cda-client

API definition for the CDA

This Python package is automatically generated by the OpenAPI Generator project:

API version: 3.0.0
Package version: 4.17.2023
Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python >=3.6

Installation & Usage

pip install

If the python package is hosted on a repository, you can install directly using:

pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git

(you may need to run pip with root permission: sudo pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git)

Then import the package:

import cda_client

Setuptools

Install via Setuptools.

python setup.py install --user

(or sudo python setup.py install to install the package for all users)

Then import the package:

import cda_client

Getting Started

Please follow the installation procedure and then run the following:

import time
import cda_client
from pprint import pprint
from cda_client.api import meta_api
from cda_client.model.dataset_description import DatasetDescription
from cda_client.model.system_status import SystemStatus
# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = cda_client.Configuration(
    host = "http://localhost"
)



# Enter a context with an instance of the API client
with cda_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = meta_api.MetaApi(api_client)

    try:
        # List descriptions of all available datasets
        api_response = api_instance.all_release_notes()
        pprint(api_response)
    except cda_client.ApiException as e:
        print("Exception when calling MetaApi->all_release_notes: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to http://localhost

Class	Method	HTTP request	Description
MetaApi	all_release_notes	GET /api/v1/dataset-description/all	List descriptions of all available datasets
MetaApi	latest_release_notes	GET /api/v1/dataset-description/latest	Description of latest dataset
MetaApi	service_status	GET /status	CDA status
QueryApi	boolean_query	POST /api/v1/boolean-query/{version}	Execute boolean query
QueryApi	bulk_data	GET /api/v1/bulk-data/{version}	Return all data in CDA
QueryApi	columns	GET /api/v1/columns/{version}	Returns all column names and definitions for schema
QueryApi	diagnosis_counts_query	POST /api/v1/diagnosis/counts/{version}	Execute Diagnosis Counts query
QueryApi	diagnosis_query	POST /api/v1/diagnosis/{version}	Execute Diagnosis query
QueryApi	file_counts_query	POST /api/v1/files/counts/{version}	Execute File Counts query
QueryApi	files	POST /api/v1/files/{version}	Returns a list of files given a boolean query
QueryApi	global_counts	POST /api/v1/global-counts/{version}	Returns counts of the DCS
QueryApi	job_status	GET /api/v1/job-status/{id}	Return the running status of long running queries.
QueryApi	mutation_counts_query	POST /api/v1/mutations/counts/{version}	Execute Mutation Counts query
QueryApi	mutation_query	POST /api/v1/mutations/{version}	Execute Mutation query
QueryApi	query	GET /api/v1/query/{id}	Given a query ID, return the a page of data from the query result.
QueryApi	research_subject_counts_query	POST /api/v1/researchsubjects/counts/{version}	Execute ResearchSubjects Counts query
QueryApi	research_subject_file_counts_query	POST /api/v1/researchsubjects/files/counts/{version}	Execute ResearchSubjects File Counts query
QueryApi	research_subject_files_query	POST /api/v1/researchsubjects/files/{version}	Execute ResearchSubject Files query
QueryApi	research_subject_query	POST /api/v1/researchsubjects/{version}	Execute Research Subject query
QueryApi	specimen_counts_query	POST /api/v1/specimen/counts/{version}	Execute Specimen Counts query
QueryApi	specimen_file_counts_query	POST /api/v1/specimen/files/counts/{version}	Execute Specimen File Counts query
QueryApi	specimen_files_query	POST /api/v1/specimen/files/{version}	Execute Specimen Files query
QueryApi	specimen_query	POST /api/v1/specimens/{version}	Execute Specimens query
QueryApi	subject_counts_query	POST /api/v1/subjects/counts/{version}	Execute Subjects Counts query
QueryApi	subject_file_counts_query	POST /api/v1/subjects/files/counts/{version}	Execute Subjects File Counts query
QueryApi	subject_files_query	POST /api/v1/subjects/files/{version}	Execute Subject Files query
QueryApi	subject_query	POST /api/v1/subjects/{version}	Execute Subject query
QueryApi	treatment_counts_query	POST /api/v1/treatments/counts/{version}	Execute Treatments Counts query
QueryApi	treatments_query	POST /api/v1/treatments/{version}	Execute Treatments query
QueryApi	unique_values	POST /api/v1/unique-values/{version}	Returns all unique values

Documentation For Models

Documentation For Authorization

All endpoints do not require authorization.

Author

Notes for Large OpenAPI documents

If the OpenAPI document is large, imports in cda_client.apis and cda_client.models may fail with a RecursionError indicating the maximum recursion limit has been exceeded. In that case, there are a couple of solutions:

Solution 1: Use specific imports for apis and models like:

from cda_client.api.default_api import DefaultApi
from cda_client.model.pet import Pet

Solution 2: Before importing the package, adjust the maximum recursion limit as shown below:

import sys
sys.setrecursionlimit(1500)
import cda_client
from cda_client.apis import *
from cda_client.models import *

CancerDataAggregator/cda-service-python-client