docs/GA4GHToolRegistryApi.md

In vjcitn/terraClientR: R Package Client for FireCloud

GA4GHToolRegistryApi

All URIs are relative to http://localhost

Method | HTTP request | Description ------------- | ------------- | ------------- Ga4ghV1MetadataGet | GET /ga4gh/v1/metadata | Return some metadata that is useful for describing this registry Ga4ghV1ToolClassesGet | GET /ga4gh/v1/tool-classes | List all tool types Ga4ghV1ToolsGet | GET /ga4gh/v1/tools | List all tools Ga4ghV1ToolsIdGet | GET /ga4gh/v1/tools/{id} | List one specific tool, acts as an anchor for self references Ga4ghV1ToolsIdVersionsGet | GET /ga4gh/v1/tools/{id}/versions | List versions of a tool Ga4ghV1ToolsIdVersionsVersionIdGet | GET /ga4gh/v1/tools/{id}/versions/{version-id} | List one specific tool version, acts as an anchor for self references Ga4ghV1ToolsIdVersionsVersionIdTypeDescriptorGet | GET /ga4gh/v1/tools/{id}/versions/{version-id}/{type}/descriptor | Get the tool descriptor (WDL) for the specified tool.

Ga4ghV1MetadataGet

Metadata Ga4ghV1MetadataGet()

Return some metadata that is useful for describing this registry

Return some metadata that is useful for describing this registry

Example

library(openapi)


#Return some metadata that is useful for describing this registry
api.instance <- GA4GHToolRegistryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$Ga4ghV1MetadataGet()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

Metadata

Authorization

googleoauth

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A Metadata object describing this service. | - |

Ga4ghV1ToolClassesGet

array[ToolClass] Ga4ghV1ToolClassesGet()

List all tool types

This endpoint returns all tool-classes available

Example

library(openapi)


#List all tool types
api.instance <- GA4GHToolRegistryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$Ga4ghV1ToolClassesGet()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

array[ToolClass]

Authorization

googleoauth

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | An array of methods that match the filter. | - |

Ga4ghV1ToolsGet

array[Tool] Ga4ghV1ToolsGet()

List all tools

This endpoint returns all tools available.

Example

library(openapi)


#List all tools
api.instance <- GA4GHToolRegistryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$Ga4ghV1ToolsGet()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

array[Tool]

Authorization

googleoauth

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | An array of Tools that match the filter. | - |

Ga4ghV1ToolsIdGet

Tool Ga4ghV1ToolsIdGet(id)

List one specific tool, acts as an anchor for self references

This endpoint returns one specific tool (which has ToolVersions nested inside it)

Example

library(openapi)

var.id <- 'id_example' # character | A unique identifier of the tool, scoped to this registry, for example `123456`

#List one specific tool, acts as an anchor for self references
api.instance <- GA4GHToolRegistryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$Ga4ghV1ToolsIdGet(var.id)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- id | character| A unique identifier of the tool, scoped to this registry, for example `123456` |

Return type

Tool

Authorization

googleoauth

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A tool. | - |

Ga4ghV1ToolsIdVersionsGet

array[ToolVersion] Ga4ghV1ToolsIdVersionsGet(id)

List versions of a tool

Returns all versions of the specified tool

Example

library(openapi)

var.id <- 'id_example' # character | A unique identifier of the tool, scoped to this registry, for example `123456`

#List versions of a tool
api.instance <- GA4GHToolRegistryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$Ga4ghV1ToolsIdVersionsGet(var.id)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- id | character| A unique identifier of the tool, scoped to this registry, for example `123456` |

Return type

array[ToolVersion]

Authorization

googleoauth

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | An array of tool versions | - |

Ga4ghV1ToolsIdVersionsVersionIdGet

ToolVersion Ga4ghV1ToolsIdVersionsVersionIdGet(id, version.id)

List one specific tool version, acts as an anchor for self references

This endpoint returns one specific tool version

Example

library(openapi)

var.id <- 'id_example' # character | A unique identifier of the tool, scoped to this registry, for example `123456`
var.version.id <- 'version.id_example' # character | An identifier of the tool version, scoped to this registry, for example `v1`

#List one specific tool version, acts as an anchor for self references
api.instance <- GA4GHToolRegistryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$Ga4ghV1ToolsIdVersionsVersionIdGet(var.id, var.version.id)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- id | character| A unique identifier of the tool, scoped to this registry, for example `123456` | version.id | character| An identifier of the tool version, scoped to this registry, for example `v1` |

Return type

ToolVersion

Authorization

googleoauth

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A tool version. | - |

Ga4ghV1ToolsIdVersionsVersionIdTypeDescriptorGet

ToolDescriptor Ga4ghV1ToolsIdVersionsVersionIdTypeDescriptorGet(type, id, version.id)

Get the tool descriptor (WDL) for the specified tool.

Returns the WDL descriptor for the specified tool.

Example

library(openapi)

var.type <- 'type_example' # character | The output type of the descriptor. If not specified it is up to the underlying implementation to determine which output type to return. Plain types return the bare descriptor while the \"non-plain\" types return a descriptor wrapped with metadata. 
var.id <- 'id_example' # character | A unique identifier of the tool, scoped to this registry, for example `123456`.    *In FireCloud, this must be a namespace + \":\" + name. For instance, if your namespace   is 'foo' and name is 'bar', this must be 'foo:bar'.* 
var.version.id <- 'version.id_example' # character | An identifier of the tool version for this particular tool registry, for example `v1`.    *In FireCloud, this must be an integer representing the FireCloud snapshot id.* 

#Get the tool descriptor (WDL) for the specified tool.
api.instance <- GA4GHToolRegistryApi$new()
# Configure OAuth2 access token for authorization: googleoauth
api.instance$apiClient$accessToken <- 'TODO_YOUR_ACCESS_TOKEN';
result <- api.instance$Ga4ghV1ToolsIdVersionsVersionIdTypeDescriptorGet(var.type, var.id, var.version.id)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- type | Enum [WDL, plain-WDL] | The output type of the descriptor. If not specified it is up to the underlying implementation to determine which output type to return. Plain types return the bare descriptor while the \"non-plain\" types return a descriptor wrapped with metadata. | id | character| A unique identifier of the tool, scoped to this registry, for example `123456`. In FireCloud, this must be a namespace + \":\" + name. For instance, if your namespace is 'foo' and name is 'bar', this must be 'foo:bar'. | version.id | character| An identifier of the tool version for this particular tool registry, for example `v1`. In FireCloud, this must be an integer representing the FireCloud snapshot id. |

Return type

ToolDescriptor

Authorization

googleoauth

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | The tool descriptor. | - | | 404 | The tool can not be output in the specified type. | - |

vjcitn/terraClientR documentation built on Dec. 23, 2021, 4:07 p.m.