vjcitn/terraClientR
R Package Client for FireCloud

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docs/MethodConfigurationsApi.md

docs/MethodConfigurationsApi.md
In vjcitn/terraClientR: R Package Client for FireCloud

MethodConfigurationsApi

All URIs are relative to http://localhost

Method | HTTP request | Description ------------- | ------------- | ------------- CopyFromMethodRepo | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/copyFromMethodRepo | Copy a Method Repository Configuration into a workspace CopyToMethodRepo | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/copyToMethodRepo | Copy a Method Config in a workspace to the Method Repository DeleteWorkspaceMethodConfig | DELETE /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/{configNamespace}/{configName} | Delete a method configuration in a workspace GetWorkspaceMethodConfig | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/{configNamespace}/{configName} | Get a method configuration in a workspace ImportStatus | GET /api/profile/importstatus | Check the user's ability to import a method config into a workspace ListWorkspaceMethodConfigs | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/methodconfigs | List method configurations in a workspace OverwriteWorkspaceMethodConfig | PUT /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/{configNamespace}/{configName} | Add or overwrite a method configuration in a workspace PostWorkspaceMethodConfig | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/methodconfigs | Create a Method Configuration in a workspace RenameWorkspaceMethodConfig | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/{configNamespace}/{configName}/rename | Rename a method configuration in a workspace UpdateWorkspaceMethodConfig | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/{configNamespace}/{configName} | Update a method configuration in a workspace ValidateMethodConfiguration | GET /api/workspaces/{workspaceNamespace}/{workspaceName}/method_configs/{configNamespace}/{configName}/validate | get syntax validation information for a method configuration WorkspacePermissionReport | POST /api/workspaces/{workspaceNamespace}/{workspaceName}/permissionReport | Retrieve user permissions for the workspace and the workspace's method references

CopyFromMethodRepo

CopyFromMethodRepo(workspace.namespace, workspace.name, config.to.copy)

Copy a Method Repository Configuration into a workspace

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.config.to.copy <- CopyConfigurationIngest$new("configurationNamespace_example", "configurationName_example", 123, "destinationNamespace_example", "destinationName_example") # CopyConfigurationIngest | Method Configuration to Copy

#Copy a Method Repository Configuration into a workspace
api.instance <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$CopyFromMethodRepo(var.workspace.namespace, var.workspace.name, var.config.to.copy)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | config.to.copy | CopyConfigurationIngest| Method Configuration to Copy |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 201 | Successful request | - | | 404 | Source method configuration does not exist | - | | 409 | Destination method configuration by that name already exists | - | | 422 | Error parsing source method configuration | - | | 500 | Internal Server Error | - |

CopyToMethodRepo

CopyToMethodRepo(workspace.namespace, workspace.name, config.to.copy)

Copy a Method Config in a workspace to the Method Repository

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.config.to.copy <- PublishConfigurationIngest$new("configurationNamespace_example", "configurationName_example", "sourceNamespace_example", "sourceName_example") # PublishConfigurationIngest | Method Configuration to Copy

#Copy a Method Config in a workspace to the Method Repository
api.instance <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$CopyToMethodRepo(var.workspace.namespace, var.workspace.name, var.config.to.copy)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | config.to.copy | PublishConfigurationIngest| Method Configuration to Copy |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 201 | Successful request | - | | 404 | Source method configuration does not exist | - | | 409 | Destination method configuration by that name already exists | - | | 422 | Error parsing source method configuration | - | | 500 | Internal Server Error | - |

DeleteWorkspaceMethodConfig

DeleteWorkspaceMethodConfig(workspace.namespace, workspace.name, config.namespace, config.name)

Delete a method configuration in a workspace

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.config.namespace <- 'config.namespace_example' # character | Configuration Namespace
var.config.name <- 'config.name_example' # character | Configuration Name

#Delete a method configuration in a workspace
api.instance <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$DeleteWorkspaceMethodConfig(var.workspace.namespace, var.workspace.name, var.config.namespace, var.config.name)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | config.namespace | character| Configuration Namespace | config.name | character| Configuration Name |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful request | - | | 404 | Workspace or Method Configuration not found | - | | 500 | Internal Server Error | - |

GetWorkspaceMethodConfig

GetWorkspaceMethodConfig(workspace.namespace, workspace.name, config.namespace, config.name)

Get a method configuration in a workspace

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.config.namespace <- 'config.namespace_example' # character | Configuration Namespace
var.config.name <- 'config.name_example' # character | Configuration Name

#Get a method configuration in a workspace
api.instance <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$GetWorkspaceMethodConfig(var.workspace.namespace, var.workspace.name, var.config.namespace, var.config.name)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | config.namespace | character| Configuration Namespace | config.name | character| Configuration Name |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful | - | | 404 | Workspace or Method Configuration not found | - | | 500 | Internal Server Error | - |

ImportStatus

UserImportPermission ImportStatus()

Check the user's ability to import a method config into a workspace

Example

library(openapi)


#Check the user's ability to import a method config into a workspace
api.instance <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$ImportStatus()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

UserImportPermission

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | OK | - | | 500 | Internal Server 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 <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$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

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | List of Method Configurations | - | | 404 | Workspace does not exist | - | | 500 | Internal Server Error | - |

OverwriteWorkspaceMethodConfig

OverwriteWorkspaceMethodConfig(workspace.namespace, workspace.name, config.namespace, config.name, body)

Add or overwrite a method configuration in a workspace

Add or overwrite a method configuration in a workspace. The method configuration name and namespace in the URI must match the values in the JSON.

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.config.namespace <- 'config.namespace_example' # character | Configuration Namespace
var.config.name <- 'config.name_example' # character | Configuration Name
var.body <- ConfigurationIngest$new("namespace_example", "name_example", "rootEntityType_example", TODO, TODO, TODO, TODO, TODO) # ConfigurationIngest | Method Config to Update

#Add or overwrite a method configuration in a workspace
api.instance <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$OverwriteWorkspaceMethodConfig(var.workspace.namespace, var.workspace.name, var.config.namespace, var.config.name, var.body)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | config.namespace | character| Configuration Namespace | config.name | character| Configuration Name | body | ConfigurationIngest| Method Config to Update |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful | - | | 400 | Method configuration name and namespace in URI do not match those in JSON body | - | | 404 | Workspace or Method Configuration not found | - | | 500 | Internal Server 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 <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$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

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 201 | Successful Request | - | | 404 | Workspace not found | - | | 409 | Method Configuration already exists | - | | 500 | Internal Server Error | - |

RenameWorkspaceMethodConfig

RenameWorkspaceMethodConfig(workspace.namespace, workspace.name, config.namespace, config.name, rename)

Rename a method configuration in a workspace

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.config.namespace <- 'config.namespace_example' # character | Configuration Namespace
var.config.name <- 'config.name_example' # character | Configuration Name
var.rename <- MethodConfigRename$new("namespace_example", "name_example", TODO) # MethodConfigRename | Method Config Rename

#Rename a method configuration in a workspace
api.instance <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$RenameWorkspaceMethodConfig(var.workspace.namespace, var.workspace.name, var.config.namespace, var.config.name, var.rename)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | config.namespace | character| Configuration Namespace | config.name | character| Configuration Name | rename | MethodConfigRename| Method Config Rename |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 204 | Successful request | - | | 400 | Workspace details in payload don't match the URI | - | | 404 | Workspace or Method Configuration not found | - | | 409 | Method Configuration with that name already exists | - | | 500 | Internal Server Error | - |

UpdateWorkspaceMethodConfig

UpdateWorkspaceMethodConfig(workspace.namespace, workspace.name, config.namespace, config.name, body)

Update a method configuration in a workspace

Update method configuration. Updates and moves the method configuration at the URI to the location in the request body. The location in the URI may be the same as the location in the request body. If the location in the request body matches the location in the URI, it is overwritten. If the location in the request body is different to the location in the URI, and there is a method config already at that location, 409 is returned.

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.config.namespace <- 'config.namespace_example' # character | Configuration Namespace
var.config.name <- 'config.name_example' # character | Configuration Name
var.body <- ConfigurationIngest$new("namespace_example", "name_example", "rootEntityType_example", TODO, TODO, TODO, TODO, TODO) # ConfigurationIngest | Method Config to Update

#Update a method configuration in a workspace
api.instance <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
api.instance$UpdateWorkspaceMethodConfig(var.workspace.namespace, var.workspace.name, var.config.namespace, var.config.name, var.body)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | config.namespace | character| Configuration Namespace | config.name | character| Configuration Name | body | ConfigurationIngest| Method Config to Update |

Return type

void (empty response body)

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful | - | | 403 | Invalid attribute namespace(s) in outputs | - | | 404 | Workspace or Method Configuration not found | - | | 409 | Method configuration with the new name already exists in the workspace | - | | 500 | Internal Server Error | - |

ValidateMethodConfiguration

ValidatedMethodConfiguration ValidateMethodConfiguration(workspace.namespace, workspace.name, config.namespace, config.name)

get syntax validation information for a method configuration

Example

library(openapi)

var.workspace.namespace <- 'workspace.namespace_example' # character | Workspace Namespace
var.workspace.name <- 'workspace.name_example' # character | Workspace Name
var.config.namespace <- 'config.namespace_example' # character | Method Configuration Namespace
var.config.name <- 'config.name_example' # character | Method Configuration Name

#get syntax validation information for a method configuration
api.instance <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$ValidateMethodConfiguration(var.workspace.namespace, var.workspace.name, var.config.namespace, var.config.name)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- workspace.namespace | character| Workspace Namespace | workspace.name | character| Workspace Name | config.namespace | character| Method Configuration Namespace | config.name | character| Method Configuration Name |

Return type

ValidatedMethodConfiguration

Authorization

googleoauth

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Request | - | | 404 | Workspace or Method Configuration does not exist | - | | 500 | Rawls Internal 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 <- MethodConfigurationsApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$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

PermissionReport

Authorization

googleoauth

HTTP request headers

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.

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