plugin2cube 2.2.14

A ChRIS helper app that registers a plugin to a CUBE instance

Abstract

Small utility app that “registers” a ChRIS plugin to a CUBE instance from the CLI. As of January 2023, CUBE no longer needs a companion store for plugin registration. It is now possible to register a plugin directly to CUBE itself using updates to the CUBE API. This utility script leverages this API to allow for direct registration of plugins.

Overview

plugin2cube is a simple app that allows for the registration of a plugin image directly to a CUBE instance without the need of a ChRIS Store as intermediary. This allows for simpler, more portable management of plugins in a given CUBE.

The script does need to determine the plugin JSON representation. There are two broad mechanisms for resolving this. The first is to simply read this representation from a file. The second is to actually run the plugin image to determine the representation.

Running the image does require docker to be present on the host executing this script. Two assumptions are made in this case:

• The plugin has been created using the chris_plugin_template in which case the chris_plugin_info mechanism is used to determine the JSON representation. This is attempted, and if successful, the representation is used.

• Failing that, the plugin is assumed to be created using the cookiecutter mechanism (or similar) and that the plugin code supports the --json flag to describe its representation. In this case, the script, if not explicitly told what the actual plugin executable within the image (from –pluginexec) is, will assume that the executable can be found from the docker image name <prefix>/<prefix>/.../pl-<pluginexec>

Arguments

--dock_image <container_name>
The name of the plugin container image. This is typically something like

                        fnndsc/pl-someAnalysis
                               -- or --
                    localhost/fnndsc/pl-someAnalysis

and is a REQUIRED parameter.

[--nodockerpull]
If specified, the app will not try and pull the image, but will assume
the image exists in the local repository space. This is useful for
container images that are purely local and have not been pushed to any
container registry.

[--name <pluginNameInCUBE>]
The name of the plugin within CUBE. Typically something like
"pl-someAnalysis". If not supplied, name will be inferred from
the <container_name>, by stripping and leading prefices and trailing
versioning.

[--public_repobase <basename>]
The base URL of the plugin code, typically on github. If not specified,
is assumed to be

            https://github.com/FNNDSC

[--public_repo <repo_name>]
The URL of the plugin code, typically on github. This is accessed to
find a README.[rst|md] which is used by the ChRIS UI when providing
plugin details. If not supplied, the repo will be assumed to be

            <public_repobase>/<pluginNameInCUBE>

[--pluginexec <exec>]
The name of the actual plugin executable within the image if this
executable does not conform to standard conventions.

[--computenames <commalist,of,envs>] ("host")
A comma separted list of compute environments within a CUBE to which
the plugin can be registered.

[--CUBEurl <CUBEURL>] ("http://localhost:8000/api/v1/")
The URL of the CUBE to manage.

[--CUBEuser <user>] ("chris")
The name of the administration CUBE user.

[--CUBEpasswd <password>] ("chris1234")
The admin password.

[--jsonFile <jsonRepFile>]
If provided, read the representation from <jsonRepFile> and do not
attempt to run the plugin with docker.

[--inputdir <inputdir>]
An optional input directory specifier.

[--outputdir <outputdir>]
An optional output directory specifier. Some files are typically created
and executed from the <outputdir>.

[--man]
If specified, show this help page and quit.

[--verbosity <level>]
Set the verbosity level. The app is currently chatty at level 0 and level 1
provides even more information.

[--debug]
If specified, toggle internal debugging. This will break at any breakpoints
specified with 'Env.set_trace()'

[--debugTermsize <253,62>]
Debugging is via telnet session. This specifies the <cols>,<rows> size of
the terminal.

[--debugHost <0.0.0.0>]
Debugging is via telnet session. This specifies the host to which to connect.

[--debugPort <7900>]
Debugging is via telnet session. This specifies the port on which the telnet
session is listening.

Installation

Easiest vector for installation is

pip install plugin2cube

Examples

plugin2cube accepts several CLI flags/arguments that together specify the CUBE instance, the plugin JSON description, as well as additional parameters needed for registration. For a full list of supported arguments, do

plugin2cube --man

To register a plugin, do

# Simplest way -- json representation is determined by running the container
# This requires of course that the machine running this script has docker installed!
plugin2cube     --CUBEurl http://localhost:8000/api/v1/                 \
                --CUBEuser chris --CUBEpassword chris1234               \
                --dock_image local/pl-imageProc                         \
                --name pl-imageProc                                     \
                --public_repo https://github.com/FNNDSC/pl-imageProc

Note that the above can also be equivalently specified with

# Simplest way -- json representation is determined by running the container
# This requires of course that the machine running this script has docker installed!
plugin2cube     --CUBEurl http://localhost:8000/api/v1/                 \
                --CUBEuser chris --CUBEpassword chris1234               \
                --dock_image local/pl-imageProc

where the --name and --public_repo are inferred from the --dock_image and a default --public_repobase

Development

Instructions for developers.

To debug, the simplest mechanism is to trigger the internal remote telnet session with the --debug CLI. Then, in the code, simply add Env.set_trace() calls where appropriate. These can remain in the codebase (i.e. you don’t need to delete/comment them out) since they are only live when a --debug flag is passed.

Testing

Run unit tests using pytest. Coming soon!

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