These are chat archives for openworm/ChannelWorm

14th
Mar 2015
Vahid Ghayoomie
@VahidGh
Mar 14 2015 07:22
@wilzh40, cool! So by reading the spreadsheet via this script, now we can get needed info from the WormBase, by one of these mechanisms:
  1. WormBase REST APIs
  2. Some script which is able to send a request like http://www.wormbase.org/species/c_elegans/gene/WBGene00000529 and then interpret the response to extract needed content
Milad Jafary
@miladjafary
Mar 14 2015 08:40
@VahidGh what's different between 1 and 2? Both of them send a REST request to wormbase.
Vahid Ghayoomie
@VahidGh
Mar 14 2015 10:27
The first one uses some specific APIs, but when I was working with the APIs, I couldn't find all needed info in the response, so in this case we can use the second method
@wilzh40, that would be great if you could push your work to the repo, so we could also play with
Vahid Ghayoomie
@VahidGh
Mar 14 2015 10:42
@miladjafary, also would you please define your proposed structure based on the design, abstracts, etc to manage scripts in repo?
I mean the structure to better keep/upload files here based on your preferred design pattern
Vahid Ghayoomie
@VahidGh
Mar 14 2015 11:58
@travs, I have a question, which I think was also the question asked by Milad -- You've added PyOW, as a module to CW, once I've cloned the repo to my local host, how can I access the PyOW, from the CW scripts?
Travis Jacobs
@travs
Mar 14 2015 19:13
Hmm I'm not sure I understand the question completely
If you bring in PyOW as a submodule you can just access it directly, using ChannelWorm/data/PyOpenWorm as a regular directory
@VahidGh
So the same way you would use PyOW in its own repo
Which is just descried in the Readme.
Can you explain the question a little further if that doesn't answer it?
Travis Jacobs
@travs
Mar 14 2015 19:24
@miladjafary I agree about having only one abstract access layer.
Vahid Ghayoomie
@VahidGh
Mar 14 2015 19:45
I think the first thing is to use the git command in this way: git clone --recursive git://github.com/VahidGH/ChannelWorm.git
is this enough or we also need to checkout the ChannelWorm branch?
Vahid Ghayoomie
@VahidGh
Mar 14 2015 20:36
Also when I clone CW with PyOW as sub-module, it's ~100 MB, which I don't think we need that much of data from the PyOW project! Is there a way to include only needed parts in CW?
Vahid Ghayoomie
@VahidGh
Mar 14 2015 20:59
This message was deleted
Wilson Zhao
@wilzh40
Mar 14 2015 22:29
https://github.com/wilzh40/DataWorm
Had to do a bit of fiddling to find the expression endpoint haha, it's hard when there's no documentation