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()

TDR()

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$listRuntimes().

Details

Note the services Terra(), Rawls(), and Leonardo() require the AnVILGCP package for authentication to the Google Cloud Platform. See ?AnVILGCP::gcloud_access_token() for 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 Leonardo container deployment service at https://leonardo.dsde-prod.broadinstitute.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

TDR() creates the API of the Terra Data Repository to work with snapshot data in the Terra Data Repository at https://data.terra.bio.

Examples

empty_object

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

library(AnVILGCP)
if (gcloud_exists()) {
    tags(Terra())
    tags(Terra(), "Billing")
}

library(AnVILGCP)
if (gcloud_exists()) {
    tags(Rawls())
    tags(Rawls(), "billing")
}

Dockstore()

library(AnVILGCP)
if (gcloud_exists())
    TDR()

Bioconductor/AnVIL documentation built on June 10, 2025, 5:25 p.m.