diff --git a/.github/workflows/test-cov.yml b/.github/workflows/test-cov.yml new file mode 100644 index 0000000..baa27f4 --- /dev/null +++ b/.github/workflows/test-cov.yml @@ -0,0 +1,45 @@ +# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-nodejs-with-github-actions + +name: Test + +on: ["push", "pull_request"] + +jobs: + build: + name: Generate coverage report + runs-on: ubuntu-latest + steps: + + - name: Get branch name + id: branch-name + uses: tj-actions/branch-names@v6 + + - uses: actions/checkout@v3 + with: + repository: biothings/biothings_explorer + ref: ${{ steps.branch-name.outputs.current_branch }} + + - name: Use Node.js 18.x + uses: actions/setup-node@v3 + with: + node-version: 18.x + + - name: Use pnpm + uses: pnpm/action-setup@v2 + with: + version: 8 + + - name: pnpm install, generate coverage report + run: | + pnpm run clone + pnpm run git checkout ${{ steps.branch-name.outputs.current_branch }} + pnpm i + pnpm --filter node-expansion test-cov + + - name: Send coverage report to codecov for visualization + uses: codecov/codecov-action@v3 + with: + # working-directory: ./packages/@biothings-explorer/bte-trapi + files: ./coverage/lcov.info + verbose: true diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml deleted file mode 100644 index c9aeb43..0000000 --- a/.github/workflows/test.yml +++ /dev/null @@ -1,26 +0,0 @@ -# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-nodejs-with-github-actions - -name: Test - -on: ["push", "pull_request"] - -jobs: - build: - - runs-on: ubuntu-latest - - strategy: - matrix: - node-version: [16.x] - # See supported Node.js release schedule at https://nodejs.org/en/about/releases/ - - steps: - - uses: actions/checkout@v3 - - name: Use Node.js ${{ matrix.node-version }} - uses: actions/setup-node@v3 - with: - node-version: ${{ matrix.node-version }} - cache: 'npm' - - run: npm ci - - run: npm test diff --git a/.gitignore b/.gitignore index e52977d..b65fe00 100644 --- a/.gitignore +++ b/.gitignore @@ -130,4 +130,7 @@ dist .yarn/unplugged .yarn/build-state.yml .yarn/install-state.gz -.pnp.* \ No newline at end of file +.pnp.* + +# Built output +built diff --git a/README.md b/README.md index 02fd534..e6a9df7 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ Module for expanding terms to children. ## Install ``` -npm i @biothings-explorer/node-expansion +pnpm i @biothings-explorer/node-expansion ``` ## Usage @@ -61,4 +61,4 @@ console.log(getDescendants(['GO:0022010', 'DOID:0060524', 'DOID:4'], recursive=f ``` node download.js ``` - - downloads, converts, and parses all the owl files listed in the config file \ No newline at end of file + - downloads, converts, and parses all the owl files listed in the config file diff --git a/package-lock.json b/package-lock.json deleted file mode 100644 index 7020a47..0000000 --- a/package-lock.json +++ /dev/null @@ -1,6151 +0,0 @@ -{ - 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"dev": true - }, - "yocto-queue": { - "version": "0.1.0", - "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", - "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", - "dev": true - } - } -} diff --git a/package.json b/package.json index 4574e25..639e58c 100644 --- a/package.json +++ b/package.json @@ -2,9 +2,17 @@ "name": "@biothings-explorer/node-expansion", "version": "1.0.1", "description": "Module for expanding terms to children.", - "main": "src/index.js", + "main": "built/index.js", "scripts": { - "test": "jest" + "build": "tsc -b", + "prepare": "pnpm run build", + "clean": "rimraf ./built './**/tsconfig.tsbuildinfo'", + "test": "jest", + "test-cov": "jest --coverage", + "format": "prettier --check 'src/**/*.js'", + "format:fix": "prettier --write 'src/**/*.js'", + "lint": "eslint . --ext .js", + "lint:fix": "pnpm lint --fix" }, "author": "", "license": "ISC", @@ -13,6 +21,18 @@ "lodash": "^4.17.21" }, "devDependencies": { - "jest": "^28.1.3" + "@types/debug": "^4.1.10", + "@types/lodash": "^4.14.200", + "@types/node": "^20.8.7", + "@typescript-eslint/eslint-plugin": "^6.8.0", + "@typescript-eslint/parser": "^6.8.0", + "eslint": "^8.52.0", + "eslint-config-prettier": "^9.0.0", + "eslint-plugin-prettier": "^5.0.1", + "jest": "^29.7.0", + "prettier": "^3.0.3", + "rimraf": "^3.0.2", + "ts-jest": "^29.1.1", + "typescript": "^5.2.2" } } diff --git a/src/config.js b/src/config.js index 01f66f2..dd950af 100644 --- a/src/config.js +++ b/src/config.js @@ -1,34 +1,36 @@ exports.ONTOLOGIES = { - 'doid': { - 'name': 'doid', - 'url': 'http://purl.obolibrary.org/obo/doid.owl' + doid: { + name: "doid", + url: "http://purl.obolibrary.org/obo/doid.owl", }, - 'go': { - 'name': 'go', - 'url': 'http://purl.obolibrary.org/obo/go.owl' - }, - 'mondo': { - 'name': 'mondo', - 'url': 'http://purl.obolibrary.org/obo/mondo.owl' + go: { + name: "go", + url: "http://purl.obolibrary.org/obo/go.owl", }, - 'hp': { - 'name': 'hp', - 'url': 'http://purl.obolibrary.org/obo/hp.owl' + mondo: { + name: "mondo", + url: "http://purl.obolibrary.org/obo/mondo.owl", }, - 'chebi': { // not sure why but downloading chebi.owl using curl or node js fails - 'name': 'chebi', - 'url': 'https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl' - }, - 'umls': { // manually processed from MRREL.REF file in UMLS dump - 'name': 'umls' - } -} + hp: { + name: "hp", + url: "http://purl.obolibrary.org/obo/hp.owl", + }, + chebi: { + // not sure why but downloading chebi.owl using curl or node js fails + name: "chebi", + url: "https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl", + }, + umls: { + // manually processed from MRREL.REF file in UMLS dump + name: "umls", + }, +}; exports.CHILD_RELATIONS = { - 'is_a': true, + is_a: true, // 'http://purl.obolibrary.org/obo/BFO_0000050': true, // part of -} +}; exports.PARENT_RELATIONS = { - 'http://purl.obolibrary.org/obo/BFO_0000051': true, // has part -} + "http://purl.obolibrary.org/obo/BFO_0000051": true, // has part +}; diff --git a/src/download.js b/src/download.js index 493351c..a968c66 100644 --- a/src/download.js +++ b/src/download.js @@ -1,7 +1,7 @@ //find and download and parse -const { ONTOLOGIES } = require('./config'); -const { parseFile } = require('./parser'); -const child_process = require('child_process'); +const { ONTOLOGIES } = require("./config"); +const { parseFile } = require("./parser"); +const child_process = require("child_process"); //iterate over ontologies obj for (let ontology of Object.values(ONTOLOGIES)) { @@ -11,21 +11,22 @@ for (let ontology of Object.values(ONTOLOGIES)) { let download_process = child_process.exec(`curl -o ../data/${ontology.name}.owl -L ${url}`); download_process.stdout.pipe(process.stdout); download_process.stderr.pipe(process.stderr); - - download_process.on('close', (code) => { + + download_process.on("close", code => { if (code !== 0) { console.log(`Error downloading ${url}`); return; } console.log(`Done downloading ${url} with code ${code}`); - + // use robot to convert owl to json - child_process.execSync(`../robot convert -i ../data/${ontology.name}.owl --format json -o ../data/${ontology.name}.json`); + child_process.execSync( + `../robot convert -i ../data/${ontology.name}.owl --format json -o ../data/${ontology.name}.json`, + ); console.log(`Parsing ${url}`); parseFile(`../data/${ontology.name}.json`); console.log(`Cleaning up ${url}`); child_process.exec(`rm ../data/${ontology.name}.owl`); child_process.exec(`rm ../data/${ontology.name}.json`); }); - } diff --git a/src/index.js b/src/index.js index 4cf2482..ebec271 100644 --- a/src/index.js +++ b/src/index.js @@ -1,5 +1,5 @@ -const { ONTOLOGIES } = require('./config'); -const _ = require('lodash'); +const { ONTOLOGIES } = require("./config"); +const _ = require("lodash"); let data = {}; let loaded = false; @@ -13,12 +13,12 @@ const loadData = () => { for (let ontology in ONTOLOGIES) { const filename = `../data/${ontology}-parsed.json`; const ontologyData = require(filename); - data = {...data, ...ontologyData}; + data = { ...data, ...ontologyData }; } // const end = performance.now(); // console.log(`loadData took ${end - start} milliseconds.`); loaded = true; -} +}; //get all children of a list of curies exports.getDescendants = (curies, recursive = true) => { @@ -43,8 +43,7 @@ exports.getDescendants = (curies, recursive = true) => { children[curie] = _.uniq(children[curie]).slice(0, ENTITY_CAP); } return children; - } else - { + } else { return _.pick(data, curies); } -} +}; diff --git a/src/parser.js b/src/parser.js index ae6625c..3d904a9 100644 --- a/src/parser.js +++ b/src/parser.js @@ -1,29 +1,26 @@ -var fs = require('fs'); -const { CHILD_RELATIONS, PARENT_RELATIONS } = require('./config'); +var fs = require("fs"); +const { CHILD_RELATIONS, PARENT_RELATIONS } = require("./config"); -const urltoCurie = (url) => { - if (url.startsWith('http://purl.obolibrary.org/obo/')) { - return url.replace('http://purl.obolibrary.org/obo/', '').replace('_', ':'); +const urltoCurie = url => { + if (url.startsWith("http://purl.obolibrary.org/obo/")) { + return url.replace("http://purl.obolibrary.org/obo/", "").replace("_", ":"); } -} +}; -const parseFile = (filename) => { - let f = JSON.parse(fs.readFileSync(filename, 'utf8')); +const parseFile = filename => { + let f = JSON.parse(fs.readFileSync(filename, "utf8")); let map_edges = {}; - for (let edge of f.graphs[0].edges) - { - if (CHILD_RELATIONS[edge.pred]) - { + for (let edge of f.graphs[0].edges) { + if (CHILD_RELATIONS[edge.pred]) { let obj = urltoCurie(edge.obj); let sub = urltoCurie(edge.sub); - if (!map_edges[obj]) - { + if (!map_edges[obj]) { map_edges[obj] = []; } map_edges[obj].push(sub); - } + } // else if (PARENT_RELATIONS[edge.pred]) { // let obj = urltoCurie(edge.sub); // let sub = urltoCurie(edge.obj); @@ -34,9 +31,9 @@ const parseFile = (filename) => { // map_edges[obj].push(sub); // } } - + //export map_edges into json file - fs.writeFileSync(filename.replace('.json', '-parsed.json'), JSON.stringify(map_edges)); -} + fs.writeFileSync(filename.replace(".json", "-parsed.json"), JSON.stringify(map_edges)); +}; exports.parseFile = parseFile; diff --git a/tsconfig.json b/tsconfig.json new file mode 100644 index 0000000..c19044d --- /dev/null +++ b/tsconfig.json @@ -0,0 +1,14 @@ +{ + "extends": "../../tsconfig.base.json", + "compilerOptions": { + "rootDir": "./src", + "outDir": "./built" + }, + "include": [ + "./src/**/*" + ], + "exclude": [ + "**/node_modules/**", + "**/__test__/**" + ] +}