girder-slicer-cli-web 1.1.2.dev5

A girder plugin for exposing slicer CLIs over the web

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 serve

To use Girder Worker:

pip install girder-slicer-cli-web[worker]
GW_DIRECT_PATHS=true girder_worker -l info -Ofair --prefetch-multiplier=1

The 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.

• Some input types (image, file, item, directory) can have defaultNameMatch and defaultPathMatch properties. These are regular expressions designed to give a UI a value to match to prepopulate default values from files or paths that match the regex. defaultNameMatch is intended to match the final path element, whereas defaultPathMatch is used on the entire path as a combined string.

• There are some special string parameters that, if unspecified or blank, are autopopulated. String parameters with the names of girderApiUrl and girderToken are populated with the appropriate url and token so that a running job could use girder_client to communicate with Girder.

Small Example CLI Docker

The small example CLI docker image can be built locally via docker build --force-rm -t girder/slicer_cli_web:small ., or pulled from Docker Hub.