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Merged
XingY merged 9 commits into from
Oct 10, 2025
Merged

Issue 53063: Support "Aliquoted From" with space #7099

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516c267
Issue 53063: Support "Aliquoted From" with space
XingY Oct 3, 2025
042b81e
Merge branch 'develop' into fb_issue53063
labkey-danield Oct 7, 2025
4320765
comment
XingY Oct 7, 2025
7aff2ef
Merge branch 'develop' into fb_issue53063
XingY Oct 8, 2025
2009b56
code review changes
XingY Oct 8, 2025
0075347
Fix aliquot name using MaterialInput syntax
XingY Oct 8, 2025
a94cbab
Switch to use set instead of List to avoid duplicate names
XingY Oct 8, 2025
81efd9e
Fix cross type import
XingY Oct 8, 2025
a5fb5ac
Issue 53963: Cross-sample-type import gives incorrect row number in m…
XingY Oct 9, 2025
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30 changes: 15 additions & 15 deletions api/src/org/labkey/api/data/NameGeneratorState.java
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Original file line number Diff line number Diff line change
Expand Up @@ -50,9 +50,9 @@
import java.util.stream.Collectors;

import static org.labkey.api.data.NameGenerator.getParentImportAliasFieldKeys;
import static org.labkey.api.exp.api.ExpMaterial.ALIQUOTED_FROM_INPUT;
import static org.labkey.api.exp.api.ExpRunItem.INPUT_PARENT;
import static org.labkey.api.exp.api.ExpRunItem.PARENT_IMPORT_ALIAS_MAP_PROP;
import static org.labkey.api.exp.api.ExperimentService.isAliquotedFromColumn;

public class NameGeneratorState implements AutoCloseable
{
Expand Down Expand Up @@ -362,7 +362,7 @@ private void addParentLookupValues(String parentTypeName,
boolean isMaterialParent,
@Nullable Map<String, FieldKey> parentImportAliases,
ExpObject parentObject,
Map<FieldKey, ArrayList<Object>> inputLookupValues,
Map<FieldKey, LinkedHashSet<Object>> inputLookupValues,
@Nullable NameGenerator altNameGenerator)
{
String inputType = isMaterialParent ? ExpMaterial.MATERIAL_INPUT_PARENT : ExpData.DATA_INPUT_PARENT;
Expand All @@ -384,7 +384,7 @@ private void addParentLookupValues(String parentTypeName,
continue;

// add to Input/<LookupField>
inputLookupValues.computeIfAbsent(FieldKey.fromParts(INPUT_PARENT, fieldName), (s) -> new ArrayList<>()).add(lookupValue);
inputLookupValues.computeIfAbsent(FieldKey.fromParts(INPUT_PARENT, fieldName), (s) -> new LinkedHashSet<>()).add(lookupValue);

// add to importAlias/<LookupField>
if (parentImportAliases != null)
Expand All @@ -393,19 +393,19 @@ private void addParentLookupValues(String parentTypeName,
.entrySet()
.stream()
.filter(entry -> inputFK.equals(entry.getValue()))
.forEach(entry -> inputLookupValues.computeIfAbsent(FieldKey.fromParts(entry.getKey(), fieldName), (s) -> new ArrayList<>()).add(lookupValue));
.forEach(entry -> inputLookupValues.computeIfAbsent(FieldKey.fromParts(entry.getKey(), fieldName), (s) -> new LinkedHashSet<>()).add(lookupValue));
}

// add to <Type>Inputs/<LookupField>
inputLookupValues.computeIfAbsent(FieldKey.fromParts(inputType, fieldName), (s) -> new ArrayList<>()).add(lookupValue);
inputLookupValues.computeIfAbsent(FieldKey.fromParts(inputType, fieldName), (s) -> new LinkedHashSet<>()).add(lookupValue);
// add to <Type>Inputs/<TypeName>/<LookupField>
inputLookupValues.computeIfAbsent(FieldKey.fromParts(inputType, parentTypeName, fieldName), (s) -> new ArrayList<>()).add(lookupValue);
inputLookupValues.computeIfAbsent(FieldKey.fromParts(inputType, parentTypeName, fieldName), (s) -> new LinkedHashSet<>()).add(lookupValue);
}
}

private void addAncestorLookupValues(
ExpRunItem parentObject,
Map<FieldKey, ArrayList<Object>> inputLookupValues,
Map<FieldKey, LinkedHashSet<Object>> inputLookupValues,
@Nullable NameGenerator altNameGenerator)
{
String parentLsid = parentObject.getLSID();
Expand Down Expand Up @@ -481,8 +481,8 @@ else if (parentObject instanceof ExpData expData)

if (!ancestorLookupValues.isEmpty())
{
inputLookupValues.putIfAbsent(ancestorFieldKey, new ArrayList<>());
List<Object> lookupValues = inputLookupValues.get(ancestorFieldKey);
inputLookupValues.putIfAbsent(ancestorFieldKey, new LinkedHashSet<>());
Set<Object> lookupValues = inputLookupValues.get(ancestorFieldKey);
for (Object lookupVal : ancestorLookupValues)
{
if (!lookupValues.contains(lookupVal))
Expand All @@ -497,7 +497,7 @@ private void addParentLookupContext(String parentTypeName/* already decoded */,
String parentName,
boolean isMaterialParent,
@Nullable Map<String, FieldKey> parentImportAliases,
Map<FieldKey, ArrayList<Object>> inputLookupValues,
Map<FieldKey, LinkedHashSet<Object>> inputLookupValues,
@Nullable NameGenerator altNameGenerator)
{
NameGenerator.ExpressionSummary expressionSummary = getExpressionSummary(altNameGenerator);
Expand Down Expand Up @@ -591,7 +591,7 @@ private Map<FieldKey, Object> additionalContext(@NotNull Map<String, Object> row
if (expressionSummary.hasParentLookup() || expressionSummary.hasParentInputs())
{
Map<FieldKey, Set<String>> inputs = new HashMap<>();
Map<FieldKey, ArrayList<Object>> inputLookupValues = new HashMap<>();
Map<FieldKey, LinkedHashSet<Object>> inputLookupValues = new HashMap<>();

inputs.put(FieldKey.fromParts(INPUT_PARENT), new LinkedHashSet<>());
inputs.put(FieldKey.fromParts(ExpData.DATA_INPUT_PARENT), new LinkedHashSet<>());
Expand Down Expand Up @@ -663,7 +663,7 @@ else if (value.isEmpty())
ctx.putAll(inputValues);

Map<FieldKey, Object> lookupValues = new HashMap<>();
inputLookupValues.forEach((key, value) -> lookupValues.put(key, value.size() > 1 ? value : (value.size() == 1 ? value.get(0) : null)));
inputLookupValues.forEach((key, value) -> lookupValues.put(key, value.size() > 1 ? value : (value.size() == 1 ? value.iterator().next() : null)));
ctx.putAll(lookupValues);
}

Expand Down Expand Up @@ -740,12 +740,12 @@ else if (value.isEmpty())
private void addParentLookupInput(String colName,
Object value,
@Nullable Map<String, FieldKey> parentImportAliases,
Map<FieldKey, ArrayList<Object>> inputLookupValues,
Map<FieldKey, LinkedHashSet<Object>> inputLookupValues,
@Nullable NameGenerator altNameGenerator)
{
String prefix = null;
String dataType = null;
if (ALIQUOTED_FROM_INPUT.equalsIgnoreCase(colName))
if (isAliquotedFromColumn(colName))
{
prefix = ExpMaterial.MATERIAL_INPUT_PARENT;
dataType = getParentTable() != null ? getParentTable().getName() : null;
Expand Down Expand Up @@ -791,7 +791,7 @@ private void addInputs(String colName,
String[] parts = colName.split("/", 2);
String prefix = null;
String decodedDataType = null;
if (ALIQUOTED_FROM_INPUT.equalsIgnoreCase(colName))
if (isAliquotedFromColumn(colName))
{
prefix = ExpMaterial.MATERIAL_INPUT_PARENT;
decodedDataType = getParentTable() != null ? getParentTable().getName() : null;
Expand Down
1 change: 1 addition & 0 deletions api/src/org/labkey/api/exp/api/ExpMaterial.java
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Expand Up @@ -35,6 +35,7 @@ public interface ExpMaterial extends ExpRunItem
String MATERIAL_INPUTS_PREFIX_LC = MATERIAL_INPUTS_PREFIX.toLowerCase();
String MATERIAL_OUTPUT_CHILD = "MaterialOutputs";
String ALIQUOTED_FROM_INPUT = "AliquotedFrom";
String ALIQUOTED_FROM_INPUT_LABEL = "Aliquoted From";

@Nullable
ExpSampleType getSampleType();
Expand Down
10 changes: 10 additions & 0 deletions api/src/org/labkey/api/exp/api/ExpSampleType.java
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Expand Up @@ -18,6 +18,7 @@

import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerFilter;
import org.labkey.api.exp.ExperimentException;
Expand Down Expand Up @@ -242,6 +243,15 @@ String createSampleName(@NotNull Map<String, Object> rowMap,

@NotNull Map<String, String> getImportAliases() throws IOException;

// Issue 53063: support "Aliquoted From"
@NotNull
default Map<String, String> getImportAliasesIncludingAliquot() throws IOException
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@labkey-susanh labkey-susanh Oct 7, 2025

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Add an issue number reference here? Or with one of these updates (not sure which is the most obvious), just so it's easier to find what's changed for this issue.

{
Map<String, String> aliases = new CaseInsensitiveHashMap<>(getImportAliases());
aliases.put(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL, ExpMaterial.ALIQUOTED_FROM_INPUT);
return aliases;
}

@NotNull Map<String, String> getRequiredImportAliases() throws IOException;

@NotNull Map<String, Map<String, Object>> getImportAliasMap() throws IOException;
Expand Down
6 changes: 6 additions & 0 deletions api/src/org/labkey/api/exp/api/ExperimentService.java
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Expand Up @@ -506,6 +506,12 @@ static boolean isInputOutputColumn(String columnName)
ExpMaterial.MATERIAL_OUTPUT_CHILD.equalsIgnoreCase(prefix);
}

static boolean isAliquotedFromColumn(String columnName)
{
return ExpMaterial.ALIQUOTED_FROM_INPUT.equalsIgnoreCase(columnName) ||
ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL.equalsIgnoreCase(columnName);
}

// convert MaterialInputs/Blood/Type to MaterialInputs/Blood$SType
static @Nullable String getEncodedLineageKey(String inputColumn /*not encoded*/)
{
Expand Down
1 change: 1 addition & 0 deletions api/src/org/labkey/api/query/QueryUpdateService.java
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Expand Up @@ -109,6 +109,7 @@ enum ConfigParameters
SkipRequiredFieldValidation, // (Bool) skip validation of required fields, used during import when the import of data happens in two hitches (e.g., samples in one file and sample statuses in a second)
BulkLoad, // (Bool) skips detailed auditing
CheckForCrossProjectData, // (Bool) Check if data belong to other projects
ProcessingPartition, // (Bool) Importing a partitioned file from original file
SkipInsertOptionValidation, // (Bool) Skip assert(supportsInsertOption(context.getInsertOption())) for special scenarios (e.g., folder import uses merge action that's otherwise not supported for a table),
PreferPKOverObjectUriAsKey, // (Bool) Prefer getPkColumnNames instead of getObjectURIColumnName to use as keys
SkipReselectRows, // (Bool) If true, skip qus.getRows and use raw returned rows. Applicable for CommandType.insert/insertWithKeys/update/updateChangingKeys
Expand Down
4 changes: 4 additions & 0 deletions experiment/src/org/labkey/experiment/ExpDataIterators.java
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Expand Up @@ -162,6 +162,7 @@
import static org.labkey.api.exp.api.ExpData.DATA_INPUTS_PREFIX_LC;
import static org.labkey.api.exp.api.ExpData.DATA_INPUT_PARENT;
import static org.labkey.api.exp.api.ExpMaterial.ALIQUOTED_FROM_INPUT;
import static org.labkey.api.exp.api.ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL;
import static org.labkey.api.exp.api.ExpMaterial.MATERIAL_INPUTS_PREFIX_LC;
import static org.labkey.api.exp.api.ExpMaterial.MATERIAL_INPUT_PARENT;
import static org.labkey.api.exp.api.ExpRunItem.INPUTS_PREFIX_LC;
Expand Down Expand Up @@ -2591,6 +2592,7 @@ public boolean next() throws BatchValidationException
{
_context.setCrossTypeImport(false);
_context.setCrossFolderImport(false);
_context.putConfigParameter(QueryUpdateService.ConfigParameters.ProcessingPartition, true);

boolean hasCrossFolderImport = false;

Expand All @@ -2610,6 +2612,7 @@ public boolean next() throws BatchValidationException
if (_isCrossFolder && !_context.getInsertOption().updateOnly && hasCrossFolderImport) // all updates are cross-folder due to lack of Container column
SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, _isSamples ? "sampleImport" : "dataClassImport", "multiFolderImport");

_context.putConfigParameter(QueryUpdateService.ConfigParameters.ProcessingPartition, false);
_context.setCrossTypeImport(_isCrossType);
_context.setCrossFolderImport(_isCrossFolder);
}
Expand Down Expand Up @@ -2861,6 +2864,7 @@ private TypeData createSampleHeaderRow(ExpSampleTypeImpl sampleType, Container c
Map<String, String> aliasMap = sampleType.getImportAliases();
validFields.addAll(aliasMap.keySet());
validFields.add(ALIQUOTED_FROM_INPUT);
validFields.add(ALIQUOTED_FROM_INPUT_LABEL);
validFields.add("StorageUnit");
validFields.add("Storage Unit");
validFields.add("StorageUnitLabel");
Expand Down
26 changes: 26 additions & 0 deletions experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java
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Expand Up @@ -1370,6 +1370,32 @@ else if (name != null)
return dataRow;
}


@Override
protected Map<String, Object> updateRow(User user, Container container, Map<String, Object> row, @NotNull Map<String, Object> oldRow, boolean allowOwner, boolean retainCreation)
throws InvalidKeyException, ValidationException, QueryUpdateServiceException, SQLException
{
Map<String, Object> result = super.updateRow(user, container, row, oldRow, allowOwner, retainCreation);

// add MaterialInput/DataInputs field from parent alias
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@labkey-susanh labkey-susanh Oct 7, 2025

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I'm unclear why this wasn't necessary before. Can you enlighten me?

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@XingY XingY Oct 7, 2025 •
edited
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There was a bug that row by row update using alias gets silently ignored. It's reproducible only from API, since our UI will never send the request using alias, and file import will never hit the row by row code. Due to its narrow repro, I didn't create a separate issue for it. In a way, one could argue ignoring import alias for query api update is per design, since this feature was called importAliases.

try
{
Map<String, String> parentAliases = _dataClass.getImportAliases();
for (String alias : parentAliases.keySet())
{
if (row.containsKey(alias))
result.put(parentAliases.get(alias), result.get(alias));
}
}
catch (IOException e)
{
throw new RuntimeException(e);
}

return result;

}

@Override
protected Map<String, Object> _update(User user, Container c, Map<String, Object> row, Map<String, Object> oldRow, Object[] keys) throws SQLException, ValidationException
{
Expand Down
2 changes: 1 addition & 1 deletion experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java
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Expand Up @@ -1725,7 +1725,7 @@ public DataIteratorBuilder persistRows(DataIteratorBuilder data, DataIteratorCon
// TODO: subclass PersistDataIteratorBuilder to index Materials! not DataClass!
try
{
var persist = new ExpDataIterators.PersistDataIteratorBuilder(data, this, propertiesTable, _ss, getUserSchema().getContainer(), getUserSchema().getUser(), _ss.getImportAliases(), sampleTypeObjectId)
var persist = new ExpDataIterators.PersistDataIteratorBuilder(data, this, propertiesTable, _ss, getUserSchema().getContainer(), getUserSchema().getUser(), _ss.getImportAliasesIncludingAliquot(), sampleTypeObjectId)
.setFileLinkDirectory(SAMPLETYPE_FILE_DIRECTORY);
ExperimentServiceImpl experimentServiceImpl = ExperimentServiceImpl.get();
SearchService.TaskIndexingQueue queue = SearchService.get().defaultTask().getQueue(getContainer(), SearchService.PRIORITY.modified);
Expand Down
73 changes: 65 additions & 8 deletions experiment/src/org/labkey/experiment/api/ExpSampleTypeTestCase.jsp
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Expand Up @@ -468,23 +468,80 @@ public void testNameExpression() throws Exception

List<Map<String, Object>> aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("aliquotedFrom", expectedName1, "AliquotCount", 10));
aliquotRows.add(CaseInsensitiveHashMap.of("Aliquotedfrom", expectedName2, "aliquotCount", 5));
aliquotRows.add(CaseInsensitiveHashMap.of("ALIQUOTEDFROM", expectedName1, "Aliquotcount", 15));
aliquotRows.add(CaseInsensitiveHashMap.of("AliquotedFrom", expectedName3, "ALIQUOTCOUNT", 2));

List<Map<String, Object>> aliquots = insertSampleRows(sampleTypeName, aliquotRows);

assertExpectedName(st, expectedName1 + "-ALI-0004");
assertEquals(expectedName1, aliquots.get(0).get("AliquotedFrom"));

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("Aliquotedfrom", expectedName2, "aliquotCount", 5));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName2 + "-ALI-0005");
assertEquals(expectedName2, aliquots.get(1).get("aliquotedFrom"));
assertEquals(expectedName2, aliquots.get(0).get("aliquotedFrom"));

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("ALIQUOTEDFROM", expectedName1, "Aliquotcount", 15));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName1 + "-ALI-0006");
assertEquals(expectedName1, aliquots.get(2).get("aliquotedfrom"));
assertEquals(expectedName1, aliquots.get(0).get("aliquotedfrom"));

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("AliquotedFrom", expectedName3, "ALIQUOTCOUNT", 2));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName3 + "-ALI-0007");
assertEquals(expectedName3, aliquots.get(3).get("ALIQUOTEDFROM"));
assertEquals(expectedName3, aliquots.get(0).get("ALIQUOTEDFROM"));

// Issue 53063: Support "Aliquoted From"
aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("Aliquoted From", expectedName2, "ALIQUOTCOUNT", 2));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName2 + "-ALI-0008");
assertEquals(expectedName2, aliquots.get(0).get("ALIQUOTEDFROM"));

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("aliquoted from", expectedName3, "ALIQUOTCOUNT", 3));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName3 + "-ALI-0009");
assertEquals(expectedName3, aliquots.get(0).get("aliquotedFrom"));

// test the default aliquot naming pattern (${${AliquotedFrom}-:withCounter}
st.setAliquotNameExpression("");
st.save(user);

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("aliquotedFrom", expectedName1));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName1 + "-1");
assertEquals(expectedName1, aliquots.get(0).get("AliquotedFrom"));

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("Aliquotedfrom", expectedName1));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName1 + "-2");
assertEquals(expectedName1, aliquots.get(0).get("aliquotedFrom"));

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("ALIQUOTEDFROM", expectedName1));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName1 + "-3");
assertEquals(expectedName1, aliquots.get(0).get("aliquotedfrom"));

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("AliquotedFrom", expectedName1));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName1 + "-4");
assertEquals(expectedName1, aliquots.get(0).get("ALIQUOTEDFROM"));

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("Aliquoted From", expectedName1));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName1 + "-5");
assertEquals(expectedName1, aliquots.get(0).get("ALIQUOTEDFROM"));

aliquotRows = new ArrayList<>();
aliquotRows.add(CaseInsensitiveHashMap.of("aliquoted from", expectedName1));
aliquots = insertSampleRows(sampleTypeName, aliquotRows);
assertExpectedName(st, expectedName1 + "-6");
assertEquals(expectedName1, aliquots.get(0).get("aliquotedFrom"));
}

@Test
Expand Down
3 changes: 2 additions & 1 deletion experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
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Expand Up @@ -10252,6 +10252,7 @@ else if (inputColumns != null)
allColumns.addAll(inputColumns);

Map<String, String> parentAliasColumnMap = new CaseInsensitiveHashMap<>();
parentAliasColumnMap.put(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL, ExpMaterial.ALIQUOTED_FROM_INPUT);
try
{
if (currentDataType instanceof ExpDataClass dataClass)
Expand All @@ -10270,7 +10271,7 @@ else if (currentDataType instanceof ExpSampleType sampleType)
String columnName = inputColName;
if (parentAliasColumnMap.containsKey(columnName))
columnName = parentAliasColumnMap.get(columnName);
if (ExperimentService.isInputOutputColumn(columnName) || "parent".equalsIgnoreCase(columnName))
if (ExperimentService.isInputOutputColumn(columnName) || ExperimentService.isAliquotedFromColumn(columnName) || "parent".equalsIgnoreCase(columnName))
{
if (seenColumns.contains(columnName))
throw new ApiUsageException(String.format(DUPLICATE_COLUMN_IN_DATA_ERROR, columnName));
Expand Down
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