Description:

chrispile 1.2.4

ChRISPile



Syntactical sugar for running ChRIS plugins locally.
Abstract
chrispile generates wrapper scripts around docker run (or podman run).
These scripts automatically locate mount points for the position arguments
/incoming and /outgoing for
ChRIS plugin apps.
Additionally, the wrapper sets sane defaults for running the container.
Background
Traditionally, docker run is a very verbose command with user-unfriendly defaults.
Of course there are good reasons for this design (security isolation)
but it is tedious and confusing to work with.

the default user is root so you will need sudo to remove outputdir.
container timezone is UTC
stopped containers occupy disk space
GPU is invisible
user needs to specify image name and command
folders containing data need to be typed out

chrispile aims to hide this complexity from users.
WARNING: it is not a good idea to use chrispile unless you understand why it is helpful. You gotta learn the basics: what is docker?
Example
mkdir data output
cp scan.nii.gz data

chrispile run -- fnndsc/pl-fetal-brain-mask:1.0.0 --inputPathFilter scan.nii.gz data output

The command above is translated to:
docker run
# clean up the stopped container after it exists
--rm
# run as yourself so that the output is readable+writable by you
--user $(id -u):$(id -g)
# if plugin meta specifies min_gpu_limit, GPU is enabled
# GPU support is detected as --runtime=nvidia (legacy) or --gpus all (native)
--gpus all
# set the timezone in case your plugin logs timestamps
-v /etc/localtime:/etc/localtime:ro
# resolve input and output paths
# SELinux label flag ':z' is appended to volume options if necessary
-v /home/jenni/data:/incoming:ro -v /home/jenni/output:rw
# container image name and command
fnndsc/pl-fetal-brain-mask:1.0.0 fetal_brain_mask
# user specified options
--inputPathFilter scan.nii.gz
# volume mountpoints
/incoming /outgoing

Installation
pip install chrispile

Usage
$ chrispile --help
usage: chrispile [-h] [-V] {run,api,install,list,uninstall} ...

Generate wrapper scripts around docker or podman run to easily run ChRIS plugins

optional arguments:
-h, --help show this help message and exit

info:
-V, --version show program's version number and exit

subcommands:
{run,api,install,list,uninstall}
run run a ChRIS plugin
api query the system for information
install install a ChRIS plugin as an executable
list list installed ChRIS plugins
uninstall uninstall a ChRIS plugin

Run Plugin
$ chrispile run --help
usage: chrispile run [--dry-run] [--reload-from] -- dock_image [args ...] inputdir/ outputdir/

positional arguments:
dock_image container image of the ChRIS plugin
args arguments to pass to the ChRIS plugin

optional arguments:
-h, --help show this help message and exit
-d, --dry-run print command to run withour running it
-e src, --reload-from src
mount given host directory as source folder for rapid development

Run Example
docker pull fnndsc/pl-simpledsapp:2.0.0

# setup test data
mkdir input output
touch input/{a,b,c}

Dry Run
$ chrispile run --dry-run -- fnndsc/pl-simpledsapp:2.0.0 --dummyFloat 3.5 input output

docker run --rm --user 1000:1003 \
-v /etc/localtime:/etc/localtime:ro \
-v /home/chris/input:/incoming:ro \
-v /home/chris/output:/outgoing:rw \
fnndsc/pl-simpledsapp:2.0.0 simpledsapp \
--dummyFloat 3.5 \
/incoming /outgoing

Real Run
$ chrispile run -- fnndsc/pl-simpledsapp:2.0.0 --dummyFloat 3.5 input output

_ _ _
(_) | | | |
___ _ _ __ ___ _ __ | | ___ __| |___ __ _ _ __ _ __
/ __| | '_ ` _ \| '_ \| |/ _ \/ _` / __|/ _` | '_ \| '_ \
\__ \ | | | | | | |_) | | __/ (_| \__ \ (_| | |_) | |_) |
|___/_|_| |_| |_| .__/|_|\___|\__,_|___/\__,_| .__/| .__/
| | | | | |
|_| |_| |_|

Version: 2.0.0
Sleeping for 0
Creating new file... /outgoing/b
Creating new file... /outgoing/a
Creating new file... /outgoing/c

Check Outputs
$ ls -lh output

total 0
-rw-r--r-- 1 chris grantlab 0 Feb 13 22:21 a
-rw-r--r-- 1 chris grantlab 0 Feb 13 22:21 b
-rw-r--r-- 1 chris grantlab 0 Feb 13 22:21 c

$ rm -rv output

removed 'output/b'
removed 'output/a'
removed 'output/c'
removed directory 'output'

Run With Live Code
Mount the source code directory into the installed library's location
within the container for a convenient developer experience.
The container will run changes you've made to the code without having
to rebuild the docker image.
chrispile run --reload-from ~/Github/pl-simpledsapp/simpledsapp \
-- fnndsc/pl-simpledsapp:2.0.0 --dummyFloat 3.2 input output

Install Plugin
docker pull fnndsc/pl-brainmgz:2.0.3
chrispile install fnndsc/pl-brainmgz:2.0.3

docker pull fnndsc/pl-lungct:latest
chrispile install fnndsc/pl-lungct:latest

Now you can simply run
mkidr out
lungct out

Uninstall Plugin
$ chrispile list
lungct
simpledsapp
med2img.py

$ chrispile uninstall lungct

Planned Features

Github Actions build matrix to test docker and podman separately
store repeated $(chrispile api ...) calls as variables in bash script
chrispile create as an alias for cookiecutter-chrisapp
chrispile run --clobber deletes the /outgoing directory before start
chrispile install from https://chrisstore.co and pulls for you
chrispile list also shows container image tags
chrispile uninstall --rm also runs docker rmi

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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