node-ncbi - npm Package Compare versions

Comparing version 0.7.0 to 0.7.1

package.json

 {
   "name": "node-ncbi",
-  "version": "0.7.0",
+  "version": "0.7.1",
   "description": "Access and parse the NCBI eUtils API in Node or the Browser",
@@ -27,6 +27,4 @@ "keywords": [
   "dependencies": {
-    "check-types": "^7.0.1",
+    "immutability-helper": "^3.1.1",
     "popsicle": "^9.2.0",
-    "react": "^15.3.2",
-    "react-addons-update": "^15.0.2",
     "xml2js": "^0.4.9"
@@ -36,3 +34,4 @@ },
     "babel-preset-es2015": "^6.24.1",
-    "mocha": "^6.1.4",
+    "check-types": "^7.0.1",
+    "mocha": "^10.1.0",
     "open": "^6.3.0"
@@ -39,0 +38,0 @@ },

src/gateways/createGateway.js

@@ -1,5 +0,5 @@
-const update = require('react-addons-update');
-const popsicle = require('popsicle');
+const update = require("immutability-helper");
+const popsicle = require("popsicle");
 
-const parse = require('./parse');
+const parse = require("./parse");
 
@@ -11,3 +11,3 @@ /**
  * http://www.ncbi.nlm.nih.gov/books/NBK25500/
-*/
+ */
 
@@ -20,5 +20,8 @@ var Gateway = {};
  */
-Gateway.getBase = function() {
-  return this.base = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/' + this.settings.utility + '.fcgi?';
-}
+Gateway.getBase = function () {
+  return (this.base =
+    "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" +
+    this.settings.utility +
+    ".fcgi?");
+};
 
@@ -30,9 +33,9 @@ /**
  */
-Gateway.generateUrl = function() {
+Gateway.generateUrl = function () {
   var url = this.getBase();
   for (var key in this.settings.params) {
     try {
-      url += key + '=' + this.settings.params[key].toString();
-      url += '&';
-    } catch(e) {
+      url += key + "=" + this.settings.params[key].toString();
+      url += "&";
+    } catch (e) {
       //skip if this parameter cannot be converted to a string
@@ -45,3 +48,3 @@ continue;
   return encodeURI(url);
-}
+};
 
@@ -53,11 +56,10 @@ /**
  */
-Gateway.send = function() {
+Gateway.send = function () {
   var url = this.generateUrl();
   return popsicle.get({
-    method: 'GET',
-    url: url
+    method: "GET",
+    url: url,
   });
-}
+};
 
-
 /**
@@ -72,4 +74,4 @@ * Send off the request and parse the returned data.
  */
-Gateway.resolve = function(query) {
-  return this.send().then(res => {
+Gateway.resolve = function (query) {
+  return this.send().then((res) => {
     const dataObj = parse(res.body);
@@ -81,29 +83,32 @@ return query(dataObj);
 /**
-* Use an Object literal to instatiate via the setup method:
-* @arg: documentType: string | 'esearch', 'esummary', 'efetch', 'einfo', see
-* http://www.ncbi.nlm.nih.gov/books/NBK25499/ for more info
-* @arg: responseType: string | 'json', 'xml', 'text'
-* @arg: params: Object | indexed object of other URL parameters, eg 'term' (for searches),
-* 'retstart', 'retmax'
-* @arg: test: Boolean | enable test mode. When in test mode, an actual call will
-* never happen, the search method will return a simple Promise instead.
-*/
-module.exports = function(args) {
+ * Use an Object literal to instatiate via the setup method:
+ * @arg: documentType: string | 'esearch', 'esummary', 'efetch', 'einfo', see
+ * http://www.ncbi.nlm.nih.gov/books/NBK25499/ for more info
+ * @arg: responseType: string | 'json', 'xml', 'text'
+ * @arg: params: Object | indexed object of other URL parameters, eg 'term' (for searches),
+ * 'retstart', 'retmax'
+ * @arg: test: Boolean | enable test mode. When in test mode, an actual call will
+ * never happen, the search method will return a simple Promise instead.
+ */
+module.exports = function (args) {
   const defaults = {
-    utility: 'esearch',
+    utility: "esearch",
     params: {
-      retmode: 'json',
-      db: 'pubmed'
-    }
+      retmode: "json",
+      db: "pubmed",
+    },
   };
-  let settings = update(defaults, {$merge: args, params: {$merge: args.params}});
+  let settings = update(defaults, {
+    $merge: args,
+    params: { $merge: args.params },
+  });
   if (process.env.NCBI_API_KEY) {
-    settings = update(settings, {params:
-      {$merge: {api_key: process.env.NCBI_API_KEY} }
-    })
+    settings = update(settings, {
+      params: { $merge: { api_key: process.env.NCBI_API_KEY } },
+    });
   }
   const gateway = Object.assign(Object.create(Gateway), {
-    settings: settings
+    settings: settings,
   });
   return gateway;
-}
+};

src/queries/index.js

@@ -1,4 +0,4 @@
-const update = require('react-addons-update');
+const update = require("immutability-helper");
 
-const summaryQueries = require('./summaries');
+const summaryQueries = require("./summaries");
 
@@ -15,21 +15,21 @@ const queries = {
    */
-   deepSearch: function _deepSearch(find, data) {
-     var found = [];
-     //if data is not an object, return an empty array.
-     if (typeof data !== 'object') {
-       return found;
-     }
-     //go through each property, and assign it to found if the key
-     //matches the key we're looking for
-     Object.keys(data).forEach(key => {
-       const value = data[key];
-       if (String(key).toLowerCase() === String(find).toLowerCase()) {
-         found.push(value);
-       }
-       //now add in the nodes from the sub-object. If the value of the
-       //property is not an object, deepSearch will just return an empty array.
-       found = found.concat(_deepSearch(find, value));
-     });
-     return found;
-   },
+  deepSearch: function _deepSearch(find, data) {
+    var found = [];
+    //if data is not an object, return an empty array.
+    if (typeof data !== "object") {
+      return found;
+    }
+    //go through each property, and assign it to found if the key
+    //matches the key we're looking for
+    Object.keys(data).forEach((key) => {
+      const value = data[key];
+      if (String(key).toLowerCase() === String(find).toLowerCase()) {
+        found.push(value);
+      }
+      //now add in the nodes from the sub-object. If the value of the
+      //property is not an object, deepSearch will just return an empty array.
+      found = found.concat(_deepSearch(find, value));
+    });
+    return found;
+  },
 
@@ -48,7 +48,7 @@ /**
   nodeValue: function nodeValue(node) {
-    if (typeof node === 'string') {
+    if (typeof node === "string") {
       return node;
     } else if (Array.isArray(node)) {
       return nodeValue(node[0]);
-    } else if (typeof node === 'object') {
+    } else if (typeof node === "object") {
       return nodeValue(node._);
@@ -65,12 +65,14 @@ } else {
    */
-  nodeValues: function(nodes) {
-    return update(nodes, {$apply: (node) => {
-      return queries.nodeValue(node);
-    }});
+  nodeValues: function (nodes) {
+    return update(nodes, {
+      $apply: (node) => {
+        return queries.nodeValue(node);
+      },
+    });
   },
 
-  count: function(data) {
+  count: function (data) {
     try {
       return data.esearchresult.count;
-    } catch(e) {
+    } catch (e) {
       return 0;
@@ -80,6 +82,6 @@ }
 
-  ids: function(data) {
+  ids: function (data) {
     try {
       return data.esearchresult.idlist;
-    } catch(e) {
+    } catch (e) {
       return [];
@@ -89,10 +91,10 @@ }
 
-  summaries: function(data) {
+  summaries: function (data) {
     var found = [];
     try {
       var results = data.result;
-    } catch(e) {
+    } catch (e) {
       return [];
     }
-    Object.keys(results).forEach(key => {
+    Object.keys(results).forEach((key) => {
       //papers are indexed by their uid, so if the key can be a number,
@@ -114,7 +116,7 @@ // we should include it in the summary array. Otherwise we should skip it.
    */
-  findLinks: function(linkname, data) {
+  findLinks: function (linkname, data) {
     try {
       var linksets = [];
       //have not found a case where there is more than one linkset
-      data.linksets[0].linksetdbs.forEach(linksetdb => {
+      data.linksets[0].linksetdbs.forEach((linksetdb) => {
         if (linksetdb.linkname === linkname) {
@@ -125,3 +127,3 @@ linksets = linksets.concat(linksetdb.links);
       return linksets;
-    } catch(e) {
+    } catch (e) {
       return [];
@@ -136,4 +138,4 @@ }
    */
-  abstract: function(data) {
-    const nodes = queries.deepSearch('abstracttext', data);
+  abstract: function (data) {
+    const nodes = queries.deepSearch("abstracttext", data);
     const values = queries.nodeValues(nodes);
@@ -144,8 +146,7 @@ return values;
   isOa: (data) => {
-    const nodes = queries.deepSearch('body', data);
+    const nodes = queries.deepSearch("body", data);
     return !!nodes.length;
-  }
+  },
+};
 
-}
-
 module.exports = queries;

test/helpers.js

 /* eslint-env mocha, node */
 
-const check = require('check-types').assert;
+const check = require("check-types").assert;
 
 module.exports = {
-
   /**
@@ -11,14 +10,17 @@ * Define helper functions to get JSON data as JavaScript so that we can
    */
-  getDoc: function(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));
-    });
+  getDoc: function (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 */
-  isPubmedSummary: function(obj) {
+  isPubmedSummary: function (obj) {
     check.object(obj.raw);
@@ -29,4 +31,3 @@ check.string(obj.pubDate);
     check.number(obj.pmid);
-  }
-
-}
+  },
+};

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This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Filesystem access

Supply chain risk

Accesses the file system, and could potentially read sensitive data.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Filesystem access

Supply chain risk

Accesses the file system, and could potentially read sensitive data.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

223957

increased by0.04%

Dependency count

3

decreased by-40%

Lines of code

2469

increased by0.49%

Worsened metrics

Dev dependency count

4

increased by33.33%

Dependency changes

• + Addedimmutability-helper@^3.1.1

• + Addedimmutability-helper@3.1.1(transitive)

• - Removedcheck-types@^7.0.1

• - Removedreact@^15.3.2

• - Removedreact-addons-update@^15.0.2

• - Removedasap@2.0.6(transitive)

• - Removedcheck-types@7.4.0(transitive)

• - Removedcore-js@1.2.7(transitive)

• - Removedcreate-react-class@15.7.0(transitive)

• - Removedencoding@0.1.13(transitive)

• - Removedfbjs@0.8.18(transitive)

• - Removediconv-lite@0.6.3(transitive)

• - Removedis-stream@1.1.0(transitive)

• - Removedisomorphic-fetch@2.2.1(transitive)

• - Removedjs-tokens@4.0.0(transitive)

• - Removedloose-envify@1.4.0(transitive)

• - Removednode-fetch@1.7.3(transitive)

• - Removedobject-assign@4.1.1(transitive)

• - Removedpromise@7.3.1(transitive)

• - Removedprop-types@15.8.1(transitive)

• - Removedreact@15.7.0(transitive)

• - Removedreact-addons-update@15.6.3(transitive)

• - Removedreact-is@16.13.1(transitive)

• - Removedsafer-buffer@2.1.2(transitive)

• - Removedsetimmediate@1.0.5(transitive)

• - Removedua-parser-js@0.7.39(transitive)

• - Removedwhatwg-fetch@3.6.20(transitive)