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GH Issue 1736: Keep calculated fields when renaming a sample type #8186

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Merged
cnathe merged 2 commits into from
Oct 19, 2026
Merged

GH Issue 1736: Keep calculated fields when renaming a sample type #8186

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b9de1b4
Don't let a stale cached QueryDef undo a rename
cnathe Oct 15, 2026
54818f7
Use an UncacheTask record instead of a lambda
cnathe Oct 15, 2026
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9 changes: 7 additions & 2 deletions query/src/org/labkey/query/MetadataTableJSON.java
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Original file line number Diff line number Diff line change
Expand Up @@ -152,9 +152,14 @@ public static void saveMetadata(String schemaName, String queryName, @Nullable S
TableInfo rawTableInfo = getRawTableInfo(schema, queryName, updatedQueryName);
TablesDocument doc = null;
TableType xmlTable = null;
String savedQueryName = updatedQueryName != null ? updatedQueryName : queryName;

@XingY XingY Oct 16, 2026

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Debugging reveals that QueryManager.get().getQueryDef returns the queryDef under a different casing. So if a "Blood" sample type is renamed to "blood", QueryManager.get().getQueryDef("blood") returns the cached def for "Blood". This is probably harmless, especially for sample types since we don't allow casing different sample types.


if (queryDef != null)
{
// GH Issue 1736: make sure to put the updated query name into the queryDef
if (updatedQueryName != null)
queryDef.setName(updatedQueryName);

try
{
doc = parseDocument(queryDef.getMetaData());
Expand All @@ -180,7 +185,7 @@ else if (updatedQueryName != null)
queryDef = new QueryDef();
queryDef.setSchema(schemaName);
queryDef.setContainer(container.getId());
queryDef.setName(queryName);
queryDef.setName(savedQueryName);
}

if (doc == null)
Expand All @@ -192,7 +197,7 @@ else if (updatedQueryName != null)
{
TablesType tables = doc.addNewTables();
xmlTable = tables.addNewTable();
xmlTable.setTableName(queryName);
xmlTable.setTableName(savedQueryName);
}

if (xmlTable.getColumns() == null)
Expand Down
64 changes: 64 additions & 0 deletions query/src/org/labkey/query/QueryServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@
import org.labkey.api.data.ConvertHelper;
import org.labkey.api.data.DbSchema;
import org.labkey.api.data.DbSchemaType;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.DisplayColumn;
import org.labkey.api.data.Filter;
import org.labkey.api.data.ForeignKey;
Expand All @@ -76,6 +77,7 @@
import org.labkey.api.data.TableSelector;
import org.labkey.api.data.VirtualTable;
import org.labkey.api.data.dialect.SqlDialect;
import org.labkey.api.exp.PropertyType;
import org.labkey.api.exp.property.DomainKind;
import org.labkey.api.exp.query.ExpTable;
import org.labkey.api.gwt.client.AuditBehaviorType;
Expand Down Expand Up @@ -206,6 +208,7 @@
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ConcurrentMap;
import java.util.concurrent.CopyOnWriteArrayList;
import java.util.concurrent.TimeUnit;
import java.util.function.Consumer;
import java.util.function.Supplier;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -3878,5 +3881,66 @@ public void testRightAndIsnumeric() throws SQLException
assertEquals("isnumeric(NULL) on " + dialect, 0, results.getInt("n4"));
}
}

// GH Issue 1736
@Test
public void testRenameWithConcurrentCacheReload() throws Exception
{
DbScope scope = QueryManager.get().getDbSchema().getScope();
Container c = JunitUtil.getTestContainer();
User user = TestContext.get().getUser();
String oldName = "Users";
String newName = "junit" + GUID.makeHash();

QueryDef def = new QueryDef();
def.setSchema("core");
def.setName(oldName);
def.setContainer(c.getId());
def.setMetaData("<tables xmlns=\"http://labkey.org/data/xml\"><table tableName=\"" + oldName + "\" tableDbType=\"NOT_IN_DB\"><columns>" +
"<column columnName=\"junitCalc\"><conceptURI>http://www.labkey.org/exp/xml#calculated</conceptURI><valueExpression>1</valueExpression></column>" +
"</columns></table></tables>");
int queryDefId = QueryManager.get().insert(user, def).getQueryDefId();

GWTPropertyDescriptor calcField = new GWTPropertyDescriptor("junitCalc", PropertyType.INTEGER.getTypeUri());
calcField.setValueExpression("1");
// reloads the cache from committed data, as search indexing can while the rename is uncommitted
Runnable concurrentReload = () -> QueryManager.get().getQueryDef(c, "core", oldName, false);

try
{
try (DbScope.Transaction tx = scope.ensureTransaction())
{
QueryManager.get().renameQuery(user, c, "core", oldName, newName);
runOnOtherThread(concurrentReload);
assertNull("Expected the cache to hold the pre-rename row", QueryManager.get().getQueryDef(c, "core", newName, false));

QueryService.get().saveCalculatedFieldsMetadata("core", oldName, newName, List.of(calcField), true, user, c);
runOnOtherThread(concurrentReload);
tx.commit();
}

QueryDef saved = new TableSelector(QueryManager.get().getTableInfoQueryDef()).getObject(queryDefId, QueryDef.class);
assertEquals(newName, saved.getName());
assertTrue(saved.getMetaData(), saved.getMetaData().contains("tableName=\"" + newName + "\""));
assertTrue(saved.getMetaData(), saved.getMetaData().contains("junitCalc"));

assertNotNull("Cache should reload after commit", QueryManager.get().getQueryDef(c, "core", newName, false));
assertNull(QueryManager.get().getQueryDef(c, "core", oldName, false));
}
finally
{
QueryDef toDelete = new TableSelector(QueryManager.get().getTableInfoQueryDef()).getObject(queryDefId, QueryDef.class);
if (toDelete != null)
QueryManager.get().delete(toDelete);
}
}

private void runOnOtherThread(Runnable r) throws InterruptedException
{
Thread t = new Thread(r);
t.start();
t.join(TimeUnit.SECONDS.toMillis(30));
assertFalse("Reader thread did not finish", t.isAlive());
}
}
}
16 changes: 14 additions & 2 deletions query/src/org/labkey/query/persist/QueryDefCache.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
import org.labkey.api.collections.CaseInsensitiveMapWrapper;
import org.labkey.api.collections.IntHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.TableSelector;
import org.labkey.query.QueryDefinitionImpl;
Expand Down Expand Up @@ -166,9 +167,20 @@ QueryDef getQueryDefById(Container container, int queryDefId)
return QUERY_DEF_DB_CACHE.get(container)._queryDefIdMap.get(queryDefId);
}

// GH Issue 1736: a thread outside the transaction can reload pre-commit rows after the immediate remove, so remove again after commit
public static void uncache(Container c)
{
QUERY_DEF_DB_CACHE.remove(c);
QueryDefinitionImpl.clearHasPkColumnCache();
QueryManager.get().getDbSchema().getScope().addCommitTask(new UncacheTask(c), DbScope.CommitTaskOption.IMMEDIATE, DbScope.CommitTaskOption.POSTCOMMIT, DbScope.CommitTaskOption.POSTROLLBACK);
}

// record equality lets the transaction dedupe repeated uncaches of the same container
private record UncacheTask(Container c) implements Runnable
{
@Override
public void run()
{
QUERY_DEF_DB_CACHE.remove(c);
QueryDefinitionImpl.clearHasPkColumnCache();
}
}
}
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