

tests/Action/InstanceActionTest.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);
+
+namespace App\Tests\Action;
+
+use PHPUnit\Framework\TestCase;
+use Nyholm\Psr7\ServerRequest;
+use Nyholm\Psr7\Response;
+use Slim\Exception\HttpNotFoundException;
+use Slim\Exception\HttpBadRequestException;
+use App\tests\EntityManagerBuilder;
+use App\Entity\Instance;
+