vsm-dictionary-ensembl - npm Package Compare versions

Comparing version 1.0.2 to 1.0.3

package.json

 {
   "name": "vsm-dictionary-ensembl",
-  "version": "1.0.2",
+  "version": "1.0.3",
   "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

@@ -69,4 +69,6 @@ # vsm-dictionary-ensembl
 
-Since `vsm-dictionary-ensembl` has only one sub-dictionary
-(it's a uni-dictionary!), `getDictInfos` returns a static object with properties:
+If the `options.filter.id` is not properly defined 
+or the `https://www.ensembl.org` dictID is included in the 
+list of ids used for filtering, `getDictInfos` returns a static object 
+with the following properties:
 - `id`: 'https://www.ensembl.org' (will be used as a `dictID`)
@@ -76,2 +78,4 @@ - `abbrev`: 'Ensembl'
 
+Otherwise, an empty result is returned.
+
 ### Map Ensembl to Entry VSM object
@@ -82,2 +86,6 @@
 
+Firstly, if the `options.filter.dictID` is properly defined and in the list of 
+dictIDs the `https://www.ensembl.org` dictID is not included, then 
+an **empty array** of entry objects is returned.
+
 If the `options.filter.id` is properly defined (with IDs like
@@ -148,4 +156,8 @@ `https://www.ensembl.org/id/ENSG00000142208`) then we use a query like this:
 
-An example of a URL string that is being built and send to the EBI Search's REST 
-API when requesting for `tp53`, is:
+Firstly, if the `options.filter.dictID` is properly defined and in the list of 
+dictIDs the `https://www.ensembl.org` dictID is not included, then 
+an **empty array** of match objects is returned.
+
+Otherwise, an example of a URL string that is being built and send to the EBI 
+Search's REST API when requesting for `tp53`, is:
 ```
@@ -152,0 +164,0 @@ https://www.ebi.ac.uk/ebisearch/ws/rest/ensembl_gene?query=tp53&fields=id%2Cname%2Cdescription%2Cgene_name%2Cgene_synonym%2Ctranscript_count%2Cspecies&size=20&start=0&format=json

src/DictionaryEnsembl.js

@@ -32,15 +32,40 @@ const Dictionary = require('vsm-dictionary');
   getDictInfos(options, cb) {
-    return cb(null,
-      {
-        items: [
-          {
-            id: this.ensemblDictID,
-            abbrev: 'Ensembl',
-            name: 'Ensembl'
-          }
-        ]
-      });
+    let res = {
+      items: [
+        {
+          id: this.ensemblDictID,
+          abbrev: 'Ensembl',
+          name: 'Ensembl'
+        }
+      ]
+    };
+
+    if (!this.hasProperFilterIDProperty(options)) {
+      return cb(null, res);
+    } 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);
+      }
+    }
   }
 
   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: [] });
+      }
+    }
+
     const url = this.prepareEntrySearchURL(options);
@@ -73,2 +98,13 @@
 
+    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: [] });
+      }
+    }
+
     const url = this.prepareMatchStringSearchURL(str, options);
@@ -283,2 +319,9 @@
 
+  hasProperFilterDictIDProperty(options) {
+    return options.hasOwnProperty('filter')
+      && options.filter.hasOwnProperty('dictID')
+      && Array.isArray(options.filter.dictID)
+      && options.filter.dictID.length !== 0;
+  }
+
   hasProperFilterIDProperty(options) {
@@ -285,0 +328,0 @@ return options.hasOwnProperty('filter')

src/DictionaryEnsembl.test.js

@@ -36,17 +36,83 @@ const DictionaryEnsembl = require('./DictionaryEnsembl');
   describe('getDictInfos', () => {
-    it('returns proper RNAcentral dictInfo object', cb => {
+    it('returns empty result when the list of dictIDs does not '
+      + ' include the domain\'s dictID', cb => {
+      dict.getDictInfos({ filter: { id: [
+        ' ',
+        'https://www.uniprot.org',
+        'https://www.ensemblgenomes.org' ]}},
+      (err, res) => {
+        expect(err).to.equal(null);
+        res.should.deep.equal({ items: [] });
+        cb();
+      });
+    });
 
+    it('returns proper dictInfo object when `options.filter` is not properly ' +
+      'defined or the domain\'s dictID is in the list of specified dictIDs', cb => {
+      let expectedResult = { items: [
+        {
+          id: 'https://www.ensembl.org',
+          abbrev: 'Ensembl',
+          name: 'Ensembl'
+        }
+      ]};
+
       dict.getDictInfos({}, (err, res) => {
-        expect(err).to.be.null;
-        res.should.deep.equal({
-          items: [
-            {
-              id: 'https://www.ensembl.org',
-              abbrev: 'Ensembl',
-              name: 'Ensembl'
-            }
-          ]
+        expect(err).to.equal(null);
+        res.should.deep.equal(expectedResult);
+      });
+
+      dict.getDictInfos({ filter: { id: [
+        'http://www.ensemblgenomes.org',
+        'https://www.ebi.ac.uk/complexportal',
+        'https://www.ensembl.org' ]}},
+      (err, res) => {
+        expect(err).to.equal(null);
+        res.should.deep.equal(expectedResult);
+      });
+
+      cb();
+    });
+  });
+
+  describe('getEntries', () => {
+    it('returns empty result when the `options.filter.dictID` is properly ' +
+      'defined and in the list of dictIDs the domain\'s dictID is not included', cb => {
+      dict.getEntries({filter: { dictID: ['']}}, (err, res) => {
+        expect(err).to.equal(null);
+        res.should.deep.equal({ items: [] });
+      });
+
+      dict.getEntries({filter: { dictID: [
+        ' ',
+        'https://www.uniprot.org',
+        'http://www.ensemblgenomes.org'
+      ]}}, (err, res) => {
+        expect(err).to.equal(null);
+        res.should.deep.equal({ items: [] });
+      });
+
+      cb();
+    });
+  });
+
+  describe('getEntryMatchesForString', () => {
+    it('returns empty result when the `options.filter.dictID` is properly ' +
+      'defined and in the list of dictIDs the domain\'s dictID is not included', cb => {
+      dict.getEntryMatchesForString(melanomaStr, {filter: { dictID: ['']}},
+        (err, res) => {
+          expect(err).to.equal(null);
+          res.should.deep.equal({ items: [] });
         });
-        cb();
+
+      dict.getEntryMatchesForString(melanomaStr, {filter: { dictID: [
+        ' ',
+        'https://www.uniprot.org',
+        'http://www.ensemblgenomes.org']}},
+      (err, res) => {
+        expect(err).to.equal(null);
+        res.should.deep.equal({ items: [] });
       });
+
+      cb();
     });
@@ -53,0 +119,0 @@ });

No alert changes

Improved metrics

Total package byte prevSize

148225

increased by3.07%

Lines of code

1208

increased by8.54%

Number of lines in readme file

167

increased by7.74%

No dependency changes