Nothing
R/class-tasks.R
In sevenbridges2: The 'Seven Bridges Platform' API Client
# nolint start
#' @title R6 Class representing tasks endpoints
#'
#' @description
#' R6 Class representing tasks resource endpoints.
#'
#' @importFrom R6 R6Class
#'
#' @export
Tasks <- R6::R6Class(
"Tasks",
# nolint end
inherit = Resource,
portable = FALSE,
public = list(
#' @field URL List of URL endpoints for this resource.
URL = list(
"query" = "tasks/",
"get" = "tasks/{id}",
"delete" = "tasks",
"bulk_get" = "bulk/tasks/get"
),
#' @description Create new Tasks resource object.
#'
#' @param ... Other response arguments.
initialize = function(...) {
# Initialize Resource class
super$initialize(...)
},
# List tasks you can access ------------------------------------------
#' @description This call lists all tasks you can access. \cr \cr
#' Read more about how to use query parameters properly
# nolint start
#' [here](https://docs.sevenbridges.com/reference/list-tasks-you-can-access).
# nolint end
#'
#' @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 parent Provide task ID or Task object of the parent task to return
#' all child tasks from that parent. A parent task is a task that specifies
#' criteria by which to batch its inputs into a series of further
#' sub-tasks, called child tasks. See the documentation on
# nolint start
#' [batching tasks](https://docs.sevenbridges.com/docs/about-batch-analyses)
# nolint end
#' for more details on how to run tasks in batches.
#' @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 checkmate assert_string
#'
#' @return \code{\link{Collection}} of \code{\link{Task}} objects.
query = function(status = NULL,
parent = NULL,
project = NULL,
created_from = NULL,
created_to = NULL,
started_from = NULL,
started_to = NULL,
ended_from = NULL,
ended_to = NULL,
order_by = c(
"created_time", "start_time", "name",
"end_time", "created_by"
),
order = c("asc", "desc"),
origin_id = NULL,
limit = getOption("sevenbridges2")$limit,
offset = getOption("sevenbridges2")$offset,
...) {
if (!is_missing(status)) {
if (!(status %in% c(
"QUEUED",
"DRAFT",
"RUNNING",
"COMPLETED",
"ABORTED",
"FAILED"
))) {
rlang::abort(
"Status must be one of the following: QUEUED, DRAFT, RUNNING, COMPLETED, ABORTED, FAILED" # nolint
)
}
}
if (!is_missing(parent)) {
parent <-
check_and_transform_id(parent, class_name = "Task")
}
if (!is_missing(project)) {
project <-
check_and_transform_id(project, class_name = "Project")
}
if (!is_missing(created_from)) {
created_from <- check_and_transform_datetime(created_from)
}
if (!is_missing(created_to)) {
created_to <- check_and_transform_datetime(created_to)
}
if (!is_missing(started_from)) {
started_from <- check_and_transform_datetime(started_from)
}
if (!is_missing(started_to)) {
started_to <- check_and_transform_datetime(started_to)
}
if (!is_missing(ended_from)) {
ended_from <- check_and_transform_datetime(ended_from)
}
if (!is_missing(ended_to)) {
ended_to <- check_and_transform_datetime(ended_to)
}
order_by <- match.arg(order_by)
order <- match.arg(order)
checkmate::assert_string(origin_id, null.ok = TRUE)
# nocov start
res <- super$query(
path = self$URL[["query"]],
status = status,
parent = parent,
project = project,
created_from = created_from,
created_to = created_to,
started_from = started_from,
started_to = started_to,
ended_from = ended_from,
ended_to = ended_to,
order_by = order_by,
order = order,
origin_id = origin_id,
offset = offset,
limit = limit,
...
)
res$items <- asTaskList(res, auth = self$auth)
return(asCollection(res, auth = self$auth))
# nocov end
},
# Get single task -------------------------------------------------------
#' @description This call returns 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 task details include its creator, its
#' start and end time, the number of jobs completed in it, and its input
#' and output files. You can also see the status of the task.
#'
#' @param id The ID of the task you are querying.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_string
#' @importFrom rlang abort
#'
#' @return \code{\link{Task}} object.
get = function(id, ...) {
if (is_missing(id)) {
rlang::abort("Task ID must be provided!")
}
checkmate::assert_string(id)
# nocov start
res <- super$get(
cls = self,
id = id,
...
)
return(asTask(res, auth = self$auth))
}, # nocov end
# Delete task ----------------------------------------------------------
#' @description This call deletes a task from the Seven Bridges Platform.
#' Tasks are specified by their IDs, which you can obtain by using
#' \code{Tasks$query()} to list tasks or by getting a single task
#' using \code{Tasks$get()}.
#'
#' @param task \code{\link{Task}} object or task ID.
#' @param ... Other arguments that can be passed to core `api()` function
#' as 'fields', etc.
#'
#' @importFrom glue glue
delete = function(task, ...) {
id <- check_and_transform_id(task, "Task")
# nocov start
res <- super$delete(
id = id,
...
)
rlang::inform(
message = glue::glue("Task {id} has been deleted.")
)
},
# nocov end
# Create a new draft task --------------------------------------------------
#' @description This call creates a new task. You can create either a single
#' task or a batch task by using the app's default batching, override
#' batching, or disable batching completely. A parent task is a task that
#' specifies criteria by which to batch its inputs into a series of further
#' sub-tasks, called child tasks. the documentation on
# nolint start
#' [batching tasks](https://docs.sevenbridges.com/docs/about-batch-analyses)
# nolint end
#' for more details on batching criteria.
#'
#' @param project The ID of a project or a Project object where you
#' want to create the task in.
#' @param app The ID of an app or an App object you want to run.
#' Recall that apps are specified by their projects, in the form
#' `<project_id>/<app_name>`.
#' @param revision The app
#' [revision (version)](https://docs.sevenbridges.com/docs/app-versions)
#' number.
#' @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>/` \cr
#' or a path on an attached volume, such as \cr
#' `volumes://volume_name/<project_id>/html`. \cr
#' 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 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 action If set to `run`, the task will be run immediately upon
#' creation.
#' @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
#'
#' @return \code{\link{Task}} object.
create = function(project,
app,
revision = NULL,
name = NULL,
description = NULL,
execution_settings = NULL,
inputs = NULL,
output_location = NULL,
batch = NULL,
batch_input = NULL,
batch_by = NULL,
use_interruptible_instances = NULL,
action = NULL,
...) {
if (is_missing(project)) {
rlang::abort("Project parameter must be provided!")
}
if (is_missing(app)) {
rlang::abort("App parameter must be provided!")
}
project_id <-
check_and_transform_id(project, class_name = "Project")
app_id <- check_and_transform_id(app, class_name = "App")
if (!is_missing(revision)) {
checkmate::check_int(revision, null.ok = TRUE)
app_id <- glue::glue("{app_id}/{revision}")
} else if (checkmate::test_r6(app)) {
app_id <- glue::glue("{app_id}/{app$revision}")
}
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)
checkmate::assert_logical(use_interruptible_instances, null.ok = TRUE)
checkmate::assert_string(action, null.ok = TRUE)
task_inputs <- list()
task_data <- list()
params <- list()
task_meta <- list(
"name" = name,
"project" = project_id,
"app" = app_id,
"description" = description
)
task_data <- c(task_data, task_meta)
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 <- private$serialize_inputs(inputs)
task_data[["inputs"]] <- task_inputs
}
if (!is_missing(output_location)) {
task_data[["output_location"]] <- output_location
}
task_data[["use_interruptible_instances"]] <-
use_interruptible_instances
task_data[["execution_settings"]] <- execution_settings
params[["action"]] <- action
params[["batch"]] <- batch
res <- self$auth$api(
path = self$URL[["query"]],
method = "POST",
query = params,
body = task_data
)
return(asTask(res, auth = self$auth))
}, # nocov end
# Get details of multiple tasks
#'
#' @description This call returns statistics for all specified tasks.
#'
#' @param tasks A list of \code{\link{Task}} objects or list of strings
#' (IDs) of the tasks you are requesting the statistics for.
#'
#' @importFrom rlang abort
#' @importFrom checkmate assert_list
#' @importFrom glue glue
#'
#' @return \code{\link{Collection}} (list of \code{\link{Task}} objects).
#'
#' @examples
#' \dontrun{
#' # Get details of multiple tasks
#' a$tasks$bulk_get(
#' tasks = list("task_1_ID", "task_2_ID")
#' )
#' }
#'
bulk_get = function(tasks) {
if (is_missing(tasks)) {
rlang::abort(
"Please provide the 'tasks' parameter as a list of task IDs or Task objects." # nolint
)
}
checkmate::assert_list(tasks)
# nocov start
tasks <- lapply(tasks, check_and_transform_id, "Task")
body <- list(
"task_ids" = tasks
)
path <- glue::glue(self$URL[["bulk_get"]])
res <- self$auth$api(
path = path,
method = "POST",
body = body
)
res$items <- asTaskList(res, auth = self$auth, bulk = TRUE)
return(asCollection(res, auth = self$auth))
# nocov end
}
),
private = list(
# Serialize input values --------------------------------------------------
#' @importFrom checkmate test_r6
serialize_inputs = function(input_value) { # nocov start
if (is.list(input_value)) {
return_value <- list()
if (is.null(names(input_value))) {
for (x in input_value) {
elem <- private$serialize_inputs(x)
return_value <- c(return_value, list(elem))
}
} else {
for (name in names(input_value)) {
elem <- private$serialize_inputs(input_value[[name]])
return_value[[name]] <- elem
}
}
} else if (checkmate::test_r6(input_value, classes = "File")) {
return_value <- private$to_api_file_format(input_value)
} else {
return_value <- input_value
}
return(return_value)
},
# Convert input value to File format --------------------------------------
#' @importFrom stringr str_to_title
to_api_file_format = function(file) {
return(list(
"class" = stringr::str_to_title(file[["type"]]),
"path" = file[["id"]]
))
} # nocov end
)
)
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# nolint start
#' @title R6 Class representing tasks endpoints
#'
#' @description
#' R6 Class representing tasks resource endpoints.
#'
#' @importFrom R6 R6Class
#'
#' @export
Tasks <- R6::R6Class(
"Tasks",
# nolint end
inherit = Resource,
portable = FALSE,
public = list(
#' @field URL List of URL endpoints for this resource.
URL = list(
"query" = "tasks/",
"get" = "tasks/{id}",
"delete" = "tasks",
"bulk_get" = "bulk/tasks/get"
),
#' @description Create new Tasks resource object.
#'
#' @param ... Other response arguments.
initialize = function(...) {
# Initialize Resource class
super$initialize(...)
},
# List tasks you can access ------------------------------------------
#' @description This call lists all tasks you can access. \cr \cr
#' Read more about how to use query parameters properly
# nolint start
#' [here](https://docs.sevenbridges.com/reference/list-tasks-you-can-access).
# nolint end
#'
#' @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 parent Provide task ID or Task object of the parent task to return
#' all child tasks from that parent. A parent task is a task that specifies
#' criteria by which to batch its inputs into a series of further
#' sub-tasks, called child tasks. See the documentation on
# nolint start
#' [batching tasks](https://docs.sevenbridges.com/docs/about-batch-analyses)
# nolint end
#' for more details on how to run tasks in batches.
#' @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 checkmate assert_string
#'
#' @return \code{\link{Collection}} of \code{\link{Task}} objects.
query = function(status = NULL,
parent = NULL,
project = NULL,
created_from = NULL,
created_to = NULL,
started_from = NULL,
started_to = NULL,
ended_from = NULL,
ended_to = NULL,
order_by = c(
"created_time", "start_time", "name",
"end_time", "created_by"
),
order = c("asc", "desc"),
origin_id = NULL,
limit = getOption("sevenbridges2")$limit,
offset = getOption("sevenbridges2")$offset,
...) {
if (!is_missing(status)) {
if (!(status %in% c(
"QUEUED",
"DRAFT",
"RUNNING",
"COMPLETED",
"ABORTED",
"FAILED"
))) {
rlang::abort(
"Status must be one of the following: QUEUED, DRAFT, RUNNING, COMPLETED, ABORTED, FAILED" # nolint
)
}
}
if (!is_missing(parent)) {
parent <-
check_and_transform_id(parent, class_name = "Task")
}
if (!is_missing(project)) {
project <-
check_and_transform_id(project, class_name = "Project")
}
if (!is_missing(created_from)) {
created_from <- check_and_transform_datetime(created_from)
}
if (!is_missing(created_to)) {
created_to <- check_and_transform_datetime(created_to)
}
if (!is_missing(started_from)) {
started_from <- check_and_transform_datetime(started_from)
}
if (!is_missing(started_to)) {
started_to <- check_and_transform_datetime(started_to)
}
if (!is_missing(ended_from)) {
ended_from <- check_and_transform_datetime(ended_from)
}
if (!is_missing(ended_to)) {
ended_to <- check_and_transform_datetime(ended_to)
}
order_by <- match.arg(order_by)
order <- match.arg(order)
checkmate::assert_string(origin_id, null.ok = TRUE)
# nocov start
res <- super$query(
path = self$URL[["query"]],
status = status,
parent = parent,
project = project,
created_from = created_from,
created_to = created_to,
started_from = started_from,
started_to = started_to,
ended_from = ended_from,
ended_to = ended_to,
order_by = order_by,
order = order,
origin_id = origin_id,
offset = offset,
limit = limit,
...
)
res$items <- asTaskList(res, auth = self$auth)
return(asCollection(res, auth = self$auth))
# nocov end
},
# Get single task -------------------------------------------------------
#' @description This call returns 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 task details include its creator, its
#' start and end time, the number of jobs completed in it, and its input
#' and output files. You can also see the status of the task.
#'
#' @param id The ID of the task you are querying.
#' @param ... Other arguments that can be passed to core `api()` function
#' like 'fields', etc.
#'
#' @importFrom checkmate assert_string
#' @importFrom rlang abort
#'
#' @return \code{\link{Task}} object.
get = function(id, ...) {
if (is_missing(id)) {
rlang::abort("Task ID must be provided!")
}
checkmate::assert_string(id)
# nocov start
res <- super$get(
cls = self,
id = id,
...
)
return(asTask(res, auth = self$auth))
}, # nocov end
# Delete task ----------------------------------------------------------
#' @description This call deletes a task from the Seven Bridges Platform.
#' Tasks are specified by their IDs, which you can obtain by using
#' \code{Tasks$query()} to list tasks or by getting a single task
#' using \code{Tasks$get()}.
#'
#' @param task \code{\link{Task}} object or task ID.
#' @param ... Other arguments that can be passed to core `api()` function
#' as 'fields', etc.
#'
#' @importFrom glue glue
delete = function(task, ...) {
id <- check_and_transform_id(task, "Task")
# nocov start
res <- super$delete(
id = id,
...
)
rlang::inform(
message = glue::glue("Task {id} has been deleted.")
)
},
# nocov end
# Create a new draft task --------------------------------------------------
#' @description This call creates a new task. You can create either a single
#' task or a batch task by using the app's default batching, override
#' batching, or disable batching completely. A parent task is a task that
#' specifies criteria by which to batch its inputs into a series of further
#' sub-tasks, called child tasks. the documentation on
# nolint start
#' [batching tasks](https://docs.sevenbridges.com/docs/about-batch-analyses)
# nolint end
#' for more details on batching criteria.
#'
#' @param project The ID of a project or a Project object where you
#' want to create the task in.
#' @param app The ID of an app or an App object you want to run.
#' Recall that apps are specified by their projects, in the form
#' `<project_id>/<app_name>`.
#' @param revision The app
#' [revision (version)](https://docs.sevenbridges.com/docs/app-versions)
#' number.
#' @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>/` \cr
#' or a path on an attached volume, such as \cr
#' `volumes://volume_name/<project_id>/html`. \cr
#' 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 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 action If set to `run`, the task will be run immediately upon
#' creation.
#' @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
#'
#' @return \code{\link{Task}} object.
create = function(project,
app,
revision = NULL,
name = NULL,
description = NULL,
execution_settings = NULL,
inputs = NULL,
output_location = NULL,
batch = NULL,
batch_input = NULL,
batch_by = NULL,
use_interruptible_instances = NULL,
action = NULL,
...) {
if (is_missing(project)) {
rlang::abort("Project parameter must be provided!")
}
if (is_missing(app)) {
rlang::abort("App parameter must be provided!")
}
project_id <-
check_and_transform_id(project, class_name = "Project")
app_id <- check_and_transform_id(app, class_name = "App")
if (!is_missing(revision)) {
checkmate::check_int(revision, null.ok = TRUE)
app_id <- glue::glue("{app_id}/{revision}")
} else if (checkmate::test_r6(app)) {
app_id <- glue::glue("{app_id}/{app$revision}")
}
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)
checkmate::assert_logical(use_interruptible_instances, null.ok = TRUE)
checkmate::assert_string(action, null.ok = TRUE)
task_inputs <- list()
task_data <- list()
params <- list()
task_meta <- list(
"name" = name,
"project" = project_id,
"app" = app_id,
"description" = description
)
task_data <- c(task_data, task_meta)
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 <- private$serialize_inputs(inputs)
task_data[["inputs"]] <- task_inputs
}
if (!is_missing(output_location)) {
task_data[["output_location"]] <- output_location
}
task_data[["use_interruptible_instances"]] <-
use_interruptible_instances
task_data[["execution_settings"]] <- execution_settings
params[["action"]] <- action
params[["batch"]] <- batch
res <- self$auth$api(
path = self$URL[["query"]],
method = "POST",
query = params,
body = task_data
)
return(asTask(res, auth = self$auth))
}, # nocov end
# Get details of multiple tasks
#'
#' @description This call returns statistics for all specified tasks.
#'
#' @param tasks A list of \code{\link{Task}} objects or list of strings
#' (IDs) of the tasks you are requesting the statistics for.
#'
#' @importFrom rlang abort
#' @importFrom checkmate assert_list
#' @importFrom glue glue
#'
#' @return \code{\link{Collection}} (list of \code{\link{Task}} objects).
#'
#' @examples
#' \dontrun{
#' # Get details of multiple tasks
#' a$tasks$bulk_get(
#' tasks = list("task_1_ID", "task_2_ID")
#' )
#' }
#'
bulk_get = function(tasks) {
if (is_missing(tasks)) {
rlang::abort(
"Please provide the 'tasks' parameter as a list of task IDs or Task objects." # nolint
)
}
checkmate::assert_list(tasks)
# nocov start
tasks <- lapply(tasks, check_and_transform_id, "Task")
body <- list(
"task_ids" = tasks
)
path <- glue::glue(self$URL[["bulk_get"]])
res <- self$auth$api(
path = path,
method = "POST",
body = body
)
res$items <- asTaskList(res, auth = self$auth, bulk = TRUE)
return(asCollection(res, auth = self$auth))
# nocov end
}
),
private = list(
# Serialize input values --------------------------------------------------
#' @importFrom checkmate test_r6
serialize_inputs = function(input_value) { # nocov start
if (is.list(input_value)) {
return_value <- list()
if (is.null(names(input_value))) {
for (x in input_value) {
elem <- private$serialize_inputs(x)
return_value <- c(return_value, list(elem))
}
} else {
for (name in names(input_value)) {
elem <- private$serialize_inputs(input_value[[name]])
return_value[[name]] <- elem
}
}
} else if (checkmate::test_r6(input_value, classes = "File")) {
return_value <- private$to_api_file_format(input_value)
} else {
return_value <- input_value
}
return(return_value)
},
# Convert input value to File format --------------------------------------
#' @importFrom stringr str_to_title
to_api_file_format = function(file) {
return(list(
"class" = stringr::str_to_title(file[["type"]]),
"path" = file[["id"]]
))
} # nocov end
)
)
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