vsm-dictionary-ensembl - npm Package Compare versions

Comparing version 1.0.6 to 1.0.7

package.json

 {
   "name": "vsm-dictionary-ensembl",
-  "version": "1.0.6",
+  "version": "1.0.7",
   "description": "Implementation of a VSM-dictionary that uses the EBI search RESTful Web Services to interact with the Ensembl genome database",
@@ -5,0 +5,0 @@ "main": "src/DictionaryEnsembl.js",

README.md

@@ -64,2 +64,15 @@ # vsm-dictionary-ensembl
 
+Note that if we receive an error response from the EBI Search servers (see the 
+URL requests for `getEnties` and `getEntryMatchesForString` below) that is not a
+JSON string that we can parse, we formulate the error as a JSON object ourselves 
+in the following format:
+```
+{
+  status: <number>,
+  error: <response> 
+}
+```
+where the *response* from the server is JSON stringified.
+
+
 ### Map Ensembl to DictInfo VSM object
@@ -96,3 +109,3 @@
 
-From the above URL, we provide a brief description for each sub-part: 
+For the above URL, we provide a brief description for each sub-part: 
 - The first part refers to the EBI Search's main REST endpoint: https://www.ebi.ac.uk/ebisearch/ws/rest/
@@ -156,3 +169,3 @@ - The second part refers to the **domain** of search (*ensembl_gene*)
 entry/match object property takes the combined value of the `species`, the gene
-names (`name`, `gene_name`, `gene_synonym`) and the `description` (in that order). 
+names (`gene_synonym`, `name`) and the `description` (in that order). 
 The reason behind this is that the `description` is sometimes the same for different
@@ -159,0 +172,0 @@ genes when `optimap: false` and thus not distinguishable, so we had to provide

src/DictionaryEnsembl.js

 const Dictionary = require('vsm-dictionary');
-const { getLastPartOfURL, fixedEncodeURIComponent, removeDuplicates } = require('./fun');
+const { getLastPartOfURL, fixedEncodeURIComponent,
+  removeDuplicates, isJSONString } = require('./fun');
 
@@ -50,12 +51,5 @@ module.exports = class DictionaryEnsembl extends Dictionary {
     } else {
-      // keep only the domain-specific dictID(s)
-      let idList = options.filter.id.filter(dictID =>
-        dictID.trim() === this.ensemblDictID
-      );
-
-      if (idList.length === 0) {
-        return cb(null, {items: []});
-      } else {
-        return cb(null, res);
-      }
+      return (options.filter.id.includes(this.ensemblDictID))
+        ? cb(null, res)
+        : cb(null, { items: [] });
     }
@@ -65,11 +59,5 @@ }
   getEntries(options, cb) {
-    if (this.hasProperFilterDictIDProperty(options)) {
-      // keep only the domain-specific dictID(s)
-      let idList = options.filter.dictID.filter(dictID =>
-        dictID.trim() === this.ensemblDictID
-      );
-
-      if (idList.length === 0) {
-        return cb(null, { items: [] });
-      }
+    if (this.hasProperFilterDictIDProperty(options)
+      && !options.filter.dictID.includes(this.ensemblDictID)) {
+      return cb(null, { items: [] });
     }
@@ -86,3 +74,3 @@
 
-      // When requesting specific list of ids, do sorting and triming
+      // When requesting specific list of ids, do sorting and trimming
       let arr = entryObjArray;
@@ -105,11 +93,5 @@ if (this.hasProperFilterIDProperty(options)) {
 
-    if (this.hasProperFilterDictIDProperty(options)) {
-      // keep only the domain-specific dictID(s)
-      let idList = options.filter.dictID.filter(dictID =>
-        dictID.trim() === this.ensemblDictID
-      );
-
-      if (idList.length === 0) {
-        return cb(null, { items: [] });
-      }
+    if (this.hasProperFilterDictIDProperty(options)
+      && !options.filter.dictID.includes(this.ensemblDictID)) {
+      return cb(null, { items: [] });
     }
@@ -385,4 +367,9 @@
       if (req.readyState === 4) {
-        if (req.status !== 200)
-          cb(JSON.parse(req.responseText));
+        if (req.status !== 200) {
+          let response = req.responseText;
+          isJSONString(response)
+            ? cb(JSON.parse(response))
+            : cb(JSON.parse('{ "status": ' + req.status
+            + ', "errors": [' + JSON.stringify(response) + ']}'));
+        }
         else {
@@ -389,0 +376,0 @@ try {

src/fun.js

 module.exports = { getLastPartOfURL, fixedEncodeURIComponent,
-  getElementsInParentheses, getStringBeforeFirstSeparator, removeDuplicates };
+  getElementsInParentheses, getStringBeforeFirstSeparator,
+  removeDuplicates, isJSONString };
 
@@ -34,2 +35,11 @@ function getLastPartOfURL(entryId) {
   return [...new Set(arr)];
+}
+
+function isJSONString(str) {
+  try {
+    let json = JSON.parse(str);
+    return (json && typeof json === 'object');
+  } catch (e) {
+    return false;
+  }
 }

src/fun.test.js

 const { getLastPartOfURL, fixedEncodeURIComponent, getElementsInParentheses,
-  getStringBeforeFirstSeparator, removeDuplicates } = require('./fun');
+  getStringBeforeFirstSeparator, removeDuplicates, isJSONString } = require('./fun');
 const chai = require('chai'); chai.should();
+const expect = chai.expect;
+const fs = require('fs');
+const path = require('path');
 
 describe('fun.js', () => {
 
+  const getIDPath = path.join(__dirname, '..', 'resources', 'id.json');
+  const getMelanomaPath = path.join(__dirname, '..', 'resources', 'melanoma.json');
+
+  const getIDStr = fs.readFileSync(getIDPath, 'utf8');
+  const getMatchesForMelanomaStr = fs.readFileSync(getMelanomaPath, 'utf8');
+
   describe('getLastPartOfURL', () => {
@@ -85,2 +94,23 @@ it('returns the last part of a URL', cb => {
   });
+
+  describe('isJSONString', () => {
+    it('returns true or false whether the given string is a JSON string or ' +
+      'not!', cb => {
+      expect(isJSONString('')).to.equal(false);
+      expect(isJSONString('melanoma')).to.equal(false);
+      expect(isJSONString('<h1>Not Found</h1>')).to.equal(false);
+      expect(isJSONString([])).to.equal(false);
+      expect(isJSONString({})).to.equal(false);
+      expect(isJSONString('This is not a JSON string.')).to.equal(false);
+
+      expect(isJSONString('{}')).to.equal(true);
+      expect(isJSONString('[]')).to.equal(true);
+      expect(isJSONString('["foo","bar",{"foo":"bar"}]')).to.equal(true);
+      expect(isJSONString('{"myCount": null}')).to.equal(true);
+      expect(isJSONString(getIDStr)).to.equal(true);
+      expect(isJSONString(getMatchesForMelanomaStr)).to.equal(true);
+
+      cb();
+    });
+  });
 });

No alert changes

Improved metrics

Total package byte prevSize

155139

increased by1.12%

Lines of code

1343

increased by1.82%

Number of lines in readme file

191

increased by7.3%

Worsened metrics

Number of low supply chain risk alerts

2

increased by100%

No dependency changes