Make generating c302 from PyOpenWorm work in the OpenWorm Docker image

[slarson]

We currently have a start on a docker image that contains PyOpenWorm.

Inside that image is the dev version of the master_openworm.py script

The first step of this script is to generate c302 from the latest contents of PyOpenWorm.

We have previously made a few steps towards accomplishing this:

• Use OpenWormReader to generate connectome CElegansNeuroML#49
• Adapt current data loading process in c302.py to pull data from PyOpenWorm CElegansNeuroML#27

We need to consolidate progress on these from a code perspective, and move on to making this runnable by modifying the dev version of the master_openworm.py script and committing a new version of the docker image that has this working correctly.

[pgleeson]

As mentioned in the issues above, #177 is the key to updating c302 to use PyOpenWorm...

[perfortnight]

November 29, 2015 9:43 AM

Conversation specifying more details about this ticket.

[slarson]

OK now that #177 is done, let's see if we can make more progress. @perfortnight ; any updates?

[perfortnight]

No. I've been away.
But on that note, the docker image I have (openworm_test) does not appear to have the file structure that the https://github.com/openworm/OpenWorm/blob/development/master_openworm.py file expects. For example, there is no /home/openworm directory.

Is this the right docker image to be working with? Are there necessary installations to make before it is ready to work with? If so, are they documented somewhere?

[slarson]

@perfortnight ok try again; you are right; the image didn't seem to have that stuff. I have pushed a new version; this time it should work