R API client for icar1

Installation

install.packages("remotes")
remotes::install_github("umccr-illumina/icar1")

Usage

Setup Auth

require(icar1)
token <- Sys.getenv("ICA_ACCESS_TOKEN")
headers <- c(
  "Accept" = "application/vnd.illumina.v3+json",
  "Authorization" = paste0("Bearer ", token)
  )

Documentation for API Endpoints

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

Documentation for Models

• 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

Documentation for Authorization

Bearer

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