[DT-3788] Migrate eligible AuthUser resource endpoints to DuosUser

src/main/java/org/broadinstitute/consent/http/resources/DACAutomationRuleResource.java

@@ -15,28 +15,23 @@
 import jakarta.ws.rs.core.Response;
 import java.util.List;
 import org.broadinstitute.consent.http.enumeration.UserRoles;
-import org.broadinstitute.consent.http.models.AuthUser;
 import org.broadinstitute.consent.http.models.DuosUser;
 import org.broadinstitute.consent.http.models.User;
 import org.broadinstitute.consent.http.rules.AuditPageResults;
 import org.broadinstitute.consent.http.rules.DACAutomationRule;
 import org.broadinstitute.consent.http.service.DACAutomationRuleService;
 import org.broadinstitute.consent.http.service.DacService;
-import org.broadinstitute.consent.http.service.UserService;
 
 @Path("api/dac/")
 public class DACAutomationRuleResource extends Resource {
 
   private final DACAutomationRuleService ruleService;
   private final DacService dacService;
-  private final UserService userService;
 
   @Inject
-  public DACAutomationRuleResource(
-      DACAutomationRuleService ruleService, DacService dacService, UserService userService) {
+  public DACAutomationRuleResource(DACAutomationRuleService ruleService, DacService dacService) {
     this.ruleService = ruleService;
     this.dacService = dacService;
-    this.userService = userService;
   }
 
   @GET
@@ -56,9 +51,9 @@ public Response getAllRules(@Auth DuosUser duosUser) {
   @Path("{dacId}/rules")
   @Produces(MediaType.APPLICATION_JSON)
   @RolesAllowed({Resource.ADMIN, Resource.CHAIRPERSON})
-  public Response getAvailableRules(@Auth AuthUser authUser, @PathParam("dacId") Integer dacId) {
+  public Response getAvailableRules(@Auth DuosUser duosUser, @PathParam("dacId") Integer dacId) {
     try {
-      User user = userService.findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       validateAdminOrChairForDAC(user, dacId);
 
       if (dacService.findById(dacId) == null) {
@@ -78,12 +73,12 @@ public Response getAvailableRules(@Auth AuthUser authUser, @PathParam("dacId") I
   @Produces(MediaType.APPLICATION_JSON)
   @RolesAllowed({Resource.ADMIN, Resource.CHAIRPERSON})
   public Response getDacRuleAuditRecords(
-      @Auth AuthUser authUser,
+      @Auth DuosUser duosUser,
       @PathParam("dacId") Integer dacId,
       @QueryParam("page") Integer page,
       @QueryParam("pageSize") Integer pageSize) {
     try {
-      User user = userService.findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       validateAdminOrChairForDAC(user, dacId);
 
       if (dacService.findById(dacId) == null) {
@@ -103,11 +98,11 @@ public Response getDacRuleAuditRecords(
   @Produces(MediaType.APPLICATION_JSON)
   @RolesAllowed({Resource.CHAIRPERSON})
   public Response toggleRule(
-      @Auth AuthUser authUser,
+      @Auth DuosUser duosUser,
       @PathParam("dacId") Integer dacId,
       @PathParam("ruleId") Integer ruleId) {
     try {
-      User user = userService.findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       validateIsChairOfDAC(user, dacId);
 
       if (dacService.findById(dacId) == null) {

src/main/java/org/broadinstitute/consent/http/resources/DacResource.java

@@ -22,7 +22,6 @@
 import java.util.Objects;
 import java.util.Optional;
 import org.broadinstitute.consent.http.enumeration.UserRoles;
-import org.broadinstitute.consent.http.models.AuthUser;
 import org.broadinstitute.consent.http.models.Dac;
 import org.broadinstitute.consent.http.models.DacDatasetExternalizationRequest;
 import org.broadinstitute.consent.http.models.DacDatasetExternalizationResponse;
@@ -51,7 +50,7 @@ public DacResource(DacService dacService, DatasetService datasetService) {
   @Produces("application/json")
   @RolesAllowed({ADMIN, MEMBER, CHAIRPERSON, RESEARCHER})
   public Response findAll(
-      @Auth AuthUser authUser, @QueryParam("withUsers") Optional<Boolean> withUsers) {
+      @Auth DuosUser duosUser, @QueryParam("withUsers") Optional<Boolean> withUsers) {
     try {
       final Boolean includeUsers = withUsers.orElse(true);
       List<Dac> dacs = dacService.findDacsWithMembersOption(includeUsers);
@@ -143,7 +142,7 @@ public Response updateDac(@Auth DuosUser duosUser, String json) {
   @Path("{dacId}")
   @Produces("application/json")
   @RolesAllowed({ADMIN, MEMBER, CHAIRPERSON})
-  public Response findDacById(@Auth AuthUser authUser, @PathParam("dacId") Integer dacId) {
+  public Response findDacById(@Auth DuosUser duosUser, @PathParam("dacId") Integer dacId) {
     try {
       Dac dac = findDacOrThrow(dacId);
       return Response.ok().entity(unmarshal(dac)).build();
@@ -264,7 +263,7 @@ public Response findAllDacDatasets(@Auth DuosUser duosUser, @PathParam("dacId")
   @Path("users/{term}")
   @Produces("application/json")
   @RolesAllowed({ADMIN, MEMBER, CHAIRPERSON})
-  public Response filterUsers(@Auth AuthUser authUser, @PathParam("term") String term) {
+  public Response filterUsers(@Auth DuosUser duosUser, @PathParam("term") String term) {
     try {
       List<User> users = dacService.findAllDACUsersBySearchString(term);
       return Response.ok().entity(users).build();

src/main/java/org/broadinstitute/consent/http/resources/DataAccessRequestResource.java

@@ -41,7 +41,6 @@
 import org.broadinstitute.consent.http.enumeration.UserRoles;
 import org.broadinstitute.consent.http.exceptions.LibraryCardRequiredException;
 import org.broadinstitute.consent.http.exceptions.SubmittedDARCannotBeEditedException;
-import org.broadinstitute.consent.http.models.AuthUser;
 import org.broadinstitute.consent.http.models.Dac;
 import org.broadinstitute.consent.http.models.DataAccessAgreement;
 import org.broadinstitute.consent.http.models.DataAccessRequest;
@@ -117,9 +116,9 @@ public Response getDataAccessRequests(@Auth DuosUser duosUser) {
   @RolesAllowed(RESEARCHER)
   @Path("/v2")
   public Response createDataAccessRequest(
-      @Auth AuthUser authUser, @Context Request request, @Context UriInfo info, String dar) {
+      @Auth DuosUser duosUser, @Context Request request, @Context UriInfo info, String dar) {
     try {
-      User user = findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
 
       DataAccessRequest payload = populateDarFromJsonString(user, dar);
       DataAccessRequest newDar =
@@ -205,9 +204,9 @@ public Response getDatasetDaaSnapshotsByReferenceId(
   @Produces("application/json")
   @RolesAllowed(RESEARCHER)
   public Response updateByReferenceId(
-      @Auth AuthUser authUser, @PathParam("referenceId") String referenceId, String dar) {
+      @Auth DuosUser duosUser, @PathParam("referenceId") String referenceId, String dar) {
     try {
-      User user = findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       DataAccessRequest originalDar = dataAccessRequestService.findByReferenceId(referenceId);
       checkAuthorizedUpdateUser(user, originalDar);
       DataAccessRequestData data = DataAccessRequestData.fromString(dar);
@@ -228,9 +227,9 @@ public Response updateByReferenceId(
   @Produces("application/json")
   @Path("/v2/draft")
   @RolesAllowed(RESEARCHER)
-  public Response getDraftDataAccessRequests(@Auth AuthUser authUser) {
+  public Response getDraftDataAccessRequests(@Auth DuosUser duosUser) {
     try {
-      User user = findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       List<DataAccessRequest> draftDars =
           dataAccessRequestService.findAllDraftDataAccessRequestsByUser(user.getUserId());
       return Response.ok().entity(draftDars).build();
@@ -243,9 +242,9 @@ public Response getDraftDataAccessRequests(@Auth AuthUser authUser) {
   @Produces("application/json")
   @Path("/v2/draft/{referenceId}")
   @RolesAllowed(RESEARCHER)
-  public Response getDraftDar(@Auth AuthUser authUser, @PathParam("referenceId") String id) {
+  public Response getDraftDar(@Auth DuosUser duosUser, @PathParam("referenceId") String id) {
     try {
-      User user = findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       DataAccessRequest dar = dataAccessRequestService.findByReferenceId(id);
       if (dar.getUserId().equals(user.getUserId())) {
         return Response.ok().entity(dar).build();
@@ -262,9 +261,9 @@ public Response getDraftDar(@Auth AuthUser authUser, @PathParam("referenceId") S
   @Path("/v2/draft")
   @RolesAllowed(RESEARCHER)
   public Response createDraftDataAccessRequest(
-      @Auth AuthUser authUser, @Context UriInfo info, String dar) {
+      @Auth DuosUser duosUser, @Context UriInfo info, String dar) {
     try {
-      User user = findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       DataAccessRequest newDar = populateDarFromJsonString(user, dar);
       DataAccessRequest result =
           dataAccessRequestService.insertDraftDataAccessRequest(user, newDar);
@@ -281,9 +280,9 @@ public Response createDraftDataAccessRequest(
   @Path("/v2/draft/{referenceId}")
   @RolesAllowed(RESEARCHER)
   public Response updatePartialDataAccessRequest(
-      @Auth AuthUser authUser, @PathParam("referenceId") String referenceId, String dar) {
+      @Auth DuosUser duosUser, @PathParam("referenceId") String referenceId, String dar) {
     try {
-      User user = findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       DataAccessRequest originalDar = dataAccessRequestService.findByReferenceId(referenceId);
       checkAuthorizedUpdateUser(user, originalDar);
       DataAccessRequestData data = DataAccessRequestData.fromString(dar);
@@ -333,12 +332,12 @@ public Response getIrbDocument(
   @Path("/v2/{referenceId}/irbDocument")
   @RolesAllowed({RESEARCHER})
   public Response uploadIrbDocument(
-      @Auth AuthUser authUser,
+      @Auth DuosUser duosUser,
       @PathParam("referenceId") String referenceId,
       @FormDataParam("file") InputStream uploadInputStream,
       @FormDataParam("file") FormDataContentDisposition fileDetail) {
     try {
-      User user = findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       DataAccessRequest dar = getDarById(referenceId);
       checkAuthorizedUpdateUser(user, dar);
       DataAccessRequest updatedDar =
@@ -376,7 +375,7 @@ public Response approveCloseout(
   @Path("/v2/progress_report/{parentReferenceId}")
   @RolesAllowed({RESEARCHER})
   public Response postProgressReport(
-      @Auth AuthUser authUser,
+      @Auth DuosUser duosUser,
       @Context Request request,
       @PathParam("parentReferenceId") String parentReferenceId,
       @FormDataParam("dar") String dar,
@@ -385,7 +384,7 @@ public Response postProgressReport(
       @FormDataParam("ethicsApprovalRequiredFile") InputStream ethicsInputStream,
       @FormDataParam("ethicsApprovalRequiredFile") FormDataContentDisposition ethicsFileDetails) {
     try {
-      User user = userService.findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       // added here because other dataAccessRequestServices calls are invoked that do not normally
       // require this sequence.  hasValidActiveERACredentials will also check for a LC so no
       // additional LC check needed.
@@ -522,12 +521,12 @@ public Response getCollaborationDocument(
   @Path("/v2/{referenceId}/collaborationDocument")
   @RolesAllowed({RESEARCHER})
   public Response uploadCollaborationDocument(
-      @Auth AuthUser authUser,
+      @Auth DuosUser duosUser,
       @PathParam("referenceId") String referenceId,
       @FormDataParam("file") InputStream uploadInputStream,
       @FormDataParam("file") FormDataContentDisposition fileDetail) {
     try {
-      User user = findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       DataAccessRequest dar = getDarById(referenceId);
       checkAuthorizedUpdateUser(user, dar);
       DataAccessRequest updatedDar =
@@ -554,14 +553,6 @@ public Response deleteDar(@Auth DuosUser duosUser, @PathParam("referenceId") Str
     }
   }
 
-  private User findUserByEmail(String email) {
-    User user = userService.findUserByEmail(email);
-    if (user == null) {
-      throw new NotFoundException("Unable to find User with the provided email: " + email);
-    }
-    return user;
-  }
-
   private DataAccessRequest populateDarFromJsonString(User user, String json) {
     DataAccessRequest newDar = new DataAccessRequest();
     DataAccessRequestData data = DataAccessRequestData.populateDARData(json);

src/main/java/org/broadinstitute/consent/http/resources/DatasetResource.java

@@ -41,7 +41,6 @@
 import org.broadinstitute.consent.http.cloudstore.GCSService;
 import org.broadinstitute.consent.http.enumeration.UserRoles;
 import org.broadinstitute.consent.http.exceptions.UnprocessableEntityException;
-import org.broadinstitute.consent.http.models.AuthUser;
 import org.broadinstitute.consent.http.models.DataUse;
 import org.broadinstitute.consent.http.models.Dataset;
 import org.broadinstitute.consent.http.models.DatasetPatch;
@@ -107,7 +106,7 @@
    * With that object, we can fully create datasets from the provided values.
    */
   public Response createDatasetRegistration(
-      @Auth AuthUser authUser, FormDataMultiPart multipart, @FormDataParam("dataset") String json) {
+      @Auth DuosUser duosUser, FormDataMultiPart multipart, @FormDataParam("dataset") String json) {
     try {
       if (json == null || json.isEmpty()) {
         throw new BadRequestException("Dataset is required");
@@ -120,7 +119,9 @@
         throw new BadRequestException("Please correct the following fields:\n" + errorMessage);
       }
 
-      User user = userService.findUserByEmail(authUser.getEmail());
+      DatasetRegistrationSchemaV1 registration =
+          GsonUtil.getInstance().fromJson(json, DatasetRegistrationSchemaV1.class);
+      User user = duosUser.getUser();
 
       // key: field name (not file name), value: file body part
       Map<String, FormDataBodyPart> files = extractFilesFromMultiPart(multipart);
@@ -406,7 +407,7 @@
   @POST
   @Path("/index")
   @RolesAllowed(ADMIN)
-  public Response indexDatasets(@Auth AuthUser authUser) {
+  public Response indexDatasets(@Auth DuosUser duosUser) {
     try {
       var datasetIds = datasetService.findAllDatasetIds();
       StreamingOutput indexResponse = elasticSearchService.indexDatasetIds(datasetIds);
@@ -419,7 +420,7 @@
   @POST
   @Path("/index/{datasetId}")
   @RolesAllowed(ADMIN)
-  public Response indexDataset(@Auth AuthUser authUser, @PathParam("datasetId") Integer datasetId) {
+  public Response indexDataset(@Auth DuosUser duosUser, @PathParam("datasetId") Integer datasetId) {
     try {
       return elasticSearchService.indexDataset(datasetId);
     } catch (Exception e) {
@@ -431,9 +432,9 @@
   @Path("/index/{datasetId}")
   @RolesAllowed(ADMIN)
   public Response deleteDatasetIndex(
-      @Auth AuthUser authUser, @PathParam("datasetId") Integer datasetId) {
+      @Auth DuosUser duosUser, @PathParam("datasetId") Integer datasetId) {
     try {
-      User user = userService.findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       return elasticSearchService.deleteIndex(datasetId, user.getUserId());
     } catch (Exception e) {
       return createExceptionResponse(e);
@@ -475,9 +476,9 @@
   @RolesAllowed(ADMIN)
   @Path("/{id}/datause")
   public Response updateDatasetDataUse(
-      @Auth AuthUser authUser, @PathParam("id") Integer id, String dataUseJson) {
+      @Auth DuosUser duosUser, @PathParam("id") Integer id, String dataUseJson) {
     try {
-      User user = userService.findUserByEmail(authUser.getEmail());
+      User user = duosUser.getUser();
       // TODO: Replace new Gson() with GsonUtil.buildGson() — deferred pending Gson configuration
       // investigation
       Gson gson = new Gson();