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Merged
labkey-nicka merged 4 commits into from
Aug 10, 2026
Merged

Experiment: cache data classes by LSID #7922

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3049de2
getDataClassByLsid
labkey-nicka Aug 7, 2026
ae45ec1
Cache data classes by LSID (just like sample types)
labkey-nicka Aug 10, 2026
9c9d812
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labkey-nicka Aug 10, 2026
418210e
Tests
labkey-nicka Aug 10, 2026
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75 changes: 75 additions & 0 deletions experiment/src/org/labkey/experiment/api/ExpDataClassDataTestCase.jsp
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@
<%@ page import="org.labkey.api.exp.api.DataClassDomainKindProperties" %>
<%@ page import="org.labkey.api.exp.api.ExpData" %>
<%@ page import="org.labkey.api.exp.api.ExpDataClass" %>
<%@ page import="org.labkey.api.exp.api.ExperimentJSONConverter" %>
<%@ page import="org.labkey.api.exp.api.ExperimentService" %>
<%@ page import="org.labkey.api.exp.list.ListDefinition" %>
<%@ page import="org.labkey.api.exp.list.ListItem" %>
Expand Down Expand Up @@ -94,6 +95,7 @@
<%@ page import="java.util.ArrayList" %>
<%@ page import="java.util.Collection" %>
<%@ page import="java.util.Collections" %>
<%@ page import="java.util.HashMap" %>
<%@ page import="java.util.HashSet" %>
<%@ page import="static java.util.Collections.emptyList" %>
<%@ page import="static org.junit.Assert.*" %>
Expand Down Expand Up @@ -1175,6 +1177,79 @@ public void testUpdateAuditForLongField() throws Exception
}
}

@Test
public void testDataClassLsidCache() throws Exception
{
final Container sub = ContainerManager.createContainer(c, "subLsidCache", _user);
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ExpDataClassImpl projectDataClass = ExperimentServiceImpl.get().createDataClass(c, _user, "lsidCacheProject", null, List.of(new GWTPropertyDescriptor("prop", "string")), emptyList(), null, null);
ExpDataClassImpl subDataClass = ExperimentServiceImpl.get().createDataClass(sub, _user, "lsidCacheSub", null, List.of(new GWTPropertyDescriptor("prop", "string")), emptyList(), null, null);
String projectLsid = projectDataClass.getLSID();
String subLsid = subDataClass.getLSID();

// first lookup populates the mapping, second is served from the container's data class cache
for (int i = 0; i < 2; i++)
{
ExpDataClass fromProject = ExperimentService.get().getDataClass(projectLsid);
assertNotNull("Lookup " + i + " by LSID should resolve the data class", fromProject);
assertEquals("lsidCacheProject", fromProject.getName());
assertEquals(projectDataClass.getRowId(), fromProject.getRowId());
assertEquals(c.getId(), fromProject.getContainer().getId());

ExpDataClass fromSub = ExperimentService.get().getDataClass(subLsid);
assertNotNull("Lookup " + i + " by LSID should resolve the subfolder data class", fromSub);
assertEquals("lsidCacheSub", fromSub.getName());
assertEquals(sub.getId(), fromSub.getContainer().getId());
}

projectDataClass.delete(_user);
assertNull("Deleted data class should not resolve from a stale LSID mapping", ExperimentService.get().getDataClass(projectLsid));
assertNotNull("Sibling data class should be unaffected", ExperimentService.get().getDataClass(subLsid));
}

@Test
public void testFailedDataClassUpdateDoesNotCorruptCache() throws Exception
{
ExperimentServiceImpl.get().createDataClass(c, _user, "failedUpdateParent", null, List.of(new GWTPropertyDescriptor("prop", "string")), emptyList(), null, null);

DataClassDomainKindProperties createOptions = new DataClassDomainKindProperties();
createOptions.setDescription("original description");
ExpDataClassImpl child = ExperimentServiceImpl.get().createDataClass(c, _user, "failedUpdateChild", createOptions, List.of(new GWTPropertyDescriptor("prop", "string")), emptyList(), null, null);

// hasMissingRequiredParent() short-circuits on an empty data class, so the rejection needs a parentless row
List<Map<String, Object>> rows = new ArrayList<>();
Map<String, Object> row = new CaseInsensitiveHashMap<>();
row.put("name", "failedUpdateChild-1");
rows.add(row);
helper.insertRows(c, rows, child.getName());

// warm the mapping so the second lookup comes back from the container's data class cache
assertNotNull(ExperimentService.get().getDataClass(child.getLSID()));
final ExpDataClass toUpdate = ExperimentService.get().getDataClass(child.getLSID());
assertNotNull(toUpdate);

Map<String, Object> parentAlias = new HashMap<>();
parentAlias.put("inputType", ExperimentJSONConverter.DATA_INPUTS_ALIAS_PREFIX + "failedUpdateParent");
parentAlias.put("required", true);

final DataClassDomainKindProperties options = new DataClassDomainKindProperties();
options.setRowId(child.getRowId());
options.setName("failedUpdateChildRenamed");
options.setDescription("attempted description");
options.setImportAliases(Map.of("parentAlias", parentAlias));

final GWTDomain<GWTPropertyDescriptor> original = DomainUtil.getDomainDescriptor(_user, child.getDomain());
final GWTDomain<GWTPropertyDescriptor> update = DomainUtil.getDomainDescriptor(_user, child.getDomain());

ApiUsageException e = assertThrows(ApiUsageException.class,
() -> ExperimentService.get().updateDataClass(c, _user, toUpdate, options, original, update, null));
assertThat(e.getMessage(), containsString("cannot be required as a parent type"));

ExpDataClass reloaded = ExperimentService.get().getDataClass(c, "failedUpdateChild");
assertNotNull("Original name should still resolve after a rejected update", reloaded);
assertEquals("Description should not reflect the rejected update", "original description", reloaded.getDescription());
assertNull("Attempted name should not resolve after a rejected update", ExperimentService.get().getDataClass(c, "failedUpdateChildRenamed"));
}

private @NotNull TableInfo getDataClassTable(String dataClassName)
{
UserSchema schema = QueryService.get().getUserSchema(_user, c, ExpSchema.SCHEMA_EXP_DATA);
Expand Down
37 changes: 31 additions & 6 deletions experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -336,6 +336,10 @@ public class ExperimentServiceImpl implements ExperimentService, ObjectReference

private final Cache<String, ExperimentRun> EXPERIMENT_RUN_CACHE = DatabaseCache.get(getExpSchema().getScope(), getTinfoExperimentRun().getCacheSize(), "Experiment Run by LSID", new ExperimentRunCacheLoader());

/** DataClass LSID -> Container */
private final Cache<String, String> dataClassLsidCache = CacheManager.getStringKeyCache(CacheManager.UNLIMITED, CacheManager.DAY, "DataClass to container");

/** ContainerId -> DataClasses */
private final Cache<String, SortedSet<DataClass>> dataClassCache = CacheManager.getBlockingStringKeyCache(CacheManager.UNLIMITED, CacheManager.DAY, "Data classes", (containerId, _) ->
{
Container c = ContainerManager.getForId(containerId);
Expand Down Expand Up @@ -1874,12 +1878,30 @@ public ExpDataClassImpl getDataClass(long rowId)
@Override
public @Nullable ExpDataClassImpl getDataClass(@NotNull String lsid)
{
SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("lsid"), lsid);
DataClass dataClass = new TableSelector(getTinfoDataClass(), filter, null).getObject(DataClass.class);
if (dataClass == null)
return null;
String containerId = dataClassLsidCache.get(lsid);
Container c = null;
if (containerId != null)
c = ContainerManager.getForId(containerId);

return new ExpDataClassImpl(dataClass);
ExpDataClassImpl dataClass = null;
if (null != c)
dataClass = getDataClass(c, false, dc -> lsid.equals(dc.getLSID()));
if (null == dataClass)
{
Filter filter = new SimpleFilter(ExpDataClassTable.Column.LSID.fieldKey(), lsid);
DataClass dc = new TableSelector(getTinfoDataClass(), filter, null).getObject(DataClass.class);
if (dc != null)
dataClass = new ExpDataClassImpl(dc);
}

if (null != dataClass)
{
Container dcContainer = dataClass.getContainer();
if (dcContainer != null && dcContainer.getId().equals(containerId))
dataClassLsidCache.put(lsid, dataClass.getContainer().getId());
}

return dataClass;
}

@Override
Expand Down Expand Up @@ -8133,7 +8155,10 @@ public ValidationException updateDataClass(@NotNull Container c, @NotNull User u
GWTDomain<? extends GWTPropertyDescriptor> update,
@Nullable String auditUserComment)
{
ExpDataClassImpl dataClass = (ExpDataClassImpl) dc;
// Re-read so the mutations below don't write through to a DataClass bean shared via dataClassCache
ExpDataClassImpl dataClass = getDataClass(dc.getRowId());
if (dataClass == null)
return new ValidationException("Data class not found: " + dc.getName());

Map<String, Object> oldProps = dataClass.getAuditRecordMap();
Map<String, Object> newProps = properties != null ? properties.getAuditRecordMap() : dataClass.getAuditRecordMap() /* no update */;
Expand Down