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Merge pull request #1302 from hallieswan/AG-1328
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AG-1328: improve handling of target nominations table display strings
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@hallieswan
hallieswan authored May 14, 2024
2 parents 35506d5 + a5157c3 commit e7bf92e
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Showing 4 changed files with 176 additions and 56 deletions.
121 changes: 120 additions & 1 deletion ...features/genes/components/gene-nominated-targets/gene-nominated-targets.component.spec.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,22 @@ import { HttpClientTestingModule } from '@angular/common/http/testing';
// -------------------------------------------------------------------------- //
import { GeneNominatedTargetsComponent } from './';
import { ApiService, HelperService } from '../../../../core/services';
import { Gene, GenesResponse } from '../../../../models';
import { geneMock1, targetNominationMock1 } from '../../../../testing/gene-mocks';
import { of } from 'rxjs';

// -------------------------------------------------------------------------- //
// Tests
// -------------------------------------------------------------------------- //
describe('Component: Gene Nominated Targets', () => {
let fixture: ComponentFixture<GeneNominatedTargetsComponent>;
let component: GeneNominatedTargetsComponent;
let element: HTMLElement;
let mockApiService: ApiService;

const COLUMN_INDICES = {
'cohort_study': 4
};

beforeEach(async () => {
await TestBed.configureTestingModule({
Expand All @@ -29,10 +38,120 @@ describe('Component: Gene Nominated Targets', () => {
beforeEach(async () => {
fixture = TestBed.createComponent(GeneNominatedTargetsComponent);
component = fixture.componentInstance;
fixture.detectChanges();
});

const setUp = (genes: Gene[]) => {
const genesResponse: GenesResponse = {
items: genes
};
mockApiService = TestBed.inject(ApiService);
spyOn(mockApiService, 'getNominatedGenes').and.returnValue(
of(genesResponse)
);
fixture.detectChanges();
element = fixture.nativeElement;

expect(mockApiService.getNominatedGenes).toHaveBeenCalled();

const table = element.querySelector('table');
expect(table).not.toBeNull();

const rows = Array.from(
table?.querySelectorAll('tbody tr') || []
) as HTMLTableRowElement[];

return { rows };
};

it('should create', () => {
setUp([geneMock1]);
expect(component).toBeTruthy();
});

it('should not show null study values', () => {
const gene: Gene = {
...geneMock1,
target_nominations: [
{ ...targetNominationMock1, study: null },
{ ...targetNominationMock1, study: 'XYZ Study, ABC Study' },
{ ...targetNominationMock1, study: '' },
{ ...targetNominationMock1, study: 'Study 123, Study 456' },
],
};
const { rows } = setUp([gene]);
expect(rows.length).toBe(1);

const cols = rows[0].cells;
expect(cols.length).toBeGreaterThan(COLUMN_INDICES.cohort_study);

expect(cols[COLUMN_INDICES.cohort_study].textContent?.trim()).toEqual(
'ABC Study, Study 123, Study 456, XYZ Study'
);
});

it('should display sorted, unique study values', () => {
const expectedStudyString = 'ACT, Banner, BLSA, Kronos, MSBB, ROSMAP';
const { rows } = setUp([geneMock1]);

expect(rows.length).toBe(1);

const cols = rows[0].cells;
expect(cols.length).toBeGreaterThan(COLUMN_INDICES.cohort_study);

expect(cols[COLUMN_INDICES.cohort_study].textContent?.trim()).toEqual(
expectedStudyString
);
});

it('should correctly flatten comma separated arrays', () => {
setUp([]);

expect(component.commaFlattenArray([])).toEqual([]);

expect(
component.commaFlattenArray(['ACT, BLSA, Banner', 'ACT, BLSA, Banner'])
).toEqual(['ACT', 'BLSA', 'Banner', 'ACT', 'BLSA', 'Banner']);

expect(component.commaFlattenArray(['A, B, C', 'D', 'E, F, G, H'])).toEqual(
['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']
);

expect(component.commaFlattenArray(['A', 'B', 'C'])).toEqual([
'A',
'B',
'C',
]);
});

it('should correctly format display values', () => {
setUp([]);

expect(
component.getCommaSeparatedStringOfUniqueSortedValues([])
).toEqual('');

expect(
component.getCommaSeparatedStringOfUniqueSortedValues([
'ACT',
'BLSA',
'Banner',
'ACT',
'BLSA',
'Banner',
])
).toEqual('ACT, Banner, BLSA');

expect(
component.getCommaSeparatedStringOfUniqueSortedValues([
'Z',
'Y',
'X',
'A',
'B',
'C',
'B',
'C',
])
).toEqual('A, B, C, X, Y, Z');
});
});
89 changes: 36 additions & 53 deletions src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -97,8 +97,8 @@ export class GeneNominatedTargetsComponent implements OnInit {
// First map all entries nested in the data to a new array
if (de.target_nominations?.length) {
teamsArray = de.target_nominations.map((nt: TargetNomination) => nt.team);
studyArray = de.target_nominations.map(
(nt: TargetNomination) => nt.study
studyArray = this.removeNullAndEmptyStrings(
de.target_nominations.map((nt: TargetNomination) => nt.study)
);
programsArray = de.target_nominations.map(
(nt: TargetNomination) => nt.source
Expand All @@ -120,37 +120,14 @@ export class GeneNominatedTargetsComponent implements OnInit {
inputDataArray = this.commaFlattenArray(inputDataArray);

// Populate targetNomination display fields
de.teams_display_value = '';
if (teamsArray.length) {
de.teams_display_value = teamsArray
.filter(this.getUnique)
.sort((a: string, b: string) => a.localeCompare(b))
.join(', ');
}

de.study_display_value = '';
if (teamsArray.length) {
de.study_display_value = studyArray
.filter(this.getUnique)
.sort((a: string, b: string) => a.localeCompare(b))
.join(', ');
}

de.programs_display_value = '';
if (programsArray.length) {
de.programs_display_value = programsArray
.filter(this.getUnique)
.sort((a: string, b: string) => a.localeCompare(b))
.join(', ');
}

de.input_data_display_value = '';
if (inputDataArray.length) {
de.input_data_display_value = inputDataArray
.filter(this.getUnique)
.sort((a: string, b: string) => a.localeCompare(b))
.join(', ');
}
de.teams_display_value =
this.getCommaSeparatedStringOfUniqueSortedValues(teamsArray);
de.study_display_value =
this.getCommaSeparatedStringOfUniqueSortedValues(studyArray);
de.programs_display_value =
this.getCommaSeparatedStringOfUniqueSortedValues(programsArray);
de.input_data_display_value =
this.getCommaSeparatedStringOfUniqueSortedValues(inputDataArray);

de.initial_nomination_display_value = initialNominationArray.length
? Math.min(...initialNominationArray)
Expand Down Expand Up @@ -185,31 +162,37 @@ export class GeneNominatedTargetsComponent implements OnInit {
});
}

removeNullAndEmptyStrings(items: (string | null)[]) {
return items.filter((item) => Boolean(item)) as string[];
}

getUnique(value: string, index: number, self: any) {
return self.indexOf(value) === index;
}

commaFlattenArray(array: any[]): any[] {
const finalArray: any[] = [];
if (array.length) {
array.forEach((t) => {
if (t) {
const i = t.indexOf(', ');
if (i > -1) {
const tmpArray = t.split(', ');
finalArray.push(tmpArray[0]);
finalArray.push(tmpArray[1]);
} else {
finalArray.push(t);
}
} else {
finalArray.push('');
}
});
array = finalArray;
}
commaFlattenArray(array: string[]): string[] {
const finalArray: string[] = [];
array.forEach((t) => {
const i = t.indexOf(', ');
if (i > -1) {
const tmpArray = t.split(', ');
tmpArray.forEach((val) => finalArray.push(val));
} else {
finalArray.push(t);
}
});
return finalArray;
}

return array;
getCommaSeparatedStringOfUniqueSortedValues(inputArray: string[]) {
let display_value = '';
if (inputArray.length) {
display_value = inputArray
.filter(this.getUnique)
.sort((a: string, b: string) => a.localeCompare(b))
.join(', ');
}
return display_value;
}

onSearch(event: any) {
Expand Down
2 changes: 1 addition & 1 deletion src/app/models/genes.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ export interface TargetNomination {
predicted_therapeutic_direction: string;
data_used_to_support_target_selection: string;
data_synapseid: string;
study: string;
study: string | null;
input_data: string;
validation_study_details: string;
initial_nomination: number;
Expand Down
20 changes: 19 additions & 1 deletion src/app/testing/gene-mocks.ts
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Original file line number Diff line number Diff line change
@@ -1,6 +1,24 @@
/* eslint-disable */

import { Gene, GCTGene } from '../models';
import { Gene, GCTGene, TargetNomination } from '../models';

export const targetNominationMock1: TargetNomination = {
source: 'Treat-AD',
team: 'Emory-Sage-SGC',
rank: '7',
hgnc_symbol: 'MSN',
target_choice_justification:
'MSN was identified as a potential driver protein based on protein coexpression analysis. The group of proteins coexpressed with MSN is conserved across the 3 datasets considered, is enriched for inflammatory processes, and for protein products of genes near loci previously associated with AD risk. MSN has increased abundance in AD across all 3 cohorts examined, and progressively increases in asymptomatic (prodromal) AD to symptomatic AD, and also correlates with both hallmark AD pathology scores (CERAD for amyloid burden; and Braak for Tau extent of spread). MSN is highly expressed as a marker of disease-associated microglia and/or endothelial cell types.',
predicted_therapeutic_direction:
'Antagonism predicted to reduce disease progression. Phosphorylation downstream of Rho/Rock influences actin, focal adhesion binding; may have redundancy with EZR and RDX, complicating targeting. MSN-directed therapeutics that improve microglial motility and/or phagocytosis competence would reduce abeta/amyloid plaque burden.',
data_used_to_support_target_selection:
'Discovery quantitative proteomics of FrCx \r\n WPCNA of multiple and consensus cohorts\r\n ANOVA',
data_synapseid: 'syn17008058',
study: 'ACT, BLSA, Banner',
input_data: 'Protein',
validation_study_details: 'validation studies ongoing',
initial_nomination: 2018,
};

export const geneMock1: Gene = {
_id: '628ea1be0e8d04279fdbaa26',
Expand Down

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