Package 'AnVIL'

Description

Functions documented on this page are primarily intended for package developers wishing to implement gadgets (graphical interfaces) to navigating AnVIL-generated tables.

.gadget_run() presents the user with a tibble-navigating gadget, returning the value of DONE_FUN if a row of the tibble is selected, or NULL.

Usage

.gadget_run(title, tibble, DONE_FUN)

Arguments

Value

.gadget_run() returns the result of DONE_FUN() if a row has been selected by the user, or NULL if no row is selected (the user presses Cancel, or Done prior to selecting any row).

Examples

tibble <- avworkspaces(platform = AnVILGCP::gcp())
DONE_FUN <- function(tibble, row_selected) {
    selected <- slice(tibble, row_selected)
    with(selected, paste0(namespace, "/", name))
}
.gadget_run("AnVIL Example", tibble, DONE_FUN)

Description

anvil_set_auth_json() stores the content of an auth.json file in the system keyring. This is the recommended way to store credentials safely.

Usage

anvil_set_auth_json(service, path)

Arguments

Value

anvil_set_auth_json() returns NULL invisibly.

Examples

jsonlite::write_json(
   list(token = "example_token"),
   "terratcgadata-test-key.json",
)
anvil_set_auth_json(
    "terra",
    "terratcgadata-test-key.json"
)
AnVIL:::.authenticate_get_access("terra")
unlink("terratcgadata-test-key.json")

Description

workspace() allows choice of workspace for subsequent use. It is the equivalent of displaying workspaces with avworkspaces(), and setting the selected workspace with avworkspace().

browse_workspace() uses browseURL() to open a browser window pointing to the Terra workspace.

table() allows choice of table in the current workspace (selected by avworkspace() or workspace()) to be returned as a tibble. It is equivalent to invoking avtables() to show available tables, and avtable() to retrieve the selected table.

workflow() allows choice of workflow for retrieval. It is the equivalent of avworkflows() for listing available workflows, and avworkflow_configuration_get() for retrieving the workflow.

Usage

avworkspace_gadget()

browse_workspace(use_avworkspace = TRUE)

avtable_gadget()

avworkflow_gadget()

Arguments

Value

workspace() returns the selected workspace as a character(1) using the format namespace/name, or character(0) if no workspace is selected.

browse_workspace() returns the status of a system() call to launch the browser, invisibly. The default app URL prefix (https://app.terra.bio) can be changed with the AnVIL.terra_app_url option.

table() returns a tibble representing the selected AnVIL table.

workflow() returns an avworkflow_configuration object representing the inputs and outputs of the selected workflow. This can be edited and updated as described in the "Running an AnVIL workflow within R" vigenette.

Examples

workspace()
browse_workspace(use_avworkspace = FALSE)
tbl <- table()
wkflw <- avworkflow_gadget()

Description

RESTful service constructor

Usage

Service(
  service,
  host,
  config = httr::config(),
  authenticate = TRUE,
  api_url = character(),
  package = "AnVIL",
  schemes = "https",
  api_reference_url = api_url,
  api_reference_md5sum = character(),
  api_reference_version = character(),
  api_reference_headers = NULL,
  ...
)

Arguments

Details

This function creates a RESTful interface to a service provided by a host, e.g., "leonardo.dsde-prod.broadinstitute.org". The function requires an OpenAPI .json or .yaml specification. The specification file is located in the source directory of a package, at ⁠<package>/inst/service/<service>/api.json⁠, or at api_url.

Authentication credentials can be stored securely in the system
keyring using `anvil_set_auth_json()`.

When provided, the api_reference_md5sum is used to check that the file described at api_reference_url has the same checksum as an author-validated version.

The service is usually a singleton, created at the package level during .onLoad().

Value

An object of class Service.

Examples

.MyService <- setClass("MyService", contains = "Service")

MyService <- function() {
    .MyService(Service("my_service", host="my.api.org"))
}

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

Format

An object of class list of length 0.

Details

Note the services Terra(), Rawls(), and Leonardo() require the GCPtools package for authentication to the Google Cloud Platform. See ?GCPtools::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. The default API url value can be changed with the AnVIL.leonardo_api_url option.

Terra() creates the API of the Terra cloud computational environment at https://api.firecloud.org/. The default API url value can be changed with the AnVIL.firecloud_api_url option.

Rawls() creates the API of the Rawls cloud computational environment at https://rawls.dsde-prod.broadinstitute.org. The default API url value can be changed with the AnVIL.rawls_api_url option.

Dockstore() represents the API of the Dockstore platform to share Docker-based tools in CWL or WDL or Nextflow at https://dockstore.org. The default API url value can be changed with the AnVIL.dockstore_api_url option.

TDR() creates the API of the Terra Data Repository to work with snapshot data in the Terra Data Repository at https://data.terra.bio. The default API url value can be changed with the AnVIL.tdr_api_url option.

Examples

empty_object


## Arguments to be used as the 'body' (`.__body__=`) of a REST query
Terra()$createBillingProjectFull       # 6 arguments...
## ... passed as `.__body__ = list(...)`
args(Terra()$createBillingProjectFull)

library(GCPtools)
if (gcloud_exists())
    Leonardo()

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

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

Dockstore()

library(GCPtools)
if (gcloud_exists())
    TDR()

Description

add_libpaths(): Add local library paths to .libPaths().

Usage

add_libpaths(paths)

Arguments

Value

add_libpaths(): updated .libPaths(), invisibly.

Examples

add_libpaths("/tmp/host-site-library")