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node-ncbi

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node-ncbi - npm Package Compare versions

Comparing version 0.0.4 to 0.1.0

.eslintrc
bin/repl.js
src/controllers/createCitationCtlr.js
src/controllers/createSearchCtlr.js
src/controllers/index.js
src/documents/document.js
src/documents/efetch.js
src/documents/elink.js
src/documents/esearch.js
src/documents/esummary.js
src/documents/index.js
src/gateways/createGateway.js
src/gateways/index.js
test/docs/elink.json

19

gulpfile.js
var gulp = require('gulp');
var mocha = require('gulp-mocha');
var gutil = require('gulp-util');
var eslint = require('gulp-eslint');

@@ -9,10 +10,20 @@ /*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

gulp.task('lint', function() {
return gulp.src(['**/*.js','!node_modules/**'])
// eslint() attaches the lint output to the "eslint" property
// of the file object so it can be used by other modules.
.pipe(eslint())
// eslint.format() outputs the lint results to the console.
// Alternatively use eslint.formatEach() (see Docs).
.pipe(eslint.format());
});
gulp.task('test', function() {
return gulp.src(['test/*.js'], { read: false })
.pipe(mocha({ reporter: 'list' }))
.on('error', gutil.log);
return gulp.src(['test/*.js'], { read: false })
.pipe(mocha({ reporter: 'list' }))
.on('error', gutil.log);
});
gulp.task('test-watch', function() {
gulp.watch(['./**/*.js'], ['test']);
gulp.watch(['./**/*.js'], ['test']);
});

73

index.js

@@ -1,72 +0,3 @@

var _ = require('underscore');
var createGateway = require('./createGateway');
'use strict';
module.exports = {
pubmedSearch : function(query, args) {
var defaults = {
start : 0,
end : 10
}
var settings = _.extend(defaults, args);
var search = createGateway({
method : 'esearch',
params : {
db : 'pubmed',
term : query,
retstart : settings.start,
retmax : settings.end - settings.start
}
});
var summary = createGateway({
method : 'esummary',
params : {
db : 'pubmed'
}
});
return new Promise(function(resolve, reject) {
var data = {};
search.get().then(function(document) {
data.count = document.count();
var ids = document.ids();
if ( ! ids.length ) {
data.papers = [];
resolve(data);
}
summary.addIds(ids);
summary.get().then(function(document) {
data.papers = document.summaries();
resolve(data);
}, function(err) {
reject(err);
});
}, function(err) {
reject(err);
})
});
},
getAbstract : function(pmids, single) {
var gateway = createGateway({
method : 'efetch',
responseType : 'xml',
params : {
db : 'pubmed'
}
});
gateway.addIds(pmids);
return gateway.get().then(function(document) {
return document.abstracts(single);
});
}
}
module.exports = require('./src/controllers');

15

package.json
{
"name": "node-ncbi",
"version": "0.0.4",
"version": "0.1.0",
"description": "Access and parse the NCBI eUtils API in Node or the Browser",

@@ -13,2 +13,5 @@ "keywords": [

"main": "index.js",
"scripts": {
"start": "node ./bin/repl"
},
"author": {

@@ -24,2 +27,3 @@ "name": "Casey Ydenberg",

"dependencies": {
"gulp-util": "^3.0.7",
"popsicle": "^0.5.12",

@@ -30,6 +34,9 @@ "underscore": "^1.8.3",

"devDependencies": {
"gulp": "^3.9.0",
"gulp": "^3.9.1",
"gulp-eslint": "^2.0.0",
"gulp-mocha": "^2.1.2",
"mocha": "^2.2.5"
}
"mocha": "^2.2.5",
"open": "0.0.5"
},
"license": "MIT"
}

98

README.md
# node-ncbi
A nodejs wrapper for the NCBI eUtils API. You can use it to search PubMed or other databases and get the results as a JavaScript object.
A nodejs wrapper for the NCBI eUtils. You can use it to search PubMed or other databases and get the results as a JavaScript object.
[Read the full documentation of the API](http://www.ncbi.nlm.nih.gov/books/NBK25500/).
[Read the full documentation of eUtils](http://www.ncbi.nlm.nih.gov/books/NBK25500/).

@@ -15,72 +15,94 @@ ## Getting started

### PubMed Searches
```js
ncbi.pubmedSearch('actin').then(function(results) {
let pubmedSearch = ncbi.createSearch('actin');
pubmedSearch.search().then((results) => {
console.log(results);
})
});
```
Will display `{count: 101882, papers: {...}}`
Will log an array of objects. The objects represent PubMed "summaries" containing title, authors, journal and citation information, etc..
By default, 10 results will be retrieved at a time. To get the next set of results:
```js
ncbi.getAbstract(6365930, true).then(function(result) {
console.log(result);
});
pubmedSearch.nextPage().then( ... );
```
will display the abstract, where 6365930 is a PubMed ID number, a true indicates that only a single result is expected.
## Advanced usage
To change the number of results retrieved at a time:
node-ncbi consists of three components: a gateway, a parser, and a few functions that wrap around them to create simple interfaces.
```js
let pubmedSearch = ncbi.createSearch('actin', {
resultsPerPage: 100
});
```
### Gateway
###Getting the details of a paper
```js
var gateway = require('node-ncbi/createGateway')({
method: 'esearch',
responseType: 'json',
params: {
term: 'actin'
},
test: false
});
var paper = ncbi.createCitation(20517925);
```
`method` may be esearch, esummary, efetch, etc.
where the only argument is a PMID (PubMed ID #).
The following methods are available:
`responseType` may be json or xml. Note that efetch only returns XML.
- `abstract()` - get the abstract
- `summary()` - get the "summary" - an object of fields containing title, authors, citation info, etc.
- `cites()` - papers which this paper cites.
- `citedBy()` - papers which cite this paper (only includes citing papers in PubMed central)
- `similar()` - papers similar to this one (similarity is calculated on NCBI's side of the API, not ours).
Params can be [any of the parameters that the eUtils API accepts](http://www.ncbi.nlm.nih.gov/books/NBK25500/), as key-value pairs.
All methods return a promise accessible by `.then()`. Except for `.abstract()` the parameter passed to the callback is a PubMed summary or an array of summaries.
**Methods**
## Contributing
`gateway.addParams({parameterKey: parameterValue})` - add new parameters after instantiating the object.
I'd love to get PRs improving the code or expanding the search methods beyond PubMed.
`gateway.addIds(ids)` - special way to add a list of IDs as a parameter; an array of ids will be concatenated into a string.
You can build for development by navigating to the project folder and running `npm install`. You'll also need to have gulp installed globally `npm install -g gulp`.
`gateway.send().then(function(response) {...})` - send off the request. The entire, unfiltered response will be the first argument of the callback passed to `then`.
### Overview
`gateway.get().then(function(doc) {...})` - send of the request and created a parser object. The parser object will be the first argument of the callback passed to `then`.
The module consists of three main parts: a Gateway class that controls access to the API, a set of Document parsers for finding the required information in the returned documents, and Controllers for tying the two together.
###Parser###
Since many of the exposed methods require accessing the API multiple times (ie - perform a search and get ID numbers, then find the individual documents by sending those ID numbers) controllers configure as many gateways and parsers as needed to accomplish a particular task.
Gateways are instantiated with an object literal as follows:
```js
var doc = require('node-ncbi/createNcbiDataDocument')(data);
let gateway = Gateway({
documentType: 'esearch' | 'esummary' | 'elink' | 'efetch' (default: 'esearch'),
responseType: 'json' | 'xml' (default: 'json'),
params: {} (set of parameters for the API)
test: false
});
```
Data may be JSON or XML (or a JavaScript object). It will stored in the property `doc.record`.
See the [API documentaion](http://www.ncbi.nlm.nih.gov/books/NBK25500/) for more information on document types and available parameters.
**Methods**
A set of PubMed IDs can be added like so:
`doc.count()` - return the count (total results) from a search.
```js
gateway.addIds([1111111, 2222222]);
```
`doc.ids()` - return all IDs (such as PubMed ID numbers) from a search.
The most important method is `gateway.send()` which returns a Promise resolving to the appropriate parser for the returned document type. The parser methods are pretty self-explanatory and are named for the type of information that they will return.
`doc.summaries(single)` - return the complete record of each summary found in an esummary search. If *single* is false, return an array, otherwise a single object.
### REPL
`doc.abstracts(single)` - return the abstract from one or more results, as a string. If *single* is false, return an array, otherwise a single string.
To help with creating Gateways are seeing the data structures returned by the API, node-ncbi provides a custom REPL. Start it with `npm start`. You can then run `url({object})` or `open({object})` where {object} is an object literal for creating gateways as described above. `url` will log the URL needed to access eUtils while `open` will open that URL in a browser. This can help to see the actual data which is useful to create new parsers.
### License
### Unit tests
Copyright (c) 2015 Casey A. Ydenberg
The Gateway and the Parsers are tested independetly in `test/test.js`. Run with `gulp test`.
### ESLint
Run with `gulp lint`.
## License
Copyright (c) 2016 Casey A. Ydenberg
Permission is hereby granted, free of charge, to any person obtaining a copy

@@ -87,0 +109,0 @@ of this software and associated documentation files (the "Software"), to deal

0

test/docs/search.json

@@ -0,0 +0,0 @@ {

0

test/docs/summary.json

@@ -0,0 +0,0 @@ {

79

test/test.js

@@ -0,1 +1,5 @@

"use strict";
/*eslint-env mocha */
//test the tests

@@ -10,19 +14,11 @@ var assert = require("assert")

})
})
});
var createGateway = require('../src/gateways');
describe('Search Gateway', function() {
var createGateway = require('../createGateway');
describe('Gateway', function() {
var search = createGateway({
method : 'esearch',
params : {
db : 'pubmed',
term : 'ydenberg ca'
},
test : true
});
describe('generateUrl', function() {
var search = createGateway.pubmedSearch('ydenberg ca', 0, 10);
describe('generateUrl search', function() {
it('should build a valid search url from parameters', function() {
assert.equal(search.generateUrl(), 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=ydenberg%20ca&retmode=json');
assert.equal(search.generateUrl(), 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=ydenberg%20ca&retstart=0&retmax=10&retmode=json');
});

@@ -33,9 +29,20 @@ });

describe('Links gateway', function() {
describe('generateUrl links', function() {
var links = createGateway.pubmedLinks(22588722);
it('should build a valid link url from parameters', function() {
assert.equal(links.generateUrl(), 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?db=pubmed&dbfrom=pubmed&cmd=neighbor&retmode=json&id=22588722');
});
});
});
function getDoc(filename, callback) {
fs = require('fs');
path = require('path');
var fs = require('fs');
var path = require('path');
fs.readFile(path.join(__dirname, 'docs', filename), 'UTF-8', callback);
}
var createParser = require('../createNcbiDataDocument');
var createParser = require('../src/documents');
describe('parser', function() {

@@ -46,3 +53,3 @@

getDoc('search.json', function(err, contents) {
var parser = createParser(contents);
var parser = createParser(contents, 'esearch');
assert.equal(parser.count(), 9);

@@ -57,3 +64,3 @@ done();

getDoc('search.json', function(err, contents) {
var parser = createParser(contents);
var parser = createParser(contents, 'esearch');
assert.equal(parser.ids().length, 9);

@@ -68,3 +75,3 @@ done();

getDoc('summary.json', function(err, contents) {
var parser = createParser(contents);
var parser = createParser(contents, 'esummary');
var summaries = parser.summaries();

@@ -80,3 +87,3 @@ assert.equal(summaries.length, 9);

getDoc('fetch.xml', function(err, contents) {
var parser = createParser(contents);
var parser = createParser(contents, 'efetch');
assert.ok( parser.abstracts(true) );

@@ -88,2 +95,32 @@ done();

describe('citedBy', function() {
it('should find all of the papers that have cited this one', function(done) {
getDoc('elink.json', function(err, contents) {
var parser = createParser(contents, 'elink');
assert.equal(parser.citedBy().length, 2);
done();
});
})
});
describe('cites', function() {
it('should find all the papers this paper cites', function(done) {
getDoc('elink.json', function(err, contents) {
var parser = createParser(contents, 'elink');
assert.ok(parser.cites());
done();
});
});
});
describe('similar', function() {
it('should find all the papers PubMed flags as similar to this one', function(done) {
getDoc('elink.json', function(err, contents) {
var parser = createParser(contents, 'elink');
assert.ok(parser.similar());
done();
});
});
});
});
createGateway.js
createNcbiDataDocument.js
.npmignore

Sorry, the diff of this file is not supported yet

test/docs/fetch.xml

Sorry, the diff of this file is not supported yet

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