Support additional unit types #7243

XingY · 2025-12-03T17:40:33Z

Rationale

This pull request adds support for additional unit types in the sample type system, particularly extending the Count kind of quantity with new unit types (pcs, pack, blocks, slides, cells, box, kit, tests, bottle) and expanding mass units to include smaller units (ug, ng).

Related Pull Requests

Changes

Extended Count unit types to support real-world counting units beyond generic "unit" and "count"
Enhanced mass unit precision scales to handle very small measurements (picogram to megagram range)
Implemented optimized SQL-based rollup calculations for samples with display units to improve performance
Added validation logic to prevent incompatible unit changes on sample types with existing data

…ty initial amount

labkey-susanh · 2025-12-04T22:05:22Z

api/src/org/labkey/api/ontology/Unit.java

            "count", "count"),
+    pcs(KindOfQuantity.Count, unit, 1.0, 2, "pcs",
+            Quantity.class,
+            "pcs", "pcs"),


I think singular here is "piece", but might want to confirm that with @labkey-hannah.

Agreed, we should switch this to "piece"/"pieces"

labkey-susanh · 2025-12-04T22:10:02Z

api/src/org/labkey/api/ontology/Unit.java

+            assertTrue(Unit.unit.isCompatible(Unit.bottle));
+            assertTrue(Unit.unit.isCompatible(Unit.blocks));
+            assertTrue(Unit.unit.isCompatible(Unit.box));
+            assertTrue(Unit.unit.isCompatible(Unit.slides));


There are some missing here. Not that I think there's risk or regression here, just for completeness.

labkey-susanh · 2025-12-04T22:14:57Z

experiment/src/client/test/integration/SampleTypeCrud.ispec.ts

+            {name: 'S-kg', amount: 4.56, units: 'kg'},
+        ], 'samples', sampleTypeMass, topFolderOptions, editorUserOptions);
+
+        // check for storedamount in g


check for raw amount in g and display amount in ug

labkey-susanh · 2025-12-04T22:26:22Z

experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java

            {
                var ret = wrapColumn(alias, _rootTable.getColumn(AliquotVolume.name()));
-                ret.setLabel(ALIQUOT_VOLUME_LABEL);
+                ret.setLabel("Raw " + ALIQUOT_VOLUME_LABEL);


Would be good to use the label specified from the ExpMaterialTable.Column enum here an for the other new columns so the labels get properly reserved.

labkey-susanh · 2025-12-04T22:28:45Z

experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java

+                {
+                    SampleTypeAmountDisplayColumn columnInfo = new SampleTypeAmountDisplayColumn(this, Column.AvailableAliquotVolume.name(), Column.AliquotUnit.name(), AVAILABLE_ALIQUOT_VOLUME_LABEL, Collections.emptySet(), typeUnit);
+                    columnInfo.setDisplayColumnFactory(colInfo -> new SampleTypeAmountPrecisionDisplayColumn(colInfo, typeUnit));
+                    columnInfo.setDescription("The total amount of this sample's aliquots that's available, in the display unit for the sample type, currently on hand.");


This doesn't parse very well. Perhaps "The total amount of this sample's available aliquots currently on hand, in the display unit for the sample type."

labkey-susanh · 2025-12-04T22:32:42Z

experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java

+                    public void addQueryFieldKeys(Set<FieldKey> keys)
+                    {
+                        super.addQueryFieldKeys(keys);
+                        keys.add(FieldKey.fromParts(AvailableAliquotVolume));


Same here AvailableAliquotVolume.fieldKey()

labkey-susanh · 2025-12-04T22:33:45Z

api/src/org/labkey/api/exp/query/ExpMaterialTable.java

        QueryableInputs,
+        RawAliquotUnit,
+        RawAliquotVolume,
+        RawAvailableAliquotVolume,


Should set the labels for these fields here.

labkey-susanh · 2025-12-04T22:49:45Z

experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java

+                TableInfo tableInfo = ExperimentService.get().getTinfoMaterial();

-                ListUtils.partition(sampleAliquotAmountsList, 1000).forEach(sublist ->
+                ListUtils.partition(new ArrayList<>(withAmountsParents), 1000).forEach(sublist ->


Do you need a new array here? Can you not partition withAmountsParents?

A list is needed, but withAmountsParents is a Collection.

labkey-susanh · 2025-12-04T22:58:38Z

experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java

        String totalUnitsStr;
        if (!StringUtils.isEmpty(sampleTypeUnitsStr))
            totalUnitsStr = sampleTypeUnitsStr;
+        else if (hasSameAliquotUnit && !StringUtils.isEmpty(volumeUnits.get(0).unit)) // if all aliquots have the same unit, prefer it over parent's unit


Doesn't this lead to divergence from base units?

Not really. In the case of an absent display unit, we don't know if aliquot unit or parent unit would be more likely to be in base unit. We don't do conversion when there is no sampleTypeUnitsStr.

Oh right. Missed that this is the sampletypeUnitStr is empty case.

labkey-susanh · 2025-12-04T22:59:41Z

experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java

    }

-    private Map<Long, Pair<Integer, String>> getSampleAvailableAliquotCounts(Collection<Long> sampleIds, Collection<Long> availableSampleStates, boolean useRootMaterialLSID) throws SQLException
+    private Map<Long, Pair<Integer, String>> getSampleAvailableAliquotCounts(Collection<Long> sampleIds, Collection<Long> availableSampleStates) throws SQLException


Nice to get rid of the useRootMaterialLSID complexity.

XingY added 13 commits November 25, 2025 21:34

Support additional unit types

2fc9a02

fix test

fee03af

jest integration tests

9b41448

crlf

4bd66f9

Support additional unit types

0f5d249

crlf

a46c8ec

Aliquot amount in display unit

e896781

Validate amount range on bulk/detail form. Show delta warning for emp…

40e2b23

…ty initial amount

Merge branch 'develop' into fb_unitTypes

4173429

bug fixes and test updates

1e21a46

fix tests

345e495

Merge branch 'develop' into fb_unitTypes

d292860

CRLF

59500c1

This was referenced Dec 3, 2025

Amounts and units polish, part 2 LabKey/labkey-ui-components#1902

Open

Update domain designer to select unit kind before selecting unit LabKey/testAutomation#2803

Open

fix metrics

4994155

XingY requested a review from Copilot December 3, 2025 22:00

Copilot started reviewing on behalf of XingY December 3, 2025 22:00 View session

Copilot finished reviewing on behalf of XingY December 3, 2025 22:02

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XingY added 4 commits December 3, 2025 14:36

remove support for pg unit

d93154b

clean

59893fd

Merge branch 'develop' into fb_unitTypes

15de63f

Merge branch 'develop' into fb_unitTypes

d3560fd

XingY requested a review from labkey-susanh December 4, 2025 18:21

labkey-susanh requested changes Dec 4, 2025

View reviewed changes

bug fixes

d87cd54

XingY requested a review from labkey-susanh December 5, 2025 05:25

XingY added 2 commits December 5, 2025 10:09

fix tests

23d06d3

fix updating other unit from sample detail panel

30c5a6d

Support additional unit types #7243

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Support additional unit types #7243

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XingY commented Dec 3, 2025 •

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