Implementation of a VSM-dictionary that interfaces with the Uniprot REST API. 

Implementation of a VSM-dictionary that interfaces with the UniProt REST API

stcruy

bblodfon

vsm-dictionary-uniprot

Implementation of a VSM-dictionary that interfaces with the Uniprot REST API

Error

Ignore

Warn

License

Maintenance

Miscellaneous

Quality

Supply chain risk

Vulnerability

Admins only

Organization members

Dashboard

<upgradeLink>Upgrade</upgradeLink> to access this feature

About

Blog

Socket CLI

Customers

Socket Dependency Search

Docs

Socket for GitHub

Love

Impersonation Mode Active

Update your browser to the latest version for the best experience.

Your web browser is outdated

Use another browser for the best experience.

Your web browser is unsupported

{{count, number}} commits last two months

{{count, number}} critical severity alert

{{count, number}} critical severity alerts

{{count, number}} dependency vulnerability

{{count, number}} dependency vulnerabilities

{{count, number}} development dependencies

{{count, number}} transitive dependencies

{{count, number}} version published last month

{{count, number}} versions published last month

{{count, number}} version published in last two months

{{count, number}} versions published in last two months

{{count, number}} version published last week

{{count, number}} versions published last week

{{count, number}} version published last year

{{count, number}} versions published last year

Socket undergoes annual SOC2 Type II audits. Socket customers can request a copy of the full SOC2 Type II report.

Allows organization owners and admins to access detailed records of actions taken by members of their organization, complete with timestamps.

Prevent compromised packages from infiltrating your supply chain by monitoring for changes in real-time.

Join our Discord community to get help from Socket engineers and other Socket users.

Compare millions of open source packages on socket.dev

Detect malicious code and risky behavior (e.g. network) in your dependencies using "deep package inspection"

All data is encrypted in transit and at rest using industry standard encryption algorithms.

Get a dedicated Socket account manager and access to Socket’s Customer Success team.

Get dedicated support from Socket engineers via email and Slack.

"Shift left" with the Socket Chrome extension and give intervene early, before developers choose risky or low quality dependencies.

Catch developers using risky dependencies and give them a "speed bump" to encourage good behavior

Install the Socket GitHub app to receive real-time dependency scanning and reports with every pull request.

Integrate Socket into your GitHub SCM to prevent risky dependencies from being installed.

Socket scans for vulnerabilities in your dependencies, including CVEs, security advisories, and more.

Socket supports dependencies in many languages, with most popular ecosystems coming in 2024. We've got you covered no matter what languages you use.

Enforce license policies across your organization

Receive a Microsoft Teams message to the channel of your choice anytime Socket runs a new analysis, has a new finding, or a policy has changed.

Get help migrating from Socket's free plan to Socket's paid plans.

Run Socket on-premises or in your own cloud environment.

Query for any dependency (at any version) across your entire organization

Integrate Socket into your CI/CD pipeline to prevent risky dependencies from being deployed to production.

Analyze an entire project to find supply chain risks

Tag projects to organize and filter your projects

Restrict access based on the roles of individual users within an organization.

Receive a Slack message to the channel of your choice anytime Socket runs a new analysis, has a new finding, or a policy has changed.

Socket is SOC2 Type II compliant and undergoes annual audits.

The Socket CLI allows teams to prevent risky dependencies from being installed, and to get dependency insights from the command line.

Socket supports SAML SSO for single sign-on and identity management.

Integrate Socket into your VS Code IDE to prevent risky dependencies from being installed.

Get a POST request anytime Socket runs a new analysis, has a new finding, or a policy has changed.

Socket will analyzed your SBOMs up to a maximum number of dependencies.

API that allows you to analyze a project, lookup package scores and alerts, and more.

Create API tokens to authenticate with the Socket API and CLI.

The number of developers in your team. A developer is someone who made a commit to your organization's repositories scanned by Socket in the past month.

Use Socket to protect your private repositories.

Socket is always free for open source projects.

Socket retains all reporting data for 3 months, 1 year, or a custom term of your choice.

Access the threat feed that powers Socket.

Unlimited scale, self-hosting, and priority support for large teams.

For open-source projects, individuals, and small teams.

For growing teams with enhanced scale, security, and support.

There is a package with a similar name that is downloaded much more often.

There are packages with similar names that are downloaded much more often.

This may not be the package you want!

Instance

Alert Locations

Package

The {{ecosystem}} package {{- packageName}} receives a total of <strong>{{numWeeklyDownloadCount, number}}</strong> weekly downloads. As such, {{- packageName}} popularity was classified as <strong>{{popularity}}</strong>.

Is {{- packageName}} popular?

Is {{- packageName}} safe to use?

Is {{- packageName}} well maintained?

What is {{- packageName}}?

{{packageDescription}}Version: {{versionString}} was published by {{publisherName}}. Start using Socket to analyze {{- packageName}} and its {{dependencyCount, number}} dependencies to secure your app from supply chain attacks.

Sorry, it seems this package was removed from the registry

Package was removed

This package version has been unpublished, mostly likely due to security reasons

Package version was removed

Provide a detailed description of the malware...

Socket fights vulnerabilities and provides visibility, defense-in-depth, and proactive supply chain protection for JavaScript, Python, and Go dependencies.

Socket - Secure your dependencies. Ship with confidence.

Compare versions

{{- packageName}} - npm Package Compare versions

  "description": "Implementation of a VSM-dictionary that interfaces with the Uniprot REST API",

    "test": "mocha \"src/**/*.test.js\" --check-leaks",

    "build": "webpack --config webpack.config.js"

    "url": "git+https://github.com/vsmjs/vsm-dictionary-uniprot"

[![Travis build status](https://travis-ci.org/vsmjs/vsm-dictionary-uniprot.svg?branch=master)](https://travis-ci.org/vsmjs/vsm-dictionary-uniprot)

[![npm version](https://img.shields.io/npm/v/vsm-dictionary-uniprot)](https://www.npmjs.com/package/vsm-dictionary-uniprot)

[![Downloads](https://img.shields.io/npm/dm/vsm-dictionary-uniprot)](https://www.npmjs.com/package/vsm-dictionary-uniprot)

`vsm-dictionary-uniprot` is an implementation 

of the 'VsmDictionary' parent-class/interface (from the package

[`vsm-dictionary`](https://github.com/vsmjs/vsm-dictionary)), that

communicates with [UniProt's](https://www.uniprot.org) 

REST API and translates the provided protein data into a VSM-specific format.

Create a `test.js` file and include this code:

const DictionaryUniprot = require('./DictionaryUniprot');

const dict = new DictionaryUniprot({log: true});

dict.getEntryMatchesForString('tp53', { page: 1, perPage: 10 }, 

      console.log(JSON.stringify(err, null, 4));

      console.log(JSON.stringify(res, null, 4));

Run `npm test`, which runs the source code tests with Mocha.  

If you want to quickly live test the Uniprot API, go to the 

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 &lt;script&gt;-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. 

`<script src="../dist/vsm-dictionary-uniprot.min.js"></script>` in the

Like all VsmDictionary subclass implementations, this package follows

[specification](https://github.com/vsmjs/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

- https://www.uniprot.org/help/query-fields

- https://www.uniprot.org/help/uniprotkb_column_names

- https://www.uniprot.org/help/api_queries

- https://www.uniprot.org/help/text-search

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 

specifications below), if one of them returns an error (either a string or an 

error JSON object response), then the result will be an error object (no matter 

if all the rest of the calls returned proper results). 

If the error response in not a JSON string that we can parse, we formulate the 

error as a JSON object ourselves in the following format:

where the *response* from the server is JSON stringified.

This specification relates to the function:  

If the `options.filter.id` is not properly defined 

or the `https://www.uniprot.org` dictID is included in the 

list of ids used for filtering, `getDictInfos` returns a static object 

- `id`: 'https://www.uniprot.org' (will be used as a `dictID`)

after the results are returned from Uniprot's REST API. 

This project is licensed under the AGPL license - see [LICENSE.md](LICENSE.md).

		{
		"name": "vsm-dictionary-uniprot",
		"version": "1.0.11",
		"version": "1.0.12",
		"description": "Implementation of a VSM-dictionary that interfaces with the Uniprot REST API",
		@@ -25,2 +25,3 @@ "main": "src/DictionaryUniprot.js",
		"author": "John Zobolas",
		"license": "AGPL-3.0",
		"devDependencies": {
		@@ -27,0 +28,0 @@ "@babel/core": "^7.0.0-rc.1",

New alerts

Fixed alerts

Improved metrics

Worsened metrics

		@@ -190,1 +190,5 @@ # vsm-dictionary-uniprot
		after the results are returned from Uniprot's REST API.

		## License

		This project is licensed under the AGPL license - see [LICENSE.md](LICENSE.md).