Enum To Describe User Requirement

virtualcell · Jan 14, 2025 · a342c95 · a342c95
1 parent e3f5490
commit a342c95
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Showing 7 changed files with 25 additions and 25 deletions.
diff --git a/vcell-rest/src/main/java/org/vcell/restq/db/UserRestDB.java b/vcell-rest/src/main/java/org/vcell/restq/db/UserRestDB.java
@@ -10,7 +10,6 @@
 import jakarta.ws.rs.WebApplicationException;
 import org.eclipse.microprofile.jwt.JsonWebToken;
 import org.vcell.auth.JWTUtils;
-import org.vcell.restq.Main;
 import org.vcell.restq.auth.CustomSecurityIdentityAugmentor;
 import org.vcell.restq.handlers.UsersResource;
 import org.vcell.util.DataAccessException;
@@ -51,14 +50,16 @@ public UserRestDB(AgroalConnectionFactory agroalConnectionFactory) throws DataAc
      * and error will be thrown about the user being unauthenticated.
      * Tokens generated by the old API for guest users will have no effect on this function because the securityIdentity
      * is something only our designated Auth0 provider can create.
-     * @param securityIdentity
-     * @param defaultGuest
      * @throws DataAccessException
      */
-    public User getUserFromIdentity(SecurityIdentity securityIdentity, boolean defaultGuest) throws DataAccessException {
+    public enum UserRequirement{
+        ALLOW_ANONYMOUS,
+        REQUIRE_USER
+    }
+    public User getUserFromIdentity(SecurityIdentity securityIdentity, UserRequirement allowAnonymous) throws DataAccessException {
         List<UserIdentity> userIdentities = getUserIdentities(securityIdentity);
         if (userIdentities == null || userIdentities.isEmpty()){
-            if (defaultGuest){
+            if (allowAnonymous == UserRequirement.ALLOW_ANONYMOUS){
                 return null;
             } else {
                 throw new WebApplicationException("User is not authenticated.", HTTP.UNAUTHORIZED);

diff --git a/vcell-rest/src/main/java/org/vcell/restq/handlers/AdminResource.java b/vcell-rest/src/main/java/org/vcell/restq/handlers/AdminResource.java
@@ -4,7 +4,6 @@
 import com.lowagie.text.html.simpleparser.HTMLWorker;
 import com.lowagie.text.pdf.PdfWriter;
 import io.quarkus.security.identity.SecurityIdentity;
-import jakarta.annotation.security.RolesAllowed;
 import jakarta.enterprise.context.RequestScoped;
 import jakarta.inject.Inject;
 import jakarta.ws.rs.GET;
@@ -62,7 +61,7 @@ public Response getUsage() throws DataAccessException {
         if (securityIdentity.isAnonymous()){
             throw new WebApplicationException("not authenticated", 401);
         }
-        User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, false);
+        User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
         try {
             String htmlString = adminRestDB.getUsageSummaryHtml(vcellUser);
             StreamingOutput fileStream = output -> {

diff --git a/vcell-rest/src/main/java/org/vcell/restq/handlers/BioModelResource.java b/vcell-rest/src/main/java/org/vcell/restq/handlers/BioModelResource.java
@@ -11,7 +11,6 @@
 import org.eclipse.microprofile.openapi.annotations.Operation;
 import org.eclipse.microprofile.openapi.annotations.responses.APIResponse;
 import org.eclipse.microprofile.openapi.annotations.responses.APIResponses;
-import org.vcell.restq.Main;
 import org.vcell.restq.db.BioModelRestDB;
 import org.vcell.restq.db.UserRestDB;
 import org.vcell.restq.models.BioModel;
@@ -45,7 +44,7 @@ public BioModelResource(BioModelRestDB bioModelRestDB, UserRestDB userRestDB) {
     })
     @Produces(MediaType.APPLICATION_JSON)
     public BioModel getBioModelInfo(@PathParam("bioModelID") String bioModelID) throws SQLException, DataAccessException, ExpressionException {
-        User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, true);
+        User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.ALLOW_ANONYMOUS);
         try {
             BioModelRep bioModelRep = bioModelRestDB.getBioModelRep(new KeyValue(bioModelID), vcellUser);
             return BioModel.fromBioModelRep(bioModelRep);
@@ -102,7 +101,7 @@ public void getBioModelDiagram(@PathParam("bioModelID") String bioModelID){
     @Produces(MediaType.TEXT_PLAIN)
     @RolesAllowed("user")
     public String uploadBioModel(String bioModelXML) throws DataAccessException, XmlParseException {
-        User user = userRestDB.getUserFromIdentity(securityIdentity, false);
+        User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
         KeyValue keyValue = bioModelRestDB.saveBioModel(user, bioModelXML);
         return keyValue.toString();
     }
@@ -111,7 +110,7 @@ public String uploadBioModel(String bioModelXML) throws DataAccessException, Xml
     @Path("{bioModelID}")
     @Operation(operationId = "deleteBioModel", summary = "Delete the BioModel from VCell's database.")
     public void deleteBioModel(@PathParam("bioModelID") String bioModelID) throws DataAccessException {
-        User user = userRestDB.getUserFromIdentity(securityIdentity, false);;
+        User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);;
         bioModelRestDB.deleteBioModel(user, new KeyValue(bioModelID));
     }
 }
diff --git a/vcell-rest/src/main/java/org/vcell/restq/handlers/FieldData/FieldDataResource.java b/vcell-rest/src/main/java/org/vcell/restq/handlers/FieldData/FieldDataResource.java
@@ -54,7 +54,7 @@ public FieldDataResource(FieldDataDB fieldDataDB, UserRestDB userRestDB){
     @Operation(operationId = "getAllFieldDataIDs", summary = "Get all of the ids used to identify, and retrieve field data.")
     public ArrayList<FieldDataReference> getAllFieldDataIDs(){
         try {
-            return fieldDataDB.getAllFieldDataIDs(userRestDB.getUserFromIdentity(securityIdentity, false));
+            return fieldDataDB.getAllFieldDataIDs(userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER));
         } catch (SQLException e) {
             throw new WebApplicationException("Can't retrieve field data ID's.", 500);
         } catch (DataAccessException e) {
@@ -67,7 +67,7 @@ public ArrayList<FieldDataReference> getAllFieldDataIDs(){
     @Operation(operationId = "getFieldDataShapeFromID", summary = "Get the shape of the field data. That is it's size, origin, extent, and data identifiers.")
     public FieldDataShape getFieldDataShapeFromID(@PathParam("fieldDataID") String fieldDataID){
         try {
-            FieldDataFileOperationResults results = fieldDataDB.getFieldDataFromID(userRestDB.getUserFromIdentity(securityIdentity, false), fieldDataID, 0);
+            FieldDataFileOperationResults results = fieldDataDB.getFieldDataFromID(userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER), fieldDataID, 0);
             return new FieldDataShape(results.extent, results.origin, results.iSize, results.dataIdentifierArr,results.times);
         } catch (DataAccessException e) {
             if (e.getCause() instanceof FileNotFoundException){
@@ -99,6 +99,7 @@ public FieldDataShape getFieldDataShapeFromID(@PathParam("fieldDataID") String f
     @Operation(operationId = "analyzeFieldDataFile", summary = "Analyze the field data from the uploaded file. Filenames must be lowercase alphanumeric, and can contain underscores.")
     public AnalyzedResultsFromFieldData analyzeFieldData(@RestForm File file, @RestForm String fileName){
         try{
+            userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
             if (!Pattern.matches("^[a-z0-9_]*$", fileName) || fileName.length() > 100 || fileName.isEmpty()){
                 throw new WebApplicationException("Invalid file name.", 400);
             }
@@ -116,7 +117,7 @@ public AnalyzedResultsFromFieldData analyzeFieldData(@RestForm File file, @RestF
     public FieldDataSaveResults createNewFieldDataFromFile(AnalyzedResultsFromFieldData saveFieldData){
         FieldDataSaveResults fieldDataSaveResults;
         try{
-            User user = userRestDB.getUserFromIdentity(securityIdentity, false);
+            User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
             FieldDataFileOperationResults fileResults = fieldDataDB.saveNewFieldDataFromFile(saveFieldData, user);
             fieldDataSaveResults = new FieldDataSaveResults(fileResults.externalDataIdentifier.getName(), fileResults.externalDataIdentifier.getKey().toString());
         } catch (ImageException | DataFormatException | DataAccessException e) {
@@ -145,7 +146,7 @@ public FieldDataSaveResults createNewFieldDataFromFile(AnalyzedResultsFromFieldD
     @Operation(operationId = "deleteFieldData", summary = "Delete the selected field data.")
     public void deleteFieldData(@PathParam("fieldDataID") String fieldDataID){
         try{
-            fieldDataDB.deleteFieldData(userRestDB.getUserFromIdentity(securityIdentity, false), fieldDataID);
+            fieldDataDB.deleteFieldData(userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER), fieldDataID);
         } catch (DataAccessException e) {
             throw new WebApplicationException(e.getMessage(), 500);
         }

diff --git a/vcell-rest/src/main/java/org/vcell/restq/handlers/PublicationResource.java b/vcell-rest/src/main/java/org/vcell/restq/handlers/PublicationResource.java
@@ -40,7 +40,7 @@ public PublicationResource(PublicationService publicationService) {
     @Operation(operationId = "getPublicationById", summary = "Get publication by ID")
     public Publication get_by_id(@PathParam("id") Long publicationID) throws SQLException, DataAccessException {
         try {
-            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, true);
+            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.ALLOW_ANONYMOUS);
             return publicationService.getPublication(new KeyValue(publicationID.toString()), vcellUser);
         } catch (DataAccessException | SQLException e) {
             Log.error(e);
@@ -53,7 +53,7 @@ public Publication get_by_id(@PathParam("id") Long publicationID) throws SQLExce
     @Operation(operationId = "getPublications", summary = "Get all publications")
     public Publication[] get_list() {
         try {
-            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, true);
+            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.ALLOW_ANONYMOUS);
             return publicationService.getPublications(DatabaseServerImpl.OrderBy.year_desc, vcellUser);
         } catch (PermissionException ee) {
             Log.error(ee);
@@ -71,7 +71,7 @@ public Publication[] get_list() {
     public Long add(Publication publication) throws DataAccessException {
         Log.debug(securityIdentity.getPrincipal().getName()+" with roles " + securityIdentity.getRoles() + " is adding publication "+publication.title());
         try {
-            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, false);
+            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
             KeyValue key = publicationService.savePublication(publication, vcellUser);
             return Long.parseLong(key.toString());
         } catch (PermissionException ee) {
@@ -87,11 +87,11 @@ public Long add(Publication publication) throws DataAccessException {
     @PUT
     @Consumes(MediaType.APPLICATION_JSON)
 //    @RolesAllowed("curator")
-    @Operation(operationId = "updatePublication", summary = "Create publication")
+    @Operation(operationId = "updatePublication", summary = "Update publication")
     public Publication update(Publication publication) {
         Log.debug(securityIdentity.getPrincipal().getName()+" with roles " + securityIdentity.getRoles() + " is adding publication "+publication.title());
         try {
-            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, false);
+            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
             Publication pub = publicationService.updatePublication(publication, vcellUser);
             return pub;
         } catch (PermissionException ee) {
@@ -110,7 +110,7 @@ public Publication update(Publication publication) {
     @Operation(operationId = "deletePublication", summary = "Delete publication")
     public void delete(@PathParam("id") Long publicationID) {
         try {
-            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, false);
+            User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
             int numRecordsDeleted = publicationService.deletePublication(new KeyValue(publicationID.toString()), vcellUser);
             if (numRecordsDeleted != 1) {
                 throw new ObjectNotFoundException("failed to delete publication, record not found");

diff --git a/vcell-rest/src/main/java/org/vcell/restq/handlers/SimulationResource.java b/vcell-rest/src/main/java/org/vcell/restq/handlers/SimulationResource.java
@@ -40,7 +40,7 @@ public SimulationResource(SimulationRestDB simulationRestDB, UserRestDB userRest
     @Produces(MediaType.APPLICATION_JSON)
     public ArrayList<StatusMessage> startSimulation(@PathParam("simID") String simID) {
         try {
-            User user = userRestDB.getUserFromIdentity(securityIdentity, false);
+            User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
             return simulationRestDB.startSimulation(simID, user);
         } catch (DataAccessException | SQLException e) {
             throw new RuntimeException(e);
@@ -53,7 +53,7 @@ public ArrayList<StatusMessage> startSimulation(@PathParam("simID") String simID
     @Operation(operationId = "stopSimulation", summary = "Stop a simulation.")
     public ArrayList<StatusMessage> stopSimulation(@PathParam("simID") String simID) {
         try {
-            User user = userRestDB.getUserFromIdentity(securityIdentity, false);
+            User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
             return simulationRestDB.stopSimulation(simID, user);
         } catch (DataAccessException | SQLException | VCMessagingException e) {
             throw new RuntimeException(e);
@@ -67,7 +67,7 @@ public ArrayList<StatusMessage> stopSimulation(@PathParam("simID") String simID)
     public SimulationStatusPersistentRecord getSimulationStatus(@PathParam("simID") String simID,
                                     @QueryParam("bioModelID") String bioModelID, @QueryParam("mathModelID") String mathModelID){
         try {
-            User user = userRestDB.getUserFromIdentity(securityIdentity, false);
+            User user = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
             return simulationRestDB.getBioModelSimulationStatus(simID, bioModelID, user);
         } catch (DataAccessException | SQLException e) {
             throw new RuntimeException(e);

diff --git a/vcell-rest/src/main/java/org/vcell/restq/handlers/UsersResource.java b/vcell-rest/src/main/java/org/vcell/restq/handlers/UsersResource.java
@@ -252,7 +252,7 @@ public AccesTokenRepresentationRecord generateBearerToken() throws DataAccessExc
         if(securityIdentity.isAnonymous()){
             return new AccesTokenRepresentationRecord(null, 0, 0, null, null);
         }
-        org.vcell.util.document.User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, false);
+        org.vcell.util.document.User vcellUser = userRestDB.getUserFromIdentity(securityIdentity, UserRestDB.UserRequirement.REQUIRE_USER);
         ApiAccessToken apiAccessToken = userRestDB.generateApiAccessToken(userRestDB.getAPIClient().getKey(), vcellUser);
         return AccesTokenRepresentationRecord.getRecordFromAccessTokenRepresentation(apiAccessToken);
     }