From ff1c338db4ed6275c764160b226324b221ef0f04 Mon Sep 17 00:00:00 2001 From: KeithKelleher Date: Fri, 13 Oct 2023 15:15:54 -0400 Subject: [PATCH 1/2] Deidre's changes and framework updates --- app.ts | 7 + data_sources/coexpression-data/index.ts | 105 +++ .../pairwise-relationship-data/index.ts | 40 + .../pairwiseService.ts | 53 ++ index.js | 6 +- models/prediction.ts | 7 +- package-lock.json | 881 +++++++++++++----- package.json | 13 +- 8 files changed, 857 insertions(+), 255 deletions(-) create mode 100644 data_sources/coexpression-data/index.ts create mode 100644 data_sources/pairwise-relationship-data/index.ts create mode 100644 data_sources/pairwise-relationship-data/pairwiseService.ts diff --git a/app.ts b/app.ts index 62351a3..b81e5b0 100644 --- a/app.ts +++ b/app.ts @@ -3,6 +3,9 @@ import express, {Application, Request, Response} from 'express'; import {ping, sample} from "./models/endpoints"; // @ts-ignore import {predictions} from "./data_sources/kinase-cancer-predictions/index" +import {interactorScores} from "./data_sources/pairwise-relationship-data"; +import {coexpressionData} from "./data_sources/coexpression-data"; + const app: Application = express() const port: number = 3001 @@ -13,6 +16,10 @@ app.get("/sample?*", (req: Request, res: Response) => sample(req, res)); app.get("/predictions?*", (req: Request, res: Response) => predictions(req, res)); +app.get("/interactorScores?*", (req: Request, res: Response) => interactorScores(req, res)); + +app.get("/coexpressionData?*", (req: Request, res: Response) => coexpressionData(req, res)); + app.listen(port, function () { console.log(`App is listening on port ${port} !`) }); diff --git a/data_sources/coexpression-data/index.ts b/data_sources/coexpression-data/index.ts new file mode 100644 index 0000000..5266d91 --- /dev/null +++ b/data_sources/coexpression-data/index.ts @@ -0,0 +1,105 @@ +import {Request, Response} from "express"; +import {setHeaders} from "../../models/endpoints"; +import url from "url"; +import querystring from "querystring"; +import PairwiseService from "../pairwise-relationship-data/pairwiseService"; +import {PredictionSet} from "../../models/prediction"; +import {getMinimalCitation} from "../../models/modelData"; + +function formatCancerSpecificData(data: any) { + const ps = new PredictionSet("Cancer Specific Coexpression", "Protein", "", + "", 1, 0, null, "Coexpressed Target", + ["Data Source", "Cancer Type", "Coexpressed Target"]); + Object.entries(data).forEach((match: any) => { + { + match = match[1]; + let dataSource = match.dataDesc.id.split("|")[0]; + let cancerType = match.dataDesc.id.split("|")[1]; + match.posGenes.forEach((gene: any) => { + const extraFields: any = + { + identifier: [ + { + "@type": "PropertyValue", + "name": "Data Source", + "value": dataSource + }, + { + "@type": "PropertyValue", + "name": "Cancer Type", + "value": cancerType + } + ], + }; + ps.addPrediction(gene, "", null, extraFields); + }) + } + }) + return ps; +} + +function formatTissueSpecificData(data: any) { + const ps = new PredictionSet("Tissue Specific Coexpression", "Protein", "", + "", 1, 0, null, "Coexpressed Target", + ["Data Source", "Tissue", "Coexpressed Target"]); + Object.entries(data).forEach((match: any) => { + { + match = match[1]; + let dataSource = match.dataDesc.id.split("|")[0]; + let tissue = match.dataDesc.id.split("|")[1]; + match.posGenes.forEach((gene: any) => { + const extraFields: any = + { + identifier: [ + { + "@type": "PropertyValue", + "name": "Data Source", + "value": dataSource + }, { + "@type": "PropertyValue", + "name": "Tissue", + "value": tissue + }], + }; + ps.addPrediction(gene, "", null, extraFields); + }) + } + }) + ps.addCitation(getMinimalCitation(37333417)); + return ps; +} + +export async function coexpressionData(req: Request, res: Response): Promise{ + setHeaders(res); + const parsedUrl = url.parse(req.url); + const queryMap = querystring.parse(parsedUrl.query); + if (queryMap.target) { + const targetQuery = queryMap.target.toString(); + const csDataDescriptions: any = PairwiseService.getAllDataDescs('TCGA', 'Gene_Coexpression'); + const tsDataDescriptions: any = PairwiseService.getAllDataDescs('GTEx', 'Gene_Coexpression'); + + return Promise.all([csDataDescriptions, tsDataDescriptions]).then((dataDescriptionResults: any[]) => { + const csDataDescIds = dataDescriptionResults[0].map((o: any) => Object(o.id)); + const tsDataDescIds = dataDescriptionResults[1].map((o: any) => Object(o.id)); + + const csPairwiseSearch = PairwiseService.searchTermSecondaryPathways( + { + "genes": [targetQuery], + "dataDescs": csDataDescIds + }); + const tsPairwiseSearch = PairwiseService.searchTermSecondaryPathways( + { + "genes": [targetQuery], + "dataDescs": tsDataDescIds + }); + return Promise.all([csPairwiseSearch, tsPairwiseSearch]).then((pwSearchResults: any[]) => { + const csPs = formatCancerSpecificData(pwSearchResults[0]); + const tsPs = formatTissueSpecificData(pwSearchResults[1]); + res.end(JSON.stringify([tsPs.asJSON(), csPs.asJSON()])); + }) + }); + } + res.end("No Protein Provided!"); +} + +exports.coexpressionData = coexpressionData; \ No newline at end of file diff --git a/data_sources/pairwise-relationship-data/index.ts b/data_sources/pairwise-relationship-data/index.ts new file mode 100644 index 0000000..e9c8791 --- /dev/null +++ b/data_sources/pairwise-relationship-data/index.ts @@ -0,0 +1,40 @@ +import {Request, Response} from "express"; +import {setHeaders} from "../../models/endpoints"; +import querystring from "querystring"; +import PairwiseService from "./pairwiseService"; +import url from "url"; +import {PredictionSet} from "../../models/prediction"; +import {getMinimalCitation} from "../../models/modelData"; + +export async function interactorScores(req: Request, res: Response): Promise { + setHeaders(res); + const parsedUrl = url.parse(req.url); + const queryMap = querystring.parse(parsedUrl.query); + + if (queryMap.target) { + const targetQuery = queryMap.target.toString(); + const score = +queryMap.score || 0.5; + try { + await PairwiseService.getInteractorScoresForTerm(targetQuery, score) + .then(data => { + const ps = new PredictionSet("Reactome Functional Interactions (FIs)", "Protein", "FI Score", + "Score of how likely two proteins are to interact with each other functionally", + 1, 0, null, "FI Partner"); + Object.entries(data).forEach((intScore: any) => { + { + intScore = intScore[1] + ps.addPrediction(intScore.gene, "", intScore.score); + } + }) + ps.addCitation(getMinimalCitation(37333417)); + res.end(JSON.stringify([ps.asJSON()])) + }); + return; + } catch (err) { + console.error(err); + } + } + res.end("No Protein Provided!"); +} + +exports.interactorScores = interactorScores; diff --git a/data_sources/pairwise-relationship-data/pairwiseService.ts b/data_sources/pairwise-relationship-data/pairwiseService.ts new file mode 100644 index 0000000..0ccb54a --- /dev/null +++ b/data_sources/pairwise-relationship-data/pairwiseService.ts @@ -0,0 +1,53 @@ +import axios from "axios"; + +class PairwiseService { + static getInteractorScoresForTerm(term: string, cutoff: number) { + return new Promise((resolve, reject) => { + axios + .get(`https://idg.reactome.org/idgpairwise/relationships/combinedScoreGenesForTerm/${term}`) + .then((res) => { + resolve( + Object.entries(res.data).map(([gene, score]) => ({ + gene: gene, + score: score, + // @ts-ignore + })).filter(({score}) => score >= cutoff) + ); + }) + .catch((err) => { + reject(err); + }); + }); + } + + static searchTermSecondaryPathways(postData: {}) { + return new Promise((resolve, reject) => { + axios + .post(`https://idg.reactome.org/idgpairwise/pairwise/term/false`, postData) + .then((res) => { + resolve(res.data); + }) + .catch((err) => { + reject(err); + }); + }); + } + + static getAllDataDescs(provenance: string, dataType: string) { + return new Promise((resolve, reject) => { + axios + .get(`https://idg.reactome.org/idgpairwise/datadesc`) + .then((res) => { + resolve( + res.data.filter((desc: any) => + desc.provenance === provenance && + desc.dataType === dataType)) + }) + .catch((err) => { + reject(err); + }); + }); + } +} + +export default PairwiseService; \ No newline at end of file diff --git a/index.js b/index.js index 1436fc1..851c2a6 100644 --- a/index.js +++ b/index.js @@ -1,6 +1,10 @@ const endpoints = require("./models/endpoints"); const kinasecancer = require("./data_sources/kinase-cancer-predictions/index") +const interactorScores = require("./data_sources/pairwise-relationship-data/index"); +const coexpressionData = require("./data_sources/coexpression-data/index"); exports.ping = endpoints.ping; exports.sample = endpoints.sample; -exports.predictions = kinasecancer.predictions; \ No newline at end of file +exports.predictions = kinasecancer.predictions; +exports.interactorScores = interactorScores.interactorScores; +exports.coexpressionData = coexpressionData.coexpressionData; \ No newline at end of file diff --git a/models/prediction.ts b/models/prediction.ts index bcfdd88..3cfbd95 100644 --- a/models/prediction.ts +++ b/models/prediction.ts @@ -23,6 +23,7 @@ export class PredictionSet { confMin: number; style: "table" | "card"; citation: any; + facetFields: string[]; predictions: Prediction[] = []; @@ -33,7 +34,7 @@ export class PredictionSet { confMax: number, confMin: number, style: "table" | "card" = "table", - alternateName?: string) { + alternateName?: string, facetFields: string[] = ['confidence']) { this.name = name; this.schemaType = schemaType; this.confidenceName = confidenceName; @@ -41,6 +42,7 @@ export class PredictionSet { this.confMax = confMax; this.confMin = confMin; this.style = style; + this.facetFields = facetFields; if (alternateName) { this.alternateName = alternateName; } @@ -70,7 +72,8 @@ export class PredictionSet { "description": this.confidenceDescription, "maxValue": this.confMax, "minValue": this.confMin - } + }, + "facetFields": this.facetFields }; if (this.alternateName) { predictionObj.alternateName = this.alternateName; diff --git a/package-lock.json b/package-lock.json index 10363e3..b878e54 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,185 +1,238 @@ { "name": "pharos-predictions-test-api", "version": "1.0.5", - "lockfileVersion": 1, + "lockfileVersion": 3, "requires": true, - "dependencies": { - "@cspotcode/source-map-support": { + "packages": { + "": { + "name": "pharos-predictions-test-api", + "version": "1.0.5", + "license": "MIT", + "dependencies": { + "@types/express": "^4.17.14", + "@types/node": "^18.11.9", + "axios": "^0.21.1", + "csv": "^6.0.5", + "csv-parse": "^5.3.3", + "csv-parser": "^3.0.0", + "express": "^4.18.2", + "fast-xml-parser": "^4.2.4", + "ts-node": "^10.9.1", + "typescript": "^4.8.4", + "typescript-require": "^0.3.0" + }, + "devDependencies": { + "nodemon": "^2.0.20" + } + }, + "node_modules/@cspotcode/source-map-support": { 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"echo \"Error: no test specified\" && exit 1" + "test": "echo \"Error: no test specified\" && exit 1", + "deploy-interactorScores": "gcloud functions deploy interactorScores --project=ncatsidg --region=us-east4 --runtime=nodejs18 --entry-point=interactorScores --trigger-http", + "deploy-coexpressionData": "gcloud functions deploy coexpressionData --project=ncatsidg --region=us-east4 --runtime=nodejs18 --entry-point=coexpressionData --trigger-http", + "deploy-predictions": "gcloud functions deploy predictions --project=ncatsidg --region=us-east4 --runtime=nodejs18 --entry-point=predictions --trigger-http", + "deploy-sample": "gcloud functions deploy sample --project=ncatsidg --region=us-east4 --runtime=nodejs18 --entry-point=sample --trigger-http", + "deploy-ping": "gcloud functions deploy ping --project=ncatsidg --region=us-east4 --runtime=nodejs18 --entry-point=ping --trigger-http" }, "repository": { "type": "git", @@ -27,15 +32,17 @@ }, "homepage": "https://github.com/KeithKelleher/pharos-predictions-test-api#readme", "dependencies": { - "csv": "^6.0.5", "@types/express": "^4.17.14", "@types/node": "^18.11.9", + "csv": "^6.0.5", "csv-parse": "^5.3.3", + "csv-parser": "^3.0.0", "express": "^4.18.2", "fast-xml-parser": "^4.2.4", "ts-node": "^10.9.1", "typescript": "^4.8.4", - "typescript-require": "^0.3.0" + "typescript-require": "^0.3.0", + "axios": "^0.21.1" }, "devDependencies": { "nodemon": "^2.0.20" From 87b63f223407c8c818fd49c446d477ab478e7d7d Mon Sep 17 00:00:00 2001 From: = <=> Date: Fri, 20 Sep 2024 12:38:14 -0400 Subject: [PATCH 2/2] fix error when there's no data --- data_sources/coexpression-data/index.ts | 72 +++++++++++++------------ 1 file changed, 38 insertions(+), 34 deletions(-) diff --git a/data_sources/coexpression-data/index.ts b/data_sources/coexpression-data/index.ts index 5266d91..6044ded 100644 --- a/data_sources/coexpression-data/index.ts +++ b/data_sources/coexpression-data/index.ts @@ -15,24 +15,26 @@ function formatCancerSpecificData(data: any) { match = match[1]; let dataSource = match.dataDesc.id.split("|")[0]; let cancerType = match.dataDesc.id.split("|")[1]; - match.posGenes.forEach((gene: any) => { - const extraFields: any = - { - identifier: [ - { - "@type": "PropertyValue", - "name": "Data Source", - "value": dataSource - }, - { - "@type": "PropertyValue", - "name": "Cancer Type", - "value": cancerType - } - ], - }; - ps.addPrediction(gene, "", null, extraFields); - }) + if (match && match.posGenes) { + match.posGenes.forEach((gene: any) => { + const extraFields: any = + { + identifier: [ + { + "@type": "PropertyValue", + "name": "Data Source", + "value": dataSource + }, + { + "@type": "PropertyValue", + "name": "Cancer Type", + "value": cancerType + } + ], + }; + ps.addPrediction(gene, "", null, extraFields); + }); + } } }) return ps; @@ -47,22 +49,24 @@ function formatTissueSpecificData(data: any) { match = match[1]; let dataSource = match.dataDesc.id.split("|")[0]; let tissue = match.dataDesc.id.split("|")[1]; - match.posGenes.forEach((gene: any) => { - const extraFields: any = - { - identifier: [ - { - "@type": "PropertyValue", - "name": "Data Source", - "value": dataSource - }, { - "@type": "PropertyValue", - "name": "Tissue", - "value": tissue - }], - }; - ps.addPrediction(gene, "", null, extraFields); - }) + if (match && match.posGenes) { + match.posGenes.forEach((gene: any) => { + const extraFields: any = + { + identifier: [ + { + "@type": "PropertyValue", + "name": "Data Source", + "value": dataSource + }, { + "@type": "PropertyValue", + "name": "Tissue", + "value": tissue + }], + }; + ps.addPrediction(gene, "", null, extraFields); + }) + } } }) ps.addCitation(getMinimalCitation(37333417));