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GitHub Issue 827: Cannot aliquot samples using lineage search naming pattern #7399

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Merged
XingY merged 4 commits into from
Feb 13, 2026
Merged

GitHub Issue 827: Cannot aliquot samples using lineage search naming pattern #7399

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0b24fe0
GitHub Issue 827: Cannot aliquot samples where parent sample has a co…
XingY Feb 8, 2026
5d53ef1
use string util
XingY Feb 8, 2026
ce703ce
fix build
XingY Feb 8, 2026
577db2f
Merge remote-tracking branch 'origin/develop' into fb_aliquotComma
XingY Feb 13, 2026
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11 changes: 11 additions & 0 deletions api/src/org/labkey/api/data/NameGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
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 java.io.IOException;
Expand Down Expand Up @@ -78,6 +79,7 @@
import java.util.stream.Stream;

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.ExpRunItem.INPUT_PARENT;
import static org.labkey.api.exp.api.ExperimentJSONConverter.DATA_INPUTS;
import static org.labkey.api.exp.api.ExperimentJSONConverter.MATERIAL_INPUTS;
Expand Down Expand Up @@ -739,6 +741,15 @@ public static Stream<String> parentNames(Object value, String parentColName, TSV
if (StringUtils.isEmpty((valueStr).trim()))
return Stream.empty();

// GitHub Issue 827: Cannot aliquot samples where parent sample has a comma in the name AND the aliquot naming pattern references ancestor lineage
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@labkey-susanh labkey-susanh Feb 13, 2026

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Good to have the GitHub Issue reference here, but I think it would be better to explain in the text why there is special handling for ALIQUOTED_FROM here (you can get it from the PR rationale, but it takes an extra hop).

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@XingY XingY Feb 13, 2026

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Good reminder. I'll add the explanation in my other branch.

if (ALIQUOTED_FROM_INPUT.equalsIgnoreCase(parentColName) || ALIQUOTED_FROM_INPUT_LABEL.equalsIgnoreCase(parentColName))
{
boolean isQuoted = (valueStr.contains(",") || valueStr.contains("\n") || valueStr.contains("\r")) && (valueStr.startsWith("\"") && valueStr.endsWith("\""));
if (isQuoted)
valueStr = StringUtilsLabKey.unquoteString(valueStr).trim();
return Stream.of(valueStr);
}

// Issue 44841: The names of the parents may include commas, so we parse the set of parent names
// using TabLoader instead of just splitting on the comma.
boolean likelyAlreadyQuoted = valueStr.contains(",") || valueStr.contains("\n") || valueStr.contains("\r") || (valueStr.startsWith("\"") && valueStr.endsWith("\""));
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