python-chrisclient

A python client for the ChRIS API.

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\"}]"}'

Search

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.

The plugin space (plugin id and plugin instance id ) in a CUBE instance can be searched using the chrispl-search script. This returns information either in tabular text form or a richer JSON payload. The search.py module is of course suitable for inclusion into other scripts/projects.

Search Examples

Find the plugin ID given a name substring search term

A common use case of the search script is to return the plugin ID for a plugin name substring:

chrispl-search  --for id,name                   \
                --using name=surfer             \
                --onCUBE '{
                    "protocol":     "http",
                    "port":         "8000",
                    "address":      "%HOSTIP",
                    "user":         "chris",
                    "password":     "chris1234"}'

(note the above onCUBE specification assumes an instance on the localhost. The special construction, %HOSTIP (if specified) will be replaced by the actual IP of the host machine. This construct is useful in some cases where the string localhost might have issues on proxied networks.)

The above call will return the plugin id as well as the complete name for all plugins that have a substring of surfer in their name:

(searchSubstr:name=surfer)  id 12  name pl-freesurfer_pp
(searchSubstr:name=surfer)  id 11  name pl-fastsurfer_inference

Find a list of all plugins registered to a CUBE instance

chrispl-search  --for name,id,type          \
                --using name=''             \
                --onCUBE '{
                    "protocol":     "http",
                    "port":         "8000",
                    "address":      "%HOSTIP",
                    "user":         "chris",
                    "password":     "chris1234"}'

will return

(searchSubstr:name=)      name pl-pfdo_med2img           id 17  type ds
(searchSubstr:name=)      name pl-pfdo_mgz2img           id 16  type ds
(searchSubstr:name=)      name pl-mgz2lut_report         id 15  type ds
(searchSubstr:name=)      name pl-z2labelmap             id 13  type ds
(searchSubstr:name=)      name pl-freesurfer_pp          id 12  type ds
(searchSubstr:name=)      name pl-fastsurfer_inference   id 11  type ds
(searchSubstr:name=)      name pl-fshack                 id 10  type ds
(searchSubstr:name=)      name pl-mpcs                   id 9   type ds
(searchSubstr:name=)      name pl-pfdicom_tagsub         id 8   type ds
(searchSubstr:name=)      name pl-pfdicom_tagextract     id 7   type ds
(searchSubstr:name=)      name pl-s3push                 id 6   type ds
(searchSubstr:name=)      name pl-dsdircopy              id 5   type ds
(searchSubstr:name=)      name pl-s3retrieve             id 3   type ds
(searchSubstr:name=)      name pl-simpledsapp            id 2   type ds
(searchSubstr:name=)      name pl-lungct                 id 18  type fs
(searchSubstr:name=)      name pl-mri10yr06mo01da_normal id 14  type fs
(searchSubstr:name=)      name pl-dircopy                id 4   type fs
(searchSubstr:name=)      name pl-simplefsapp            id 1   type fs

Search plugin instances

The actual space of executed plugin instances can also be searched. For instance, find the instance IDs of all plugins with name substring surfer and list their status. Note that to search the instance space, the --across plugininstances is specified:

chrispl-search --for id,status,plugin_name          \
               --using plugin_name=surfer           \
               --across plugininstances             \
               --onCUBE '{
                    "protocol":     "http",
                    "port":         "8000",
                    "address":      "%HOSTIP",
                    "user":         "chris",
                    "password":     "chris1234"}'

which will return something similar to:

(searchSubstr:plugin_name=surfer)  id 12 status finishedSuccessfully  plugin_name pl-freesurfer_pp
(searchSubstr:plugin_name=surfer)  id 11 status finishedSuccessfully  plugin_name pl-freesurfer_pp
(searchSubstr:plugin_name=surfer)  id 10 status finishedSuccessfully  plugin_name pl-freesurfer_pp
(searchSubstr:plugin_name=surfer)  id 9  status finishedSuccessfully  plugin_name pl-freesurfer_pp

Search plugin files

The actual list of file data associated with the outputs of a plugin instance can also be searched. For instance, search for the names of files by looking for the fname across files using plugin_inst_id of 9:

chrispl-search --for fname                              \
               --using plugin_inst_id=9                 \
               --across files                           \
               --onCUBEaddress megalodon.local

which will return something similar to:

(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/PatientF.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/PatientE.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/PatientD.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/PatientC.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/PatientB.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/PatientA.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/jobStatusSummary.json
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/jobStatus.json
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/input.meta.json
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/ex-covid.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/ex-covid-ct.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/0006.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/0005.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/0004.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/0003.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/0002.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/0001.dcm
(searchSubstr:plugin_inst_id=9)     fname chris/feed_9/pl-lungct_9/data/0000.dcm

Search plugin downloadable file resources

A list of web accessible locations to downloadable files can be found by searching across links for a file_resource associated with a given plugin_inst_id=9 (with an example of onCUBEaddress and onCUBEport:

chrispl-search  --for file_resource                     \
                --using plugin_inst_id=9                \
                --across links                          \
                --onCUBEaddress localhost               \
                --onCUBEport 8333

which will return something similar to:

(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/157/PatientF.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/156/PatientE.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/155/PatientD.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/154/PatientC.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/153/PatientB.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/152/PatientA.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/162/jobStatusSummary.json
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/161/jobStatus.json
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/160/input.meta.json
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/159/ex-covid.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/158/ex-covid-ct.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/151/0006.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/150/0005.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/149/0004.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/148/0003.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/147/0002.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/146/0001.dcm
(searchSubstr:plugin_inst_id=9)  file_resource http://localhost:8333/api/v1/files/145/0000.dcm

Search the space of parameters for a plugin id

To get a list of CLI flags, internal name, and help string associated with plugin id 8

chrispl-search  --for flag,name,help                \
                --using plugin_id=8                 \
                --across parameters                 \
                --onCUBEaddress localhost --onCUBEport 8333

(searchSubstr:plugin_id=8)  flag --subjectDir            name subjectDir             help directory (relative to <inputDir>) of subjects to process
(searchSubstr:plugin_id=8)  flag --in_name               name iname                  help name of the input (raw) file to process (default: brain.mgz)
(searchSubstr:plugin_id=8)  flag --out_name              name oname                  help name of the output segmented file
(searchSubstr:plugin_id=8)  flag --order                 name order                  help interpolation order
(searchSubstr:plugin_id=8)  flag --subject               name subject                help subject(s) to process. This expression is globbed.
(searchSubstr:plugin_id=8)  flag --log                   name logfile                help name of logfile (default: deep-seg.log)
(searchSubstr:plugin_id=8)  flag --network_sagittal_path name network_sagittal_path  help path to pre-trained sagittal network weights
(searchSubstr:plugin_id=8)  flag --network_coronal_path  name network_coronal_path   help path to pre-trained coronal network weights
(searchSubstr:plugin_id=8)  flag --network_axial_path    name network_axial_path     help path to pre-trained axial network weights
(searchSubstr:plugin_id=8)  flag --clean                 name cleanup                help if specified, clean up segmentation
(searchSubstr:plugin_id=8)  flag --no_cuda               name no_cuda                help if specified, do not use GPU
(searchSubstr:plugin_id=8)  flag --batch_size            name batch_size             help batch size for inference (default: 8
(searchSubstr:plugin_id=8)  flag --simple_run            name simple_run             help simplified run: only analyze one subject
(searchSubstr:plugin_id=8)  flag --run_parallel          name run_parallel           help if specified, allows for execute on multiple GPUs
(searchSubstr:plugin_id=8)  flag --copyInputImage        name copyInputImage         help if specified, copy input file to output dir.

Sub filter a parameter space for a single CLI and return the name to POST to CUBE

Determine the internal value to POST to CUBE for a given plugin CLI flag: (note this is an exact flag / string search – thus flag filters must have leading ‘–’ where appropriate):

chrispl-search      --for flag,name                     \
                    --using plugin_id=8                 \
                    --across parameters                 \
                    --filterFor " --in_name,--out_name" \
                    --onCUBEaddress localhost --onCUBEport 8333

(searchSubstr:plugin_id=8)  flag --in_name               name iname
(searchSubstr:plugin_id=8)  flag --out_name              name oname

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.

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