node-ncbi/src/pubmed.js

Access and parse the NCBI eUtils API in Node or the Browser

"use strict";

const gateways = require("./gateways");
const queries = require("./queries");

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));
        });
      });
  },

  summaries: function (pmids) {
    return gateways.pubmedSummary(pmids).resolve(queries.summaries);
  },

  summary: function (pmid) {
    return gateways.pubmedSummary(pmid).resolve((data) => {
      const summaries = queries.summaries(data);
      if (summaries.length) {
        return summaries[0];
      } else {
        return null;
      }
    });
  },

  citedBy: function (pmid) {
    return gateways.pubmedLinks(pmid).resolve((data) => {
      var pmids = queries.findLinks("pubmed_pubmed_citedin", data);
      if (!pmids.length) return [];
      return this.summaries(pmids);
    });
  },

  cites: function (pmid) {
    return gateways.pubmedLinks(pmid).resolve((data) => {
      var pmids = queries.findLinks("pubmed_pubmed_refs", data);
      if (!pmids.length) return [];
      return this.summaries(pmids);
    });
  },

  similar: function (pmid) {
    return gateways.pubmedLinks(pmid).resolve((data) => {
      var pmids = queries.findLinks("pubmed_pubmed", data);
      if (!pmids.length) return [];
      return this.summaries(pmids);
    });
  },

  abstract: function (pmid) {
    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.data);
      }
    });
  },
};