install.packages("remotes")
remotes::install_github("umccr-illumina/icar1")
require(icar1)
token <- Sys.getenv("ICA_ACCESS_TOKEN")
headers <- c(
"Accept" = "application/vnd.illumina.v3+json",
"Authorization" = paste0("Bearer ", token)
)
All URIs are relative to http://aps2.platform.illumina.com
Class | Method | HTTP request | Description |
---|---|---|---|
FilesApi | ArchiveFile | POST /v1/files/{fileId}:archive | Archive a file |
FilesApi | BulkFileUpdate | PATCH /v1/files | Updates list of files with metadata |
FilesApi | CompleteFileUpload | POST /v1/files/{fileId}:completeUpload | Complete a file Upload |
FilesApi | CopyFiles | POST /v1/files/copy | Copy list of files |
FilesApi | CreateFile | POST /v1/files | Create a file entry in GDS and get temporary credentials for upload |
FilesApi | DeleteFile | DELETE /v1/files/{fileId} | Permanently delete a file |
FilesApi | GetFile | GET /v1/files/{fileId} | Get details about a file, including a pre-signed URL for download |
FilesApi | ListFiles | GET /v1/files | Get a list of files |
FilesApi | ListVolumeFiles | POST /v1/files/list | Get a list of volume files |
FilesApi | UnarchiveFile | POST /v1/files/{fileId}:unarchive | Unarchive a file |
FilesApi | UpdateFile | PATCH /v1/files/{fileId} | Update a file entry in GDS and get temporary credentials for upload |
FoldersApi | ArchiveFolder | POST /v1/folders/{folderId}:archive | Archive a folder |
FoldersApi | BulkFolderUpdate | PATCH /v1/folders | Updates list of folders with metadata |
FoldersApi | BulkMetadataFolderUpdate | PATCH /v1/folders/bulkMetadataFolderUpdate | Updates list of folders with metadata |
FoldersApi | CompleteFolderSession | POST /v1/folders/{folderId}/sessions/{sessionId}:complete | Complete a folder upload in GDS |
FoldersApi | CopyFolder | POST /v1/folders/{folderId}:copy | Copy a folder |
FoldersApi | CreateFolder | POST /v1/folders | Create a folder in GDS and receive credentials for upload |
FoldersApi | CreateFolderSession | POST /v1/folders/{folderId}/sessions | Create a session |
FoldersApi | DeleteFolder | DELETE /v1/folders/{folderId} | Deletes a folder by id |
FoldersApi | GetFolder | GET /v1/folders/{folderId} | Get information about a folder in GDS. |
FoldersApi | GetFolderJob | GET /v1/folders/{folderId}/jobs/{jobId} | Get status of a folder job in GDS |
FoldersApi | GetFolderSession | GET /v1/folders/{folderId}/sessions/{sessionId} | Get status of a folder upload in GDS |
FoldersApi | ListFolders | GET /v1/folders | Get a list of folders |
FoldersApi | UnarchiveFolder | POST /v1/folders/{folderId}:unarchive | Unarchive a folder |
FoldersApi | UpdateFolder | PATCH /v1/folders/{folderId} | Update a folder content or acl |
JobsApi | AbortJob | POST /v1/jobs/{jobId}:abort | Abort a job in GDS. |
JobsApi | GetJob | GET /v1/jobs/{jobId} | Get information about a job in GDS. |
JobsApi | ListJobs | GET /v1/jobs | Get a list of jobs for a given folder |
SubscriptionsApi | CreateSubscription | POST /v1/subscriptions | Creates a subscription to an event type and defines how those events get delivered. |
SubscriptionsApi | DisableSubscription | DELETE /v1/subscriptions/{subscriptionId} | Given a subscription id, disables the specified subscription. |
SubscriptionsApi | GetSubscription | GET /v1/subscriptions/{subscriptionId} | Given a subscription id, returns information about that subscription. |
SubscriptionsApi | ListSubscriptions | GET /v1/subscriptions | Get a list of subscriptions. |
TaskRunsApi | AbortTaskRun | PUT /v1/tasks/runs/{runId}:abort | Abort a task run |
TaskRunsApi | CreateTaskRun | POST /v1/tasks/runs | Create and launch a task run |
TaskRunsApi | GetTaskRun | GET /v1/tasks/runs/{runId} | Get the status of a task run |
TaskRunsApi | HeartbeatTaskRun | POST /v1/tasks/runs/{runId}:heartbeat | Heartbeat for a task run |
TaskRunsApi | ListTaskRuns | GET /v1/tasks/runs | Get a list of task runs |
TaskVersionsApi | CreateTaskVersion | POST /v1/tasks/{taskId}/versions | Create a task version |
TaskVersionsApi | GetTaskVersion | GET /v1/tasks/{taskId}/versions/{versionId} | Get the details of a task version |
TaskVersionsApi | LaunchTaskRun | POST /v1/tasks/{taskId}/versions/{versionId}:launch | Launch a task version |
TaskVersionsApi | ListTaskVersions | GET /v1/tasks/{taskId}/versions | Get a list of versions |
TaskVersionsApi | UpdateTaskVersion | PATCH /v1/tasks/{taskId}/versions/{versionId} | Update task version properties |
TasksApi | CreateTask | POST /v1/tasks | Create a Task |
TasksApi | GetTask | GET /v1/tasks/{taskId} | Get the details of a Task |
TasksApi | ListTasks | GET /v1/tasks | Get a list of tasks |
TasksApi | UpdateTask | PATCH /v1/tasks/{taskId} | Update an existing task. |
VolumeConfigurationsApi | CreateVolumeConfiguration | POST /v1/volumeconfigurations | Create a volume configuration in GDS. |
VolumeConfigurationsApi | DeleteVolumeConfiguration | DELETE /v1/volumeconfigurations/{volumeConfigurationName} | Deletes a volume configuration by Id or name |
VolumeConfigurationsApi | GetVolumeConfiguration | GET /v1/volumeconfigurations/{volumeConfigurationName} | Get information for the specified volume configuration name or Id |
VolumeConfigurationsApi | ListVolumeConfigurations | GET /v1/volumeconfigurations | Get a list of volumes |
VolumeConfigurationsApi | ValidateVolumeConfiguration | POST /v1/volumeconfigurations/{volumeConfigurationName}:validate | Validate a volume configuration |
VolumesApi | CreateVolume | POST /v1/volumes | Create a volume in GDS and receive temporary credentials for upload |
VolumesApi | DeleteVolume | DELETE /v1/volumes/{volumeId} | Deletes a volume by Id |
VolumesApi | GetVolume | GET /v1/volumes/{volumeId} | Get information for the specified volume ID or volume name |
VolumesApi | ListVolumes | GET /v1/volumes | Get a list of volumes |
VolumesApi | UpdateVolume | PATCH /v1/volumes/{volumeId} | Update a volume content |
WorkflowRunsApi | AbortWorkflowRun | PUT /v1/workflows/runs/{runId}:abort | Abort a workflow run |
WorkflowRunsApi | GetWorkflowRun | GET /v1/workflows/runs/{runId} | Get the details of a workflow run |
WorkflowRunsApi | ListWorkflowRunHistory | GET /v1/workflows/runs/{runId}/history | Get a list of workflow run history events |
WorkflowRunsApi | ListWorkflowRuns | GET /v1/workflows/runs | Get a list of workflow runs |
WorkflowSignalsApi | FailSignal | PATCH /v1/workflows/signals/{signalId}:fail | Fail a workflow signal |
WorkflowSignalsApi | GetSignal | GET /v1/workflows/signals/{signalId} | Get the details of a workflow signal |
WorkflowSignalsApi | ListSignals | GET /v1/workflows/signals | Get a list of workflow signals |
WorkflowSignalsApi | SucceedSignal | PATCH /v1/workflows/signals/{signalId}:succeed | Succeed a workflow signal |
WorkflowVersionsApi | CreateWorkflowVersion | POST /v1/workflows/{workflowId}/versions | Create a new workflow version |
WorkflowVersionsApi | GetWorkflowVersion | GET /v1/workflows/{workflowId}/versions/{versionName} | Get the details of a workflow version |
WorkflowVersionsApi | LaunchWorkflowVersion | POST /v1/workflows/{workflowId}/versions/{versionName}:launch | Launch a workflow version |
WorkflowVersionsApi | ListAllWorkflowVersions | GET /v1/workflows/versions | Get a list of all workflow versions |
WorkflowVersionsApi | ListWorkflowVersions | GET /v1/workflows/{workflowId}/versions | Get a list of workflow versions |
WorkflowVersionsApi | UpdateWorkflowVersion | PATCH /v1/workflows/{workflowId}/versions/{versionName} | Update an existing workflow version |
WorkflowsApi | CreateWorkflow | POST /v1/workflows | Create a workflow |
WorkflowsApi | GetWorkflow | GET /v1/workflows/{workflowId} | Get the details of a workflow |
WorkflowsApi | ListWorkflows | GET /v1/workflows | Get a list of workflows |
WorkflowsApi | UpdateWorkflow | PATCH /v1/workflows/{workflowId} | Update an existing workflow |
- AWSS3ObjectStoreSetting
- AbortWorkflowRunRequest
- AgentTaskRun
- ArchiveStatuses
- AwsS3PresignedUrlForUpload
- AwsS3TemporaryReadOnlyCredentials
- AwsS3TemporaryUploadCredentials
- BulkFailedItem
- BulkFileUpdateItem
- BulkFileUpdateRequest
- BulkFileUpdateResponse
- BulkFolderMetadataUpdateRequest
- BulkFolderUpdateItem
- BulkFolderUpdateRequest
- BulkFolderUpdateResponse
- BulkMetadataUpdateOperationParameters
- BulkUpdateFailedItem
- CheckOutQueuedTaskRunRequest
- Cluster
- ClusterSummary
- ClusterSummaryPagedItems
- CompleteSessionRequest
- ContainerState
- ContainerStateRunning
- ContainerStateTerminated
- ContainerStateWaiting
- ContainerStatus
- CreateClusterRequest
- CreateFileRequest
- CreateFolderRequest
- CreateSessionRequest
- CreateSessionResponse
- CreateSubscriptionRequest
- CreateTaskRequest
- CreateTaskRunRequest
- CreateTaskVersionRequest
- CreateVolumeConfigurationRequest
- CreateVolumeRequest
- CreateVolumeResponse
- CreateWorkflowRequest
- CreateWorkflowVersionRequest
- Credentials
- DeliveryTarget
- DeliveryTargetAwsSnsTopic
- DeliveryTargetAwsSqsQueue
- DeliveryTargetWorkflowRunLaunch
- Environment
- ErrorResponse
- ErrorResponse1
- ErrorResponse2
- ErrorResponse3
- Execution
- FailWorkflowSignalRequest
- FileArchiveRequest
- FileArchiveStorageTier
- FileCopyOperationParameters
- FileCopyOutput
- FileLifeCycleSettings
- FileListCopyRequest
- FileListResponse
- FileResponse
- FileStatus
- FileUnarchiveRequest
- FileUploadCompleteRequest
- FileWriteableResponse
- FolderArchiveRequest
- FolderArchiveStorageTier
- FolderCopyOperationParameters
- FolderCopyRequest
- FolderDeleteOperationParameters
- FolderListResponse
- FolderResponse
- FolderUnarchiveRequest
- FolderUpdateRequest
- FolderWriteableResponse
- GracePeriodEndAction
- HeartbeatTaskRunRequest
- Image
- InputMountMappingWithCreds
- InputStreamSettings
- JobListResponse
- JobOperationParameters
- JobOperationType
- JobOutput
- JobProgressStatus
- JobResponse
- JobStatus
- LaunchTaskRequest
- LaunchWorkflowVersionRequest
- MetadataUpdateOutput
- MetadataUpdateRequest
- MountMappingWithCreds
- ObjectStoreAccess
- ObjectStoreSettings
- PartEtag
- PartInfo
- Resources
- RestoreType
- SessionResponse
- SessionStatus
- SortDirection
- StorageTier
- Subscription
- SubscriptionList
- SubscriptionListSortFields
- SucceedWorkflowSignalRequest
- SystemFiles
- Task
- TaskRun
- TaskRunHeartbeat
- TaskRunLogs
- TaskRunSummary
- TaskRunSummaryPagedItems
- TaskSummary
- TaskSummaryPagedItems
- TaskVersion
- TaskVersionSummary
- TaskVersionSummaryPagedItems
- UpdateClusterRequest
- UpdateFileRequest
- UpdateTaskRequest
- UpdateTaskRunStateRequest
- UpdateTaskVersionRequest
- UpdateVolumeRequest
- UpdateWorkflowRequest
- UpdateWorkflowVersionRequest
- VolumeConfigurationListResponse
- VolumeConfigurationOnlineStatus
- VolumeConfigurationResponse
- VolumeFileListRequest
- VolumeFileListResponse
- VolumeLifeCycleSettings
- VolumeListResponse
- VolumeMigrationOperationParameters
- VolumeResponse
- Workflow
- WorkflowArgument
- WorkflowCompact
- WorkflowConnection
- WorkflowLanguage
- WorkflowList
- WorkflowRun
- WorkflowRunCompact
- WorkflowRunHistoryEvent
- WorkflowRunHistoryEventList
- WorkflowRunList
- WorkflowSignal
- WorkflowSignalCompact
- WorkflowSignalList
- WorkflowVersion
- WorkflowVersionCompact
- WorkflowVersionList
- Type: API key
- API key parameter name: Authorization
- Location: HTTP header