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GitHub Issue #443: AbstractAssayTsvDataHandler to lookup field values by titleColumn before primaryKey in checkData() #7226

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Merged
cnathe merged 1 commit into from
Nov 25, 2025
Merged

GitHub Issue #443: AbstractAssayTsvDataHandler to lookup field values by titleColumn before primaryKey in checkData() #7226

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12 changes: 9 additions & 3 deletions api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -706,7 +706,8 @@ private DataIterator checkData(
DomainProperty wellLocationPropFinder = null;
DomainProperty wellLsidPropFinder = null;

RemapCache cache = new RemapCache();
RemapCache cacheWithoutPkLookup = new RemapCache();
RemapCache cacheWithPkLookup = new RemapCache();
Map<DomainProperty, TableInfo> remappableLookup = new HashMap<>();
Map<Long, ExpMaterial> materialCache = new LongHashMap<>();
Map<Long, Map<String, Long>> plateWellCache = new LongHashMap<>();
Expand Down Expand Up @@ -879,7 +880,12 @@ else if (entry.getKey().equalsIgnoreCase(ProvenanceService.PROVENANCE_INPUT_PROP
{
String s = o instanceof String ? (String) o : o.toString();
TableInfo lookupTable = remappableLookup.get(pd);
Object remapped = cache.remap(lookupTable, s, true);

// GitHub Issue #443: similar to LookupResolutionType.alternateThenPrimaryKey, we want to check if the string value remaps using alternate keys (titleColumn) first
Object remapped = cacheWithoutPkLookup.remap(lookupTable, s, false);
if (remapped == null)
remapped = cacheWithPkLookup.remap(lookupTable, s, true);

if (remapped == null)
{
if (SAMPLE_CONCEPT_URI.equals(pd.getConceptURI()))
Expand Down Expand Up @@ -1026,7 +1032,7 @@ else if (o instanceof MvFieldWrapper mvWrapper)
try
{
if (material == null)
material = exp.findExpMaterial(lookupContainer, user, materialName, byNameSS, cache, materialCache);
material = exp.findExpMaterial(lookupContainer, user, materialName, byNameSS, cacheWithoutPkLookup, materialCache);
}
catch (ValidationException ve)
{
Expand Down
23 changes: 22 additions & 1 deletion study/test/src/org/labkey/test/tests/study/AssayTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1036,7 +1036,10 @@ public void testAssayLookupValidatorConversion()
_listHelper.bulkImportData(TestDataUtils.tsvStringFromRowMaps(List.of(
Map.of(valueField.getName(), "One"),
Map.of(valueField.getName(), "Two"),
Map.of(valueField.getName(), "123")
Map.of(valueField.getName(), "123"),
// GitHub Issue #443: value is the primary key for another row
Map.of(valueField.getName(), "5"), // pk = 4
Map.of(valueField.getName(), "6") // pk = 5
), List.of(valueField.getName()), true));

log("Create an assay with a results lookup field to the list, with lookup validator set");
Expand All @@ -1060,6 +1063,24 @@ public void testAssayLookupValidatorConversion()
.setLookupValidatorEnabled(false);
designerPage.clickFinish();
verifyAssayImportForLookupValidator(ISSUE_53625_ASSAY, lookupField, "RunWithoutLookupValidator", false);

log("GitHub Issue #443: Verify that importing a value that is also a primary key maps to the titleColumn value");
verifyAssayImportForPKValueThatIsTitleColumn(ISSUE_53625_ASSAY, lookupField, "RunWithPKandTitleColumn");
}

private void verifyAssayImportForPKValueThatIsTitleColumn(String assayName, FieldInfo lookupField, String runName)
{
String runDataStr = TestDataUtils.tsvStringFromRowMaps(List.of(
Map.of(lookupField.getName(), "4"), // pk 4, value 5
Map.of(lookupField.getName(), "5"), // pk 4, value 5
Map.of(lookupField.getName(), "6")), // pk 5, value 6
List.of(lookupField.getName()), true
);
importAssayData(assayName, runName, runDataStr);
clickAndWait(Locator.linkWithText(runName));
DataRegionTable dataTable = new DataRegionTable("Data", getDriver());
checker().verifyEquals("Incorrect number of results shown.", 3, dataTable.getDataRowCount());
checker().fatal().verifyEquals("Lookup values not as expected.", List.of("5", "5", "6"), dataTable.getColumnDataAsText(lookupField.getLabel()));
}

private void verifyAssayImportForLookupValidator(String assayName, FieldInfo lookupField, String runName, boolean validatorOn)
Expand Down