node-ncbi - npm Package Compare versions

Comparing version 0.4.0 to 0.5.0

bin/repl.js

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

gulpfile.js

@@ -0,0 +0,0 @@ var gulp = require('gulp');

index.js

@@ -0,0 +0,0 @@ 'use strict';

package.json

 {
   "name": "node-ncbi",
-  "version": "0.4.0",
+  "version": "0.5.0",
   "description": "Access and parse the NCBI eUtils API in Node or the Browser",
@@ -5,0 +5,0 @@ "keywords": [

README.md

@@ -0,0 +0,0 @@ # node-ncbi

src/gateways/createGateway.js

@@ -20,3 +20,3 @@ const update = require('react-addons-update');
 Gateway.getBase = function() {
-  return this.base = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/' + this.settings.utility + '.fcgi?';
+  return this.base = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/' + this.settings.utility + '.fcgi?';
 }
@@ -23,0 +23,0 @@

src/gateways/index.js

@@ -72,4 +72,13 @@ 'use strict';
     });
-  }
+  },
 
+  pmcFullText: (id) => createGateway({
+    utility: 'efetch',
+    params: {
+      db: 'pmc',
+      retmode: 'xml',
+      id: id
+    }
+  })
+
 }

src/gateways/parse.js

@@ -0,0 +0,0 @@ const parseString = require('xml2js').parseString;

src/pubmed.js

@@ -73,4 +73,26 @@ 'use strict';
     return gateways.pubmedRecord(pmid).resolve(queries.abstract);
+  },
+
+  isOa: function(pmid) {
+    return this.summary(pmid).then(summary => {
+      if (!summary) {
+        return null;
+      } else {
+        const pmcid = summary.pmc;
+        return gateways.pmcFullText(pmcid).resolve(queries.isOa);
+      }
+    });
+  },
+
+  fulltext: function(pmid) {
+    return this.summary(pmid).then(summary => {
+      if (!summary) {
+        return null;
+      } else {
+        const pmcid = summary.pmc;
+        return gateways.pmcFullText(pmcid).send().then(res => res.body);
+      }
+    });
   }
 
 }

src/queries/index.js

@@ -133,2 +133,7 @@ const update = require('react-addons-update');
     return values;
+  },
+
+  isOa: (data) => {
+    const nodes = queries.deepSearch('body', data);
+    return !!nodes.length;
   }
@@ -135,0 +140,0 @@

src/queries/summaries.js

@@ -0,0 +0,0 @@ const update = require('react-addons-update');

test/docs/elink.json

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

test/docs/search.json

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

test/docs/summary_single.json

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

test/docs/summary.json

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

test/test.js

 /* eslint-env mocha, node */
 
-const check = require('check-types').assert;
+//test the tests
+var assert = require('assert');
 
-//test the tests
-var assert = require('assert')
 describe('Array', function() {
@@ -27,3 +26,3 @@ describe('#indexOf()', 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?retmode=json&db=pubmed&term=ydenberg%20ca&retstart=0&retmax=10');
+      assert.equal(search.generateUrl(), 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmode=json&db=pubmed&term=ydenberg%20ca&retstart=0&retmax=10');
     });
@@ -39,3 +38,3 @@ });
     it('should build a valid link url from parameters', function() {
-      assert.equal(links.generateUrl(), 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=json&db=pubmed&dbfrom=pubmed&cmd=neighbor&id=22588722');
+      assert.equal(links.generateUrl(), 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=json&db=pubmed&dbfrom=pubmed&cmd=neighbor&id=22588722');
     });
@@ -46,189 +45,11 @@ });
 
+describe('PMC full text gateway', () => {
+  describe('generateUrl', () => {
 
-/**
- * PARSERS
- *
- */
-
-/**
- * Define helper functions to get JSON data as JavaScript so that we can
- * query it
- */
-function getDoc(filename, callback) {
-  const parse = require('../src/gateways/parse');
-  var fs = require('fs');
-  var path = require('path');
-  fs.readFile(path.join(__dirname, 'docs', filename), 'UTF-8', (err, data) => {
-    callback(err, parse(data));
-  });
-}
-
-/** Define helper function to determine if an object is a pubmed summary */
-function isPubmedSummary(obj) {
-  check.number(obj.pmid);
-  check.object(obj.raw);
-  check.string(obj.title);
-  check.string(obj.authors);
-  check.emptyString(obj.abstract);
-  check.string(obj.pubDate);
-}
-
-
-describe('Summary parser', function() {
-  const sq = require('../src/queries/summaries');
-  // Parser of a single summary
-
-  describe('formatAuthors', function() {
-
-    it('should return the article authors as a string', function() {
-      const authors = [
-        {name: 'Ydenberg CA'},
-        {name: 'Johnstone A'}
-      ]
-      var result = sq.formatAuthors(authors);
-      assert.equal('Ydenberg CA, Johnstone A', result);
+    it('should build a valid url from parameters', () => {
+      const fetch = createGateway.pmcFullText(3315798);
+      assert.equal(fetch.generateUrl(), 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=xml&db=pmc&id=3315798');
     });
 
-    it("should return an empty string in response to an empty array", function() {
-      var result = sq.formatAuthors([])
-      check.emptyString(result);
-    });
-
   });
-
-  describe('summary', function() {
-
-    it("should return an object containing the important data at the top level and the entire summary embedded under the 'raw' sub-object", function(done) {
-      getDoc('summary_single.json', (err, contents) => {
-        const result = sq.summary(contents);
-        isPubmedSummary(result);
-        done();
-      })
-    });
-
-  });
-
-  describe("sort", function() {
-
-    it("should sort by reverse publication date order, by default", function(done) {
-      const papers = [
-        {pubDate: '1990'},
-        {pubDate: '2010'},
-        {pubDate: '2000'}
-      ];
-      const result = sq.sortSummaries(papers);
-      assert.equal(result[0].pubDate, 2010);
-      done();
-    });
-  });
-
 });
-
-describe('parser', function() {
-  var q = require('../src/queries');
-
-  describe('count', function() {
-    it('should find the count field in a JSON search result', function(done) {
-      getDoc('search.json', function(err, contents) {
-        assert.equal(q.count(contents), 9);
-        done();
-      });
-    });
-  });
-
-  describe('ids', function() {
-    it('should return an array of ids', function(done) {
-      getDoc('search.json', function(err, contents) {
-        assert.equal(q.ids(contents).length, 9);
-        done();
-      })
-    });
-  });
-
-  describe('summary', function() {
-    it('should find all of the info for each summary in the result set', function(done) {
-      getDoc('summary.json', function(err, contents) {
-        q.summaries(contents).forEach(summary => {
-          isPubmedSummary(summary);
-        })
-        done();
-      });
-    });
-  });
-
-  describe('abstract', function() {
-    it('should retrieve the abstract from an xml string', function(done) {
-      getDoc('fetch.xml', function(err, contents) {
-        assert.equal(typeof q.abstract(contents), 'string');
-        done();
-      });
-    });
-  });
-
-  describe('findLinks', function() {
-    it('should find all of the papers that have cited this one', function(done) {
-      getDoc('elink.json', function(err, contents) {
-        assert.equal(q.findLinks('pubmed_pubmed_citedin', contents).length, 2);
-        done();
-      });
-    })
-  });
-
-});
-
-
-
-var pubmed = require('../src/pubmed');
-describe('Pubmed module', function() {
-  this.timeout(10000);
-
-  it('should perform a search', function(done) {
-    pubmed.search('ydenberg ca').then(results => {
-      results.papers.forEach(isPubmedSummary);
-      done();
-    })
-  });
-
-  it('should return papers that cite this one', function(done) {
-    pubmed.citedBy(19188495).then(results => {
-      results.forEach(isPubmedSummary);
-      done();
-    });
-  });
-
-  it('should return papers that are similar to this one', function(done) {
-    pubmed.similar(19188495).then(results => {
-      results.forEach(isPubmedSummary);
-      done();
-    });
-  });
-
-  it('should return a count of 0 if the search returns no results', function(done) {
-    pubmed.search('boioioioioioioioioioioing').then(results => {
-      assert.equal(results.count, 0);
-      done();
-    })
-  });
-
-  it('should return null if an invalid pmid is passed', function(done) {
-    pubmed.summary(0).then(results => {
-      assert.equal(results, null);
-      done();
-    });
-  });
-
-  it('should return an empty array if an invalid pmid is passed to a linking method', function(done) {
-    pubmed.citedBy(0).then(results => {
-      assert.equal(results.length, 0);
-      done();
-    });
-  });
-
-  it('should return null if an invalid pmid is passed to the abstract method', function(done) {
-    pubmed.abstract(0).then(results => {
-      assert.equal(results, null);
-      done();
-    });
-  });
-
-});

New alerts

Network access

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This module accesses the network.

Found 1 instance in 1 package

URL strings

Supply chain risk

Package contains fragments of external URLs or IP addresses, which the package may be accessing at runtime.

Found 1 instance in 1 package

Fixed alerts

URL strings

Supply chain risk

Package contains fragments of external URLs or IP addresses, which the package may be accessing at runtime.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

232228

182.81%

Number of package files

25

31.58%

Lines of code

2479

9.4%

Worsened metrics

Number of medium supply chain risk alerts

1

Infinity%

No dependency changes