Protein Kinase Ontology (ProKinO)'s browser

This repo contains the dev version (untested and not stable) of the ProKinO browser's front-end source code (view online). The University of Georgia hosts the main version at https://prokino.uga.edu.

Ontology

The Protein Kinase Ontology (ProKinO), is a protein kinase-specific ontology, which provides a controlled vocabulary of terms, their hierarchy, and relationships unifying sequence, structure, function, mutation and pathway information on kinases. The conceptual representation of such diverse information in one place enables not only rapid discovery of significant information related to a specific protein kinase, but also enables large scale integrative analysis of the protein kinase family.

Available to download from: https://prokino.uga.edu/downloads

Running on Local Machine

1. Run node -v to check the version of node. If the version is not 18.12.1, you can install it using the following commands:

   Using nvm you can run nvm install 18.12.1 to install the preferred version. To select the version, run nvm use 18.12.1.

2. Global packages:

   • sudo npm install -g gatsby-cli@5.2.0

3. In the project directory and run: npm install For the first time, you may get errors related to peer dependencies. To fix this, run the following command, then run npm install again:

   1. npm config set legacy-peer-deps true
   2. npm install react-html-parser @material-ui/core@4.12.4 --legacy-peer-deps
   3. npm audit fix (It is likely that you will get errors related to npm permissions. To fix this, run the suggested command that is shown on your terminal. Alternatively, you can run sudo chown -R $USER ~/.npm and try again.)

4. npm run develop

NOTE: If there was an error, you can hard reset by deleting the node_modules directory and running the above commands again. - rm -rf node_modules.

Preparing a version to upload on prokino.uga.edu

Run local-pulish.sh to produce new-public.zip: - ./local-publish.sh

You can extract the zip file on the server's website directory.

Publishing on Netlify

• Prerequisites:

  • On netlify.com, create a new website.
  • When asked for GitHub address, set it to the https://github.com/prokino/nb-gatsby
  • Set Build command to: gatsby build
  • Set Publish directory to: public/
  • Set the following Environment variables:
    • HOST_NAME=netlify
    • NODE_ENV=production
    • NODE_OPTIONS=--max_old_space_size= 4096
  • Follow instructions to enable netlify cli from the official documentation

• Steps

  • ./local-pulish.sh,
  • ./netlify-publish.sh

Development

Maintaining the code

The code is written in React.js and Gatsby.js. It uses npm as a package manager. The version numbers of the packages are specified in the package.json file. Each package has its own version number as x.y.z where x is the major version, y is the minor version, and z is the patch version.

To update npm packages, it is suggested to follow the steps below:

1. Install the npm-check-update package: npm install -g npm-check-updates
2. Run ncu -u -t patch to update the packages to the latest patch version.
3. If still needed, run ncu -u -t minor to update the packages to the latest minor version.
4. If still needed, run ncu -u -t major to update the packages to the latest major version.
5. If still needed, run ncu -u to update the packages to the latest version, then run npm install.

NOTES:

1. Updating packages to the latest version may cause errors.
2. After each of the steps above, run npm install to install the updated packages.
3. If there is an error, you can hard reset by running:
   • rm -rf node_modules.
   • npm install react-html-parser @material-ui/core@4.12.4 --legacy-peer-deps

Licence

This work is licensed under a Creative Commons Attribution 4.0 International License.