Relevance search

README.md

@@ -62,6 +62,14 @@ pubmed.search("actin", 0, 20).then((results) => {
 });
 ```
 
+You can also search by relevance (instead of publication date):
+
+```javascript
+pubmed.searchByRelevance("actin").then((results) => {
+  console.log(results);
+});
+```
+
 ### Looking up a specific paper
 
 ```javascript
@@ -84,6 +92,14 @@ In addition, following methods are available:
 
 All methods return a promise accessible by `.then()`; the value retrieved is passed to the promise.
 
+### Searching by PubMedCentral (PMC) ID number
+
+```javascript
+pmc.summary(3315798).then((paper) => {
+  console.log(paper);
+});
+```
+
 ## Contributing
 
 I'd love to get PRs improving the code or expanding the search methods beyond PubMed.

src/gateways/index.js

@@ -1,55 +1,65 @@
-'use strict';
+"use strict";
 
-const createGateway = require('./createGateway');
+const createGateway = require("./createGateway");
 
 /**
  * Wrapper factory functions for the Gateway. Create and configure Gateways
  * for a specific purpose.
  */
 module.exports = {
-
   /**
    * pubmedSearch. Return a Gateway for a pubmed search, with start and end parameters.
    * (ie first and last results.)
    */
-  pubmedSearch: function(query, page, resultsPerPage) {
+  pubmedSearch: function (query, page, resultsPerPage, sort) {
     const start = page * resultsPerPage;
     return createGateway({
-      utility: 'esearch',
+      utility: "esearch",
       params: {
-        db: 'pubmed',
+        db: "pubmed",
         term: query,
         retstart: start,
-        retmax: resultsPerPage
-      }
+        retmax: resultsPerPage,
+        sort: sort,
+      },
     });
   },
 
   /**
    * pubmedSummary. Get a set of pubmedSummaries, specified by an array of pmid (pubmed identifiers.)
    */
-  pubmedSummary: function(ids) {
+  pubmedSummary: function (ids) {
+    return createGateway({
+      utility: "esummary",
+      params: {
+        db: "pubmed",
+        id: ids,
+      },
+    });
+  },
+
+  pmcSummary: function (ids) {
     return createGateway({
       utility: 'esummary',
       params: {
-        db: 'pubmed',
-        id: ids
+        db: 'pmc',
+        id: ids,
       }
-    });
+    })
   },
 
   /**
-  * Get a set of full/efetch documents from pubmed, specified by an array of pmids (pubmed identifiers).
-  * Note that efetch documents can only be returned via XML (or flatfile).
-  */
-  pubmedRecord: function(ids) {
+   * Get a set of full/efetch documents from pubmed, specified by an array of pmids (pubmed identifiers).
+   * Note that efetch documents can only be returned via XML (or flatfile).
+   */
+  pubmedRecord: function (ids) {
     return createGateway({
-      utility: 'efetch',
+      utility: "efetch",
       params: {
-        db: 'pubmed',
-        retmode: 'xml',
-        id: ids
-      }
+        db: "pubmed",
+        retmode: "xml",
+        id: ids,
+      },
     });
   },
 
@@ -59,25 +69,25 @@ module.exports = {
    * similar articles, articles that cite this article, and articles cited by
    * this article.
    */
-  pubmedLinks: function(id) {
+  pubmedLinks: function (id) {
     return createGateway({
-      utility: 'elink',
+      utility: "elink",
       params: {
-        db: 'pubmed',
-        dbfrom: 'pubmed',
-        cmd: 'neighbor',
-        id: id
-      }
+        db: "pubmed",
+        dbfrom: "pubmed",
+        cmd: "neighbor",
+        id: id,
+      },
     });
   },
 
-  pmcFullText: (id) => createGateway({
-    utility: 'efetch',
-    params: {
-      db: 'pmc',
-      retmode: 'xml',
-      id: id
-    }
-  })
-
-}
+  pmcFullText: (id) =>
+    createGateway({
+      utility: "efetch",
+      params: {
+        db: "pmc",
+        retmode: "xml",
+        id: id,
+      },
+    }),
+};

src/pmc.js

@@ -0,0 +1,17 @@
+'use strict';
+
+const gateways = require('./gateways');
+const queries = require('./queries');
+
+module.exports = {
+  summary: function(pmc) {
+    return gateways.pmcSummary(pmc).resolve(data => {
+      const summaries = queries.summaries(data);
+      if (summaries.length) {
+        return summaries[0];
+      } else {
+        return null;
+      }
+    });
+  }
+}

src/pubmed.js

@@ -3,30 +3,37 @@
 const gateways = require('./gateways');
 const queries = require('./queries');
 
+function pubmedSearch(query, page, resultsPerPage, sort) {
+  let count;
+  page = page || 0;
+  resultsPerPage = resultsPerPage || 10;
+  sort = sort || 'most+recent'
+  return gateways.pubmedSearch(query, page, resultsPerPage).resolve(data => {
+    count = queries.count(data);
+    const pmids = queries.ids(data);
+    if (!pmids.length) {
+      return {
+        count: 0,
+        papers: []
+      };
+    }
+    return new Promise((resolve, reject) => {
+      this.summaries(pmids).then(summaries => {
+        resolve({
+          count: count,
+          papers: summaries
+        });
+      }).catch(err => reject(err));
+    });
+  });
+}
+
 module.exports = {
 
-  search: function(query, page, resultsPerPage) {
-    let count;
-    page = page || 0;
-    resultsPerPage = resultsPerPage || 10;
-    return gateways.pubmedSearch(query, page, resultsPerPage).resolve(data => {
-      count = queries.count(data);
-      const pmids = queries.ids(data);
-      if (!pmids.length) {
-        return {
-          count: 0,
-          papers: []
-        };
-      }
-      return new Promise((resolve, reject) => {
-        this.summaries(pmids).then(summaries => {
-          resolve({
-            count: count,
-            papers: summaries
-          });
-        }).catch(err => reject(err));
-      });
-    });
+  search: pubmedSearch,
+
+  searchByRelevance: function(query, page, resultsPerPage) {
+    return pubmedSearch(query, page, resultsPerPage, 'relevance');
   },
 
   summaries: function(pmids) {

src/queries/summaries.js

@@ -12,15 +12,15 @@ const summaryQueries = {
       raw: data,
       title: data.title || '',
       authors: summaryQueries.formatAuthors(data.authors) || '',
-      pubDate: data.sortpubdate
+      pubDate: data.sortpubdate || data.sortdate,
     };
     data.articleids.forEach((idObject) => {
-      if (idObject.idtype === 'pubmed') {
+      if (['pubmed', 'pmid'].includes(idObject.idtype)) {
         //Change pubmed to pmid. Make sure it's an integer.
         summary.pmid = parseInt(idObject.value, 10);
       } else if (idObject.idtype === 'pmc') {
         //Remove PMC from the beginning of the string and make sure it's an integer.
-        summary.pmc = parseInt(idObject.value.replace('PMC', ''));
+        summary.pmc = parseInt(idObject.value.replace('PMC', ''), 10);
       } else if (idObject.idtype === 'doi') {
         //Move DOI to the top level
         summary.doi = idObject.value;

test/integration.js

@@ -5,6 +5,7 @@ const {isPubmedSummary} = require('./helpers.js');
 const assert = require('assert');
 
 var pubmed = require('../src/pubmed');
+var pmc = require('../src/pmc')
 
 describe('Pubmed module', function() {
   this.timeout(10000);
@@ -72,6 +73,13 @@ describe('Pubmed module', function() {
     });
   });
 
+  it('should retrieve a summary from pmc', function(done) {
+    pmc.summary(3315798).then(result => {
+      isPubmedSummary(result);
+      done();
+    });
+  });
+
   it('should retrieve the full NLM XML of a paper', function(done) {
     pubmed.fulltext(22323294).then(result => {
       check.string(result);

test/test.js

@@ -40,6 +40,17 @@ describe('Links gateway', function() {
 
 });
 
+describe('PMC summary gateway', () => {
+  describe('generateUrl', () => {
+
+    it('should build a valid url from parameters', () => {
+      const fetch = createGateway.pmcSummary(3315798);
+      assert.equal(fetch.generateUrl(), 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmode=json&db=pmc&id=3315798');
+    });
+
+  });
+});
+
 describe('PMC full text gateway', () => {
   describe('generateUrl', () => {
 

types/node-ncbi.d.ts

@@ -1,15 +1,15 @@
 declare module "node-ncbi" {
+  interface Paper {
+    raw: object;
+    pubDate: string;
+    title: string;
+    authors: string;
+    pmid: number;
+    pmc?: number;
+    doi?: string;
+  }
+
   module pubmed {
-    interface Paper {
-      raw: object;
-      pubDate: string;
-      title: string;
-      authors: string;
-      pmid: number;
-      pmc?: number;
-      doi?: string;
-    }
-
     function search(
       term: string,
       page?: number,
@@ -19,6 +19,15 @@ declare module "node-ncbi" {
       papers: Array<Paper>;
     }>;
 
+    function searchByRelevance(
+      term: string,
+      page?: number,
+      limit?: number
+    ): Promise<{
+      count: number;
+      papers: Array<Paper>;
+    }>;
+
     function summary(pmid: number): Promise<Paper>;
 
     function summaries(pmids: string): Promise<Paper[]>;
@@ -35,4 +44,8 @@ declare module "node-ncbi" {
 
     function fullText(pmid: number): Promise<string>;
   }
+
+  module pmc {
+    function summary(pmc: number): Promise<Paper>;
+  }
 }