├── .gitignore ├── index.js ├── .travis.yml ├── docs ├── fonts │ ├── OpenSans-Bold-webfont.eot │ ├── OpenSans-Bold-webfont.woff │ ├── OpenSans-Italic-webfont.eot │ ├── OpenSans-Light-webfont.eot │ ├── OpenSans-Light-webfont.woff │ ├── OpenSans-Italic-webfont.woff │ ├── OpenSans-Regular-webfont.eot │ ├── OpenSans-Regular-webfont.woff │ ├── OpenSans-BoldItalic-webfont.eot │ ├── OpenSans-BoldItalic-webfont.woff │ ├── OpenSans-LightItalic-webfont.eot │ ├── OpenSans-LightItalic-webfont.woff │ └── OpenSans-Light-webfont.svg ├── README.hbs ├── scripts │ ├── linenumber.js │ └── prettify │ │ ├── lang-css.js │ │ ├── Apache-License-2.0.txt │ │ └── prettify.js ├── index.html ├── styles │ ├── prettify-jsdoc.css │ ├── prettify-tomorrow.css │ └── jsdoc-default.css ├── emitter.js.html ├── util.js.html ├── module-emitter.html ├── obo.js.html ├── module-util.html └── module-bionode-obo.html ├── README.md ├── test ├── obo.spec.js ├── test.js └── SyRO.obo ├── src ├── emitter.js ├── util.js └── obo.js ├── package.json └── CODE_OF_CONDUCT.md /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | *.swp 3 | node_modules 4 | -------------------------------------------------------------------------------- /index.js: -------------------------------------------------------------------------------- 1 | module.exports = require('./src/obo.js') 2 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: node_js 2 | node_js: 3 | - "7" 4 | -------------------------------------------------------------------------------- /docs/fonts/OpenSans-Bold-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-obo/master/docs/fonts/OpenSans-Bold-webfont.eot 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-obo/master/docs/fonts/OpenSans-Regular-webfont.woff -------------------------------------------------------------------------------- /docs/fonts/OpenSans-BoldItalic-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-obo/master/docs/fonts/OpenSans-BoldItalic-webfont.eot -------------------------------------------------------------------------------- /docs/fonts/OpenSans-BoldItalic-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-obo/master/docs/fonts/OpenSans-BoldItalic-webfont.woff -------------------------------------------------------------------------------- /docs/fonts/OpenSans-LightItalic-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-obo/master/docs/fonts/OpenSans-LightItalic-webfont.eot -------------------------------------------------------------------------------- /docs/fonts/OpenSans-LightItalic-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bionode/bionode-obo/master/docs/fonts/OpenSans-LightItalic-webfont.woff -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # bionode-obo 2 | 3 | Parse OBO files, with streams! 4 | 5 | ## API Documentation 6 | 7 | See [here](https://rawgit.com/thejmazz/bionode-obo/master/docs/module-bionode-obo.html). 8 | 9 | ## License 10 | 11 | MIT [http://jmazz.mit-license.org](http://jmazz.mit-license.org) 12 | -------------------------------------------------------------------------------- /docs/README.hbs: -------------------------------------------------------------------------------- 1 | # bionode-obo 2 | 3 | Parse OBO files, with streams! 4 | 5 | ## API Documentation 6 | 7 | See [here](https://rawgit.com/thejmazz/bionode-obo/master/docs/module-bionode-obo.html). 8 | 9 | ## License 10 | 11 | MIT [http://jmazz.mit-license.org](http://jmazz.mit-license.org) 12 | -------------------------------------------------------------------------------- /test/obo.spec.js: -------------------------------------------------------------------------------- 1 | 'use strict' 2 | 3 | const chai = require('chai') 4 | const should = chai.should() 5 | 6 | const obo = require('../index.js') 7 | 8 | describe('obo', function() { 9 | describe('#parse()', function() { 10 | 11 | it('should be a function', function() { 12 | obo.parse.should.be.a('function') 13 | }) 14 | 15 | it.skip('should return `foo`', function() { 16 | obo.parse().should.equal('foo') 17 | }) 18 | }) 19 | }) 20 | -------------------------------------------------------------------------------- /src/emitter.js: -------------------------------------------------------------------------------- 1 | const EventEmitter = require('events') 2 | const util = require('util') 3 | 4 | /** 5 | * A small wrapper around custom event emitters. 6 | * @module emitter 7 | */ 8 | 9 | /** 10 | * Return a new custom event emitter 11 | * @return {object} a function inheriting from EventEmitter with a default 12 | * `#write()` method 13 | */ 14 | module.exports = function() { 15 | function customEmitter() { 16 | EventEmitter.call(this) 17 | } 18 | util.inherits(customEmitter, EventEmitter) 19 | 20 | customEmitter.prototype.write = function(data) { 21 | this.emit('data', data) 22 | } 23 | 24 | customEmitter.prototype.writeline = function(chunk) { 25 | this.emit('line', chunk) 26 | } 27 | 28 | return new customEmitter() 29 | } 30 | -------------------------------------------------------------------------------- /docs/scripts/linenumber.js: -------------------------------------------------------------------------------- 1 | /*global document */ 2 | (function() { 3 | var source = document.getElementsByClassName('prettyprint source linenums'); 4 | var i = 0; 5 | var lineNumber = 0; 6 | var lineId; 7 | var lines; 8 | var totalLines; 9 | var anchorHash; 10 | 11 | if (source && source[0]) { 12 | anchorHash = document.location.hash.substring(1); 13 | lines = source[0].getElementsByTagName('li'); 14 | totalLines = lines.length; 15 | 16 | for (; i < totalLines; i++) { 17 | lineNumber++; 18 | lineId = 'line' + lineNumber; 19 | lines[i].id = lineId; 20 | if (lineId === anchorHash) { 21 | lines[i].className += ' selected'; 22 | } 23 | } 24 | } 25 | })(); 26 | -------------------------------------------------------------------------------- /docs/scripts/prettify/lang-css.js: -------------------------------------------------------------------------------- 1 | PR.registerLangHandler(PR.createSimpleLexer([["pln",/^[\t\n\f\r ]+/,null," \t\r\n "]],[["str",/^"(?:[^\n\f\r"\\]|\\(?:\r\n?|\n|\f)|\\[\S\s])*"/,null],["str",/^'(?:[^\n\f\r'\\]|\\(?:\r\n?|\n|\f)|\\[\S\s])*'/,null],["lang-css-str",/^url\(([^"')]*)\)/i],["kwd",/^(?:url|rgb|!important|@import|@page|@media|@charset|inherit)(?=[^\w-]|$)/i,null],["lang-css-kw",/^(-?(?:[_a-z]|\\[\da-f]+ ?)(?:[\w-]|\\\\[\da-f]+ ?)*)\s*:/i],["com",/^\/\*[^*]*\*+(?:[^*/][^*]*\*+)*\//],["com", 2 | /^(?:<\!--|--\>)/],["lit",/^(?:\d+|\d*\.\d+)(?:%|[a-z]+)?/i],["lit",/^#[\da-f]{3,6}/i],["pln",/^-?(?:[_a-z]|\\[\da-f]+ ?)(?:[\w-]|\\\\[\da-f]+ ?)*/i],["pun",/^[^\s\w"']+/]]),["css"]);PR.registerLangHandler(PR.createSimpleLexer([],[["kwd",/^-?(?:[_a-z]|\\[\da-f]+ ?)(?:[\w-]|\\\\[\da-f]+ ?)*/i]]),["css-kw"]);PR.registerLangHandler(PR.createSimpleLexer([],[["str",/^[^"')]+/]]),["css-str"]); 3 | -------------------------------------------------------------------------------- /package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "bionode-obo", 3 | "version": "0.1.1", 4 | "description": "OBO flat file format parser for ontologies", 5 | "main": "index.js", 6 | "scripts": { 7 | "test": "mocha test/obo.spec.js", 8 | "docs": "jsdoc2md --template docs/README.hbs src/*.js > README.md && jsdoc src/*.js -d docs" 9 | }, 10 | "repository": { 11 | "type": "git", 12 | "url": "git+https://github.com/thejmazz/bionode-obo.git" 13 | }, 14 | "author": "Julian Mazzitelli ", 15 | "license": "MIT", 16 | "bugs": { 17 | "url": "https://github.com/thejmazz/bionode-obo/issues" 18 | }, 19 | "homepage": "https://github.com/thejmazz/bionode-obo#readme", 20 | "devDependencies": { 21 | "chai": "^4.0.1", 22 | "mocha": "^3.4.2" 23 | }, 24 | "dependencies": { 25 | "bl": "^1.2.1", 26 | "eventemitter2": "^4.1.0", 27 | "highland": "^2.10.5", 28 | "lodash": "^4.17.4", 29 | "pumpify": "^1.3.5", 30 | "request": "^2.81.0", 31 | "split": "^1.0.0", 32 | "through2": "^2.0.3", 33 | "through2-filter": "^2.0.0" 34 | } 35 | } 36 | -------------------------------------------------------------------------------- /src/util.js: -------------------------------------------------------------------------------- 1 | 'use strict' 2 | 3 | /** 4 | * Utility functions. 5 | * @module util 6 | */ 7 | 8 | /** 9 | * Return an object mapping characters to their respective codes. 10 | * @param {string} str a string of characters 11 | * @return {object} an object with keys as single characters and values as 12 | * their character code 13 | */ 14 | exports.charCodeMap = function (str) { 15 | // could this be made more function? `reduce` on an object? 16 | // http://stackoverflow.com/questions/15748656/javascript-reduce-on-object 17 | let map = {} 18 | str.split('').forEach( (char) => { 19 | map[char] = char.charCodeAt(0) 20 | }) 21 | return map 22 | } 23 | 24 | /** 25 | * Return position of next newline in a binary chunk starting from pos. 26 | * @param {number} pos the start position 27 | * @param {object} chunk binary object emitted from stream 28 | * @return {number} Index of the next newline from pos. 29 | */ 30 | exports.getNextNewline = function (pos, chunk) { 31 | for (let i=pos; i < chunk.length; i++) { 32 | if (chunk[i] === 10) { 33 | return i 34 | } 35 | } 36 | } 37 | -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | JSDoc: Home 6 | 7 | 8 | 9 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
19 | 20 |

Home

21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 |

30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 |
51 | 52 | 55 | 56 |
57 | 58 | 61 | 62 | 63 | 64 | 65 | -------------------------------------------------------------------------------- /test/test.js: -------------------------------------------------------------------------------- 1 | 'use strict' 2 | 3 | const fs = require('fs') 4 | const through = require('through2') 5 | const request = require('request') 6 | const hl = require('highland') 7 | 8 | const obo = require('../src/obo') 9 | 10 | // const readStream = fs.createReadStream(__dirname + '/SyRO.obo') 11 | const readStream = fs.createReadStream(__dirname + '/ff-phase2-140729.obo') 12 | const liveStream = request.get('http://purl.obolibrary.org/obo/go/go-basic.obo') 13 | 14 | // readStream 15 | // .pipe(obo.parse) 16 | // .pipe(process.stdout) 17 | 18 | // readStream 19 | // .pipe(through()) 20 | // .on('data', () => { 21 | // console.log('got data') 22 | // }) 23 | // .on('end', () => console.log('finished')) 24 | 25 | 26 | const receiveHeader = (data) => { 27 | console.log(data) 28 | } 29 | 30 | readStream 31 | .pipe(obo.parse(receiveHeader)) 32 | // .on('header', receiveHeader) 33 | // .map(obj => JSON.stringify(obj)) 34 | .pipe(process.stdout) 35 | 36 | // hl(obo.parse(readStream).on('header', receiveHeader)) 37 | // // .map(chunk => chunk.toString() + '=========') 38 | // .each(chunk => console.log(chunk)) 39 | // .done(() => console.log('DONE')) 40 | 41 | // hl(readStream.pipe(through())) 42 | // .each(chunk => console.log(chunk.toString())) 43 | // .done(() => console.log('done')) 44 | 45 | // obo.terms(readStream) 46 | // .pipe(through.obj( function(chunk, enc, cb) { 47 | // console.log(chunk) 48 | // 49 | // cb() 50 | // } )) 51 | 52 | // obo.termsNdjson(liveStream) 53 | // .pipe(process.stdout) 54 | 55 | // obo.parse(liveStream) 56 | 57 | // liveStream 58 | // .pipe(obo.parse) 59 | // .pipe(process.stdout) 60 | -------------------------------------------------------------------------------- /docs/styles/prettify-jsdoc.css: -------------------------------------------------------------------------------- 1 | /* JSDoc prettify.js theme */ 2 | 3 | /* plain text */ 4 | .pln { 5 | color: #000000; 6 | font-weight: normal; 7 | font-style: normal; 8 | } 9 | 10 | /* string content */ 11 | .str { 12 | color: #006400; 13 | font-weight: normal; 14 | font-style: normal; 15 | } 16 | 17 | /* a keyword */ 18 | .kwd { 19 | color: #000000; 20 | font-weight: bold; 21 | font-style: normal; 22 | } 23 | 24 | /* a comment */ 25 | .com { 26 | font-weight: normal; 27 | font-style: italic; 28 | } 29 | 30 | /* a type name */ 31 | .typ { 32 | color: #000000; 33 | font-weight: normal; 34 | font-style: normal; 35 | } 36 | 37 | /* a literal value */ 38 | .lit { 39 | color: #006400; 40 | font-weight: normal; 41 | font-style: normal; 42 | } 43 | 44 | /* punctuation */ 45 | .pun { 46 | color: #000000; 47 | font-weight: bold; 48 | font-style: normal; 49 | } 50 | 51 | /* lisp open bracket */ 52 | .opn { 53 | color: #000000; 54 | font-weight: bold; 55 | font-style: normal; 56 | } 57 | 58 | /* lisp close bracket */ 59 | .clo { 60 | color: #000000; 61 | font-weight: bold; 62 | font-style: normal; 63 | } 64 | 65 | /* a markup tag name */ 66 | .tag { 67 | color: #006400; 68 | font-weight: normal; 69 | font-style: normal; 70 | } 71 | 72 | /* a markup attribute name */ 73 | .atn { 74 | color: #006400; 75 | font-weight: normal; 76 | font-style: normal; 77 | } 78 | 79 | /* a markup attribute value */ 80 | .atv { 81 | color: #006400; 82 | font-weight: normal; 83 | font-style: normal; 84 | } 85 | 86 | /* a declaration */ 87 | .dec { 88 | color: #000000; 89 | font-weight: bold; 90 | font-style: normal; 91 | } 92 | 93 | /* a variable name */ 94 | .var { 95 | color: #000000; 96 | font-weight: normal; 97 | font-style: normal; 98 | } 99 | 100 | /* a function name */ 101 | .fun { 102 | color: #000000; 103 | font-weight: bold; 104 | font-style: normal; 105 | } 106 | 107 | /* Specify class=linenums on a pre to get line numbering */ 108 | ol.linenums { 109 | margin-top: 0; 110 | margin-bottom: 0; 111 | } 112 | -------------------------------------------------------------------------------- /docs/emitter.js.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | JSDoc: Source: emitter.js 6 | 7 | 8 | 9 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
19 | 20 |

Source: emitter.js

21 | 22 | 23 | 24 | 25 | 26 | 27 |
28 |
29 | 
const EventEmitter = require('events')
30 | const util = require('util')
31 | 
32 | /**
33 |  * A small wrapper around custom event emitters.
34 |  * @module emitter
35 |  */
36 | 
37 | /**
38 |  * Return a new custom event emitter
39 |  * @return {object} a function inheriting from EventEmitter with a default
40 |  *                  `#write()` method
41 |  */
42 | module.exports = function() {
43 |   function customEmitter() {
44 |     EventEmitter.call(this)
45 |   }
46 |   util.inherits(customEmitter, EventEmitter)
47 | 
48 |   customEmitter.prototype.write = function(data) {
49 |     this.emit('data', data)
50 |   }
51 | 
52 |   customEmitter.prototype.writeline = function(chunk) {
53 |     this.emit('line', chunk)
54 |   }
55 | 
56 |   return new customEmitter()
57 | }
58 |
59 |
60 |
61 | 62 | 63 | 64 | 65 |
66 | 67 | 70 | 71 |
72 | 73 | 76 | 77 | 78 | 79 | 80 | 81 | -------------------------------------------------------------------------------- /src/obo.js: -------------------------------------------------------------------------------- 1 | 'use strict' 2 | 3 | const through = require('through2') 4 | const filter = require('through2-filter') 5 | const split = require('split') 6 | const BufferList = require('bl') 7 | const pumpify = require('pumpify') 8 | 9 | const charCode = (char) => new Buffer(char)[0] 10 | 11 | // Flags and buffers 12 | let header = true 13 | let stanzaBuffer = new BufferList() 14 | 15 | const skipEmpties = filter(chunk => chunk.length !== 0) 16 | 17 | const parseStanza = (stanzaBuffer) => stanzaBuffer 18 | .toString() 19 | .trim() 20 | .split('\n') 21 | .reduce((stanza, currentLine) => { 22 | // add key:val to stanza 23 | const keyValSeperatorIndex = currentLine.indexOf(':') 24 | let key = currentLine.slice(0, keyValSeperatorIndex) 25 | let val = currentLine.slice(keyValSeperatorIndex+1).trim() 26 | 27 | if (currentLine[0] === '[') { 28 | key = '' 29 | val = val.replace(/^\[/, '').replace(/\]$/, '') 30 | } 31 | 32 | // TODO know ahead of time which keys should be arrays 33 | if (stanza[key]) { 34 | if (stanza[key].constructor !== Array) { 35 | stanza[key] = new Array(stanza[key]) 36 | } 37 | 38 | stanza[key].push(val) 39 | } else { 40 | stanza[key] = val 41 | } 42 | 43 | return stanza 44 | }, {}) 45 | 46 | const parse = (h) => { 47 | 48 | const transform = function (chunk, enc, next) { 49 | // Line starts with [ 50 | if (chunk[0] === charCode('[')) { 51 | if (header) { 52 | this.emit('header', parseStanza(stanzaBuffer.slice())) 53 | h(parseStanza(stanzaBuffer.slice())) 54 | header = false 55 | } else { 56 | // Push what we have collected for the current set of key:value pairs 57 | this.push(JSON.stringify(parseStanza(stanzaBuffer.slice())) + '\n') 58 | } 59 | 60 | // and start again 61 | stanzaBuffer = new BufferList() 62 | } 63 | 64 | stanzaBuffer.append(chunk).append('\n') 65 | next() 66 | } 67 | 68 | const flush = function() { 69 | this.push(JSON.stringify(parseStanza(stanzaBuffer.slice())) + '\n') 70 | this.push(null) 71 | } 72 | 73 | // return stream 74 | // .pipe(split()) 75 | // .pipe(skipEmpties) 76 | // .pipe(through.obj(transform, flush)) 77 | return through(transform, flush) 78 | } 79 | 80 | exports.parse = (h) => { 81 | return pumpify(split(), skipEmpties, parse(h)) 82 | } 83 | 84 | exports.parseNdjson = (stream) => { 85 | return parse(stream) 86 | .pipe(through.obj(function (obj, enc, next) { 87 | this.push(JSON.stringify(obj)) 88 | next() 89 | })) 90 | } 91 | -------------------------------------------------------------------------------- /docs/util.js.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | JSDoc: Source: util.js 6 | 7 | 8 | 9 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
19 | 20 |

Source: util.js

21 | 22 | 23 | 24 | 25 | 26 | 27 |
28 |
29 | 
'use strict'
30 | 
31 | /**
32 |  * Utility functions.
33 |  * @module util
34 |  */
35 | 
36 |  /**
37 |   * Return an object mapping characters to their respective codes.
38 |   * @param  {string} str a string of characters
39 |   * @return {object}     an object with keys as single characters and values as
40 |   *                      their character code
41 |   */
42 | exports.charCodeMap = function (str) {
43 |   // could this be made more function? `reduce` on an object?
44 |   // http://stackoverflow.com/questions/15748656/javascript-reduce-on-object
45 |   let map = {}
46 |   str.split('').forEach( (char) => {
47 |     map[char] = char.charCodeAt(0)
48 |   })
49 |   return map
50 | }
51 | 
52 | /**
53 |  * Return position of next newline in a binary chunk starting from pos.
54 |  * @param  {number} pos   the start position
55 |  * @param  {object} chunk binary object emitted from stream
56 |  * @return {number}       Index of the next newline from pos.
57 |  */
58 | exports.getNextNewline = function (pos, chunk) {
59 |   for (let i=pos; i < chunk.length; i++) {
60 |     if (chunk[i] === 10) {
61 |       return i
62 |     }
63 |   }
64 | }
65 |
66 |
67 |
68 | 69 | 70 | 71 | 72 |
73 | 74 | 77 | 78 |
79 | 80 | 83 | 84 | 85 | 86 | 87 | 88 | -------------------------------------------------------------------------------- /docs/styles/prettify-tomorrow.css: -------------------------------------------------------------------------------- 1 | /* Tomorrow Theme */ 2 | /* Original theme - https://github.com/chriskempson/tomorrow-theme */ 3 | /* Pretty printing styles. Used with prettify.js. */ 4 | /* SPAN elements with the classes below are added by prettyprint. */ 5 | /* plain text */ 6 | .pln { 7 | color: #4d4d4c; } 8 | 9 | @media screen { 10 | /* string content */ 11 | .str { 12 | color: #718c00; } 13 | 14 | /* a keyword */ 15 | .kwd { 16 | color: #8959a8; } 17 | 18 | /* a comment */ 19 | .com { 20 | color: #8e908c; } 21 | 22 | /* a type name */ 23 | .typ { 24 | color: #4271ae; } 25 | 26 | /* a literal value */ 27 | .lit { 28 | color: #f5871f; } 29 | 30 | /* punctuation */ 31 | .pun { 32 | color: #4d4d4c; } 33 | 34 | /* lisp open bracket */ 35 | .opn { 36 | color: #4d4d4c; } 37 | 38 | /* lisp close bracket */ 39 | .clo { 40 | color: #4d4d4c; } 41 | 42 | /* a markup tag name */ 43 | .tag { 44 | color: #c82829; } 45 | 46 | /* a markup attribute name */ 47 | .atn { 48 | color: #f5871f; } 49 | 50 | /* a markup attribute value */ 51 | .atv { 52 | color: #3e999f; } 53 | 54 | /* a declaration */ 55 | .dec { 56 | color: #f5871f; } 57 | 58 | /* a variable name */ 59 | .var { 60 | color: #c82829; } 61 | 62 | /* a function name */ 63 | .fun { 64 | color: #4271ae; } } 65 | /* Use higher contrast and text-weight for printable form. */ 66 | @media print, projection { 67 | .str { 68 | color: #060; } 69 | 70 | .kwd { 71 | color: #006; 72 | font-weight: bold; } 73 | 74 | .com { 75 | color: #600; 76 | font-style: italic; } 77 | 78 | .typ { 79 | color: #404; 80 | font-weight: bold; } 81 | 82 | .lit { 83 | color: #044; } 84 | 85 | .pun, .opn, .clo { 86 | color: #440; } 87 | 88 | .tag { 89 | color: #006; 90 | font-weight: bold; } 91 | 92 | .atn { 93 | color: #404; } 94 | 95 | .atv { 96 | color: #060; } } 97 | /* Style */ 98 | /* 99 | pre.prettyprint { 100 | background: white; 101 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 102 | font-size: 12px; 103 | line-height: 1.5; 104 | border: 1px solid #ccc; 105 | padding: 10px; } 106 | */ 107 | 108 | /* Specify class=linenums on a pre to get line numbering */ 109 | ol.linenums { 110 | margin-top: 0; 111 | margin-bottom: 0; } 112 | 113 | /* IE indents via margin-left */ 114 | li.L0, 115 | li.L1, 116 | li.L2, 117 | li.L3, 118 | li.L4, 119 | li.L5, 120 | li.L6, 121 | li.L7, 122 | li.L8, 123 | li.L9 { 124 | /* */ } 125 | 126 | /* Alternate shading for lines */ 127 | li.L1, 128 | li.L3, 129 | li.L5, 130 | li.L7, 131 | li.L9 { 132 | /* */ } 133 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Covenant Code of Conduct 2 | 3 | ## Our Pledge 4 | 5 | In the interest of fostering an open and welcoming environment, we as 6 | contributors and maintainers pledge to making participation in our project and 7 | our community a harassment-free experience for everyone, regardless of age, body 8 | size, disability, ethnicity, gender identity and expression, level of experience, 9 | nationality, personal appearance, race, religion, or sexual identity and 10 | orientation. 11 | 12 | ## Our Standards 13 | 14 | Examples of behavior that contributes to creating a positive environment 15 | include: 16 | 17 | * Using welcoming and inclusive language 18 | * Being respectful of differing viewpoints and experiences 19 | * Gracefully accepting constructive criticism 20 | * Focusing on what is best for the community 21 | * Showing empathy towards other community members 22 | 23 | Examples of unacceptable behavior by participants include: 24 | 25 | * The use of sexualized language or imagery and unwelcome sexual attention or 26 | advances 27 | * Trolling, insulting/derogatory comments, and personal or political attacks 28 | * Public or private harassment 29 | * Publishing others' private information, such as a physical or electronic 30 | address, without explicit permission 31 | * Other conduct which could reasonably be considered inappropriate in a 32 | professional setting 33 | 34 | ## Our Responsibilities 35 | 36 | Project maintainers are responsible for clarifying the standards of acceptable 37 | behavior and are expected to take appropriate and fair corrective action in 38 | response to any instances of unacceptable behavior. 39 | 40 | Project maintainers have the right and responsibility to remove, edit, or 41 | reject comments, commits, code, wiki edits, issues, and other contributions 42 | that are not aligned to this Code of Conduct, or to ban temporarily or 43 | permanently any contributor for other behaviors that they deem inappropriate, 44 | threatening, offensive, or harmful. 45 | 46 | ## Scope 47 | 48 | This Code of Conduct applies both within project spaces and in public spaces 49 | when an individual is representing the project or its community. Examples of 50 | representing a project or community include using an official project e-mail 51 | address, posting via an official social media account, or acting as an appointed 52 | representative at an online or offline event. Representation of a project may be 53 | further defined and clarified by project maintainers. 54 | 55 | ## Enforcement 56 | 57 | Instances of abusive, harassing, or otherwise unacceptable behavior may be 58 | reported by contacting the project team at mail@bionode.io. All 59 | complaints will be reviewed and investigated and will result in a response that 60 | is deemed necessary and appropriate to the circumstances. The project team is 61 | obligated to maintain confidentiality with regard to the reporter of an incident. 62 | Further details of specific enforcement policies may be posted separately. 63 | 64 | Project maintainers who do not follow or enforce the Code of Conduct in good 65 | faith may face temporary or permanent repercussions as determined by other 66 | members of the project's leadership. 67 | 68 | ## Attribution 69 | 70 | This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, 71 | available at [http://contributor-covenant.org/version/1/4][version] 72 | 73 | [homepage]: http://contributor-covenant.org 74 | [version]: http://contributor-covenant.org/version/1/4/ 75 | -------------------------------------------------------------------------------- /docs/module-emitter.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | JSDoc: Module: emitter 6 | 7 | 8 | 9 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
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Module: emitter

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A small wrapper around custom event emitters.
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(require("emitter"))() → {object}

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58 | Return a new custom event emitter 59 |
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Source:
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Returns:
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129 | a function inheriting from EventEmitter with a default 130 | `#write()` method 131 |
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137 | Type 138 |
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140 | 141 | object 142 | 143 | 144 |
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258 | 259 | 262 | 263 | 264 | 265 | 266 | -------------------------------------------------------------------------------- /docs/obo.js.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | JSDoc: Source: obo.js 6 | 7 | 8 | 9 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
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Source: obo.js

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'use strict'
 30 | 
 31 | const _ = require('lodash')
 32 | const highland = require('highland')
 33 | const EventEmitter2 = require('eventemitter2').EventEmitter2
 34 | 
 35 | /**
 36 |  * Parse OBO files from an input stream.
 37 |  * Emits a [Term] object stream or ndjson stream.
 38 |  * @module bionode-obo
 39 |  */
 40 | 
 41 | // Setting up event emitter
 42 | const emitter = new EventEmitter2({
 43 |   wildcard: false,
 44 |   delimiter: '.',
 45 |   newListener: true,
 46 |   maxListeners: 10
 47 | })
 48 | 
 49 | // emitter.addListener('header', header => console.log('HEADER: ' + JSON.stringify(stanzaParser(header), null, 2)))
 50 | 
 51 | // highland('stanza', emitter)
 52 | //   .map(stanza => stanzaParser(stanza))
 53 | //   .map(stanza => JSON.stringify(stanza, null, 2))
 54 | //   .each(stanza => console.log('STANZA: ' + stanza))
 55 | 
 56 | // Flags and buffers
 57 | let header = true
 58 | let headerComplete = false
 59 | let headerStr = ''
 60 | 
 61 | let term = false
 62 | let termStr = ''
 63 | 
 64 | // Watch for `line` events from the emitter
 65 | // TODO stop using events, as this stream "never ends"
 66 | highland('line', emitter)
 67 |   .each(line => {
 68 |     // If we found a new stanza, swap term flag
 69 |     if (line.match(/^\[[a-z]+\]/i)) {
 70 |       // Found a stanza
 71 |       header = false
 72 |       term = !term
 73 |     }
 74 | 
 75 |     // Emit header once
 76 |     // TODO headerStr buffer can be termStr
 77 |     if (header) {
 78 |       headerStr += line + '\n'
 79 |     } else if (!headerComplete) {
 80 |       emitter.emit('header', headerStr)
 81 |       headerComplete = true
 82 |     }
 83 | 
 84 | 
 85 |     if (term) {
 86 |       // If we are currently buffering a stanza, continue to do so
 87 |       termStr += line + '\n'
 88 |     } else if (!term && !header) {
 89 |       // Term flag will have been swapped if we encountered a [Term], [Typedef], etc
 90 |       // Then emit the currently completed stanza, and swap the flag back so we
 91 |       // continue to buffer a new stanza
 92 |       term = !term
 93 |       emitter.emit('stanza', termStr)
 94 |       termStr = line + '\n'
 95 |     }
 96 |   })
 97 | 
 98 | // Emits a `line` event with each line passed in
 99 | // TODO mitigate using events, event stream doesn't know when it ends
100 | const getLines = (stream) => {
101 |   return stream
102 |     .splitBy('\n')
103 |     .each(line => emitter.emit('line', line))
104 | }
105 | 
106 | // map stanza text to an object representation
107 | const parseStanzas = (stream) => {
108 |   return stream.map(stanza => stanzaParser(stanza))
109 | }
110 | 
111 | // map objects to stringified lines
112 | const ndjsonIfy = (stream) => {
113 |   return stream.map(obj => JSON.stringify(obj) + '\n')
114 | }
115 | 
116 | // filter out [Term]s
117 | const termsFilter = (stream) => {
118 |   return stream.filter(obj => obj[''] === '[Term]')
119 | }
120 | 
121 | /**
122 |  * Parse OBO 1.2 file
123 |  * @return {stream} the readable stream of an OBO file from fs or www
124 |  */
125 | exports.parse = highland.pipeline(highland.through(getLines))
126 | 
127 | /**
128 |  * Produce [Term]s object stream
129 |  * @param  {stream} stream stream from fs or www
130 |  * @return {stream}        object stream
131 |  */
132 | exports.terms = (stream) => {
133 |   highland(stream).through(getLines)
134 | 
135 |   return highland('stanza', emitter)
136 |     .through(parseStanzas)
137 |     .through(termsFilter)
138 | }
139 | 
140 | /**
141 |  * Produce [Term]s ndjson stream
142 |  * @param  {stream} stream strem from fs or www
143 |  * @return {stream}        ndjson stream
144 |  */
145 | exports.termsNdjson = (stream) => {
146 |   highland(stream).through(getLines)
147 | 
148 |   return highland('stanza', emitter)
149 |     .through(parseStanzas)
150 |     .through(termsFilter)
151 |     .through(ndjsonIfy)
152 | }
153 | 
154 | /**
155 |  * Parse one [Term] at once.
156 |  *
157 |  * NOTE Although this parser is a stream, this function requires one term to be
158 |  * stored in memory at once. How else to create an Object stream? One
159 |  * could append a string until it is JSON.parse()''able, but that still requires
160 |  * storing the object in memory at once, on the other side. Better to provide
161 |  * an Object stream as well as an ndjson stream.
162 |  */
163 | const stanzaParser = (stanza) => {
164 |   return stanza
165 |     .split('\n')
166 |     // Filter out empty lines
167 |     .filter(l => l.length !== 0)
168 |     // Reduce array into object of key:val
169 |     .reduce( (prev, curr) => {
170 |       const sep = curr.indexOf(':')
171 |       const key = curr.substring(0, sep)
172 |       const val = _.trim(curr.substring(sep+1))
173 | 
174 |       prev[key] = val
175 | 
176 |       return prev
177 |     }, {} )
178 | }
179 |
180 |
181 |
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187 | 188 | 191 | 192 |
193 | 194 | 197 | 198 | 199 | 200 | 201 | 202 | -------------------------------------------------------------------------------- /test/SyRO.obo: -------------------------------------------------------------------------------- 1 | format-version: 1.2 2 | date: 27:10:2015 18:58 3 | saved-by: steipe 4 | auto-generated-by: OBO-Edit 2.3.1 5 | default-namespace: default_namespace 6 | 7 | [Term] 8 | id: ID:0000000 9 | name: structural role 10 | def: "A role relating to establishing the physical existence or the integrity of a system." [] 11 | creation_date: 2015-10-25T22:04:05Z 12 | 13 | [NewTermType] 14 | id: ID:0000055 15 | name: Test 16 | 17 | [Term] 18 | id: ID:0000001 19 | name: functional role 20 | def: "A role that relates to the realization of the purpose of the system, i.e. those aspects of its behaviour that are maintained under purifying selection." [] 21 | created_by: steipe 22 | creation_date: 2015-10-25T22:07:16Z 23 | 24 | [Term] 25 | id: ID:0000002 26 | name: create 27 | def: "Roles that contribute to the physical realization of a system." [] 28 | is_a: ID:0000000 ! structural role 29 | created_by: steipe 30 | creation_date: 2015-10-25T22:15:58Z 31 | 32 | [Term] 33 | id: ID:0000003 34 | name: maintain 35 | def: "Roles that contribute to the structural integrity of a system's components. This would include repair of damage, and replacement of components. Distinguish between replacement e.g. of cofactors, and replenishing of substrates and similar: the latter is a functional role." [] 36 | is_a: ID:0000000 ! structural role 37 | created_by: steipe 38 | creation_date: 2015-10-25T22:16:54Z 39 | 40 | [Term] 41 | id: ID:0000004 42 | name: destroy 43 | def: "Roles that contribute to the disestablishment of a system." [] 44 | is_a: ID:0000000 ! structural role 45 | created_by: steipe 46 | creation_date: 2015-10-25T22:18:12Z 47 | 48 | [Term] 49 | id: ID:0000005 50 | name: synthesize component 51 | def: "Roles that create a component from metabolic building blocks." [] 52 | relationship: ID:0000006 ID:0000002 ! create 53 | created_by: steipe 54 | creation_date: 2015-10-25T22:32:20Z 55 | 56 | [Term] 57 | id: ID:0000007 58 | name: assemble components 59 | def: "Roles that place system components into their functional spatial relationship." [] 60 | relationship: ID:0000006 ID:0000002 ! create 61 | created_by: steipe 62 | creation_date: 2015-10-25T22:39:39Z 63 | 64 | [Term] 65 | id: ID:0000008 66 | name: localize component 67 | def: "Roles that place system components into their correct location or compartment." [] 68 | relationship: ID:0000006 ID:0000002 ! create 69 | created_by: steipe 70 | creation_date: 2015-10-25T22:41:23Z 71 | 72 | [Term] 73 | id: ID:0000009 74 | name: modify component 75 | def: "Roles that physically modify individual components of a system. Examples include signal-peptide or pro-domain cleavage, myristoilation, or covalent and non-covalent addition of prosthetic groups. However phosphorylation would typically be a part of system regulation: a functional role; and ubiquitination would be a part of system destruction." [] 76 | relationship: ID:0000006 ID:0000002 ! create 77 | created_by: steipe 78 | creation_date: 2015-10-25T22:47:44Z 79 | 80 | [Term] 81 | id: ID:0000010 82 | name: tag component for localization 83 | def: "Roles that specifically tag components of a particular system, so that these components can become engaged by generic transport and localization systems." [] 84 | relationship: ID:0000006 ID:0000008 ! localize component 85 | created_by: steipe 86 | creation_date: 2015-10-27T10:44:00Z 87 | 88 | [Term] 89 | id: ID:0000011 90 | name: translocate component 91 | def: "Roles that physically displace a system component from one location into another." [] 92 | relationship: ID:0000006 ID:0000008 ! localize component 93 | created_by: steipe 94 | creation_date: 2015-10-27T10:46:33Z 95 | 96 | [Term] 97 | id: ID:0000012 98 | name: tether component 99 | def: "Roles that keep a system component in a specific location, either by physically constraining or confining the component, or relocating displaced components." [] 100 | relationship: ID:0000006 ID:0000008 ! localize component 101 | created_by: steipe 102 | creation_date: 2015-10-27T10:57:21Z 103 | 104 | [Term] 105 | id: ID:0000013 106 | name: tag component for destruction 107 | def: "Roles that specifically tag components of a particular system, so that these components can become engaged by generic disassembly and decomposition systems." [] 108 | relationship: ID:0000006 ID:0000004 ! destroy 109 | created_by: steipe 110 | creation_date: 2015-10-27T11:03:27Z 111 | 112 | [Term] 113 | id: ID:0000014 114 | name: disassemble components 115 | def: "Roles that remove system components from their functional spatial relationship." [] 116 | relationship: ID:0000006 ID:0000004 ! destroy 117 | created_by: steipe 118 | creation_date: 2015-10-27T11:06:03Z 119 | 120 | [Term] 121 | id: ID:0000015 122 | name: decompose component 123 | def: "Roles that reduce a component to its metabolic building blocks." [] 124 | relationship: ID:0000006 ID:0000004 ! destroy 125 | created_by: steipe 126 | creation_date: 2015-10-27T11:07:20Z 127 | 128 | [Term] 129 | id: ID:0000016 130 | name: input 131 | is_a: ID:0000001 ! functional role 132 | created_by: steipe 133 | creation_date: 2015-10-27T11:13:42Z 134 | 135 | [Term] 136 | id: ID:0000017 137 | name: transmit 138 | is_a: ID:0000001 ! functional role 139 | created_by: steipe 140 | creation_date: 2015-10-27T11:13:42Z 141 | 142 | [Term] 143 | id: ID:0000018 144 | name: transform 145 | is_a: ID:0000001 ! functional role 146 | created_by: steipe 147 | creation_date: 2015-10-27T11:13:42Z 148 | 149 | [Term] 150 | id: ID:0000019 151 | name: set 152 | is_a: ID:0000001 ! functional role 153 | created_by: steipe 154 | creation_date: 2015-10-27T11:13:42Z 155 | 156 | [Term] 157 | id: ID:0000020 158 | name: regulate 159 | is_a: ID:0000001 ! functional role 160 | created_by: steipe 161 | creation_date: 2015-10-27T11:13:42Z 162 | 163 | [Term] 164 | id: ID:0000021 165 | name: output 166 | is_a: ID:0000001 ! functional role 167 | created_by: steipe 168 | creation_date: 2015-10-27T11:13:42Z 169 | 170 | [Term] 171 | id: ID:0000022 172 | name: integrate signals 173 | def: "Roles that combine signals to a common signal." [] 174 | is_a: ID:0000016 ! input 175 | created_by: steipe 176 | creation_date: 2015-10-27T18:57:08Z 177 | 178 | [Typedef] 179 | id: ID:0000006 180 | name: Part_of 181 | def: "Child term is a part of the parent term." [] 182 | created_by: steipe 183 | creation_date: 2015-10-25T22:37:02Z 184 | 185 | 186 | [Term] 187 | id: ID:0000009 188 | name: Test 189 | -------------------------------------------------------------------------------- /docs/styles/jsdoc-default.css: -------------------------------------------------------------------------------- 1 | @font-face { 2 | font-family: 'Open Sans'; 3 | font-weight: normal; 4 | font-style: normal; 5 | src: url('../fonts/OpenSans-Regular-webfont.eot'); 6 | src: 7 | local('Open Sans'), 8 | local('OpenSans'), 9 | url('../fonts/OpenSans-Regular-webfont.eot?#iefix') format('embedded-opentype'), 10 | url('../fonts/OpenSans-Regular-webfont.woff') format('woff'), 11 | url('../fonts/OpenSans-Regular-webfont.svg#open_sansregular') format('svg'); 12 | } 13 | 14 | @font-face { 15 | font-family: 'Open Sans Light'; 16 | font-weight: normal; 17 | font-style: normal; 18 | src: url('../fonts/OpenSans-Light-webfont.eot'); 19 | src: 20 | local('Open Sans Light'), 21 | local('OpenSans Light'), 22 | url('../fonts/OpenSans-Light-webfont.eot?#iefix') format('embedded-opentype'), 23 | url('../fonts/OpenSans-Light-webfont.woff') format('woff'), 24 | url('../fonts/OpenSans-Light-webfont.svg#open_sanslight') format('svg'); 25 | } 26 | 27 | html 28 | { 29 | overflow: auto; 30 | background-color: #fff; 31 | font-size: 14px; 32 | } 33 | 34 | body 35 | { 36 | font-family: 'Open Sans', sans-serif; 37 | line-height: 1.5; 38 | color: #4d4e53; 39 | background-color: white; 40 | } 41 | 42 | a, a:visited, a:active { 43 | color: #0095dd; 44 | text-decoration: none; 45 | } 46 | 47 | a:hover { 48 | text-decoration: underline; 49 | } 50 | 51 | header 52 | { 53 | display: block; 54 | padding: 0px 4px; 55 | } 56 | 57 | tt, code, kbd, samp { 58 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 59 | } 60 | 61 | .class-description { 62 | font-size: 130%; 63 | line-height: 140%; 64 | margin-bottom: 1em; 65 | margin-top: 1em; 66 | } 67 | 68 | .class-description:empty { 69 | margin: 0; 70 | } 71 | 72 | #main { 73 | float: left; 74 | width: 70%; 75 | } 76 | 77 | article dl { 78 | margin-bottom: 40px; 79 | } 80 | 81 | section 82 | { 83 | display: block; 84 | background-color: #fff; 85 | padding: 12px 24px; 86 | border-bottom: 1px solid #ccc; 87 | margin-right: 30px; 88 | } 89 | 90 | .variation { 91 | display: none; 92 | } 93 | 94 | .signature-attributes { 95 | font-size: 60%; 96 | color: #aaa; 97 | font-style: italic; 98 | font-weight: lighter; 99 | } 100 | 101 | nav 102 | { 103 | display: block; 104 | float: right; 105 | margin-top: 28px; 106 | width: 30%; 107 | box-sizing: border-box; 108 | border-left: 1px solid #ccc; 109 | padding-left: 16px; 110 | } 111 | 112 | nav ul { 113 | font-family: 'Lucida Grande', 'Lucida Sans Unicode', arial, sans-serif; 114 | font-size: 100%; 115 | line-height: 17px; 116 | padding: 0; 117 | margin: 0; 118 | list-style-type: none; 119 | } 120 | 121 | nav ul a, nav ul a:visited, nav ul a:active { 122 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 123 | line-height: 18px; 124 | color: #4D4E53; 125 | } 126 | 127 | nav h3 { 128 | margin-top: 12px; 129 | } 130 | 131 | nav li { 132 | margin-top: 6px; 133 | } 134 | 135 | footer { 136 | display: block; 137 | padding: 6px; 138 | margin-top: 12px; 139 | font-style: italic; 140 | font-size: 90%; 141 | } 142 | 143 | h1, h2, h3, h4 { 144 | font-weight: 200; 145 | margin: 0; 146 | } 147 | 148 | h1 149 | { 150 | font-family: 'Open Sans Light', sans-serif; 151 | font-size: 48px; 152 | letter-spacing: -2px; 153 | margin: 12px 24px 20px; 154 | } 155 | 156 | h2, h3 157 | { 158 | font-size: 30px; 159 | font-weight: 700; 160 | letter-spacing: -1px; 161 | margin-bottom: 12px; 162 | } 163 | 164 | h4 165 | { 166 | font-size: 18px; 167 | letter-spacing: -0.33px; 168 | margin-bottom: 12px; 169 | color: #4d4e53; 170 | } 171 | 172 | h5, .container-overview .subsection-title 173 | { 174 | font-size: 120%; 175 | font-weight: bold; 176 | letter-spacing: -0.01em; 177 | margin: 8px 0 3px 0; 178 | } 179 | 180 | h6 181 | { 182 | font-size: 100%; 183 | letter-spacing: -0.01em; 184 | margin: 6px 0 3px 0; 185 | font-style: italic; 186 | } 187 | 188 | .ancestors { color: #999; } 189 | .ancestors a 190 | { 191 | color: #999 !important; 192 | text-decoration: none; 193 | } 194 | 195 | .clear 196 | { 197 | clear: both; 198 | } 199 | 200 | .important 201 | { 202 | font-weight: bold; 203 | color: #950B02; 204 | } 205 | 206 | .yes-def { 207 | text-indent: -1000px; 208 | } 209 | 210 | .type-signature { 211 | color: #aaa; 212 | } 213 | 214 | .name, .signature { 215 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 216 | } 217 | 218 | .details { margin-top: 14px; border-left: 2px solid #DDD; } 219 | .details dt { width: 120px; float: left; padding-left: 10px; padding-top: 6px; } 220 | .details dd { margin-left: 70px; } 221 | .details ul { margin: 0; } 222 | .details ul { list-style-type: none; } 223 | .details li { margin-left: 30px; padding-top: 6px; } 224 | .details pre.prettyprint { margin: 0 } 225 | .details .object-value { padding-top: 0; } 226 | 227 | .description { 228 | margin-bottom: 1em; 229 | margin-top: 1em; 230 | } 231 | 232 | .code-caption 233 | { 234 | font-style: italic; 235 | font-size: 107%; 236 | margin: 0; 237 | } 238 | 239 | .prettyprint 240 | { 241 | border: 1px solid #ddd; 242 | width: 80%; 243 | overflow: auto; 244 | } 245 | 246 | .prettyprint.source { 247 | width: inherit; 248 | } 249 | 250 | .prettyprint code 251 | { 252 | font-size: 100%; 253 | line-height: 18px; 254 | display: block; 255 | padding: 4px 12px; 256 | margin: 0; 257 | background-color: #fff; 258 | color: #4D4E53; 259 | } 260 | 261 | .prettyprint code span.line 262 | { 263 | display: inline-block; 264 | } 265 | 266 | .prettyprint.linenums 267 | { 268 | padding-left: 70px; 269 | -webkit-user-select: none; 270 | -moz-user-select: none; 271 | -ms-user-select: none; 272 | user-select: none; 273 | } 274 | 275 | .prettyprint.linenums ol 276 | { 277 | padding-left: 0; 278 | } 279 | 280 | .prettyprint.linenums li 281 | { 282 | border-left: 3px #ddd solid; 283 | } 284 | 285 | .prettyprint.linenums li.selected, 286 | .prettyprint.linenums li.selected * 287 | { 288 | background-color: lightyellow; 289 | } 290 | 291 | .prettyprint.linenums li * 292 | { 293 | -webkit-user-select: text; 294 | -moz-user-select: text; 295 | -ms-user-select: text; 296 | user-select: text; 297 | } 298 | 299 | .params, .props 300 | { 301 | border-spacing: 0; 302 | border: 0; 303 | border-collapse: collapse; 304 | } 305 | 306 | .params .name, .props .name, .name code { 307 | color: #4D4E53; 308 | font-family: Consolas, Monaco, 'Andale Mono', monospace; 309 | font-size: 100%; 310 | } 311 | 312 | .params td, .params th, .props td, .props th 313 | { 314 | border: 1px solid #ddd; 315 | margin: 0px; 316 | text-align: left; 317 | vertical-align: top; 318 | padding: 4px 6px; 319 | display: table-cell; 320 | } 321 | 322 | .params thead tr, .props thead tr 323 | { 324 | background-color: #ddd; 325 | font-weight: bold; 326 | } 327 | 328 | .params .params thead tr, .props .props thead tr 329 | { 330 | background-color: #fff; 331 | font-weight: bold; 332 | } 333 | 334 | .params th, .props th { border-right: 1px solid #aaa; } 335 | .params thead .last, .props thead .last { border-right: 1px solid #ddd; } 336 | 337 | .params td.description > p:first-child, 338 | .props td.description > p:first-child 339 | { 340 | margin-top: 0; 341 | padding-top: 0; 342 | } 343 | 344 | .params td.description > p:last-child, 345 | .props td.description > p:last-child 346 | { 347 | margin-bottom: 0; 348 | padding-bottom: 0; 349 | } 350 | 351 | .disabled { 352 | color: #454545; 353 | } 354 | -------------------------------------------------------------------------------- /docs/module-util.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | JSDoc: Module: util 6 | 7 | 8 | 9 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
19 | 20 |

Module: util

21 | 22 | 23 | 24 | 25 | 26 | 27 |
28 | 29 |
30 | 31 | 32 | 33 | 34 | 35 |
36 | 37 |
38 |
39 | 40 | 41 |
Utility functions.
42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 |
62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 |
Source:
89 |
92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 |
100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 |
119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 132 | 133 |

Methods

134 | 135 | 136 | 137 | 138 | 139 | 140 |

(static) charCodeMap(str) → {object}

141 | 142 | 143 | 144 | 145 | 146 |
147 | Return an object mapping characters to their respective codes. 148 |
149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | 158 |
Parameters:
159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | 201 | 202 | 203 | 204 |
NameTypeDescription
str 187 | 188 | 189 | string 190 | 191 | 192 | 193 | a string of characters
205 | 206 | 207 | 208 | 209 | 210 | 211 |
212 | 213 | 214 | 215 | 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | 234 | 235 | 236 | 237 | 238 |
Source:
239 |
242 | 243 | 244 | 245 | 246 | 247 | 248 | 249 |
250 | 251 | 252 | 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 261 | 262 | 263 |
Returns:
264 | 265 | 266 |
267 | an object with keys as single characters and values as 268 | their character code 269 |
270 | 271 | 272 | 273 |
274 |
275 | Type 276 |
277 |
278 | 279 | object 280 | 281 | 282 |
283 |
284 | 285 | 286 | 287 | 288 | 289 | 290 | 291 | 292 | 293 | 294 |

(static) getNextNewline(pos, chunk) → {number}

295 | 296 | 297 | 298 | 299 | 300 |
301 | Return position of next newline in a binary chunk starting from pos. 302 |
303 | 304 | 305 | 306 | 307 | 308 | 309 | 310 | 311 | 312 |
Parameters:
313 | 314 | 315 | 316 | 317 | 318 | 319 | 320 | 321 | 322 | 323 | 324 | 325 | 326 | 327 | 328 | 329 | 330 | 331 | 332 | 333 | 334 | 335 | 336 | 337 | 338 | 339 | 340 | 348 | 349 | 350 | 351 | 352 | 353 | 354 | 355 | 356 | 357 | 358 | 359 | 360 | 361 | 362 | 363 | 371 | 372 | 373 | 374 | 375 | 376 | 377 | 378 | 379 | 380 | 381 |
NameTypeDescription
pos 341 | 342 | 343 | number 344 | 345 | 346 | 347 | the start position
chunk 364 | 365 | 366 | object 367 | 368 | 369 | 370 | binary object emitted from stream
382 | 383 | 384 | 385 | 386 | 387 | 388 |
389 | 390 | 391 | 392 | 393 | 394 | 395 | 396 | 397 | 398 | 399 | 400 | 401 | 402 | 403 | 404 | 405 | 406 | 407 | 408 | 409 | 410 | 411 | 412 | 413 | 414 | 415 |
Source:
416 |
419 | 420 | 421 | 422 | 423 | 424 | 425 | 426 |
427 | 428 | 429 | 430 | 431 | 432 | 433 | 434 | 435 | 436 | 437 | 438 | 439 | 440 |
Returns:
441 | 442 | 443 |
444 | Index of the next newline from pos. 445 |
446 | 447 | 448 | 449 |
450 |
451 | Type 452 |
453 |
454 | 455 | number 456 | 457 | 458 |
459 |
460 | 461 | 462 | 463 | 464 | 465 | 466 | 467 | 468 | 469 | 470 | 471 |
472 | 473 |
474 | 475 | 476 | 477 | 478 |
479 | 480 | 483 | 484 |
485 | 486 | 489 | 490 | 491 | 492 | 493 | -------------------------------------------------------------------------------- /docs/module-bionode-obo.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | JSDoc: Module: bionode-obo 6 | 7 | 8 | 9 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
19 | 20 |

Module: bionode-obo

21 | 22 | 23 | 24 | 25 | 26 | 27 |
28 | 29 |
30 | 31 | 32 | 33 | 34 | 35 |
36 | 37 |
38 |
39 | 40 | 41 |
Parse OBO files from an input stream. 42 | Emits a [Term] object stream or ndjson stream.
43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 |
63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 |
Source:
90 |
93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 |
101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 |
120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 132 |

Members

133 | 134 | 135 | 136 |

(static) parse

137 | 138 | 139 | 140 | 141 |
142 | Parse OBO 1.2 file 143 |
144 | 145 | 146 | 147 | 148 | 149 | 150 | 151 |
152 | 153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 |
Source:
179 |
182 | 183 | 184 | 185 | 186 | 187 | 188 | 189 |
190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 |

Methods

201 | 202 | 203 | 204 | 205 | 206 | 207 |

(static) terms(stream) → {stream}

208 | 209 | 210 | 211 | 212 | 213 |
214 | Produce [Term]s object stream 215 |
216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 |
Parameters:
226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | 234 | 235 | 236 | 237 | 238 | 239 | 240 | 241 | 242 | 243 | 244 | 245 | 246 | 247 | 248 | 249 | 250 | 251 | 252 | 253 | 261 | 262 | 263 | 264 | 265 | 266 | 267 | 268 | 269 | 270 | 271 |
NameTypeDescription
stream 254 | 255 | 256 | stream 257 | 258 | 259 | 260 | stream from fs or www
272 | 273 | 274 | 275 | 276 | 277 | 278 |
279 | 280 | 281 | 282 | 283 | 284 | 285 | 286 | 287 | 288 | 289 | 290 | 291 | 292 | 293 | 294 | 295 | 296 | 297 | 298 | 299 | 300 | 301 | 302 | 303 | 304 | 305 |
Source:
306 |
309 | 310 | 311 | 312 | 313 | 314 | 315 | 316 |
317 | 318 | 319 | 320 | 321 | 322 | 323 | 324 | 325 | 326 | 327 | 328 | 329 | 330 |
Returns:
331 | 332 | 333 |
334 | object stream 335 |
336 | 337 | 338 | 339 |
340 |
341 | Type 342 |
343 |
344 | 345 | stream 346 | 347 | 348 |
349 |
350 | 351 | 352 | 353 | 354 | 355 | 356 | 357 | 358 | 359 | 360 |

(static) termsNdjson(stream) → {stream}

361 | 362 | 363 | 364 | 365 | 366 |
367 | Produce [Term]s ndjson stream 368 |
369 | 370 | 371 | 372 | 373 | 374 | 375 | 376 | 377 | 378 |
Parameters:
379 | 380 | 381 | 382 | 383 | 384 | 385 | 386 | 387 | 388 | 389 | 390 | 391 | 392 | 393 | 394 | 395 | 396 | 397 | 398 | 399 | 400 | 401 | 402 | 403 | 404 | 405 | 406 | 414 | 415 | 416 | 417 | 418 | 419 | 420 | 421 | 422 | 423 | 424 |
NameTypeDescription
stream 407 | 408 | 409 | stream 410 | 411 | 412 | 413 | strem from fs or www
425 | 426 | 427 | 428 | 429 | 430 | 431 |
432 | 433 | 434 | 435 | 436 | 437 | 438 | 439 | 440 | 441 | 442 | 443 | 444 | 445 | 446 | 447 | 448 | 449 | 450 | 451 | 452 | 453 | 454 | 455 | 456 | 457 | 458 |
Source:
459 |
462 | 463 | 464 | 465 | 466 | 467 | 468 | 469 |
470 | 471 | 472 | 473 | 474 | 475 | 476 | 477 | 478 | 479 | 480 | 481 | 482 | 483 |
Returns:
484 | 485 | 486 |
487 | ndjson stream 488 |
489 | 490 | 491 | 492 |
493 |
494 | Type 495 |
496 |
497 | 498 | stream 499 | 500 | 501 |
502 |
503 | 504 | 505 | 506 | 507 | 508 | 509 | 510 | 511 | 512 | 513 |

(inner) stanzaParser()

514 | 515 | 516 | 517 | 518 | 519 |
520 | Parse one [Term] at once. 521 | 522 | NOTE Although this parser is a stream, this function requires one term to be 523 | stored in memory at once. How else to create an Object stream? One 524 | could append a string until it is JSON.parse()''able, but that still requires 525 | storing the object in memory at once, on the other side. Better to provide 526 | an Object stream as well as an ndjson stream. 527 |
528 | 529 | 530 | 531 | 532 | 533 | 534 | 535 | 536 | 537 | 538 | 539 | 540 | 541 |
542 | 543 | 544 | 545 | 546 | 547 | 548 | 549 | 550 | 551 | 552 | 553 | 554 | 555 | 556 | 557 | 558 | 559 | 560 | 561 | 562 | 563 | 564 | 565 | 566 | 567 | 568 |
Source:
569 |
572 | 573 | 574 | 575 | 576 | 577 | 578 | 579 |
580 | 581 | 582 | 583 | 584 | 585 | 586 | 587 | 588 | 589 | 590 | 591 | 592 | 593 | 594 | 595 | 596 | 597 | 598 | 599 | 600 | 601 | 602 |
603 | 604 |
605 | 606 | 607 | 608 | 609 |
610 | 611 | 614 | 615 |
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