haplohub 2.0.4

HaploHub API

haplohub

The HaploHub is a turnkey solution to securely store and interpret biomarkers, genetics, and 'omics data. Our customers use the HaploHub to:

• Store WGS, WES, low-pass, and array data with uniform REST interfaces to access variants
• Interpret genomic variants
• Generate risk scores for an individual
• Run the typical algorithms (phasing, imputation, etc.)
• Calculate 'biological age' or 'organ age' biomarkers
• Generate custom reports

The HaploHub platform is continually updated to remain at the forefront of scientific understanding.

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

• API version: 2.0.1
• Package version: 1.0.0
• Generator version: 7.22.0-SNAPSHOT
• Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python 3.10+

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 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:

    try:
        # List Accessions
        api_response = api_client.accession_api.list_accession()
        print("The response of AccessionApi->list_accession:\n")
        pprint(api_response)
    except ApiException as e:
        print("Exception when calling AccessionApi->list_accession: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to http://localhost

Class	Method	HTTP request	Description
AccessionApi	list_accession	GET /api/v1/metadata/accession/	List Accessions
AlgorithmApi	get_algorithm	GET /api/v1/algorithm/{algorithm_id}/	Get algorithm
AlgorithmApi	list_algorithms	GET /api/v1/algorithm/	List algorithms
AlgorithmResultApi	create_algorithm_result	POST /api/v1/algorithm-result/	Create algorithm result
AlgorithmResultApi	get_algorithm_result	GET /api/v1/algorithm-result/{algorithm_result_id}/	Get algorithm result
AlgorithmResultApi	list_algorithm_results	GET /api/v1/algorithm-result/	List algorithm results
AlgorithmVersionApi	get_algorithm_version	GET /api/v1/algorithm-version/{algorithm_version_id}/	Get algorithm version
AlgorithmVersionApi	list_algorithm_versions	GET /api/v1/algorithm-version/	List algorithm versions
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
BiomarkerApi	list_biomarker_results	GET /api/v1/cohort/{cohort_id}/biomarker/result/	List biomarker results
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
ConfigApi	haplohub_api_v1_config_config	GET /api/v1/config/	Config
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
MemberPGSScoreApi	get_member_pgs_score	GET /api/v1/member-pgs-score/{score_id}/	Get member PGS score
MemberPGSScoreApi	list_member_pgs_scores	GET /api/v1/member-pgs-score/	List member PGS scores
MemberReportApi	create_member_report	POST /api/v1/cohort/{cohort_id}/member/{member_id}/report/{report_template_id}/create/	Create member report
OrganizationApi	haplohub_api_v1_organization_get_organization_settings	GET /api/v1/organization/settings/	Get Organization Settings
OrganizationApi	haplohub_api_v1_organization_sync_cors	POST /api/v1/organization/sync-cors/	Sync Cors
OrganizationApi	haplohub_api_v1_organization_update_organization_settings	PATCH /api/v1/organization/settings/	Update Organization Settings
ReportTemplateApi	create_report_template	POST /api/v1/report-template/	Create report template
ReportTemplateApi	delete_report_template	DELETE /api/v1/report-template/{report_template_id}/	Delete report template
ReportTemplateApi	get_report_template	GET /api/v1/report-template/{report_template_id}/	Get report template
ReportTemplateApi	list_report_templates	GET /api/v1/report-template/	List report templates
ReportTemplateApi	preview_report_template	GET /api/v1/report-template/{report_template_id}/preview/	Preview report template
ReportTemplateApi	update_report_template	PUT /api/v1/report-template/{report_template_id}/	Update report template
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	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
TaskApi	get_task	GET /api/v1/cohort/{cohort_id}/task/{task_id}/	Get task
TaskApi	list_tasks	GET /api/v1/cohort/{cohort_id}/task/	List tasks
TraitApi	get_trait	GET /api/v1/trait/{trait_id}/	Get trait
TraitApi	list_traits	GET /api/v1/trait/	List traits
TraitCategoryApi	get_trait_category	GET /api/v1/trait-category/{trait_category_id}/	Get trait category
TraitCategoryApi	list_trait_categories	GET /api/v1/trait-category/	List trait categories
UploadRequestApi	cancel_upload_request	POST /api/v1/cohort/{cohort_id}/upload-request/{upload_request_id}/cancel/	Cancel upload request
UploadRequestApi	create_upload_request	POST /api/v1/cohort/{cohort_id}/upload-request/	Create upload request
UploadRequestApi	get_upload_request	GET /api/v1/cohort/{cohort_id}/upload-request/{upload_request_id}/	Get upload request
UploadRequestApi	list_upload_requests	GET /api/v1/cohort/{cohort_id}/upload-request/	List upload requests
UserApi	haplohub_api_v1_user_check_slug	POST /api/v1/user/check-slug/	Check Slug
UserApi	haplohub_api_v1_user_get_user	GET /api/v1/user/	Get User
UserApi	haplohub_api_v1_user_init_user	POST /api/v1/user/init/	Init User
VariantApi	get_variant	POST /api/v1/cohort/{cohort_id}/variant/	Get Variant
VariantReferenceApi	lookup_variant_references_by_rsid	POST /api/v1/variant-reference/rsid/	Lookup variant references by rsID
DefaultApi	status	GET /api/v1/status/	Status

Documentation For Models

• AccessionSchema
• AlgorithmResultSchema
• AlgorithmSchema
• AlgorithmVersionSchema
• ApiKeySchema
• AuthSchema
• BiomarkerResultSchema
• CheckSlugRequest
• CliSchema
• ClinvarAttachmentSchema
• ClinvarTargetSchema
• CohortDetailSchema
• CohortSchema
• ConfigSchema
• CreateAlgorithmResultRequest
• CreateApiKeySchema
• CreateCohortRequest
• CreateCohortResponse
• CreateEnvironmentRequest
• CreateEnvironmentResponse
• CreateMemberRequest
• CreateReportTemplateRequest
• CreateReportTemplateResponse
• CreateSampleRequest
• CreateUploadRequestRequest
• CreateUploadRequestResult
• DirSchema
• DownloadLinkSchema
• EnvironmentSchema
• ErrorResponse
• ErrorSchema
• FileDirSchema
• FileInfo
• FileSchema
• GenericResponse
• GetCohortResponse
• GetReportTemplateResponse
• GetTraitCategoryResponse
• GetTraitResponse
• GetVariantRequest
• HgvsTargetSchema
• InfinityPaginatedResponseLogSchema
• InitUserRequest
• ListFilesFilter
• ListTraitCategoriesResponse
• ListTraitsResponse
• LogSchema
• MemberPgsScoreQueryParams
• MemberSchema
• OrderSchema
• OrganizationSchema
• OrganizationSettingsSchema
• PaginatedResponseAccessionSchema
• PaginatedResponseAlgorithmResultSchema
• PaginatedResponseAlgorithmSchema
• PaginatedResponseAlgorithmVersionSchema
• PaginatedResponseApiKeySchema
• PaginatedResponseCohortSchema
• PaginatedResponseEnvironmentSchema
• PaginatedResponseMemberSchema
• PaginatedResponseReportTemplateListSchema
• PaginatedResponseSampleSchema
• PaginatedResponseScoreSchema
• PaginatedResponseTaskSchema
• PaginatedResponseUploadRequestSchema
• RegionTargetSchema
• ReportTemplateListSchema
• ReportTemplateSchema
• ReportType
• RequestSchema
• Response
• Response1
• Response2
• ResponseSchema
• ResultListResponseBiomarkerResultSchema
• ResultListResponseVariantReferenceLookupResult
• ResultListResponseVariantResultSchema
• ResultResponse
• ResultResponseAlgorithmResultSchema
• ResultResponseAlgorithmSchema
• ResultResponseAlgorithmVersionSchema
• ResultResponseApiKeySchema
• ResultResponseBool
• ResultResponseConfigSchema
• ResultResponseCreateUploadRequestResult
• ResultResponseDownloadLinkSchema
• ResultResponseFileDirSchema
• ResultResponseFileSchema
• ResultResponseMemberSchema
• ResultResponseOrganizationSettingsSchema
• ResultResponseSampleSchema
• ResultResponseScoreSchema
• ResultResponseTaskSchema
• ResultResponseUnionUserSchemaNoneType
• ResultResponseUploadRequestSchema
• ResultSchema
• SampleSchema
• SampleVariantCallSchema
• ScoreSchema
• SuccessResponse
• SwitchEnvironmentResponse
• TargetReferenceSchema
• TargetsInner
• TaskSchema
• TaskStatus
• TenantSchema
• TraitCategorySchema
• TraitSchema
• UpdateAllowedOriginsRequest
• UpdateCohortRequest
• UpdateCohortResponse
• UpdateMemberRequest
• UpdateReportTemplateRequest
• UpdateReportTemplateResponse
• UpdateSampleRequest
• UploadLink
• UploadRequestSchema
• UploadRequestStatus
• UploadType
• UserSchema
• VariantAttachmentSchema
• VariantFilterSchema
• VariantReferenceLookupRequest
• VariantReferenceLookupResult
• VariantReferenceSchema
• VariantResultSchema
• VariantSchema

Documentation For Authorization

Authentication schemes defined for the API:

JWTBearer

• Type: Bearer authentication

ApiKeyAuth

• Type: API key
• API key parameter name: X-API-Key
• Location: HTTP header

Author