Services: RESTful services useful for AnVIL developers

In Bioconductor/AnVIL: Bioconductor on the AnVIL compute environment

Description

RESTful services useful for AnVIL developers

Usage

empty_object

operations(x, ..., .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?
.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 identifiied.

'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 May 4, 2021, 9:39 a.m.