style: prettier formatting

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
+};

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`);
   });
-
 }

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);
   }
-}
+};

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;