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: 3.5.0
• Package version: 1.0.0
• Generator version: 7.22.0
• 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 os

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.
# When no argument is given, Configuration falls back to the
# HAPLOHUB_API_HOST, HAPLOHUB_API_KEY and HAPLOHUB_ACCESS_TOKEN environment variables.

# Configure API key authorization (X-API-Key header): ApiKeyAuth
configuration = haplohub.Configuration(
    api_key=os.environ["HAPLOHUB_API_KEY"]
)

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

# 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

Documentation For Models

• AccessionSchema
• AlgorithmAutoRunSchema
• AlgorithmResultIssueSchema
• AlgorithmResultIssueSeverity
• AlgorithmResultResponse
• AlgorithmResultSchema
• AlgorithmSchema
• AlgorithmVersionSchema
• ApiKeySchema
• Assay
• AuthSchema
• BiomarkerResultSchema
• CheckSlugRequest
• CheckSlugResponse
• CliSchema
• ClingenDosageSchema
• ClingenGeneValiditySchema
• ClinvarAttachmentSchema
• ClinvarTargetSchema
• CohortDetailSchema
• CohortSchema
• ConfigResponse
• ConfigSchema
• CpicDiplotypeSchema
• CpicPairSchema
• CpicRecommendationSchema
• CreateAlgorithmAutoRunRequest
• CreateAlgorithmAutoRunResponse
• CreateAlgorithmResultRequest
• CreateApiKeyResponse
• CreateApiKeySchema
• CreateCohortRequest
• CreateCohortResponse
• CreateEnvironmentRequest
• CreateEnvironmentResponse
• CreateMemberRequest
• CreateReportTemplateRequest
• CreateReportTemplateResponse
• CreateSampleRequest
• CreateUploadRequestRequest
• CurrentUserResponse
• DeleteMode
• DirSchema
• DownloadLinkResponse
• DownloadLinkSchema
• EnvironmentSchema
• ErrorResponse
• ErrorSchema
• FileDirSchema
• FileInfo
• FilePageParams
• FileSchema
• GenericResponse
• GetAlgorithmResponse
• GetAlgorithmVersionResponse
• GetCohortResponse
• GetFileResponse
• GetGwasAssociationResponse
• GetMemberPgsScoreResponse
• GetOrganizationSettingsResponse
• GetPgsScoreResponse
• GetReportTemplateResponse
• GetSampleLineageResponse
• GetTaskResponse
• GetVariantRequest
• GetVariantResponse
• GwasAssociationSchema
• GwasAttachmentSchema
• GwasTargetSchema
• HgvsTargetSchema
• InitUserRequest
• LineageConsumedFileSchema
• LineageFileSchema
• LineageResultSchema
• ListAccessionResponse
• ListAlgorithmAutoRunsResponse
• ListAlgorithmResultsResponse
• ListAlgorithmVersionsResponse
• ListAlgorithmsResponse
• ListApiKeysResponse
• ListBiomarkerResultsResponse
• ListCohortsResponse
• ListCpicDiplotypesResponse
• ListCpicPairsResponse
• ListCpicRecommendationsResponse
• ListDosageResponse
• ListEnvironmentsResponse
• ListFilesFilter
• ListFilesResponse
• ListGeneValidityResponse
• ListGwasAssociationsResponse
• ListLogsResponse
• ListMemberPgsScoresResponse
• ListMembersResponse
• ListPgsCategoriesResponse
• ListPgsScoresResponse
• ListReportTemplatesResponse
• ListSamplesResponse
• ListTasksResponse
• ListUploadRequestsResponse
• LogSchema
• MemberPgsScoreQueryParams
• MemberResponse
• MemberSchema
• OrderSchema
• OrganizationSchema
• OrganizationSettingsSchema
• PageParams
• PgsCategorySchema
• PgsScoreSchema
• PgsTraitSchema
• RegionTargetSchema
• ReportTemplateListSchema
• ReportTemplateSchema
• ReportType
• RequestSchema
• ResponseSchema
• ResultSchema
• SampleLineageSchema
• SampleResponse
• SampleSchema
• SampleVariantCallSchema
• ScoreSchema
• SuccessResponse
• SwitchEnvironmentResponse
• TargetReferenceSchema
• TaskSchema
• TaskStatus
• TenantSchema
• UpdateAllowedOriginsRequest
• UpdateCohortRequest
• UpdateCohortResponse
• UpdateMemberRequest
• UpdateReportTemplateRequest
• UpdateReportTemplateResponse
• UpdateSampleRequest
• UploadLink
• UploadRequestResponse
• UploadRequestResult
• UploadRequestSchema
• UploadRequestStatus
• UploadType
• UserSchema
• VariantAttachmentSchema
• VariantFilterSchema
• VariantReferenceLookupRequest
• VariantReferenceLookupResponse
• VariantReferenceLookupResult
• VariantReferenceSchema
• VariantResultSchema
• VariantSchema
• VariantTargetSchema

Documentation For Authorization

Authentication schemes defined for the API:

ApiKeyAuth

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

JWTBearer

• Type: Bearer authentication

Author