arbor_nova

Arbor easy-mode apps for Girder 3.

Installation

This is descriptive rather than prescriptive, but it is what has been tested.

• Do this work with Python3
• Have two virtualenvs, one for girder named girder and one for girder-worker named gw.
• Install mongo and rabbitmq
• In virtualenv girder run the following commands, it doesn't matter where you run them from:

$ pip install --pre girder[plugins]
$ girder build

• These commands need to be run in the girder virtualenv from specific locations.

$ cd arbor_nova/girder_worker_tasks    
$ pip install -e .                     # install gw tasks for producer
$ cd ../../arbor_nova/girder_plugin
$ pip install -e .                     # install girder plugin
$ girder serve                         # start serving girder

• In virtualenv gw run the following command, it doesn't matter where you run it from:

$ pip install --pre girder-worker

• These commands need to be run in the gw virtualenv from a specific location

$ cd arbor_nova/girder_worker_tasks    
$ pip install -e .                     # install gw tasks for consumer
$ girder-worker                        # start girder-worker

Features

Installs a REST endpoint for launching a GW job. The endpoint will take in a csv file id, and an output item id, then call the GW job. The GW job will download the csv file, append a new column to each line, then upload the resulting file to the output item.

TODO

• Should we have to enable the jobs or other dependent plugins? how to get those enabled automatically?
• Need to cleanup the output file on the GW task side. Is there a way to do that automatically?