add column formatter and fisher two sided unit tests

src/pages/groupComparison/FisherExactTwoSidedTestLabel.tsx

@@ -5,8 +5,7 @@ import MutationMapperDataStore from 'shared/components/mutationMapper/MutationMa
 import { ComparisonGroup } from './GroupComparisonUtils';
 import { toConditionalPrecisionWithMinimum } from 'shared/lib/FormatUtils';
 import _ from 'lodash';
-import { getTwoTailedPValue } from 'shared/lib/FisherExactTestCalculator';
-import { formatPercentValue } from 'cbioportal-utils';
+import { getTwoTailedPValue } from 'shared/lib/calculation/FisherExactTestCalculator';
 import intersect from 'fast_array_intersect';
 import InfoIcon from 'shared/components/InfoIcon';
 import { MutationOverlapOverlay } from 'shared/components/mutationTable/column/mutationOverlap/MutationOverlapOverlay';

src/pages/groupComparison/GroupComparisonUtils.tsx

@@ -45,7 +45,7 @@ import {
     SessionGroupData,
 } from 'shared/api/session-service/sessionServiceModels';
 import { GroupComparisonMutation } from 'shared/model/GroupComparisonMutation';
-import { getTwoTailedPValue } from 'shared/lib/FisherExactTestCalculator';
+import { getTwoTailedPValue } from 'shared/lib/calculation/FisherExactTestCalculator';
 import { calculateQValues } from 'shared/lib/calculation/BenjaminiHochbergFDRCalculator';
 
 type Omit<T, K> = Pick<T, Exclude<keyof T, K>>;

src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.spec.tsx

@@ -265,11 +265,11 @@ describe('MutualExclusivityUtil', () => {
     });
 
     describe('#calculatePValue()', () => {
-        it('returns 0.3653846153846146 for 4, 3, 7, 2', () => {
+        it('returns 0.5961538461538457 for 4, 3, 7, 2', () => {
             assert.equal(calculatePValue(4, 3, 7, 2), 0.5961538461538457);
         });
 
-        it('returns 0.07706146926536687 for 13, 7, 3, 7', () => {
+        it('returns 0.12163918040979466 for 13, 7, 3, 7', () => {
             assert.equal(calculatePValue(13, 7, 3, 7), 0.12163918040979466);
         });
     });

src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.tsx

@@ -1,5 +1,5 @@
 import * as React from 'react';
-import { getTwoTailedPValue } from '../../../shared/lib/FisherExactTestCalculator';
+import { getTwoTailedPValue } from '../../../shared/lib/calculation/FisherExactTestCalculator';
 import { MutualExclusivity } from '../../../shared/model/MutualExclusivity';
 import { calculateQValues } from '../../../shared/lib/calculation/BenjaminiHochbergFDRCalculator';
 import Combinatorics from 'js-combinatorics';

src/shared/components/mutationTable/column/EnrichedInColumnFormatter.spec.tsx

@@ -0,0 +1,140 @@
+import { assert } from 'chai';
+import { initMutation } from 'test/MutationMockUtils';
+import { Mutation } from 'cbioportal-ts-api-client';
+import { GroupComparisonMutation } from 'shared/model/GroupComparisonMutation';
+import { enrichedInRenderFunction } from './EnrichedInColumnFormatter';
+import { mount, ReactWrapper } from 'enzyme';
+import { ComparisonGroup } from 'pages/groupComparison/GroupComparisonUtils';
+import styles from 'pages/resultsView/enrichments/styles.module.scss';
+
+describe('EnrichedInColumnFormatter', () => {
+    const mutation1: Mutation = initMutation({
+        proteinChange: 'L702H',
+    });
+
+    const mutation2: Mutation = initMutation({
+        proteinChange: 'H875Y',
+    });
+
+    const mutation3: Mutation = initMutation({
+        proteinChange: 'A646D',
+    });
+
+    const rowDataByProteinChange: {
+        [proteinChange: string]: GroupComparisonMutation;
+    } = {
+        L702H: {
+            proteinChange: 'L702H',
+            enrichedGroup: '(A) Metastasis',
+            groupAMutatedCount: 9,
+            groupAMutatedPercentage: 3.2490974729241873,
+            groupBMutatedCount: 0,
+            groupBMutatedPercentage: 0,
+            logRatio: Infinity,
+            pValue: 0.00036917378321091467,
+            qValue: 0.005906780531374635,
+        },
+        H875Y: {
+            proteinChange: 'H875Y',
+            enrichedGroup: '(A) Metastasis',
+            groupAMutatedCount: 9,
+            groupBMutatedCount: 1,
+            groupAMutatedPercentage: 3.2490974729241873,
+            groupBMutatedPercentage: 0.26041666666666663,
+            logRatio: 3.6411453361142803,
+            pValue: 0.0023260213212133113,
+            qValue: 0.01860817056970649,
+        },
+        A646D: {
+            proteinChange: 'A646D',
+            enrichedGroup: '(B) Primary',
+            groupAMutatedCount: 0,
+            groupBMutatedCount: 1,
+            groupAMutatedPercentage: 0,
+            groupBMutatedPercentage: 0.26041666666666663,
+            logRatio: -Infinity,
+            pValue: 0.999999999999234,
+            qValue: 0.999999999999234,
+        },
+    };
+
+    const groups: ComparisonGroup[] = [
+        {
+            color: '#DC3912',
+            uid: 'Metastasis',
+            name: 'Metastasis',
+            nameWithOrdinal: '(A) Metastasis',
+            ordinal: 'A',
+            studies: [],
+            nonExistentSamples: [],
+            origin: ['msk_impact_2017'],
+            description: '',
+        },
+        {
+            color: '#2986E2',
+            uid: 'Primary',
+            name: 'Primary',
+            nameWithOrdinal: '(B) Primary',
+            ordinal: 'B',
+            studies: [],
+            nonExistentSamples: [],
+            origin: ['msk_impact_2017'],
+            description: '',
+        },
+    ];
+
+    let component1: ReactWrapper<any, any>;
+    let component2: ReactWrapper<any, any>;
+    let component3: ReactWrapper<any, any>;
+
+    beforeAll(() => {
+        component1 = mount(
+            enrichedInRenderFunction(
+                rowDataByProteinChange,
+                [mutation1],
+                groups
+            )
+        );
+        component2 = mount(
+            enrichedInRenderFunction(
+                rowDataByProteinChange,
+                [mutation2],
+                groups
+            )
+        );
+        component3 = mount(
+            enrichedInRenderFunction(
+                rowDataByProteinChange,
+                [mutation3],
+                groups
+            )
+        );
+    });
+
+    function testRenderedValues(
+        component: ReactWrapper<any, any>,
+        classNames: string[],
+        value: string
+    ) {
+        assert.isTrue(
+            classNames.every(c =>
+                component.find(`div.${(styles as any)[c]}`).exists()
+            )
+        );
+        assert.equal(component.find(`div`).text(), value);
+    }
+
+    it('renders enriched in column correctly', () => {
+        testRenderedValues(
+            component1,
+            ['Tendency', 'Significant', 'ColoredBackground'],
+            '(A) Metastasis'
+        );
+        testRenderedValues(
+            component2,
+            ['Tendency', 'Significant', 'ColoredBackground'],
+            '(A) Metastasis'
+        );
+        testRenderedValues(component3, ['Tendency'], '(B) Primary');
+    });
+});

src/shared/components/mutationTable/column/GroupMutatedCountPercentageColumnFormatter.spec.tsx

@@ -0,0 +1,98 @@
+import { assert } from 'chai';
+import { initMutation } from 'test/MutationMockUtils';
+import { Mutation } from 'cbioportal-ts-api-client';
+import { getGroupMutatedCountPercentageTextValue } from './GroupMutatedCountPercentageColumnFormatter';
+import { GroupComparisonMutation } from 'shared/model/GroupComparisonMutation';
+
+describe('GroupMutatedCountPercentageColumnFormatter', () => {
+    const mutation1: Mutation = initMutation({
+        proteinChange: 'L702H',
+    });
+
+    const mutation2: Mutation = initMutation({
+        proteinChange: 'H875Y',
+    });
+
+    const mutation3: Mutation = initMutation({
+        proteinChange: 'A646D',
+    });
+
+    const rowDataByProteinChange: {
+        [proteinChange: string]: GroupComparisonMutation;
+    } = {
+        L702H: {
+            proteinChange: 'L702H',
+            enrichedGroup: '(A) Metastasis',
+            groupAMutatedCount: 9,
+            groupAMutatedPercentage: 3.2490974729241873,
+            groupBMutatedCount: 0,
+            groupBMutatedPercentage: 0,
+            logRatio: Infinity,
+            pValue: 0.00036917378321091467,
+            qValue: 0.005906780531374635,
+        },
+        H875Y: {
+            proteinChange: 'H875Y',
+            enrichedGroup: '(A) Metastasis',
+            groupAMutatedCount: 9,
+            groupBMutatedCount: 1,
+            groupAMutatedPercentage: 3.2490974729241873,
+            groupBMutatedPercentage: 0.26041666666666663,
+            logRatio: 3.6411453361142803,
+            pValue: 0.0023260213212133113,
+            qValue: 0.01860817056970649,
+        },
+        A646D: {
+            proteinChange: 'A646D',
+            enrichedGroup: '(B) Primary',
+            groupAMutatedCount: 0,
+            groupBMutatedCount: 1,
+            groupAMutatedPercentage: 0,
+            groupBMutatedPercentage: 0.26041666666666663,
+            logRatio: -Infinity,
+            pValue: 0.999999999999234,
+            qValue: 0.999999999999234,
+        },
+    };
+
+    it('gets mutated count percentage text value properly', () => {
+        assert.equal(
+            getGroupMutatedCountPercentageTextValue(rowDataByProteinChange, 0, [
+                mutation1,
+            ]),
+            '9 (3.25%)'
+        );
+        assert.equal(
+            getGroupMutatedCountPercentageTextValue(rowDataByProteinChange, 1, [
+                mutation1,
+            ]),
+            '0 (0.00%)'
+        );
+
+        assert.equal(
+            getGroupMutatedCountPercentageTextValue(rowDataByProteinChange, 0, [
+                mutation2,
+            ]),
+            '9 (3.25%)'
+        );
+        assert.equal(
+            getGroupMutatedCountPercentageTextValue(rowDataByProteinChange, 1, [
+                mutation2,
+            ]),
+            '1 (0.26%)'
+        );
+
+        assert.equal(
+            getGroupMutatedCountPercentageTextValue(rowDataByProteinChange, 0, [
+                mutation3,
+            ]),
+            '0 (0.00%)'
+        );
+        assert.equal(
+            getGroupMutatedCountPercentageTextValue(rowDataByProteinChange, 1, [
+                mutation3,
+            ]),
+            '1 (0.26%)'
+        );
+    });
+});

src/shared/components/mutationTable/column/LogRatioColumnFormatter.spec.tsx

@@ -0,0 +1,74 @@
+import { assert } from 'chai';
+import { initMutation } from 'test/MutationMockUtils';
+import { Mutation } from 'cbioportal-ts-api-client';
+import { GroupComparisonMutation } from 'shared/model/GroupComparisonMutation';
+import { getLogRatioTextValue } from './LogRatioColumnFormatter';
+
+describe('LogRatioColumnFormatter', () => {
+    const mutation1: Mutation = initMutation({
+        proteinChange: 'L702H',
+    });
+
+    const mutation2: Mutation = initMutation({
+        proteinChange: 'H875Y',
+    });
+
+    const mutation3: Mutation = initMutation({
+        proteinChange: 'A646D',
+    });
+
+    const rowDataByProteinChange: {
+        [proteinChange: string]: GroupComparisonMutation;
+    } = {
+        L702H: {
+            proteinChange: 'L702H',
+            enrichedGroup: '(A) Metastasis',
+            groupAMutatedCount: 9,
+            groupAMutatedPercentage: 3.2490974729241873,
+            groupBMutatedCount: 0,
+            groupBMutatedPercentage: 0,
+            logRatio: Infinity,
+            pValue: 0.00036917378321091467,
+            qValue: 0.005906780531374635,
+        },
+        H875Y: {
+            proteinChange: 'H875Y',
+            enrichedGroup: '(A) Metastasis',
+            groupAMutatedCount: 9,
+            groupBMutatedCount: 1,
+            groupAMutatedPercentage: 3.2490974729241873,
+            groupBMutatedPercentage: 0.26041666666666663,
+            logRatio: 3.6411453361142803,
+            pValue: 0.0023260213212133113,
+            qValue: 0.01860817056970649,
+        },
+        A646D: {
+            proteinChange: 'A646D',
+            enrichedGroup: '(B) Primary',
+            groupAMutatedCount: 0,
+            groupBMutatedCount: 1,
+            groupAMutatedPercentage: 0,
+            groupBMutatedPercentage: 0.26041666666666663,
+            logRatio: -Infinity,
+            pValue: 0.999999999999234,
+            qValue: 0.999999999999234,
+        },
+    };
+
+    it('gets mutated count percentage text value properly', () => {
+        assert.equal(
+            getLogRatioTextValue(rowDataByProteinChange, [mutation1]),
+            '>10'
+        );
+
+        assert.equal(
+            getLogRatioTextValue(rowDataByProteinChange, [mutation2]),
+            '3.64'
+        );
+
+        assert.equal(
+            getLogRatioTextValue(rowDataByProteinChange, [mutation3]),
+            '<-10'
+        );
+    });
+});