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();
 
  /**