docs/WorkspacesApi.md
In vjcitn/terraClientR: R Package Client for FireCloud
WorkspacesApi
All URIs are relative to http://localhost
Method | HTTP request | Description
------------- | ------------- | -------------
BrowserDownloadAttributes | GET /cookie-authed/workspaces/{workspaceNamespace}/{workspaceName}/exportAttributesTSV | TSV file containing workspace attributes (allows cookie-based authentication)
ChangedWorkspaceNotification | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/sendChangeNotification | Sends notifications for change to workspace
CheckIamActionWithLock | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/checkIamActionWithLock/{samActionName} | Check IAM action with lock
CloneWorkspace | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/clone | Clone Workspace
CreateWorkspace | POST /api/workspaces | Create workspace
DeleteWorkspace | DELETE /api/workspaces/{workspaceNamespace}/{workspaceName} | Delete workspace
DeleteWorkspaceTags | DELETE /api/workspaces/{workspaceNamespace}/{workspaceName}/tags | Remove the user-supplied tags from the workspace.
ExportAttributesTSV | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/exportAttributesTSV | TSV file containing workspace attributes
GetBucketUsage | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/bucketUsage | Get bucket usage
GetCatalog | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/catalog | Get workspace catalog permission
GetStorageCostEstimate | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/storageCostEstimate | Calculate an estimate of the monthly storage cost for the workspace bucket
GetTags | GET /api/workspaces/tags | Get all tags used in FireCloud (for autocomplete)
GetWorkspace | GET /api/workspaces/{workspaceNamespace}/{workspaceName} | Get workspace
GetWorkspaceAccessInstructions | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/accessInstructions | Get workspace access instructions (if any)
GetWorkspaceAcl | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/acl | Get workspace ACL
GetWorkspaceBucketOptions | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/bucketOptions | Get metadata about the workspace bucket
GetWorkspaceTags | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/tags | Get the tags for this workspace.
ImportAttributesTSV | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/importAttributesTSV | Import workspace attributes from a tsv file
ListWorkspaceMethodConfigs | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/methodconfigs | List method configurations in a workspace
ListWorkspaces | GET /api/workspaces | Lists workspaces.
LockWorkspace | PUT /api/workspaces/{workspaceNamespace}/{workspaceName}/lock | Lock Workspace
PatchWorkspaceTags | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/tags | Add tags to the workspace without modifying pre-existing tags.
PostWorkspaceMethodConfig | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/methodconfigs | Create a Method Configuration in a workspace
PutWorkspaceTags | PUT /api/workspaces/{workspaceNamespace}/{workspaceName}/tags | Replace all tags for this workspace with the user input.
ReadBucket | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/checkBucketReadAccess | Read workspace bucket
SetAttributes | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/setAttributes | Set attributes on a workspace.
UnlockWorkspace | PUT /api/workspaces/{workspaceNamespace}/{workspaceName}/unlock | Unlock Workspace
UpdateAttributes | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/updateAttributes | Modify attributes on a workspace.
UpdateCatalog | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/catalog | Update catalog permission
UpdateWorkspaceACL | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/acl | Update workspace ACL
WorkspacePermissionReport | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/permissionReport | Retrieve user permissions for the workspace and the workspace's method references
BrowserDownloadAttributes
data.frame BrowserDownloadAttributes(workspace.namespace, workspace.name)
TSV file containing workspace attributes (allows cookie-based authentication)
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#TSV file containing workspace attributes (allows cookie-based authentication)
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$BrowserDownloadAttributes(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
data.frame
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: text/plain
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Workspace attributes in TSV format | - |
| 404 | Workspace does not exist | - |
| 500 | Internal Server Error | - |
ChangedWorkspaceNotification
ChangedWorkspaceNotification(workspace.namespace, workspace.name)
Sends notifications for change to workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | workspace namespace
var.workspace.name <- 'workspace.name_example' # character | workspace name
#Sends notifications for change to workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$ChangedWorkspaceNotification(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| workspace namespace |
workspace.name | character| workspace name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Success | - |
| 403 | Insufficient permisions to send notification on this workspace | - |
CheckIamActionWithLock
CheckIamActionWithLock(workspace.namespace, workspace.name, sam.action.name)
Check IAM action with lock
Check to see if the user has the given action on a workspace in Sam. Takes into account if the workspace is locked too.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.sam.action.name <- 'sam.action.name_example' # character | Sam action
#Check IAM action with lock
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$CheckIamActionWithLock(var.workspace.namespace, var.workspace.name, var.sam.action.name)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
sam.action.name | character| Sam action |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 204 | User can perform the given action on the workspace | - |
| 403 | User may not perform the given action on the workspace (including if it doesn't exist) | - |
| 500 | Internal Server Error | - |
CloneWorkspace
WorkspaceDetails CloneWorkspace(workspace.namespace, workspace.name, workspace)
Clone Workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.workspace <- WorkspaceRequestClone$new("namespace_example", "name_example", 123, list(ManagedGroupRef$new("membersGroupName_example")), "copyFilesWithPrefix_example", "noWorkspaceOwner_example") # WorkspaceRequestClone | Cloned workspace information
#Clone Workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$CloneWorkspace(var.workspace.namespace, var.workspace.name, var.workspace)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
workspace | WorkspaceRequestClone| Cloned workspace information |
Return type
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 201 | Successful Request | - |
| 400 | Unable to create resources for workspace | - |
| 404 | Source workspace not found | - |
| 409 | Destination workspace already exists | - |
| 500 | Internal Server Error | - |
CreateWorkspace
WorkspaceDetails CreateWorkspace(workspace)
Create workspace
Example
library(openapi)
var.workspace <- WorkspaceRequest$new("namespace_example", "name_example", 123, list(ManagedGroupRef$new("membersGroupName_example")), "noWorkspaceOwner_example") # WorkspaceRequest | New workspace information
#Create workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$CreateWorkspace(var.workspace)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace | WorkspaceRequest| New workspace information |
Return type
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 201 | Successful Request | - |
| 400 | Bad request | - |
| 403 | Unable to create bucket for workspace | - |
| 409 | Workspace by that name already exists | - |
| 500 | Internal Server Error | - |
DeleteWorkspace
DeleteWorkspace(workspace.namespace, workspace.name)
Delete workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Delete workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$DeleteWorkspace(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 202 | Request Accepted | - |
| 403 | User does not have correct permissions to delete a published workspace | - |
| 404 | Workspace does not exist | - |
| 500 | Internal Server Error | - |
DeleteWorkspaceTags
array[character] DeleteWorkspaceTags(workspace.namespace, workspace.name, tags)
Remove the user-supplied tags from the workspace.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.tags <- list("property_example") # array[character] | List of tags.
#Remove the user-supplied tags from the workspace.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$DeleteWorkspaceTags(var.workspace.namespace, var.workspace.name, var.tags)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
tags | list( character )| List of tags. |
Return type
array[character]
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Workspace tags | - |
| 400 | Invalid input | - |
| 404 | Workspace not found | - |
| 500 | Internal Error | - |
ExportAttributesTSV
data.frame ExportAttributesTSV(workspace.namespace, workspace.name)
TSV file containing workspace attributes
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#TSV file containing workspace attributes
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$ExportAttributesTSV(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
data.frame
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: text/plain
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Workspace attributes in TSV format | - |
| 404 | Workspace does not exist | - |
| 500 | Internal Server Error | - |
GetBucketUsage
GetBucketUsage(workspace.namespace, workspace.name)
Get bucket usage
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get bucket usage
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$GetBucketUsage(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
GetCatalog
array[WorkspaceCatalog] GetCatalog(workspace.namespace, workspace.name)
Get workspace catalog permission
Get catalog permissions for a workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get workspace catalog permission
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetCatalog(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
| 404 | Workspace not found | - |
| 500 | Rawls Internal Error | - |
GetStorageCostEstimate
GetStorageCostEstimate(workspace.namespace, workspace.name)
Calculate an estimate of the monthly storage cost for the workspace bucket
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Calculate an estimate of the monthly storage cost for the workspace bucket
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$GetStorageCostEstimate(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Storage cost estimate | - |
| 404 | Workspace not found | - |
| 500 | Internal Error | - |
GetTags
array[WorkspaceTag] GetTags(q=var.q)
Get all tags used in FireCloud (for autocomplete)
list of all tags used in FireCloud and their associated frequencies
Example
library(openapi)
var.q <- 'q_example' # character | Query string
#Get all tags used in FireCloud (for autocomplete)
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetTags(q=var.q)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
q | character| Query string | [optional]
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | list of all tags used in FireCloud | - |
| 500 | Rawls Internal Error | - |
GetWorkspace
WorkspaceResponse GetWorkspace(workspace.namespace, workspace.name, fields=var.fields)
Get workspace
Get a single workspace's details, optionally filtered to only the specified fields. See additional GET methods in this section to retrieve additional details about the workspace. For instance, this API only returns the workspace's owners; use the GET .../acl method to retrieve the full list of all users at all permission levels.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.fields <- list("inner_example") # array[character] | When specified, include only these keys in the response payload and exclude other keys. Accepts a comma-delimited list of values. To include a nested key, specify the key's path using a dot delimiter; for example, to include {\"workspace\": {\"attributes\": {}}}, specify \"workspace.attributes\". Legal values are any first-level key in the response, any first-level key inside the {\"workspace\": {}} object, and any first-level key inside the {\"workspace\": {\"attributes\": {}}} object. If omitted, will return the full response payload.
#Get workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspace(var.workspace.namespace, var.workspace.name, fields=var.fields)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
fields | list( character )| When specified, include only these keys in the response payload and exclude other keys. Accepts a comma-delimited list of values. To include a nested key, specify the key's path using a dot delimiter; for example, to include {\"workspace\": {\"attributes\": {}}}, specify \"workspace.attributes\". Legal values are any first-level key in the response, any first-level key inside the {\"workspace\": {}} object, and any first-level key inside the {\"workspace\": {\"attributes\": {}}} object. If omitted, will return the full response payload. | [optional]
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
| 400 | Unrecognized query parameters | - |
| 404 | Workspace does not exist | - |
| 500 | Internal Server Error | - |
GetWorkspaceAccessInstructions
array[ManagedGroupAccessInstructions] GetWorkspaceAccessInstructions(workspace.namespace, workspace.name)
Get workspace access instructions (if any)
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get workspace access instructions (if any)
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspaceAccessInstructions(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
array[ManagedGroupAccessInstructions]
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
| 404 | Workspace not found | - |
| 500 | Internal Server Error | - |
GetWorkspaceAcl
WorkspaceACL GetWorkspaceAcl(workspace.namespace, workspace.name)
Get workspace ACL
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get workspace ACL
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspaceAcl(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
| 400 | Can't retrieve ACL for workspace | - |
| 404 | Workspace not found | - |
| 500 | Internal Server Error | - |
GetWorkspaceBucketOptions
WorkspaceBucketOptions GetWorkspaceBucketOptions(workspace.namespace, workspace.name)
Get metadata about the workspace bucket
Returns metadata about the workspace bucket.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get metadata about the workspace bucket
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspaceBucketOptions(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
| 404 | Workspace not found | - |
| 500 | Rawls Internal Error | - |
GetWorkspaceTags
array[character] GetWorkspaceTags(workspace.namespace, workspace.name)
Get the tags for this workspace.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get the tags for this workspace.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspaceTags(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
array[character]
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Workspace tags | - |
| 404 | Workspace not found | - |
| 500 | Internal Error | - |
ImportAttributesTSV
ImportAttributesTSV(workspace.namespace, workspace.name, attributes)
Import workspace attributes from a tsv file
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.attributes <- File.new('/path/to/file') # data.frame | A valid TSV import file
#Import workspace attributes from a tsv file
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$ImportAttributesTSV(var.workspace.namespace, var.workspace.name, var.attributes)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
attributes | data.frame| A valid TSV import file |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: multipart/form-data
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
| 400 | Bad Request | - |
| 404 | Source Workspace not found | - |
| 500 | Internal Error | - |
ListWorkspaceMethodConfigs
ListWorkspaceMethodConfigs(workspace.namespace, workspace.name, all.repos=FALSE)
List method configurations in a workspace
List method configurations in a workspace. By default, only Agora method configs are returned. To return configs for all repos, specify allRepos to be true. #### Expanded discussion on the methodRepoMethod field This endpoint returns method references to Agora in the format \"methodRepoMethod\": { \"methodNamespace\": \"namespace\", \"methodName\": \"name\", \"methodVersion\": 1, \"sourceRepo\": \"agora\", \"methodUri\": \"agora://namespace/name/1\" } and for Dockstore in the format \"methodRepoMethod\": { \"methodPath\": \"path\", \"methodVersion\": \"version\", \"sourceRepo\": \"agora\", \"methodUri\": \"dockstore://path/version\" } If you are only working with Agora methods, the fields \"sourceRepo\" and \"methodUri\" can be considered informational and do not need to be round-tripped (see the corresponding POST /api/workspaces/{workspaceNamespace}/{workspaceName}/methodconfigs for more details).
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.all.repos <- FALSE # character | Configs for all repos, not just Agora
#List method configurations in a workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$ListWorkspaceMethodConfigs(var.workspace.namespace, var.workspace.name, all.repos=var.all.repos)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
all.repos | character| Configs for all repos, not just Agora | [optional] [default to FALSE]
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | List of Method Configurations | - |
| 404 | Workspace does not exist | - |
| 500 | Internal Server Error | - |
ListWorkspaces
array[WorkspaceListResponse] ListWorkspaces(fields=var.fields)
Lists workspaces.
Example
library(openapi)
var.fields <- list("inner_example") # array[character] | When specified, include only these keys in the response payload and exclude other keys. Accepts a comma-delimited list of values. To include a nested key, specify the key's path using a dot delimiter; for example, to include {\"workspace\": {\"attributes\": {}}}, specify \"workspace.attributes\". Legal values are any first-level key in the response, any first-level key inside the {\"workspace\": {}} object, and any first-level key inside the {\"workspace\": {\"attributes\": {}}} object. If omitted, will return the full response payload.
#Lists workspaces.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$ListWorkspaces(fields=var.fields)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
fields | list( character )| When specified, include only these keys in the response payload and exclude other keys. Accepts a comma-delimited list of values. To include a nested key, specify the key's path using a dot delimiter; for example, to include {\"workspace\": {\"attributes\": {}}}, specify \"workspace.attributes\". Legal values are any first-level key in the response, any first-level key inside the {\"workspace\": {}} object, and any first-level key inside the {\"workspace\": {\"attributes\": {}}} object. If omitted, will return the full response payload. | [optional]
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json, text/plain
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | List of workspaces. | - |
| 400 | Unrecognized query parameters | - |
LockWorkspace
LockWorkspace(workspace.namespace, workspace.name)
Lock Workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Lock Workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$LockWorkspace(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | No response was specified | - |
| 204 | Successful Request | - |
| 403 | Not Owner | - |
| 404 | Workspace Not Found | - |
| 500 | Internal Server Error | - |
PatchWorkspaceTags
array[character] PatchWorkspaceTags(workspace.namespace, workspace.name, tags)
Add tags to the workspace without modifying pre-existing tags.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.tags <- list("property_example") # array[character] | List of tags.
#Add tags to the workspace without modifying pre-existing tags.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$PatchWorkspaceTags(var.workspace.namespace, var.workspace.name, var.tags)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
tags | list( character )| List of tags. |
Return type
array[character]
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Workspace tags | - |
| 400 | Invalid input | - |
| 404 | Workspace not found | - |
| 500 | Internal Error | - |
PostWorkspaceMethodConfig
PostWorkspaceMethodConfig(workspace.namespace, workspace.name, method.config.json)
Create a Method Configuration in a workspace
Create method configurations. #### Expanded discussion on the methodRepoMethod field To create a method config for an Agora method, \"sourceRepo\": \"agora\" is optional; the following is sufficient: \"methodRepoMethod\": { \"methodNamespace\": \"namespace\", \"methodName\": \"name\", \"methodVersion\": 1 } To create a method config for a Dockstore method, \"sourceRepo\": \"dockstore\" is required: \"methodRepoMethod\": { \"sourceRepo\": \"dockstore\", \"methodPath\": \"path\", \"methodVersion\": \"version\" } You may also use the URI on its own to create a config referencing any supported repo (currently Agora and Dockstore): \"methodRepoMethod\": { \"methodUri\": \"agora://namespace/name/1\" } \"methodRepoMethod\": { \"methodUri\": \"dockstore://path/version\" } The system is specified to check for a URI first before falling back to the legacy fields. Unsupported repos will return a 400 Bad Request.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.method.config.json <- NewMethodConfigIngest$new("namespace_example", "name_example", "rootEntityType_example", TODO, TODO, TODO, TODO, 123, "deleted_example") # NewMethodConfigIngest | Method Configuration contents
#Create a Method Configuration in a workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$PostWorkspaceMethodConfig(var.workspace.namespace, var.workspace.name, var.method.config.json)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
method.config.json | NewMethodConfigIngest| Method Configuration contents |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 201 | Successful Request | - |
| 404 | Workspace not found | - |
| 409 | Method Configuration already exists | - |
| 500 | Internal Server Error | - |
PutWorkspaceTags
array[character] PutWorkspaceTags(workspace.namespace, workspace.name, tags)
Replace all tags for this workspace with the user input.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.tags <- list("property_example") # array[character] | List of tags.
#Replace all tags for this workspace with the user input.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$PutWorkspaceTags(var.workspace.namespace, var.workspace.name, var.tags)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
tags | list( character )| List of tags. |
Return type
array[character]
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Workspace tags | - |
| 400 | Invalid input | - |
| 404 | Workspace not found | - |
| 500 | Internal Error | - |
ReadBucket
ReadBucket(workspace.namespace, workspace.name)
Read workspace bucket
Read a workspace bucket
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Read workspace bucket
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$ReadBucket(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
| 403 | Insufficient permissions to access workspace bucket | - |
| 404 | Workspace Not Found | - |
| 500 | Internal Server Error | - |
SetAttributes
SetAttributes(workspace.namespace, workspace.name, new.attributes)
Set attributes on a workspace.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.new.attributes <- TODO # map(object) | New attribute values, as Map[String, Attribute]. WARNING! This should not be used to change library metadata (republish will not happen). Use UpdateAttributes in the library section
#Set attributes on a workspace.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$SetAttributes(var.workspace.namespace, var.workspace.name, var.new.attributes)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
new.attributes | named list( map(object) )| New attribute values, as Map[String, Attribute]. WARNING! This should not be used to change library metadata (republish will not happen). Use UpdateAttributes in the library section |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Success | - |
| 400 | Malformed request | - |
| 404 | Workspace not found | - |
| 500 | Internal Error | - |
UnlockWorkspace
UnlockWorkspace(workspace.namespace, workspace.name)
Unlock Workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Unlock Workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$UnlockWorkspace(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | No response was specified | - |
| 204 | Successful Request | - |
| 403 | Not Owner | - |
| 404 | Workspace Not Found | - |
| 500 | Internal Server Error | - |
UpdateAttributes
WorkspaceDetails UpdateAttributes(workspace.namespace, workspace.name, workspace.update.json)
Modify attributes on a workspace.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.workspace.update.json <- list(AttributeUpdateOperation$new("AddUpdateAttribute")) # array[AttributeUpdateOperation] | Attribute operations. WARNING! This should not be used to change library metadata (republish will not happen). Use UpdateAttributes in the library section.
#Modify attributes on a workspace.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$UpdateAttributes(var.workspace.namespace, var.workspace.name, var.workspace.update.json)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
workspace.update.json | list( AttributeUpdateOperation )| Attribute operations. WARNING! This should not be used to change library metadata (republish will not happen). Use UpdateAttributes in the library section. |
Return type
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Success | - |
| 400 | Invalid operation | - |
| 404 | Workspace not found | - |
| 500 | Internal Error | - |
UpdateCatalog
WorkspaceCatalogUpdateResponseList UpdateCatalog(workspace.namespace, workspace.name, catalog.updates)
Update catalog permission
Set catalog permisisons for a workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.catalog.updates <- list(WorkspaceCatalog$new("email_example", "catalog_example")) # array[WorkspaceCatalog] | Series of Catalog updates for workspace
#Update catalog permission
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$UpdateCatalog(var.workspace.namespace, var.workspace.name, var.catalog.updates)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
catalog.updates | list( WorkspaceCatalog )| Series of Catalog updates for workspace |
Return type
WorkspaceCatalogUpdateResponseList
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
| 403 | Insufficient permissions to change catalog permissions (must be owner or admin) | - |
| 404 | Workspace, user or group not found | - |
| 500 | Rawls Internal Error | - |
UpdateWorkspaceACL
WorkspaceACLUpdateResponseList UpdateWorkspaceACL(workspace.namespace, workspace.name, invite.users.not.found, acl.updates)
Update workspace ACL
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.invite.users.not.found <- FALSE # character | true to invite unregistered users, false to ignore
var.acl.updates <- list(WorkspaceACLUpdate$new("email_example", "accessLevel_example", "canShare_example", "canCompute_example")) # array[WorkspaceACLUpdate] | Series of ACL updates for workspace
#Update workspace ACL
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$UpdateWorkspaceACL(var.workspace.namespace, var.workspace.name, var.invite.users.not.found, var.acl.updates)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
invite.users.not.found | character| true to invite unregistered users, false to ignore | [default to FALSE]
acl.updates | list( WorkspaceACLUpdate )| Series of ACL updates for workspace |
Return type
WorkspaceACLUpdateResponseList
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Successful Request | - |
| 400 | Can't set ACL for workspace | - |
| 404 | Workspace not found | - |
| 500 | Internal Server Error | - |
WorkspacePermissionReport
PermissionReport WorkspacePermissionReport(workspace.namespace, workspace.name, report.input)
Retrieve user permissions for the workspace and the workspace's method references
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.report.input <- PermissionReportRequest$new(list("users_example"), list(MethodConfigurationName$new("namespace_example", "name_example"))) # PermissionReportRequest | Users and/or configs on which to report, both optional
#Retrieve user permissions for the workspace and the workspace's method references
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$WorkspacePermissionReport(var.workspace.namespace, var.workspace.name, var.report.input)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
workspace.namespace | character| Workspace Namespace |
workspace.name | character| Workspace Name |
report.input | PermissionReportRequest| Users and/or configs on which to report, both optional |
Return type
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
| 200 | Permission Report | - |
| 404 | Workspace does not exist | - |
| 500 | Internal Server Error | - |
vjcitn/terraClientR documentation built on Dec. 23, 2021, 4:07 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
WorkspacesApi
All URIs are relative to http://localhost
Method | HTTP request | Description ------------- | ------------- | ------------- BrowserDownloadAttributes | GET /cookie-authed/workspaces/{workspaceNamespace}/{workspaceName}/exportAttributesTSV | TSV file containing workspace attributes (allows cookie-based authentication) ChangedWorkspaceNotification | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/sendChangeNotification | Sends notifications for change to workspace CheckIamActionWithLock | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/checkIamActionWithLock/{samActionName} | Check IAM action with lock CloneWorkspace | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/clone | Clone Workspace CreateWorkspace | POST /api/workspaces | Create workspace DeleteWorkspace | DELETE /api/workspaces/{workspaceNamespace}/{workspaceName} | Delete workspace DeleteWorkspaceTags | DELETE /api/workspaces/{workspaceNamespace}/{workspaceName}/tags | Remove the user-supplied tags from the workspace. ExportAttributesTSV | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/exportAttributesTSV | TSV file containing workspace attributes GetBucketUsage | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/bucketUsage | Get bucket usage GetCatalog | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/catalog | Get workspace catalog permission GetStorageCostEstimate | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/storageCostEstimate | Calculate an estimate of the monthly storage cost for the workspace bucket GetTags | GET /api/workspaces/tags | Get all tags used in FireCloud (for autocomplete) GetWorkspace | GET /api/workspaces/{workspaceNamespace}/{workspaceName} | Get workspace GetWorkspaceAccessInstructions | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/accessInstructions | Get workspace access instructions (if any) GetWorkspaceAcl | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/acl | Get workspace ACL GetWorkspaceBucketOptions | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/bucketOptions | Get metadata about the workspace bucket GetWorkspaceTags | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/tags | Get the tags for this workspace. ImportAttributesTSV | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/importAttributesTSV | Import workspace attributes from a tsv file ListWorkspaceMethodConfigs | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/methodconfigs | List method configurations in a workspace ListWorkspaces | GET /api/workspaces | Lists workspaces. LockWorkspace | PUT /api/workspaces/{workspaceNamespace}/{workspaceName}/lock | Lock Workspace PatchWorkspaceTags | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/tags | Add tags to the workspace without modifying pre-existing tags. PostWorkspaceMethodConfig | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/methodconfigs | Create a Method Configuration in a workspace PutWorkspaceTags | PUT /api/workspaces/{workspaceNamespace}/{workspaceName}/tags | Replace all tags for this workspace with the user input. ReadBucket | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/checkBucketReadAccess | Read workspace bucket SetAttributes | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/setAttributes | Set attributes on a workspace. UnlockWorkspace | PUT /api/workspaces/{workspaceNamespace}/{workspaceName}/unlock | Unlock Workspace UpdateAttributes | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/updateAttributes | Modify attributes on a workspace. UpdateCatalog | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/catalog | Update catalog permission UpdateWorkspaceACL | PATCH /api/workspaces/{workspaceNamespace}/{workspaceName}/acl | Update workspace ACL WorkspacePermissionReport | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/permissionReport | Retrieve user permissions for the workspace and the workspace's method references
BrowserDownloadAttributes
data.frame BrowserDownloadAttributes(workspace.namespace, workspace.name)
TSV file containing workspace attributes (allows cookie-based authentication)
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#TSV file containing workspace attributes (allows cookie-based authentication)
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$BrowserDownloadAttributes(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
data.frame
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: text/plain
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Workspace attributes in TSV format | - | | 404 | Workspace does not exist | - | | 500 | Internal Server Error | - |
ChangedWorkspaceNotification
ChangedWorkspaceNotification(workspace.namespace, workspace.name)
Sends notifications for change to workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | workspace namespace
var.workspace.name <- 'workspace.name_example' # character | workspace name
#Sends notifications for change to workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$ChangedWorkspaceNotification(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| workspace namespace | workspace.name | character| workspace name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Success | - | | 403 | Insufficient permisions to send notification on this workspace | - |
CheckIamActionWithLock
CheckIamActionWithLock(workspace.namespace, workspace.name, sam.action.name)
Check IAM action with lock
Check to see if the user has the given action on a workspace in Sam. Takes into account if the workspace is locked too.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.sam.action.name <- 'sam.action.name_example' # character | Sam action
#Check IAM action with lock
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$CheckIamActionWithLock(var.workspace.namespace, var.workspace.name, var.sam.action.name)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | sam.action.name | character| Sam action |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 204 | User can perform the given action on the workspace | - | | 403 | User may not perform the given action on the workspace (including if it doesn't exist) | - | | 500 | Internal Server Error | - |
CloneWorkspace
WorkspaceDetails CloneWorkspace(workspace.namespace, workspace.name, workspace)
Clone Workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.workspace <- WorkspaceRequestClone$new("namespace_example", "name_example", 123, list(ManagedGroupRef$new("membersGroupName_example")), "copyFilesWithPrefix_example", "noWorkspaceOwner_example") # WorkspaceRequestClone | Cloned workspace information
#Clone Workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$CloneWorkspace(var.workspace.namespace, var.workspace.name, var.workspace)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | workspace | WorkspaceRequestClone| Cloned workspace information |
Return type
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 201 | Successful Request | - | | 400 | Unable to create resources for workspace | - | | 404 | Source workspace not found | - | | 409 | Destination workspace already exists | - | | 500 | Internal Server Error | - |
CreateWorkspace
WorkspaceDetails CreateWorkspace(workspace)
Create workspace
Example
library(openapi)
var.workspace <- WorkspaceRequest$new("namespace_example", "name_example", 123, list(ManagedGroupRef$new("membersGroupName_example")), "noWorkspaceOwner_example") # WorkspaceRequest | New workspace information
#Create workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$CreateWorkspace(var.workspace)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace | WorkspaceRequest| New workspace information |
Return type
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 201 | Successful Request | - | | 400 | Bad request | - | | 403 | Unable to create bucket for workspace | - | | 409 | Workspace by that name already exists | - | | 500 | Internal Server Error | - |
DeleteWorkspace
DeleteWorkspace(workspace.namespace, workspace.name)
Delete workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Delete workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$DeleteWorkspace(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 202 | Request Accepted | - | | 403 | User does not have correct permissions to delete a published workspace | - | | 404 | Workspace does not exist | - | | 500 | Internal Server Error | - |
DeleteWorkspaceTags
array[character] DeleteWorkspaceTags(workspace.namespace, workspace.name, tags)
Remove the user-supplied tags from the workspace.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.tags <- list("property_example") # array[character] | List of tags.
#Remove the user-supplied tags from the workspace.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$DeleteWorkspaceTags(var.workspace.namespace, var.workspace.name, var.tags)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | tags | list( character )| List of tags. |
Return type
array[character]
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Workspace tags | - | | 400 | Invalid input | - | | 404 | Workspace not found | - | | 500 | Internal Error | - |
ExportAttributesTSV
data.frame ExportAttributesTSV(workspace.namespace, workspace.name)
TSV file containing workspace attributes
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#TSV file containing workspace attributes
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$ExportAttributesTSV(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
data.frame
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: text/plain
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Workspace attributes in TSV format | - | | 404 | Workspace does not exist | - | | 500 | Internal Server Error | - |
GetBucketUsage
GetBucketUsage(workspace.namespace, workspace.name)
Get bucket usage
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get bucket usage
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$GetBucketUsage(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - |
GetCatalog
array[WorkspaceCatalog] GetCatalog(workspace.namespace, workspace.name)
Get workspace catalog permission
Get catalog permissions for a workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get workspace catalog permission
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetCatalog(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 404 | Workspace not found | - | | 500 | Rawls Internal Error | - |
GetStorageCostEstimate
GetStorageCostEstimate(workspace.namespace, workspace.name)
Calculate an estimate of the monthly storage cost for the workspace bucket
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Calculate an estimate of the monthly storage cost for the workspace bucket
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$GetStorageCostEstimate(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Storage cost estimate | - | | 404 | Workspace not found | - | | 500 | Internal Error | - |
GetTags
array[WorkspaceTag] GetTags(q=var.q)
Get all tags used in FireCloud (for autocomplete)
list of all tags used in FireCloud and their associated frequencies
Example
library(openapi)
var.q <- 'q_example' # character | Query string
#Get all tags used in FireCloud (for autocomplete)
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetTags(q=var.q)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- q | character| Query string | [optional]
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | list of all tags used in FireCloud | - | | 500 | Rawls Internal Error | - |
GetWorkspace
WorkspaceResponse GetWorkspace(workspace.namespace, workspace.name, fields=var.fields)
Get workspace
Get a single workspace's details, optionally filtered to only the specified fields. See additional GET methods in this section to retrieve additional details about the workspace. For instance, this API only returns the workspace's owners; use the GET .../acl method to retrieve the full list of all users at all permission levels.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.fields <- list("inner_example") # array[character] | When specified, include only these keys in the response payload and exclude other keys. Accepts a comma-delimited list of values. To include a nested key, specify the key's path using a dot delimiter; for example, to include {\"workspace\": {\"attributes\": {}}}, specify \"workspace.attributes\". Legal values are any first-level key in the response, any first-level key inside the {\"workspace\": {}} object, and any first-level key inside the {\"workspace\": {\"attributes\": {}}} object. If omitted, will return the full response payload.
#Get workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspace(var.workspace.namespace, var.workspace.name, fields=var.fields)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | fields | list( character )| When specified, include only these keys in the response payload and exclude other keys. Accepts a comma-delimited list of values. To include a nested key, specify the key's path using a dot delimiter; for example, to include {\"workspace\": {\"attributes\": {}}}, specify \"workspace.attributes\". Legal values are any first-level key in the response, any first-level key inside the {\"workspace\": {}} object, and any first-level key inside the {\"workspace\": {\"attributes\": {}}} object. If omitted, will return the full response payload. | [optional]
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 400 | Unrecognized query parameters | - | | 404 | Workspace does not exist | - | | 500 | Internal Server Error | - |
GetWorkspaceAccessInstructions
array[ManagedGroupAccessInstructions] GetWorkspaceAccessInstructions(workspace.namespace, workspace.name)
Get workspace access instructions (if any)
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get workspace access instructions (if any)
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspaceAccessInstructions(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
array[ManagedGroupAccessInstructions]
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 404 | Workspace not found | - | | 500 | Internal Server Error | - |
GetWorkspaceAcl
WorkspaceACL GetWorkspaceAcl(workspace.namespace, workspace.name)
Get workspace ACL
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get workspace ACL
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspaceAcl(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 400 | Can't retrieve ACL for workspace | - | | 404 | Workspace not found | - | | 500 | Internal Server Error | - |
GetWorkspaceBucketOptions
WorkspaceBucketOptions GetWorkspaceBucketOptions(workspace.namespace, workspace.name)
Get metadata about the workspace bucket
Returns metadata about the workspace bucket.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get metadata about the workspace bucket
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspaceBucketOptions(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 404 | Workspace not found | - | | 500 | Rawls Internal Error | - |
GetWorkspaceTags
array[character] GetWorkspaceTags(workspace.namespace, workspace.name)
Get the tags for this workspace.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Get the tags for this workspace.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$GetWorkspaceTags(var.workspace.namespace, var.workspace.name)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
array[character]
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Workspace tags | - | | 404 | Workspace not found | - | | 500 | Internal Error | - |
ImportAttributesTSV
ImportAttributesTSV(workspace.namespace, workspace.name, attributes)
Import workspace attributes from a tsv file
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.attributes <- File.new('/path/to/file') # data.frame | A valid TSV import file
#Import workspace attributes from a tsv file
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$ImportAttributesTSV(var.workspace.namespace, var.workspace.name, var.attributes)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | attributes | data.frame| A valid TSV import file |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: multipart/form-data
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 400 | Bad Request | - | | 404 | Source Workspace not found | - | | 500 | Internal Error | - |
ListWorkspaceMethodConfigs
ListWorkspaceMethodConfigs(workspace.namespace, workspace.name, all.repos=FALSE)
List method configurations in a workspace
List method configurations in a workspace. By default, only Agora method configs are returned. To return configs for all repos, specify allRepos to be true. #### Expanded discussion on the methodRepoMethod field This endpoint returns method references to Agora in the format \"methodRepoMethod\": { \"methodNamespace\": \"namespace\", \"methodName\": \"name\", \"methodVersion\": 1, \"sourceRepo\": \"agora\", \"methodUri\": \"agora://namespace/name/1\" } and for Dockstore in the format \"methodRepoMethod\": { \"methodPath\": \"path\", \"methodVersion\": \"version\", \"sourceRepo\": \"agora\", \"methodUri\": \"dockstore://path/version\" } If you are only working with Agora methods, the fields \"sourceRepo\" and \"methodUri\" can be considered informational and do not need to be round-tripped (see the corresponding POST /api/workspaces/{workspaceNamespace}/{workspaceName}/methodconfigs for more details).
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.all.repos <- FALSE # character | Configs for all repos, not just Agora
#List method configurations in a workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$ListWorkspaceMethodConfigs(var.workspace.namespace, var.workspace.name, all.repos=var.all.repos)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | all.repos | character| Configs for all repos, not just Agora | [optional] [default to FALSE]
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | List of Method Configurations | - | | 404 | Workspace does not exist | - | | 500 | Internal Server Error | - |
ListWorkspaces
array[WorkspaceListResponse] ListWorkspaces(fields=var.fields)
Lists workspaces.
Example
library(openapi)
var.fields <- list("inner_example") # array[character] | When specified, include only these keys in the response payload and exclude other keys. Accepts a comma-delimited list of values. To include a nested key, specify the key's path using a dot delimiter; for example, to include {\"workspace\": {\"attributes\": {}}}, specify \"workspace.attributes\". Legal values are any first-level key in the response, any first-level key inside the {\"workspace\": {}} object, and any first-level key inside the {\"workspace\": {\"attributes\": {}}} object. If omitted, will return the full response payload.
#Lists workspaces.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$ListWorkspaces(fields=var.fields)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- fields | list( character )| When specified, include only these keys in the response payload and exclude other keys. Accepts a comma-delimited list of values. To include a nested key, specify the key's path using a dot delimiter; for example, to include {\"workspace\": {\"attributes\": {}}}, specify \"workspace.attributes\". Legal values are any first-level key in the response, any first-level key inside the {\"workspace\": {}} object, and any first-level key inside the {\"workspace\": {\"attributes\": {}}} object. If omitted, will return the full response payload. | [optional]
Return type
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: application/json, text/plain
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | List of workspaces. | - | | 400 | Unrecognized query parameters | - |
LockWorkspace
LockWorkspace(workspace.namespace, workspace.name)
Lock Workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Lock Workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$LockWorkspace(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | No response was specified | - | | 204 | Successful Request | - | | 403 | Not Owner | - | | 404 | Workspace Not Found | - | | 500 | Internal Server Error | - |
PatchWorkspaceTags
array[character] PatchWorkspaceTags(workspace.namespace, workspace.name, tags)
Add tags to the workspace without modifying pre-existing tags.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.tags <- list("property_example") # array[character] | List of tags.
#Add tags to the workspace without modifying pre-existing tags.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$PatchWorkspaceTags(var.workspace.namespace, var.workspace.name, var.tags)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | tags | list( character )| List of tags. |
Return type
array[character]
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Workspace tags | - | | 400 | Invalid input | - | | 404 | Workspace not found | - | | 500 | Internal Error | - |
PostWorkspaceMethodConfig
PostWorkspaceMethodConfig(workspace.namespace, workspace.name, method.config.json)
Create a Method Configuration in a workspace
Create method configurations. #### Expanded discussion on the methodRepoMethod field To create a method config for an Agora method, \"sourceRepo\": \"agora\" is optional; the following is sufficient: \"methodRepoMethod\": { \"methodNamespace\": \"namespace\", \"methodName\": \"name\", \"methodVersion\": 1 } To create a method config for a Dockstore method, \"sourceRepo\": \"dockstore\" is required: \"methodRepoMethod\": { \"sourceRepo\": \"dockstore\", \"methodPath\": \"path\", \"methodVersion\": \"version\" } You may also use the URI on its own to create a config referencing any supported repo (currently Agora and Dockstore): \"methodRepoMethod\": { \"methodUri\": \"agora://namespace/name/1\" } \"methodRepoMethod\": { \"methodUri\": \"dockstore://path/version\" } The system is specified to check for a URI first before falling back to the legacy fields. Unsupported repos will return a 400 Bad Request.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.method.config.json <- NewMethodConfigIngest$new("namespace_example", "name_example", "rootEntityType_example", TODO, TODO, TODO, TODO, 123, "deleted_example") # NewMethodConfigIngest | Method Configuration contents
#Create a Method Configuration in a workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$PostWorkspaceMethodConfig(var.workspace.namespace, var.workspace.name, var.method.config.json)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | method.config.json | NewMethodConfigIngest| Method Configuration contents |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 201 | Successful Request | - | | 404 | Workspace not found | - | | 409 | Method Configuration already exists | - | | 500 | Internal Server Error | - |
PutWorkspaceTags
array[character] PutWorkspaceTags(workspace.namespace, workspace.name, tags)
Replace all tags for this workspace with the user input.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.tags <- list("property_example") # array[character] | List of tags.
#Replace all tags for this workspace with the user input.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$PutWorkspaceTags(var.workspace.namespace, var.workspace.name, var.tags)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | tags | list( character )| List of tags. |
Return type
array[character]
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Workspace tags | - | | 400 | Invalid input | - | | 404 | Workspace not found | - | | 500 | Internal Error | - |
ReadBucket
ReadBucket(workspace.namespace, workspace.name)
Read workspace bucket
Read a workspace bucket
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Read workspace bucket
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$ReadBucket(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 403 | Insufficient permissions to access workspace bucket | - | | 404 | Workspace Not Found | - | | 500 | Internal Server Error | - |
SetAttributes
SetAttributes(workspace.namespace, workspace.name, new.attributes)
Set attributes on a workspace.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.new.attributes <- TODO # map(object) | New attribute values, as Map[String, Attribute]. WARNING! This should not be used to change library metadata (republish will not happen). Use UpdateAttributes in the library section
#Set attributes on a workspace.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$SetAttributes(var.workspace.namespace, var.workspace.name, var.new.attributes)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | new.attributes | named list( map(object) )| New attribute values, as Map[String, Attribute]. WARNING! This should not be used to change library metadata (republish will not happen). Use UpdateAttributes in the library section |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Success | - | | 400 | Malformed request | - | | 404 | Workspace not found | - | | 500 | Internal Error | - |
UnlockWorkspace
UnlockWorkspace(workspace.namespace, workspace.name)
Unlock Workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
#Unlock Workspace
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$UnlockWorkspace(var.workspace.namespace, var.workspace.name)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name |
Return type
void (empty response body)
Authorization
HTTP request headers
- Content-Type: Not defined
- Accept: Not defined
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | No response was specified | - | | 204 | Successful Request | - | | 403 | Not Owner | - | | 404 | Workspace Not Found | - | | 500 | Internal Server Error | - |
UpdateAttributes
WorkspaceDetails UpdateAttributes(workspace.namespace, workspace.name, workspace.update.json)
Modify attributes on a workspace.
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.workspace.update.json <- list(AttributeUpdateOperation$new("AddUpdateAttribute")) # array[AttributeUpdateOperation] | Attribute operations. WARNING! This should not be used to change library metadata (republish will not happen). Use UpdateAttributes in the library section.
#Modify attributes on a workspace.
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$UpdateAttributes(var.workspace.namespace, var.workspace.name, var.workspace.update.json)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | workspace.update.json | list( AttributeUpdateOperation )| Attribute operations. WARNING! This should not be used to change library metadata (republish will not happen). Use UpdateAttributes in the library section. |
Return type
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Success | - | | 400 | Invalid operation | - | | 404 | Workspace not found | - | | 500 | Internal Error | - |
UpdateCatalog
WorkspaceCatalogUpdateResponseList UpdateCatalog(workspace.namespace, workspace.name, catalog.updates)
Update catalog permission
Set catalog permisisons for a workspace
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.catalog.updates <- list(WorkspaceCatalog$new("email_example", "catalog_example")) # array[WorkspaceCatalog] | Series of Catalog updates for workspace
#Update catalog permission
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$UpdateCatalog(var.workspace.namespace, var.workspace.name, var.catalog.updates)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | catalog.updates | list( WorkspaceCatalog )| Series of Catalog updates for workspace |
Return type
WorkspaceCatalogUpdateResponseList
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 403 | Insufficient permissions to change catalog permissions (must be owner or admin) | - | | 404 | Workspace, user or group not found | - | | 500 | Rawls Internal Error | - |
UpdateWorkspaceACL
WorkspaceACLUpdateResponseList UpdateWorkspaceACL(workspace.namespace, workspace.name, invite.users.not.found, acl.updates)
Update workspace ACL
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.invite.users.not.found <- FALSE # character | true to invite unregistered users, false to ignore
var.acl.updates <- list(WorkspaceACLUpdate$new("email_example", "accessLevel_example", "canShare_example", "canCompute_example")) # array[WorkspaceACLUpdate] | Series of ACL updates for workspace
#Update workspace ACL
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$UpdateWorkspaceACL(var.workspace.namespace, var.workspace.name, var.invite.users.not.found, var.acl.updates)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | invite.users.not.found | character| true to invite unregistered users, false to ignore | [default to FALSE] acl.updates | list( WorkspaceACLUpdate )| Series of ACL updates for workspace |
Return type
WorkspaceACLUpdateResponseList
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 400 | Can't set ACL for workspace | - | | 404 | Workspace not found | - | | 500 | Internal Server Error | - |
WorkspacePermissionReport
PermissionReport WorkspacePermissionReport(workspace.namespace, workspace.name, report.input)
Retrieve user permissions for the workspace and the workspace's method references
Example
library(openapi)
var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.report.input <- PermissionReportRequest$new(list("users_example"), list(MethodConfigurationName$new("namespace_example", "name_example"))) # PermissionReportRequest | Users and/or configs on which to report, both optional
#Retrieve user permissions for the workspace and the workspace's method references
api.instance <- WorkspacesApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$WorkspacePermissionReport(var.workspace.namespace, var.workspace.name, var.report.input)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | report.input | PermissionReportRequest| Users and/or configs on which to report, both optional |
Return type
Authorization
HTTP request headers
- Content-Type: application/json
- Accept: application/json
HTTP response details
| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Permission Report | - | | 404 | Workspace does not exist | - | | 500 | Internal Server Error | - |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.