(Python) client for the ChRIS API

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License: MIT

Author: FNNDSC

Project description

A python client for the ChRIS API.

https://travis-ci.org/FNNDSC/python-chrisclient.svg?branch=master

Quick Overview

This repository contains various python scripts and modules that provide a rich client experience for interacting with a CUBE backend instance. Interaction is typically either via the command line interface (CLI) or directly in python using relevant modules.

Overview

At time of writing (early 2021), two scripts/modules are in production:

  • a plugin search utility

  • a plugin run schedule utility

Note that in the instructions below, the details of a CUBE instance are passed in a JSON structure using the --onCUBE flag. In many cases you might only want to pass the address of a CUBE instance. For this purpose, the --onCUBEaddress can be used that will only set the address and keep other default information intact.

Installation

Use the PyPI, Luke!

pip install -U python-chrisclient

Run

Plugins can be run/scheduled on a CUBE instance using the chrispl-run script. The CLI parameters are broadly similar to chrispl-search with some semantic changes more pertinent to the run call – the for search is fixed to the plugin id and the search --pluginSpec becomes the --using CLI.

Run Examples

Run an FS plugin, pl-mri10yr06mo01da_normal

chrispl-run --plugin name=pl-mri10yr06mo01da_normal \
            --onCUBE '{
                "protocol":     "http",
                "port":         "8000",
                "address":      "%HOSTIP",
                "user":         "chris",
                "password":     "chris1234"}'

This plugin does not require any specific CLI args when run in the default state. Once posted to CUBE, a string is returned to the shell:

(name=pl-mri10yr06mo01da_normal) id 14

Indicating that the plugin instance ID of the plugin in CUBE is 14 (for example).

For convenience, let’s set:

CUBE='{
    "protocol":     "http",
    "port":         "8000",
    "address":      "%HOSTIP",
    "user":         "chris",
    "password":     "chris1234"
}'

This return construct lends itself easily to scripting:

ROOTNODE=$(./chrispl-run --plugin name=pl-mri10yr06mo01da_normal --onCUBE "$CUBE" | awk '{print $3}')

or with some formatting:

ROOTNODE=$(
    chrispl-run --plugin name=pl-mri10yr06mo01da_normal     \
                --onCUBE="$CUBE"                            |
                     awk '{print $3}'
)

Run a DS plugin, pl-freesurfer_pp, that builds on the previous node

In this manner, a workflow can be constructed. First construct the arguments for the next plugin:

ARGS="                              \
--ageSpec=10-06-01;                 \
--copySpec=sag,cor,tra,stats,3D;    \
--previous_id=$ROOTNODE             \
"

and now schedule the run:

chrispl-run --plugin name="pl-freesurfer_pp"    \
            --args="$ARGS"                      \
            --onCUBE="$CUBE"

which will return:

(name=pl-freesurfer_pp)        id 19

As before, this can be captured and used for subsequent chaining:

FSNODE=$(
    chrispl-run --plugin name=pl-freesurfer_pp  \
                --args="$ARGS"                  \
                --onCUBE="$CUBE"                |
                     awk '{print $3}'
)

Additional Reading

Consult the ChRIS_docs workflow directory for examples of workflows built using these tools.

-30-

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License: MIT

Author: FNNDSC


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