vsm-dictionary-uniprot - npm Package Compare versions

Comparing version 1.0.14 to 1.0.15

.eslintrc.js

@@ -9,3 +9,3 @@ module.exports = {
   globals: {
-    VsmDictionaryUniprot: true,
+    VsmDictionaryUniProt: true,
   },
@@ -12,0 +12,0 @@ parserOptions: {

package.json

 {
   "name": "vsm-dictionary-uniprot",
-  "version": "1.0.14",
-  "description": "Implementation of a VSM-dictionary that interfaces with the Uniprot REST API",
-  "main": "src/DictionaryUniprot.js",
+  "version": "1.0.15",
+  "description": "Implementation of a VSM-dictionary that interfaces with the UniProt REST API",
+  "main": "src/DictionaryUniProt.js",
   "scripts": {
@@ -28,26 +28,26 @@ "lint": "eslint src test",
   "devDependencies": {
-    "@babel/core": "^7.10.2",
-    "@babel/preset-env": "^7.10.2",
+    "@babel/core": "^7.11.6",
+    "@babel/preset-env": "^7.11.5",
     "babel-loader": "^8.1.0",
     "chai": "^4.2.0",
     "clean-webpack-plugin": "^1.0.1",
-    "codecov": "^3.7.0",
-    "copy-webpack-plugin": "^5.1.1",
+    "codecov": "^3.7.2",
+    "copy-webpack-plugin": "^5.1.2",
     "eslint": "^5.13.0",
     "html-webpack-plugin": "^3.2.0",
     "js-yaml": "^3.14.0",
-    "lodash": "^4.17.15",
+    "lodash": "^4.17.20",
     "mocha": "^7.2.0",
     "nock": "^9.6.1",
     "nyc": "^15.1.0",
-    "terser-webpack-plugin": "^2.3.7",
+    "terser-webpack-plugin": "^2.3.8",
     "text-transform-loader": "^2.0.0",
-    "webpack": "^4.43.0",
-    "webpack-cli": "^3.3.11",
+    "webpack": "^4.44.1",
+    "webpack-cli": "^3.3.12",
     "webpack-dev-server": "^3.11.0"
   },
   "dependencies": {
-    "vsm-dictionary": "^2.6.5",
+    "vsm-dictionary": "^2.6.6",
     "xmlhttprequest": "^1.8.0"
   }
 }

README.md

@@ -15,3 +15,3 @@ # vsm-dictionary-uniprot
 of the 'VsmDictionary' parent-class/interface (from the package
-[`vsm-dictionary`](https://github.com/vsmjs/vsm-dictionary)), that
+[`vsm-dictionary`](https://github.com/vsm/vsm-dictionary)), that
 communicates with [UniProt's](https://www.uniprot.org) 
@@ -26,7 +26,8 @@ REST API and translates the provided protein data into a VSM-specific format.
 
-Create a `test.js` file and include this code:
+Create a directory `test-dir` and inside run `npm install vsm-dictionary-uniprot`.
+Then, create a `test.js` file and include this code:
 
 ```javascript
-const DictionaryUniprot = require('./DictionaryUniprot');
-const dict = new DictionaryUniprot({log: true});
+const DictionaryUniProt = require('vsm-dictionary-uniprot');
+const dict = new DictionaryUniProt({log: true});
 
@@ -44,6 +45,13 @@ dict.getEntryMatchesForString('tp53', { page: 1, perPage: 10 },
 
+### Browsers
+
+```html
+<script src="https://unpkg.com/vsm-dictionary-uniprot@^1.0.0/dist/vsm-dictionary-uniprot.min.js"></script>
+```
+after which it is accessible as the global variable `VsmDictionaryUniProt`.
+
 ## Tests
 
 Run `npm test`, which runs the source code tests with Mocha.  
-If you want to quickly live test the Uniprot API, go to the 
+If you want to quickly live test the UniProt API, go to the 
 `test` directory and run:
@@ -73,5 +81,5 @@ ```
 the parent class
-[specification](https://github.com/vsmjs/vsm-dictionary/blob/master/Dictionary.spec.md).
+[specification](https://github.com/vsm/vsm-dictionary/blob/master/Dictionary.spec.md).
 In the next sections we will explain the mapping between the data 
-offered by Uniprot's API and the corresponding VSM objects. Useful
+offered by UniProt's API and the corresponding VSM objects. Useful
 links for the API are: 
@@ -84,3 +92,3 @@ - https://www.uniprot.org/help/query-fields
 Note also that we implement **strict error handling** in the sense that whenever 
-we launch multiple parallel queries to Uniprot's REST API (see the functions 
+we launch multiple parallel queries to UniProt's REST API (see the functions 
 specifications below), if one of them returns an error (either a string or an 
@@ -100,3 +108,3 @@ error JSON object response), then the result will be an error object (no matter
 
-### Map Uniprot to DictInfo VSM object
+### Map UniProt to DictInfo VSM object
 
@@ -116,3 +124,3 @@ This specification relates to the function:
 
-### Map Uniprot to Entry VSM object
+### Map UniProt to Entry VSM object
 
@@ -151,3 +159,3 @@ This specification relates to the function:
 
-At July 2019, Uniprot offered the results from its REST API in various formats 
+At July 2019, UniProt offered the results from its REST API in various formats 
 but not JSON :( We chose thus the tab-separated format as shown in the above 
@@ -157,5 +165,5 @@ queries (`&format=tab`). The returned tab-separated lines are mapped to VSM
 
-Uniprot column | Type | Required | VSM entry/match object property | Notes  
+UniProt column | Type | Required | VSM entry/match object property | Notes  
 :---:|:---:|:---:|:---:|:---:
-`Entry` | String | YES | `id` | the full URL of the Uniprot ID
+`Entry` | String | YES | `id` | the full URL of the UniProt ID
 `FUNCTION [CC]` | String | NO | `descr` | The protein's function
@@ -166,3 +174,3 @@ `Protein names` | String | NO? | `str`,`terms[i].str` | Recommended and alternative names for the protein
 `Status` | String | NO | `z.status` | Is the protein information *reviewed*, *unreviewed*, *deleted* (obsolete), etc.
-`Entry name` | String | YES | `z.entry` | A Uniprot-specific ID for the entry, e.g. `VPS73_YEAST`
+`Entry name` | String | YES | `z.entry` | A UniProt-specific ID for the entry, e.g. `VPS73_YEAST`
 `Annotation` | String | NO | `z.score` | Annotation score, a quality index for the protein information (e.g. '4 out of 5')
@@ -172,11 +180,11 @@
 reasonable. There is though a global option `optimap` that you can pass to the 
-`DictionaryUniprot` object, which optimizes the above mapping for curator clarity
+`DictionaryUniProt` object, which optimizes the above mapping for curator clarity
 and use. The **default value is true** and what changes in the mapping table
 above (which is the mapping for `optimap: false` actually) is that the VSM's `str` 
 entry/match object property takes the value of the `Entry name`. The reason behind 
-this is that the `Entry name` is always different for every returned result (Uniprot's
+this is that the `Entry name` is always different for every returned result (UniProt's
 internal id) and thus distinguishable, whereas in the original mapping the first 
 protein name (which was used as `str`) is not. 
 
-### Map Uniprot to Match VSM object
+### Map UniProt to Match VSM object
 
@@ -190,3 +198,3 @@ This specification relates to the function:
 
-Otherwise, an example of a URL string that is being built and send to Uniprot's 
+Otherwise, an example of a URL string that is being built and send to UniProt's 
 REST API when requesting for `tp53`, is:
@@ -199,11 +207,11 @@ ```
 well as the mapping shown in the table above. Queries requesting for string 
-matches **always** return results sorted based on an internal, Uniprot-specific 
+matches **always** return results sorted based on an internal, UniProt-specific 
 score value (note the `sort=score` in the URL). This practically ensures that 
 the most requested and best-quality results will be the ones returned first and 
 they are the same as what you would expect when searching a term in the the main 
-search box of the Uniprot website: `https://www.uniprot.org/uniprot/?query=tp53&sort=score`.
+search box of the UniProt website: `https://www.uniprot.org/uniprot/?query=tp53&sort=score`.
 
 For the `limit` and `offset` parameters the same things apply as in 
 the `getEntries` specification. No sorting whatsoever is done on the client
-after the results are returned from Uniprot's REST API. 
+after the results are returned from UniProt's REST API. 
 
@@ -210,0 +218,0 @@ ## License

src/DictionaryUniprot.test.js

@@ -1,2 +0,2 @@
-const DictionaryUniprot = require('./DictionaryUniprot');
+const DictionaryUniProt = require('./DictionaryUniProt');
 const chai = require('chai'); chai.should();
@@ -8,9 +8,9 @@ const expect = chai.expect;
 
-describe('DictionaryUniprot.js', () => {
+describe('DictionaryUniProt.js', () => {
 
   const testURLBase = 'http://test';
   const dict =
-    new DictionaryUniprot({ baseURL: testURLBase, log: true, optimap: false });
+    new DictionaryUniProt({ baseURL: testURLBase, log: true, optimap: false });
   const dictOptimized =
-    new DictionaryUniprot({ baseURL: testURLBase, log: true }); // optimap: true
+    new DictionaryUniProt({ baseURL: testURLBase, log: true }); // optimap: true
 
@@ -140,3 +140,3 @@ const melanomaStr = 'melanoma';
   describe('buildEntryURLs', () => {
-    it('returns proper array of URLs to send to Uniprot REST API', cb => {
+    it('returns proper array of URLs to send to UniProt REST API', cb => {
       const options1 = {};
@@ -195,6 +195,6 @@ const options2 = { filter: {}, sort: 'str' };
 
-  describe('mapUniprotResToEntryObj', () => {
-    it('properly maps Uniprot\'s tab-seperated lines to VSM entry '
+  describe('mapUniProtResToEntryObj', () => {
+    it('properly maps UniProt\'s tab-seperated lines to VSM entry '
       + 'objects', cb => {
-      dict.mapUniprotResToEntryObj(getIDsStr).should.deep.equal(
+      dict.mapUniProtResToEntryObj(getIDsStr).should.deep.equal(
         [{
@@ -246,3 +246,3 @@ id: 'https://www.uniprot.org/uniprot/P52413',
 
-      dictOptimized.mapUniprotResToEntryObj(getIDsStr).should.deep.equal(
+      dictOptimized.mapUniProtResToEntryObj(getIDsStr).should.deep.equal(
         [{
@@ -304,6 +304,6 @@ id: 'https://www.uniprot.org/uniprot/P52413',
 
-  describe('mapUniprotResToMatchObj', () => {
-    it('properly maps Uniprot\'s tab-seperated lines to VSM match '
+  describe('mapUniProtResToMatchObj', () => {
+    it('properly maps UniProt\'s tab-seperated lines to VSM match '
       + 'objects', cb => {
-      dict.mapUniprotResToMatchObj(getMatchesForMelanomaStr, 'melanoma')
+      dict.mapUniProtResToMatchObj(getMatchesForMelanomaStr, 'melanoma')
         .should.deep.equal([
@@ -383,3 +383,3 @@ {
 
-      dictOptimized.mapUniprotResToMatchObj(getMatchesForMelanomaStr, 'melanoma')
+      dictOptimized.mapUniProtResToMatchObj(getMatchesForMelanomaStr, 'melanoma')
         .should.deep.equal([
@@ -476,3 +476,3 @@ {
       const url5 = dict.prepareEntrySearchURL({ page: 1, perPage: 2 }, 'https://www.uniprot.org/uniprot/Q7T2N5');
-      const url6 = dict.prepareEntrySearchURL({}, 'notAUniprotID');
+      const url6 = dict.prepareEntrySearchURL({}, 'notAUniProtID');
 
@@ -490,3 +490,3 @@ const columnsURLPart = '&columns=id%2Ccomment%28FUNCTION%29%2Cprotein%20names%2Cgenes%2Corganism%2Creviewed%2Centry%20name%2Cannotation%20score';
         + '&format=tab';
-      const expectedURL6 = testURLBase + '/?query=id:notAUniprotID' + columnsURLPart
+      const expectedURL6 = testURLBase + '/?query=id:notAUniProtID' + columnsURLPart
         + '&format=tab';
@@ -493,0 +493,0 @@

test/getEntries.test.js

 /**
  * File used to quick test the `getEntries` function of
- * `DictionaryUniprot.js`
+ * `DictionaryUniProt.js`
  */
 
-const DictionaryUniprot = require('../src/DictionaryUniprot');
+const DictionaryUniProt = require('../src/DictionaryUniProt');
 
-const dict = new DictionaryUniprot({log: true});
+const dict = new DictionaryUniProt({log: true});
 
@@ -10,0 +10,0 @@ dict.getEntries({

test/getEntryMatchesForString.test.js

 /**
  * File used to quick test the `getEntryMatchesForString` function of
- * `DictionaryUniprot.js`
+ * `DictionaryUniProt.js`
  */
 
-const DictionaryUniprot = require('../src/DictionaryUniprot');
+const DictionaryUniProt = require('../src/DictionaryUniProt');
 
-const dict = new DictionaryUniprot({log: true});
+const dict = new DictionaryUniProt({log: true});
 
@@ -10,0 +10,0 @@ dict.getEntryMatchesForString('tp53', { page: 1, perPage: 20 },

webpack.config.js

 /*
-This Webpack-config builds a version of VsmDictionaryUniprot that can be
+This Webpack-config builds a version of VsmDictionaryUniProt that can be
 loaded in browsers, where it can be accessed as a global variable.
@@ -16,7 +16,7 @@ */
 
-module.exports = (env = {}) => ({
+module.exports = () => ({
 
   mode: 'production',
 
-  entry: src + '/DictionaryUniprot.js',
+  entry: src + '/DictionaryUniProt.js',
 
@@ -58,5 +58,5 @@ devtool: addSourceMap ? 'hidden-source-map' : false,
     filename: 'vsm-dictionary-uniprot.min.js',
-    library: 'VsmDictionaryUniprot',
+    library: 'VsmDictionaryUniProt',
     libraryTarget: 'var'
   }
 });

No alert changes

Improved metrics

Total package byte prevSize

199254

increased by0.31%

Number of lines in readme file

208

increased by4%

Dependency changes

• Updatedvsm-dictionary@^2.6.6