chore: execute prettier and linter

GenomicDataInfrastructure · Mar 20, 2024 · 6d1aadb · 6d1aadb
1 parent df946f0
commit 6d1aadb
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Showing 12 changed files with 107 additions and 129 deletions.
diff --git a/checkstyle.xml.license b/checkstyle.xml.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2024 PNED G.I.E.
+
+SPDX-License-Identifier: Apache-2.0
diff --git a/src/main/java/io/github/genomicdatainfrastructure/daam/api/ApplicationCommandApiImpl.java b/src/main/java/io/github/genomicdatainfrastructure/daam/api/ApplicationCommandApiImpl.java
@@ -1,98 +1,79 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
+
 package io.github.genomicdatainfrastructure.daam.api;
-import java.io.File;
-import java.util.List;
 
-import io.github.genomicdatainfrastructure.daam.services.CreateApplicationService;
 import io.github.genomicdatainfrastructure.daam.model.AddApplicationEvent;
 import io.github.genomicdatainfrastructure.daam.model.AddedAttachments;
 import io.github.genomicdatainfrastructure.daam.model.CreateApplication;
 import io.github.genomicdatainfrastructure.daam.model.RemoveMember;
 import io.github.genomicdatainfrastructure.daam.model.SaveFormsAndDuos;
 import io.github.genomicdatainfrastructure.daam.model.UpdateDatasets;
+import io.github.genomicdatainfrastructure.daam.services.CreateApplicationService;
 import jakarta.ws.rs.core.Response;
+import java.io.File;
+import java.util.List;
 import lombok.RequiredArgsConstructor;
 
 @RequiredArgsConstructor
 public class ApplicationCommandApiImpl implements ApplicationCommandApi {
 
-    private final CreateApplicationService createApplicationService;
+  private final CreateApplicationService createApplicationService;
 
-    @Override
-    public Response acceptApplicationTermsV1(String id) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'acceptApplicationTermsV1'"
-        );
-    }
+  @Override
+  public Response acceptApplicationTermsV1(String id) {
+    throw new UnsupportedOperationException("Unimplemented method 'acceptApplicationTermsV1'");
+  }
 
-    @Override
-    public List<AddedAttachments> addAttachmentToApplicationV1(String id, File body) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'addAttachmentToApplicationV1'"
-        );
-    }
+  @Override
+  public List<AddedAttachments> addAttachmentToApplicationV1(String id, File body) {
+    throw new UnsupportedOperationException("Unimplemented method 'addAttachmentToApplicationV1'");
+  }
 
-    @Override
-    public Response addEventToApplicationV1(String id, AddApplicationEvent addApplicationEvent) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'addEventToApplicationV1'"
-        );
-    }
+  @Override
+  public Response addEventToApplicationV1(String id, AddApplicationEvent addApplicationEvent) {
+    throw new UnsupportedOperationException("Unimplemented method 'addEventToApplicationV1'");
+  }
 
-    @Override
-    public Response cancelApplicationV1(String id) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'cancelApplicationV1'"
-        );
-    }
+  @Override
+  public Response cancelApplicationV1(String id) {
+    throw new UnsupportedOperationException("Unimplemented method 'cancelApplicationV1'");
+  }
 
-    @Override
-    public Response copyApplicationAsNewV1(String id) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'copyApplicationAsNewV1'"
-        );
-    }
+  @Override
+  public Response copyApplicationAsNewV1(String id) {
+    throw new UnsupportedOperationException("Unimplemented method 'copyApplicationAsNewV1'");
+  }
 
-    @Override
-    public Response createApplicationV1(CreateApplication createApplication) {
-        createApplicationService.createRemsApplication(createApplication);
-        return Response.noContent().build();
-    }
+  @Override
+  public Response createApplicationV1(CreateApplication createApplication) {
+    createApplicationService.createRemsApplication(createApplication);
+    return Response.noContent().build();
+  }
 
-    @Override
-    public Response inviteMemberToApplicationV1(String id) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'inviteMemberToApplicationV1'"
-        );
-    }
+  @Override
+  public Response inviteMemberToApplicationV1(String id) {
+    throw new UnsupportedOperationException("Unimplemented method 'inviteMemberToApplicationV1'");
+  }
 
-    @Override
-    public Response removeMemberFromApplicationV1(String id, RemoveMember removeMember) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'removeMemberFromApplicationV1'"
-        );
-    }
+  @Override
+  public Response removeMemberFromApplicationV1(String id, RemoveMember removeMember) {
+    throw new UnsupportedOperationException("Unimplemented method 'removeMemberFromApplicationV1'");
+  }
 
-    @Override
-    public Response saveApplicationFormsAndDuosV1(String id, SaveFormsAndDuos saveFormsAndDuos) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'saveApplicationFormsAndDuosV1'"
-        );
-    }
+  @Override
+  public Response saveApplicationFormsAndDuosV1(String id, SaveFormsAndDuos saveFormsAndDuos) {
+    throw new UnsupportedOperationException("Unimplemented method 'saveApplicationFormsAndDuosV1'");
+  }
 
-    @Override
-    public Response submitApplicationV1(String id) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'submitApplicationV1'"
-        );
-    }
+  @Override
+  public Response submitApplicationV1(String id) {
+    throw new UnsupportedOperationException("Unimplemented method 'submitApplicationV1'");
+  }
 
-    @Override
-    public Response updateDatasetsOfApplicationV1(String id, List<UpdateDatasets> updateDatasets) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'updateDatasetsOfApplicationV1'"
-        );
-    }
+  @Override
+  public Response updateDatasetsOfApplicationV1(String id, List<UpdateDatasets> updateDatasets) {
+    throw new UnsupportedOperationException("Unimplemented method 'updateDatasetsOfApplicationV1'");
+  }
 }
diff --git a/src/main/java/io/github/genomicdatainfrastructure/daam/api/ApplicationQueryApiImpl.java b/src/main/java/io/github/genomicdatainfrastructure/daam/api/ApplicationQueryApiImpl.java
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
+
 package io.github.genomicdatainfrastructure.daam.api;
 
 import static io.github.genomicdatainfrastructure.daam.security.PostAuthenticationFilter.USER_ID_CLAIM;
@@ -35,7 +36,6 @@ public RetrievedApplication retrieveApplicationV1(String id) {
   @Override
   public File retrieveAttachmentFromApplicationV1(String id, String attachmentId) {
     throw new UnsupportedOperationException(
-        "Unimplemented method 'retrieveAttachmentFromApplicationV1'"
-    );
+        "Unimplemented method 'retrieveAttachmentFromApplicationV1'");
   }
 }
diff --git a/...main/java/io/github/genomicdatainfrastructure/daam/security/PostAuthenticationFilter.java b/...main/java/io/github/genomicdatainfrastructure/daam/security/PostAuthenticationFilter.java
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
+
 package io.github.genomicdatainfrastructure.daam.security;
 
 import io.github.genomicdatainfrastructure.daam.services.CreateRemsUserService;
@@ -25,9 +26,8 @@ public class PostAuthenticationFilter implements ContainerRequestFilter {
   private final CreateRemsUserService createRemsUserService;
 
   @Inject
-  public PostAuthenticationFilter(SecurityIdentity identity,
-      CreateRemsUserService createRemsUserService
-  ) {
+  public PostAuthenticationFilter(
+      SecurityIdentity identity, CreateRemsUserService createRemsUserService) {
     this.identity = identity;
     this.createRemsUserService = createRemsUserService;
   }

diff --git a/...main/java/io/github/genomicdatainfrastructure/daam/services/CreateApplicationService.java b/...main/java/io/github/genomicdatainfrastructure/daam/services/CreateApplicationService.java
@@ -5,46 +5,44 @@
 package io.github.genomicdatainfrastructure.daam.services;
 
 import static io.github.genomicdatainfrastructure.daam.security.PostAuthenticationFilter.USER_ID_CLAIM;
+
 import io.github.genomicdatainfrastructure.daam.model.CreateApplication;
 import io.github.genomicdatainfrastructure.daam.remote.rems.api.RemsApplicationCommandApi;
 import io.github.genomicdatainfrastructure.daam.remote.rems.model.CreateApplicationCommand;
 import io.quarkus.oidc.runtime.OidcJwtCallerPrincipal;
 import io.quarkus.security.identity.SecurityIdentity;
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
+import java.util.List;
 import org.eclipse.microprofile.config.inject.ConfigProperty;
 import org.eclipse.microprofile.rest.client.inject.RestClient;
 
-import java.util.List;
-
 @ApplicationScoped
 public class CreateApplicationService {
 
-    private final SecurityIdentity identity;
-    private final String remsApiKey;
-    private final RemsApplicationCommandApi remsApplicationCommandApi;
-
-    @Inject
-    public CreateApplicationService(
-        @ConfigProperty(name = "quarkus.rest-client.rems_yaml.api-key") String remsApiKey,
-        SecurityIdentity identity,
-        @RestClient RemsApplicationCommandApi applicationsApi
-    ) {
-        this.remsApiKey = remsApiKey;
-        this.identity = identity;
-        this.remsApplicationCommandApi = applicationsApi;
-    }
-
-    public void createRemsApplication(CreateApplication createApplication) {
-        var principal = (OidcJwtCallerPrincipal) identity.getPrincipal();
-        String userId = principal.getClaim(USER_ID_CLAIM);
-
-        List<String> catalogueItemIds = createApplication.getDatasetIds();
-
-        CreateApplicationCommand command = CreateApplicationCommand.builder()
-                .catalogueItemIds(catalogueItemIds)
-                .build();
-
-        remsApplicationCommandApi.apiApplicationsCreatePost(command, remsApiKey, userId);
-    }
+  private final SecurityIdentity identity;
+  private final String remsApiKey;
+  private final RemsApplicationCommandApi remsApplicationCommandApi;
+
+  @Inject
+  public CreateApplicationService(
+      @ConfigProperty(name = "quarkus.rest-client.rems_yaml.api-key") String remsApiKey,
+      SecurityIdentity identity,
+      @RestClient RemsApplicationCommandApi applicationsApi) {
+    this.remsApiKey = remsApiKey;
+    this.identity = identity;
+    this.remsApplicationCommandApi = applicationsApi;
+  }
+
+  public void createRemsApplication(CreateApplication createApplication) {
+    var principal = (OidcJwtCallerPrincipal) identity.getPrincipal();
+    String userId = principal.getClaim(USER_ID_CLAIM);
+
+    List<String> catalogueItemIds = createApplication.getDatasetIds();
+
+    CreateApplicationCommand command =
+        CreateApplicationCommand.builder().catalogueItemIds(catalogueItemIds).build();
+
+    remsApplicationCommandApi.apiApplicationsCreatePost(command, remsApiKey, userId);
+  }
 }
diff --git a/src/main/java/io/github/genomicdatainfrastructure/daam/services/CreateRemsUserService.java b/src/main/java/io/github/genomicdatainfrastructure/daam/services/CreateRemsUserService.java
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
+
 package io.github.genomicdatainfrastructure.daam.services;
 
 import io.github.genomicdatainfrastructure.daam.remote.rems.api.RemsUsersApi;
@@ -21,8 +22,7 @@ public class CreateRemsUserService {
   public CreateRemsUserService(
       @ConfigProperty(name = "quarkus.rest-client.rems_yaml.api-key") String remsApiKey,
       @ConfigProperty(name = "quarkus.rest-client.rems_yaml.bot-user") String remsBotUser,
-      @RestClient RemsUsersApi usersApi
-  ) {
+      @RestClient RemsUsersApi usersApi) {
     this.remsApiKey = remsApiKey;
     this.remsBotUser = remsBotUser;
     this.usersApi = usersApi;

diff --git a/src/main/java/io/github/genomicdatainfrastructure/daam/services/ListApplicationsService.java b/src/main/java/io/github/genomicdatainfrastructure/daam/services/ListApplicationsService.java
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
+
 package io.github.genomicdatainfrastructure.daam.services;
 
 import io.github.genomicdatainfrastructure.daam.model.ListedApplication;
@@ -21,8 +22,7 @@ public class ListApplicationsService {
   @Inject
   public ListApplicationsService(
       @ConfigProperty(name = "quarkus.rest-client.rems_yaml.api-key") String remsApiKey,
-      @RestClient RemsApplicationsApi applicationsApi
-  ) {
+      @RestClient RemsApplicationsApi applicationsApi) {
     this.remsApiKey = remsApiKey;
     this.applicationsApi = applicationsApi;
   }

diff --git a/src/test/java/io/github/genomicdatainfrastructure/daam/api/ApplicationCommandApiImplIT.java b/src/test/java/io/github/genomicdatainfrastructure/daam/api/ApplicationCommandApiImplIT.java
@@ -1,11 +1,10 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
+
 package io.github.genomicdatainfrastructure.daam.api;
 
 import io.quarkus.test.junit.QuarkusIntegrationTest;
 
 @QuarkusIntegrationTest
-public class ApplicationCommandApiImplIT extends ApplicationCommandApiImplTest {
-
-}
+public class ApplicationCommandApiImplIT extends ApplicationCommandApiImplTest {}
diff --git a/...test/java/io/github/genomicdatainfrastructure/daam/api/ApplicationCommandApiImplTest.java b/...test/java/io/github/genomicdatainfrastructure/daam/api/ApplicationCommandApiImplTest.java
@@ -1,17 +1,16 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
+
 package io.github.genomicdatainfrastructure.daam.api;
 
-import io.github.genomicdatainfrastructure.daam.model.CreateApplication;
-import org.junit.jupiter.api.Test;
+import static io.restassured.RestAssured.given;
 
-import static org.hamcrest.Matchers.equalTo;
+import io.github.genomicdatainfrastructure.daam.model.CreateApplication;
 import io.quarkus.test.junit.QuarkusTest;
-import static io.restassured.RestAssured.given;
 import io.quarkus.test.keycloak.client.KeycloakTestClient;
 import java.util.Arrays;
-
+import org.junit.jupiter.api.Test;
 
 @QuarkusTest
 public class ApplicationCommandApiImplTest {
@@ -23,13 +22,13 @@ void unauthorized_when_no_user() {
     given().when().get("/api/v1/applications/create").then().statusCode(401);
   }
 
-
   @Test
   void createApplication_when_authenticated() {
-    CreateApplication createApplication = CreateApplication.builder()
-    .datasetIds(Arrays.asList("dataset1", "dataset2", "dataset3"))
-    .build();
-
+    CreateApplication createApplication =
+        CreateApplication.builder()
+            .datasetIds(Arrays.asList("dataset1", "dataset2", "dataset3"))
+            .build();
+
     given()
         .auth()
         .oauth2(getAccessToken("alice"))

diff --git a/src/test/java/io/github/genomicdatainfrastructure/daam/api/ApplicationQueryApiImplIT.java b/src/test/java/io/github/genomicdatainfrastructure/daam/api/ApplicationQueryApiImplIT.java
@@ -1,11 +1,10 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
+
 package io.github.genomicdatainfrastructure.daam.api;
 
 import io.quarkus.test.junit.QuarkusIntegrationTest;
 
 @QuarkusIntegrationTest
-public class ApplicationQueryApiImplIT extends ApplicationQueryApiImplTest {
-
-}
+public class ApplicationQueryApiImplIT extends ApplicationQueryApiImplTest {}
diff --git a/src/test/java/io/github/genomicdatainfrastructure/daam/api/ApplicationQueryApiImplTest.java b/src/test/java/io/github/genomicdatainfrastructure/daam/api/ApplicationQueryApiImplTest.java
@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2024 PNED G.I.E.
 //
 // SPDX-License-Identifier: Apache-2.0
+
 package io.github.genomicdatainfrastructure.daam.api;
 
 import static io.restassured.RestAssured.given;