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#318. Add datasets download for experiments related to a gene
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@const8ine
const8ine committed Sep 29, 2024
1 parent e557505 commit 9c6286f
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Showing 9 changed files with 378 additions and 157 deletions.
2 changes: 2 additions & 0 deletions src/app/core/models/open-genes-api/studies.model.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -180,6 +180,8 @@ export interface PinkTable extends Research {
ethnicity: string | null;
studyType: string | null;
location?: string | null; // TODO: Will be added according to OG-809
significance?: string | null;
pValue?: string | null;
}

// gray form
Expand Down
200 changes: 106 additions & 94 deletions src/app/core/services/csv-export-service.ts
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
import { Injectable } from '@angular/core';
import { AdditionalInterventionResolver } from '../utils/additional-intervention-resolver';
import { PurpleTable } from '../models/open-genes-api/studies.model';
import { BlueTable, GreenTable, PinkTable, PurpleTable, YellowTable } from '../models/open-genes-api/studies.model';
import { environment } from '../../../environments/environment';


@Injectable({
providedIn: 'root',
})
Expand All @@ -19,6 +20,7 @@ export class CsvExportService extends AdditionalInterventionResolver {
super();
}

// Basic service functionality
static wait(delay) {
return new Promise((resolve) => setTimeout(resolve, delay));
}
Expand Down Expand Up @@ -82,6 +84,21 @@ export class CsvExportService extends AdditionalInterventionResolver {
return null;
}

// eslint-disable-next-line @typescript-eslint/ban-types
public async fetchStudyFromEndpoint(url: string, fn: Function): Promise<void> {
const response: Response = await CsvExportService.FetchData(
url,
0,
1,
{}
);
if (response) {
const resJson = await response.json();
fn(resJson.items)
}
}

// Other datasets
public async generateGenesDiseasesTable() {
return await this.generateSimplePairCsv(["hgnc", "diseases"], 'diseases');
}
Expand Down Expand Up @@ -177,7 +194,73 @@ export class CsvExportService extends AdditionalInterventionResolver {
return null;
}

public async generatePinkTable() {
public async generateGeneEvolutionTable() {
let items = [];
let resultingString = '';
const fetchedItems = await CsvExportService.FetchData(
`${this.apiUrl}/api/gene/search?pageSize=${this.maxPageSize}`,
0,
1,
{}
);
const resItems = await fetchedItems.json();
items = resItems.items;
const csvHeader = this.makeRow(['hgnc', 'gene_origin', 'gene_family_origin', 'conservative_in']);
resultingString = resultingString + csvHeader;

if (items.length !== 0) {
for (const gene of items) {
const origin = this.checkBlankValues(gene.origin?.phylum);
const familyOrigin = this.checkBlankValues(gene.familyOrigin?.phylum);
const conservativeIn = this.checkBlankValues(gene.homologueTaxon);
const arrRow = this.makeRow([gene.symbol, origin, familyOrigin, conservativeIn]);
resultingString = resultingString + arrRow;
}
return resultingString;
}
return null;
}

// Studies
// - Fetch data

public async fetchPinkTable(): Promise<void> {
await this.fetchStudyFromEndpoint(
`${this.apiUrl}/api/research/associations-with-lifespan?pageSize=${this.maxPageSize}`,
this.generatePinkTable.bind(CsvExportService)
);
}

public async fetchPurpleTable(): Promise<void> {
await this.fetchStudyFromEndpoint(
`${this.apiUrl}/api/research/lifespan-change?pageSize=${this.maxPageSize}`,
this.generatePurpleTable.bind(CsvExportService)
);
}

public async fetchGreenTable(): Promise<void> {
await this.fetchStudyFromEndpoint(
`${this.apiUrl}/api/research/gene-activity-change-impact?pageSize=${this.maxPageSize}`,
this.generateGreenTable.bind(CsvExportService)
);
}

public async fetchBlueTable(): Promise<void> {
await this.fetchStudyFromEndpoint(
`${this.apiUrl}/api/research/age-related-changes?pageSize=${this.maxPageSize}`,
this.generateBlueTable.bind(CsvExportService)
);
}

public async fetchYellowTable(): Promise<void> {
await this.fetchStudyFromEndpoint(
`${this.apiUrl}/api/research/gene-regulation?pageSize=${this.maxPageSize}`,
this.generateYellowTable.bind(CsvExportService)
);
}

// - Generate datasets
public generatePinkTable(studies: PinkTable[]) {
let resultingString = '';
const csvHeader = this.makeRow([
'hgnc',
Expand Down Expand Up @@ -212,17 +295,8 @@ export class CsvExportService extends AdditionalInterventionResolver {
]);
resultingString = resultingString + csvHeader;

const response = await CsvExportService.FetchData(
`${this.apiUrl}/api/research/associations-with-lifespan?pageSize=${this.maxPageSize}`,
0,
1,
{}
);
if (response) {
const resJson = await response.json();
const researches = resJson.items;
if (researches) {
for (const form of researches) {
if (studies) {
for (const form of studies) {
if (typeof form !== undefined) {
let comment = this.sanitize(form?.comment);
comment = this.checkBlankValues(comment);
Expand Down Expand Up @@ -291,11 +365,11 @@ export class CsvExportService extends AdditionalInterventionResolver {
}
return resultingString;
}
}

return null;
}

public async generateYellowTable() {
public generateYellowTable(studies: YellowTable[]) {
let resultingString = '';
const csvHeader = this.makeRow([
'hgnc',
Expand All @@ -308,17 +382,8 @@ export class CsvExportService extends AdditionalInterventionResolver {
]);
resultingString = resultingString + csvHeader;

const response = await CsvExportService.FetchData(
`${this.apiUrl}/api/research/gene-regulation?pageSize=${this.maxPageSize}`,
0,
1,
{}
);
if (response) {
const resJson = await response.json();
const researches = resJson.items;
if (researches) {
for (const form of researches) {
if (studies) {
for (const form of studies) {
if (typeof form !== undefined) {
let comment = this.sanitize(form?.comment);
comment = this.checkBlankValues(comment);
Expand All @@ -335,11 +400,11 @@ export class CsvExportService extends AdditionalInterventionResolver {
}
return resultingString;
}
}

return null;
}

public async generatePurpleTable() {
public generatePurpleTable(studies: PurpleTable[]) {
let resultingString = '';
const csvHeader = this.makeRow([
'hgnc',
Expand Down Expand Up @@ -388,18 +453,8 @@ export class CsvExportService extends AdditionalInterventionResolver {
]);
resultingString = resultingString + csvHeader;

// TODO: OG-811
const response = await CsvExportService.FetchData(
`${this.apiUrl}/api/research/lifespan-change?pageSize=${this.maxPageSize}`,
0,
1,
{}
);
if (response) {
const resJson = await response.json();
const researches: PurpleTable[] = resJson.items;
if (researches) {
for (const form of researches) {
if (studies) {
for (const form of studies) {
if (typeof form !== undefined) {
const isNoAdditionalIntervention = this.resolveAdditionalIntervention(form);

Expand Down Expand Up @@ -553,16 +608,18 @@ export class CsvExportService extends AdditionalInterventionResolver {
pmid,
]);
resultingString = resultingString + csvRow;
} else {
resultingString = 'All experiments contain additional interventions. Generation of datasets with additional interventions is not yet implemented.'
}
}
}
return resultingString;
}
}

return null;
}

public async generateGreenTable() {
public generateGreenTable(studies: GreenTable[]) {
let resultingString = '';
const csvHeader = this.makeRow([
'hgnc',
Expand All @@ -582,17 +639,8 @@ export class CsvExportService extends AdditionalInterventionResolver {
]);
resultingString = resultingString + csvHeader;

const response = await CsvExportService.FetchData(
`${this.apiUrl}/api/research/gene-activity-change-impact?pageSize=${this.maxPageSize}`,
0,
1,
{}
);
if (response) {
const resJson = await response.json();
const researches = resJson.items;
if (researches) {
for (const form of researches) {
if (studies) {
for (const form of studies) {
if (typeof form !== undefined) {
const geneSymbol = this.sanitize(form?.geneSymbol);
let comment = this.sanitize(form?.comment);
Expand Down Expand Up @@ -647,11 +695,11 @@ export class CsvExportService extends AdditionalInterventionResolver {
}
return resultingString;
}
}

return null;
}

public async generateBlueTable() {
public generateBlueTable(studies: BlueTable[]) {
let resultingString = '';
const csvHeader = this.makeRow([
'hgnc',
Expand Down Expand Up @@ -680,17 +728,8 @@ export class CsvExportService extends AdditionalInterventionResolver {
]);
resultingString = resultingString + csvHeader;

const response = await CsvExportService.FetchData(
`${this.apiUrl}/api/research/age-related-changes?pageSize=${this.maxPageSize}`,
0,
1,
{}
);
if (response) {
const resJson = await response.json();
const researches = resJson.items;
if (researches) {
for (const form of researches) {
if (studies) {
for (const form of studies) {
if (typeof form !== undefined) {
const geneSymbol = this.sanitize(form?.geneSymbol);
let comment = this.sanitize(form?.comment);
Expand Down Expand Up @@ -746,7 +785,7 @@ export class CsvExportService extends AdditionalInterventionResolver {
}
return resultingString;
}
}

return null;
}

Expand Down Expand Up @@ -943,31 +982,4 @@ export class CsvExportService extends AdditionalInterventionResolver {
}
return null;
}

public async generateGeneEvolutionTable() {
let items = [];
let resultingString = '';
const fetchedItems = await CsvExportService.FetchData(
`${this.apiUrl}/api/gene/search?pageSize=${this.maxPageSize}`,
0,
1,
{}
);
const resItems = await fetchedItems.json();
items = resItems.items;
const csvHeader = this.makeRow(['hgnc', 'gene_origin', 'gene_family_origin', 'conservative_in']);
resultingString = resultingString + csvHeader;

if (items.length !== 0) {
for (const gene of items) {
const origin = this.checkBlankValues(gene.origin?.phylum);
const familyOrigin = this.checkBlankValues(gene.familyOrigin?.phylum);
const conservativeIn = this.checkBlankValues(gene.homologueTaxon);
const arrRow = this.makeRow([gene.symbol, origin, familyOrigin, conservativeIn]);
resultingString = resultingString + arrRow;
}
return resultingString;
}
return null;
}
}
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