Merge pull request #22 from GenomicDataInfrastructure/issue-5/submit-…

…application

feat: implement submit application endpoint

src/main/java/io/github/genomicdatainfrastructure/daam/api/ApplicationCommandApiImpl.java

@@ -6,6 +6,7 @@
 import java.util.List;
 
 import io.github.genomicdatainfrastructure.daam.services.CreateApplicationService;
+import io.github.genomicdatainfrastructure.daam.services.SubmitApplicationService;
 import io.github.genomicdatainfrastructure.daam.model.AddApplicationEvent;
 import io.github.genomicdatainfrastructure.daam.model.AddedAttachments;
 import io.github.genomicdatainfrastructure.daam.model.CreateApplication;
@@ -19,6 +20,7 @@
 public class ApplicationCommandApiImpl implements ApplicationCommandApi {
 
     private final CreateApplicationService createApplicationService;
+    private final SubmitApplicationService submitApplicationService;
 
     @Override
     public Response acceptApplicationTermsV1(String id) {
@@ -84,9 +86,8 @@ public Response saveApplicationFormsAndDuosV1(String id, SaveFormsAndDuos saveFo
 
     @Override
     public Response submitApplicationV1(String id) {
-        throw new UnsupportedOperationException(
-            "Unimplemented method 'submitApplicationV1'"
-        );
+        submitApplicationService.submitApplication(id);
+        return Response.noContent().build();
     }
 
     @Override
@@ -95,4 +96,4 @@ public Response updateDatasetsOfApplicationV1(String id, List<UpdateDatasets> up
             "Unimplemented method 'updateDatasetsOfApplicationV1'"
         );
     }
-}
+}

src/main/java/io/github/genomicdatainfrastructure/daam/services/SubmitApplicationService.java

@@ -0,0 +1,46 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.daam.services;
+
+import static io.github.genomicdatainfrastructure.daam.security.PostAuthenticationFilter.USER_ID_CLAIM;
+import io.github.genomicdatainfrastructure.daam.remote.rems.api.RemsApplicationCommandApi;
+import io.github.genomicdatainfrastructure.daam.remote.rems.model.SubmitApplicationCommand;
+import io.quarkus.oidc.runtime.OidcJwtCallerPrincipal;
+import io.quarkus.security.identity.SecurityIdentity;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
+import org.eclipse.microprofile.config.inject.ConfigProperty;
+import org.eclipse.microprofile.rest.client.inject.RestClient;
+
+
+@ApplicationScoped
+public class SubmitApplicationService {
+
+    private final SecurityIdentity identity;
+    private final String remsApiKey;
+    private final RemsApplicationCommandApi remsApplicationCommandApi;
+
+    @Inject
+    public SubmitApplicationService(
+        @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 submitApplication(String id) {
+        var principal = (OidcJwtCallerPrincipal) identity.getPrincipal();
+        String userId = principal.getClaim(USER_ID_CLAIM);
+
+        SubmitApplicationCommand command = SubmitApplicationCommand.builder()
+                .applicationId(Long.valueOf(id))
+                .build();
+
+        remsApplicationCommandApi.apiApplicationsSubmitPost(command, remsApiKey, userId);
+    }
+}

src/main/openapi/rems.yaml

@@ -102,6 +102,38 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/CreateApplicationResponse'
+  /api/applications/submit:
+    post:
+      tags:
+        - rems-application-command
+      summary: 'Submits a submit command for an application (roles: logged-in)'
+      parameters:
+        - in: header
+          name: x-rems-api-key
+          description: REMS API-Key (optional for UI, required for API)
+          required: false
+          schema:
+            type: string
+        - in: header
+          name: x-rems-user-id
+          description: User (optional for UI, required for API). This can be a REMS internal or an external user identity attribute (specified in config.edn).
+          required: false
+          schema:
+            type: string
+      requestBody:
+        description: Application submission data
+        required: true
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/SubmitApplicationCommand'
+      responses:
+        '200':
+          description: Application submission successful
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/SubmitApplicationResponse'
 components:
   schemas:
     ApplicationOverview:
@@ -602,6 +634,30 @@ components:
       required:
         - catalogue-item-ids
     CreateApplicationResponse:
+      type: object
+      properties:
+        success:
+          type: boolean
+        errors:
+          type: array
+          items: {}
+        warnings:
+          type: array
+          items: {}
+        application-id:
+          type: integer
+          format: int64
+      required:
+        - success
+    SubmitApplicationCommand:
+      type: object
+      properties:
+        application-id:
+          type: integer
+          format: int64
+      required:
+        - application-id
+    SubmitApplicationResponse:
       type: object
       properties:
         success:

src/test/java/io/github/genomicdatainfrastructure/daam/api/ApplicationCommandApiImplTest.java

@@ -41,6 +41,17 @@ void createApplication_when_authenticated() {
         .statusCode(204);
   }
 
+  @Test
+  void submitApplication_when_authenticated() {
+    given()
+        .auth()
+        .oauth2(getAccessToken("alice"))
+        .when()
+        .post("/api/v1/applications/1/submit")
+        .then()
+        .statusCode(204);
+  }
+
   private String getAccessToken(String userName) {
     return keycloakClient.getAccessToken(userName);
   }

src/test/resources/mappings/submit_application.json

@@ -0,0 +1,16 @@
+{
+  "request": {
+    "method": "POST",
+    "url": "/api/applications/submit"
+  },
+  "response": {
+    "status": 200,
+    "headers": {
+      "Content-Type": "application/json"
+    },
+    "jsonBody": {
+      "success": true,
+      "application-id": 12345
+    }
+  }
+}

src/test/resources/mappings/submit_application.json.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2024 PNED G.I.E.
+
+SPDX-License-Identifier: Apache-2.0