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libica.openapi.v2

This API can be used to interact with Illumina Connected Analytics.

Authentication

Authentication to the API can be done in multiple ways:

  • For the entire API, except for the POST /tokens endpoint: API-key + JWT
  • Only for the POST /tokens endpoint: API-key + Basic Authentication

API-key

API keys are managed within the Illumina portal where you can manage your profile after you have logged on. The API-key has to be provided in the X-API-Key header parameter when executing API calls to ICA. In the background, a JWT will be requested at the IDP of Illumina to create a session. A good practice is to not use the API-key for every API call, but to first generate a JWT and to use that for authentication in subsequent calls.

JWT

To avoid using an API-key for each call, we recommend to request a JWT via the POST /tokens endpoint using this API-key. The JWT will expire after a pre-configured period specified by a tenant administrator through the IAM console in the Illumina portal. The JWT is the preferred way for authentication.
A not yet expired, still valid JWT could be refreshed using the POST /tokens:refresh endpoint.
Refreshing the JWT is not possible if the JWT was generated by using an API-key.

Basic Authentication

Basic authentication is only supported by the POST /tokens endpoint for generating a JWT. Use \"Basic base64encoded(emailaddress:password)\" in the \"Authorization\" header parameter for this authentication method. In case having access to multiple tenants using the same email-address, also provide the \"tenant\" request parameter to indicate what tenant you would like to request a JWT for.

Compression

If the API client provides request header 'Accept-Encoding' with value 'gzip', then the API applies GZIP compression on the JSON response. This significantly reduces the size and thus the download time of the response, which results in faster end-to-end API calls. In case of compression, the API also provides response header 'Content-Encoding' with value 'gzip', as indication for the client that decompression is required.

The libica.openapi.v2 package is automatically generated by the OpenAPI Generator project:

  • API version: 3
  • Package version: 1.0.0
  • Build date: 2025-06-05T14:43:12.864218+10:00[Australia/Melbourne]
  • Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python >=3.6

Installation & Usage

This python library package is generated without supporting files like setup.py or requirements files

To be able to use it, you will need these dependencies in your own package that uses this library:

  • urllib3 >= 1.25.3
  • python-dateutil

Getting Started

In your own code, to use this library to connect and interact with libica.openapi.v2, you can run the following:

import time
import libica.openapi.v2
from pprint import pprint
from libica.openapi.v2.api import analysis_storage_api
from libica.openapi.v2.model.analysis_storage_list_v3 import AnalysisStorageListV3
from libica.openapi.v2.model.problem import Problem
# Defining the host is optional and defaults to /ica/rest
# See configuration.py for a list of all supported configuration parameters.
configuration = libica.openapi.v2.Configuration(
    host = "/ica/rest"
)

# 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: ApiKeyAuth
configuration.api_key['ApiKeyAuth'] = 'YOUR_API_KEY'

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

# Configure Bearer authorization (JWT): JwtAuth
configuration = libica.openapi.v2.Configuration(
    access_token = 'YOUR_BEARER_TOKEN'
)


# Enter a context with an instance of the API client
with libica.openapi.v2.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = analysis_storage_api.AnalysisStorageApi(api_client)

    try:
        # Retrieve the list of analysis storage options.
        api_response = api_instance.get_analysis_storage_options()
        pprint(api_response)
    except libica.openapi.v2.ApiException as e:
        print("Exception when calling AnalysisStorageApi->get_analysis_storage_options: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to /ica/rest

Class Method HTTP request Description
AnalysisStorageApi get_analysis_storage_options GET /api/analysisStorages Retrieve the list of analysis storage options.
BundleApi accept_terms_of_use_bundle POST /api/bundles/{bundleId}/termsOfUse:accept accept terms of use for a bundle
BundleApi create_bundle POST /api/bundles Create a new bundle
BundleApi deprecate_bundle POST /api/bundles/{bundleId}:deprecate deprecate a bundle
BundleApi get_bundle GET /api/bundles/{bundleId} Retrieve a bundle.
BundleApi get_bundle_terms_of_use GET /api/bundles/{bundleId}/termsOfUse Retrieve the last version of terms of use for a bundle.
BundleApi get_bundles GET /api/bundles Retrieve a list of bundles.
BundleApi get_terms_of_use_acceptance GET /api/bundles/{bundleId}/termsOfUse/userAcceptance/currentUser Retrieve the acceptance record for a bundle for the current user.
BundleApi insert_bundle_terms_of_use POST /api/bundles/{bundleId}/termsOfUse:new Insert a new version of the terms of use for a bundle
BundleApi release_bundle POST /api/bundles/{bundleId}:release release a bundle
BundleDataApi get_bundle_data GET /api/bundles/{bundleId}/data Retrieve the list of bundle data.
BundleDataApi link_data_to_bundle POST /api/bundles/{bundleId}/data/{dataId} Link data to this bundle.
BundleDataApi unlink_data_from_bundle DELETE /api/bundles/{bundleId}/data/{dataId} Unlink data from this bundle.
BundleDataLinkingBatchApi create_bundle_data_linking_batch POST /api/bundles/{bundleId}/dataLinkingBatch Create a bundle data linking batch.
BundleDataLinkingBatchApi get_bundle_data_linking_batch GET /api/bundles/{bundleId}/dataLinkingBatch/{batchId} Retrieve a bundle data linking batch.
BundleDataLinkingBatchApi get_bundle_data_linking_batch_item GET /api/bundles/{bundleId}/dataLinkingBatch/{batchId}/items/{itemId} Retrieve a bundle data linking batch item.
BundleDataLinkingBatchApi get_bundle_data_linking_batch_items GET /api/bundles/{bundleId}/dataLinkingBatch/{batchId}/items Retrieve a list of bundle data linking batch items.
BundleDataUnlinkingBatchApi create_bundle_data_unlinking_batch POST /api/bundles/{bundleId}/dataUnlinkingBatch Create a bundle data unlinking batch.
BundleDataUnlinkingBatchApi get_bundle_data_unlinking_batch GET /api/bundles/{bundleId}/dataUnlinkingBatch/{batchId} Retrieve a bundle data unlinking batch.
BundleDataUnlinkingBatchApi get_bundle_data_unlinking_batch_item GET /api/bundles/{bundleId}/dataUnlinkingBatch/{batchId}/items/{itemId} Retrieve a bundle data unlinking batch item.
BundleDataUnlinkingBatchApi get_bundle_data_unlinking_batch_items GET /api/bundles/{bundleId}/dataUnlinkingBatch/{batchId}/items Retrieve a list of bundle data unlinking batch items.
BundlePipelineApi get_bundle_pipelines GET /api/bundles/{bundleId}/pipelines Retrieve a list of bundle pipelines.
BundlePipelineApi link_pipeline_to_bundle POST /api/bundles/{bundleId}/pipelines/{pipelineId} Link a pipeline to a bundle.
BundlePipelineApi unlink_pipeline_from_bundle DELETE /api/bundles/{bundleId}/pipelines/{pipelineId} Unlink a pipeline from a bundle.
BundleSampleApi get_bundle_samples GET /api/bundles/{bundleId}/samples Retrieve a list of bundle samples.
BundleSampleApi link_sample_to_bundle POST /api/bundles/{bundleId}/samples/{sampleId} Link a sample to a bundle.
BundleSampleApi unlink_sample_from_bundle DELETE /api/bundles/{bundleId}/samples/{sampleId} Unlink a sample from a bundle.
BundleToolApi get_bundle_tools GET /api/bundles/{bundleId}/tools Retrieve a list of bundle tools.
BundleToolApi get_tools_eligible_for_linking_to_bundle GET /api/bundles/{bundleId}/tools/eligibleForLinking Retrieve a list of tools eligible for linking to the bundle.
BundleToolApi link_tool_to_bundle POST /api/bundles/{bundleId}/tools/{toolId} Link a tool to a bundle
BundleToolApi unlink_tool_from_bundle DELETE /api/bundles/{bundleId}/tools/{toolId} Unlink a tool from this bundle.
ConnectorApi cancel_connector POST /api/connectors/{connectorId}:cancel Cancel a connector.
ConnectorApi create_connector POST /api/connectors Create a connector.
ConnectorApi create_download_rule POST /api/connectors/{connectorId}/downloadRules Create a download rule.
ConnectorApi create_upload_rule POST /api/connectors/{connectorId}/uploadRules Create an upload rule.
ConnectorApi delete_download_rule DELETE /api/connectors/{connectorId}/downloadRules/{downloadRuleId} Delete a download rule.
ConnectorApi delete_upload_rule DELETE /api/connectors/{connectorId}/uploadRules/{uploadRuleId} Delete an upload rule.
ConnectorApi disable_connector POST /api/connectors/{connectorId}:disable Disable a connector.
ConnectorApi enable_connector POST /api/connectors/{connectorId}:enable Enable a connector.
ConnectorApi get_connector GET /api/connectors/{connectorId} Retrieve a connector.
ConnectorApi get_connectors GET /api/connectors Retrieve a list of connectors.
ConnectorApi get_download_rule GET /api/connectors/{connectorId}/downloadRules/{downloadRuleId} Retrieve a download rule.
ConnectorApi get_download_rules GET /api/connectors/{connectorId}/downloadRules Retrieve a list of download rules.
ConnectorApi get_upload_rule GET /api/connectors/{connectorId}/uploadRules/{uploadRuleId} Retrieve an upload rule.
ConnectorApi get_upload_rules GET /api/connectors/{connectorId}/uploadRules Retrieve a list of upload rules.
ConnectorApi update_download_rule PUT /api/connectors/{connectorId}/downloadRules/{downloadRuleId} Update a download rule.
ConnectorApi update_upload_rule PUT /api/connectors/{connectorId}/uploadRules/{uploadRuleId} Update an upload rule.
DataApi create_download_url_for_data_without_project_context POST /api/data/{dataUrn}:createDownloadUrl Retrieve a download URL for this data.
DataApi create_inline_view_url_for_data_without_project_context POST /api/data/{dataUrn}:createInlineViewUrl Retrieve an URL for this data to use for inline view in a browser.
DataApi get_data GET /api/data/{dataUrn} Retrieve a data.
DataFormatApi get_data_formats GET /api/dataFormats Retrieve a list of data formats.
DockerImageApi add_regions POST /api/dockerImages/{imageId}:addRegions Add regions to an existing Docker image.
DockerImageApi create_external_docker_image POST /api/dockerImages:createExternal Create an external Docker image.
DockerImageApi create_internal_docker_image POST /api/dockerImages:createInternal Create an internal Docker image.
DockerImageApi get_docker_image GET /api/dockerImages/{imageId} Retrieve a Docker image. Only the Docker image the user has access to can be retrieved.
DockerImageApi get_docker_images GET /api/dockerImages Retrieve a list of Docker images. Only the Docker images the user has access to are returned.
DockerImageApi remove_regions POST /api/dockerImages/{imageId}:removeRegions Remove regions to an existing Docker image.
EntitledBundleApi accept_terms_of_use_entitled_bundle POST /api/entitledbundles/{entitledBundleId}/termsOfUse:accept Accept terms of use for an entitled bundle
EntitledBundleApi get_entitled_bundle GET /api/entitledbundles/{entitledBundleId} Retrieve an entitled bundle.
EntitledBundleApi get_entitled_bundle_terms_of_use GET /api/entitledbundles/{entitledBundleId}/termsOfUse Retrieve the last version of terms of use for an entitled bundle.
EntitledBundleApi get_entitled_bundle_terms_of_use_acceptance GET /api/entitledbundles/{entitledBundleId}/termsOfUse/userAcceptance/currentUser Retrieve the acceptance record for an entitled bundle for the current user.
EntitledBundleApi get_entitled_bundles GET /api/entitledbundles Retrieve a list of entitled bundles.
EntitlementDetailApi find_all_matching_activation_codes_for_cwl POST /api/activationCodes:findAllMatchingForCwl Search all matching activation code details for a Cwl pipeline.
EntitlementDetailApi find_all_matching_activation_codes_for_nextflow POST /api/activationCodes:findAllMatchingForNextflow Search all matching activation code details for a Nextflow pipeline.
EntitlementDetailApi find_best_matching_activation_code_for_cwl POST /api/activationCodes:findBestMatchingForCwl Search the best matching activation code detail for Cwl pipeline.
EntitlementDetailApi find_best_matching_activation_codes_for_nextflow POST /api/activationCodes:findBestMatchingForNextflow Search the best matching activation code details for Nextflow pipeline.
EventCodeApi get_event_codes GET /api/eventCodes Retrieve event codes
EventLogApi get_event_logs GET /api/eventLog Retrieve a list of event logs.
EventLogApi search_event_logs POST /api/eventLog:search Search event logs.
JobApi get_job GET /api/jobs/{jobId} Retrieve a job.
JobApi get_jobs GET /api/jobs Retrieve a list of jobs.
MetadataModelApi get_metadata_model GET /api/metadataModels/{metadataModelId} Retrieve a metadata model. Only metadata models that the user has access to can be retrieved.
MetadataModelApi get_metadata_model_fields GET /api/metadataModels/{metadataModelId}/fields Retrieve the fields of a metadata model. Only metadata models that the user has access to can be retrieved.
MetadataModelApi get_metadata_models GET /api/metadataModels Retrieve the metadata models for the tenant associated to the security context.
MetadataModelApi get_tenant_model GET /api/metadataModels/tenantModel Retrieve the tenant model for the tenant associated to the security context.
NotificationChannelApi create_notification_channel POST /api/notificationChannels Create a notification channel
NotificationChannelApi delete_notification_channel DELETE /api/notificationChannels/{channelId} Delete a notification channel
NotificationChannelApi get_notification_channel GET /api/notificationChannels/{channelId} Retrieve a notification channel
NotificationChannelApi get_notification_channels GET /api/notificationChannels Retrieve notification channels
NotificationChannelApi update_notification_channel PUT /api/notificationChannels/{channelId} Update a notification channel
PipelineApi download_pipeline_file_content GET /api/pipelines/{pipelineId}/files/{fileId}/content Download the contents of a pipeline file.
PipelineApi get_pipeline GET /api/pipelines/{pipelineId} Retrieve a pipeline.
PipelineApi get_pipeline_configuration_parameters GET /api/pipelines/{pipelineId}/configurationParameters Retrieve configuration parameters for a pipeline.
PipelineApi get_pipeline_files GET /api/pipelines/{pipelineId}/files Retrieve files for a pipeline.
PipelineApi get_pipeline_html_documentation GET /api/pipelines/{pipelineId}/documentation/HTML Retrieve HTML documentation for a project pipeline.
PipelineApi get_pipeline_input_parameters GET /api/pipelines/{pipelineId}/inputParameters Retrieve input parameters for a pipeline.
PipelineApi get_pipeline_reference_sets GET /api/pipelines/{pipelineId}/referenceSets Retrieve the reference sets of a pipeline.
PipelineApi get_pipelines GET /api/pipelines Retrieve a list of pipelines.
PipelineLanguageApi get_nextflow_versions GET /api/pipelineLanguages/nextflow/versions Retrieve a list of nextflow versions.
ProjectApi change_project_owner POST /api/projects/{projectId}:changeOwner Change the project owner.
ProjectApi create_project POST /api/projects Create a new project.
ProjectApi get_project GET /api/projects/{projectId} Retrieve a project.
ProjectApi get_project_bundle GET /api/projects/{projectId}/bundles/{bundleId} Retrieve a project bundle.
ProjectApi get_project_bundles GET /api/projects/{projectId}/bundles Retrieve project bundles.
ProjectApi get_projects GET /api/projects Retrieve a list of projects.
ProjectApi hide_project POST /api/projects/{projectId}:hide Hide a project.
ProjectApi link_project_bundle POST /api/projects/{projectId}/bundles/{bundleId} Link a bundle to a project.
ProjectApi unlink_project_bundle DELETE /api/projects/{projectId}/bundles/{bundleId} Unlink a bundle from a project.
ProjectApi update_project PUT /api/projects/{projectId} Update a project.
ProjectAnalysisApi abort_analysis POST /api/projects/{projectId}/analyses/{analysisId}:abort Abort an analysis.
ProjectAnalysisApi create_cwl_analysis POST /api/projects/{projectId}/analysis:cwl Create and start an analysis for a CWL pipeline.
ProjectAnalysisApi create_cwl_analysis_with_json_input POST /api/projects/{projectId}/analysis:cwlWithJsonInput Create and start an analysis for a CWL pipeline with an input.json.
ProjectAnalysisApi create_cwl_analysis_with_structured_input POST /api/projects/{projectId}/analysis:cwlWithStructuredInput Create and start an analysis for a CWL pipeline with a structured input.
ProjectAnalysisApi create_cwl_json_analysis POST /api/projects/{projectId}/analysis:cwlJson Create and start an analysis for a JSON based CWL pipeline.
ProjectAnalysisApi create_nextflow_analysis POST /api/projects/{projectId}/analysis:nextflow Create and start an analysis for a Nextflow pipeline.
ProjectAnalysisApi create_nextflow_analysis_with_custom_input POST /api/projects/{projectId}/analysis:nextflowWithCustomInput Create and initiate an analysis for a Nextflow pipeline using a custom input, provided in either YAML format or an escaped JSON string.
ProjectAnalysisApi create_nextflow_json_analysis POST /api/projects/{projectId}/analysis:nextflowJson Create and start an analysis for a JSON based Nextflow pipeline.
ProjectAnalysisApi get_analyses GET /api/projects/{projectId}/analyses Retrieve the list of analyses.
ProjectAnalysisApi get_analysis GET /api/projects/{projectId}/analyses/{analysisId} Retrieve an analysis.
ProjectAnalysisApi get_analysis_configurations GET /api/projects/{projectId}/analyses/{analysisId}/configurations Retrieve the configurations of an analysis.
ProjectAnalysisApi get_analysis_inputs GET /api/projects/{projectId}/analyses/{analysisId}/inputs Retrieve the inputs of an analysis.
ProjectAnalysisApi get_analysis_outputs GET /api/projects/{projectId}/analyses/{analysisId}/outputs Retrieve the outputs of an analysis (limited to the first 200.000 files per output folder). When trying to retrieve the listed data with an endpoint such as GET /api/data/{dataUrn}, data which has already been deleted will be skipped.
ProjectAnalysisApi get_analysis_reports GET /api/projects/{projectId}/analyses/{analysisId}/reports Retrieve the report configs and associated reports.
ProjectAnalysisApi get_analysis_steps GET /api/projects/{projectId}/analyses/{analysisId}/steps Retrieve the individual steps of an analysis.
ProjectAnalysisApi get_analysis_usage_details GET /api/projects/{projectId}/analyses/{analysisId}/usage Retrieve the analysis usage details.
ProjectAnalysisApi get_cwl_input_json GET /api/projects/{projectId}/analyses/{analysisId}/cwl/inputJson Retrieve the input json of a CWL analysis.
ProjectAnalysisApi get_cwl_output_json GET /api/projects/{projectId}/analyses/{analysisId}/cwl/outputJson Retrieve the output json of a CWL analysis.
ProjectAnalysisApi get_project_analysis_input_form_values GET /api/projects/{projectId}/analyses/{analysisId}/inputFormValues Retrieve the values from an input form.
ProjectAnalysisApi get_raw_analysis_output GET /api/projects/{projectId}/analyses/{analysisId}/rawOutput Retrieve the raw output of an analysis.
ProjectAnalysisApi search_analyses POST /api/projects/{projectId}/analysis:search Search analyses.
ProjectAnalysisApi update_analysis PUT /api/projects/{projectId}/analyses/{analysisId} Update an analysis.
ProjectAnalysisCreationBatchApi create_analysis_creation_batch POST /api/projects/{projectId}/analysisCreationBatch Create and start multiple analyses in batch.
ProjectAnalysisCreationBatchApi get_analysis_creation_batch GET /api/projects/{projectId}/analysisCreationBatch/{batchId} Retrieve a analysis creation batch.
ProjectAnalysisCreationBatchApi get_analysis_creation_batch_item GET /api/projects/{projectId}/analysisCreationBatch/{batchId}/items/{itemId} Retrieve a analysis creation batch item.
ProjectAnalysisCreationBatchApi get_analysis_creation_batch_items GET /api/projects/{projectId}/analysisCreationBatch/{batchId}/items Retrieve a list of analysis creation batch items.
ProjectAnalysisStorageApi get_project_analysis_storage_options GET /api/projects/{projectId}/analysisStorages Retrieve the list of project analysis storage options.
ProjectBaseApi create_base_connection_details POST /api/projects/{projectId}/base:connectionDetails Creates the connection details to snowflake instance.
ProjectBaseApi get_base_job GET /api/projects/{projectId}/base/jobs/{baseJobId} Retrieve a base job.
ProjectBaseApi get_base_jobs GET /api/projects/{projectId}/base/jobs Retrieve a list of base jobs
ProjectBaseApi get_base_tables GET /api/projects/{projectId}/base/tables Retrieve a list of base tables.
ProjectBaseApi load_data POST /api/projects/{projectId}/base/tables/{tableId}:loadData Load data in a base table.
ProjectCustomEventsApi create_custom_event POST /api/projects/{projectId}/customEvents Create a new custom event.
ProjectCustomNotificationSubscriptionsApi create_custom_notification_subscription POST /api/projects/{projectId}/customNotificationSubscriptions Create a custom notification subscription
ProjectCustomNotificationSubscriptionsApi delete_custom_notification_subscription DELETE /api/projects/{projectId}/customNotificationSubscriptions/{subscriptionId} Delete a custom notification subscription
ProjectCustomNotificationSubscriptionsApi get_custom_notification_subscription GET /api/projects/{projectId}/customNotificationSubscriptions/{subscriptionId} Retrieve a notification subscription
ProjectCustomNotificationSubscriptionsApi get_custom_notification_subscriptions GET /api/projects/{projectId}/customNotificationSubscriptions Retrieve notification subscriptions
ProjectCustomNotificationSubscriptionsApi update_custom_notification_subscription PUT /api/projects/{projectId}/customNotificationSubscriptions/{subscriptionId} Update a notification subscription
ProjectDataApi add_secondary_data POST /api/projects/{projectId}/data/{dataId}/secondaryData/{secondaryDataId} Add secondary data to data.
ProjectDataApi archive_data POST /api/projects/{projectId}/data/{dataId}:archive Schedule this data for archival.
ProjectDataApi complete_folder_upload_session POST /api/projects/{projectId}/data/{dataId}/folderUploadSessions/{folderUploadSessionId}:complete Complete a trackable folder upload session.
ProjectDataApi create_data_in_project POST /api/projects/{projectId}/data Create data in this project.
ProjectDataApi create_download_url_for_data POST /api/projects/{projectId}/data/{dataId}:createDownloadUrl Retrieve a download URL for this data.
ProjectDataApi create_download_urls_for_data POST /api/projects/{projectId}/data:createDownloadUrls Retrieve download URLs for the data.
ProjectDataApi create_file POST /api/projects/{projectId}/data:createFile Create a file in this project.
ProjectDataApi create_file_with_temporary_credentials POST /api/projects/{projectId}/data:createFileWithTemporaryCredentials Create a file in this project, and retrieve temporary credentials for it.
ProjectDataApi create_file_with_upload_url POST /api/projects/{projectId}/data:createFileWithUploadUrl Create a file in this project, and retrieve an upload url for it.
ProjectDataApi create_folder POST /api/projects/{projectId}/data:createFolder Create a folder in this project.
ProjectDataApi create_folder_upload_session POST /api/projects/{projectId}/data/{dataId}/folderUploadSessions Create a trackable folder upload session.
ProjectDataApi create_folder_with_temporary_credentials POST /api/projects/{projectId}/data:createFolderWithTemporaryCredentials Create a folder in this project, and and retrieve temporary credentials for it.
ProjectDataApi create_folder_with_upload_session POST /api/projects/{projectId}/data:createFolderWithUploadSession Create a folder in this project, and create a trackable folder upload session.
ProjectDataApi create_inline_view_url_for_data POST /api/projects/{projectId}/data/{dataId}:createInlineViewUrl Retrieve an URL for this data to use for inline view in a browser.
ProjectDataApi create_non_indexed_folder POST /api/projects/{projectId}/data:createNonIndexedFolder Create a non indexed folder in this project. The folder will be created as a top-level folder.
ProjectDataApi create_temporary_credentials_for_data POST /api/projects/{projectId}/data/{dataId}:createTemporaryCredentials Retrieve temporary credentials for this data.
ProjectDataApi create_upload_url_for_data POST /api/projects/{projectId}/data/{dataId}:createUploadUrl Retrieve an upload URL for this data.
ProjectDataApi delete_data POST /api/projects/{projectId}/data/{dataId}:delete Schedule this data for deletion.
ProjectDataApi get_data_eligible_for_linking GET /api/projects/{projectId}/data/eligibleForLinking Retrieve a list of data eligible for linking to the current project.
ProjectDataApi get_folder_upload_session GET /api/projects/{projectId}/data/{dataId}/folderUploadSessions/{folderUploadSessionId} Retrieve folder upload session details.
ProjectDataApi get_non_sample_project_data GET /api/projects/{projectId}/data/nonSampleData Retrieve a list of project data not linked to a sample.
ProjectDataApi get_project_data GET /api/projects/{projectId}/data/{dataId} Retrieve a project data.
ProjectDataApi get_project_data_children GET /api/projects/{projectId}/data/{dataId}/children Retrieve the children of this data.
ProjectDataApi get_project_data_list GET /api/projects/{projectId}/data Retrieve the list of project data.
ProjectDataApi get_projects_linked_to_data GET /api/projects/{projectId}/data/{dataId}/linkedProjects Retrieve a list of projects to which this data is linked.
ProjectDataApi get_secondary_data GET /api/projects/{projectId}/data/{dataId}/secondaryData Retrieve a list of secondary data for data.
ProjectDataApi link_data_to_project POST /api/projects/{projectId}/data/{dataId} Link data to this project.
ProjectDataApi remove_secondary_data DELETE /api/projects/{projectId}/data/{dataId}/secondaryData/{secondaryDataId} Remove secondary data from data.
ProjectDataApi schedule_download_for_data POST /api/projects/{projectId}/data/{dataId}:scheduleDownload Schedule a download.
ProjectDataApi unarchive_data POST /api/projects/{projectId}/data/{dataId}:unarchive Schedule this data for unarchival.
ProjectDataApi unlink_data_from_project POST /api/projects/{projectId}/data/{dataId}:unlink Unlink data from this project.
ProjectDataApi update_project_data PUT /api/projects/{projectId}/data/{dataId} Update this project data.
ProjectDataCopyBatchApi create_project_data_copy_batch POST /api/projects/{projectId}/dataCopyBatch Create a project data copy batch.
ProjectDataCopyBatchApi get_project_data_copy_batch GET /api/projects/{projectId}/dataCopyBatch/{batchId} Retrieve a project data copy batch.
ProjectDataCopyBatchApi get_project_data_copy_batch_item GET /api/projects/{projectId}/dataCopyBatch/{batchId}/items/{itemId} Retrieve a project data copy batch item.
ProjectDataCopyBatchApi get_project_data_copy_batch_items GET /api/projects/{projectId}/dataCopyBatch/{batchId}/items Retrieve a list of project data copy batch items.
ProjectDataLinkingBatchApi create_project_data_linking_batch POST /api/projects/{projectId}/dataLinkingBatch Create a project data linking batch.
ProjectDataLinkingBatchApi get_project_data_linking_batch GET /api/projects/{projectId}/dataLinkingBatch/{batchId} Retrieve a project data linking batch.
ProjectDataLinkingBatchApi get_project_data_linking_batch_item GET /api/projects/{projectId}/dataLinkingBatch/{batchId}/items/{itemId} Retrieve a project data linking batch item.
ProjectDataLinkingBatchApi get_project_data_linking_batch_items GET /api/projects/{projectId}/dataLinkingBatch/{batchId}/items Retrieve a list of project data linking batch items.
ProjectDataMoveBatchApi create_project_data_move_batch POST /api/projects/{projectId}/dataMoveBatch Create a project data move batch.
ProjectDataMoveBatchApi get_project_data_move_batch GET /api/projects/{projectId}/dataMoveBatch/{batchId} Retrieve a project data move batch.
ProjectDataMoveBatchApi get_project_data_move_batch_item GET /api/projects/{projectId}/dataMoveBatch/{batchId}/items/{itemId} Retrieve a project data move batch item.
ProjectDataMoveBatchApi get_project_data_move_batch_items POST /api/projects/{projectId}/dataMoveBatch/{batchId}/items:search Retrieve a list of project data move batch items.
ProjectDataTransferApi abort_data_transfer POST /api/projects/{projectId}/dataTransfers/{dataTransferId}:abort Abort a data transfer.
ProjectDataTransferApi get_data_transfer GET /api/projects/{projectId}/dataTransfers/{dataTransferId} Retrieve a data transfer.
ProjectDataTransferApi get_data_transfers GET /api/projects/{projectId}/dataTransfers Retrieve a list of data transfers.
ProjectDataUnlinkingBatchApi create_project_data_unlinking_batch POST /api/projects/{projectId}/dataUnlinkingBatch Create a project data unlinking batch.
ProjectDataUnlinkingBatchApi get_project_data_unlinking_batch GET /api/projects/{projectId}/dataUnlinkingBatch/{batchId} Retrieve a project data unlinking batch.
ProjectDataUnlinkingBatchApi get_project_data_unlinking_batch_item GET /api/projects/{projectId}/dataUnlinkingBatch/{batchId}/items/{itemId} Retrieve a project data unlinking batch item.
ProjectDataUnlinkingBatchApi get_project_data_unlinking_batch_items GET /api/projects/{projectId}/dataUnlinkingBatch/{batchId}/items Retrieve a list of project data unlinking batch items.
ProjectDataUpdateBatchApi create_project_data_update_batch POST /api/projects/{projectId}/dataUpdateBatch Create a project data update batch. Folder contents will be updated recursively. Time archive/delete cannot be defined for folders.
ProjectDataUpdateBatchApi get_project_data_update_batch GET /api/projects/{projectId}/dataUpdateBatch/{batchId} Retrieve a project data update batch.
ProjectDataUpdateBatchApi get_project_data_update_batch_item GET /api/projects/{projectId}/dataUpdateBatch/{batchId}/items/{itemId} Retrieve a project data update batch item.
ProjectDataUpdateBatchApi get_project_data_update_batch_items GET /api/projects/{projectId}/dataUpdateBatch/{batchId}/items Retrieve a list of project data update batch items.
ProjectNotificationSubscriptionsApi create_notification_subscription POST /api/projects/{projectId}/notificationSubscriptions Create a notification subscription
ProjectNotificationSubscriptionsApi delete_notification_subscription DELETE /api/projects/{projectId}/notificationSubscriptions/{subscriptionId} Delete a notification subscription
ProjectNotificationSubscriptionsApi get_notification_subscription GET /api/projects/{projectId}/notificationSubscriptions/{subscriptionId} Retrieve a notification subscription
ProjectNotificationSubscriptionsApi get_notification_subscriptions GET /api/projects/{projectId}/notificationSubscriptions Retrieve notification subscriptions
ProjectNotificationSubscriptionsApi update_notification_subscription PUT /api/projects/{projectId}/notificationSubscriptions/{subscriptionId} Update a notification subscription
ProjectPermissionApi create_project_permission POST /api/projects/{projectId}/permissions Create a project permission.
ProjectPermissionApi get_project_permission GET /api/projects/{projectId}/permissions/{permissionId} Retrieve a project permission.
ProjectPermissionApi get_project_permissions GET /api/projects/{projectId}/permissions Retrieve a list of project permissions.
ProjectPermissionApi update_project_permission PUT /api/projects/{projectId}/permissions/{permissionId} Update a project permission.
ProjectPipelineApi create_additional_project_pipeline_file POST /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/additionalFiles Create an additional input form file for a pipeline.
ProjectPipelineApi create_cwl_json_pipeline POST /api/projects/{projectId}/pipelines:createCwlJsonPipeline Create a JSON based CWL pipeline within a project.
ProjectPipelineApi create_cwl_pipeline POST /api/projects/{projectId}/pipelines:createCwlPipeline Create a CWL pipeline within a project.
ProjectPipelineApi create_nextflow_json_pipeline POST /api/projects/{projectId}/pipelines:createNextflowJsonPipeline Create a JSON based Nextflow pipeline within a project.
ProjectPipelineApi create_nextflow_pipeline POST /api/projects/{projectId}/pipelines:createNextflowPipeline Create a Nextflow pipeline within a project.
ProjectPipelineApi create_project_pipeline_file POST /api/projects/{projectId}/pipelines/{pipelineId}/files Create a file for a pipeline.
ProjectPipelineApi delete_additional_project_pipeline_file DELETE /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/additionalFiles/{fileId} Delete an additional input form file for a pipeline.
ProjectPipelineApi delete_project_pipeline_file DELETE /api/projects/{projectId}/pipelines/{pipelineId}/files/{fileId} Delete a file for a pipeline.
ProjectPipelineApi download_additional_file_content GET /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/additionalFiles/{fileId}/content Download the contents of an additional input form file.
ProjectPipelineApi download_input_form_file_content GET /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/inputFormFile Download the contents of the input form file.
ProjectPipelineApi download_on_render_file_content GET /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/onRenderFile Download the contents of the onRender file.
ProjectPipelineApi download_on_submit_file_content GET /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/onSubmitFile Download the contents of the onSubmit file.
ProjectPipelineApi download_project_pipeline_file_content GET /api/projects/{projectId}/pipelines/{pipelineId}/files/{fileId}/content Download the contents of a pipeline file.
ProjectPipelineApi get_project_pipeline GET /api/projects/{projectId}/pipelines/{pipelineId} Retrieve a project pipeline.
ProjectPipelineApi get_project_pipeline_additional_files GET /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/additionalFiles Retrieve additional input form files for a project pipeline.
ProjectPipelineApi get_project_pipeline_configuration_parameters GET /api/projects/{projectId}/pipelines/{pipelineId}/configurationParameters Retrieve configuration parameters for a project pipeline.
ProjectPipelineApi get_project_pipeline_files GET /api/projects/{projectId}/pipelines/{pipelineId}/files Retrieve files for a project pipeline.
ProjectPipelineApi get_project_pipeline_html_documentation GET /api/projects/{projectId}/pipelines/{pipelineId}/documentation/HTML Retrieve HTML documentation for a project pipeline.
ProjectPipelineApi get_project_pipeline_input_parameters GET /api/projects/{projectId}/pipelines/{pipelineId}/inputParameters Retrieve input parameters for a project pipeline.
ProjectPipelineApi get_project_pipeline_reference_sets GET /api/projects/{projectId}/pipelines/{pipelineId}/referenceSets Retrieve the reference sets of a project pipeline.
ProjectPipelineApi get_project_pipelines GET /api/projects/{projectId}/pipelines Retrieve a list of project pipelines.
ProjectPipelineApi link_pipeline_to_project POST /api/projects/{projectId}/pipelines/{pipelineId} Link a pipeline to a project.
ProjectPipelineApi release_project_pipeline POST /api/projects/{projectId}/pipelines/{pipelineId}:release Release a pipeline.
ProjectPipelineApi unlink_pipeline_from_project DELETE /api/projects/{projectId}/pipelines/{pipelineId} Unlink a pipeline from a project.
ProjectPipelineApi update_additional_file PUT /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/additionalFiles/{fileId}/content Update the contents of an additional input form file.
ProjectPipelineApi update_general_attributes_project_pipeline POST /api/projects/{projectId}/pipelines/{pipelineId}/generalAttributes Update the general attributes of a project pipeline.
ProjectPipelineApi update_input_form_file PUT /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/inputFormFile Update the contents of the input form file for a pipeline.
ProjectPipelineApi update_on_render_file PUT /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/onRenderFile Update the contents of the onRender file for a pipeline.
ProjectPipelineApi update_on_submit_file PUT /api/projects/{projectId}/pipelines/{pipelineId}/inputForm/onSubmitFile Update the contents of the onSubmit file for a pipeline.
ProjectPipelineApi update_project_pipeline_file PUT /api/projects/{projectId}/pipelines/{pipelineId}/files/{fileId}/content Update the contents of a file for a pipeline.
ProjectSampleApi add_metadata_model_to_sample POST /api/projects/{projectId}/samples/{sampleId}/metadata/{metadataModelId} Add a metadata model to a sample.
ProjectSampleApi complete_project_sample POST /api/projects/{projectId}/samples/{sampleId}:complete Completes the sample after data has been linked to it.
ProjectSampleApi create_sample_in_project POST /api/projects/{projectId}/samples Create a new sample in this project
ProjectSampleApi deep_delete_sample POST /api/projects/{projectId}/samples/{sampleId}:deleteDeep Delete a sample together with all of its data.
ProjectSampleApi delete_and_unlink_sample POST /api/projects/{projectId}/samples/{sampleId}:deleteUnlink Delete a sample and unlink its data.
ProjectSampleApi delete_sample_with_input POST /api/projects/{projectId}/samples/{sampleId}:deleteWithInput Delete a sample as well as its input data.
ProjectSampleApi get_project_sample GET /api/projects/{projectId}/samples/{sampleId} Retrieve a project sample.
ProjectSampleApi get_project_sample_analyses GET /api/projects/{projectId}/samples/{sampleId}/analyses Retrieve the list of analyses.
ProjectSampleApi get_project_samples POST /api/projects/{projectId}/samples:search Retrieve project samples.
ProjectSampleApi get_projects_for_sample GET /api/projects/{projectId}/samples/{sampleId}/projects Retrieve a list of projects for this sample.
ProjectSampleApi get_sample_data_list GET /api/projects/{projectId}/samples/{sampleId}/data Retrieve the list of sample data.
ProjectSampleApi get_sample_history GET /api/projects/{projectId}/samples/{sampleId}/history Retrieve sample history.
ProjectSampleApi get_sample_metadata_field GET /api/projects/{projectId}/samples/{sampleId}/metadata/field/{fieldId} Retrieve a metadata field.
ProjectSampleApi get_sample_metadata_field_count GET /api/projects/{projectId}/samples/{sampleId}/metadata/{fieldId}/fieldCount Retrieves the number of occurrences of a given field.
ProjectSampleApi link_data_to_sample POST /api/projects/{projectId}/samples/{sampleId}/data/{dataId} Link data to a sample.
ProjectSampleApi link_sample_to_project POST /api/projects/{projectId}/samples/{sampleId} Link a sample to a project.
ProjectSampleApi mark_sample_deleted POST /api/projects/{projectId}/samples/{sampleId}:deleteMark Mark a sample deleted.
ProjectSampleApi search_project_sample_analyses POST /api/projects/{projectId}/samples/{sampleId}/analyses:search Search analyses for sample.
ProjectSampleApi unlink_data_from_sample POST /api/projects/{projectId}/samples/{sampleId}/data/{dataId}:unlink Unlink data from a sample.
ProjectSampleApi unlink_sample_from_project POST /api/projects/{projectId}/samples/{sampleId}:unlink Unlink a sample from a project.
ProjectSampleApi update_project_sample PUT /api/projects/{projectId}/samples/{sampleId} Update a project sample.
ProjectSampleApi update_sample_metadata_fields POST /api/projects/{projectId}/samples/{sampleId}/metadata:updateFields Update metadata fields.
ProjectSampleBatchApi create_sample_creation_batch POST /api/projects/{projectId}/sampleCreationBatch Create a sample creation batch.
ProjectSampleBatchApi get_sample_creation_batch GET /api/projects/{projectId}/sampleCreationBatch/{batchId} Retrieve a sample creation batch.
ProjectSampleBatchApi get_sample_creation_batch_item GET /api/projects/{projectId}/sampleCreationBatch/{batchId}/items/{itemId} Retrieve a sample creation batch item.
ProjectSampleBatchApi get_sample_creation_batch_items GET /api/projects/{projectId}/sampleCreationBatch/{batchId}/items Retrieve a list of sample creation batch items.
ProjectWorkflowSessionApi get_workflow_session_configurations GET /api/projects/{projectId}/workflowSessions/{workflowSessionId}/configurations Retrieve the configurations of a workflow session.
ProjectWorkflowSessionApi get_workflow_session_inputs GET /api/projects/{projectId}/workflowSessions/{workflowSessionId}/inputs Retrieve the inputs of a workflow session.
ProjectWorkflowSessionApi get_workflow_sessions GET /api/projects/{projectId}/workflowSessions Retrieve the list of workflow sessions.
ProjectWorkflowSessionApi search_orchestrated_analyses POST /api/projects/{projectId}/workflowSessions/{workflowSessionId}/analyses:search Search analyses orchestrated by the workflow session.
ProjectWorkflowSessionApi search_workflow_sessions POST /api/projects/{projectId}/workflowSessions:search Search workflow sessions.
ReferenceSetApi get_reference_sets GET /api/referenceSets Retrieve a list of of reference sets.
ReferenceSetApi get_species GET /api/referenceSets/{referenceSetId}/species Retrieve a list of species linked to the reference set.
RegionApi get_region GET /api/regions/{regionId} Retrieve a region. Only the regions the user has access to through his/her entitlements can be retrieved.
RegionApi get_regions GET /api/regions Retrieve a list of regions. Only the regions the user has access to through his/her entitlements are returned.
SampleApi get_samples GET /api/samples Retrieve a list of samples.
SequencingRunApi get_sequencing_run GET /api/sequencingRuns/{sequencingRunId} Retrieve a sequencing run.
StorageBundleApi get_storage_bundles GET /api/storageBundles Retrieve a list of storage bundles.
StorageConfigurationApi create_storage_configuration POST /api/storageConfigurations Create a new storage configuration
StorageConfigurationApi get_storage_configuration GET /api/storageConfigurations/{storageConfigurationId} Retrieve a storage configuration.
StorageConfigurationApi get_storage_configuration_details GET /api/storageConfigurations/{storageConfigurationId}/details Retrieve a storage configuration detail.
StorageConfigurationApi get_storage_configurations GET /api/storageConfigurations Retrieve a list of storage configurations.
StorageConfigurationApi share_storage_configuration POST /api/storageConfigurations/{storageConfigurationId}:share Share your own storage configuration with tenant.
StorageConfigurationApi validate_storage_configuration POST /api/storageConfigurations/{storageConfigurationId}:validate Start validation of your storage configuration.
StorageCredentialsApi create_storage_credential POST /api/storageCredentials Create a new storage credential
StorageCredentialsApi get_storage_credential GET /api/storageCredentials/{storageCredentialId} Retrieve a storage credential.
StorageCredentialsApi get_storage_credentials GET /api/storageCredentials Retrieve a list of storage credentials.
StorageCredentialsApi share_storage_credential POST /api/storageCredentials/{storageCredentialId}:share Share your own storage credentials with tenant.
StorageCredentialsApi update_storage_credential_secrets POST /api/storageCredentials/{storageCredentialId}:updateSecrets Update a storage credential's secrets.
SystemApi get_system_info GET /api/system/info Retrieve system information.
TokenApi create_jwt_token POST /api/tokens Generate a JWT using an API-key, Basic Authentication or a psToken.
TokenApi refresh_jwt_token POST /api/tokens:refresh Refresh a JWT using a not yet expired, still valid JWT.
UserApi approve_user POST /api/users/{userId}:approve Approve a user.
UserApi assign_tenant_admin_rights_to_user POST /api/users/{userId}:assignTenantAdministratorRights Assign tenant administrator rights to a user.
UserApi get_user GET /api/users/{userId} Retrieve a user.
UserApi get_users GET /api/users Retrieve a list of users.
UserApi revoke_tenant_admin_rights_to_user POST /api/users/{userId}:revokeTenantAdministratorRights Revoke tenant administrator rights to a user.
UserApi update_user PUT /api/users/{userId} Update a user.
WorkgroupApi get_workgroup GET /api/workgroups/{workgroupId} Retrieve a workgroup.
WorkgroupApi get_workgroups GET /api/workgroups Retrieve a list of workgroups.

Documentation For Models

Documentation For Authorization

ApiKeyAuth

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

BasicAuth

  • Type: HTTP basic authentication

JwtAuth

  • Type: Bearer authentication (JWT)

PsTokenAuth

  • Type: Bearer authentication (psToken)

Author

Notes for Large OpenAPI documents

If the OpenAPI document is large, imports in libica.openapi.v2.apis and libica.openapi.v2.models may fail with a RecursionError indicating the maximum recursion limit has been exceeded. In that case, there are a couple of solutions:

Solution 1: Use specific imports for apis and models like: - from libica.openapi.v2.api.default_api import DefaultApi - from libica.openapi.v2.model.pet import Pet

Solution 2: Before importing the package, adjust the maximum recursion limit as shown below:

import sys
sys.setrecursionlimit(1500)
import libica.openapi.v2
from libica.openapi.v2.apis import *
from libica.openapi.v2.models import *