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Issue 52824: Don't mutate domains from the cache #891

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Merged
labkey-susanh merged 2 commits into from
Jun 4, 2025
Merged

Issue 52824: Don't mutate domains from the cache #891

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e20c2fe
Still more forUpdate parameters
labkey-susanh May 28, 2025
cfc38ba
Merge remote-tracking branch 'origin/develop' into fb_getDomainForUpdate
labkey-susanh Jun 4, 2025
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2 changes: 1 addition & 1 deletion elisa/src/org/labkey/elisa/ElisaAssayProvider.java
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Expand Up @@ -410,7 +410,7 @@ public DataExchangeHandler createDataExchangeHandler()

public Domain getConcentrationWellGroupDomain(ExpProtocol protocol)
{
return getDomainByPrefix(protocol, ASSAY_DOMAIN_DATA);
return getDomainByPrefix(protocol, ASSAY_DOMAIN_DATA, false);
}

@Override
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6 changes: 3 additions & 3 deletions elispotassay/src/org/labkey/elispot/ElispotAssayProvider.java
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Expand Up @@ -222,7 +222,7 @@ public AssayTableMetadata getTableMetadata(@NotNull ExpProtocol protocol)
}

@Override
public Domain getResultsDomain(ExpProtocol protocol)
public Domain getResultsDomain(ExpProtocol protocol, boolean forUpdate)
{
return null;
}
Expand Down Expand Up @@ -350,12 +350,12 @@ public ActionURL getImportURL(Container container, ExpProtocol protocol)

public Domain getAntigenWellGroupDomain(ExpProtocol protocol)
{
return getDomainByPrefix(protocol, ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
return getDomainByPrefix(protocol, ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);
}

public Domain getAnalyteDomain(ExpProtocol protocol)
{
return getDomainByPrefix(protocol, ASSAY_DOMAIN_ANALYTE);
return getDomainByPrefix(protocol, ASSAY_DOMAIN_ANALYTE, false);
}

@Override
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4 changes: 2 additions & 2 deletions elispotassay/src/org/labkey/elispot/ElispotDataHandler.java
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Expand Up @@ -265,7 +265,7 @@ public static void populateAntigenDataProperties(ExpRun run, Plate plate, PlateR
{
Container container = run.getContainer();

Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(run.getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(run.getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);
DomainProperty cellWellProp = antigenDomain.getPropertyByName(ElispotAssayProvider.CELLWELL_PROPERTY_NAME);

List<? extends ExpData> data = run.getOutputDatas(ElispotDataHandler.ELISPOT_DATA_TYPE);
Expand Down Expand Up @@ -324,7 +324,7 @@ public static void populateAntigenRunProperties(ExpRun run, Plate plate, PlateRe
{
Container container = run.getContainer();

Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(run.getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(run.getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);
List<? extends DomainProperty> antigenProps = antigenDomain.getProperties();
DomainProperty cellWellProp = antigenDomain.getPropertyByName(ElispotAssayProvider.CELLWELL_PROPERTY_NAME);

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2 changes: 1 addition & 1 deletion elispotassay/src/org/labkey/elispot/ElispotManager.java
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Expand Up @@ -76,7 +76,7 @@ public static TableInfo getTableInfoElispotRunData()
@NotNull
public static TableInfo getTableInfoElispotAntigen(ExpProtocol protocol)
{
Domain domain = AbstractAssayProvider.getDomainByPrefix(protocol, ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
Domain domain = AbstractAssayProvider.getDomainByPrefix(protocol, ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);
if (null != domain)
return StorageProvisioner.createTableInfo(domain);
throw new IllegalStateException("Domain not found for protocol: " + protocol.getName());
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2 changes: 1 addition & 1 deletion elispotassay/src/org/labkey/elispot/ElispotProtocolSchema.java
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Expand Up @@ -84,7 +84,7 @@ public TableInfo createProviderTable(String name, ContainerFilter cf)
{
if (name.equalsIgnoreCase(ANTIGEN_TABLE_NAME))
{
Domain domain = AbstractAssayProvider.getDomainByPrefix(getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
Domain domain = AbstractAssayProvider.getDomainByPrefix(getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);
if (null != domain)
return new ElispotRunAntigenTable(this, cf, domain, getProtocol());
}
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4 changes: 2 additions & 2 deletions elispotassay/src/org/labkey/elispot/ElispotUploadWizardAction.java
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Expand Up @@ -168,7 +168,7 @@ public PlateAnalytePropertyHelper createAnalytePropertyHelper(ElispotRunUploadFo
@Override
protected void addRunActionButtons(ElispotRunUploadForm newRunForm, InsertView insertView, ButtonBar bbar)
{
Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(_protocol, ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(_protocol, ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);
List<? extends DomainProperty> antigenColumns = antigenDomain.getProperties();
if (antigenColumns.isEmpty())
{
Expand Down Expand Up @@ -338,7 +338,7 @@ public boolean executeStep(ElispotRunUploadForm form, BindException errors) thro
}
}

Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(form.getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(form.getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);
List<? extends DomainProperty> antigenColumns = antigenDomain.getProperties();
if (antigenColumns.isEmpty())
{
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2 changes: 1 addition & 1 deletion elispotassay/src/org/labkey/elispot/pipeline/BackgroundSubtractionJob.java
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Expand Up @@ -124,7 +124,7 @@ public void run()
{
String dataLsid = data.get(0).getLSID();
Map<String, Object> propMap = new HashMap<>();
Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(run.getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(run.getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);

DomainProperty cellWellProp = antigenDomain.getPropertyByName(ElispotAssayProvider.CELLWELL_PROPERTY_NAME);
DomainProperty antigenNameProp = antigenDomain.getPropertyByName(ElispotAssayProvider.ANTIGENNAME_PROPERTY_NAME);
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2 changes: 1 addition & 1 deletion elispotassay/src/org/labkey/elispot/query/ElispotRunAntigenTable.java
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Expand Up @@ -90,7 +90,7 @@ protected ColumnInfo resolveColumn(String name)
@Override
public TableInfo getLookupTableInfo()
{
Domain domain = AbstractAssayProvider.getDomainByPrefix(_protocol, ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP);
Domain domain = AbstractAssayProvider.getDomainByPrefix(_protocol, ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);
return new ElispotRunAntigenTable(_userSchema, getLookupContainerFilter(), domain, _protocol);
}
};
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8 changes: 7 additions & 1 deletion flow/src/org/labkey/flow/data/FlowAssayProvider.java
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Expand Up @@ -198,12 +198,18 @@ public Domain getRunDomain(ExpProtocol protocol)

@Override
public Domain getBatchDomain(ExpProtocol protocol)
{
return getBatchDomain(protocol, false);
}

@Override
public Domain getBatchDomain(ExpProtocol protocol, boolean forUpdate)
{
return null;
}

@Override
public Domain getResultsDomain(ExpProtocol protocol)
public Domain getResultsDomain(ExpProtocol protocol, boolean forUpdate)
{
return null;
}
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/reports/FlowReportManager.java
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Expand Up @@ -202,7 +202,7 @@ public static Domain ensureDomain(FlowReport report, User user, FlowTableType ta
domain.setDescription("Domain for " + report.getDescriptor().getDescriptorType() + " reports on flow table " + tableType);
domain.save(user);

domain = PropertyService.get().getDomain(domain.getTypeId());
domain = PropertyService.get().getDomain(domain.getTypeId(), true);

for (PropertyDescriptor prop : properties)
{
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8 changes: 4 additions & 4 deletions luminex/src/org/labkey/luminex/LuminexAssayProvider.java
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Expand Up @@ -163,11 +163,11 @@ public AssayTableMetadata getTableMetadata(@NotNull ExpProtocol protocol)
}

@Override
public Domain getResultsDomain(ExpProtocol protocol)
public Domain getResultsDomain(ExpProtocol protocol, boolean forUpdate)
{
try
{
return getDomainByPrefix(protocol, ASSAY_DOMAIN_CUSTOM_DATA);
return getDomainByPrefix(protocol, ASSAY_DOMAIN_CUSTOM_DATA, forUpdate);
}
catch (IllegalArgumentException e)
{
Expand All @@ -177,7 +177,7 @@ public Domain getResultsDomain(ExpProtocol protocol)
addResultsDomain(protocol);
// Clear the cache so we can find the domain we just created
protocol.setObjectProperties(null);
return getDomainByPrefix(protocol, ASSAY_DOMAIN_CUSTOM_DATA);
return getDomainByPrefix(protocol, ASSAY_DOMAIN_CUSTOM_DATA, forUpdate);
}
}

Expand Down Expand Up @@ -485,7 +485,7 @@ public boolean supportsBackgroundUpload()

public static Domain getExcelRunDomain(ExpProtocol protocol)
{
return AbstractAssayProvider.getDomainByPrefix(protocol, LuminexAssayProvider.ASSAY_DOMAIN_EXCEL_RUN);
return AbstractAssayProvider.getDomainByPrefix(protocol, LuminexAssayProvider.ASSAY_DOMAIN_EXCEL_RUN, false);
}

@Override
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2 changes: 1 addition & 1 deletion luminex/src/org/labkey/luminex/LuminexRunDatabaseContext.java
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Expand Up @@ -79,7 +79,7 @@ public String[] getAnalyteNames()
public Map<DomainProperty, String> getAnalyteProperties(String analyteName)
{
Analyte analyte = getAnalyte(analyteName);
Domain domain = AbstractAssayProvider.getDomainByPrefix(_protocol, LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE);
Domain domain = AbstractAssayProvider.getDomainByPrefix(_protocol, LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE, false);
return getProperties(domain, OntologyManager.getPropertyObjects(_run.getContainer(), analyte.getLsid()));
}

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2 changes: 1 addition & 1 deletion luminex/src/org/labkey/luminex/LuminexRunUploadForm.java
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Expand Up @@ -118,7 +118,7 @@ protected Map<DomainProperty, String> getAnalytePropertyMapFromRequest(List<? ex
@Override
public Map<DomainProperty, String> getAnalyteProperties(String analyteName)
{
Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(getProtocol(), LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE);
Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(getProtocol(), LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE, false);
List<? extends DomainProperty> domainProperties = analyteDomain.getProperties();
return getAnalytePropertyMapFromRequest(domainProperties, analyteName);
}
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4 changes: 2 additions & 2 deletions luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java
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Expand Up @@ -109,7 +109,7 @@ public LuminexUploadWizardAction()
@Override
protected void addRunActionButtons(LuminexRunUploadForm newRunForm, InsertView insertView, ButtonBar bbar)
{
Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(_protocol, LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE);
Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(_protocol, LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE, false);
List<? extends DomainProperty> analyteColumns = analyteDomain.getProperties();
if (analyteColumns.isEmpty())
{
Expand Down Expand Up @@ -157,7 +157,7 @@ private ModelAndView getAnalytesView(String[] analyteNames, final LuminexRunUplo
for (String analyte : analyteNames)
view.getDataRegion().addHiddenFormField("analyteNames", analyte);

Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(_protocol, LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE);
Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(_protocol, LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE, false);
List<? extends DomainProperty> analyteColumns = analyteDomain.getProperties();
Set<String> initNegativeControlAnalytes = new TreeSet<>();
List<String> negativeBeadDefaultValues = AnalyteDefaultValueService.getAnalyteProperty(Arrays.asList(analyteNames), getContainer(), _protocol, LuminexDataHandler.NEGATIVE_BEAD_COLUMN_NAME);
Expand Down
3 changes: 1 addition & 2 deletions luminex/src/org/labkey/luminex/query/AnalyteTable.java
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Expand Up @@ -41,7 +41,6 @@
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.security.permissions.UpdatePermission;
import org.labkey.api.assay.AbstractAssayProvider;
import org.labkey.api.assay.AssaySchema;
import org.labkey.luminex.LuminexAssayProvider;
import org.labkey.luminex.model.Analyte;

Expand Down Expand Up @@ -115,7 +114,7 @@ public TableInfo getLookupTableInfo()
lsidColumn.setShownInUpdateView(false);

var colProperty = wrapColumn("Properties", getRealTable().getColumn("LSID"));
Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(_userSchema.getProtocol(), LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE);
Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(_userSchema.getProtocol(), LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE, false);
Map<String, PropertyDescriptor> map = new TreeMap<>();
for(DomainProperty pd : analyteDomain.getProperties())
{
Expand Down
11 changes: 9 additions & 2 deletions luminex/src/org/labkey/luminex/query/LuminexDataTable.java
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Expand Up @@ -282,7 +282,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
defaultCols.add(FieldKey.fromParts("Titration"));

// issue 21253: Conditional show/hide of the Negative Bead column in the Luminex assay results grid
Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(protocol, LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE);
Domain analyteDomain = AbstractAssayProvider.getDomainByPrefix(protocol, LuminexAssayProvider.ASSAY_DOMAIN_ANALYTE, false);
if (analyteDomain != null && analyteDomain.getPropertyByName(LuminexDataHandler.NEGATIVE_CONTROL_COLUMN_NAME) != null)
{
defaultCols.add(FieldKey.fromParts("Analyte", "NegativeBead"));
Expand Down Expand Up @@ -395,7 +395,14 @@ private SQLFragment getExclusionsUnionSQL()
@NotNull
public Domain getDomain()
{
return _provider.getResultsDomain(_userSchema.getProtocol());
return getDomain(false);
}

@Override
@NotNull
public Domain getDomain(boolean forUpdate)
{
return _provider.getResultsDomain(_userSchema.getProtocol(), forUpdate);
}

@Override
Expand Down
2 changes: 1 addition & 1 deletion microarray/src/org/labkey/microarray/matrix/ExpressionMatrixAssayProvider.java
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Expand Up @@ -135,7 +135,7 @@ public List<ParticipantVisitResolverType> getParticipantVisitResolverTypes()
}

@Override
public Domain getResultsDomain(ExpProtocol protocol)
public Domain getResultsDomain(ExpProtocol protocol, boolean forUpdate)
{
return null;
}
Expand Down
2 changes: 1 addition & 1 deletion nab/src/org/labkey/nab/NabAssayProvider.java
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Expand Up @@ -337,7 +337,7 @@ protected Pair<Domain, Map<DomainProperty, Object>> createVirusWellGroupDomain(C
public Domain getVirusWellGroupDomain(ExpProtocol protocol)
{
if (supportsMultiVirusPlate())
return getDomainByPrefixIfExists(protocol, ASSAY_DOMAIN_VIRUS_WELLGROUP);
return getDomainByPrefixIfExists(protocol, ASSAY_DOMAIN_VIRUS_WELLGROUP, false);
else
return null;
}
Expand Down
2 changes: 0 additions & 2 deletions viability/src/org/labkey/viability/ViabilityAssayRunUploadForm.java
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Expand Up @@ -31,11 +31,9 @@
import org.labkey.api.assay.actions.UploadWizardAction;
import org.labkey.api.assay.AssayDataCollector;
import org.labkey.api.assay.AssayFileWriter;
import org.labkey.api.util.UnexpectedException;
import org.labkey.vfs.FileLike;
import org.springframework.validation.Errors;

import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
Expand Down
2 changes: 1 addition & 1 deletion viability/src/org/labkey/viability/ViabilityAssayUploadWizardAction.java
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Expand Up @@ -173,7 +173,7 @@ protected InsertView _getResultsView(ViabilityAssayRunUploadForm form, boolean e
List<Map<String, Object>> rows = errorReshow ? form.getResultProperties(errors) : form.getParsedResultData();
Map<String, Map<String, Object>> reRunResults = form.getReRunResults();

Domain resultDomain = AbstractAssayProvider.getDomainByPrefix(_protocol, ExpProtocol.ASSAY_DOMAIN_DATA);
Domain resultDomain = AbstractAssayProvider.getDomainByPrefix(_protocol, ExpProtocol.ASSAY_DOMAIN_DATA, false);
List<? extends DomainProperty> resultDomainProperties = resultDomain.getProperties();
String lsidCol = "RowID";
InsertView view = createInsertView(ViabilitySchema.getTableInfoResults(), lsidCol, resultDomainProperties, errorReshow, ResultsStepHandler.NAME, form, errors);
Expand Down