immport-client 1.0.0

Shared Data API

immport-client

Unofficial ImmPort Python client generated via OpenAPI Generator Some patches for missspecifications have been manually applied to the ImmPort API, when methods actually returned arrays instead of single objects.

Overview

The Shared Data API supports the downloading of data hosted in the ImmPort Shared Data Warehouse. Endpoints that download Study and Subject level data require Authorization to use these endpoints. Registration to use ImmPort Shared Data is free, visit ImmPort to explore the types of data available for download. Click on this Link to register.

Additional Help

For more details on the endpoints visit the API Documentation Site for more information. In addition, How-To tutorials on using the endpoints and examples of exploring the data are available here

Note

The Swagger UI can be used to try out endpoints but the Browser can freeze when the endpoint returns large result sets. Either try to add filters to reduce the amount of data returned or test the endpoints with shell scripts using curl or wget.

Controllers

Controller	Description	Authorization
Study Search	Endpoints to support text and facted search of Study and Subject Metadata	No
Study Data	These endpoints support the retrieval of study data for a single study including subject, experiment, etc	Yes
Study Result	Endpoints to download study, experiment, assay results	Yes
Study File Manifest	These endpoints support retrieving a manifest of all files associated with a given study	Yes
Download Study Files	These endpoints support the download of study package files including release files, study files, protocol files and result files using GA4GH DRS ID's. Use the manifest endpoint to retrieve DRS ID for each file	Yes
Lookup or Controlled Vocabulary	Endpoints to download controlled vocabulary information	No

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

• API version: v1
• Package version: 1.0.0
• Generator version: 7.21.0
• Build package: org.openapitools.codegen.languages.PythonClientCodegen For more information, please visit https://immport.org

Requirements.

Python 3.9+

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 immport_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 immport_client

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:

import os
import immport_client

from immport_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://immport.org/data/query
# See configuration.py for a list of all supported configuration parameters.
configuration = immport_client.Configuration(
    host = "https://immport.org/data/query"
)

# 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.

configuration.access_token = os.environ["ACCESS_TOKEN"]


# Enter a context with an instance of the API client
with immport_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = immport_client.DownloadStudyFilesApi(api_client)
    file_uuid = '81944983-0aaf-4b55-a1ef-e2681c8b258b' # str | DRS file UUID
    access_method = 's3' # str | Access method to retrieve the file: s3 or stream

    try:
        # Get download URL using DRS ID
        api_response = api_instance.get_url_from_drs(file_uuid, access_method)
        print("The response of DownloadStudyFilesApi->get_url_from_drs:\n")
        pprint(api_response)
    except ApiException as e:
        print("Exception when calling DownloadStudyFilesApi->get_url_from_drs: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to https://immport.org/data/query

Class	Method	HTTP request	Description
DownloadStudyFilesApi	get_url_from_drs	GET /drs/download/{accessMethod}/{fileUUID}	Get download URL using DRS ID
LookupOrControlledVocabularyApi	get_lk_adverse_event_severity	GET /api/lookup/lkAdverseEventSeverity	Retrieve LkAdverseEventSeverity Information
LookupOrControlledVocabularyApi	get_lk_age_event	GET /api/lookup/lkAgeEvent	Retrieve LkAgeEvent Information
LookupOrControlledVocabularyApi	get_lk_analyte	GET /api/lookup/lkAnalyte	Retrieve LkAnalyte Information
LookupOrControlledVocabularyApi	get_lk_ancestral_population	GET /api/lookup/lkAncestralPopulation	Retrieve LkAncestralPopulation Information
LookupOrControlledVocabularyApi	get_lk_cell_population	GET /api/lookup/lkCellPopulation	Retrieve LkCellPopulation Information
LookupOrControlledVocabularyApi	get_lk_cell_population_marker	GET /api/lookup/lkCellPopulationMarker	Retrieve LkCellPopulationMarker Information
LookupOrControlledVocabularyApi	get_lk_compound_role	GET /api/lookup/lkCompoundRole	Retrieve LkCompoundRole Information
LookupOrControlledVocabularyApi	get_lk_criterion_category	GET /api/lookup/lkCriterionCategory	Retrieve LkCriterionCategory Information
LookupOrControlledVocabularyApi	get_lk_data_completeness	GET /api/lookup/lkDataCompleteness	Retrieve LkDataCompleteness Information
LookupOrControlledVocabularyApi	get_lk_disease	GET /api/lookup/lkDisease	Retrieve LkDisease Information
LookupOrControlledVocabularyApi	get_lk_disease_stage	GET /api/lookup/lkDiseaseStage	Retrieve LkDiseaseStage Information
LookupOrControlledVocabularyApi	get_lk_ethnicity	GET /api/lookup/lkEthnicity	Retrieve LkEthnicity Information
LookupOrControlledVocabularyApi	get_lk_exp_measurement_tech	GET /api/lookup/lkExpMeasurementTech	Retrieve LkExpMeasurementTech Information
LookupOrControlledVocabularyApi	get_lk_exposure_material	GET /api/lookup/lkExposureMaterial	Retrieve LkExposureMaterial Information
LookupOrControlledVocabularyApi	get_lk_exposure_process	GET /api/lookup/lkExposureProcess	Retrieve LkExposureProcess Information
LookupOrControlledVocabularyApi	get_lk_expsample_result_schema	GET /api/lookup/lkExpsampleResultSchema	Retrieve LkExpsampleResultSchema Information
LookupOrControlledVocabularyApi	get_lk_file_detail	GET /api/lookup/lkFileDetail	Retrieve LkFileDetail Information
LookupOrControlledVocabularyApi	get_lk_gender	GET /api/lookup/lkSex	Retrieve LkSex Information
LookupOrControlledVocabularyApi	get_lk_hmdb	GET /api/lookup/lkHmdb	Retrieve LkHmdb Information
LookupOrControlledVocabularyApi	get_lk_lab_test_name	GET /api/lookup/lkLabTestName	Retrieve LkLabTestName Information
LookupOrControlledVocabularyApi	get_lk_lab_test_panel_name	GET /api/lookup/lkLabTestPanelName	Retrieve LkLabTestPanelName Information
LookupOrControlledVocabularyApi	get_lk_locus_name	GET /api/lookup/lkLocusName	Retrieve LkLocusName Information
LookupOrControlledVocabularyApi	get_lk_mass_spectrometry_type	GET /api/lookup/lkMassSpectrometryType	Retrieve LkMassSpectrometryType Information
LookupOrControlledVocabularyApi	get_lk_organization	GET /api/lookup/lkOrganization	Retrieve LkOrganization Information
LookupOrControlledVocabularyApi	get_lk_personnel_role	GET /api/lookup/lkPersonnelRole	Retrieve LkPersonnelRole Information
LookupOrControlledVocabularyApi	get_lk_plate_type	GET /api/lookup/lkPlateType	Retrieve LkPlateType Information
LookupOrControlledVocabularyApi	get_lk_protein_name	GET /api/lookup/lkProteinName	Retrieve LkProteinName Information
LookupOrControlledVocabularyApi	get_lk_protocol_type	GET /api/lookup/lkProtocolType	Retrieve LkProtocolType Information
LookupOrControlledVocabularyApi	get_lk_public_repository	GET /api/lookup/lkPublicRepository	Retrieve LkPublicRepository Information
LookupOrControlledVocabularyApi	get_lk_race	GET /api/lookup/lkRace	Retrieve LkRace Information
LookupOrControlledVocabularyApi	get_lk_reagent_type	GET /api/lookup/lkReagentType	Retrieve LkReagentType Information
LookupOrControlledVocabularyApi	get_lk_research_focus	GET /api/lookup/lkResearchFocus	Retrieve LkResearchFocus Information
LookupOrControlledVocabularyApi	get_lk_sample_type	GET /api/lookup/lkSampleType	Retrieve LkSampleType Information
LookupOrControlledVocabularyApi	get_lk_source_type	GET /api/lookup/lkSourceType	Retrieve LkSourceType Information
LookupOrControlledVocabularyApi	get_lk_species	GET /api/lookup/lkSpecies	Retrieve LkSpecies Information
LookupOrControlledVocabularyApi	get_lk_study_file_type	GET /api/lookup/lkStudyFileType	Retrieve LkStudyFileType Information
LookupOrControlledVocabularyApi	get_lk_study_panel	GET /api/lookup/lkStudyPanel	Retrieve LkStudyPanel Information
LookupOrControlledVocabularyApi	get_lk_subject_location	GET /api/lookup/lkSubjectLocation	Retrieve LkSubjectLocation Information
LookupOrControlledVocabularyApi	get_lk_t0_event	GET /api/lookup/lkT0Event	Retrieve LkT0Event Information
LookupOrControlledVocabularyApi	get_lk_time_unit	GET /api/lookup/lkTimeUnit	Retrieve LkTimeUnit Information
LookupOrControlledVocabularyApi	get_lk_transcript_type	GET /api/lookup/lkTranscriptType	Retrieve LkTranscriptType Information
LookupOrControlledVocabularyApi	get_lk_unit_of_measure	GET /api/lookup/lkUnitOfMeasure	Retrieve LkUnitOfMeasure Information
LookupOrControlledVocabularyApi	get_lk_user_role_type	GET /api/lookup/lkUserRoleType	Retrieve LkUserRoleType Information
LookupOrControlledVocabularyApi	get_lk_virus_strain	GET /api/lookup/lkVirusStrain	Retrieve LkVirusStrain Information
LookupOrControlledVocabularyApi	get_lk_visibility_category	GET /api/lookup/lkVisibilityCategory	Retrieve LkVisibilityCategory Information
StudyDataApi	get_all_file_details_api	GET /api/study/filePath/{studyAccession}	Retrieve All File Path Information
StudyDataApi	get_protocol_file_details_api	GET /api/study/filePath/protocolFiles/{studyAccession}	Retrieve Protocol File Path Information
StudyDataApi	get_restricted_study_accessions	GET /api/study/getRestrictedStudyAccessions
StudyDataApi	get_result_file_details_api	GET /api/study/filePath/resultFiles/{studyAccession}	Retrieve Result File Path Information
StudyDataApi	get_study	GET /api/study/{studyAccession}	Retrieve Basic Study Information
StudyDataApi	get_study_adverse_event_api	GET /api/study/adverseEvent/{studyAccession}	Retrieve Study Adverse Event Information
StudyDataApi	get_study_arm_api	GET /api/study/arm/{studyAccession}	Retrieve Study Arm Information
StudyDataApi	get_study_condition_or_disease	GET /api/study/condition/{studyAccession}	Retrieve Study ConditionOrDisease
StudyDataApi	get_study_contract_program	GET /api/study/contract/{studyAccession}	Retrieve Study Contract and Program Information
StudyDataApi	get_study_experiment_api	GET /api/study/experiment/{studyAccession}	Retrieve Study Experiments
StudyDataApi	get_study_file_api	GET /api/study/file/{studyAccession}	Retrieve Study File Information
StudyDataApi	get_study_file_details_api	GET /api/study/filePath/studyFiles/{studyAccession}	Retrieve Study File Path Information
StudyDataApi	get_study_immune_exposure_api	GET /api/study/immuneExposure/{studyAccession}	Retrieve Study Subject Immune Exposure Information
StudyDataApi	get_study_inclusion_exclusion_api	GET /api/study/inclusionExclusion/{studyAccession}	Retrieve Study Inclusion/Exclusion critera
StudyDataApi	get_study_intervention_api	GET /api/study/intervention/{studyAccession}	Retrieve Study Subject Intervention Information
StudyDataApi	get_study_link	GET /api/study/link/{studyAccession}	Retrieve Study Links
StudyDataApi	get_study_personnel	GET /api/study/personnel/{studyAccession}	Retrieve Study Personnel Information
StudyDataApi	get_study_planned_visit	GET /api/study/plannedVisit/{studyAccession}	Retrieve Planned Visit Information
StudyDataApi	get_study_protocol	GET /api/study/protocol/{studyAccession}	Retrieve Protocol Information
StudyDataApi	get_study_pubmed	GET /api/study/pubmed/{studyAccession}	Retrieve Pubmed Information
StudyDataApi	get_study_subject_assessment_api	GET /api/study/assessment/{studyAccession}	Retrieve Study Subject Assessments
StudyDataApi	get_study_subject_bio_sample_api	GET /api/study/biosample/{studyAccession}	Retrieve Study Subject BioSample Information
StudyDataApi	get_study_subject_demographic_api	GET /api/study/demographic/{studyAccession}	Retrieve Study Subject Demographics
StudyDataApi	get_study_subject_exp_sample_api	GET /api/study/expsample/{studyAccession}	Retrieve Study Subject ExpSample Information
StudyDataApi	get_study_subject_lab_test_api	GET /api/study/labtest/{studyAccession}	Retrieve Study Subject Lab Tests
StudyDataApi	get_study_summary	GET /api/study/summary/{studyAccession}
StudyFileManifestApi	get_file_details	GET /api/study/manifest/{studyAccession}	Retrieve file manifest with DRS ID's for a study
StudyResultApi	get_elisa_result	GET /result/elisa	Retrieve ELISA results using filters
StudyResultApi	get_elispot_result	GET /result/elispot	Retrieve Elispot results using filters
StudyResultApi	get_fcs_analyzed_result	GET /result/fcsAnalyzed	Retrieve FcsAnalyzed results using filters
StudyResultApi	get_file_path	GET /result/filePath	Retrieve File Paths using filters
StudyResultApi	get_hai_result	GET /result/hai	Retrieve HAI results using filters
StudyResultApi	get_hla_typing_result	GET /result/hlaTyping	Retrieve HLA Typing results using filters
StudyResultApi	get_kir_typing_result	GET /result/kirTyping	Retrieve kIR Typing results using filters
StudyResultApi	get_mass_spectrometry_result	GET /result/massSpectrometryResult	Retrieve Mass Spectrometry results using filters
StudyResultApi	get_mbaa_result	GET /result/mbaa	Retrieve MBAA results using filters
StudyResultApi	get_neut_ab_titer_result	GET /result/neutAbTiter	Retrieve Neutralizing Antibody Titer results using filters
StudyResultApi	get_pcr_result	GET /result/pcr	Retrieve PCR results using filters
StudySearchApi	study_search	GET /api/search/study	Search studies
StudySearchApi	subject_search	GET /api/search/subject	Search subjects

Documentation For Models

• FileDetails
• FileDownloadURL
• FilterCriteriaFields
• LkAdverseEventSeverity
• LkAgeEvent
• LkAnalyte
• LkAncestralPopulation
• LkCellPopulation
• LkCellPopulationMarker
• LkCompoundRole
• LkCriterionCategory
• LkDataCompleteness
• LkDisease
• LkDiseaseStage
• LkEthnicity
• LkExpMeasurementTech
• LkExposureMaterial
• LkExposureProcess
• LkExpsampleResultSchema
• LkFileDetail
• LkGender
• LkHmdb
• LkLabTestName
• LkLabTestPanelName
• LkLocusName
• LkMassSpectrometryType
• LkOrganization
• LkPersonnelRole
• LkPlateType
• LkProteinName
• LkProtocolType
• LkPublicRepository
• LkRace
• LkReagentType
• LkResearchFocus
• LkSampleType
• LkSourceType
• LkSpecies
• LkStudyFileType
• LkStudyPanel
• LkSubjectLocation
• LkT0Event
• LkTimeUnit
• LkTranscriptType
• LkUnitOfMeasure
• LkUserRoleType
• LkVirusStrain
• LkVisibilityCategory
• MassSpectrometryResult
• ResultFilePath
• StudyAdverseEventApi
• StudyApi
• StudyArmApi
• StudyConditionOrDiseaseApi
• StudyContractProgramApi
• StudyExperimentApi
• StudyFileApi
• StudyFileDetailsApi
• StudyInclusionExclusionApi
• StudyLink
• StudyLinkApi
• StudyPersonnel
• StudyPersonnelApi
• StudyPlannedVisitApi
• StudyProtocolApi
• StudyPubmed
• StudyPubmedApi
• StudyPubmedId
• StudySubjectAssessmentsApi
• StudySubjectBioSampleApi
• StudySubjectDemographicsApi
• StudySubjectExpSampleApi
• StudySubjectImmuneExposureApi
• StudySubjectInterventionApi
• StudySubjectLabTestsApi
• StudySummary
• VElisaResult
• VElispotResult
• VFcsAnalyzedResult
• VHaiResult
• VHlaTypingResult
• VKirTypingResult
• VMbaaResult
• VNeutAbTiterResult
• VPcrResult
• VResultFilePath

Documentation For Authorization

Authentication schemes defined for the API:

immport-security

• Type: OAuth
• Flow: accessCode
• Authorization URL: https://www.immport.org/auth/oauth2/authorize
• Scopes:
• browse: Browse scope
• download: Download scope

Author

[e-mail]