Nothing
R/class-task.R
In sevenbridges2: The 'Seven Bridges Platform' API Client
Defines functions
asTaskList
asTask
# nolint start
#' @title R6 Class representing a Task
#'
#' @description
#' R6 Class representing a resource for managing tasks.
#'
#' @importFrom R6 R6Class
#' @export
Task <- R6::R6Class(
# nolint end
"Task",
inherit = Item,
portable = FALSE,
public = list(
#' @field URL List of URL endpoints for this resource.
URL = list(
"get" = "tasks/{id}",
"run" = "tasks/{self$id}/actions/run",
"abort" = "tasks/{self$id}/actions/abort",
"clone" = "tasks/{self$id}/actions/clone",
"execution_details" = "tasks/{self$id}/execution_details",
"task" = "tasks/{self$id}"
),
#' @field id The ID of the task.
id = NULL,
#' @field name The name of the task.
name = NULL,
#' @field status Task status (different from execution_status).
#' Allowed values:
#' * QUEUED
#' * DRAFT
#' * RUNNING
#' * COMPLETED
#' * ABORTED
#' * FAILED
status = NULL,
#' @field description An optional description of a task.
description = NULL,
#' @field project Identifier of the project that
#' the task is located in.
project = NULL,
#' @field app The identifier of the app that was used for the task.
app = NULL,
#' @field created_by Username of the task creator.
created_by = NULL,
#' @field executed_by Username of the task executor.
executed_by = NULL,
#' @field created_on The time in form of string when the task was created.
created_on = NULL,
#' @field start_time Task start time in form of string.
start_time = NULL,
#' @field end_time Task end time in form of string .
end_time = NULL,
#' @field origin Id of the entity that created the task, e.g.
#' automation run, if task was created by an automation run.
origin = NULL,
#' @field use_interruptable_instances This field can be `TRUE` or
#' `FALSE`. Set this field to `TRUE` to allow the use of spot instances.
use_interruptable_instances = NULL,
#' @field batch `TRUE` for batch tasks, `FALSE` for regular and child
#' tasks (batch this task; if `FALSE`, will not create a batch task).
batch = NULL,
#' @field batch_by Batching criteria (list).
batch_by = NULL,
#' @field batch_group Batch group for a batch task (list). Represents the
#' group that is assigned to the child task from the batching criteria that
#' was used when the task was started.
batch_group = NULL,
#' @field batch_input Input identifier on to which to apply batching.
batch_input = NULL,
#' @field batch_parent Parent task ID for a batch child. (batch task
#' which is the parent of this task).
batch_parent = NULL,
#' @field execution_settings Execution settings list for the task.
execution_settings = NULL,
#' @field execution_status Task execution status list - info about current
#' execution status.
execution_status = NULL,
#' @field errors Validations errors list stored as a high-level errors
#' array property in the API response.
errors = NULL,
#' @field warnings Validation warnings list from API response.
warnings = NULL,
#' @field price Task cost (list) - contains amount and currency.
price = NULL,
#' @field inputs List of inputs that were submitted to the task.
inputs = NULL,
#' @field outputs List of generated outputs from the task.
outputs = NULL,
#' @field output_location List of locations where task outputs will be
#' stored.
output_location = NULL,
#'
# Initialize Task object ----------------------------------------------
#' @description Create new Task object.
#'
#' @param res Response containing Task object information.
#' @param ... Other response arguments.
initialize = function(res = NA, ...) {
# Initialize Item class
super$initialize(...)
self$id <- res$id
self$name <- res$name
self$status <- res$status
self$description <- res$description
self$project <- res$project
self$app <- res$app
self$created_by <- res$created_by
self$executed_by <- res$executed_by
self$created_on <- res$created_on
self$start_time <- res$start_time
self$end_time <- res$end_time
self$origin <- res$origin
self$use_interruptable_instances <-
res$use_interruptable_instances
self$batch <- res$batch
self$batch_by <- res$batch_by
self$batch_group <- res$batch_group
self$batch_input <- res$batch_input
self$batch_parent <- res$batch_parent
self$execution_settings <- res$execution_settings
self$execution_status <- res$execution_status
self$errors <- res$errors
self$warnings <- res$warnings
self$inputs <- private$map_input_output(res$inputs)
self$outputs <- private$map_input_output(res$outputs)
self$output_location <- res$output_location
},
# Print Task object ------------------------------------------------------
#' @description Print method for Task class.
#'
#' @importFrom purrr discard
#' @importFrom glue glue_col
#' @importFrom cli cli_h1 cli_li cli_end
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Print task object
#' task_object$print()
#' }
#'
print = function() {
x <- as.list(self)
# Extract all except 'raw'
x$raw <- NULL
x <- purrr::discard(x, .p = is.function)
x <- purrr::discard(x, .p = is.environment)
x <- purrr::discard(x, .p = is.null)
# Extract name, description and status from service to print
x <- append(x, x$service[c("name", "description", "status")])
# Remove lists
x <- purrr::discard(x, .p = is.list)
# Remove copy_of field if it's empty (NA)
x <- purrr::discard(x, .p = is.na)
string <- glue::glue_col("{green {names(x)}}: {x}")
cli::cli_h1("Task")
cli::cli_li(string)
# Close container elements
cli::cli_end()
},
# nocov start
# Reload Task object ------------------------------------------------------
#' @description Reload Task object information.
#'
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Reload task object
#' task_object$reload()
#' }
#'
#' @return \code{\link{Task}} object.
reload = function(...) {
super$reload(
cls = self,
...
)
rlang::inform("Task object is refreshed!")
}, # nocov end
# Run task ---------------------------------------------------------------
#' @description This call runs (executes) the task. Only tasks whose status
#' is `DRAFT` can be run.
#'
#' @param batch Set this to `FALSE` to disable the default batching
#' for this task. Running a batch task is a recommended way to run multiple
#' tasks considering the API rate limit
#' ([learn more](https://docs.sevenbridges.com/docs/api-rate-limit)).
#' @param use_interruptible_instances This field can be `TRUE` or
#' `FALSE`. Set this field to `TRUE` to allow the use of
# nolint start
#' [spot instances](https://docs.sevenbridges.com/docs/about-spot-instances).
# nolint end
#' @param in_place Default `TRUE`. Should the new object of
#' Task class be returned or the current to be reinitialized.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_logical
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Run task
#' task_object$run()
#' }
#'
#' @return \code{\link{Task}} object.
run = function(batch = NULL,
use_interruptible_instances = NULL,
in_place = TRUE,
...) {
checkmate::assert_logical(batch, null.ok = TRUE)
checkmate::assert_logical(use_interruptible_instances, null.ok = TRUE)
checkmate::assert_logical(in_place, null.ok = FALSE)
# nocov start
path <- glue::glue(self$URL[["run"]])
params <- list()
params[["batch"]] <- batch
params[["use_interruptible_instances"]] <-
use_interruptible_instances
res <- self$auth$api(
path = path,
method = "POST",
query = params,
body = list(),
...
)
rlang::inform(
glue::glue_col(
"Execution of task {green {self$name}} has started."
)
)
if (in_place) {
self$initialize(
res = res,
href = res$href,
auth = self$auth,
response = attr(res, "response")
)
} else {
return(asTask(res, auth = self$auth))
}
}, # nocov end
# Abort task -------------------------------------------------------------
#' @description This call aborts the specified task. Only tasks whose
#' status is `RUNNING` or `QUEUED` may be aborted.
#' @param in_place Default `TRUE`. Should the new object of
#' Task class be returned or the current to be reinitialized.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_logical
#' @importFrom glue glue glue_col
#' @importFrom rlang inform
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' . # Run task
#' task_object$run()
#'
#' # Then abort task
#' task_object$abort()
#' }
#'
#' @return \code{\link{Task}} object.
abort = function(in_place = TRUE, ...) {
checkmate::assert_logical(in_place, null.ok = FALSE)
# nocov start
res <- self$auth$api(
path = glue::glue(self$URL[["abort"]]),
method = "POST",
...
)
rlang::inform(
glue::glue_col(
"Task {green {self$name}} has been aborted."
)
)
if (in_place) {
self$initialize(
res = res,
href = res$href,
auth = self$auth,
response = attr(res, "response")
)
} else {
return(asTask(res, auth = self$auth))
}
}, # nocov end
# Clone task ------------------------------------------------------------
#' @description This call clones the specified task. Once cloned, the task
#' can either be in `DRAFT` mode or immediately ran, by setting the `run`
#' parameter to `TRUE`.
#' @param run Set this to `TRUE` in order to create a draft task
#' and execute it immediately. Default: `FALSE`.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_logical
#' @importFrom glue glue glue_col
#' @importFrom rlang inform
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Clone task object
#' task_object$clone_task()
#' }
#'
#' @return \code{\link{Task}} object.
clone_task = function(run = FALSE, ...) {
# nocov start
action <- NULL
checkmate::assert_logical(run, null.ok = TRUE)
if (!is_missing(run)) {
if (run) {
action <- "run"
}
}
path <- glue::glue(self$URL[["clone"]])
params <- list("action" = action)
res <- self$auth$api(
path = path,
method = "POST",
query = params,
...
)
rlang::inform(
glue::glue_col(
"New cloned draft task with id {green {res$id}} has been created."
)
)
return(asTask(res, auth = self$auth))
}, # nocov end
# Get execution details of a task -----------------------------------------
#' @description This call returns execution details of the specified task.
#' The task is referred to by its ID, which you can obtain by making the
#' call to list all tasks you can access. The call breaks down the
#' information into the task's distinct jobs. A job is a single subprocess
#' carried out in a task. The information returned by this call is broadly
#' similar to that which can be found in the task stats and logs provided
#' on the Platform.
#' The task execution details include the following information:
#' * The name of the command line job that executed
#' * The start time of the job
#' * End time of the job (if it completed)
#' * The status of the job (`DONE`, `FAILED`, or `RUNNING`)
#' * Information on the computational instance that the job was run on,
#' including the provider ID, the type of instance used and the cloud
#' service provider
#' * A link that can be used to download the standard error logs for the
#' job.
#' * SHA hash of the Docker image ('checksum').
#'
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom glue glue
#' @importFrom rlang inform
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Get task execution details
#' task_object$get_execution_details()
#' }
#'
#' @return List of execution details.
get_execution_details = function(...) {
# nocov start
res <- self$auth$api(
path = glue::glue(self$URL[["execution_details"]]),
method = "GET",
...
)
if (self$batch) {
rlang::inform("Execution details can be seen on each child task.")
}
return(res)
}, # nocov end
# List batch child tasks -------------------------------------------------
#' @description This call retrieves batch child tasks for this task if its
#' a batch task.
#'
#' @param status You can filter the returned tasks by their status.
#' Set the value of status to one of the following values:
#' * QUEUED
#' * DRAFT
#' * RUNNING
#' * COMPLETED
#' * ABORTED
#' * FAILED.
#' @param project Provide the project ID or Project object you wish to list
#' the tasks from.
#' @param created_from Enter the starting date string for querying tasks
#' created on the specified date and onwards.
#' @param created_to Enter the ending date string for querying tasks
#' created until the specified date. You can use it in combination with
#' `created_from` to specify a time interval.
#' @param started_from Enter the starting date string for querying tasks
#' started on the specified date and onwards.
#' @param started_to Enter the ending date string for querying tasks
#' started until the specified date.
#' @param ended_from Enter the starting date string for querying tasks
#' that ended on a specified date.
#' @param ended_to Enter the ending date string for querying tasks that
#' ended until a specified date.
#' @param order_by Order returned results by the specified field.
#' Allowed values: \cr `created_time`, `start_time`, `name`, `end_time` and
#' `created_by`. \cr Sort can be done only by one column. The default
#' value is `created_time`.
#' @param order Sort results in ascending or descending order by
#' specifying `asc` or `desc`, respectively. Only taken into account if
#' `order_by` is explicitly specified. The default value is `asc`.
#' @param origin_id Enter an automation run ID to list all tasks
#' created from the specified automation run.
#' @param limit The maximum number of collection items to return
#' for a single request. Minimum value is `1`.
#' The maximum value is `100` and the default value is `50`.
#' This is a pagination-specific attribute.
#' @param offset The zero-based starting index in the entire collection
#' of the first item to return. The default value is `0`.
#' This is a pagination-specific attribute.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom rlang abort
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # List batch children of a task
#' task_object$list_batch_children()
#' }
#'
#' @return \code{\link{Collection}} of \code{\link{Task}} objects.
list_batch_children = function(status = NULL,
project = NULL,
created_from = NULL,
created_to = NULL,
started_from = NULL,
started_to = NULL,
ended_from = NULL,
ended_to = NULL,
order_by = NULL,
order = NULL,
origin_id = NULL,
limit = getOption("sevenbridges2")$limit,
offset = getOption("sevenbridges2")$offset,
...) {
if (is_missing(self$batch) || !self$batch) {
rlang::abort("This task is not a batch task.")
}
# nocov start
parent <- self$id
self$auth$tasks$query(
status = status,
parent = parent,
project = project,
created_from = created_from,
created_to = created_to,
started_from = started_from,
started_to = started_to,
ended_from = ended_from,
ended_to = ended_to,
order_by = order_by,
order = order,
origin_id = origin_id,
offset = offset,
limit = limit,
...
)
}, # nocov end
# Delete task -----------------------------------------------------------
#' @description This call deletes the specified task. The task is referred
#' to by its ID, which you can obtain by making the call to list all tasks
#' you can access.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom glue glue glue_col
#' @importFrom rlang inform
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Delete task
#' task_object$delete()
#' }
#'
delete = function(...) {
# nocov start
res <- self$auth$api(
path = glue::glue(self$URL[["task"]]),
method = "DELETE",
...
)
rlang::inform(
glue::glue_col(
"The task with the following ID {green {id}} has been deleted."
)
)
}, # nocov end
# Rerun task -----------------------------------------------------------
#' @description This call reruns (executes) the specified task.
#'
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom glue glue
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Rerun task
#' task_object$rerun()
#' }
#'
#' @return \code{\link{Task}} object.
rerun = function(...) {
# nocov start
self$clone_task(run = TRUE, ...)
}, # nocov end
# Update task -----------------------------------------------------------
#' @description Change the details of the specified task, including its
#' name, description, and inputs. Note that you can only modify tasks with
#' a task status of `DRAFT`. Tasks which are `RUNNING`, `QUEUED`,
#' `ABORTED`, `COMPLETED` or `FAILED` cannot be modified in order to
#' enable the reproducibility of analyses which have been queued for
#' execution or has initiated executing.
#' There are two things to note if you are editing a batch task:
#' \itemize{
#' \item `1` If you want to change the input on which to batch and
#' the batch criteria, you need to specify the batch_input and batch_by
#' parameters together in the same function call.
#' \item `2` If you want to disable batching on a task, set batch to
#' false. Or, you can also set the parameters batch_input and batch_by
#' to NULL.
#' }
#' @param name The name of the task.
#' @param description An optional description of the task.
#' @param execution_settings Named list with detailed task execution
#' parameters. Detailed task execution parameters:
#' \itemize{
#' \item `instance_type`: Possible value is the specific instance type,
#' e.g. `"instance_type" = "c4.2xlarge;ebs-gp2;2000"`;
#' \item `max_parallel_instances`: Maximum number of instances
#' running at the same time. Takes any integer value equal to or
#' greater than 1, e.g. `"max_parallel_instances" = 2.`;
#' \item `use_memoization`: Set to `FALSE` by default. Set to `TRUE`
#' to enable
#' [memoization](https://docs.sevenbridges.com/docs/about-memoization);
#' \item `use_elastic_disk`: Set to `TRUE` to enable
#' [Elastic Disk](https://docs.sevenbridges.com/page/elastic-disk).
#' }
#'
#' Here is an example:
#' ```{r}
#' execution_settings <- list(
#' "instance_type" = "c4.2xlarge;ebs-gp2;2000",
#' "max_parallel_instances" = 2,
#' "use_memoization" = TRUE,
#' "use_elastic_disk" = TRUE
#' )
#' ```
#' @param inputs List of objects. See the section on
# nolint start
#' [specifying task inputs](https://docs.sevenbridges.com/docs/the-api#section-inputs)
# nolint end
#' for information on creating task input objects. Here is an example with
#' various input types:
#' ```{r}
#' inputs <- list(
#' "input_file"= "<file_id/file_object>",
#' "input_directory" = "<folder_id/folder_object>",
#' "input_array_string" = list("<string_elem_1>", "<string_elem_2>"),
#' "input_boolean" = TRUE,
#' "input_double" = 54.6,
#' "input_enum" = "enum_1",
#' "input_float" = 11.2,
#' "input_integer" = "asdf",
#' "input_long" = 4212,
#' "input_string" = "test_string",
#' "input_record" = list(
#' "input_record_field_file" = "<file_id/file_object>",
#' "input_record_field_integer" = 42
#' )
#' )
#' ```
#' @param output_location The output location list allows you to
#' define the exact location where your task outputs will be stored.
#' The location can either be defined for the entire project using the
#' main_location parameter, or individually per each output node, by
#' setting the nodes_override parameter to true and defining individual
#' output node locations within nodes_location.
#' See below for more details.
#' \itemize{
#' \item `main_location` - Defines the output location for all
#' output nodes in the task. Can be a string path within the project in
#' which the task is created, for example \cr
#' `/Analysis/<task_id>_<task_name>/`
#' or a path on an attached volume, such as \cr
#' `volumes://volume_name/<project_id>/html`.
#' Parts of the path enclosed in angle brackets <> are tokens that are
#' dynamically replaced with corresponding values during task
#' execution.
#' \item `main_location_alias`: The string location (path) in the
#' project that will point to the actual location where the outputs are
#' stored. Used if main_location is defined as a volume path (starting
#' with volumes://), to provide an easy way of accessing output data
#' directly from project files.
#' \item `nodes_override`: Enables defining of output locations
#' for output nodes individually through nodes_location (see below).
#' Set to `TRUE` to be able to define individual locations per output
#' node. Default: `FALSE`.
#' Even if nodes_override is set to `TRUE`, it is not necessary to
#' define output locations for each of the output nodes individually.
#' Data from those output nodes that don't have their locations
#' explicitly defined through nodes_location is either placed in
#' main_location (if defined) or at the project files root if a main
#' output location is not defined for the task.
#' \item `nodes_location`: List of output paths for individual
#' task output nodes in the following format for each output node:\cr
#' `<output-node-id> = list(` \cr
#' `"output_location" = "<output-path>",` \cr
#' `"output_location_alias" = "<alias-path>"` \cr
#' `)` \cr
#' Example:
#' ```{r}
#' b64html = list(
#' "output_location" = "volumes://outputs/tasks/mar-19",
#' "output_location_alias" = "/rfranklin/tasks/picard"
#' )
#' ```
#' In the example above, b64html is the ID of the output node for which
#' you want to define the output location, while the parameters are
#' defined as follows:
#' \itemize{
#' \item `output_location` - Can be a path within the project in which
#' the task is created, for example
#' `/Analysis/<task_id>_<task_name>/`
#' or a path on an attached volume, such as
#' `volumes://volume_name/<project_id>/html`. Also accepts tokens.
#' \item `output_location_alias` - The location (path) in the project
#' that will point to the exact location where the output is stored.
#' Used if output_location is defined as a volume path
#' (starting with volumes://).
#' }
#' }
#' @param batch This is set to `FALSE` by default. Set to `TRUE` to
#' create a batch task and specify the `batch_input` and `batch-by`
#' criteria as described below.
#' @param batch_input The ID of the input on which you wish to batch.
#' You would typically batch on the input consisting of a list of files.
#' If this parameter is omitted, the default batching criteria defined for
#' the app will be used.
#' @param batch_by Batching criteria in form of list. For example:
#' ```{r}
#' batch_by = list(
#' type = "CRITERIA",
#' criteria = list("metadata.condition")
#' )
#' ```
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_string assert_list assert_logical
#' @importFrom rlang abort
#' @importFrom glue glue glue_col
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Update task
#' task_object$update(name = new_name)
#' }
#'
#' @return \code{\link{Task}} object.
update = function(name = NULL,
description = NULL,
execution_settings = NULL,
inputs = NULL,
output_location = NULL,
batch = NULL,
batch_input = NULL,
batch_by = NULL,
...) {
checkmate::assert_string(name, null.ok = TRUE)
checkmate::assert_string(description, null.ok = TRUE)
check_execution_settings(execution_settings)
checkmate::assert_list(inputs, null.ok = TRUE)
checkmate::assert_list(output_location, null.ok = TRUE)
checkmate::assert_logical(batch, null.ok = TRUE)
checkmate::assert_string(batch_input, null.ok = TRUE)
checkmate::assert_list(batch_by, null.ok = TRUE)
task_inputs <- list()
task_data <- list()
task_data <- list(
"name" = name,
"description" = description
)
if (!is_missing(batch) && batch) {
if (!is_missing(batch_input) && !is_missing(batch_by)) {
task_data[["batch_input"]] <- batch_input
task_data[["batch_by"]] <- batch_by
} else {
rlang::abort("Batch is set to TRUE, therefore, please set batching criteria (batch_by) and batch inputs.") # nolint
}
}
# nocov start
if (!is_missing(inputs)) {
task_inputs <- self$auth$tasks$private$serialize_inputs(inputs)
task_data[["inputs"]] <- task_inputs
}
if (!is_missing(output_location)) {
task_data[["output_location"]] <- output_location
}
task_data[["execution_settings"]] <- execution_settings
task_data[["batch"]] <- batch
res <- self$auth$api(
path = glue::glue(self$URL[["task"]]),
method = "PATCH",
body = task_data,
...
)
rlang::inform(
glue::glue_col(
"Task {green {self$name}} has been updated."
)
)
self$initialize(
res = res,
href = res$href,
auth = self$auth,
response = attr(res, "response")
)
} # nocov end
),
private = list(
# Map input/output values -----------------------------------------------
#' @importFrom checkmate test_list
map_input_output = function(input) {
return_value <- list()
if (checkmate::test_list(input)) {
if ("class" %in% names(input)) {
if (tolower(input[["class"]]) %in% c("file", "folder")) {
f_data <- map_fields_util(input)
f_data <- append(f_data, input)
if (!is.null(input[["secondaryFiles"]])) {
secondary_files <- list()
for (sf in input[["secondaryFiles"]]) {
sf_data <- map_fields_util(sf)
sf_data <- append(sf_data, sf)
secondary_files <- append(secondary_files, list(sf_data))
}
f_data[["secondary_files"]] <- secondary_files
}
return_value <- asFile(f_data, auth = self$auth)
}
} else {
for (i in seq_len(length(input))) {
elem_name <- names(input[i])
vals <- private$map_input_output(input[[i]])
if (!is.null(elem_name)) {
return_value[[elem_name]] <- vals
} else {
return_value <- c(return_value, list(vals))
}
}
}
} else {
return_value <- input
}
return(return_value)
},
# Map fields -------------------------------------------------------------
map_fields_util = function(input) {
mapped_data <- list(
id = input[["path"]],
type = tolower(input[["class"]])
)
if ("basename" %in% names(input)) {
mapped_data[["name"]] <- input[["basename"]]
}
if ("name" %in% names(input)) {
mapped_data[["name"]] <- input[["name"]]
}
return(mapped_data)
}
)
)
# nocov start
# Helper functions for creating Task objects --------------------------------
asTask <- function(x = NULL, auth = NULL, bulk = FALSE) {
if (bulk) {
x <- x$resource
}
Task$new(
res = x,
href = x$href,
response = attr(x, "response"),
auth = auth
)
}
asTaskList <- function(x, auth, bulk = FALSE) {
obj <- lapply(x$items, asTask, auth = auth, bulk = bulk)
obj
}
# nocov end
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Defines functions asTaskList asTask
# nolint start
#' @title R6 Class representing a Task
#'
#' @description
#' R6 Class representing a resource for managing tasks.
#'
#' @importFrom R6 R6Class
#' @export
Task <- R6::R6Class(
# nolint end
"Task",
inherit = Item,
portable = FALSE,
public = list(
#' @field URL List of URL endpoints for this resource.
URL = list(
"get" = "tasks/{id}",
"run" = "tasks/{self$id}/actions/run",
"abort" = "tasks/{self$id}/actions/abort",
"clone" = "tasks/{self$id}/actions/clone",
"execution_details" = "tasks/{self$id}/execution_details",
"task" = "tasks/{self$id}"
),
#' @field id The ID of the task.
id = NULL,
#' @field name The name of the task.
name = NULL,
#' @field status Task status (different from execution_status).
#' Allowed values:
#' * QUEUED
#' * DRAFT
#' * RUNNING
#' * COMPLETED
#' * ABORTED
#' * FAILED
status = NULL,
#' @field description An optional description of a task.
description = NULL,
#' @field project Identifier of the project that
#' the task is located in.
project = NULL,
#' @field app The identifier of the app that was used for the task.
app = NULL,
#' @field created_by Username of the task creator.
created_by = NULL,
#' @field executed_by Username of the task executor.
executed_by = NULL,
#' @field created_on The time in form of string when the task was created.
created_on = NULL,
#' @field start_time Task start time in form of string.
start_time = NULL,
#' @field end_time Task end time in form of string .
end_time = NULL,
#' @field origin Id of the entity that created the task, e.g.
#' automation run, if task was created by an automation run.
origin = NULL,
#' @field use_interruptable_instances This field can be `TRUE` or
#' `FALSE`. Set this field to `TRUE` to allow the use of spot instances.
use_interruptable_instances = NULL,
#' @field batch `TRUE` for batch tasks, `FALSE` for regular and child
#' tasks (batch this task; if `FALSE`, will not create a batch task).
batch = NULL,
#' @field batch_by Batching criteria (list).
batch_by = NULL,
#' @field batch_group Batch group for a batch task (list). Represents the
#' group that is assigned to the child task from the batching criteria that
#' was used when the task was started.
batch_group = NULL,
#' @field batch_input Input identifier on to which to apply batching.
batch_input = NULL,
#' @field batch_parent Parent task ID for a batch child. (batch task
#' which is the parent of this task).
batch_parent = NULL,
#' @field execution_settings Execution settings list for the task.
execution_settings = NULL,
#' @field execution_status Task execution status list - info about current
#' execution status.
execution_status = NULL,
#' @field errors Validations errors list stored as a high-level errors
#' array property in the API response.
errors = NULL,
#' @field warnings Validation warnings list from API response.
warnings = NULL,
#' @field price Task cost (list) - contains amount and currency.
price = NULL,
#' @field inputs List of inputs that were submitted to the task.
inputs = NULL,
#' @field outputs List of generated outputs from the task.
outputs = NULL,
#' @field output_location List of locations where task outputs will be
#' stored.
output_location = NULL,
#'
# Initialize Task object ----------------------------------------------
#' @description Create new Task object.
#'
#' @param res Response containing Task object information.
#' @param ... Other response arguments.
initialize = function(res = NA, ...) {
# Initialize Item class
super$initialize(...)
self$id <- res$id
self$name <- res$name
self$status <- res$status
self$description <- res$description
self$project <- res$project
self$app <- res$app
self$created_by <- res$created_by
self$executed_by <- res$executed_by
self$created_on <- res$created_on
self$start_time <- res$start_time
self$end_time <- res$end_time
self$origin <- res$origin
self$use_interruptable_instances <-
res$use_interruptable_instances
self$batch <- res$batch
self$batch_by <- res$batch_by
self$batch_group <- res$batch_group
self$batch_input <- res$batch_input
self$batch_parent <- res$batch_parent
self$execution_settings <- res$execution_settings
self$execution_status <- res$execution_status
self$errors <- res$errors
self$warnings <- res$warnings
self$inputs <- private$map_input_output(res$inputs)
self$outputs <- private$map_input_output(res$outputs)
self$output_location <- res$output_location
},
# Print Task object ------------------------------------------------------
#' @description Print method for Task class.
#'
#' @importFrom purrr discard
#' @importFrom glue glue_col
#' @importFrom cli cli_h1 cli_li cli_end
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Print task object
#' task_object$print()
#' }
#'
print = function() {
x <- as.list(self)
# Extract all except 'raw'
x$raw <- NULL
x <- purrr::discard(x, .p = is.function)
x <- purrr::discard(x, .p = is.environment)
x <- purrr::discard(x, .p = is.null)
# Extract name, description and status from service to print
x <- append(x, x$service[c("name", "description", "status")])
# Remove lists
x <- purrr::discard(x, .p = is.list)
# Remove copy_of field if it's empty (NA)
x <- purrr::discard(x, .p = is.na)
string <- glue::glue_col("{green {names(x)}}: {x}")
cli::cli_h1("Task")
cli::cli_li(string)
# Close container elements
cli::cli_end()
},
# nocov start
# Reload Task object ------------------------------------------------------
#' @description Reload Task object information.
#'
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Reload task object
#' task_object$reload()
#' }
#'
#' @return \code{\link{Task}} object.
reload = function(...) {
super$reload(
cls = self,
...
)
rlang::inform("Task object is refreshed!")
}, # nocov end
# Run task ---------------------------------------------------------------
#' @description This call runs (executes) the task. Only tasks whose status
#' is `DRAFT` can be run.
#'
#' @param batch Set this to `FALSE` to disable the default batching
#' for this task. Running a batch task is a recommended way to run multiple
#' tasks considering the API rate limit
#' ([learn more](https://docs.sevenbridges.com/docs/api-rate-limit)).
#' @param use_interruptible_instances This field can be `TRUE` or
#' `FALSE`. Set this field to `TRUE` to allow the use of
# nolint start
#' [spot instances](https://docs.sevenbridges.com/docs/about-spot-instances).
# nolint end
#' @param in_place Default `TRUE`. Should the new object of
#' Task class be returned or the current to be reinitialized.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_logical
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Run task
#' task_object$run()
#' }
#'
#' @return \code{\link{Task}} object.
run = function(batch = NULL,
use_interruptible_instances = NULL,
in_place = TRUE,
...) {
checkmate::assert_logical(batch, null.ok = TRUE)
checkmate::assert_logical(use_interruptible_instances, null.ok = TRUE)
checkmate::assert_logical(in_place, null.ok = FALSE)
# nocov start
path <- glue::glue(self$URL[["run"]])
params <- list()
params[["batch"]] <- batch
params[["use_interruptible_instances"]] <-
use_interruptible_instances
res <- self$auth$api(
path = path,
method = "POST",
query = params,
body = list(),
...
)
rlang::inform(
glue::glue_col(
"Execution of task {green {self$name}} has started."
)
)
if (in_place) {
self$initialize(
res = res,
href = res$href,
auth = self$auth,
response = attr(res, "response")
)
} else {
return(asTask(res, auth = self$auth))
}
}, # nocov end
# Abort task -------------------------------------------------------------
#' @description This call aborts the specified task. Only tasks whose
#' status is `RUNNING` or `QUEUED` may be aborted.
#' @param in_place Default `TRUE`. Should the new object of
#' Task class be returned or the current to be reinitialized.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_logical
#' @importFrom glue glue glue_col
#' @importFrom rlang inform
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' . # Run task
#' task_object$run()
#'
#' # Then abort task
#' task_object$abort()
#' }
#'
#' @return \code{\link{Task}} object.
abort = function(in_place = TRUE, ...) {
checkmate::assert_logical(in_place, null.ok = FALSE)
# nocov start
res <- self$auth$api(
path = glue::glue(self$URL[["abort"]]),
method = "POST",
...
)
rlang::inform(
glue::glue_col(
"Task {green {self$name}} has been aborted."
)
)
if (in_place) {
self$initialize(
res = res,
href = res$href,
auth = self$auth,
response = attr(res, "response")
)
} else {
return(asTask(res, auth = self$auth))
}
}, # nocov end
# Clone task ------------------------------------------------------------
#' @description This call clones the specified task. Once cloned, the task
#' can either be in `DRAFT` mode or immediately ran, by setting the `run`
#' parameter to `TRUE`.
#' @param run Set this to `TRUE` in order to create a draft task
#' and execute it immediately. Default: `FALSE`.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_logical
#' @importFrom glue glue glue_col
#' @importFrom rlang inform
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Clone task object
#' task_object$clone_task()
#' }
#'
#' @return \code{\link{Task}} object.
clone_task = function(run = FALSE, ...) {
# nocov start
action <- NULL
checkmate::assert_logical(run, null.ok = TRUE)
if (!is_missing(run)) {
if (run) {
action <- "run"
}
}
path <- glue::glue(self$URL[["clone"]])
params <- list("action" = action)
res <- self$auth$api(
path = path,
method = "POST",
query = params,
...
)
rlang::inform(
glue::glue_col(
"New cloned draft task with id {green {res$id}} has been created."
)
)
return(asTask(res, auth = self$auth))
}, # nocov end
# Get execution details of a task -----------------------------------------
#' @description This call returns execution details of the specified task.
#' The task is referred to by its ID, which you can obtain by making the
#' call to list all tasks you can access. The call breaks down the
#' information into the task's distinct jobs. A job is a single subprocess
#' carried out in a task. The information returned by this call is broadly
#' similar to that which can be found in the task stats and logs provided
#' on the Platform.
#' The task execution details include the following information:
#' * The name of the command line job that executed
#' * The start time of the job
#' * End time of the job (if it completed)
#' * The status of the job (`DONE`, `FAILED`, or `RUNNING`)
#' * Information on the computational instance that the job was run on,
#' including the provider ID, the type of instance used and the cloud
#' service provider
#' * A link that can be used to download the standard error logs for the
#' job.
#' * SHA hash of the Docker image ('checksum').
#'
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom glue glue
#' @importFrom rlang inform
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Get task execution details
#' task_object$get_execution_details()
#' }
#'
#' @return List of execution details.
get_execution_details = function(...) {
# nocov start
res <- self$auth$api(
path = glue::glue(self$URL[["execution_details"]]),
method = "GET",
...
)
if (self$batch) {
rlang::inform("Execution details can be seen on each child task.")
}
return(res)
}, # nocov end
# List batch child tasks -------------------------------------------------
#' @description This call retrieves batch child tasks for this task if its
#' a batch task.
#'
#' @param status You can filter the returned tasks by their status.
#' Set the value of status to one of the following values:
#' * QUEUED
#' * DRAFT
#' * RUNNING
#' * COMPLETED
#' * ABORTED
#' * FAILED.
#' @param project Provide the project ID or Project object you wish to list
#' the tasks from.
#' @param created_from Enter the starting date string for querying tasks
#' created on the specified date and onwards.
#' @param created_to Enter the ending date string for querying tasks
#' created until the specified date. You can use it in combination with
#' `created_from` to specify a time interval.
#' @param started_from Enter the starting date string for querying tasks
#' started on the specified date and onwards.
#' @param started_to Enter the ending date string for querying tasks
#' started until the specified date.
#' @param ended_from Enter the starting date string for querying tasks
#' that ended on a specified date.
#' @param ended_to Enter the ending date string for querying tasks that
#' ended until a specified date.
#' @param order_by Order returned results by the specified field.
#' Allowed values: \cr `created_time`, `start_time`, `name`, `end_time` and
#' `created_by`. \cr Sort can be done only by one column. The default
#' value is `created_time`.
#' @param order Sort results in ascending or descending order by
#' specifying `asc` or `desc`, respectively. Only taken into account if
#' `order_by` is explicitly specified. The default value is `asc`.
#' @param origin_id Enter an automation run ID to list all tasks
#' created from the specified automation run.
#' @param limit The maximum number of collection items to return
#' for a single request. Minimum value is `1`.
#' The maximum value is `100` and the default value is `50`.
#' This is a pagination-specific attribute.
#' @param offset The zero-based starting index in the entire collection
#' of the first item to return. The default value is `0`.
#' This is a pagination-specific attribute.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom rlang abort
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # List batch children of a task
#' task_object$list_batch_children()
#' }
#'
#' @return \code{\link{Collection}} of \code{\link{Task}} objects.
list_batch_children = function(status = NULL,
project = NULL,
created_from = NULL,
created_to = NULL,
started_from = NULL,
started_to = NULL,
ended_from = NULL,
ended_to = NULL,
order_by = NULL,
order = NULL,
origin_id = NULL,
limit = getOption("sevenbridges2")$limit,
offset = getOption("sevenbridges2")$offset,
...) {
if (is_missing(self$batch) || !self$batch) {
rlang::abort("This task is not a batch task.")
}
# nocov start
parent <- self$id
self$auth$tasks$query(
status = status,
parent = parent,
project = project,
created_from = created_from,
created_to = created_to,
started_from = started_from,
started_to = started_to,
ended_from = ended_from,
ended_to = ended_to,
order_by = order_by,
order = order,
origin_id = origin_id,
offset = offset,
limit = limit,
...
)
}, # nocov end
# Delete task -----------------------------------------------------------
#' @description This call deletes the specified task. The task is referred
#' to by its ID, which you can obtain by making the call to list all tasks
#' you can access.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom glue glue glue_col
#' @importFrom rlang inform
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Delete task
#' task_object$delete()
#' }
#'
delete = function(...) {
# nocov start
res <- self$auth$api(
path = glue::glue(self$URL[["task"]]),
method = "DELETE",
...
)
rlang::inform(
glue::glue_col(
"The task with the following ID {green {id}} has been deleted."
)
)
}, # nocov end
# Rerun task -----------------------------------------------------------
#' @description This call reruns (executes) the specified task.
#'
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom glue glue
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Rerun task
#' task_object$rerun()
#' }
#'
#' @return \code{\link{Task}} object.
rerun = function(...) {
# nocov start
self$clone_task(run = TRUE, ...)
}, # nocov end
# Update task -----------------------------------------------------------
#' @description Change the details of the specified task, including its
#' name, description, and inputs. Note that you can only modify tasks with
#' a task status of `DRAFT`. Tasks which are `RUNNING`, `QUEUED`,
#' `ABORTED`, `COMPLETED` or `FAILED` cannot be modified in order to
#' enable the reproducibility of analyses which have been queued for
#' execution or has initiated executing.
#' There are two things to note if you are editing a batch task:
#' \itemize{
#' \item `1` If you want to change the input on which to batch and
#' the batch criteria, you need to specify the batch_input and batch_by
#' parameters together in the same function call.
#' \item `2` If you want to disable batching on a task, set batch to
#' false. Or, you can also set the parameters batch_input and batch_by
#' to NULL.
#' }
#' @param name The name of the task.
#' @param description An optional description of the task.
#' @param execution_settings Named list with detailed task execution
#' parameters. Detailed task execution parameters:
#' \itemize{
#' \item `instance_type`: Possible value is the specific instance type,
#' e.g. `"instance_type" = "c4.2xlarge;ebs-gp2;2000"`;
#' \item `max_parallel_instances`: Maximum number of instances
#' running at the same time. Takes any integer value equal to or
#' greater than 1, e.g. `"max_parallel_instances" = 2.`;
#' \item `use_memoization`: Set to `FALSE` by default. Set to `TRUE`
#' to enable
#' [memoization](https://docs.sevenbridges.com/docs/about-memoization);
#' \item `use_elastic_disk`: Set to `TRUE` to enable
#' [Elastic Disk](https://docs.sevenbridges.com/page/elastic-disk).
#' }
#'
#' Here is an example:
#' ```{r}
#' execution_settings <- list(
#' "instance_type" = "c4.2xlarge;ebs-gp2;2000",
#' "max_parallel_instances" = 2,
#' "use_memoization" = TRUE,
#' "use_elastic_disk" = TRUE
#' )
#' ```
#' @param inputs List of objects. See the section on
# nolint start
#' [specifying task inputs](https://docs.sevenbridges.com/docs/the-api#section-inputs)
# nolint end
#' for information on creating task input objects. Here is an example with
#' various input types:
#' ```{r}
#' inputs <- list(
#' "input_file"= "<file_id/file_object>",
#' "input_directory" = "<folder_id/folder_object>",
#' "input_array_string" = list("<string_elem_1>", "<string_elem_2>"),
#' "input_boolean" = TRUE,
#' "input_double" = 54.6,
#' "input_enum" = "enum_1",
#' "input_float" = 11.2,
#' "input_integer" = "asdf",
#' "input_long" = 4212,
#' "input_string" = "test_string",
#' "input_record" = list(
#' "input_record_field_file" = "<file_id/file_object>",
#' "input_record_field_integer" = 42
#' )
#' )
#' ```
#' @param output_location The output location list allows you to
#' define the exact location where your task outputs will be stored.
#' The location can either be defined for the entire project using the
#' main_location parameter, or individually per each output node, by
#' setting the nodes_override parameter to true and defining individual
#' output node locations within nodes_location.
#' See below for more details.
#' \itemize{
#' \item `main_location` - Defines the output location for all
#' output nodes in the task. Can be a string path within the project in
#' which the task is created, for example \cr
#' `/Analysis/<task_id>_<task_name>/`
#' or a path on an attached volume, such as \cr
#' `volumes://volume_name/<project_id>/html`.
#' Parts of the path enclosed in angle brackets <> are tokens that are
#' dynamically replaced with corresponding values during task
#' execution.
#' \item `main_location_alias`: The string location (path) in the
#' project that will point to the actual location where the outputs are
#' stored. Used if main_location is defined as a volume path (starting
#' with volumes://), to provide an easy way of accessing output data
#' directly from project files.
#' \item `nodes_override`: Enables defining of output locations
#' for output nodes individually through nodes_location (see below).
#' Set to `TRUE` to be able to define individual locations per output
#' node. Default: `FALSE`.
#' Even if nodes_override is set to `TRUE`, it is not necessary to
#' define output locations for each of the output nodes individually.
#' Data from those output nodes that don't have their locations
#' explicitly defined through nodes_location is either placed in
#' main_location (if defined) or at the project files root if a main
#' output location is not defined for the task.
#' \item `nodes_location`: List of output paths for individual
#' task output nodes in the following format for each output node:\cr
#' `<output-node-id> = list(` \cr
#' `"output_location" = "<output-path>",` \cr
#' `"output_location_alias" = "<alias-path>"` \cr
#' `)` \cr
#' Example:
#' ```{r}
#' b64html = list(
#' "output_location" = "volumes://outputs/tasks/mar-19",
#' "output_location_alias" = "/rfranklin/tasks/picard"
#' )
#' ```
#' In the example above, b64html is the ID of the output node for which
#' you want to define the output location, while the parameters are
#' defined as follows:
#' \itemize{
#' \item `output_location` - Can be a path within the project in which
#' the task is created, for example
#' `/Analysis/<task_id>_<task_name>/`
#' or a path on an attached volume, such as
#' `volumes://volume_name/<project_id>/html`. Also accepts tokens.
#' \item `output_location_alias` - The location (path) in the project
#' that will point to the exact location where the output is stored.
#' Used if output_location is defined as a volume path
#' (starting with volumes://).
#' }
#' }
#' @param batch This is set to `FALSE` by default. Set to `TRUE` to
#' create a batch task and specify the `batch_input` and `batch-by`
#' criteria as described below.
#' @param batch_input The ID of the input on which you wish to batch.
#' You would typically batch on the input consisting of a list of files.
#' If this parameter is omitted, the default batching criteria defined for
#' the app will be used.
#' @param batch_by Batching criteria in form of list. For example:
#' ```{r}
#' batch_by = list(
#' type = "CRITERIA",
#' criteria = list("metadata.condition")
#' )
#' ```
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_string assert_list assert_logical
#' @importFrom rlang abort
#' @importFrom glue glue glue_col
#'
#' @examples
#' \dontrun{
#' # x is API response when task is requested
#' task_object <- Task$new(
#' res = x,
#' href = x$href,
#' auth = auth,
#' response = attr(x, "response")
#' )
#'
#' # Update task
#' task_object$update(name = new_name)
#' }
#'
#' @return \code{\link{Task}} object.
update = function(name = NULL,
description = NULL,
execution_settings = NULL,
inputs = NULL,
output_location = NULL,
batch = NULL,
batch_input = NULL,
batch_by = NULL,
...) {
checkmate::assert_string(name, null.ok = TRUE)
checkmate::assert_string(description, null.ok = TRUE)
check_execution_settings(execution_settings)
checkmate::assert_list(inputs, null.ok = TRUE)
checkmate::assert_list(output_location, null.ok = TRUE)
checkmate::assert_logical(batch, null.ok = TRUE)
checkmate::assert_string(batch_input, null.ok = TRUE)
checkmate::assert_list(batch_by, null.ok = TRUE)
task_inputs <- list()
task_data <- list()
task_data <- list(
"name" = name,
"description" = description
)
if (!is_missing(batch) && batch) {
if (!is_missing(batch_input) && !is_missing(batch_by)) {
task_data[["batch_input"]] <- batch_input
task_data[["batch_by"]] <- batch_by
} else {
rlang::abort("Batch is set to TRUE, therefore, please set batching criteria (batch_by) and batch inputs.") # nolint
}
}
# nocov start
if (!is_missing(inputs)) {
task_inputs <- self$auth$tasks$private$serialize_inputs(inputs)
task_data[["inputs"]] <- task_inputs
}
if (!is_missing(output_location)) {
task_data[["output_location"]] <- output_location
}
task_data[["execution_settings"]] <- execution_settings
task_data[["batch"]] <- batch
res <- self$auth$api(
path = glue::glue(self$URL[["task"]]),
method = "PATCH",
body = task_data,
...
)
rlang::inform(
glue::glue_col(
"Task {green {self$name}} has been updated."
)
)
self$initialize(
res = res,
href = res$href,
auth = self$auth,
response = attr(res, "response")
)
} # nocov end
),
private = list(
# Map input/output values -----------------------------------------------
#' @importFrom checkmate test_list
map_input_output = function(input) {
return_value <- list()
if (checkmate::test_list(input)) {
if ("class" %in% names(input)) {
if (tolower(input[["class"]]) %in% c("file", "folder")) {
f_data <- map_fields_util(input)
f_data <- append(f_data, input)
if (!is.null(input[["secondaryFiles"]])) {
secondary_files <- list()
for (sf in input[["secondaryFiles"]]) {
sf_data <- map_fields_util(sf)
sf_data <- append(sf_data, sf)
secondary_files <- append(secondary_files, list(sf_data))
}
f_data[["secondary_files"]] <- secondary_files
}
return_value <- asFile(f_data, auth = self$auth)
}
} else {
for (i in seq_len(length(input))) {
elem_name <- names(input[i])
vals <- private$map_input_output(input[[i]])
if (!is.null(elem_name)) {
return_value[[elem_name]] <- vals
} else {
return_value <- c(return_value, list(vals))
}
}
}
} else {
return_value <- input
}
return(return_value)
},
# Map fields -------------------------------------------------------------
map_fields_util = function(input) {
mapped_data <- list(
id = input[["path"]],
type = tolower(input[["class"]])
)
if ("basename" %in% names(input)) {
mapped_data[["name"]] <- input[["basename"]]
}
if ("name" %in% names(input)) {
mapped_data[["name"]] <- input[["name"]]
}
return(mapped_data)
}
)
)
# nocov start
# Helper functions for creating Task objects --------------------------------
asTask <- function(x = NULL, auth = NULL, bulk = FALSE) {
if (bulk) {
x <- x$resource
}
Task$new(
res = x,
href = x$href,
response = attr(x, "response"),
auth = auth
)
}
asTaskList <- function(x, auth, bulk = FALSE) {
obj <- lapply(x$items, asTask, auth = auth, bulk = bulk)
obj
}
# nocov end
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