These are chat archives for biojs/biojs

30th
Jun 2018
Sarthak Sehgal
@sarthak-sehgal
Jun 30 2018 18:21
Screen Shot 2018-06-30 at 11.50.52 PM.png
Screen Shot 2018-06-30 at 11.49.43 PM.png
Yo Yehudi
@yochannah
Jun 30 2018 18:22
fancy - what's the implementation method?
Sarthak Sehgal
@sarthak-sehgal
Jun 30 2018 18:28

Visualizations are almost complete!
A static index.html is now being served by backend.
https://github.com/biojs/biojs-backend/tree/visualization-frontend

Few important things:

  1. To implement this method, Megh and I both had to go through the code and workflow of the registry-workmen in detail. The workmen is indeed very well designed and we would have definitely insisted to use it if it didn't require a node server to be run!
    The node server though is not the reason of the visualizations being slow. The reason is indeed "Wzrd"! As I tested a lot of visualizations to make sure that the code works, I observed that most of the times a "Gateway Time-Out" error comes in Wzrd and we can't actually do anything about it! :(
    In a nutshell, though the code of the current implementation compiles quite quick, the visualization takes time to render and even might not render a few times due to Wzrd. I searched for alternatives, couldn't find one.
  2. There's a discrepancy in the component version, more about which we will discuss in the weekly call. Will attach the details in the meeting notes.
Yo Yehudi
@yochannah
Jun 30 2018 18:30
sounds like you've been doing some great work! is wzrd this? https://github.com/browserify/wzrd.in
(I'm just curious)
Sarthak Sehgal
@sarthak-sehgal
Jun 30 2018 18:32
Yes, @yochannah
Wzrd is used for components which use Browserify as the module bundler. It basically installs all the npm dependencies, bundles them and returns the final build file, all of the tasks performed by Browserify in a local environment.
Yo Yehudi
@yochannah
Jun 30 2018 18:33
totally makes sense that it runs slowly based on my experience with browserify!
Sarthak Sehgal
@sarthak-sehgal
Jun 30 2018 18:36
This reminds me:
You can observe the difference yourself!
"msa" doesn't use browserify and thus the bundled JS is on its github repo/hosted online (I'm not sure).
Whereas "cytoscape" uses browserify.
Thus when you open http://biojs.io/d/msa the visualization loads pretty fast!
Whereas if you open http://biojs.io/d/cytoscape the visualization will take a bit time to load (and sometimes even might not if a time-out occurs!)
Yo Yehudi
@yochannah
Jun 30 2018 18:36
nice summary!!
Sarthak Sehgal
@sarthak-sehgal
Jun 30 2018 18:50
Thank you @yochannah! :smiley:
Megh Thakkar
@Megh-Thakkar
Jun 30 2018 19:06
As @sarthak-sehgal pointed out there is a discrepancy I think I would just describe it in short: It is again with wzrd!!!
In the current biojs.io website, the database is not completely updated so cytoscape visualizations are loaded using the version 3.2.6(url)
But the latest version is 3.2.14
Now, wzrd is able to successfully create the bundle for 3.2.6 but not for 3.2.14. Since the version is not updated for biojs.io, the visualizations are loaded successfully from their side, but we are getting issues on our end.
I thought of opening an issue for the same on the cytoscape repository, but it has already been opened cytoscape/cytoscape.js#1778