@genspectrum/dashboard-components 1.16.0 → 1.17.0

package/src/preact/mutationsOverTime/getFilteredMutationsOverTime.spec.ts

@@ -1,417 +0,0 @@
-import { describe, expect, it } from 'vitest';
-
-import { BaseMutationOverTimeDataMap } from './MutationOverTimeData';
-import { getFilteredMutationOverTimeData, type MutationFilter } from './getFilteredMutationsOverTimeData';
-import { type ProportionValue } from '../../query/queryMutationsOverTime';
-import { type DeletionEntry, type SubstitutionEntry } from '../../types';
-import { type Deletion, type Substitution } from '../../utils/mutations';
-import { type TemporalClass } from '../../utils/temporalClass';
-import { yearMonthDay } from '../../utils/temporalTestHelpers';
-import { type MutationAnnotations } from '../../web-components/mutation-annotations-context';
-import { getMutationAnnotationsContext, getMutationAnnotationsProvider } from '../MutationAnnotationsContext';
-
-describe('getFilteredMutationOverTimeData', () => {
-    it('should filter by displayed segments', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            someSubstitutionEntry,
-            anotherSubstitutionEntry,
-            someDeletionEntry,
-        ]);
-
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [
-                { segment: 'someSegment', checked: false, label: 'Some Segment' },
-                { segment: 'someOtherSegment', checked: true, label: 'Some Other Segment' },
-            ],
-            displayedMutationTypes: [],
-            proportionInterval,
-            hideGaps: false,
-            displayMutations: undefined,
-            mutationFilterValue: { textFilter: '', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getFirstAxisKeys()).to.deep.equal([anotherSubstitution]);
-    });
-
-    it('should filter by mutation types', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            someSubstitutionEntry,
-            anotherSubstitutionEntry,
-            someDeletionEntry,
-        ]);
-
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [],
-            displayedMutationTypes: [
-                {
-                    type: 'substitution',
-                    checked: false,
-                    label: 'Substitution',
-                },
-                {
-                    type: 'deletion',
-                    checked: true,
-                    label: 'Deletion',
-                },
-            ],
-            proportionInterval,
-            hideGaps: false,
-            mutationFilterValue: { textFilter: '', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getFirstAxisKeys()).to.deep.equal([someDeletion]);
-    });
-
-    it('should remove mutations where overall proportion is below filter', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            { ...someSubstitutionEntry, proportion: belowFilter },
-            { ...anotherSubstitutionEntry, proportion: inFilter },
-            { ...someDeletionEntry, proportion: inFilter },
-        ]);
-
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [],
-            displayedMutationTypes: [],
-            proportionInterval,
-            hideGaps: false,
-            mutationFilterValue: { textFilter: '', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getFirstAxisKeys()).to.deep.equal([anotherSubstitution, someDeletion]);
-    });
-
-    it('should remove mutations where overall proportion is above filter', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            { ...someSubstitutionEntry, proportion: aboveFilter },
-            { ...anotherSubstitutionEntry, proportion: inFilter },
-            { ...someDeletionEntry, proportion: inFilter },
-        ]);
-
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [],
-            displayedMutationTypes: [],
-            proportionInterval,
-            hideGaps: false,
-            mutationFilterValue: { textFilter: '', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getFirstAxisKeys()).to.deep.equal([anotherSubstitution, someDeletion]);
-    });
-
-    it('should not remove mutations where overall proportion is above filter but single proportion is below filter', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            someSubstitutionEntry,
-            anotherSubstitutionEntry,
-            someDeletionEntry,
-        ]);
-        data.set(someSubstitution, someTemporal, { ...someMutationOverTimeValue, proportion: belowFilter });
-
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [],
-            displayedMutationTypes: [],
-            proportionInterval,
-            hideGaps: false,
-            mutationFilterValue: { textFilter: '', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getFirstAxisKeys()).to.deep.equal([someSubstitution, anotherSubstitution, someDeletion]);
-    });
-
-    it('should not remove mutations where overall proportion is below max but single proportion is above max', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            someSubstitutionEntry,
-            anotherSubstitutionEntry,
-            someDeletionEntry,
-        ]);
-        data.set(someSubstitution, someTemporal, { ...someMutationOverTimeValue, proportion: aboveFilter });
-
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [],
-            displayedMutationTypes: [],
-            proportionInterval,
-            hideGaps: false,
-            mutationFilterValue: { textFilter: '', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getFirstAxisKeys()).to.deep.equal([someSubstitution, anotherSubstitution, someDeletion]);
-    });
-
-    it('should not remove mutations where overall proportion is at lower bound of filter', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            { ...someSubstitutionEntry, proportion: atFilterMin },
-            { ...anotherSubstitutionEntry, proportion: inFilter },
-            { ...someDeletionEntry, proportion: inFilter },
-        ]);
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [],
-            displayedMutationTypes: [],
-            proportionInterval,
-            hideGaps: false,
-            mutationFilterValue: { textFilter: '', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getFirstAxisKeys()).to.deep.equal([someSubstitution, anotherSubstitution, someDeletion]);
-    });
-
-    it('should not remove mutations where overall proportion is at upper bound of filter', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            { ...someSubstitutionEntry, proportion: atFilterMax },
-            { ...anotherSubstitutionEntry, proportion: inFilter },
-            { ...someDeletionEntry, proportion: inFilter },
-        ]);
-
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [],
-            displayedMutationTypes: [],
-            proportionInterval,
-            hideGaps: false,
-            mutationFilterValue: { textFilter: '', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getFirstAxisKeys()).to.deep.equal([someSubstitution, anotherSubstitution, someDeletion]);
-    });
-
-    it('should filter by mutation filter text value', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            someSubstitutionEntry,
-            anotherSubstitutionEntry,
-            someDeletionEntry,
-        ]);
-
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [],
-            displayedMutationTypes: [],
-            proportionInterval,
-            hideGaps: false,
-            mutationFilterValue: { textFilter: '23T', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getFirstAxisKeys()).to.deep.equal([someSubstitution]);
-    });
-
-    describe('should filter by annotation', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([
-            someSubstitutionEntry,
-            anotherSubstitutionEntry,
-            someDeletionEntry,
-        ]);
-
-        const expectFilteredValue = (filterValue: MutationFilter, annotations: MutationAnnotations) => {
-            const annotationProvider = getMutationAnnotationsProvider(getMutationAnnotationsContext(annotations));
-
-            const result = getFilteredMutationOverTimeData({
-                data,
-                overallMutationData,
-                displayedSegments: [],
-                displayedMutationTypes: [],
-                proportionInterval,
-                hideGaps: false,
-                mutationFilterValue: filterValue,
-                sequenceType: 'nucleotide',
-                annotationProvider,
-            });
-
-            expect(result.getFirstAxisKeys()).to.deep.equal([someSubstitution]);
-        };
-
-        it('with filter value in symbol', () => {
-            expectFilteredValue({ textFilter: '#', annotationNameFilter: new Set() }, [
-                {
-                    name: 'Annotation 1',
-                    description: 'Description 1',
-                    symbol: '#',
-                    nucleotideMutations: ['A123T'],
-                },
-            ]);
-        });
-
-        it('with filter value in name', () => {
-            expectFilteredValue({ textFilter: 'Annota', annotationNameFilter: new Set() }, [
-                {
-                    name: 'Annotation 1 #',
-                    description: 'Description 1',
-                    symbol: '+',
-                    nucleotideMutations: ['A123T'],
-                },
-            ]);
-        });
-
-        it('with filter value in name', () => {
-            expectFilteredValue({ textFilter: 'Descr', annotationNameFilter: new Set() }, [
-                {
-                    name: 'Annotation 1',
-                    description: 'Description 1',
-                    symbol: '#',
-                    nucleotideMutations: ['A123T'],
-                },
-            ]);
-        });
-
-        it('with annotation name filter', () => {
-            expectFilteredValue({ textFilter: '', annotationNameFilter: new Set(['Annotation 1']) }, [
-                {
-                    name: 'Annotation 1',
-                    description: 'Description 1',
-                    symbol: '#',
-                    nucleotideMutations: ['A123T'],
-                },
-            ]);
-        });
-    });
-
-    it('should remove date ranges that have no samples', () => {
-        const { data, overallMutationData } = prepareMutationOverTimeData([someSubstitutionEntry, someDeletionEntry]);
-        data.set(someSubstitution, anotherTemporal, emptyMutationOverTimeValue);
-        data.set(someDeletion, anotherTemporal, emptyMutationOverTimeValue);
-
-        const result = getFilteredMutationOverTimeData({
-            data,
-            overallMutationData,
-            displayedSegments: [],
-            displayedMutationTypes: [],
-            proportionInterval,
-            hideGaps: true,
-            mutationFilterValue: { textFilter: '', annotationNameFilter: new Set() },
-            sequenceType: 'nucleotide',
-            annotationProvider: () => {
-                return [];
-            },
-        });
-
-        expect(result.getSecondAxisKeys()).to.deep.equal([someTemporal]);
-    });
-
-    const belowFilter = 0.1;
-    const atFilterMin = 0.2;
-    const inFilter = 0.5;
-    const atFilterMax = 0.9;
-    const aboveFilter = 0.99;
-    const proportionInterval = { min: atFilterMin, max: atFilterMax };
-
-    const someSubstitution: Substitution = {
-        type: 'substitution',
-        valueAtReference: 'A',
-        substitutionValue: 'T',
-        code: 'A123T',
-        segment: 'someSegment',
-        position: 123,
-    };
-    const someSubstitutionEntry: SubstitutionEntry<Substitution> = {
-        type: 'substitution',
-        mutation: someSubstitution,
-        count: 234,
-        proportion: inFilter,
-    };
-
-    const anotherSubstitution: Substitution = {
-        type: 'substitution',
-        valueAtReference: 'G',
-        substitutionValue: 'C',
-        code: 'G345C',
-        segment: 'someOtherSegment',
-        position: 345,
-    };
-    const anotherSubstitutionEntry: SubstitutionEntry<Substitution> = {
-        type: 'substitution',
-        mutation: anotherSubstitution,
-        count: 456,
-        proportion: inFilter,
-    };
-
-    const someDeletion: Deletion = {
-        type: 'deletion',
-        valueAtReference: 'A',
-        segment: 'someSegment',
-        position: 567,
-        code: 'A123-',
-    };
-    const someDeletionEntry: DeletionEntry<Deletion> = {
-        type: 'deletion',
-        mutation: someDeletion,
-        count: 789,
-        proportion: inFilter,
-    };
-    const someTemporal = yearMonthDay('2021-01-01');
-    const anotherTemporal = yearMonthDay('2021-02-02');
-    const someMutationOverTimeValue = {
-        type: 'value',
-        count: 1,
-        proportion: inFilter,
-        totalCount: 10,
-    } satisfies ProportionValue;
-    const emptyMutationOverTimeValue = {
-        type: 'value',
-        count: 0,
-        proportion: NaN,
-        totalCount: 0,
-    } satisfies ProportionValue;
-
-    function prepareMutationOverTimeData(
-        mutationEntries: (SubstitutionEntry<Substitution> | DeletionEntry<Deletion>)[],
-        temporals: TemporalClass[] = [someTemporal, anotherTemporal],
-    ) {
-        const data = new BaseMutationOverTimeDataMap();
-
-        temporals.forEach((temporal) => {
-            mutationEntries.forEach((entry) => {
-                data.set(entry.mutation, temporal, someMutationOverTimeValue);
-            });
-        });
-
-        return { data, overallMutationData: mutationEntries };
-    }
-});