Services: RESTful services useful for AnVIL developers

In Bioconductor/AnVIL: Bioconductor on the AnVIL compute environment

RESTful services useful for AnVIL developers

Description

RESTful services useful for AnVIL developers

Usage

empty_object

operations(x, ..., .deprecated = FALSE)

## S4 method for signature 'Service'
operations(x, ..., auto_unbox = FALSE, .deprecated = FALSE)

schemas(x)

tags(x, .tags, .deprecated = FALSE)

## S4 method for signature 'Service'
x$name

Leonardo()

Terra()

Rawls()

Dockstore()

Gen3Fence()

Gen3Indexd()

Gen3Sheepdog()

Gen3Peregrine()

Arguments

x	A Service instance, usually a singleton provided by the package and documented on this page, e.g., leonardo or terra.
...	additional arguments passed to methods or, for operations,Service-method, to the internal get_operation() function.
.deprecated	optional logical(1) include deprecated operations?
auto_unbox	logical(1) If FALSE (default) do not automatically 'unbox' R scalar values from JSON arrays to JSON scalers.
.tags	optional character() of tags to use to filter operations.
name	A symbol representing a defined operation, e.g., leonardo$listClusters().

Details

When using $ to select a service, some arguments appear in 'body' of the REST request. Specify these using the .__body__= argument, as illustrated for createBillingProjectFull(), below.

Value

empty_object returns a representation to be used as arguments in function calls expecting the empty json object \{\}.

Leonardo() creates the API of the Leonard container deployment service at https://notebooks.firecloud.org/api-docs.yaml.

Terra() creates the API of the Terra cloud computational environemnt at https://api.firecloud.org/.

Rawls() creates the API of the Rawls cloud computational environemnt at https://rawls.dsde-prod.broadinstitute.org.

Dockstore() represents the API of the Dockstore platform to share Docker-based tools in CWL or WDL or Nextflow at https://dockstore.org

gen3_* APIs are not fully implemented, because a service endpoint has not been identified.

Gen3Fence() returns the authentication API at https://raw.githubusercontent.com/uc-cdis/fence/master/openapis/swagger.yaml

Gen3Indexd() returns the indexing service API documented at https://raw.githubusercontent.com/uc-cdis/indexd/master/openapis/swagger.yaml

Gen3Sheepdog returns the submission services API at https://raw.githubusercontent.com/uc-cdis/sheepdog/master/openapi/swagger.yml

Gen3Peregrine returns the graphQL query services API at https://raw.githubusercontent.com/uc-cdis/peregrine/master/openapis/swagger.yaml

Examples

empty_object

if (gcloud_exists()) {
    ## Arguments to be used as the 'body' (`.__body__=`) of a REST query
    terra <- Terra()
    terra$createBillingProjectFull       # 6 arguments...
    args(terra$createBillingProjectFull) # ... passed as `.__body__ = list(...)`
}
if (gcloud_exists())
    Leonardo()

if (gcloud_exists()) {
    terra <- Terra()
    tags(terra)
    tags(terra, "Billing")
}

if (gcloud_exists()) {
    rawls <- Rawls()
    tags(rawls)
    tags(rawls, "billing")
}

Dockstore()

Bioconductor/AnVIL documentation built on June 25, 2022, 9:42 p.m.