Issue 52824: Don't mutate domains from the cache

api/src/org/labkey/api/assay/AbstractAssayProvider.java

@@ -382,31 +382,37 @@ public static String getDomainURIForPrefixIfExists(ExpProtocol protocol, String
         return result;
     }
 
-    public static Domain getDomainByPrefix(ExpProtocol protocol, String domainPrefix)
+    public static Domain getDomainByPrefix(ExpProtocol protocol, String domainPrefix, boolean forUpdate)
     {
         Container container = protocol.getContainer();
-        return PropertyService.get().getDomain(container, getDomainURIForPrefix(protocol, domainPrefix));
+        return PropertyService.get().getDomain(container, getDomainURIForPrefix(protocol, domainPrefix), forUpdate);
     }
 
     @Nullable
-    public static Domain getDomainByPrefixIfExists(ExpProtocol protocol, String domainPrefix)
+    public static Domain getDomainByPrefixIfExists(ExpProtocol protocol, String domainPrefix, boolean forUpdate)
     {
         String domainURI = getDomainURIForPrefixIfExists(protocol, domainPrefix);
         if (null == domainURI)
             return null;
         Container container = protocol.getContainer();
-        return PropertyService.get().getDomain(container, domainURI);
+        return PropertyService.get().getDomain(container, domainURI, forUpdate);
     }
 
     @Override
     public Domain getResultsDomain(ExpProtocol protocol)
     {
-        return getDomainByPrefix(protocol, ExpProtocol.ASSAY_DOMAIN_DATA);
+        return getResultsDomain(protocol, false);
+    }
+
+    @Override
+    public Domain getResultsDomain(ExpProtocol protocol, boolean forUpdate)
+    {
+        return getDomainByPrefix(protocol, ExpProtocol.ASSAY_DOMAIN_DATA, forUpdate);
     }
 
     protected @Nullable Domain getResultsDomainIfExists(ExpProtocol protocol)
     {
-        return getDomainByPrefixIfExists(protocol, ExpProtocol.ASSAY_DOMAIN_DATA);
+        return getDomainByPrefixIfExists(protocol, ExpProtocol.ASSAY_DOMAIN_DATA, false);
     }
 
     @Override
@@ -422,13 +428,25 @@ public void afterDomainChange(User user, ExpProtocol protocol, GWTDomain<GWTProp
     @Override
     public Domain getBatchDomain(ExpProtocol protocol)
     {
-        return getDomainByPrefix(protocol, ExpProtocol.ASSAY_DOMAIN_BATCH);
+        return getBatchDomain(protocol, false);
+    }
+
+    @Override
+    public Domain getBatchDomain(ExpProtocol protocol, boolean forUpdate)
+    {
+        return getDomainByPrefix(protocol, ExpProtocol.ASSAY_DOMAIN_BATCH, forUpdate);
     }
 
     @Override
     public Domain getRunDomain(ExpProtocol protocol)
     {
-        return getDomainByPrefix(protocol, ExpProtocol.ASSAY_DOMAIN_RUN);
+        return getRunDomain(protocol,false);
+    }
+
+    @Override
+    public Domain getRunDomain(ExpProtocol protocol, boolean forUpdate)
+    {
+        return getDomainByPrefix(protocol, ExpProtocol.ASSAY_DOMAIN_RUN, forUpdate);
     }
 
     protected PropertyDescriptor addProperty(Container sourceContainer, String name, Integer value, Map<String, Object> dataMap, Collection<PropertyDescriptor> types)

api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java

@@ -395,7 +395,7 @@ public void beforeDeleteData(List<ExpData> data, User user) throws ExperimentExc
                 // results/data domain for TSV-style assays
                 try
                 {
-                    domain = AbstractAssayProvider.getDomainByPrefixIfExists(protocol, ExpProtocol.ASSAY_DOMAIN_DATA) ;
+                    domain = AbstractAssayProvider.getDomainByPrefixIfExists(protocol, ExpProtocol.ASSAY_DOMAIN_DATA, false) ;
                 }
                 catch (IllegalStateException ignored)
                 {

api/src/org/labkey/api/assay/AssayProvider.java

@@ -97,12 +97,19 @@ enum ReRunSupport
     /** Get a schema that includes queries like Batch, Run, Results, and any additional tables. */
     AssayProtocolSchema createProtocolSchema(User user, Container container, @NotNull ExpProtocol protocol, @Nullable Container targetStudy);
 
+    /** Get a domain that is not intended to be mutated */
     Domain getBatchDomain(ExpProtocol protocol);
 
+    Domain getBatchDomain(ExpProtocol protocol, boolean forUpdate);
+
     Domain getRunDomain(ExpProtocol protocol);
 
+    Domain getRunDomain(ExpProtocol protocol, boolean forUpdate);
+
     Domain getResultsDomain(ExpProtocol protocol);
 
+    Domain getResultsDomain(ExpProtocol protocol, boolean forUpdate);
+
     void beforeDomainChange(User user, ExpProtocol protocol, GWTDomain<GWTPropertyDescriptor> orig, GWTDomain<GWTPropertyDescriptor> update) throws ValidationException;
     void afterDomainChange(User user, ExpProtocol protocol, GWTDomain<GWTPropertyDescriptor> orig, GWTDomain<GWTPropertyDescriptor> update) throws ValidationException;
 

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

@@ -124,7 +124,7 @@ 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)
@@ -138,7 +138,7 @@ public void initializeProvider(User user)
                     domain.addPropertyOfPropertyDescriptor(pd);
                 }
                 domain.save(user);
-                domain = getDomain();
+                domain = getDomain(true);
             }
             catch (ChangePropertyDescriptorException e)
             {
@@ -299,12 +299,18 @@ private void copyTo(DomainProperty dp, PropertyDescriptor pd, Container c)
 
     @Override
     public final Domain getDomain()
+    {
+        return getDomain(false);
+    }
+
+    @Override
+    public final 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/audit/AuditTypeProvider.java

@@ -44,6 +44,8 @@ public interface AuditTypeProvider
 
     Domain getDomain();
 
+    Domain getDomain(boolean forUpdate);
+
     TableInfo createTableInfo(UserSchema schema, ContainerFilter cf);
 
     <K extends AuditTypeEvent> Class<K> getEventClass();

api/src/org/labkey/api/audit/query/AbstractAuditDomainKind.java

@@ -241,7 +241,7 @@ public JSONObject getDomainKindProperties(GWTDomain domain, Container container,
     }
 
     @Override
-    public Domain createDomain(GWTDomain domain, JSONObject arguments, Container container, User user, @Nullable TemplateInfo templateInfo)
+    public Domain createDomain(GWTDomain domain, JSONObject arguments, Container container, User user, @Nullable TemplateInfo templateInfo, boolean forUpdate)
     {
         throw new UnsupportedOperationException();
     }

api/src/org/labkey/api/audit/query/DefaultAuditTypeTable.java

@@ -142,7 +142,14 @@ protected void initColumn(MutableColumnInfo col)
     @Override
     public Domain getDomain()
     {
-        return _provider.getDomain();
+        return getDomain(false);
+    }
+
+    @Nullable
+    @Override
+    public Domain getDomain(boolean forUpdate)
+    {
+        return _provider.getDomain(forUpdate);
     }
 
     @Nullable

api/src/org/labkey/api/data/AbstractTableInfo.java

@@ -1769,6 +1769,13 @@ public Domain getDomain()
         return null;
     }
 
+    @Nullable
+    @Override
+    public Domain getDomain(boolean forUpdate)
+    {
+        return getDomain();
+    }
+
     @Nullable
     @Override
     public DomainKind getDomainKind()

api/src/org/labkey/api/data/MutableColumnInfo.java

@@ -97,7 +97,7 @@ default void setSortFieldKeysFromXml(String xml)
 
     void setLocked(boolean b);
 
-    // return a ColumnInfo that does not suppport MutableColumnInfo or a MutableColumnInfo that is locked
+    // return a ColumnInfo that does not support MutableColumnInfo or a MutableColumnInfo that is locked
     default ColumnInfo lock()
     {
         setLocked(true);

api/src/org/labkey/api/data/NameGenerator.java

@@ -15,8 +15,6 @@
  */
 package org.labkey.api.data;
 
-import org.apache.commons.beanutils.ConversionException;
-import org.apache.commons.beanutils.ConvertUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -26,17 +24,12 @@
 import org.junit.Test;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.collections.CaseInsensitiveHashSet;
-import org.labkey.api.exp.Identifiable;
-import org.labkey.api.exp.LsidManager;
 import org.labkey.api.exp.PropertyType;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExpDataClass;
-import org.labkey.api.exp.api.ExpLineage;
 import org.labkey.api.exp.api.ExpLineageOptions;
-import org.labkey.api.exp.api.ExpLineageService;
 import org.labkey.api.exp.api.ExpMaterial;
 import org.labkey.api.exp.api.ExpObject;
-import org.labkey.api.exp.api.ExpRunItem;
 import org.labkey.api.exp.api.ExpSampleType;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.exp.api.SampleTypeService;
@@ -47,7 +40,6 @@
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryKey;
 import org.labkey.api.query.QueryService;
-import org.labkey.api.query.RuntimeValidationException;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.reader.TabLoader;
@@ -59,12 +51,9 @@
 import org.labkey.api.util.StringExpressionFactory;
 import org.labkey.api.util.StringExpressionFactory.AbstractStringExpression.NullValueBehavior;
 import org.labkey.api.util.StringExpressionFactory.FieldKeyStringExpression;
-import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.SubstitutionFormat;
-import org.labkey.api.util.Tuple3;
 
 import java.io.IOException;
-import java.sql.SQLException;
 import java.sql.Time;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
@@ -73,12 +62,10 @@
 import java.util.Calendar;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.Date;
 import java.util.GregorianCalendar;
 import java.util.HashMap;
 import java.util.HashSet;
-import java.util.LinkedHashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.ListIterator;
@@ -88,7 +75,6 @@
 import java.util.function.Supplier;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import static org.labkey.api.data.NameGenerator.NameGenerationExpression.findFirstOpenOrCloseTag;

api/src/org/labkey/api/data/SchemaTableInfo.java

@@ -857,6 +857,15 @@ public Domain getDomain()
         return null;
     }
 
+    @Nullable
+    @Override
+    public Domain getDomain(boolean forUpdate)
+    {
+        if (forUpdate)
+            throw new UnsupportedOperationException("Cannot get domain for update.");
+        return getDomain();
+    }
+
     @Nullable
     @Override
     public DomainKind getDomainKind()

api/src/org/labkey/api/data/TableInfo.java

@@ -445,6 +445,12 @@ default List<Pair<String, String>> getValidatedImportTemplates(ViewContext ctx)
     @Nullable
     Domain getDomain();
 
+    /**
+     * Get Domain associated with this TableInfo if any.
+     */
+    @Nullable
+    Domain getDomain(boolean forUpdate);
+
     /**
      * Get DomainKind associated with this TableInfo if any.
      * Domain may or may not exist even if DomainKind is available.

api/src/org/labkey/api/data/generator/DataGenerator.java

@@ -17,7 +17,6 @@
 import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.dataiterator.DataIteratorBuilder;
 import org.labkey.api.dataiterator.DetailedAuditLogDataIterator;
-import org.labkey.api.dataiterator.ListofMapsDataIterator;
 import org.labkey.api.dataiterator.MapDataIterator;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.DataClassDomainKindProperties;

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

@@ -2441,25 +2441,55 @@ public DomainDescriptor load(@NotNull Integer key, @Nullable Object argument)
         }
     }
 
-
     public static DomainDescriptor getDomainDescriptor(int id)
     {
+        return getDomainDescriptor(id, false);
+    }
+
+    public static DomainDescriptor getDomainDescriptor(int id, boolean forUpdate)
+    {
+        if (forUpdate)
+            return new DomainDescriptorLoader().load(id, null);
+
         return DOMAIN_DESC_BY_ID_CACHE.get(id);
     }
 
     @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;
 
+        if (forUpdate)
+            return getDomainDescriptorForUpdate(domainURI, c);
+
         // 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)
             return dd;
 
         // Try in the /Shared container too
-        return DOMAIN_DESCRIPTORS_BY_URI_CACHE.get(getCacheKey(domainURI, _sharedContainer));
+        key = getCacheKey(domainURI, _sharedContainer);
+        return DOMAIN_DESCRIPTORS_BY_URI_CACHE.get(key);
+    }
+
+    @Nullable
+    private static DomainDescriptor getDomainDescriptorForUpdate(String domainURI, Container c)
+    {
+        if (c == null)
+            return null;
+
+        DomainDescriptor dd = fetchDomainDescriptorFromDB(domainURI, c);
+        if (dd == null)
+            dd = fetchDomainDescriptorFromDB(domainURI, _sharedContainer);
+        return dd;
     }
 
     /**

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

@@ -58,9 +58,11 @@ public interface ExpDataClass extends ExpObject, ExpSearchable
 
     void setSampleType(Integer sampleType);
 
+    @NotNull
     Domain getDomain();
 
-    void setDomain(Domain d);
+    @NotNull
+    Domain getDomain(boolean forUpdate);
 
     String getDescription();
 

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

@@ -66,6 +66,9 @@ public interface ExpSampleType extends ExpObject, ExpSearchable
     @NotNull
     Domain getDomain();
 
+    @NotNull
+    Domain getDomain(boolean forUpdate);
+
     String getDescription();
 
     /**