This API can be used to interact with Illumina Connected Analytics.
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 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.
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 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.
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.
Tests created by Illumina are in the tests/test_integration/ folder, they are run using pytest, but modification will be required to update domain specific parameters. This is an active area of change in the repository and will be updated over time.
This Python package is automatically generated by the OpenAPI Generator project:
- API version: 3
- Package version: 1.0.0
- Build package: org.openapitools.codegen.languages.PythonClientCodegen
This is the command used to generate this SDK:
openapi-generator-cli generate \
-i openapi_public.yaml \
-g python \
-t template \
--additional-properties packageName=icasdk,packageVersion=1.0.0,projectName=ica-sdk-python \
--global-property skipFormModel=false &> generate.log
After code generation, a few manual corrections are made:
input_part.py
andinput_part.pyi
type foradditionalProperties
Python >=3.7
- This generator uses spec case for all (object) property names and parameter names.
- So if the spec has a property name like camelCase, it will use camelCase rather than camel_case
- So you will need to update how you input and read properties to use spec case
- Endpoint parameters are stored in dictionaries to prevent collisions (explanation below)
- So you will need to update how you pass data in to endpoints
- Endpoint responses now include the original response, the deserialized response body, and (todo)the deserialized headers
- So you will need to update your code to use response.body to access deserialized data
- All validated data is instantiated in an instance that subclasses all validated Schema classes and Decimal/str/list/tuple/frozendict/NoneClass/BoolClass/bytes/io.FileIO
- This means that you can use isinstance to check if a payload validated against a schema class
- This means that no data will be of type None/True/False
- ingested None will subclass NoneClass
- ingested True will subclass BoolClass
- ingested False will subclass BoolClass
- So if you need to check is True/False/None, instead use instance.is_true_oapg()/.is_false_oapg()/.is_none_oapg()
- All validated class instances are immutable except for ones based on io.File
- This is because if properties were changed after validation, that validation would no longer apply
- So no changing values or property values after a class has been instantiated
- String + Number types with formats
- String type data is stored as a string and if you need to access types based on its format like date, date-time, uuid, number etc then you will need to use accessor functions on the instance
- type string + format: See .as_date_oapg, .as_datetime_oapg, .as_decimal_oapg, .as_uuid_oapg
- type number + format: See .as_float_oapg, .as_int_oapg
- this was done because openapi/json-schema defines constraints. string data may be type string with no format keyword in one schema, and include a format constraint in another schema
- So if you need to access a string format based type, use as_date_oapg/as_datetime_oapg/as_decimal_oapg/as_uuid_oapg
- So if you need to access a number format based type, use as_int_oapg/as_float_oapg
- Property access on AnyType(type unset) or object(dict) schemas
- Only required keys with valid python names are properties like .someProp and have type hints
- All optional keys may not exist, so properties are not defined for them
- One can access optional values with dict_instance['optionalProp'] and KeyError will be raised if it does not exist
- Use get_item_oapg if you need a way to always get a value whether or not the key exists
- If the key does not exist, schemas.unset is returned from calling dict_instance.get_item_oapg('optionalProp')
- All required and optional keys have type hints for this method, and @typing.overload is used
- A type hint is also generated for additionalProperties accessed using this method
- So you will need to update you code to use some_instance['optionalProp'] to access optional property and additionalProperty values
- The location of the api classes has changed
- Api classes are located in your_package.apis.tags.some_api
- This change was made to eliminate redundant code generation
- Legacy generators generated the same endpoint twice if it had > 1 tag on it
- This generator defines an endpoint in one class, then inherits that class to generate apis by tags and by paths
- This change reduces code and allows quicker run time if you use the path apis
- path apis are at your_package.apis.paths.some_path
- Those apis will only load their needed models, which is less to load than all of the resources needed in a tag api
- So you will need to update your import paths to the api classes
Classes can have arbitrarily named properties set on them Endpoints can have arbitrary operationId method names set For those reasons, I use the prefix Oapg and _oapg to greatly reduce the likelihood of collisions on protected + public classes/methods. oapg stands for OpenApi Python Generator.
This was done because when payloads are ingested, they can be validated against N number of schemas. If the input signature used a different property name then that has mutated the payload. So SchemaA and SchemaB must both see the camelCase spec named variable. Also, it is possible to send in two properties, named camelCase and camel_case in the same payload. That use case should be supported so spec case is used.
Parameters can be included in different locations including:
- query
- path
- header
- cookie
Any of those parameters could use the same parameter names, so if every parameter was included as an endpoint parameter in a function signature, they would collide. For that reason, each of those inputs have been separated out into separate typed dictionaries:
- query_params
- path_params
- header_params
- cookie_params
So when updating your code, you will need to pass endpoint parameters in using those dictionaries.
Endpoint responses have been enriched to now include more information. Any response reom an endpoint will now include the following properties: response: urllib3.HTTPResponse body: typing.Union[Unset, Schema] headers: typing.Union[Unset, TODO] Note: response header deserialization has not yet been added
If the python package is hosted on a repository, you can install directly using:
pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git
(you may need to run pip
with root permission: sudo pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git
)
Then import the package:
import icasdk
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 icasdk
Please follow the installation procedure and then see the following sample.py:
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. |
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. |
EntitledBundleApi | get_entitled_bundle | get /api/entitledbundles/{entitledBundleId} | Retrieve an entitled bundle. |
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. |
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 | 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_nextflow_analysis | post /api/projects/{projectId}/analysis:nextflow | Create and start an analysis for a 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. The list might be incomplete if a folder contains too many output files, but all the data can always be retrieved through the GET data endpoint. |
ProjectAnalysisApi | get_analysis_steps | get /api/projects/{projectId}/analyses/{analysisId}/steps | Retrieve the individual steps of an analysis. |
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_raw_analysis_output | get /api/projects/{projectId}/analyses/{analysisId}/rawOutput | Retrieve the raw output of an analysis. |
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 | Retrieve a list of analysis creation batch items. |
ProjectAnalysisCreationBatchApi | get_analysis_creation_batch_item1 | get /api/projects/{projectId}/analysisCreationBatch/{batchId}/items/{itemId} | Retrieve a analysis creation batch item. |
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_notification_subscription | post /api/projects/{projectId}/customNotificationSubscriptions | Create a custom notification subscription |
ProjectCustomNotificationSubscriptionsApi | delete_notification_subscription | delete /api/projects/{projectId}/customNotificationSubscriptions/{subscriptionId} | Delete a custom notification subscription |
ProjectCustomNotificationSubscriptionsApi | get_notification_subscription | get /api/projects/{projectId}/customNotificationSubscriptions/{subscriptionId} | Retrieve a notification subscription |
ProjectCustomNotificationSubscriptionsApi | get_notification_subscriptions | get /api/projects/{projectId}/customNotificationSubscriptions | Retrieve notification subscriptions |
ProjectCustomNotificationSubscriptionsApi | update_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_folder_upload_session | post /api/projects/{projectId}/data/{dataId}/folderUploadSessions | 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_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. |
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. |
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. |
ProjectDataUpdateBatchApi | create_project_data_update_batch | post /api/projects/{projectId}/dataUpdateBatch | Create a project data update batch. |
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_subscription1 | post /api/projects/{projectId}/notificationSubscriptions | Create a notification subscription |
ProjectNotificationSubscriptionsApi | delete_notification_subscription1 | delete /api/projects/{projectId}/notificationSubscriptions/{subscriptionId} | Delete a notification subscription |
ProjectNotificationSubscriptionsApi | get_notification_subscription1 | get /api/projects/{projectId}/notificationSubscriptions/{subscriptionId} | Retrieve a notification subscription |
ProjectNotificationSubscriptionsApi | get_notification_subscriptions1 | get /api/projects/{projectId}/notificationSubscriptions | Retrieve notification subscriptions |
ProjectNotificationSubscriptionsApi | update_notification_subscription1 | 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_cwl_pipeline | post /api/projects/{projectId}/pipelines:createCwlPipeline | Create a CWL pipeline within a project. |
ProjectPipelineApi | create_nextflow_pipeline | post /api/projects/{projectId}/pipelines:createNextflowPipeline | Create a Nextflow pipeline within a project. |
ProjectPipelineApi | create_pipeline_file | post /api/projects/{projectId}/pipelines/{pipelineId}/files | Create a file for a pipeline. |
ProjectPipelineApi | delete_pipeline_file | delete /api/projects/{projectId}/pipelines/{pipelineId}/files/{fileId} | Delete a file for a pipeline. |
ProjectPipelineApi | download_pipeline_file_content1 | get /api/projects/{projectId}/pipelines/{pipelineId}/files/{fileId}/content | Download the contents of a pipeline file. |
ProjectPipelineApi | get_pipeline_files1 | get /api/projects/{projectId}/pipelines/{pipelineId}/files | Retrieve files for a project pipeline. |
ProjectPipelineApi | get_project_pipeline | get /api/projects/{projectId}/pipelines/{pipelineId} | Retrieve 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_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_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_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 | 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. |
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. |
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. |
- AWSDetails
- ActivationCodeDetail
- ActivationCodeDetailList
- ActivationCodeDetailUsage
- Analysis
- AnalysisCreationBatch
- AnalysisCreationBatchItem
- AnalysisCreationBatchItemPagedList
- AnalysisCreationBatchItemProcessing
- AnalysisCreationBatchItemRequest
- AnalysisData
- AnalysisDataInput
- AnalysisExternalData
- AnalysisInput
- AnalysisInputDataMount
- AnalysisInputExternalData
- AnalysisInputList
- AnalysisOutput
- AnalysisOutputList
- AnalysisOutputMapping
- AnalysisPagedList
- AnalysisParameterInput
- AnalysisRawOutput
- AnalysisReferenceDataParameter
- AnalysisS3DataDetails
- AnalysisStep
- AnalysisStepList
- AnalysisStepLogs
- AnalysisStorage
- AnalysisStorageList
- AnalysisTag
- Application
- AwsCredentials
- AwsTempCredentials
- BaseConnection
- BaseJob
- BaseJobList
- Bundle
- BundleData
- BundleDataPagedList
- BundleList
- BundlePagedList
- BundlePipeline
- BundlePipelineList
- BundleSample
- BundleSamplePagedList
- BundleTool
- BundleToolsList
- CWLToolDefinition
- CompleteFolderUploadSession
- Connector
- ConnectorList
- Country
- CreateAnalysisCreationBatch
- CreateBundle
- CreateConnector
- CreateCustomEvent
- CreateCustomNotificationSubscription
- CreateCwlAnalysis
- CreateCwlPipeline
- CreateData
- CreateDownloadRule
- CreateNextflowAnalysis
- CreateNextflowPipeline
- CreateNotificationChannel
- CreateNotificationSubscription
- CreateProject
- CreateProjectDataLinkingBatch
- CreateProjectDataLinkingBatchItem
- CreateProjectDataUpdateBatch
- CreateProjectPermission
- CreateProjectPermissionV4
- CreateSample
- CreateSampleCreationBatch
- CreateSampleCreationBatchDataItem
- CreateSampleCreationBatchSampleItem
- CreateStorageConfiguration
- CreateStorageCredential
- CreateTemporaryCredentials
- CreateTermsOfUse
- CreateUploadRule
- CustomNotificationSubscription
- CustomNotificationSubscriptionList
- CwlAnalysisInput
- CwlAnalysisInputJson
- CwlAnalysisJsonInput
- CwlAnalysisOutputJson
- CwlAnalysisStructuredInput
- CwlToolDefinitionList
- Data
- DataDetails
- DataFormat
- DataFormatPagedList
- DataIdOrPathList
- DataList
- DataPagedList
- DataTag
- DataTransfer
- DataTransferPagedList
- DataUpdateGroup
- DataUrlWithPath
- DataUrlWithPathList
- Download
- DownloadRule
- DownloadRuleList
- EventCode
- EventCodeList
- EventLog
- EventLogList
- ExecutionConfiguration
- ExecutionConfigurationList
- Field
- FieldId
- FieldList
- FindProjectSamples
- FindSampleBooleanCondition
- FindSampleCondition
- FindSampleDateCondition
- FindSampleNumberCondition
- FolderUploadSession
- InlineView
- InputParameter
- InputParameterList
- InputPart
- IntegerSettings
- Job
- JobPagedList
- Link
- Links
- LoadDataInBaseRequest
- MetadataField
- MetadataModel
- MetadataModelList
- Model
- MultipartFormDataInput
- NextflowAnalysisInput
- NotificationChannel
- NotificationChannelList
- NotificationSubscription
- NotificationSubscriptionList
- OptionSettings
- OptionalSampleTags
- Pipeline
- PipelineBundle
- PipelineConfigurationParameter
- PipelineConfigurationParameterList
- PipelineFile
- PipelineFileContentSpec
- PipelineFileList
- PipelineHtmlDocumentation
- PipelineLanguageVersion
- PipelineLanguageVersionList
- PipelineList
- PipelineTag
- Problem
- Project
- ProjectBaseTable
- ProjectBaseTableList
- ProjectBundle
- ProjectBundleList
- ProjectData
- ProjectDataLinkingBatch
- ProjectDataLinkingBatchItem
- ProjectDataLinkingBatchItemPagedList
- ProjectDataLinkingBatchItemProcessing
- ProjectDataLinkingBatchItemRequest
- ProjectDataPagedList
- ProjectDataUpdateBatch
- ProjectDataUpdateBatchItem
- ProjectDataUpdateBatchItemPagedList
- ProjectDataUpdateBatchItemProcessing
- ProjectDataUpdateBatchItemRequest
- ProjectList
- ProjectPagedList
- ProjectPermission
- ProjectPermissionList
- ProjectPermissionListV4
- ProjectPermissionV4
- ProjectPipeline
- ProjectPipelineList
- ProjectSample
- ProjectSamplePagedList
- ProjectTag
- RcloneTempCredentials
- ReferenceData
- ReferenceDataList
- ReferenceSet
- ReferenceSetList
- Region
- RegionList
- Sample
- SampleCreationBatch
- SampleCreationBatchItemPagedList
- SampleCreationBatchItemProcessing
- SampleCreationBatchItemRequest
- SampleCreationBatchSampleItem
- SampleHistory
- SampleHistoryList
- SamplePagedList
- SampleTag
- ScheduleDownload
- SearchMatchingActivationCodesForCwlAnalysis
- SearchMatchingActivationCodesForNextflowAnalysis
- SequencingRun
- Settings
- Species
- SpeciesList
- StorageBundle
- StorageBundleList
- StorageConfiguration
- StorageConfigurationDetails
- StorageConfigurationWithDetails
- StorageConfigurationWithDetailsList
- StorageCredential
- StorageCredentialList
- StringSettings
- SystemInfo
- TagUpdate
- TempCredentials
- TermsOfUse
- TermsOfUseAcceptance
- Token
- Type
- TypeList
- UpdateMetadata
- UpdateMetadataFieldGroup
- UpdateSingleMetadataField
- UpdateStorageCredentialSecrets
- Upload
- UploadRule
- UploadRuleList
- User
- UserList
- Workflow
- WorkflowSession
- WorkflowSessionTag
- Workgroup
- WorkgroupList
- Type: Bearer authentication (JWT)
- Type: Bearer authentication (psToken)
- Type: API key
- API key parameter name: X-API-Key
- Location: HTTP header
Authentication schemes defined for the API:
- Type: HTTP basic authentication
If the OpenAPI document is large, imports in icasdk.apis and icasdk.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 icasdk.apis.default_api import DefaultApi
from icasdk.model.pet import Pet
Solution 1: Before importing the package, adjust the maximum recursion limit as shown below:
import sys
sys.setrecursionlimit(1500)
import icasdk
from icasdk.apis import *
from icasdk.models import *