Integrate into Refinery

[mccalluc]

@scottx611x : Here's one attempt at an IGV wrapper. What's the simplest contract we can require for integrating this or any future visualization into refinery? What still needs to happen here?

• How do you want to manage the dependencies? Should I just download then all and put them in a vendor directory? Or should I try a package.json or something like that and leave it to Refinery to pull everything during build?
• (Assuming we do want to avoid dependencies on CDNs?)
• Extra input from the user: Getting the genome from the user, if it's missing, is pretty adhoc, but it gets the job done? I think that trying to get more user input from inside the refinery space doesn't scale well.
• Naming: On the refinery side it needs to know which repo to check out, and what the key js file is, and what the human-readable name for the menu is: we could agree that the same name might be shared across more roles, or the convention could be index.js?
• Since there's no compilation here, everything is src... but probably not a pattern to rely on.
• I need to write a real refinery.js: There are probably tools that build js from an API spec... but if we only need one method, writing it by hand seems fine for now?

[mccalluc]

In my view, part of the contract may be for vis packages to identify themselves as such, rather than maintaining a separate configuration list with all the details. This script does that... but it is unacceptably slow: Perhaps figure out where the package.jsons are stored and parse them directly?

import os
import json

look_for = 'refinery-vis'
matches = []

npm_list_json = os.popen('npm list --json true --depth 0').read()
dependencies = json.loads(npm_list_json)['dependencies']
for name, info in dependencies.iteritems():
  command = 'npm view %s@%s keywords --json' % (name, info['version']) # Security of string interpolation?
  npm_view_json = os.popen(command).read()
  if npm_view_json:
    keywords = json.loads(npm_view_json)
    if look_for in keywords:
      matches.append(name)

print matches

Alternatively parse the each package.json yourself: I think it would suffice to iterate over

node_modules/*/package.json # for locals
`npm root -g`/*/package.json # for globals