(Python) client for the ChRIS API
Project description
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
At time of writing (early 2022), three scripts/modules are in production:
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
General CUBE client usage
Python programmatic interface
Instantiate the client:
from chrisclient import client
cl = client.Client('http://localhost:8000/api/v1/', 'cube', 'cube1234')
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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