Pydra2App - XNAT

An extension for the Pydra2App framework that support for building XNAT "apps" (container service docker images) from Pydra tasks.

Quick Installation

This extension can be installed for Python 3 using pip:

$ pip3 install pydra2app-xnat

This will also install the core Pydra2App package and any required dependencies.

Reconcile XNAT pipelines

deploy-pipelines performs one reconciliation against a release catalogue and exits:

PIPELINE_CATALOGUE_URL=https://example.org/pipeline-release.json \
XNAT_HOST=https://xnat.example.org \
XNAT_USER=username \
XNAT_PASS=password \
pydra2app ext xnat deploy-pipelines

The catalogue may instead be passed as a local file or URL argument. The command reports each pipeline as installed, updated, unchanged, or failed, with how many of its commands were enabled, and exits nonzero if any pipeline fails. Existing commands are updated in place (keeping their site and project enablement), and commands absent from the catalogue are not removed. The XNAT user must be an administrator or a Container Service manager.

Selecting and enabling pipelines

A YAML config file passed to --config (or PIPELINE_RECONCILER_CONFIG) selects which catalogue pipelines are reconciled and whether their commands are enabled:

include:              # optional; leave out to take every pipeline
  - mri.human.neuro.*
exclude:              # optional; wins over include
  - mri.human.neuro.bidsapp.*
enablement: approval  # or "auto"; default is approval

Patterns are case-sensitive wildcards matched against the whole catalogue pipeline ID, where * also matches .. Excluded pipelines are left untouched even if already installed: their commands are not downloaded, updated or enabled. Invalid config fails before XNAT is contacted, and a pattern matching no pipeline logs a warning. Without a config, every pipeline is reconciled in approval mode.

• approval: new commands are installed disabled until an administrator enables them.
• auto: every selected command is enabled for the site on each run, including any an administrator has disabled. To block a pipeline, exclude it, then disable it in XNAT.

Either way, project owners still enable commands for their own projects.

License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Creative Commons License: Attribution-NonCommercial-ShareAlike 4.0 International