This is an example of using a Singularity container to contain all dependencies for the Experiment Factory software, meaning installation of python and the
expfactory package, and then giving the command to generate the experiment battery to the container as an executable. The goal of this example is to show how easily you can wrap an entire analysis, environment, or whatever other dependencies you might have, and then serve something easily to a user. If you haven't installed singularity, do that with these instructions. Then Download the repo if you haven't already:
git clone https://www.github.com/vsoch/singularity-web cd singularity-web
Let's now generate our expfactory.img from the build file (called Singularity) and run it!
cd nginx-expfactory sudo singularity create --size 4000 expfactory.img sudo singularity bootstrap expfactory.img Singularity
You will see the image bootstrapping, including downloading of Docker layers, installation of nginx. What happens when we run it like an executable?
optional arguments: -h, --help show this help message and exit --folder FOLDER full path to single experiment folder (for single experiment run with --run) or folder with many experiments (for battery run with --run) --subid SUBID subject id to embed in experiments data in the case of a battery run with --run --experiments EXPERIMENTS comma separated list of experiments for a local battery --port PORT port to preview experiment --battery BATTERY_FOLDER full path to local battery folder to use as template --time TIME maximum number of minutes for battery to endure, to select experiments --preview preview an experiment locally (development function) --run run a single experiment/survey or battery locally --survey SURVEY survey to run for a local assessment --game GAME game to run for a local assessment --validate validate an experiment folder --psiturk to be used with the --generate command, to generate a psiturk battery instead of local folder deployment --generate generate (and don't run) a battery with --experiments to a --folder --output OUTPUT output folder for --generate command, if a temporary directory is not desired. Must not exist. --test test an experiment folder with the experiment robot
We see the command line usage for the executable! If you look at the
%runscript, we've enforced that the user is using the container to run one or more experiments, represented by the
$@ which takes the input arguments we give the executable and gives them to our script.
%runscript cd /data exec /usr/local/bin/expfactory --run --experiments "$@"
In the case above, we ran this:
/usr/local/bin/expfactory --run --experiments
which was not correct usage, so it spat out the correct usage for us. What happens if we give an experiment name?
./expfactory stroop No battery folder specified. Will pull latest battery from expfactory-battery repo No experiments, games, or surveys folder specified. Will pull latest from expfactory-experiments repo Generating custom battery selecting from experiments for maximum of 99999 minutes, please wait... Found 57 valid experiments Found 9 valid games Preview experiment at localhost:9684
In this case we are really running the command:
/usr/local/bin/expfactory --run --experiments stroop
and if we open our browser to port 9684 (randomly selected) we see our stroop task! Awesome.
Notice how you can use the
%runscript section to give the user more or less control over your executable. For example, if my runscript looked like this:
%runscript cd /data exec /usr/local/bin/expfactory "$@"
The user could have full functionality to run a command other than
--run, or specify
--surveys instead of experiments. I would need to be clear about this in whatever documentation I provide.