These are chat archives for biojs/biojs

20th
Jul 2018
Sarthak Sehgal
@sarthak-sehgal
Jul 20 2018 05:39
@mentors
Since the wzrd verison inconsistency is there with a lot of components. Can we do something like this:
Take the versions of all the components from the biojs.io website and store them in a db. The versions in the biojs.io website are outdated (eg: cytoscape's v3.2.6 was released 8 months back. The latest version is 3.2.15) but the visualizations seem to work well with it. Run a script in backend for each component and call Wzrd for a version greater than the one in database and less than or equal to the latest version, if a response other than 404 Not found, 502 Gateway timeout is received, update the version in the database and perform this for the next version else stop.
I think that this is the best we can do to ensure that maximum visualizations are up.
@Megh-Thakkar What do you think?
Ironically, biojs.io has outdated data but it seems to work well with the visualizations so why not take it as the base data (only the versions) for the new website?
Sarthak Sehgal
@sarthak-sehgal
Jul 20 2018 05:54
Also, since this will take a few minutes, we can run this cron job in every 15 days or so.
Megh Thakkar
@Megh-Thakkar
Jul 20 2018 08:34
@sarthak-sehgal only issue with that is we can back track to certain versions only. For example, in case of cytoscape, we can only go to 3.2.0 and not before that as we do not know where 3.1.x ended. Though it is worth a try. I'm working on ansible right now, will get back to this as soon as that is over.
Sarthak Sehgal
@sarthak-sehgal
Jul 20 2018 08:36
@Megh-Thakkar that's why we'll be using the base data as the current biojs.io data. For example, the version of Cytoscape in biojs.io is 3.2.6
Then, as our script runs, we check for versions like this:
Run wzrd for 3.2.7: runs, update db
Run wzrd for 3.2.8: runs, update db
...
Run wzrd for 3.2.12: runs, update db
Run wzrd for 3.2.13: doesn't work, stop process
rowlandm
@rowlandm
Jul 20 2018 12:00
I think @sarthak-sehgal that we need to know how many visualisations are working and how many aren't.
Where is the link in the demo website for the random visualisations?
I also think @sarthak-sehgal that we have to accept that not all visualisations will work
and we need to ensure that at least the rest of the website works
So that means:
at a minimum
  • Ansible has to work
  • Website has to have simple links working, eg tags are clickable, link to npm, link to github
  • Documentation page has to be cleaned up or removed
  • Contact us has to work
The visualisation is ending up being a very big black hole. We may have to wait, pause and then look at it later.
Yo Yehudi
@yochannah
Jul 20 2018 12:06
popping my head in briefly to approve of this direction :thumbsup:
rowlandm
@rowlandm
Jul 20 2018 12:06
Thanks
Sarthak Sehgal
@sarthak-sehgal
Jul 20 2018 12:19
@rowlandm, I'll work on the component page and the contact us page. Megh is currently working on Ansible. Have you checked the latest documentation page? I updated it last week and added the API responses, etc. so that the viewer gets better info about the whole workflow.
rowlandm
@rowlandm
Jul 20 2018 12:19
Hey @sarthak-sehgal - I think there is some confusion
Documentation probably means (to the user) how to setup a BioJS component, rather than the documentation about the website
Sarthak Sehgal
@sarthak-sehgal
Jul 20 2018 12:47
Rowland and I had a quick meet regarding the progress and how to go about the project. Here's what we discussed:
  1. Visualizations came out to be a black hole. We need to draw a line and sought it out in an elegant way as engineers. The idea is to create an excel sheet having list of components having visualizations, a column depicting whether it is working on biojs.io, and a column depicting whether it is working on new website and URLs to both the website.
    To go about this, Megh and I will be creating a page on the website. Something like URL/visualizations/<n> which gives a list of <n> components having visualizations.
  1. Link to the component in biojs.io has to be added in the components' page in the new website.
  1. Link to gitter and a text has to be added in the Contact Us page.
rowlandm
@rowlandm
Jul 20 2018 12:48
  • if you have time, think about clicking on tags to use as a search
After that has all been sorted, we could look at using workmen / biojs.io visualisations as a place holder while we try and sort out a longer term solution
rowlandm
@rowlandm
Jul 20 2018 12:55
Thansk @sarthak-sehgal
Sarthak Sehgal
@sarthak-sehgal
Jul 20 2018 13:07

@rowlandm, Megh has made the API for random components having visualizations: http://139.59.93.32/api/random_snippets/?q=5
For 5 components

Incorporating it in the website

Megh Thakkar
@Megh-Thakkar
Jul 20 2018 13:36
The 'q' parameter is the components you need generated.
Also, @/all anyone knows what's up with npm?
On Tuesday, the "biojs" search returned 11 components.
Wednesday it was around 45
12 hours ago it was around 64
And now it shows 75!
Two days ago, I was not able to find the original cytoscape package!
And it showed up today. They are going through something critical I guess.
Megh Thakkar
@Megh-Thakkar
Jul 20 2018 13:42
Jumping back to Ansible, I have implemented and tested the plays for Gunjcorn, Nginx and Supervisor. They work great! The play for setting up the database is the only one left and I'm working on it right now. It will be done soon.
Link to Github repository.
Yo Yehudi
@yochannah
Jul 20 2018 13:49
that sounds really weird, megh! (the npm thing)
Sarthak Sehgal
@sarthak-sehgal
Jul 20 2018 14:48
Max Franz
@maxkfranz
Jul 20 2018 19:41
The npm search on npmjs.org has never been particularly stable or effective to my knowledge. It ihas been especially unstable over the past few weeks.
Is there any update on the status of wzrd?
rowlandm
@rowlandm
Jul 20 2018 21:04
Nice work @sarthak-sehgal
Nice work @Megh-Thakkar
@sarthak-sehgal - can we have a on the page http://139.59.93.32/api/random_snippets/?q=5 to the new and the old website please?
Saves me having to copy and paste
have them open in new tabs too