A girder plugin for exposing slicer CLIs over the web
Project description
A Girder plugin for exposing slicer execution model CLIs over the web using docker and girder_worker.
Installation
Slicer CLI Web is both a Girder plugin and a Girder Worker plugin. It allows dockerized tasks to be run from the Girder user interface.
Linux
In linux with Python 2.7, Python 3.5, 3.6, or 3.7:
Prerequisites:
An appropriate version of Python must be installed.
MongoDB must be installed and running.
RabbitMQ or another broker is needed to use Girder Worker.
Docker must be installed and the current user must be part of the docker group.
To use Girder:
pip install girder-slicer-cli-web[girder]
girder build
girder serveTo use Girder Worker:
pip install girder-slicer-cli-web[worker]
GW_DIRECT_PATHS=true girder_worker -l info -Ofair --prefetch-multiplier=1The first time you start Girder, you’ll need to configure it with at least one user and one assetstore (see the Girder documentation). Additionally, it is recommended that you install some dockerized tasks, such as the HistomicsTK algorithms. This can be done going to the Admin Console, Plugins, Slicer CLI Web settings. Set a default task upload folder, then import the dsarchive/histomicstk:latest docker image.
Girder Plugin
Importing Docker Images
When installed in Girder, an admin user can go to the Admin Console -> Plugins -> Slicer CLI Web to add Docker images. Select a Docker image and an existing folder and then select Import Image. Slicer CLI Web will pull the Docker image if it is not available on the Girder machine.
For each docker image that is imported, a folder is created with the image tag. Within this folder, a subfolder is created with the image version. The subfolder will have one item per CLI that the Docker image reports. These items can be moved after they have been imported, just like standard Girder items.
Running CLIs
When you visit the item page of an imported CLI, an extra Configure Task section is shown. You can set all of the inputs for the CLI and indicate where output files should be stored. Selecting Run Task will have Girder Worker execute the CLI. See the Jobs panel for progress and error messages.
Docker CLIs
Slicer CLI Web executes programs from docker images. Any docker image can be used that complies with some basic responses from its ENTRYPOINT.
Specifically, when a docker image is invoked like:
docker run <docker image tag> --list_cli
it needs to respond with with a JSON dictionary of CLIs, where the keys of this dictionary are the names of the CLIs. See cli_list.json for an example.
Each available CLI needs to report what it takes as inputs and outputs. When the docker image is invoked like:
docker run <docker image tag> <cli name> --xml
it needs to return an XML specification to stdout. See Example1.xml for an example.
The XML must conform to the Slicer Execution Schema, with a few minor additions:
Some types (image, file, transform, geometry, table) can have a reference property.
The region type can have a coordinateSystem property.
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