test: add integration tests

GenomicDataInfrastructure · Mar 21, 2024 · 215f8a9 · 215f8a9
1 parent b3f5fda
commit 215f8a9
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Showing 12 changed files with 578 additions and 96 deletions.
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;
@@ -30,14 +31,12 @@ public List<ListedApplication> listApplicationsV1() {
   }
 
   @Override
-  public RetrievedApplication retrieveApplicationV1(String id) {
-    var principal = (OidcJwtCallerPrincipal) identity.getPrincipal();
-    String userId = principal.getClaim(USER_ID_CLAIM);
-    return retrieveApplicationService.retrieveApplication(Long.parseLong(id), userId);
+  public RetrievedApplication retrieveApplicationV1(Long id) {
+    return retrieveApplicationService.retrieveApplication(id);
   }
 
   @Override
-  public File retrieveAttachmentFromApplicationV1(String id, String attachmentId) {
+  public File retrieveAttachmentFromApplicationV1(Long id, Long attachmentId) {
     throw new UnsupportedOperationException(
         "Unimplemented method 'retrieveAttachmentFromApplicationV1'"
     );

diff --git a/...ava/io/github/genomicdatainfrastructure/daam/exceptions/ApplicationNotFoundException.java b/...ava/io/github/genomicdatainfrastructure/daam/exceptions/ApplicationNotFoundException.java
@@ -0,0 +1,14 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.daam.exceptions;
+
+public class ApplicationNotFoundException extends RuntimeException {
+
+    private static final String MESSAGE = "Application %s not found";
+
+    public ApplicationNotFoundException(Long applicationId) {
+        super(MESSAGE.formatted(applicationId));
+    }
+}
diff --git a/.../io/github/genomicdatainfrastructure/daam/mappers/ApplicationNotFoundExceptionMapper.java b/.../io/github/genomicdatainfrastructure/daam/mappers/ApplicationNotFoundExceptionMapper.java
@@ -0,0 +1,30 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.daam.mappers;
+import io.github.genomicdatainfrastructure.daam.exceptions.ApplicationNotFoundException;
+import io.github.genomicdatainfrastructure.daam.model.ErrorResponse;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.ext.Provider;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.ext.ExceptionMapper;
+
+@Provider
+public class ApplicationNotFoundExceptionMapper implements ExceptionMapper<ApplicationNotFoundException> {
+
+    @Override
+    public Response toResponse(ApplicationNotFoundException exception) {
+        ErrorResponse errorResponse = new ErrorResponse(
+                "Application Not Found",
+                Response.Status.NOT_FOUND.getStatusCode(),
+                exception.getMessage()
+        );
+
+        return Response
+                .status(Response.Status.NOT_FOUND)
+                .entity(errorResponse)
+                .type(MediaType.APPLICATION_JSON)
+                .build();
+    }
+}
diff --git a/src/main/java/io/github/genomicdatainfrastructure/daam/model/RemsApplicationMapper.java b/src/main/java/io/github/genomicdatainfrastructure/daam/model/RemsApplicationMapper.java
@@ -17,11 +17,10 @@ public static RetrievedApplication toRetrievedApplication(Application remsApplic
                 .builder()
                 .workflow(toRetrievedApplicationWorkflow(remsApplication.getApplicationWorkflow()))
                 .externalId(remsApplication.getApplicationExternalId())
-                .id(remsApplication.getApplicationId().toString())
+                .id(remsApplication.getApplicationId())
                 .applicant(toRetrievedApplicationApplicant(remsApplication.getApplicationApplicant()))
                 .members(toRetrievedApplicationMembers(remsApplication.getApplicationMembers()))
                 .datasets(toRetrievedApplicationDatasets(remsApplication.getApplicationResources()))
-                .acceptedLicenses(toRetrievedApplicationAcceptedLicences(remsApplication.getApplicationAcceptedLicenses()))
                 .forms(toRetrievedApplicationForms(remsApplication.getApplicationForms()))
                 .invitedMembers(toRetrievedApplicationInvitedMembers(remsApplication.getApplicationInvitedMembers()))
                 .description(remsApplication.getApplicationDescription())
@@ -39,7 +38,7 @@ public static RetrievedApplication toRetrievedApplication(Application remsApplic
     }
 
     private static RetrievedApplicationWorkflow toRetrievedApplicationWorkflow(Response10953Workflow remsWorkflow) {
-        return new RetrievedApplicationWorkflow(remsWorkflow.getWorkflowId().toString(),
+        return new RetrievedApplicationWorkflow(remsWorkflow.getWorkflowId(),
                 remsWorkflow.getWorkflowType());
     }
 
@@ -62,24 +61,16 @@ private static List<RetrievedApplicationMember> toRetrievedApplicationMembers(Se
     private static List<RetrievedApplicationDataset> toRetrievedApplicationDatasets(List<V2Resource> remsResources) {
         return remsResources
                 .stream()
-                .map(resource -> new RetrievedApplicationDataset(resource.getCatalogueItemId().toString(),
+                .map(resource -> new RetrievedApplicationDataset(resource.getCatalogueItemId(),
                                                                  toLabelObject(resource.getCatalogueItemTitle()),
                                                                  toLabelObject(resource.getCatalogueItemInfourl())))
                 .toList();
     }
 
-    private static List<RetrievedAcceptedLicense> toRetrievedApplicationAcceptedLicences(Map<String, Set<Long>> remsAcceptedLicenses) {
-        return remsAcceptedLicenses
-                .entrySet()
-                .stream()
-                .flatMap(entry -> entry.getValue().stream().map(licenseId -> new RetrievedAcceptedLicense(entry.getKey(), licenseId.toString())))
-                .toList();
-    }
-
     private static List<RetrievedApplicationForm> toRetrievedApplicationForms(List<Form> remsApplicationForms) {
         return remsApplicationForms
                 .stream()
-                .map(form -> new RetrievedApplicationForm(form.getFormId().toString(),
+                .map(form -> new RetrievedApplicationForm(form.getFormId(),
                                                          form.getFormInternalName(),
                                                          toLabelObject(form.getFormExternalTitle()),
                                                          form.getFormFields()
@@ -118,7 +109,7 @@ private static List<RetrievedApplicationEvent> toRetrievedApplicationEvents(List
         return remsApplicationEvents
                 .stream()
                 .map(event -> new RetrievedApplicationEvent(
-                                                            event.getEventActor(),
+                                                            event.getEventActorAttributes().getUserid(),
                                                             event.getEventTime(),
                                                             event.getEventType()))
                 .toList();
@@ -127,7 +118,7 @@ private static List<RetrievedApplicationEvent> toRetrievedApplicationEvents(List
     private static List<RetrievedApplicationAttachment> toRetrievedApplicationAttachments(List<ApplicationAttachment> remsApplicationAttachments) {
         return remsApplicationAttachments
                 .stream()
-                .map(attachment -> new RetrievedApplicationAttachment(attachment.getAttachmentId().toString(),
+                .map(attachment -> new RetrievedApplicationAttachment(attachment.getAttachmentId(),
                                                                      attachment.getAttachmentFilename().toString(),
                                                                      attachment.getAttachmentType()))
                 .toList();

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;
@@ -35,7 +36,7 @@ public List<ListedApplication> listApplications(String userId) {
 
   public ListedApplication parse(ApplicationOverview applicationOverview) {
     return ListedApplication.builder()
-        .id(applicationOverview.getApplicationId().toString())
+        .id(applicationOverview.getApplicationId())
         .title(applicationOverview.getApplicationExternalId())
         .currentState(applicationOverview.getApplicationState())
         .stateChangedAt(applicationOverview.getApplicationLastActivity())

diff --git a/...in/java/io/github/genomicdatainfrastructure/daam/services/RetrieveApplicationService.java b/...in/java/io/github/genomicdatainfrastructure/daam/services/RetrieveApplicationService.java
@@ -3,30 +3,51 @@
 // SPDX-License-Identifier: Apache-2.0
 
 package io.github.genomicdatainfrastructure.daam.services;
+import io.github.genomicdatainfrastructure.daam.exceptions.ApplicationNotFoundException;
 import io.github.genomicdatainfrastructure.daam.model.RemsApplicationMapper;
 import io.github.genomicdatainfrastructure.daam.model.RetrievedApplication;
 import io.github.genomicdatainfrastructure.daam.remote.rems.api.RemsApplicationsApi;
+import io.quarkus.oidc.runtime.OidcJwtCallerPrincipal;
+import io.quarkus.security.identity.SecurityIdentity;
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
+import jakarta.ws.rs.WebApplicationException;
 import org.eclipse.microprofile.config.inject.ConfigProperty;
 import org.eclipse.microprofile.rest.client.inject.RestClient;
 
+import static io.github.genomicdatainfrastructure.daam.security.PostAuthenticationFilter.USER_ID_CLAIM;
+
 
 @ApplicationScoped
 public class RetrieveApplicationService {
     private final String remsApiKey;
     private final RemsApplicationsApi applicationsApi;
+    private final SecurityIdentity identity;
 
     @Inject
     public RetrieveApplicationService(
             @ConfigProperty(name = "quarkus.rest-client.rems_yaml.api-key") String remsApiKey,
+            SecurityIdentity identity,
             @RestClient RemsApplicationsApi applicationsApi
     ) {
         this.remsApiKey = remsApiKey;
         this.applicationsApi = applicationsApi;
+        this.identity = identity;
     }
 
-    public RetrievedApplication retrieveApplication(Long applicationId, String userId) {
-        return RemsApplicationMapper.toRetrievedApplication(applicationsApi.apiApplicationsApplicationIdGet(applicationId, remsApiKey, userId));
+    public RetrievedApplication retrieveApplication(Long applicationId) {
+        var principal = (OidcJwtCallerPrincipal) identity.getPrincipal();
+        String userId = principal.getClaim(USER_ID_CLAIM);
+
+        try {
+            return RemsApplicationMapper
+                    .toRetrievedApplication(applicationsApi.apiApplicationsApplicationIdGet(applicationId, remsApiKey, userId));
+        }
+        catch (WebApplicationException e) {
+            if (e.getResponse().getStatus() == 404) {
+                throw new ApplicationNotFoundException(applicationId);
+            }
+            throw e;
+        }
     }
 }