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vsm-dictionary-combiner

Node.js CI npm version Downloads License

Summary

vsm-dictionary-combiner is an implementation of the 'VsmDictionary' parent-class/interface (from the package vsm-dictionary). It differs though from other vsm-dictionaries in the sense that it does not communicate with any external data source directly, but gets results from other vsm-dictionary-xyz packages and combines them.

Install

Run: npm install

Example use

To see an example of how to use this package to get results from 3 vsm-dictionaries (namely vsm-dictionary-uniprot, vsm-dictionary-ensembl and vsm-dictionary-bioportal), go to the test directory and run:

node getDictInfos.test.js
node getEntries.test.js
node getEntryMatchesForString.test.js

'Build' configuration

To use a VsmDictionary in Node.js, one can simply run npm install and then use require(). But it is also convenient to have a version of the code that can just be loaded via a <script>-tag in the browser.

Therefore, we included webpack.config.js, which is a Webpack configuration file for generating such a browser-ready package.

By running npm build, the built file will appear in a 'dist' subfolder. You can use it by including: <script src="../dist/vsm-dictionary-combiner.min.js"></script> in the header of an HTML file.

Note that you should always include all other vsm-dictionaries that the combiner package will use either by using require() (in Node.js) or by including the specific script source for each package in the HTML header. See the example HTML file in the test directory for a demo of the vsm-dictionary-combiner integrated in a vsm-box and how to include the minified distribution built files for each respective vsm-dictionary.

Specification

Since the vsm-dictionary-combiner follows the parent's class specification, it supports the merging of results for the 4 functions:

  • getDictInfos
  • getEntries
  • getEntryMatchesForString
  • getRefTerms

For each of the above functions, the combiner module concatenates the results from the subsequent vsm-dictionaries calls, in the order the dictionaries were given to the constructor. This means that the options.perPage and options.page for example will be sent unchanged to each dictionary and no cutoff whatsoever will be applied to the merged result array object.

  • A key configuration option is the dictionaries property - an array of VsmDictionary classes that the combiner package will use (other objects are ignored):
const DictionaryCombiner          = require('vsm-dictionary-combiner');
const VsmDictionaryUniProt        = require('vsm-dictionary-uniprot');
const VsmDictionaryEnsembl        = require('vsm-dictionary-ensembl');
const VsmDictionaryEnsemblGenomes = require('vsm-dictionary-ensembl-genomes');

const dictCombiner = new DictionaryCombiner({
  dictionaries: [
    new VsmDictionaryUniProt(),
    new VsmDictionaryEnsembl(),
    new VsmDictionaryEnsemblGenomes()
  ]
});
  • Regarding error handling, we use the option: errorIfAllErrors. The default value is true (or absent) which means that only if all of the subsequent vsm-dictionaries return an error, only then the combiner class returns a global error object by concatenating the subsequent error objects in an array arr and sending back the object: {errors: arr}. So, in that case even if some of the underlying vsm-dictionaries have errors, we still return the results from the other dictionaries (flexible error handling). If errorIfAllErrors is false, then we return the first error (object) that occurs (strict error handling).

License

This project is licensed under the AGPL license - see LICENSE.md.