orderly_bundle_pack: Pack and run orderly "bundles"

In vimc/orderly: Lightweight Reproducible Reporting

Pack and run orderly "bundles"

Description

Pack up and run orderly reports to run elsewhere. By using these functions you can safely copy all requirements of an orderly report into a portable archive and run them on another machine (perhaps a cluster or HPC), then import the completed archive into your orderly tree. There is considerable overhead to using these functions (mostly due to transport costs) so they are intended primarily for very computationally demanding patterns.

Usage

orderly_bundle_pack(
  path,
  name,
  parameters = NULL,
  envir = NULL,
  root = NULL,
  locate = TRUE,
  message = NULL,
  instance = NULL,
  remote = NULL,
  tags = NULL
)

orderly_bundle_run(path, workdir = tempfile(), echo = TRUE, envir = NULL)

orderly_bundle_import(path, root = NULL, locate = TRUE)

orderly_bundle_list(path)

Arguments

path	A path, whose interpretation depends on the function: orderly_bundle_pack: A directory to save bundles to. If it does not exist it will be created for you. orderly_bundle_run: The path to the packed bundle (a zip file created by orderly_bundle_pack) orderly_bundle_import: The path to unpack and import (a zip file created by orderly_bundle_run) orderly_bundle_list: The path to a directory that might contain either incomplete or complete bundles (created by either orderly_bundle_pack or orderly_bundle_run)
name	Name of the report to pack (see orderly_list(). A leading ⁠src/⁠ will be removed if provided, allowing easier use of autocomplete.
parameters	Parameters passed to the report. A named list of parameters declared in the orderly.yml. Each parameter must be a scalar character, numeric, integer or logical.
envir	The parent of the environment that will be used to evaluate the report script; by default a new environment will be made with the global environment as the parent.
root	The path to an orderly root directory, or NULL (the default) to search for one from the current working directory if locate is TRUE.
locate	Logical, indicating if the configuration should be searched for. If TRUE and config is not given, then orderly looks in the working directory and up through its parents until it finds an orderly_config.yml file.
message	An optional character string containing a message explaining why the report was run
instance	Select instance of the source database to be used, where multiple instances are configured. Use a single unnamed character string to indicate an instance to match. If given, then this name must be present in all databases where instances are listed in orderly_config.yml, and will be ignored by all database where instances are not given. See the "orderly" vignette for further information.
remote	Remote to use to resolve dependencies. Use this in order to run a report with the same dependencies as are available on a remote server, particularly when using id = "latest". Note that this is not the same as running orderly_pull_dependencies(), then orderly_run with remote = NULL, as the pull/run approach will use the latest report in your archive but the remote = "remote" approach will use the latest approach in the remote archive (which might be less recent).
tags	Character vector of tags to add to the report. Tags are immutable and cannot be removed once the report is run. Tags added here will be in addition to any tags listed in the ⁠tags:⁠ field in orderly.yml and must be present in orderly_config.yml.
workdir	The path in which to run bundles. If it does not exist it will be created for you. The completed bundle will be saved in this directory as ⁠<id>.zip⁠.
echo	Print the result of running the R code to the console

Value

For orderly_bundle_pack and orderly_bundle_run, a list with elements path (the path to the bundle) and id (its orderly id). For orderly_bundle_list a data.frame with key information about the report in the bundles (id, name, parameters, status, time). The function orderly_bundle_import is called for its side effect only and does not return anything useful.

Examples

path <- orderly::orderly_example("minimal")

# A working directory to export bundles to:
workdir <- tempfile()

# Pack up the "example" report to go:
res <- orderly::orderly_bundle_pack(workdir, "example", root = path)

# The return value is a list with the id and the path to the zip
# file created:
res

# A list of reports bundled in this directory and their status
orderly::orderly_bundle_list(workdir)

# Run the bundle (this would ordinarily be done on another computer)
zip <- orderly::orderly_bundle_run(res$path, workdir)
zip

# The status has now been updated to reflect the status
orderly::orderly_bundle_list(workdir)

# We can import this into the orderly tree
orderly::orderly_bundle_import(zip$path, root = path)

# This has now been included in your orderly archive and the
# workdir can be safely deleted
unlink(workdir, recursive = TRUE)
orderly::orderly_list_archive(path)

vimc/orderly documentation built on July 8, 2023, 2:31 a.m.