Dynamic branching over input files or URLs
Source:R/tar_files_input.R
, R/tar_files_input_raw.R
tar_files_input.Rd
Dynamic branching over input files or URLs.
tar_files_input()
expects a unevaluated symbol for the name
argument,
whereas
tar_files_input_raw()
expects a character string for name
.
See the examples
for a demo.
Usage
tar_files_input(
name,
files,
batches = length(files),
format = c("file", "file_fast", "url", "aws_file"),
repository = targets::tar_option_get("repository"),
iteration = targets::tar_option_get("iteration"),
error = targets::tar_option_get("error"),
memory = targets::tar_option_get("memory"),
garbage_collection = targets::tar_option_get("garbage_collection"),
priority = targets::tar_option_get("priority"),
resources = targets::tar_option_get("resources"),
cue = targets::tar_option_get("cue"),
description = targets::tar_option_get("description")
)
tar_files_input_raw(
name,
files,
batches = length(files),
format = c("file", "file_fast", "url", "aws_file"),
repository = targets::tar_option_get("repository"),
iteration = targets::tar_option_get("iteration"),
error = targets::tar_option_get("error"),
memory = targets::tar_option_get("memory"),
garbage_collection = targets::tar_option_get("garbage_collection"),
priority = targets::tar_option_get("priority"),
resources = targets::tar_option_get("resources"),
cue = targets::tar_option_get("cue"),
description = targets::tar_option_get("description")
)
Arguments
- name
Name of the target.
tar_files_input()
expects a unevaluated symbol for thename
argument, whereastar_files_input_raw()
expects a character string forname
. See the examples for a demo.- files
Nonempty character vector of known existing input files to track for changes.
- batches
Positive integer of length 1, number of batches to partition the files. The default is one file per batch (maximum number of batches) which is simplest to handle but could cause a lot of overhead and consume a lot of computing resources. Consider reducing the number of batches below the number of files for heavy workloads.
- format
Character, either
"file"
,"file_fast"
, or"url"
. See theformat
argument oftargets::tar_target()
for details.- repository
Character of length 1, remote repository for target storage. Choices:
"local"
: file system of the local machine."aws"
: Amazon Web Services (AWS) S3 bucket. Can be configured with a non-AWS S3 bucket using theendpoint
argument oftar_resources_aws()
, but versioning capabilities may be lost in doing so. See the cloud storage section of https://books.ropensci.org/targets/data.html for details for instructions."gcp"
: Google Cloud Platform storage bucket. See the cloud storage section of https://books.ropensci.org/targets/data.html for details for instructions.A character string from
tar_repository_cas()
for content-addressable storage.
Note: if
repository
is not"local"
andformat
is"file"
then the target should create a single output file. That output file is uploaded to the cloud and tracked for changes where it exists in the cloud. The local file is deleted after the target runs.- iteration
Character, iteration method. Must be a method supported by the
iteration
argument oftargets::tar_target()
. The iteration method for the upstream target is always"list"
in order to support batching.- error
Character of length 1, what to do if the target stops and throws an error. Options:
"stop"
: the whole pipeline stops and throws an error."continue"
: the whole pipeline keeps going."null"
: The errored target continues and returnsNULL
. The data hash is deliberately wrong so the target is not up to date for the next run of the pipeline."abridge"
: any currently running targets keep running, but no new targets launch after that."trim"
: all currently running targets stay running. A queued target is allowed to start if:It is not downstream of the error, and
It is not a sibling branch from the same
tar_target()
call (if the error happened in a dynamic branch).
The idea is to avoid starting any new work that the immediate error impacts.
error = "trim"
is just likeerror = "abridge"
, but it allows potentially healthy regions of the dependency graph to begin running. (Visit https://books.ropensci.org/targets/debugging.html to learn how to debug targets using saved workspaces.)
- memory
Character of length 1, memory strategy. If
"persistent"
, the target stays in memory until the end of the pipeline (unlessstorage
is"worker"
, in which casetargets
unloads the value from memory right after storing it in order to avoid sending copious data over a network). If"transient"
, the target gets unloaded after every new target completes. Either way, the target gets automatically loaded into memory whenever another target needs the value. For cloud-based dynamic files (e.g.format = "file"
withrepository = "aws"
), this memory strategy applies to the temporary local copy of the file:"persistent"
means it remains until the end of the pipeline and is then deleted, and"transient"
means it gets deleted as soon as possible. The former conserves bandwidth, and the latter conserves local storage.- garbage_collection
Logical, whether to run
base::gc()
just before the target runs.- priority
Numeric of length 1 between 0 and 1. Controls which targets get deployed first when multiple competing targets are ready simultaneously. Targets with priorities closer to 1 get dispatched earlier (and polled earlier in
tar_make_future()
).- resources
Object returned by
tar_resources()
with optional settings for high-performance computing functionality, alternative data storage formats, and other optional capabilities oftargets
. Seetar_resources()
for details.- cue
An optional object from
tar_cue()
to customize the rules that decide whether the target is up to date. Only applies to the downstream target. The upstream target always runs.- description
Character of length 1, a custom free-form human-readable text description of the target. Descriptions appear as target labels in functions like
tar_manifest()
andtar_visnetwork()
, and they let you select subsets of targets for thenames
argument of functions liketar_make()
. For example,tar_manifest(names = tar_described_as(starts_with("survival model")))
lists all the targets whose descriptions start with the character string"survival model"
.
Value
A list of two targets, one upstream and one downstream.
The upstream one does some work and returns some file paths,
and the downstream target is a pattern that applies format = "file"
or format = "url"
.
See the "Target objects" section for background.
Details
tar_files_input()
is like tar_files()
but more convenient when the files in question already
exist and are known in advance. Whereas tar_files()
always appears outdated (e.g. with tar_outdated()
)
because it always needs to check which files it needs to
branch over, tar_files_input()
will appear up to date
if the files have not changed since last tar_make()
.
In addition, tar_files_input()
automatically groups
input files into batches to reduce overhead and
increase the efficiency of parallel processing.
tar_files_input()
creates a pair of targets, one upstream
and one downstream. The upstream target does some work
and returns some file paths, and the downstream
target is a pattern that applies format = "file"
,
format = "file_fast"
, or format = "url"
.
This is the correct way to dynamically
iterate over file/url targets. It makes sure any downstream patterns
only rerun some of their branches if the files/urls change.
For more information, visit
https://github.com/ropensci/targets/issues/136 and
https://github.com/ropensci/drake/issues/1302.
Target objects
Most tarchetypes
functions are target factories,
which means they return target objects
or lists of target objects.
Target objects represent skippable steps of the analysis pipeline
as described at https://books.ropensci.org/targets/.
Please read the walkthrough at
https://books.ropensci.org/targets/walkthrough.html
to understand the role of target objects in analysis pipelines.
For developers, https://wlandau.github.io/targetopia/contributing.html#target-factories explains target factories (functions like this one which generate targets) and the design specification at https://books.ropensci.org/targets-design/ details the structure and composition of target objects.
See also
Other Dynamic branching over files:
tar_files()
Examples
if (identical(Sys.getenv("TAR_LONG_EXAMPLES"), "true")) {
targets::tar_dir({ # tar_dir() runs code from a temporary directory.
targets::tar_script({
library(tarchetypes)
# Do not use temp files in real projects
# or else your targets will always rerun.
paths <- unlist(replicate(4, tempfile()))
file.create(paths)
list(
tar_files_input(
name = x,
files = paths,
batches = 2
),
tar_files_input_raw(
name = "y",
files = paths,
batches = 2
)
)
})
targets::tar_make()
targets::tar_read(x)
targets::tar_read(x, branches = 1)
})
}