theobarberbany / js_tag_validator

A react web app to validate manifests for Illumina single and dual index runs.

Javascript Tag Validator

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Clone the repo then run npm install or yarn install

(Currently tested and working with yarn 1.3.2, npm 5.6.0 and node version(s) 9.3.0, 8.9.4)

UI is designed with sketch, and can be found in ui.sketch

This project was bootstrapped with Create React App.

React-scripts do a lot of background work. You can find the most recent version of the guide here.

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Commands:

• start dev server: yarn start

• run tests: yarn test

• build for production: yarn build

• eject (don't do..): yarn eject

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Testing

• tests are run by Jest running "yarn test" will scan the entire src folder for "x.test.js" files, the tests folder for test files to run. Tests are run using nodejs with jsdom.

• Tests are formatted using the expect statement. Snapshot testing is also supported.

• Enzyme is used for test rendering.

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Directory / File Structure

React Components

• All components go into /src/components/{ComponentName}

Redux

• Currently using redux ducks but transitioning to re-ducks following the suggestions from here

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Sentry (Error Handling)

Sentry is used for error tracking. All config is within src/index.js,

Each new release corresponds to a new release within Sentry. This makes it easy to see if users of an older version are reporting errors from known bugs. See releases for the documentation on using releases.

Errors within the application lifecycle methods are caught by error boundaries, a react 16 feature. A single error boundary is currently used, with Sentry integration. It is defined in src/components/SentryBoundary.js. There is room for additional, more specialised error boundaries that may be added later. (e.g A parser failure should look different to a validation or database function failing to run)

The boundaries are defined in /src/components/FileHandlerContainer.js where The <SentryBoundary> component wraps the respective container component. This way, if the component fails to mount, the entire application does not unmount. Coarser, or finer grained options are possible.

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Travis CI

Travis CI is used for continuous integration. Currently the configuration runs with node v8. Node v6 does not currently work due to the lack of Object.entries added in ES17.

Documentation for changing slack integration can be found here

Codecov is used to track coverage. Results are automatically uploaded after each Travis build. The codecov token is encrypted in the same way the slack one is, and is stored in the env: section. See here for an example node repository.

Greenkeeper is used to track and keep npm dependencies up to date. Docs

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Libraries used :

• React
• Redux
• Redux thunk
• React-redux
• Isomorphic Fetch
• Carbon components design kit
• React DnD
• Redux Dev tools (chrome extension)
• React Inspector
• Raven Middleware for Redux
• Raven-js
• Redux-segment

js_tag_validator's Issues

Testing

Make use of reverse compliment function.

Add feature whereby the end user can select an option to query the reverse compliment of a tag against the cache, possibly conditionally.

Visual Feedback to user on Error

Add something like "Oops, something went wrong!" when an error is encountered

Consider SSR On load for initial view

Separate error boundary for redux failing to get cache.

An in-range update of eslint is breaking the build 🚨

Version 4.12.0 of eslint was just published.

Branch	Build failing 🚨
Dependency	eslint
Current Version	4.11.0
Type	devDependency

This version is covered by your current version range and after updating it in your project the build failed.

eslint is a devDependency of this project. It might not break your production code or affect downstream projects, but probably breaks your build or test tools, which may prevent deploying or publishing.

Status Details

• ❌ continuous-integration/travis-ci/push The Travis CI build could not complete due to an error Details

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Release Notes

v4.12.0

• 76dab18 Upgrade: doctrine@^2.0.2 (#9656) (Kevin Partington)
• 28c9c8e New: add a Linter#defineParser function (#9321) (Ives van Hoorne)
• 5619910 Update: Add autofix for sort-vars (#9496) (Trevin Hofmann)
• 71eedbf Update: add beforeStatementContinuationChars to semi (fixes #9521) (#9594) (Toru Nagashima)
• 4118f14 New: Adds implicit-arrow-linebreak rule (refs #9510) (#9629) (Sharmila Jesupaul)
• 208fb0f Fix: Use XML 1.1 on XML formatters (fixes #9607) (#9608) (Daniel Reigada)
• 6e04f14 Upgrade: globals to 11.0.1 (fixes #9614) (#9632) (Toru Nagashima)
• e13d439 Fix: space-in-parens crash (#9655) (Toru Nagashima)
• 92171cc Docs: Updating migration guide for single-line disable (#9385) (Justin Helmer)
• f39ffe7 Docs: remove extra punctuation from readme (#9640) (Teddy Katz)
• a015234 Fix: prefer-destructuring false positive on "super" (fixes #9625) (#9626) (Kei Ito)
• 0cf081e Update: add importNames option to no-restricted-imports (#9506) (Benjamin R Gibson)
• 332c214 Docs: Add @platinumazure to TSC (#9618) (Ilya Volodin)

Commits

The new version differs by 15 commits.

• f4a65c6 4.12.0
• 1cd1627 Build: changelog update for 4.12.0
• 76dab18 Upgrade: doctrine@^2.0.2 (#9656)
• 28c9c8e New: add a Linter#defineParser function (#9321)
• 5619910 Update: Add autofix for sort-vars (#9496)
• 71eedbf Update: add beforeStatementContinuationChars to semi (fixes #9521) (#9594)
• 4118f14 New: Adds implicit-arrow-linebreak rule (refs #9510) (#9629)
• 208fb0f Fix: Use XML 1.1 on XML formatters (fixes #9607) (#9608)
• 6e04f14 Upgrade: globals to 11.0.1 (fixes #9614) (#9632)
• e13d439 Fix: space-in-parens crash (#9655)
• 92171cc Docs: Updating migration guide for single-line disable (#9385)
• f39ffe7 Docs: remove extra punctuation from readme (#9640)
• a015234 Fix: prefer-destructuring false positive on "super" (fixes #9625) (#9626)
• 0cf081e Update: add importNames option to no-restricted-imports (#9506)
• 332c214 Docs: Add @platinumazure to TSC (#9618)

See the full diff

FAQ and help

There is a collection of frequently asked questions. If those don’t help, you can always ask the humans behind Greenkeeper.

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Your Greenkeeper Bot 🌴

dependencies in package.json are mixed

Some dev dependencies are in dependencies section. Better if all dev-only deps go into dev-dependencies section.

Improve manifest detection (type, indexing etc)

Add functionality to determine single / dual index

[React] Error boundaries

Version 10 of node.js has been released

Version 10 of Node.js (code name Dubnium) has been released! 🎊

To see what happens to your code in Node.js 10, Greenkeeper has created a branch with the following changes:

• Added the new Node.js version to your .travis.yml

If you’re interested in upgrading this repo to Node.js 10, you can open a PR with these changes. Please note that this issue is just intended as a friendly reminder and the PR as a possible starting point for getting your code running on Node.js 10.

More information on this issue

Greenkeeper has checked the engines key in any package.json file, the .nvmrc file, and the .travis.yml file, if present.

• engines was only updated if it defined a single version, not a range.
• .nvmrc was updated to Node.js 10
• .travis.yml was only changed if there was a root-level node_js that didn’t already include Node.js 10, such as node or lts/*. In this case, the new version was appended to the list. We didn’t touch job or matrix configurations because these tend to be quite specific and complex, and it’s difficult to infer what the intentions were.

For many simpler .travis.yml configurations, this PR should suffice as-is, but depending on what you’re doing it may require additional work or may not be applicable at all. We’re also aware that you may have good reasons to not update to Node.js 10, which is why this was sent as an issue and not a pull request. Feel free to delete it without comment, I’m a humble robot and won’t feel rejected 🤖

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FAQ and help

There is a collection of frequently asked questions. If those don’t help, you can always ask the humans behind Greenkeeper.

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Your Greenkeeper Bot 🌴

Update DEPLOY.md and README.md to reflect latest changes

Push dropped files to s3 / cog bucket

Add green / red circles for visual user feedback

An in-range update of react is breaking the build 🚨

There have been updates to the react monorepo:

• • The dependency react was updated from 16.5.2 to 16.6.0.

• The dependency react-dom was updated from 16.5.2 to 16.6.0.
• The devDependency react-test-renderer was updated from 16.5.2 to 16.6.0.

🚨 View failing branch.

This version is covered by your current version range and after updating it in your project the build failed.

This monorepo update includes releases of one or more dependencies which all belong to the react group definition.

react is a direct dependency of this project, and it is very likely causing it to break. If other packages depend on yours, this update is probably also breaking those in turn.

Status Details

• ❌ continuous-integration/travis-ci/push: The Travis CI build failed (Details).

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FAQ and help

There is a collection of frequently asked questions. If those don’t help, you can always ask the humans behind Greenkeeper.

---

Your Greenkeeper Bot 🌴

Don't hide warnings on completion. Strikethrough instead.

Leaves end user with some notion of work completed.

Add FAQ Section

Improve database evaluation

• Reverse Complement each oligo, and or its composite parts when certain conditions are met. (e.g no matches found)
• If no matches found, swap oligo cols and run again.

For dual index run return the row of the two concatenated tags in the manifest (Ease of use)