haplohub 1.0.7

HaploHub API

haplohub

No description provided (generated by Openapi Generator https://github.com/openapitools/openapi-generator)

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

• API version: 1.0
• Package version: 1.0.0
• Generator version: 7.11.0-SNAPSHOT
• Build package: org.openapitools.codegen.languages.PythonPydanticV1ClientCodegen

Requirements.

Python 3.7+

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 haplohub

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 haplohub

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:

import time
import haplohub
from haplohub.rest import ApiException
from pprint import pprint

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure Bearer authorization: 
configuration = haplohub.Configuration(
    access_token=os.environ["API_KEY"]
)


# Enter a context with an instance of the API client
with haplohub.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = haplohub.ApiKeyApi(api_client)
    create_api_key_schema = haplohub.CreateApiKeySchema() # CreateApiKeySchema | 

    try:
        # Create Api Key
        api_response = api_instance.haplohub_api_v1_api_key_create_api_key(create_api_key_schema)
        print("The response of ApiKeyApi->haplohub_api_v1_api_key_create_api_key:\n")
        pprint(api_response)
    except ApiException as e:
        print("Exception when calling ApiKeyApi->haplohub_api_v1_api_key_create_api_key: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to http://localhost

Class	Method	HTTP request	Description
ApiKeyApi	haplohub_api_v1_api_key_create_api_key	POST /api/v1/api-key/	Create Api Key
ApiKeyApi	haplohub_api_v1_api_key_delete_api_key	DELETE /api/v1/api-key/{api_key_id}/	Delete Api Key
ApiKeyApi	haplohub_api_v1_api_key_list_api_keys	GET /api/v1/api-key/	List Api Keys
CohortApi	create_cohort	POST /api/v1/cohort/	Create cohort
CohortApi	delete_cohort	DELETE /api/v1/cohort/{cohort_id}/	Delete cohort
CohortApi	get_cohort	GET /api/v1/cohort/{cohort_id}/	Get cohort
CohortApi	list_cohorts	GET /api/v1/cohort/	List cohorts
CohortApi	update_cohort	PUT /api/v1/cohort/{cohort_id}/	Update cohort
EnvironmentApi	create_environment	POST /api/v1/environment/	Create environment
EnvironmentApi	list_environments	GET /api/v1/environment/	List environments
EnvironmentApi	switch_environment	POST /api/v1/environment/{environment_id}/switch/	Switch environment
FileApi	delete_file	DELETE /api/v1/cohort/{cohort_id}/file/{file_id}/	Delete file
FileApi	download_link	POST /api/v1/cohort/{cohort_id}/file/{file_id}/download-link/	Get download link
FileApi	download_link_by_path	POST /api/v1/cohort/{cohort_id}/file/download-link/	Get download link by file path
FileApi	get_file	GET /api/v1/cohort/{cohort_id}/file/{file_id}/	Get file
FileApi	list_files	GET /api/v1/cohort/{cohort_id}/file/	List files
LogApi	list_logs	GET /api/v1/log/	List logs
MemberApi	create_member	POST /api/v1/cohort/{cohort_id}/member/	Create member
MemberApi	delete_member	DELETE /api/v1/cohort/{cohort_id}/member/{member_id}/	Delete member
MemberApi	get_member	GET /api/v1/cohort/{cohort_id}/member/{member_id}/	Get member
MemberApi	list_members	GET /api/v1/cohort/{cohort_id}/member/	List members
MemberApi	update_member	PUT /api/v1/cohort/{cohort_id}/member/{member_id}/	Update member
MetadataApi	accession	GET /api/v1/metadata/	Each accession is a string of DNA that is used as a reference. These are defined by https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38
ModelApi	create_model	POST /api/v1/model/	Create model
ModelApi	list_models	GET /api/v1/model/	List models
ModelApi	push_model	POST /api/v1/model/{model_id}/push/	Push model
PredictionApi	get_prediction	GET /api/v1/prediction/{prediction_id}/	Get prediction
PredictionApi	get_prediction_results	GET /api/v1/prediction/{prediction_id}/results/	Get prediction results
PredictionApi	list_predictions	GET /api/v1/prediction/	List predictions
PredictionApi	run_prediction	POST /api/v1/prediction/	Run prediction
ReportApi	create_report	POST /api/v1/report/	Create report
ReportApi	delete_report	DELETE /api/v1/report/{report_id}/	Delete report
ReportApi	get_report	GET /api/v1/report/{report_id}/	Get report
ReportApi	list_reports	GET /api/v1/report/	List reports
ReportApi	preview_report	GET /api/v1/report/{report_id}/preview/	Preview report
ReportApi	update_report	PUT /api/v1/report/{report_id}/	Update report
SampleApi	create_sample	POST /api/v1/cohort/{cohort_id}/sample/	Create sample
SampleApi	delete_sample	DELETE /api/v1/cohort/{cohort_id}/sample/{sample_id}/	Delete sample
SampleApi	get_sample	GET /api/v1/cohort/{cohort_id}/sample/{sample_id}/	Get sample
SampleApi	hgvs_dosage	GET /api/v1/sample/	Fetch the dosage of a given allele for a sample based on the hgvs nomenclature. For example 'NC_000001.11:g.11794419T>G'
SampleApi	list_samples	GET /api/v1/cohort/{cohort_id}/sample/	List samples
SampleApi	update_sample	PUT /api/v1/cohort/{cohort_id}/sample/{sample_id}/	Update sample
UploadApi	create_upload_request	POST /api/v1/cohort/{cohort_id}/upload/request/	Create upload request
VariantApi	get_variant	POST /api/v1/cohort/{cohort_id}/variant/	Get Variant
WorkflowApi	get_workflow_run	GET /api/v1/workflow/run/{workflow_run_id}/	Get workflow run
WorkflowApi	list_workflow_runs	GET /api/v1/workflow/run/	List workflow runs
DefaultApi	status	GET /api/v1/status/	Status

Documentation For Models

• AccessionSchema
• ApiKeySchema
• AuthSchema
• CohortDetailSchema
• CohortSchema
• CreateApiKeySchema
• CreateCohortRequest
• CreateCohortResponse
• CreateEnvironmentRequest
• CreateEnvironmentResponse
• CreateMemberRequest
• CreateModelRequest
• CreateModelResponse
• CreateReportRequest
• CreateReportResponse
• CreateSampleRequest
• CreateUploadRequestRequest
• DetailWorkflowRunSchema
• DirSchema
• DownloadLinkSchema
• EnvironmentSchema
• ErrorResponse
• ErrorSchema
• FileDirSchema
• FileInfo
• FileSchema
• GenericResponse
• GetCohortResponse
• GetHgvsResponse
• GetPredictionResponse
• GetPredictionResultsResponse
• GetReportResponse
• GetVariantRequest
• HgvsDosageSchema
• InfinityPaginatedResponseLogSchema
• ListFilesFilter
• LogSchema
• MLModelSchema
• MemberSchema
• ModelId
• PaginatedResponseAccessionSchema
• PaginatedResponseApiKeySchema
• PaginatedResponseCohortSchema
• PaginatedResponseEnvironmentSchema
• PaginatedResponseMLModelSchema
• PaginatedResponseMemberSchema
• PaginatedResponsePredictionSchema
• PaginatedResponseReportSchema2
• PaginatedResponseSampleSchema
• PaginatedResponseWorkflowRunSchema
• PredictionResultsSchema
• PredictionSchema
• PredictionStatus
• PushCredentials
• PushModelRequest
• ReportSchema2
• RequestSchema
• Response
• ResponseSchema
• ResponseStatus
• ResultListResponseVariantSchema
• ResultResponse
• ResultResponseApiKeySchema
• ResultResponseDetailWorkflowRunSchema
• ResultResponseDownloadLinkSchema
• ResultResponseFileDirSchema
• ResultResponseFileSchema
• ResultResponseMemberSchema
• ResultResponsePushCredentials
• ResultResponseSampleSchema
• ResultResponseUploadRequestResponse
• RunPredictionRequest
• RunPredictionResponse
• SampleSchema
• SuccessResponse
• SwitchEnvironmentResponse
• TenantSchema
• UpdateCohortRequest
• UpdateCohortResponse
• UpdateMemberRequest
• UpdateReportRequest
• UpdateReportResponse
• UpdateSampleRequest
• UploadLink
• UploadRequestResponse
• UploadType
• UserSchema
• VariantSchema
• WorkflowHistorySchema
• WorkflowRunSchema

Documentation For Authorization

Authentication schemes defined for the API:

Auth0JWTBearer

• Type: Bearer authentication

Author