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odm-api

This swagger page describes the variantUser API endpoints for ODM. These are typically used to find and retrieve variant data and metadata.

Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.

To try out calls in this swagger page:

  1. Click the 'Authorize' button below to enter your API token
  2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
  3. Enter parameter values that you wish to try
  4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears

The server response will be in the section that follows.

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

  • API version: default-released
  • Package version: 1.62.5
  • Generator version: 7.20.0
  • 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/genestack/openapi.git
(you may need to run pip with root permission: sudo pip install git+https://github.com/genestack/openapi.git)

Then import the package: 

import odm_api

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 odm_api

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:

import odm_api
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# 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 API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'


# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.CellIntegrationAsCuratorApi(api_client)
    source_id = 'source_id_example' # str | The ID (accession) of the cell group object
    target_id = 'target_id_example' # str | The ID (accession) of the library group object

    try:
        # Create links between cells and libraries
        api_instance.create_cell_group_library_group_link_as_curator(source_id, target_id)
    except ApiException as e:
        print("Exception when calling CellIntegrationAsCuratorApi->create_cell_group_library_group_link_as_curator: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to http://localhost

Class Method HTTP request Description
CellIntegrationAsCuratorApi create_cell_group_library_group_link_as_curator POST /api/v1/as-curator/integration/link/cell/group/{sourceId}/to/library/group/{targetId} Create links between cells and libraries
CellIntegrationAsCuratorApi create_cell_group_preparation_group_link_as_curator POST /api/v1/as-curator/integration/link/cell/group/{sourceId}/to/preparation/group/{targetId} Create links between cells and preparations
CellIntegrationAsCuratorApi create_cell_group_sample_group_link_as_curator POST /api/v1/as-curator/integration/link/cell/group/{sourceId}/to/sample/group/{targetId} Create links between cells and samples
CellsAsCuratorApi get_cell_by_id_as_curator GET /api/v1/as-curator/cells/{id} Retrieve a cell by ID
CellsAsCuratorApi get_cells_by_group_as_curator GET /api/v1/as-curator/cells/by/group/{id} Retrieve cells from a given group
CellsAsUserApi get_cell_by_id_as_user GET /api/v1/as-user/cells/{id} Retrieve a cell by ID
CellsAsUserApi get_cells_by_group_as_user GET /api/v1/as-user/cells/by/group/{id} Retrieve cells from a given group
DataImportJobsApi start_import_a_file POST /api/v1/jobs/import/file Import file as an attachment
DataImportJobsApi start_import_cells POST /api/v1/jobs/import/cells Import a group of cell data objects from a TSV file
DataImportJobsApi start_import_expression POST /api/v1/jobs/import/expression Import any tabular data from TSV or GCT files
DataImportJobsApi start_import_flow_cytometry POST /api/v1/jobs/import/flow-cytometry Import flow-cytometry data and metadata from FACS and TSV files
DataImportJobsApi start_import_libraries POST /api/v1/jobs/import/libraries Import a group of library metadata objects from a TSV file
DataImportJobsApi start_import_preparations POST /api/v1/jobs/import/preparations Import a group of preparation metadata objects from a TSV file
DataImportJobsApi start_import_samples POST /api/v1/jobs/import/samples Import a group of sample metadata objects from a TSV file
DataImportJobsApi start_import_study POST /api/v1/jobs/import/study Import study metadata from a TSV file
DataImportJobsApi start_import_variant POST /api/v1/jobs/import/variant Import variation data and metadata from VCF and TSV files
DataImportViaDirectFileUploadApi start_import_a_file_multipart POST /api/v1/jobs/import/file/multipart Import a file as an attachment, optionally with a separate TSV metadata file via multipart/form-data upload
DataImportViaDirectFileUploadApi start_import_cells_multipart POST /api/v1/jobs/import/cells/multipart Import a group of cell data objects from a TSV file via multipart/form-data upload
DataImportViaDirectFileUploadApi start_import_expression_multipart POST /api/v1/jobs/import/expression/multipart Import a TSV file containing any tabular data, optionally with a separate TSV metadata file via multipart/form-data upload
DataImportViaDirectFileUploadApi start_import_flow_cytometry_multipart POST /api/v1/jobs/import/flow-cytometry/multipart Import a FACS file containing flow-cytometry data, optionally with a separate TSV metadata file via multipart/form-data upload
DataImportViaDirectFileUploadApi start_import_libraries_multipart POST /api/v1/jobs/import/libraries/multipart Import a group of library metadata objects from a TSV file via multipart/form-data upload
DataImportViaDirectFileUploadApi start_import_preparations_multipart POST /api/v1/jobs/import/preparations/multipart Import a group of preparation metadata objects from a TSV file via multipart/form-data upload
DataImportViaDirectFileUploadApi start_import_samples_multipart POST /api/v1/jobs/import/samples/multipart Import a group of sample metadata objects from a TSV file via multipart/form-data upload
DataImportViaDirectFileUploadApi start_import_variant_multipart POST /api/v1/jobs/import/variant/multipart Import a VCF file containing variant data, optionally with a separate TSV metadata file via multipart/form-data
ExpressionSPoTAsCuratorApi get_expression_as_curator GET /api/v1/as-curator/expressions/{id} Retrieve a single expression object by ID (itemId)
ExpressionSPoTAsCuratorApi get_expression_by_version_as_curator GET /api/v1/as-curator/expressions/{id}/versions/{version} Retrieve a single expression object by run ID and its version
ExpressionSPoTAsCuratorApi get_expression_data_as_curator GET /api/v1/as-curator/expressions Retrieve multiple expression data and metadata objects
ExpressionSPoTAsCuratorApi get_expression_group_as_curator GET /api/v1/as-curator/expressions/group/{id} Retrieve a single expression group by ID (groupId)
ExpressionSPoTAsCuratorApi get_expression_group_by_run_as_curator GET /api/v1/as-curator/expressions/group/by/run/{id} Retrieve a single group object by run ID (runId)
ExpressionSPoTAsCuratorApi get_expression_versions_as_curator GET /api/v1/as-curator/expressions/{id}/versions Retrieve a list of expression object versions by run ID (runId)
ExpressionSPoTAsCuratorApi search_expression_groups_as_curator GET /api/v1/as-curator/expressions/group Retrieve groups that match a query
ExpressionSPoTAsCuratorApi search_expression_runs_as_curator GET /api/v1/as-curator/expressions/runs/by/group/{id} Retrieve run objects related to the given group
ExpressionSPoTAsCuratorApi update_expression_run_as_curator PATCH /api/v1/as-curator/expressions/{id} Update metadata object by expression object run ID (runId)
ExpressionSPoTAsUserApi get_expression_as_user GET /api/v1/as-user/expressions/{id} Retrieve a single expression object by ID (itemId)
ExpressionSPoTAsUserApi get_expression_by_version_as_user GET /api/v1/as-user/expressions/{id}/versions/{version} Retrieve a single expression object by run ID and its version
ExpressionSPoTAsUserApi get_expression_data_as_user GET /api/v1/as-user/expressions Retrieve multiple expression data and metadata objects
ExpressionSPoTAsUserApi get_expression_group_as_user GET /api/v1/as-user/expressions/group/{id} Retrieve a single expression group by ID (groupId)
ExpressionSPoTAsUserApi get_expression_group_by_run_as_user GET /api/v1/as-user/expressions/group/by/run/{id} Retrieve a single group object by run ID (runId)
ExpressionSPoTAsUserApi get_expression_versions_as_user GET /api/v1/as-user/expressions/{id}/versions Retrieve a list of expression object versions by run ID (runId)
ExpressionSPoTAsUserApi search_expression_groups_as_user GET /api/v1/as-user/expressions/group Retrieve groups that match a query
ExpressionSPoTAsUserApi search_expression_runs_as_user GET /api/v1/as-user/expressions/runs/by/group/{id} Retrieve run objects related to the given group
ExpressionIntegrationAsCuratorApi create_expression_group_cell_group_link_as_curator POST /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/cell/group/{targetId} Create a link between a group of cell expression objects and a group of cell metadata.
ExpressionIntegrationAsCuratorApi create_expression_group_library_group_link_as_curator POST /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/library/group/{targetId} Create a link between a group of expression objects and a group of library objects
ExpressionIntegrationAsCuratorApi create_expression_group_preparation_group_link_as_curator POST /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/preparation/group/{targetId} Create a link between a group of expression objects and a group of preparation objects
ExpressionIntegrationAsCuratorApi create_expression_group_sample_group_link_as_curator POST /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/sample/group/{targetId} Create a link between a group of expression objects and a group of sample objects
ExpressionIntegrationAsCuratorApi create_expression_library_link_as_curator POST /api/v1/as-curator/integration/link/expression/{sourceId}/to/library/{targetId} Create a link between an expression object and a library
ExpressionIntegrationAsCuratorApi create_expression_preparation_link_as_curator POST /api/v1/as-curator/integration/link/expression/{sourceId}/to/preparation/{targetId} Create a link between an expression object and a preparation
ExpressionIntegrationAsCuratorApi create_expression_sample_link_as_curator POST /api/v1/as-curator/integration/link/expression/{sourceId}/to/sample/{targetId} Create a link between an expression object and a sample
ExpressionIntegrationAsCuratorApi delete_expression_group_library_group_link_as_curator DELETE /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/library/group/{targetId} Delete link between a group of expression objects and a group of library objects
ExpressionIntegrationAsCuratorApi delete_expression_group_preparation_group_link_as_curator DELETE /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/preparation/group/{targetId} Delete link between a group of expression objects and a group of preparation objects
ExpressionIntegrationAsCuratorApi delete_expression_group_sample_group_link_as_curator DELETE /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/sample/group/{targetId} Delete link between a group of expression objects and a group of sample objects
ExpressionIntegrationAsCuratorApi delete_expression_library_link_as_curator DELETE /api/v1/as-curator/integration/link/expression/{sourceId}/to/library/{targetId} Delete link between an expression object and a library
ExpressionIntegrationAsCuratorApi delete_expression_preparation_link_as_curator DELETE /api/v1/as-curator/integration/link/expression/{sourceId}/to/preparation/{targetId} Delete link between an expression object and a preparation
ExpressionIntegrationAsCuratorApi delete_expression_sample_link_as_curator DELETE /api/v1/as-curator/integration/link/expression/{sourceId}/to/sample/{targetId} Delete link between an expression object and a sample
ExpressionIntegrationAsCuratorApi get_expression_by_library_as_curator GET /api/v1/as-curator/integration/link/expression/by/library/{id} Retrieve expression run-level data by querying related library ID (accession)
ExpressionIntegrationAsCuratorApi get_expression_by_preparation GET /api/v1/as-curator/integration/link/expression/by/preparation/{id} Retrieve expression run-level data by querying related preparation ID (accession)
ExpressionIntegrationAsCuratorApi get_expression_by_sample_as_curator GET /api/v1/as-curator/integration/link/expression/by/sample/{id} Retrieve expression run-level data by querying related sample ID (accession)
ExpressionIntegrationAsCuratorApi get_expression_groups_by_study_as_curator GET /api/v1/as-curator/integration/link/expression/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
ExpressionIntegrationAsCuratorApi get_expression_run_to_library_pairs_as_curator GET /api/v1/as-curator/integration/link/expression/run-to-libraries/by/group/{id} Retrieve run-library pairs by group id. Pagination is based on unique runs, not unique pairs.
ExpressionIntegrationAsCuratorApi get_expression_run_to_preparation_pairs_as_curator GET /api/v1/as-curator/integration/link/expression/run-to-preparations/by/group/{id} Retrieve run-preparation pairs by group id. Pagination is based on unique runs, not unique pairs.
ExpressionIntegrationAsCuratorApi get_expression_run_to_sample_pairs_as_curator GET /api/v1/as-curator/integration/link/expression/run-to-samples/by/group/{id} Retrieve run-sample pairs by group id. Pagination is based on unique runs, not unique pairs.
ExpressionIntegrationAsUserApi get_expression_by_library_as_user GET /api/v1/as-user/integration/link/expression/by/library/{id} Retrieve expression run-level data by querying related library ID (accession)
ExpressionIntegrationAsUserApi get_expression_by_preparation_as_user GET /api/v1/as-user/integration/link/expression/by/preparation/{id} Retrieve expression run-level data by querying related preparation ID (accession)
ExpressionIntegrationAsUserApi get_expression_by_sample_as_user GET /api/v1/as-user/integration/link/expression/by/sample/{id} Retrieve expression run-level data by querying related sample ID (accession)
ExpressionIntegrationAsUserApi get_expression_groups_by_study_as_user GET /api/v1/as-user/integration/link/expression/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
ExpressionIntegrationAsUserApi get_expression_run_to_library_pairs_as_user GET /api/v1/as-user/integration/link/expression/run-to-libraries/by/group/{id} Retrieve run-library pairs by group id. Pagination is based on unique runs, not unique pairs.
ExpressionIntegrationAsUserApi get_expression_run_to_preparation_pairs_as_user GET /api/v1/as-user/integration/link/expression/run-to-preparations/by/group/{id} Retrieve run-preparation pairs by group id. Pagination is based on unique runs, not unique pairs.
ExpressionIntegrationAsUserApi get_expression_run_to_sample_pairs_as_user GET /api/v1/as-user/integration/link/expression/run-to-samples/by/group/{id} Retrieve run-sample pairs by group id. Pagination is based on unique runs, not unique pairs.
FilesAsCuratorApi get_file_as_curator GET /api/v1/as-curator/files/{id}/download Retrieve a file by ID (accession)
FilesAsCuratorApi get_file_metadata_by_id_as_curator GET /api/v1/as-curator/files/{id} Retrieve file's metadata by ID (accession)
FilesAsCuratorApi get_files_metadata_as_curator GET /api/v1/as-curator/files Retrieve file's metadata by its fields
FilesAsCuratorApi head_file_as_curator HEAD /api/v1/as-curator/files/{id}/download
FilesAsUserApi get_file_as_user GET /api/v1/as-user/files/{id}/download Retrieve a file by ID (accession)
FilesAsUserApi get_file_metadata_by_id_as_user GET /api/v1/as-user/files/{id} Retrieve file's metadata by ID (accession)
FilesAsUserApi get_files_metadata_as_user GET /api/v1/as-user/files Retrieve file's metadata by its fields
FilesAsUserApi head_file_as_user HEAD /api/v1/as-user/files/{id}/download Check if a file exists by ID (accession).
FilesIntegrationAsCuratorApi get_files_by_study_as_curator GET /api/v1/as-curator/integration/link/files/by/study/{id} Retrieve file's metadata by study ID
FilesIntegrationAsUserApi get_files_by_study_as_user GET /api/v1/as-user/integration/link/files/by/study/{id} Retrieve file's metadata by study ID
FlowCytometrySPoTAsCuratorApi get_flow_cytometry_as_curator GET /api/v1/as-curator/flow-cytometries/{id} Retrieve a single sample flow cytometry by ID (accession)
FlowCytometrySPoTAsCuratorApi get_flow_cytometry_by_version_as_curator GET /api/v1/as-curator/flow-cytometries/{id}/versions/{version} Retrieve a single sample flow cytometry by ID (accession)
FlowCytometrySPoTAsCuratorApi get_flow_cytometry_data_as_curator GET /api/v1/as-curator/flow-cytometries Retrieve multiple flow cytometry data and metadata objects
FlowCytometrySPoTAsCuratorApi get_flow_cytometry_group_as_curator GET /api/v1/as-curator/flow-cytometries/group/{id} Retrieve a single group object by ID (accession)
FlowCytometrySPoTAsCuratorApi get_flow_cytometry_group_by_run_as_curator GET /api/v1/as-curator/flow-cytometries/group/by/run/{id} Retrieve a single group object by run ID (accession)
FlowCytometrySPoTAsCuratorApi get_flow_cytometry_versions_as_curator GET /api/v1/as-curator/flow-cytometries/{id}/versions Retrieve a list of object versions by ID
FlowCytometrySPoTAsCuratorApi search_flow_cytometry_groups_as_curator GET /api/v1/as-curator/flow-cytometries/group Retrieve groups that match a query
FlowCytometrySPoTAsCuratorApi search_flow_cytometry_runs_as_curator GET /api/v1/as-curator/flow-cytometries/runs/by/group/{id} Retrieve run objects related to the given group
FlowCytometrySPoTAsCuratorApi update_flow_cytometry_as_curator PATCH /api/v1/as-curator/flow-cytometries/{id} Update object metadata
FlowCytometrySPoTAsUserApi get_flow_cytometry_as_user GET /api/v1/as-user/flow-cytometries/{id} Retrieve a single sample flow cytometry by ID (accession)
FlowCytometrySPoTAsUserApi get_flow_cytometry_by_version_as_user GET /api/v1/as-user/flow-cytometries/{id}/versions/{version} Retrieve a single sample flow cytometry by ID (accession)
FlowCytometrySPoTAsUserApi get_flow_cytometry_data_as_user GET /api/v1/as-user/flow-cytometries Retrieve multiple flow cytometry data and metadata objects
FlowCytometrySPoTAsUserApi get_flow_cytometry_group_as_user GET /api/v1/as-user/flow-cytometries/group/{id} Retrieve a single group object by ID (accession)
FlowCytometrySPoTAsUserApi get_flow_cytometry_group_by_run_as_user GET /api/v1/as-user/flow-cytometries/group/by/run/{id} Retrieve a single group object by run ID (accession)
FlowCytometrySPoTAsUserApi get_flow_cytometry_versions_as_user GET /api/v1/as-user/flow-cytometries/{id}/versions Retrieve a list of object versions by ID
FlowCytometrySPoTAsUserApi search_flow_cytometry_groups_as_user GET /api/v1/as-user/flow-cytometries/group Retrieve groups that match a query
FlowCytometrySPoTAsUserApi search_flow_cytometry_runs_as_user GET /api/v1/as-user/flow-cytometries/runs/by/group/{id} Retrieve run objects related to the given group
FlowCytometryFACSIntegrationAsCuratorApi create_flow_cytometry_group_sample_group_link_as_curator POST /api/v1/as-curator/integration/link/flow-cytometry/group/{sourceId}/to/sample/group/{targetId} Create a link between a group of flow-cytometry objects and a group of sample objects
FlowCytometryFACSIntegrationAsCuratorApi create_flow_cytometry_sample_link_as_curator POST /api/v1/as-curator/integration/link/flow-cytometry/{sourceId}/to/sample/{targetId} Create a link between a flow-cytometry object and a sample
FlowCytometryFACSIntegrationAsCuratorApi delete_flow_cytometry_group_sample_group_link_as_curator DELETE /api/v1/as-curator/integration/link/flow-cytometry/group/{sourceId}/to/sample/group/{targetId} Delete link between a group of flow-cytometry objects and a group of sample objects
FlowCytometryFACSIntegrationAsCuratorApi delete_flow_cytometry_sample_link_as_curator DELETE /api/v1/as-curator/integration/link/flow-cytometry/{sourceId}/to/sample/{targetId} Delete link between a flow-cytometry object and a sample
FlowCytometryFACSIntegrationAsCuratorApi get_flow_cytometry_by_sample_as_curator GET /api/v1/as-curator/integration/link/flow-cytometry/by/sample/{id} Retrieve flow cytometry run-level data by querying related sample ID (accession)
FlowCytometryFACSIntegrationAsCuratorApi get_flow_cytometry_groups_by_study_as_curator GET /api/v1/as-curator/integration/link/flow-cytometry/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
FlowCytometryFACSIntegrationAsCuratorApi get_flow_cytometry_run_to_sample_pairs_as_curator GET /api/v1/as-curator/integration/link/flow-cytometry/run-to-samples/by/group/{id} Retrieve run-sample pairs by group id. Pagination is based on unique runs, not unique pairs.
FlowCytometryFACSIntegrationAsUserApi get_flow_cytometry_by_sample_as_user GET /api/v1/as-user/integration/link/flow-cytometry/by/sample/{id} Retrieve flow cytometry run-level data by querying related sample ID (accession)
FlowCytometryFACSIntegrationAsUserApi get_flow_cytometry_groups_by_study_as_user GET /api/v1/as-user/integration/link/flow-cytometry/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
FlowCytometryFACSIntegrationAsUserApi get_flow_cytometry_run_to_sample_pairs_as_user GET /api/v1/as-user/integration/link/flow-cytometry/run-to-samples/by/group/{id} Retrieve run-sample pairs by group id. Pagination is based on unique runs, not unique pairs.
GroupsApi create_group POST /api/v1/scim/Groups Add a new user group
GroupsApi delete_group DELETE /api/v1/scim/Groups/{id} Delete a group
GroupsApi find_groups GET /api/v1/scim/Groups Retrieve a list of available groups
GroupsApi get_group GET /api/v1/scim/Groups/{id} Retrieve a group by id
GroupsApi patch_group PATCH /api/v1/scim/Groups/{id} Update a group
JobOperationsApi info GET /api/v1/jobs/{jobExecId}/info get information about one particular job execution
JobOperationsApi output GET /api/v1/jobs/{jobExecId}/output retrieve job output (result)
JobOperationsApi restart PUT /api/v1/jobs/{jobExecId}/restart restart stopped (failed) job
JobOperationsApi stop PUT /api/v1/jobs/{jobExecId}/stop stop running job
LibrarySPoTAsCuratorApi get_libraries_by_group_as_curator GET /api/v1/as-curator/libraries/by/group/{id} Retrieve libraries related to the given group
LibrarySPoTAsCuratorApi get_library_as_curator GET /api/v1/as-curator/libraries/{id} Retrieve a single library object by ID (accession)
LibrarySPoTAsCuratorApi get_library_by_version_as_curator GET /api/v1/as-curator/libraries/{id}/versions/{version} Retrieve a single library object by ID (accession)
LibrarySPoTAsCuratorApi get_library_versions_as_curator GET /api/v1/as-curator/libraries/{id}/versions Retrieve a list of object versions by ID
LibrarySPoTAsCuratorApi search_libraries_as_curator GET /api/v1/as-curator/libraries List or search for library metadata objects
LibrarySPoTAsCuratorApi update_library_as_curator PATCH /api/v1/as-curator/libraries/{id} Update a library object
LibrarySPoTAsUserApi get_libraries_by_group_as_user GET /api/v1/as-user/libraries/by/group/{id} Retrieve libraries related to the given group
LibrarySPoTAsUserApi get_library_as_user GET /api/v1/as-user/libraries/{id} Retrieve a single library object by ID (accession)
LibrarySPoTAsUserApi get_library_by_version_as_user GET /api/v1/as-user/libraries/{id}/versions/{version} Retrieve a single library object by ID (accession)
LibrarySPoTAsUserApi get_library_versions_as_user GET /api/v1/as-user/libraries/{id}/versions Retrieve a list of object versions by ID
LibrarySPoTAsUserApi search_libraries_as_user GET /api/v1/as-user/libraries List or search for library metadata objects
LibraryIntegrationAsCuratorApi create_library_group_sample_group_link_as_curator POST /api/v1/as-curator/integration/link/library/group/{sourceId}/to/sample/group/{targetId} Create links between samples and libraries
LibraryIntegrationAsCuratorApi create_library_sample_link_as_curator POST /api/v1/as-curator/integration/link/library/{sourceId}/to/sample/{targetId} Create a link between a library and a sample
LibraryIntegrationAsCuratorApi delete_library_group_sample_group_link_as_curator DELETE /api/v1/as-curator/integration/link/library/group/{sourceId}/to/sample/group/{targetId} Delete links between samples and libraries related to the specified group
LibraryIntegrationAsCuratorApi delete_library_sample_link_as_curator DELETE /api/v1/as-curator/integration/link/library/{sourceId}/to/sample/{targetId} Delete a link between a library and a sample
LibraryIntegrationAsCuratorApi get_libraries_by_samples_as_curator GET /api/v1/as-curator/integration/link/libraries/by/samples Retrieve library metadata by querying related samples
LibraryIntegrationAsCuratorApi get_library_by_sample_as_curator GET /api/v1/as-curator/integration/link/library/by/sample/{id} Retrieve library metadata by querying related sample ID (accession)
LibraryIntegrationAsCuratorApi get_library_groups_by_study_as_curator GET /api/v1/as-curator/integration/link/library/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
LibraryIntegrationAsCuratorApi get_library_links_to_samples_as_curator GET /api/v1/as-curator/integration/link/library/libraries-to-samples/by/group/{id} Retrieve library-samples pairs by group id. Pagination is based on unique libraries, not unique pairs.
LibraryIntegrationAsUserApi get_libraries_by_samples_as_user GET /api/v1/as-user/integration/link/libraries/by/samples Retrieve library metadata by querying related samples
LibraryIntegrationAsUserApi get_library_by_sample_as_user GET /api/v1/as-user/integration/link/library/by/sample/{id} Retrieve library metadata by querying related sample ID (accession)
LibraryIntegrationAsUserApi get_library_groups_by_study_as_user GET /api/v1/as-user/integration/link/library/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
LibraryIntegrationAsUserApi get_library_links_to_samples_as_user GET /api/v1/as-user/integration/link/library/libraries-to-samples/by/group/{id} Retrieve library-samples pairs by group id. Pagination is based on unique libraries, not unique pairs.
LinkageAsCuratorApi delete_link_as_curator DELETE /api/v1/as-curator/links Deletes existing links matching the specified criteria.
LinkageAsCuratorApi get_data_types_as_curator GET /api/v1/as-curator/data-types Lists all available data types.
LinkageAsCuratorApi get_data_types_links_as_curator GET /api/v1/as-curator/data-types/links List all possible links between data types that match the specified criteria.
LinkageAsCuratorApi get_links_by_ids_as_curator POST /api/v1/as-curator/links/get-batch Finds existing links by passing many IDs. Pagination goes through all links matched the criteria.
LinkageAsCuratorApi get_links_by_params_as_curator GET /api/v1/as-curator/links Finds existing links matching the specified criteria.
LinkageAsCuratorApi save_links_as_curator POST /api/v1/as-curator/links Creates new links between objects.
LinkageAsUserApi get_data_types_as_user GET /api/v1/as-user/data-types Lists all available data types.
LinkageAsUserApi get_data_types_links_as_user GET /api/v1/as-user/data-types/links List all possible links between data types that match the specified criteria.
LinkageAsUserApi get_links_by_ids_as_user POST /api/v1/as-user/links/get-batch Finds existing links by passing many IDs. Pagination goes through all links matched the criteria.
LinkageAsUserApi get_links_by_params_as_user GET /api/v1/as-user/links Finds existing links matching the specified criteria.
ManageDataApi delete_data DELETE /api/v1/manage-data/data Delete objects from ODM
ManageDataApi get_detached_objects GET /api/v1/manage-data/detached-objects Retrieve a list of detached objects
MetadataVersioningAsCuratorApi publish_study_by_accession_as_curator POST /api/v1/as-curator/integration/studies/{id}/tasks/publish-versions Asynchronous task that publishes all pending versions for a single study.
OmicsQueriesAsCuratorApi omics_search_cells_as_curator GET /api/v1/as-curator/omics/cells Retrieve Cell objects by searching across multiple data types
OmicsQueriesAsCuratorApi omics_search_cells_expression_data_as_curator GET /api/v1/as-curator/omics/cells/expression/data Retrieve cell expression objects by searching across multiple metadata types
OmicsQueriesAsCuratorApi omics_search_expression_data_as_curator GET /api/v1/as-curator/omics/expression/data Retrieve data objects by searching across multiple data types
OmicsQueriesAsCuratorApi omics_search_expression_groups_as_curator GET /api/v1/as-curator/omics/expression/group Retrieve group objects by searching across multiple data types
OmicsQueriesAsCuratorApi omics_search_flow_cytometry_data_as_curator GET /api/v1/as-curator/omics/flow-cytometry/data Retrieve flow cytometry data objects by searching across multiple data types
OmicsQueriesAsCuratorApi omics_search_flow_cytometry_groups_as_curator GET /api/v1/as-curator/omics/flow-cytometry/group Retrieve group objects by searching across multiple data types
OmicsQueriesAsCuratorApi omics_search_samples_as_curator GET /api/v1/as-curator/omics/samples Retrieve sample metadata objects by searching across multiple data types
OmicsQueriesAsCuratorApi omics_search_streamed_expression_data_as_curator GET /api/v1/as-curator/omics/expression/streamed-data Stream data from a given tabular file
OmicsQueriesAsCuratorApi omics_search_streamed_variant_data_as_curator GET /api/v1/as-curator/omics/variant/streamed-data Stream data from a given VCF file
OmicsQueriesAsCuratorApi omics_search_variant_data_as_curator GET /api/v1/as-curator/omics/variant/data Retrieve variant data objects by searching across multiple data types
OmicsQueriesAsCuratorApi omics_search_variant_groups_as_curator GET /api/v1/as-curator/omics/variant/group Retrieve group objects by searching across multiple data types
OmicsQueriesAsUserApi omics_search_cells_as_user GET /api/v1/as-user/omics/cells Retrieve Cell objects by searching across multiple data types
OmicsQueriesAsUserApi omics_search_cells_expression_data_as_user GET /api/v1/as-user/omics/cells/expression/data Retrieve cell expression objects by searching across multiple metadata types
OmicsQueriesAsUserApi omics_search_expression_data_as_user GET /api/v1/as-user/omics/expression/data Retrieve data objects by searching across multiple data types
OmicsQueriesAsUserApi omics_search_expression_groups_as_user GET /api/v1/as-user/omics/expression/group Retrieve group objects by searching across multiple data types
OmicsQueriesAsUserApi omics_search_flow_cytometry_data_as_user GET /api/v1/as-user/omics/flow-cytometry/data Retrieve flow cytometry data objects by searching across multiple data types
OmicsQueriesAsUserApi omics_search_flow_cytometry_groups_as_user GET /api/v1/as-user/omics/flow-cytometry/group Retrieve group objects by searching across multiple data types
OmicsQueriesAsUserApi omics_search_samples_as_user GET /api/v1/as-user/omics/samples Retrieve sample metadata objects by searching across multiple data types
OmicsQueriesAsUserApi omics_search_streamed_expression_data_as_user GET /api/v1/as-user/omics/expression/streamed-data Stream data from a given tabular file
OmicsQueriesAsUserApi omics_search_streamed_variant_data_as_user GET /api/v1/as-user/omics/variant/streamed-data Stream data from a given VCF file
OmicsQueriesAsUserApi omics_search_variant_data_as_user GET /api/v1/as-user/omics/variant/data Retrieve variant data objects by searching across multiple data types
OmicsQueriesAsUserApi omics_search_variant_groups_as_user GET /api/v1/as-user/omics/variant/group Retrieve group objects by searching across multiple data types
PreparationSPoTAsCuratorApi get_preparation_as_curator GET /api/v1/as-curator/preparations/{id} Retrieve a single preparation object by ID (accession)
PreparationSPoTAsCuratorApi get_preparation_by_version_as_curator GET /api/v1/as-curator/preparations/{id}/versions/{version} Retrieve a single preparation object by ID (accession)
PreparationSPoTAsCuratorApi get_preparation_versions_as_curator GET /api/v1/as-curator/preparations/{id}/versions Retrieve a list of object versions by ID
PreparationSPoTAsCuratorApi get_preparations_by_group_as_curator GET /api/v1/as-curator/preparations/by/group/{id} Retrieve preparations related to the given group
PreparationSPoTAsCuratorApi search_preparations_as_curator GET /api/v1/as-curator/preparations List or search for preparation metadata objects
PreparationSPoTAsCuratorApi update_preparation_as_curator PATCH /api/v1/as-curator/preparations/{id} Update a preparation object
PreparationSPoTAsUserApi get_preparation_as_user GET /api/v1/as-user/preparations/{id} Retrieve a single preparation object by ID (accession)
PreparationSPoTAsUserApi get_preparation_by_version_as_user GET /api/v1/as-user/preparations/{id}/versions/{version} Retrieve a single preparation object by ID (accession)
PreparationSPoTAsUserApi get_preparation_versions_as_user GET /api/v1/as-user/preparations/{id}/versions Retrieve a list of object versions by ID
PreparationSPoTAsUserApi get_preparations_by_group_as_user GET /api/v1/as-user/preparations/by/group/{id} Retrieve preparations related to the given group
PreparationSPoTAsUserApi search_preparations_as_user GET /api/v1/as-user/preparations List or search for preparation metadata objects
PreparationIntegrationAsCuratorApi create_preparation_group_sample_group_link_as_curator POST /api/v1/as-curator/integration/link/preparation/group/{sourceId}/to/sample/group/{targetId} Create links between samples and preparations
PreparationIntegrationAsCuratorApi create_preparation_sample_link_as_curator POST /api/v1/as-curator/integration/link/preparation/{sourceId}/to/sample/{targetId} Create a link between a preparation and a sample
PreparationIntegrationAsCuratorApi delete_preparation_group_sample_group_link_as_curator DELETE /api/v1/as-curator/integration/link/preparation/group/{sourceId}/to/sample/group/{targetId} Delete links between samples and preparations related to the specified group
PreparationIntegrationAsCuratorApi delete_preparation_sample_link_as_curator DELETE /api/v1/as-curator/integration/link/preparation/{sourceId}/to/sample/{targetId} Delete a link between a preparation and a sample
PreparationIntegrationAsCuratorApi get_preparation_by_sample_as_curator GET /api/v1/as-curator/integration/link/preparation/by/sample/{id} Retrieve preparation metadata by querying related sample ID (accession)
PreparationIntegrationAsCuratorApi get_preparation_groups_by_study_as_curator GET /api/v1/as-curator/integration/link/preparation/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
PreparationIntegrationAsCuratorApi get_preparation_links_to_samples_as_curator GET /api/v1/as-curator/integration/link/preparation/preparations-to-samples/by/group/{id} Retrieve run-sample pairs by group id. Pagination is based on unique preparations, not unique pairs.
PreparationIntegrationAsCuratorApi get_preparations_by_samples_as_curator GET /api/v1/as-curator/integration/link/preparations/by/samples Retrieve preparation metadata by querying related samples
PreparationIntegrationAsUserApi get_preparation_by_sample_as_user GET /api/v1/as-user/integration/link/preparation/by/sample/{id} Retrieve preparation metadata by querying related sample ID (accession)
PreparationIntegrationAsUserApi get_preparation_groups_by_study_as_user GET /api/v1/as-user/integration/link/preparation/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
PreparationIntegrationAsUserApi get_preparation_links_to_samples_as_user GET /api/v1/as-user/integration/link/preparation/preparations-to-samples/by/group/{id} Retrieve run-sample pairs by group id. Pagination is based on unique preparations, not unique pairs.
PreparationIntegrationAsUserApi get_preparations_by_samples_as_user GET /api/v1/as-user/integration/link/preparations/by/samples Retrieve preparation metadata by querying related samples
ReferenceGenomeApi get_reference_genome_by_accession GET /api/v1/reference-genomes/{id} Retrieve a single Reference Genome object by ID (accession)
ReferenceGenomeApi search_reference_genomes GET /api/v1/reference-genomes List or search for Reference Genome objects
ReferenceGenomeApi upload POST /api/v1/reference-genomes Upload reference genome to ODM
SampleSPoTAsCuratorApi get_sample_as_curator GET /api/v1/as-curator/samples/{id} Retrieve a single sample object by ID (accession)
SampleSPoTAsCuratorApi get_sample_by_version_as_curator GET /api/v1/as-curator/samples/{id}/versions/{version} Retrieve a single sample object by ID (accession)
SampleSPoTAsCuratorApi get_sample_versions_as_curator GET /api/v1/as-curator/samples/{id}/versions Retrieve a list of object versions by ID
SampleSPoTAsCuratorApi search_samples_as_curator GET /api/v1/as-curator/samples List or search for sample metadata objects
SampleSPoTAsCuratorApi update_sample_as_curator PATCH /api/v1/as-curator/samples/{id} Update a sample object
SampleSPoTAsUserApi get_sample_as_user GET /api/v1/as-user/samples/{id} Retrieve a single sample object by ID (accession)
SampleSPoTAsUserApi get_sample_by_version_as_user GET /api/v1/as-user/samples/{id}/versions/{version} Retrieve a single sample object by ID (accession)
SampleSPoTAsUserApi get_sample_versions_as_user GET /api/v1/as-user/samples/{id}/versions Retrieve a list of object versions by ID
SampleSPoTAsUserApi search_samples_as_user GET /api/v1/as-user/samples List or search for sample metadata objects
SampleIntegrationAsCuratorApi create_sample_group_study_link_as_curator POST /api/v1/as-curator/integration/link/sample/group/{sourceId}/to/study/{targetId} Create a link between a group of sample objects and a study
SampleIntegrationAsCuratorApi create_sample_study_link_as_curator POST /api/v1/as-curator/integration/link/sample/{sourceId}/to/study/{targetId} Create a link between a sample and a study
SampleIntegrationAsCuratorApi delete_sample_group_study_link_as_curator DELETE /api/v1/as-curator/integration/link/sample/group/{sourceId}/to/study/{targetId} Delete link between a group of sample objects and a study
SampleIntegrationAsCuratorApi delete_sample_study_link_as_curator DELETE /api/v1/as-curator/integration/link/sample/{sourceId}/to/study/{targetId} Delete link between a sample and a study
SampleIntegrationAsCuratorApi get_samples_by_libraries_as_curator GET /api/v1/as-curator/integration/link/samples/by/libraries Retrieve sample metadata by querying related libraries
SampleIntegrationAsCuratorApi get_samples_by_preparations_as_curator GET /api/v1/as-curator/integration/link/samples/by/preparations Retrieve sample metadata by querying related preparations
SampleIntegrationAsCuratorApi get_samples_by_study_as_curator GET /api/v1/as-curator/integration/link/samples/by/study/{id} Retrieve sample metadata by querying related study ID (accession)
SampleIntegrationAsUserApi get_samples_by_libraries_as_user GET /api/v1/as-user/integration/link/samples/by/libraries Retrieve sample metadata by querying related libraries
SampleIntegrationAsUserApi get_samples_by_preparations_as_user GET /api/v1/as-user/integration/link/samples/by/preparations Retrieve sample metadata by querying related preparations
SampleIntegrationAsUserApi get_samples_by_study_as_user GET /api/v1/as-user/integration/link/samples/by/study/{id} Retrieve sample metadata by querying related study ID (accession)
StudySPoTAsCuratorApi get_study_as_curator GET /api/v1/as-curator/studies/{id} Retrieve a single study object by ID (accession)
StudySPoTAsCuratorApi get_study_by_version_as_curator GET /api/v1/as-curator/studies/{id}/versions/{version} Retrieve a single study object by ID (accession)
StudySPoTAsCuratorApi get_study_versions_as_curator GET /api/v1/as-curator/studies/{id}/versions Retrieve a list of object versions by ID
StudySPoTAsCuratorApi search_studies_as_curator GET /api/v1/as-curator/studies List or search for study metadata objects
StudySPoTAsCuratorApi update_study_as_curator PATCH /api/v1/as-curator/studies/{id} Update a study object
StudySPoTAsUserApi get_study_as_user GET /api/v1/as-user/studies/{id} Retrieve a single study object by ID (accession)
StudySPoTAsUserApi get_study_by_version_as_user GET /api/v1/as-user/studies/{id}/versions/{version} Retrieve a single study object by ID (accession)
StudySPoTAsUserApi get_study_versions_as_user GET /api/v1/as-user/studies/{id}/versions Retrieve a list of object versions by ID
StudySPoTAsUserApi search_studies_as_user GET /api/v1/as-user/studies List or search for study metadata objects
StudyIntegrationAsCuratorApi get_studies_by_files_as_curator GET /api/v1/as-curator/integration/link/studies/by/files Retrieve study metadata objects by querying related attachment files
StudyIntegrationAsCuratorApi get_studies_by_libraries_as_curator GET /api/v1/as-curator/integration/link/studies/by/libraries Retrieve study metadata objects by querying related libraries
StudyIntegrationAsCuratorApi get_studies_by_preparations_as_curator GET /api/v1/as-curator/integration/link/studies/by/preparations Retrieve study metadata objects by querying related preparations
StudyIntegrationAsCuratorApi get_studies_by_samples_as_curator GET /api/v1/as-curator/integration/link/studies/by/samples Retrieve study metadata objects by querying related samples
StudyIntegrationAsCuratorApi get_study_by_file_as_curator GET /api/v1/as-curator/integration/link/study/by/file/{id} Retrieve study metadata by querying attachment file ID (accession)
StudyIntegrationAsCuratorApi get_study_by_sample_as_curator GET /api/v1/as-curator/integration/link/study/by/sample/{id} Retrieve study metadata by querying sample ID (accession)
StudyIntegrationAsCuratorApi search_studies_by_filter_as_curator POST /api/v1/as-curator/integration/fulltext/search/studies Find and retrieve studies by full-text or facet query
StudyIntegrationAsUserApi get_studies_by_files_as_user GET /api/v1/as-user/integration/link/studies/by/files Retrieve study metadata objects by querying related attachment files
StudyIntegrationAsUserApi get_studies_by_libraries_as_user GET /api/v1/as-user/integration/link/studies/by/libraries Retrieve study metadata objects by querying related libraries
StudyIntegrationAsUserApi get_studies_by_preparations_as_user GET /api/v1/as-user/integration/link/studies/by/preparations Retrieve study metadata objects by querying related preparations
StudyIntegrationAsUserApi get_studies_by_samples_as_user GET /api/v1/as-user/integration/link/studies/by/samples Retrieve study metadata objects by querying related samples
StudyIntegrationAsUserApi get_study_by_file_as_user GET /api/v1/as-user/integration/link/study/by/file/{id} Retrieve study metadata by querying attachment file ID (accession)
StudyIntegrationAsUserApi get_study_by_sample_as_user GET /api/v1/as-user/integration/link/study/by/sample/{id} Retrieve study metadata by querying sample ID (accession)
StudyIntegrationAsUserApi search_studies_by_filter_as_user POST /api/v1/as-user/integration/fulltext/search/studies Find and retrieve studies by full-text or facet query
TasksAPIApi get_task_info GET /api/v1/tasks/{id} Retrieve information about any ODM task.
TasksAPIApi publish_all_studies POST /api/v1/tasks/publish-versions Asynchronous task that publishes all pending versions across all studies in the instance.
TransformationConfigurationsApi delete_api_v1_transformations_configurations_by_id DELETE /api/v1/transformations/configurations/{id} Delete an existing transformation configuration.
TransformationConfigurationsApi get_api_v1_transformations_configurations_by_id GET /api/v1/transformations/configurations/{id} Get details of a specific transformation configuration.
TransformationConfigurationsApi list_api_v1_transformations_configurations GET /api/v1/transformations/configurations List available transformation configurations.
TransformationConfigurationsApi post_api_v1_transformations_configurations POST /api/v1/transformations/configurations Create a new transformation configuration.
TransformationConfigurationsApi put_api_v1_transformations_configurations_by_id PUT /api/v1/transformations/configurations/{id} Update an existing transformation configuration.
TransformationImagesApi list_api_v1_transformations_images GET /api/v1/transformations/images List available transformation images with their metadata.
TransformationJobsApi delete_api_v1_transformations_jobs_by_id DELETE /api/v1/transformations/jobs/{id} Delete a transformation job by ID.
TransformationJobsApi get_api_v1_transformations_jobs_by_id GET /api/v1/transformations/jobs/{id} Get details of a specific transformation job.
TransformationJobsApi list_api_v1_transformations_jobs GET /api/v1/transformations/jobs List submitted transformation jobs.
TransformationJobsApi post_api_v1_transformations_jobs POST /api/v1/transformations/jobs Submit a new transformation job with optional configuration and version.
TransformationJobsApi post_api_v1_transformations_jobs_by_id_logs POST /api/v1/transformations/jobs/{id}/logs Retrieve logs for a transformation job.
TransformationJobsApi post_api_v1_transformations_jobs_by_id_stop POST /api/v1/transformations/jobs/{id}/stop Stop a running transformation job.
UsersApi create_user POST /api/v1/scim/Users Add a new user
UsersApi delete_user DELETE /api/v1/scim/Users/{id} Deactivate a user
UsersApi find_users GET /api/v1/scim/Users Retrieve a list of all active users
UsersApi get_user GET /api/v1/scim/Users/{id} Retrieve a user by id
UsersApi patch_user PATCH /api/v1/scim/Users/{id} Update a user
ValidationSummaryAsCuratorApi get_study_validation_summary GET /api/v1/as-curator/integration/studies/{id}/validation-summary Retrieve validation summary by querying study ID (accession)
VariantSPoTAsCuratorApi get_all_variants_as_curator GET /api/v1/as-curator/variants Retrieve multiple variant data and metadata objects
VariantSPoTAsCuratorApi get_variant_as_curator GET /api/v1/as-curator/variants/{id} Retrieve a single variant object by ID (itemId)
VariantSPoTAsCuratorApi get_variant_by_version_as_curator GET /api/v1/as-curator/variants/{id}/versions/{version} Retrieve a single variant object by run ID and its version
VariantSPoTAsCuratorApi get_variant_group_as_curator GET /api/v1/as-curator/variants/group/{id} Retrieve a single variant group by ID (groupId)
VariantSPoTAsCuratorApi get_variant_group_by_run_as_curator GET /api/v1/as-curator/variants/group/by/run/{id} Retrieve a single group object by run ID (runId)
VariantSPoTAsCuratorApi get_variant_versions_as_curator GET /api/v1/as-curator/variants/{id}/versions Retrieve a list of variant object versions by run ID (runId)
VariantSPoTAsCuratorApi search_groups_as_curator GET /api/v1/as-curator/variants/group Retrieve groups that match a query
VariantSPoTAsCuratorApi search_variant_runs_as_curator GET /api/v1/as-curator/variants/runs/by/group/{id} Retrieve run objects related to the given group
VariantSPoTAsUserApi get_all_variants_as_user GET /api/v1/as-user/variants Retrieve multiple variant data and metadata objects
VariantSPoTAsUserApi get_variant_as_user GET /api/v1/as-user/variants/{id} Retrieve a single variant object by ID (itemId)
VariantSPoTAsUserApi get_variant_by_version_as_user GET /api/v1/as-user/variants/{id}/versions/{version} Retrieve a single variant object by run ID and its version
VariantSPoTAsUserApi get_variant_group_as_user GET /api/v1/as-user/variants/group/{id} Retrieve a single variant group by ID (groupId)
VariantSPoTAsUserApi get_variant_group_by_run_as_user GET /api/v1/as-user/variants/group/by/run/{id} Retrieve a single group object by run ID (runId)
VariantSPoTAsUserApi get_variant_versions_as_user GET /api/v1/as-user/variants/{id}/versions Retrieve a list of variant object versions by run ID (runId)
VariantSPoTAsUserApi search_variant_groups_as_user GET /api/v1/as-user/variants/group Retrieve groups that match a query
VariantSPoTAsUserApi search_variant_runs_as_user GET /api/v1/as-user/variants/runs/by/group/{id} Retrieve run objects related to the given group
VariantIntegrationAsCuratorApi create_variant_group_sample_group_link_as_curator POST /api/v1/as-curator/integration/link/variant/group/{sourceId}/to/sample/group/{targetId} Create a link between a group of variant objects and a group of sample objects
VariantIntegrationAsCuratorApi create_variant_sample_link_as_curator POST /api/v1/as-curator/integration/link/variant/{sourceId}/to/sample/{targetId} Create a link between a variant object and a sample
VariantIntegrationAsCuratorApi delete_variant_group_sample_group_link_as_curator DELETE /api/v1/as-curator/integration/link/variant/group/{sourceId}/to/sample/group/{targetId} Delete link between a group of variant objects and a group of sample objects
VariantIntegrationAsCuratorApi delete_variant_sample_link_as_curator DELETE /api/v1/as-curator/integration/link/variant/{sourceId}/to/sample/{targetId} Delete link between a variant object and a sample
VariantIntegrationAsCuratorApi get_variant_by_sample_as_curator GET /api/v1/as-curator/integration/link/variant/by/sample/{id} Retrieve variant run-level data by querying related sample ID (accession)
VariantIntegrationAsCuratorApi get_variant_groups_by_study_as_curator GET /api/v1/as-curator/integration/link/variant/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
VariantIntegrationAsCuratorApi get_variant_run_to_sample_pairs_as_curator GET /api/v1/as-curator/integration/link/variant/run-to-samples/by/group/{id} Retrieve run-sample pairs by group id. Pagination is based on unique runs, not unique pairs.
VariantIntegrationAsUserApi get_variant_by_sample_as_user GET /api/v1/as-user/integration/link/variant/by/sample/{id} Retrieve variant run-level data by querying related sample ID (accession)
VariantIntegrationAsUserApi get_variant_groups_by_study_as_user GET /api/v1/as-user/integration/link/variant/group/by/study/{id} Retrieve group metadata by querying study ID (accession)
VariantIntegrationAsUserApi get_variant_run_to_sample_pairs_as_user GET /api/v1/as-user/integration/link/variant/run-to-samples/by/group/{id} Retrieve run-sample pairs by group id. Pagination is based on unique runs, not unique pairs.
XrefsetQueriesApi create POST /api/v1/xrefsets Import a new xrefset file
XrefsetQueriesApi delete_file DELETE /api/v1/xrefsets/{id} Delete a xrefset with all related data. Only users who uploaded the xrefset are allowed to delete it.
XrefsetQueriesApi get_details_by_accession GET /api/v1/xrefsets/{id}/metadata Retrieve xrefset details
XrefsetQueriesApi search_entries GET /api/v1/xrefsets/entries Retrieve a list of entries across all xrefsets for given sourceId and targetId
XrefsetQueriesApi search_entries_within_file GET /api/v1/xrefsets/{id}/entries Retrieve a list of entries for the given xrefset and given sourceId and targetId
BETAAnalyticsOmicsQueriesAsCuratorApi cell_ratio_as_curator POST /api/v1/as-curator/omics/cells/analytics/cell-ratio [BETA] Compute cell ratio statistics across groups or metadata attributes in single-cell data.
BETAAnalyticsOmicsQueriesAsCuratorApi differential_expression_as_curator POST /api/v1/as-curator/omics/cells/analytics/differential-expression [BETA] Perform differential gene expression analytics between case and control cell groups
BETAAnalyticsOmicsQueriesAsCuratorApi gene_summary_as_curator POST /api/v1/as-curator/omics/cells/analytics/gene-summary [BETA] Compute and retrieve descriptive statistics and visual summaries for single-cell data.
BETAAnalyticsOmicsQueriesAsUserApi cell_ratio_as_user POST /api/v1/as-user/omics/cells/analytics/cell-ratio [BETA] Compute cell ratio statistics across groups or metadata attributes in single-cell data.
BETAAnalyticsOmicsQueriesAsUserApi differential_expression_as_user POST /api/v1/as-user/omics/cells/analytics/differential-expression [BETA] Perform differential gene expression analytics between case and control cell groups
BETAAnalyticsOmicsQueriesAsUserApi gene_summary_as_user POST /api/v1/as-user/omics/cells/analytics/gene-summary [BETA] Compute and retrieve descriptive statistics and visual summaries for single-cell data.

Documentation For Models

Documentation For Authorization

Authentication schemes defined for the API:

Access-token

  • Type: API key
  • API key parameter name: Authorization
  • Location: HTTP header

Genestack-API-Token

  • Type: API key
  • API key parameter name: Genestack-API-Token
  • Location: HTTP header

Author