Mechanical Rob is our name for what could be considered our integration tests.
The idea is that we observe how Prof. Robert Williams (Rob) (and other scientists) use(s) GeneNetwork and create a "mechanical" facsimile of that. The purpose is to ensure that the system works correctly with each and every commit in any of our various repositories.
If any commit causes any part of the Mechanical Rob system to raise an error, then we know, immediately, that something is broken, and the culprit can get onto fixing that with haste.
Nice! I like your enthusiasm.
You can find the
within the genenetwork2 repository.
You can also see how it is triggered in the gn-machines repository in
Search for "genenetwork2-mechanical-rob" within that module and you should find how the system is triggered.
All the above is nice and all, but sometimes you just want to run the checks locally.
In that case, you can run Mechanical Rob locally by following the steps below: (note that these steps are mostly the same ones to run GN2 locally).
1. Get a guix shell for GN2 development:
$ cd genenetwork2/
$ guix shell --container --network \
--expose=</path/to/directory/with/genotypes> \
--expose=</path/to/local/genenetwork3> \
--expose=</path/to/setting/file> \
--expose=</path/to/secrets/file> \
--file=guix.scm bash
The last `bash` is to ensure we install the Bourne-Again Shell whic we use to launch the application. The `</path/to/local/genenetwork3>` can be omitted if you do not need the latest code in GN3 to be included in your running GN2.
2. Set up the appropriate environment variables:
[env]$ export HOME=</path/to/home/directory>
[env]$ export GN2_SETTINGS=</path/to/settings/file>
[env]$ export SERVER_PORT=5003
[env]$ export GN2_PROFILE="${GUIX_ENVIRONMENT}"
[env]$ export GN3_PYTHONPATH=</path/to/local/genenetwor3> # Only needed if you need to test GN3 updates
3. Run the mechanical-rob tests
[env]$ bash bin/genenetwork2 gn2/default_settings.py -c \
test/requests/test-website.py \
--all "http://localhost:${SERVER_PORT}"
Of course, here we are assuming that `SERVER_PORT` has the value of the port on which GN2 is running.
Look into using geckodriver to help with the mechanical-rob tests. `geckodriver` comes with the
which is present as a package in GNU Guix.