Remove Javascript 3rd-party dependencies from the Knetminer codebase

[marco-brandizi]

I've just copied my local clone of the Knetminer codebase and I realised there are directories with huge size, which seem to contain 3rd-party Javascript dependencies, eg, node_modules. This slows down operations like copies and Docker builds.

We should improve this and put those files out of our code base. One way to do it might be to see if there are already published Maven modules that could be linked from our POMs. Or, if no such thing exists, we could create separated Maven modules and link them.

[AjitPS]

for both Genomaps/ and KnetMaps/ in common/client-base/, fyi

[marco-brandizi]

After some investigation, this should be a reasonable plan.

Javascript refactoring

Work on the original Javascript repositories, KnetMaps and GenoMaps. For each of them:

1. Move everything about Bower into the NPM package list and build. This is hardly automatable, but there
   is a guideline.
2. Upgrade Gulp and NPM versions.
3. Upgrade dependencies in Gulp and NPM. Use a similar approach of changing version one dependency at
   a time and see if it works.
4. Ensure the Gulp/NPM files can build distribution files (in dist/) and add a build step to publish these files
   into the NPM registry. If the latter is not viable, just publish back on the package github repository.
5. Once everything works, automate the build via GitHub Actions. Consider the approach we already have in
   place for Java (here). This might be done after the KnetMiner refactorisation (see below)

KnetMiner refactorisation

Once the Js repo is re-arranged and can publish distro files, Go to KnetMiner and make client-base dependant on the distro only. At the moment this module has duplicates of both repositories and rebuilds everything (with bower, NPM, etc) during the Maven build. Clearly, this is redundant and needs to be factories. So,

1. we need to remove the Maven build steps that reproduce the Js process outlined in the previous section,
2. we need to remove non-distro files and
3. we need a different Maven build procedure that just downloads the distribution files into target/, thus preparing the .war building stage.

[marco-brandizi]

I've checked out the work done so far for knemap.js. Sounds good, I'm leaving just a few notes, in case it's useful to keep track of them:

• css/knet-style.css: any reason why background-color: white was changed to #FFF?

• When I rebuild the NPM packaging, the commandnpm install --package-lock yields many deprecated
  warnings, including a mention that bower is deprecated. Is this because of transitive dependencies?
  we should address these warnings at some point, for the moment, let's complete the re-organisation, including knetminer/client-base

• As per documentation, It should be possible to use the repository as-is (without even
  pushing dist/). When refactoring client-base, let's first try this option (ie, link knetmaps.js and
  genomaps.js via github URL), we'll use NPM registry if this doesn't work.

• Both README files and documentation need to reflect these recent changes at some point (TODO
  warning added).

[Arnedeklerk]

@manlikleo please close if completed.

[marco-brandizi]

This is practically completed, except for a few minor details:

• On the respective Js repos, we need to update the documentation, including the demos
• We also need to move these upgrades to the master branches
• On knetmaps.js, we still have static files from dependencies, which we need to put back into the Js build cycle, see Remove manual downloads from 3rd-party libraries and download them properly during the build knetmaps.js#36

[Arnedeklerk]

@marco-brandizi @lawal-olaotan please close if done