hra-api-client 0.19.0

HRA-API

hra-api-client

This API provides programmatic access to data registered to the Human Reference Atlas (HRA). See the HuBMAP HRA Portal for details.

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

• API version: 0.19.0
• Package version: 0.19.0
• Generator version: 7.19.0
• Build package: org.openapitools.codegen.languages.PythonClientCodegen

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/x-atlas-consortia/hra-api.git

(you may need to run pip with root permission: sudo pip install git+https://github.com/x-atlas-consortia/hra-api.git)

Then import the package:

import hra_api_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 hra_api_client

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:

import hra_api_client
from hra_api_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://apps.humanatlas.io/api
# See configuration.py for a list of all supported configuration parameters.
configuration = hra_api_client.Configuration(
    host = "https://apps.humanatlas.io/api"
)



# Enter a context with an instance of the API client
with hra_api_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = hra_api_client.DsGraphApi(api_client)
    token = 'token_example' # str | Authentication token to use for authenticated searches (optional)

    try:
        # Get Atlas D2K Dataset Graph
        api_response = api_instance.atlas_d2k(token=token)
        print("The response of DsGraphApi->atlas_d2k:\n")
        pprint(api_response)
    except ApiException as e:
        print("Exception when calling DsGraphApi->atlas_d2k: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to https://apps.humanatlas.io/api

Class	Method	HTTP request	Description
DsGraphApi	atlas_d2k	GET /ds-graph/atlas-d2k	Get Atlas D2K Dataset Graph
DsGraphApi	gtex	GET /ds-graph/gtex	Get GTEx Dataset Graph
DsGraphApi	hubmap	GET /ds-graph/hubmap	Get HuBMAP Dataset Graph
DsGraphApi	sennet	GET /ds-graph/sennet	Get SenNet Dataset Graph
HraKgApi	asctb_term_occurences	GET /kg/asctb-term-occurences	Get number of ASCT+B term occurrences for a search
HraKgApi	digital_objects	GET /kg/digital-objects	List all digital objects in the HRA KG
HraKgApi	do_search	GET /kg/do-search	Search for Digital Object PURLs
HraPopApi	cell_summary_report	POST /hra-pop/cell-summary-report	Given a cell summary in csv format, retrieve a predicted cell summary report from HRApop showing relative anatomical structures, datasets, and rui locations.
HraPopApi	rui_location_cell_summary	POST /hra-pop/rui-location-cell-summary	Given a SpatialEntity already placed relative to a reference SpatialEntity, retrieve a predicted cell summary from HRApop
HraPopApi	supported_organs	GET /hra-pop/supported-organs	Get all organs supported by HRApop
HraPopApi	supported_reference_organs	GET /hra-pop/supported-reference-organs	Get all reference organs supported by HRApop
HraPopApi	supported_tools	GET /hra-pop/supported-tools	Get all tools supported by HRApop
V1Api	aggregate_results	GET /v1/aggregate-results	Get aggregate results / statistics
V1Api	anatomical_systems_tree_model	GET /v1/anatomical-systems-tree-model	Get anatomical systems partonomy tree nodes
V1Api	asctb_omap_sheet_config	GET /v1/asctb-omap-sheet-config	Get OMAP sheet config data for the ASCT+B Reporter
V1Api	asctb_sheet_config	GET /v1/asctb-sheet-config	Get sheet config data for the ASCT+B Reporter
V1Api	biomarker_term_occurences	GET /v1/biomarker-term-occurences	Get number of biomarker type term occurrences for a search
V1Api	biomarker_tree_model	GET /v1/biomarker-tree-model	Get biomarker tree nodes
V1Api	cell_type_term_occurences	GET /v1/cell-type-term-occurences	Get number of cell type term occurrences for a search
V1Api	cell_type_tree_model	GET /v1/cell-type-tree-model	Get cell type tree nodes
V1Api	collisions	POST /v1/collisions	Given an extraction site, get mesh-based collisions with the reference organ.
V1Api	consortium_names	GET /v1/consortium-names	Get consortium names (for filtering)
V1Api	corridor	POST /v1/corridor	Given an extraction site, generate a corridor with the reference organ.
V1Api	db_status	GET /v1/db-status	Get current status of database
V1Api	ds_graph	GET /v1/ds-graph	Get dataset graph
V1Api	extraction_site	GET /v1/extraction-site	Lookup Extraction Site
V1Api	ftu_illustrations	GET /v1/ftu-illustrations	Get 2D FTU Illustration data
V1Api	get_spatial_placement	POST /v1/get-spatial-placement	Given a SpatialEntity already placed relative to a reference SpatialEntity, retrieve a new direct SpatialPlacement to the given SpatialEntity IRI
V1Api	gtex_rui_locations	GET /v1/gtex/rui_locations.jsonld	Get all GTEx rui locations (if enabled)
V1Api	hubmap_rui_locations	GET /v1/hubmap/rui_locations.jsonld	Get all hubmap rui locations (if enabled)
V1Api	mesh3d_cell_population	POST /v1/mesh-3d-cell-population	Given a reference organ, 3d scene node, and cell population, generate cells in that distribution to fit in that 3d scene node.
V1Api	ontology_term_occurences	GET /v1/ontology-term-occurences	Get number of ontology term occurrences for a search
V1Api	ontology_tree_model	GET /v1/ontology-tree-model	Get ontology term tree nodes
V1Api	provider_names	GET /v1/provider-names	Get tissue provider names (for filtering)
V1Api	reference_organ_scene	GET /v1/reference-organ-scene	Get all nodes to form the 3D scene for an organ
V1Api	reference_organs	GET /v1/reference-organs	Get all reference organs
V1Api	rui_reference_data	GET /v1/rui-reference-data	Get reference data for the RUI tool
V1Api	scene	GET /v1/scene	Get all nodes to form the 3D scene of reference body, organs, and tissues
V1Api	sennet_rui_locations	GET /v1/sennet/rui_locations.jsonld	Get all sennet rui locations (if enabled)
V1Api	session_token	POST /v1/session-token	Get a session token
V1Api	sparql	GET /v1/sparql	Run a SPARQL query
V1Api	sparql_post	POST /v1/sparql	Run a SPARQL query (POST)
V1Api	technology_names	GET /v1/technology-names	Get technology names (for filtering)
V1Api	tissue_blocks	GET /v1/tissue-blocks	Get Tissue Block Results

Documentation For Models

• AggregateCount
• CellSummaryReport
• CellSummaryReportRequest
• CellSummaryRow
• DatabaseStatus
• DigitalObjectInfo
• DigitalObjectsJsonLd
• ErrorMessage
• ErrorMessageObject
• Filter
• FlatSpatialPlacement
• GetSpatialPlacementRequest
• IdLabelPair
• JsonLdObject
• Mesh3dCellPopulationRequest
• MinMax
• OntologyTree
• OntologyTreeNode
• SessionToken
• SessionTokenRequest
• SourceSimilarityRow
• SpacialPlacementSource
• SpacialPlacementTarget
• SparqlQueryRequest
• SpatialEntity
• SpatialEntityCommon
• SpatialEntityCreator
• SpatialEntityDimensions
• SpatialEntityPlacement
• SpatialObjectReference
• SpatialPlacement
• SpatialPlacementCommon
• SpatialPlacementRotation
• SpatialPlacementScaling
• SpatialPlacementTranslation
• SpatialSceneNode
• SpatialSearch
• TissueBlock
• TissueCommon
• TissueDataset
• TissueDonor
• TissueSampleCommon
• TissueSection

Documentation For Authorization

Endpoints do not require authorization.

Author

[e-mail]