Issue 52824: Don't mutate domains from the cache

api/src/org/labkey/api/audit/AbstractAuditTypeProvider.java

@@ -121,7 +121,7 @@ protected AbstractAuditDomainKind getDomainKind()
     public void initializeProvider(User user)
     {
         AbstractAuditDomainKind domainKind = getDomainKind();
-        Domain domain = getDomain();
+        Domain domain = getDomain(true);
 
         // if the domain doesn't exist, create it
         if (domain == null)
@@ -296,12 +296,17 @@ private void copyTo(DomainProperty dp, PropertyDescriptor pd, Container c)
 
     @Override
     public final Domain getDomain()
+    {
+        return getDomain(false);
+    }
+
+    protected Domain getDomain(boolean forUpdate)
     {
         DomainKind domainKind = getDomainKind();
 
         String domainURI = domainKind.generateDomainURI(QUERY_SCHEMA_NAME, getEventName(), getDomainContainer(), null);
 
-        return PropertyService.get().getDomain(getDomainContainer(), domainURI);
+        return PropertyService.get().getDomain(getDomainContainer(), domainURI, forUpdate);
     }
 
 

api/src/org/labkey/api/exp/OntologyManager.java

@@ -2441,25 +2441,47 @@ public DomainDescriptor load(@NotNull Integer key, @Nullable Object argument)
         }
     }
 
-
     public static DomainDescriptor getDomainDescriptor(int id)
     {
-        return DOMAIN_DESC_BY_ID_CACHE.get(id);
+        return getDomainDescriptor(id, false);
+    }
+
+    public static DomainDescriptor getDomainDescriptor(int id, boolean forUpdate)
+    {
+        DomainDescriptor dd = DOMAIN_DESC_BY_ID_CACHE.get(id);
+        if (forUpdate)
+            DOMAIN_DESC_BY_ID_CACHE.remove(id);
+        return dd;
     }
 
     @Nullable
     public static DomainDescriptor getDomainDescriptor(String domainURI, Container c)
+    {
+        return getDomainDescriptor(domainURI, c, false);
+    }
+
+    @Nullable
+    public static DomainDescriptor getDomainDescriptor(String domainURI, Container c, boolean forUpdate)
     {
         if (c == null)
             return null;
 
         // cache lookup by project. if not found at project level, check to see if global
-        DomainDescriptor dd = DOMAIN_DESCRIPTORS_BY_URI_CACHE.get(getCacheKey(domainURI, c));
+        Pair<String, GUID> key = getCacheKey(domainURI, c);
+        DomainDescriptor dd = DOMAIN_DESCRIPTORS_BY_URI_CACHE.get(key);
         if (null != dd)
+        {
+            if (forUpdate)
+                DOMAIN_DESCRIPTORS_BY_URI_CACHE.remove(key);
             return dd;
+        }
 
         // Try in the /Shared container too
-        return DOMAIN_DESCRIPTORS_BY_URI_CACHE.get(getCacheKey(domainURI, _sharedContainer));
+        key = getCacheKey(domainURI, _sharedContainer);
+        dd = DOMAIN_DESCRIPTORS_BY_URI_CACHE.get(key);
+        if (null != dd && forUpdate)
+            DOMAIN_DESCRIPTORS_BY_URI_CACHE.remove(key);
+        return dd;
     }
 
     /**

api/src/org/labkey/api/exp/property/DomainUtil.java

@@ -751,7 +751,8 @@ public static ValidationException updateDomainDescriptor(GWTDomain<? extends GWT
         LOG.info("Updating domain descriptor for " + orig.getName());
         assert orig.getDomainURI().equals(update.getDomainURI());
 
-        Domain d = PropertyService.get().getDomain(container, update.getDomainURI());
+        // Issue 52824: when updating, remove domain descriptor from cache so others don't see a descriptor from the cache in a paritially updated state
+        Domain d = PropertyService.get().getDomain(container, update.getDomainURI(), true);
         if (null == d)
         {
             ValidationException validationException = new ValidationException();

api/src/org/labkey/api/exp/property/PropertyService.java

@@ -55,9 +55,15 @@ static void setInstance(PropertyService impl)
     @Nullable
     Domain getDomain(Container container, String domainURI);
 
+    @Nullable
+    Domain getDomain(Container container, String domainURI, boolean forUpdate);
+
     @Nullable
     Domain getDomain(int domainId);
 
+    @Nullable
+    Domain getDomain(int domainId, boolean forUpdate);
+
     List<DomainKind<?>> getDomainKinds();
 
     List<DomainKind<?>> getDomainKinds(Container container, User user, Set<String> domainKinds, boolean includeProjectAndShared);

assay/api-src/org/labkey/api/assay/plate/PlateService.java

@@ -252,7 +252,7 @@ static PlateService get()
     /**
      * Create the plate metadata domain for this container.
      */
-    @NotNull Domain ensurePlateMetadataDomain(Container container, User user) throws ValidationException;
+    @NotNull Domain ensurePlateMetadataDomain(Container container, User user, boolean forUpdate) throws ValidationException;
 
     /**
      * Name expressions for plate sets and plates.

assay/src/org/labkey/assay/AssayUpgradeCode.java

@@ -272,7 +272,7 @@ public static void deletePlateVocabDomains(ModuleContext ctx) throws Exception
                     {
                         // ensure the plate metadata domain for the top level biologics projects
                         if (container.isProject())
-                            PlateManager.get().ensurePlateMetadataDomain(container, User.getAdminServiceUser());
+                            PlateManager.get().ensurePlateMetadataDomain(container, User.getAdminServiceUser(), false);
                         biologicsFolders.add(container);
                     }
                 }
@@ -535,7 +535,7 @@ public static void renameWellMetadataFields(ModuleContext ctx) throws Exception
         DbScope scope = AssayDbSchema.getInstance().getSchema().getScope();
         for (Container container : metadataContainers)
         {
-            Domain domain = PlateManager.get().getPlateMetadataDomain(container, User.getAdminServiceUser());
+            Domain domain = PlateManager.get().getPlateMetadataDomain(container, User.getAdminServiceUser(), true);
             if (domain != null)
             {
                 try (DbScope.Transaction tx = scope.ensureTransaction())

assay/src/org/labkey/assay/PlateController.java

@@ -904,7 +904,7 @@ public static class EnsurePlateMetadataDomainAction extends MutatingApiAction<Ob
         @Override
         public Object execute(Object form, BindException errors) throws Exception
         {
-            return success(PlateManager.get().ensurePlateMetadataDomain(getContainer(), getUser()).getTypeId());
+            return success(PlateManager.get().ensurePlateMetadataDomain(getContainer(), getUser(), false).getTypeId());
         }
     }
 

assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java

@@ -913,7 +913,7 @@ public Map<String, List<GWTPropertyDescriptor>> previewFilterCriteriaColumns(@No
         if (columnNames.isEmpty())
             return Collections.emptyMap();
 
-        var replicateDomain = ensurePlateReplicateStatsDomain(container, protocolName);
+        var replicateDomain = ensurePlateReplicateStatsDomain(container, protocolName, true);
         var existingFields = getExistingFields(replicateDomain);
         var columnMap = new HashMap<String, List<GWTPropertyDescriptor>>();
 
@@ -952,7 +952,7 @@ public void updateReplicateStatsDomain(
         GWTDomain<GWTPropertyDescriptor> update
     ) throws ValidationException
     {
-        var replicateDomain = ensurePlateReplicateStatsDomain(protocol);
+        var replicateDomain = ensurePlateReplicateStatsDomain(protocol, true);
         var existingReplicateFields = getExistingFields(replicateDomain);
 
         var originalFields = new HashMap<Integer, GWTPropertyDescriptor>();
@@ -1085,13 +1085,13 @@ else if (wasValidType)
     @Override
     public @Nullable Domain getPlateReplicateStatsDomain(ExpProtocol protocol)
     {
-        return getPlateReplicateStatsDomain(protocol.getContainer(), protocol.getName());
+        return getPlateReplicateStatsDomain(protocol.getContainer(), protocol.getName(), false);
     }
 
-    private @Nullable Domain getPlateReplicateStatsDomain(Container container, String protocolName)
+    private @Nullable Domain getPlateReplicateStatsDomain(Container container, String protocolName, boolean forUpdate)
     {
         String uri = getPlateReplicateStatsDomainUri(container, protocolName);
-        return PropertyService.get().getDomain(container, uri);
+        return PropertyService.get().getDomain(container, uri, forUpdate);
     }
 
     private String getPlateReplicateStatsDomainUri(Container container, String protocolName)
@@ -1100,14 +1100,14 @@ private String getPlateReplicateStatsDomainUri(Container container, String proto
         return domainKind.generateDomainURI(AssaySchema.NAME, protocolName, container, null);
     }
 
-    private @NotNull Domain ensurePlateReplicateStatsDomain(ExpProtocol protocol)
+    private @NotNull Domain ensurePlateReplicateStatsDomain(ExpProtocol protocol, boolean forUpdate)
     {
-        return ensurePlateReplicateStatsDomain(protocol.getContainer(), protocol.getName());
+        return ensurePlateReplicateStatsDomain(protocol.getContainer(), protocol.getName(), forUpdate);
     }
 
-    private @NotNull Domain ensurePlateReplicateStatsDomain(Container container, String protocolName)
+    private @NotNull Domain ensurePlateReplicateStatsDomain(Container container, String protocolName, boolean forUpdate)
     {
-        Domain domain = getPlateReplicateStatsDomain(container, protocolName);
+        Domain domain = getPlateReplicateStatsDomain(container, protocolName, forUpdate);
         if (domain == null)
             domain = PropertyService.get().createDomain(container, getPlateReplicateStatsDomainUri(container, protocolName), PlateReplicateStatsDomainKind.NAME);
 

assay/src/org/labkey/assay/plate/PlateManager.java

@@ -172,7 +172,6 @@
 
 import static java.util.Collections.emptyList;
 import static java.util.Collections.emptyMap;
-import static java.util.Collections.emptySet;
 import static java.util.Collections.unmodifiableList;
 import static org.labkey.api.assay.plate.PlateSet.MAX_PLATES;
 import static org.labkey.api.assay.plate.WellGroup.Type.SAMPLE;
@@ -2266,10 +2265,18 @@ public static void deindexPlateSet(Container container, Integer plateSetRowId)
      * Returns the domain attached to the Well table,
      */
     public @Nullable Domain getPlateMetadataDomain(Container container, User user)
+    {
+        return getPlateMetadataDomain(container, user, false);
+    }
+
+    /**
+     * Returns the domain attached to the Well table,
+     */
+    public @Nullable Domain getPlateMetadataDomain(Container container, User user, boolean forUpdate)
     {
         // the domain is scoped at the project level (project and subfolder scoping)
         String domainURI = PlateMetadataDomainKind.generateDomainURI(getPlateMetadataDomainContainer(container));
-        return PropertyService.get().getDomain(container, domainURI);
+        return PropertyService.get().getDomain(container, domainURI, forUpdate);
     }
 
     public @Nullable TableInfo getPlateMetadataTable(Container container, User user)
@@ -2289,9 +2296,9 @@ public Container getPlateMetadataDomainContainer(Container container)
     }
 
     @Override
-    public @NotNull Domain ensurePlateMetadataDomain(Container container, User user) throws ValidationException
+    public @NotNull Domain ensurePlateMetadataDomain(Container container, User user, boolean forUpdate) throws ValidationException
     {
-        Domain metadataDomain = getPlateMetadataDomain(container, user);
+        Domain metadataDomain = getPlateMetadataDomain(container, user, forUpdate);
 
         if (metadataDomain == null)
         {
@@ -2311,7 +2318,7 @@ public Container getPlateMetadataDomainContainer(Container container)
      */
     public @NotNull List<PlateCustomField> createPlateMetadataFields(Container container, User user, List<GWTPropertyDescriptor> fields) throws Exception
     {
-        Domain metadataDomain = ensurePlateMetadataDomain(container, user);
+        Domain metadataDomain = ensurePlateMetadataDomain(container, user, true);
         DomainKind<?> domainKind = metadataDomain.getDomainKind();
 
         if (!domainKind.canEditDefinition(user, metadataDomain))
@@ -2338,7 +2345,7 @@ public Container getPlateMetadataDomainContainer(Container container)
 
     public @NotNull List<PlateCustomField> deletePlateMetadataFields(Container container, User user, List<PlateCustomField> fields) throws Exception
     {
-        Domain metadataDomain = getPlateMetadataDomain(container, user);
+        Domain metadataDomain = getPlateMetadataDomain(container, user, true);
 
         if (metadataDomain == null)
             throw new IllegalArgumentException("Unable to remove fields from the domain, the domain was not found.");

assay/src/org/labkey/assay/plate/query/WellTable.java

@@ -355,7 +355,7 @@ public QueryUpdateService getUpdateService()
         {
             try
             {
-                domain = PlateManager.get().ensurePlateMetadataDomain(container, user);
+                domain = PlateManager.get().ensurePlateMetadataDomain(container, user, false);
             }
             catch (ValidationException e)
             {

experiment/src/org/labkey/experiment/api/property/PropertyServiceImpl.java

@@ -128,7 +128,14 @@ public IPropertyType getType(Container container, String typeURI)
     @Nullable
     public DomainImpl getDomain(Container container, String domainURI)
     {
-        DomainDescriptor dd = OntologyManager.getDomainDescriptor(domainURI, container);
+        return getDomain(container, domainURI, false);
+    }
+
+    @Override
+    @Nullable
+    public DomainImpl getDomain(Container container, String domainURI, boolean forUpdate)
+    {
+        DomainDescriptor dd = OntologyManager.getDomainDescriptor(domainURI, container, forUpdate);
         if (dd == null)
             return null;
         return new DomainImpl(dd);
@@ -144,6 +151,16 @@ public Domain getDomain(int domainId)
         return new DomainImpl(dd);
     }
 
+    @Override
+    @Nullable
+    public Domain getDomain(int domainId, boolean forUpdate)
+    {
+        DomainDescriptor dd = OntologyManager.getDomainDescriptor(domainId);
+        if (dd == null)
+            return null;
+        return new DomainImpl(dd);
+    }
+
     @Override
     @NotNull
     public Domain createDomain(Container container, String typeURI, String name)