(Python) client for the ChRIS API

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for debio from gravatar.com debio Avatar for jbernal from gravatar.com jbernal

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers
Report project as malware

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 either via the command line interface (CLI) or through a Python programmatic interface using relevant modules.

Overview

Three scripts/modules are included in this repository:

  • a general CUBE client

  • a more specific plugin search utility

  • a more specific plugin run schedule utility

Installation

Use the PyPI, Luke!

pip install -U python-chrisclient

ChRIS server preconditions

These preconditions are only necessary to be able to test the client against an actual instance of a ChRIS server both during development and for the automated tests.

Install latest just command runner.

Fire up the full set of ChRIS services:

Open a terminal and run the following commands in any working directory:

$> git clone https://github.com/FNNDSC/ChRIS_ultron_backEnd.git
$> cd ChRIS_ultron_backEnd
$> just

Create a test feed and two pipelines:

Run the following shell script on the directory of this README file. NOTE: The script depends on the popular curl and jq command line tools.

$> ./pre_test.sh

Run the automated tests:

Optionally create a virtual environment and activate it and then run the automated tests.

$> pip install -e ".[dev]"
$> pytest

Tear down the full set of ChRIS services:

You can later remove all the backend containers and release storage volumes with:

$> cd ChRIS_ultron_backEnd
$> just nuke

General CUBE client usage

Python programmatic interface

Instantiate the client:

from chrisclient import client

cl = client.Client('http://localhost:8000/api/v1/', 'cube', 'cube1234')

Alternatively get a valid token for the user and instantiate the client:

token = client.Client.get_auth_token('http://localhost:8000/api/v1/auth-token/', 'cube', 'cube1234' )
cl = client.Client('http://localhost:8000/api/v1/', token=token)

Upload and create a new plugin (only works for ChRIS admins):

cl_admin = client.Client('http://localhost:8000/api/v1/', 'chris', 'chris1234')
response = cl_admin.admin_upload_plugin('host,moc', '~/simpledsapp.json')

Get plugins given search parameters:

search_params = {'name': 'pl-dircopy'}
response = cl.get_plugins(search_params)

Get a plugin by id:

plugin_id = 1
response = cl.get_plugin_by_id(plugin_id)

Get a plugin’s parameters:

plugin_id = 1
response = cl.get_plugin_parameters(plugin_id, {'limit': 50, 'offset':0})

These retrieving operations are supported for all other high level resources such as feeds, pipelines, plugin instances and workflows.

Get a pipeline’s default parameters and nodes data structure and then run a workflow from the pipeline:

pipeline_id = 2
# attempt to fetch all parameters in a single request by setting a very high limit
response = cl.get_pipeline_default_parameters(pipeline_id, {'limit': 100, 'offset':0})
nodes = cl.compute_workflow_nodes_info(response['data'])
response = cl.create_workflow(pipeline_id, {'previous_plugin_inst_id': 1, 'nodes_info': json.dumps(nodes)})

Please visit the wiki for more information about the client’s API and examples.

Standalone CLI client tool

List plugins:

chrisclient -u cube -p cube1234 http://localhost:8000/api/v1/ list plugin offset==0 limit==2 --verbose

List pipelines:

chrisclient -u cube -p cube1234 http://localhost:8000/api/v1/ list pipeline --verbose

List plugin instances:

chrisclient -u cube -p cube1234 http://localhost:8000/api/v1/ list plugininstance offset==0 limit==1

Upload and create plugin (only works for ChRIS admins):

chrisclient -u chris -p chris1234 http://localhost:8000/api/v1/ add plugin --computenames host,moc --fname ~/simpledsapp.json

Create plugin instance (run plugin):

chrisclient -u cube -p cube1234 http://localhost:8000/api/v1/ add plugininstance
 --pluginid 3 --instancedata '{"previous_id": 1, "dir": "home/cube/uploads"}'

Create pipeline:

chrisclient -u cube -p cube1234 http://localhost:8000/api/v1/ add pipeline --pipelinedata '{"name": "Pipeline1", "plugin_tree": "[{\"plugin_id\": 2, \"previous_index\": null}, {\"plugin_id\": 2, \"previous_index\": 0}]"}'

Create workflow (run pipeline):

chrisclient -u cube -p cube1234 http://localhost:8000/api/v1/ add workflow --pipelineid 2 --workflowdata '{"previous_plugin_inst_id": 1, "nodes_info": "[{\"piping_id\": 3, \"compute_resource_name\": \"host\"}, {\"piping_id\": 4, \"compute_resource_name\": \"host\"}, {\"piping_id\": 5, \"compute_resource_name\": \"host\"}]"}'

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-

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for debio from gravatar.com debio Avatar for jbernal from gravatar.com jbernal

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers

Release history Release notifications | RSS feed

This version

2.15.0

2.14.0

2.13.0

2.12.0

2.11.1

2.11.0

2.10.0

2.9.1

2.8.2

2.8.0

2.7.0

2.6.0

2.5.0

2.4.0

2.3.2

2.3.0

2.2.10

2.2.8

2.2.6

2.2.4

2.2.2

2.2.0

2.0.4

2.0.2

2.0.0

1.2.8

1.2.6

1.2.4

1.2.2

1.2.0

1.0.10

1.0.8

1.0.6

1.0.4

1.0.2

1.0.0

0.0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

python_chrisclient-2.15.0.tar.gz (33.8 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

python_chrisclient-2.15.0-py3-none-any.whl (32.9 kB view details)

Uploaded Python 3

File details

Details for the file python_chrisclient-2.15.0.tar.gz.

File metadata

  • Download URL: python_chrisclient-2.15.0.tar.gz
  • Upload date:
  • Size: 33.8 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.2.0 CPython/3.14.4

File hashes

Hashes for python_chrisclient-2.15.0.tar.gz
Algorithm Hash digest
SHA256 b5c51f4c34cccc63bb43c854a4dccd6f44ef70bb815972dd5167b450a7892ddd
MD5 0593d5245de54531d286e2fa147153a9
BLAKE2b-256 ddcdccdc92eb5afca9afcab45bfaf7d62251157c2d1577c4fbb1a5bba7385da0

See more details on using hashes here.

File details

Details for the file python_chrisclient-2.15.0-py3-none-any.whl.

File metadata

File hashes

Hashes for python_chrisclient-2.15.0-py3-none-any.whl
Algorithm Hash digest
SHA256 441240387c2b85ae9ba3d1ce69c368922b8d51f2a1842137d938079c5afd95ba
MD5 cacb3bf7ece94189a23330fbf84c4def
BLAKE2b-256 21281349d4d49fd83e484a1eb5161c6254c237efe3d159dff44ed2137122bef3

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page