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Concepts

danger

chrs is now obsolete. It only works with outdated versions of ChRIS backend, the latest supported version being 5.1.0. These documentation remain as a design reference for the future development of an updated ChRIS CLI client.

Inspirations​

chrs behaves similarly, but not exactly, like a filesystem. The chrs command-line interface is inspired by built-in shell commands and the design of kubectl.

Like a filesystem, you can run the cd command and ls commands:

chrs cd chris/feed_10/pl-dircopy_45/pl-unstack-folders_46/pl-dcm2niix_47
chrs ls
chrs ls ./data
chrs ls ..
chrs ls ../..

Unfortunately, path resolution is not fully implemented:

chrs ls '../DICOM to NIFTI simple'
Error: path not found

Like kubectl, resources should be prefixed by their resource type names, which can be abbreviated:

chrs describe 'plugin/pl-dcm2niix'
chrs describe 'pipeline/Fetal Reconstruction Pipeline'
chrs describe 'pp/Fetal Reconstruction Pipeline'

What's more is that chrs will try to guess what you mean if the resource type is not provided.

# assumed to be a plugin
chrs describe 'pl-dcm2niix'

# assumed to be a pipeline because plugin names don't usually contain spaces
chrs describe 'Fetal Reconstruction Pipeline'

Runnables​

Runnables are involved in chrs run, chrs search, and chrs describe.

A runnable is one of:

Tests: https://github.com/FNNDSC/chrs/blob/7ab5a7831bc9746b6e76727b24b6c9572fd177e1/chrs/src/arg/runnable.rs#L260-L338

Plugins​

Plugins may be specified by any of:

  • plugin name, e.g. pl-dcm2niix, pl/pl-dcm2niix, plugin/pl-dcm2niix
  • plugin name and version, e.g. pl-dcm2niix@1.0.0, pl/pl-dcm2niix@1.0.0, plugin/pl-dcm2niix@1.0.0 (preferred)
  • plugin ID, e.g. 127, pl/127, plugin/127
  • API URL, e.g. https://cube.chrisproject.org/api/v1/plugins/127/

Pipelines​

Pipelines may be specified by any of:

  • pipeline name, e.g. Fetal Brain Reconstruction, pp/Fetal Brain Reconstruction, pipeline/Fetal Brain Reconstruction
  • pipeline ID, e.g. pp/12, pipeline/12
  • API URL, e.g. https://cube.chrisproject.org/api/v1/pipelines/12/

Data Nodes​

Data nodes are involved in chrs run, chrs status, chrs list, chrs logs, chrs ls, and chrs download.

Data nodes are plugin instances, simply put. However, for flexibility they may be specified one of several ways:

  • plugin instance title, e.g. DICOM-to-NIFTI, pi/DICOM-to-NIFTI, plugininstance/DICOM-to-NIFTI
  • plugin instance ID, e.g. 42, pi/42, plugininstance/42
  • relative path, e.g. ., .., ../..
  • absolute* path, e.g. rudolph/feed_130/pl-dircopy_543
  • feed name, e.g. feed/A tractography study
  • feed ID, e.g. feed/80

*By convention, absolute paths do not start with /. Relative paths start with ./ or ...

Feeds as Data Nodes​

Be aware that the different subcommands of chrs interpret feeds differently.

  • chrs download feed/N will download all files of a feed
  • chrs status feed/N will show only the feed status, but no plugin instance statuses
  • chrs run <runnable> feed/N will append the <runnable> to the most recent plugin instance in feed/N