fix(components): gs-mutations-over-time: show 0 instead of "no data" …

…when there are sequences but no mutation resolves #635 case 2
GenSpectrum · Jan 9, 2025 · 666709a · 666709a
1 parent 3d943a1
commit 666709a
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Showing 10 changed files with 32,762 additions and 11,893 deletions.
diff --git a/components/src/preact/mutationsOverTime/__mockData__/aminoAcidMutationsByDay.ts b/components/src/preact/mutationsOverTime/__mockData__/aminoAcidMutationsByDay.ts
diff --git a/components/src/preact/mutationsOverTime/__mockData__/byWeek.ts b/components/src/preact/mutationsOverTime/__mockData__/byWeek.ts
diff --git a/components/src/preact/mutationsOverTime/__mockData__/defaultMockData.ts b/components/src/preact/mutationsOverTime/__mockData__/defaultMockData.ts
diff --git a/components/src/preact/mutationsOverTime/mutations-over-time-grid.tsx b/components/src/preact/mutationsOverTime/mutations-over-time-grid.tsx
@@ -85,7 +85,7 @@ const MutationsOverTimeGrid: FunctionComponent<MutationsOverTimeGridProps> = ({
 };
 
 function getTooltipPosition(rowIndex: number, rows: number, columnIndex: number, columns: number) {
-    const tooltipX = rowIndex < rows / 2 ? 'bottom' : 'top';
+    const tooltipX = rowIndex < rows / 2 || rowIndex < 5 ? 'bottom' : 'top';
     const tooltipY = columnIndex < columns / 2 ? 'start' : 'end';
     return `${tooltipX}-${tooltipY}` as const;
 }

diff --git a/components/src/query/queryMutationsOverTime.spec.ts b/components/src/query/queryMutationsOverTime.spec.ts
@@ -100,7 +100,11 @@ describe('queryMutationsOverTime', () => {
         });
 
         expect(mutationOverTimeData.getAsArray()).to.deep.equal([
-            [{ proportion: 0.4, count: 4, totalCount: 11 }, null, null],
+            [
+                { proportion: 0.4, count: 4, totalCount: 11 },
+                { proportion: 0, count: 0, totalCount: 12 },
+                { proportion: 0, count: 0, totalCount: 13 },
+            ],
             [
                 { proportion: 0.1, count: 1, totalCount: 11 },
                 { proportion: 0.2, count: 2, totalCount: 12 },
@@ -177,7 +181,7 @@ describe('queryMutationsOverTime', () => {
                     dateFieldTo: '2023-01-02',
                     fields: [],
                 },
-                response: { data: [{ count: 12 }] },
+                response: { data: [{ count: 0 }] },
             },
             {
                 body: {
@@ -247,7 +251,7 @@ describe('queryMutationsOverTime', () => {
         });
 
         expect(mutationOverTimeData.getAsArray()).to.deep.equal([
-            [{ proportion: 0.4, count: 4, totalCount: 11 }, null, null],
+            [{ proportion: 0.4, count: 4, totalCount: 11 }, null, { proportion: 0, count: 0, totalCount: 13 }],
             [{ proportion: 0.1, count: 1, totalCount: 11 }, null, { proportion: 0.3, count: 3, totalCount: 13 }],
         ]);
 
@@ -688,7 +692,10 @@ describe('queryMutationsOverTime', () => {
         });
 
         expect(mutationOverTimeData.getAsArray()).to.deep.equal([
-            [{ proportion: 0.4, count: 4, totalCount: 11 }, null],
+            [
+                { proportion: 0.4, count: 4, totalCount: 11 },
+                { proportion: 0, count: 0, totalCount: 12 },
+            ],
             [
                 { proportion: 0.1, count: 1, totalCount: 11 },
                 { proportion: 0.2, count: 2, totalCount: 12 },
@@ -734,6 +741,139 @@ describe('queryMutationsOverTime', () => {
         expect(dates.length).toBe(0);
     });
 
+    it('should fill with 0 if the mutation does not exist in a date range but count > 0', async () => {
+        const lapisFilter = { field1: 'value1', field2: 'value2' };
+        const dateField = 'dateField';
+
+        lapisRequestMocks.multipleAggregated([
+            {
+                body: { ...lapisFilter, fields: [dateField] },
+                response: {
+                    data: [
+                        { count: 1, [dateField]: '2023-01-01' },
+                        { count: 1, [dateField]: '2023-01-02' },
+                    ],
+                },
+            },
+            {
+                body: {
+                    ...lapisFilter,
+                    dateFieldFrom: '2023-01-01',
+                    dateFieldTo: '2023-01-01',
+                    fields: [],
+                },
+                response: { data: [{ count: 11 }] },
+            },
+            {
+                body: {
+                    ...lapisFilter,
+                    dateFieldFrom: '2023-01-02',
+                    dateFieldTo: '2023-01-02',
+                    fields: [],
+                },
+                response: { data: [{ count: 11 }] },
+            },
+        ]);
+
+        lapisRequestMocks.multipleMutations(
+            [
+                {
+                    body: {
+                        ...lapisFilter,
+                        dateFieldFrom: '2023-01-01',
+                        dateFieldTo: '2023-01-01',
+                        minProportion: 0.001,
+                    },
+                    response: { data: [getSomeTestMutation(0.1, 1)] },
+                },
+                {
+                    body: {
+                        ...lapisFilter,
+                        dateFieldFrom: '2023-01-02',
+                        dateFieldTo: '2023-01-02',
+                        minProportion: 0.001,
+                    },
+                    response: { data: [] },
+                },
+                {
+                    body: {
+                        ...lapisFilter,
+                        dateFieldFrom: '2023-01-01',
+                        dateFieldTo: '2023-01-02',
+                        minProportion: 0.001,
+                    },
+                    response: {
+                        data: [getSomeTestMutation(0.21, 6)],
+                    },
+                },
+            ],
+            'nucleotide',
+        );
+
+        const { mutationOverTimeData } = await queryMutationsOverTimeData({
+            lapisFilter,
+            sequenceType: 'nucleotide',
+            lapis: DUMMY_LAPIS_URL,
+            lapisDateField: dateField,
+            granularity: 'day',
+        });
+
+        expect(mutationOverTimeData.getAsArray()).to.deep.equal([
+            [
+                { proportion: 0.1, count: 1, totalCount: 11 },
+                { proportion: 0, count: 0, totalCount: 11 },
+            ],
+        ]);
+    });
+
+    it('should return null if count in a date range is 0', async () => {
+        const lapisFilter = { field1: 'value1', field2: 'value2' };
+        const dateField = 'dateField';
+
+        lapisRequestMocks.multipleAggregated([
+            {
+                body: { ...lapisFilter, fields: [dateField] },
+                response: {
+                    data: [{ count: 0, [dateField]: '2023-01-01' }],
+                },
+            },
+            {
+                body: {
+                    ...lapisFilter,
+                    dateFieldFrom: '2023-01-01',
+                    dateFieldTo: '2023-01-01',
+                    fields: [],
+                },
+                response: { data: [{ count: 0 }] },
+            },
+        ]);
+
+        lapisRequestMocks.multipleMutations(
+            [
+                {
+                    body: {
+                        ...lapisFilter,
+                        dateFieldFrom: '2023-01-01',
+                        dateFieldTo: '2023-01-01',
+                        minProportion: 0.001,
+                    },
+                    response: { data: [getSomeTestMutation(0.1, 1)] },
+                },
+            ],
+            'nucleotide',
+        );
+
+        const { mutationOverTimeData } = await queryMutationsOverTimeData({
+            lapisFilter,
+            sequenceType: 'nucleotide',
+            lapis: DUMMY_LAPIS_URL,
+            lapisDateField: dateField,
+            granularity: 'day',
+        });
+
+        expect(mutationOverTimeData.getAsArray()).to.deep.equal([[null]]);
+    });
+
     function getSomeTestMutation(proportion: number, count: number) {
         return {
             mutation: 'sequenceName:A123T',

diff --git a/components/src/query/queryMutationsOverTime.ts b/components/src/query/queryMutationsOverTime.ts
@@ -122,6 +122,7 @@ export async function queryMutationsOverTimeData({
 
         const data = await fetchAndPrepareSubstitutionsOrDeletions(filter, sequenceType).evaluate(lapis, signal);
         const totalCountQuery = await getTotalNumberOfSequencesInDateRange(filter).evaluate(lapis, signal);
+
         return {
             date,
             mutations: data.content,
@@ -244,9 +245,14 @@ export function groupByMutation(
     });
 
     data.forEach((mutationData) => {
+        if (mutationData.totalCount == 0) {
+            return;
+        }
+
+        const date = toTemporal(mutationData.date);
+
         mutationData.mutations.forEach((mutationEntry) => {
             const mutation = toSubstitutionOrDeletion(mutationEntry.mutation);
-            const date = toTemporal(mutationData.date);
 
             if (dataArray.get(mutation, date) !== undefined) {
                 dataArray.set(mutation, date, {
@@ -256,6 +262,16 @@ export function groupByMutation(
                 });
             }
         });
+
+        for (const firstAxisKey of dataArray.getFirstAxisKeys()) {
+            if (dataArray.get(firstAxisKey, date) === null) {
+                dataArray.set(firstAxisKey, date, {
+                    count: 0,
+                    proportion: 0,
+                    totalCount: mutationData.totalCount,
+                });
+            }
+        }
     });
 
     return dataArray;

diff --git a/...-of-visualization-mutations-over-time--by-week-should-match-snapshot-1-chromium-linux.txt b/...-of-visualization-mutations-over-time--by-week-should-match-snapshot-1-chromium-linux.txt
@@ -1,9 +1,9 @@
 mutation,2024-W03,2024-W04,2024-W05,2024-W06
-C44T,0.5851938895417156,0.5614583333333333,0.6298472385428907,0.5540540540540541
-C774T,0.26635694928377857,0.2508050767190756,0.27291549030679463,0.2662041625371655
-C1762A,0.06473724295506474,0.06412605349945034,0.04853105243584976,0.041330446762448333
-C11747T,0.0638990638990639,0.062058130400628436,0.04801873902010541,0.03954564577198149
-G17562T,0.0710909434675742,0.07296607077708865,0.06433721575152523,0.05823724838772718
-T18453C,0.21926151503616292,0.19885629957572404,0.21122050900984582,0.21082565208864484
-G21641T,0.06280500742626777,0.10792580101180438,0.06527690040008423,0.028808481216870248
-C23277T,0.06267698697375873,0.0770213542617266,0.10395856455789863,0.127443315089914
+C44T,0.5851938895417156,0,0.6298472385428907,0.5540540540540541
+C774T,0.26635694928377857,0,0.27291549030679463,0.2662041625371655
+C1762A,0.06473724295506474,0,0.04853105243584976,0.041330446762448333
+C11747T,0.0638990638990639,0,0.04801873902010541,0.03954564577198149
+G17562T,0.0710909434675742,0,0.06433721575152523,0.05823724838772718
+T18453C,0.21926151503616292,0,0.21122050900984582,0.21082565208864484
+G21641T,0.06280500742626777,0,0.06527690040008423,0.028808481216870248
+C23277T,0.06267698697375873,0,0.10395856455789863,0.127443315089914
diff --git a/...d-of-visualization-mutations-over-time--by-week-should-match-snapshot-1-firefox-linux.txt b/...d-of-visualization-mutations-over-time--by-week-should-match-snapshot-1-firefox-linux.txt
@@ -1,9 +1,9 @@
 mutation,2024-W03,2024-W04,2024-W05,2024-W06
-C44T,0.5851938895417156,0.5614583333333333,0.6298472385428907,0.5540540540540541
-C774T,0.26635694928377857,0.2508050767190756,0.27291549030679463,0.2662041625371655
-C1762A,0.06473724295506474,0.06412605349945034,0.04853105243584976,0.041330446762448333
-C11747T,0.0638990638990639,0.062058130400628436,0.04801873902010541,0.03954564577198149
-G17562T,0.0710909434675742,0.07296607077708865,0.06433721575152523,0.05823724838772718
-T18453C,0.21926151503616292,0.19885629957572404,0.21122050900984582,0.21082565208864484
-G21641T,0.06280500742626777,0.10792580101180438,0.06527690040008423,0.028808481216870248
-C23277T,0.06267698697375873,0.0770213542617266,0.10395856455789863,0.127443315089914
+C44T,0.5851938895417156,0,0.6298472385428907,0.5540540540540541
+C774T,0.26635694928377857,0,0.27291549030679463,0.2662041625371655
+C1762A,0.06473724295506474,0,0.04853105243584976,0.041330446762448333
+C11747T,0.0638990638990639,0,0.04801873902010541,0.03954564577198149
+G17562T,0.0710909434675742,0,0.06433721575152523,0.05823724838772718
+T18453C,0.21926151503616292,0,0.21122050900984582,0.21082565208864484
+G21641T,0.06280500742626777,0,0.06527690040008423,0.028808481216870248
+C23277T,0.06267698697375873,0,0.10395856455789863,0.127443315089914
diff --git a/...ation-mutations-over-time--by-week-should-match-screenshot-1-chromium-linux.png b/...ation-mutations-over-time--by-week-should-match-screenshot-1-chromium-linux.png
diff --git a/...zation-mutations-over-time--by-week-should-match-screenshot-1-firefox-linux.png b/...zation-mutations-over-time--by-week-should-match-screenshot-1-firefox-linux.png