Support additional unit types

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

@@ -52,6 +52,9 @@ enum Column
         Properties,
         Property,
         QueryableInputs,
+        RawAliquotUnit,
+        RawAliquotVolume,
+        RawAvailableAliquotVolume,
         RawAmount(true),
         RawUnits,
         RootMaterialRowId,

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

@@ -29,7 +29,7 @@ public List<Unit> getCommonUnits()
         @Override
         public List<Unit> getCommonUnits()
         {
-            return List.of(Unit.kg, Unit.g, Unit.mg);
+            return List.of(Unit.kg, Unit.g, Unit.mg, Unit.ug, Unit.ng);
         }
     },
 
@@ -39,7 +39,7 @@ public List<Unit> getCommonUnits()
         @Override
         public List<Unit> getCommonUnits()
         {
-            return List.of(Unit.unit);
+            return List.of(Unit.unit, Unit.blocks, Unit.bottle, Unit.box, Unit.cells, Unit.kit, Unit.pack, Unit.pcs, Unit.slides, Unit.tests);
         }
     };
 

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

@@ -465,6 +465,10 @@ public void testParse()
             assertEquals(Quantity.of(0, Unit.count), parse("0 units"));
             assertEquals(Quantity.of(0, Unit.count), parse("0count"));
 
+            assertEquals(Quantity.of(1, Unit.count), parse("1", Unit.box));
+            assertEquals(Quantity.of(1, Unit.unit), parse("1", Unit.blocks));
+            assertEquals(Quantity.of(1, Unit.cells), parse("1", Unit.tests));
+
             assertEquals(parse("1000mg", Unit.g), parse("0.001kg", Unit.g));
             assertEquals(parse(" 1000mg", Unit.g), parse("0.001kg", Unit.g));
             assertEquals(parse("1000mg ", Unit.g), parse("0.001kg", Unit.g));

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

@@ -19,6 +19,33 @@ public enum Unit
     count(KindOfQuantity.Count, unit, 1.0, 2, "count",
             Quantity.class,
             "count", "count"),
+    pcs(KindOfQuantity.Count, unit, 1.0, 2, "pcs",
+            Quantity.class,
+            "pcs", "pcs"),
+    pack(KindOfQuantity.Count, unit, 1.0, 2, "pack",
+            Quantity.class,
+            "pack", "packs"),
+    blocks(KindOfQuantity.Count, unit, 1.0, 2, "blocks",
+            Quantity.class,
+            "block", "blocks"),
+    slides(KindOfQuantity.Count, unit, 1.0, 2, "slides",
+            Quantity.class,
+            "slide", "slides"),
+    cells(KindOfQuantity.Count, unit, 1.0, 2, "cells",
+            Quantity.class,
+            "cell", "cells"),
+    box(KindOfQuantity.Count, unit, 1.0, 2, "box",
+            Quantity.class,
+            "box", "boxes"),
+    kit(KindOfQuantity.Count, unit, 1.0, 2, "kit",
+            Quantity.class,
+            "kit", "kits"),
+    tests(KindOfQuantity.Count, unit, 1.0, 2, "tests",
+            Quantity.class,
+            "test", "tests"),
+    bottle(KindOfQuantity.Count, unit, 1.0, 2, "bottle",
+            Quantity.class,
+            "bottle", "bottles"),
 
     mL(KindOfQuantity.Volume, null, 1e0, 6, "mL",
             Quantity.Volume_ml.class,
@@ -51,27 +78,27 @@ public enum Unit
             "picoliter", "picoliters",
             "pl", "picolitre", "picolitres"),
 
-    g(KindOfQuantity.Mass, null, 1e0, 9, "g",
+    g(KindOfQuantity.Mass, null, 1e0, 12, "g",
             Quantity.Mass_g.class,
             "gram", "grams"),
-    Mg(KindOfQuantity.Mass, g, 1e6, 12, "Mg",
+    Mg(KindOfQuantity.Mass, g, 1e6, 15, "Mg",
             Quantity.Mass_Megag.class,
             "megagram", "megagrams",
             "tonne", "tonnes"),
-    kg(KindOfQuantity.Mass, g, 1e3, 12, "kg",
+    kg(KindOfQuantity.Mass, g, 1e3, 15, "kg",
             Quantity.Mass_kg.class,
             "kilogram", "kilograms"),
-    mg(KindOfQuantity.Mass, g, 1e-3, 6, "mg",
+    mg(KindOfQuantity.Mass, g, 1e-3, 9, "mg",
             Quantity.Mass_mg.class,
             "milligram", "milligrams"),
-    ug(KindOfQuantity.Mass, g, 1e-6, 3, "ug",
+    ug(KindOfQuantity.Mass, g, 1e-6, 6, "ug",
             Quantity.Mass_ug.class,
             "microgram", "micrograms",
         "μg"),
     ng(KindOfQuantity.Mass, g, 1e-9, 3, "ng",
             Quantity.Mass_ng.class,
             "nanogram", "nanograms"),
-    pg(KindOfQuantity.Mass, g, 1e-12, 3, "pg",
+    pg(KindOfQuantity.Mass, g, 1e-12, 0, "pg",
             Quantity.Mass_pg.class,
             "picogram", "picograms");
 
@@ -206,6 +233,7 @@ public void testIsBase()
             assertFalse(Unit.kg.isBase());
             assertTrue(Unit.unit.isBase());
             assertFalse(Unit.count.isBase());
+            assertFalse(Unit.bottle.isBase());
         }
 
         @Test
@@ -217,6 +245,12 @@ public void testIsCompatible()
             assertTrue(Unit.g.isCompatible(Unit.mg));
             assertFalse(Unit.g.isCompatible(Unit.mL));
             assertTrue(Unit.unit.isCompatible(Unit.count));
+            assertTrue(Unit.unit.isCompatible(Unit.pcs));
+            assertTrue(Unit.unit.isCompatible(Unit.pack));
+            assertTrue(Unit.unit.isCompatible(Unit.bottle));
+            assertTrue(Unit.unit.isCompatible(Unit.blocks));
+            assertTrue(Unit.unit.isCompatible(Unit.box));
+            assertTrue(Unit.unit.isCompatible(Unit.slides));
             assertFalse(Unit.unit.isCompatible(Unit.mL));
             assertFalse(Unit.mL.isCompatible(null));
         }

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

@@ -974,6 +974,12 @@ describe('Amount/Unit CRUD', () => {
         expect(errorMsg.text).toContain(NO_AMOUNT_ERROR);
         errorMsg = await ExperimentCRUDUtils.importSample(server, "Name\tStoredAmount\tUnits\nData1\t1.1\tL", dataType, "INSERT", topFolderOptions, editorUserOptions);
         expect(errorMsg.text).toContain(INCOMPATIBLE_ERROR);
+        errorMsg = await ExperimentCRUDUtils.importSample(server, "Name\tStoredAmount\tUnits\nData1\t1.1\tunit", dataType, "INSERT", topFolderOptions, editorUserOptions);
+        expect(errorMsg.text).toContain('Units value (unit) is not compatible with the ' + dataType + ' display units (g).');
+        errorMsg = await ExperimentCRUDUtils.importSample(server, "Name\tStoredAmount\tUnits\nData1\t1.1\tcells", dataType, "INSERT", topFolderOptions, editorUserOptions);
+        expect(errorMsg.text).toContain('Units value (cells) is not compatible with the ' + dataType + ' display units (g).');
+        errorMsg = await ExperimentCRUDUtils.importSample(server, "Name\tStoredAmount\tUnits\nData1\t1.1\tbogus", dataType, "INSERT", topFolderOptions, editorUserOptions);
+        expect(errorMsg.text).toContain('Unsupported Units value (bogus). Supported values are: kg, g, mg, ug, ng.');
         errorMsg = await ExperimentCRUDUtils.importSample(server, "Name\tStoredAmount\tUnits\nData1\t-1.1\tkg", dataType, "INSERT", topFolderOptions, editorUserOptions);
         expect(errorMsg.text).toContain(NEGATIVE_ERROR);
         errorMsg = await ExperimentCRUDUtils.importCrossTypeData(server, "Name\tStoredAmount\tUnits\tSampleType\nData1\t-1.1\tkg\t" + dataType ,'IMPORT', topFolderOptions, adminOptions, true);
@@ -1085,5 +1091,235 @@ describe('Amount/Unit CRUD', () => {
 
     });
 
+    it ("Test units conversion on insert/update", async () => {
+        const sampleTypeMass = 'SampleTypeWithMassUnits';
+        const sampleTypeVolume = 'SampleTypeWithVolumeUnits';
+        const sampleTypeCount = 'SampleTypeWithCountUnits';
+
+        const sampleTypeUnits = {
+            [sampleTypeMass]: 'ug',
+            [sampleTypeVolume]: 'L',
+            [sampleTypeCount]: 'unit'
+        };
+
+        for (const [dataType, unit] of Object.entries(sampleTypeUnits)) {
+            const createPayload = {
+                kind: 'SampleSet',
+                domainDesign: { name: dataType, fields: [{ name: 'Name' }] },
+                options: {
+                    name: dataType,
+                    metricUnit: unit
+                }
+            };
+            await server.post('property', 'createDomain', createPayload, {...topFolderOptions, ...designerReaderOptions}).expect(successfulResponse);
+        }
+
+        let sampleRowsWithUnits = await ExperimentCRUDUtils.insertRows(server, [
+            {name: 'S-ng', amount: 4.56, units: 'ng'},
+            {name: 'S-ug', amount: 4.56, units: 'ug'},
+            {name: 'S-mg', amount: 4.56, units: 'mg'},
+            {name: 'S-g', amount: 4.56, units: 'g'},
+            {name: 'S-kg', amount: 4.56, units: 'kg'},
+        ], 'samples', sampleTypeMass, topFolderOptions, editorUserOptions);
+
+        // check for storedamount in g
+        let expectedRawAmounts : {} = {
+            'S-ng': 4.56e-9,
+            'S-ug': 4.56e-6,
+            'S-mg': 0.00456,
+            'S-g': 4.56,
+            'S-kg': 4560,
+        };
+        let expectedStoredAmounts : {} = {
+            'S-ng': 4.56e-3,
+            'S-ug': 4.56,
+            'S-mg': 4560,
+            'S-g': 4.56e6,
+            'S-kg': 4.56e9,
+        };
+
+        for (const sampleRow of sampleRowsWithUnits) {
+            const sampleName = caseInsensitive(sampleRow, 'name');
+            let sampleData = await ExperimentCRUDUtils.getSampleDataByName(server, sampleName, sampleTypeMass, 'StoredAmount,Units,RawAmount,RawUnits', topFolderOptions, readerUserOptions);
+            expect(caseInsensitive(sampleData, 'RawAmount')).toBeCloseTo(expectedRawAmounts[sampleName]);
+            expect(caseInsensitive(sampleData, 'StoredAmount')).toBeCloseTo(expectedStoredAmounts[sampleName]);
+            expect(caseInsensitive(sampleData, 'RawUnits')).toEqual('g');
+            expect(caseInsensitive(sampleData, 'Units')).toEqual('ug');
+            await server.post('query', 'updateRows', {
+                schemaName: 'samples',
+                queryName: sampleTypeMass,
+                rows: [{
+                    amount: 6.54,
+                    units: sampleName.substring(2),
+                    rowId: caseInsensitive(sampleRow, 'rowId')
+                }]
+            }, { ...topFolderOptions, ...editorUserOptions }).expect(successfulResponse);
+        }
+
+        expectedRawAmounts = {
+            'S-ng': 6.54e-9,
+            'S-ug': 6.54e-6,
+            'S-mg': 0.00654,
+            'S-g': 6.54,
+            'S-kg': 6540,
+        };
+        expectedStoredAmounts = {
+            'S-ng': 6.54e-3,
+            'S-ug': 6.54,
+            'S-mg': 6540,
+            'S-g': 6.54e6,
+            'S-kg': 6.54e9,
+        };
+        for (const sampleRow of sampleRowsWithUnits) {
+            const sampleName = caseInsensitive(sampleRow, 'name');
+            let sampleData = await ExperimentCRUDUtils.getSampleDataByName(server, sampleName, sampleTypeMass, 'StoredAmount,Units,RawAmount,RawUnits', topFolderOptions, readerUserOptions);
+            expect(caseInsensitive(sampleData, 'RawAmount')).toBeCloseTo(expectedRawAmounts[sampleName]);
+            expect(caseInsensitive(sampleData, 'StoredAmount')).toBeCloseTo(expectedStoredAmounts[sampleName]);
+            expect(caseInsensitive(sampleData, 'RawUnits')).toEqual('g');
+            expect(caseInsensitive(sampleData, 'Units')).toEqual('ug');
+        }
+
+        sampleRowsWithUnits = await ExperimentCRUDUtils.insertRows(server, [
+            {name: 'S-L', amount: 4.56, units: 'L'},
+            {name: 'S-mL', amount: 4.56, units: 'mL'},
+            {name: 'S-uL', amount: 4.56, units: 'uL'},
+        ], 'samples', sampleTypeVolume, topFolderOptions, editorUserOptions);
+
+        // check for storedamount in mL
+        expectedRawAmounts = {
+            'S-L': 4560,
+            'S-mL': 4.56,
+            'S-uL': 0.00456,
+        };
+        // stored amount is in L
+        expectedStoredAmounts = {
+            'S-L': 4.56,
+            'S-mL': 0.00456,
+            'S-uL': 4.56e-6,
+        }
+        for (const sampleRow of sampleRowsWithUnits) {
+            const sampleName = caseInsensitive(sampleRow, 'name');
+            const sampleData = await ExperimentCRUDUtils.getSampleDataByName(server, sampleName, sampleTypeVolume, 'StoredAmount,Units,RawAmount,RawUnits', topFolderOptions, readerUserOptions);
+            expect(caseInsensitive(sampleData, 'RawAmount')).toBeCloseTo(expectedRawAmounts[sampleName]);
+            expect(caseInsensitive(sampleData, 'StoredAmount')).toBeCloseTo(expectedStoredAmounts[sampleName]);
+            expect(caseInsensitive(sampleData, 'RawUnits')).toEqual('mL');
+            expect(caseInsensitive(sampleData, 'Units')).toEqual('L');
+        }
+
+        const countRows = [
+            {name: 'S-unit', amount: 4.56, units: 'unit'},
+            {name: 'S-pcs', amount: 4.56, units: 'pcs'},
+            {name: 'S-kit', amount: 4.56, units: 'kit'},
+            {name: 'S-cells', amount: 4.56, units: 'cells'}
+        ]
+        sampleRowsWithUnits = await ExperimentCRUDUtils.insertRows(server, countRows, 'samples', sampleTypeCount, topFolderOptions, editorUserOptions);
+
+        for (const sampleRow of sampleRowsWithUnits) {
+            const sampleName = caseInsensitive(sampleRow, 'name');
+            const usedUnit = sampleName.substring(2);
+            const sampleData = await ExperimentCRUDUtils.getSampleDataByName(server, sampleName, sampleTypeCount, 'StoredAmount,Units,RawAmount,RawUnits', topFolderOptions, readerUserOptions);
+            expect(caseInsensitive(sampleData, 'RawAmount')).toBeCloseTo(4.56);
+            expect(caseInsensitive(sampleData, 'StoredAmount')).toBeCloseTo(4.56);
+            expect(caseInsensitive(sampleData, 'RawUnits')).toEqual(usedUnit);
+            expect(caseInsensitive(sampleData, 'Units')).toEqual(usedUnit);
+
+            await server.post('query', 'updateRows', {
+                schemaName: 'samples',
+                queryName: sampleTypeCount,
+                rows: [{
+                    amount: 6.54,
+                    units: usedUnit,
+                    rowId: caseInsensitive(sampleRow, 'rowId')
+                }]
+            }, { ...topFolderOptions, ...editorUserOptions }).expect(successfulResponse);
+        }
+
+        for (const sampleRow of sampleRowsWithUnits) {
+            const sampleName = caseInsensitive(sampleRow, 'name');
+            const usedUnit = sampleName.substring(2);
+            const sampleData = await ExperimentCRUDUtils.getSampleDataByName(server, sampleName, sampleTypeCount, 'StoredAmount,Units,RawAmount,RawUnits', topFolderOptions, readerUserOptions);
+            expect(caseInsensitive(sampleData, 'RawAmount')).toBeCloseTo(6.54);
+            expect(caseInsensitive(sampleData, 'StoredAmount')).toBeCloseTo(6.54);
+            expect(caseInsensitive(sampleData, 'RawUnits')).toEqual(usedUnit);
+            expect(caseInsensitive(sampleData, 'Units')).toEqual(usedUnit);
+        }
+
+    })
+
+    async function verifyCountTypeAliquotRollup(sampleTypeName: string, hasSampleTypeDisplayUnit: boolean) {
+        const dataRows = [
+            {name: 'S-no-amount'},
+            {AliquotedFrom: 'S-no-amount', name: 'S-no-pcs1', amount: 2, units: 'pcs'},
+            {AliquotedFrom: 'S-no-amount', name: 'S-no-pcs2', amount: 2, units: 'pcs'},
+            {name: 'S-unit', amount: 1, units: 'unit'},
+            {AliquotedFrom: 'S-unit', name: 'S-unit-unit1', amount: 2, units: 'unit'},
+            {AliquotedFrom: 'S-unit', name: 'S-unit-unit2', amount: 2, units: 'unit'},
+            {name: 'S-pcs', amount: 1, units: 'pcs'},
+            {AliquotedFrom: 'S-pcs', name: 'S-pcs-pcs1', amount: 2, units: 'pcs'},
+            {AliquotedFrom: 'S-pcs', name: 'S-pcs-pcs2', amount: 2, units: 'pcs'},
+            {name: 'S-kit', amount: 1, units: 'kit'},
+            {AliquotedFrom: 'S-kit', name: 'S-kit-pcs1', amount: 2, units: 'pcs'},
+            {AliquotedFrom: 'S-kit', name: 'S-kit-pcs2', amount: 2, units: 'pcs'},
+            {name: 'S-cells', amount: 1, units: 'cells'},
+            {AliquotedFrom: 'S-cells', name: 'S-cells-pcs1', amount: 2, units: 'pcs'},
+            {AliquotedFrom: 'S-cells', name: 'S-cells-cells2', amount: 2, units: 'cells'},
+        ]
+
+        const insertedResults = await ExperimentCRUDUtils.insertRows(server, dataRows, 'samples', sampleTypeName, topFolderOptions, editorUserOptions);
+        const insertedMap = {};
+        for (const row of insertedResults) {
+            insertedMap[caseInsensitive(row, 'name')] = row;
+        }
+
+        let expectedAliquotUnit = {
+            'S-no-amount': 'pcs',
+            'S-unit': 'unit',
+            'S-pcs': 'pcs',
+            'S-kit': 'pcs',
+            'S-cells': hasSampleTypeDisplayUnit ? 'unit' : 'cells',
+        };
+
+        // for each expectedRollupAmounts
+        for (const [sampleName, expectedAliquotUnitValue] of Object.entries(expectedAliquotUnit)) {
+            let parentUnit = sampleName.substring(2);
+            if (parentUnit === 'no-amount') {
+                parentUnit = null;
+            }
+            const sampleData = await ExperimentCRUDUtils.getSampleDataByName(server, sampleName, sampleTypeName, 'Units,RawUnits,AliquotVolume,AliquotCount,AliquotUnit', topFolderOptions, readerUserOptions);
+            expect(caseInsensitive(sampleData, 'RawUnits')).toEqual(parentUnit);
+            expect(caseInsensitive(sampleData, 'Units')).toEqual(parentUnit);
+            expect(caseInsensitive(sampleData, 'AliquotVolume')).toEqual(4);
+            expect(caseInsensitive(sampleData, 'AliquotCount')).toEqual(2);
+            expect(caseInsensitive(sampleData, 'AliquotUnit')).toEqual(expectedAliquotUnitValue);
+
+        }
+    }
+
+    it ("Test aliquot rollup for count display unit", async () => {
+        let dataType = 'SampleTypeAliquotWithCountUnit';
+        let createPayload : {} = {
+            kind: 'SampleSet',
+            domainDesign: { name: dataType, fields: [{ name: 'Name' }] },
+            options: {
+                name: dataType,
+                metricUnit: 'unit'
+            }
+        };
+        await server.post('property', 'createDomain', createPayload, {...topFolderOptions, ...designerReaderOptions}).expect(successfulResponse);
+        await verifyCountTypeAliquotRollup(dataType, true);
+
+        dataType = 'SampleTypeAliquoNoDisplayUnit';
+        createPayload = {
+            kind: 'SampleSet',
+            domainDesign: { name: dataType, fields: [{ name: 'Name' }] },
+            options: {
+                name: dataType,
+            }
+        };
+        await server.post('property', 'createDomain', createPayload, {...topFolderOptions, ...designerReaderOptions}).expect(successfulResponse);
+        await verifyCountTypeAliquotRollup(dataType, false);
+
+    })
+
 });
 

experiment/src/org/labkey/experiment/ExperimentModule.java

@@ -740,6 +740,9 @@ SELECT COUNT(DISTINCT DD.DomainURI) FROM
                 results.put("sampleNegativeAmountCount", new SqlSelector(schema, "SELECT COUNT(*) FROM exp.material WHERE storedamount < 0").getObject(Long.class));
                 results.put("sampleUnitsDifferCount", new SqlSelector(schema, "SELECT COUNT(*) from exp.material m JOIN exp.materialSource s ON m.materialsourceid = s.rowid WHERE m.units != s.metricunit").getObject(Long.class));
                 results.put("sampleTypesWithoutUnitsCount", new SqlSelector(schema, "SELECT COUNT(*) from exp.materialSource WHERE category IS NULL AND metricunit IS NULL").getObject(Long.class));
+                results.put("sampleTypesWithMassTypeUnit", new SqlSelector(schema, "SELECT COUNT(*) from exp.materialSource WHERE category IS NULL AND metricunit IN ('kg', 'g', 'mg', 'ug', 'ng')").getObject(Long.class));
+                results.put("sampleTypesWithVolumeTypeUnit", new SqlSelector(schema, "SELECT COUNT(*) from exp.materialSource WHERE category IS NULL AND metricunit IN ('L', 'mL', 'uL')").getObject(Long.class));
+                results.put("sampleTypesWithCountTypeUnit", new SqlSelector(schema, "SELECT COUNT(*) from exp.materialSource WHERE category IS NULL AND metricunit = ?", "unit").getObject(Long.class));
 
                 results.put("duplicateSampleMaterialNameCount", new SqlSelector(schema, "SELECT COUNT(*) as duplicateCount FROM " +
                         "(SELECT name, cpastype FROM exp.material WHERE cpastype <> 'Material' GROUP BY name, cpastype HAVING COUNT(*) > 1) d").getObject(Long.class));