Pack and run orderly "bundles"Source:
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.
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)
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_import: The path to unpack and import (a zip file created by
orderly_bundle_list: The path to a directory that might contain either incomplete or complete bundles (created by either
Name of the report to pack (see
orderly_list(). A leading
src/will be removed if provided, allowing easier use of autocomplete.
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.
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.
The path to an orderly root directory, or
NULL(the default) to search for one from the current working directory if
Logical, indicating if the configuration should be searched for. If
configis not given, then orderly looks in the working directory and up through its parents until it finds an
An optional character string containing a message explaining why the report was run
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 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
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).
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
orderly.ymland must be present in
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
Print the result of running the R code to the console
orderly_bundle_run, a list with elements
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.
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) #> [ name ] example #> [ id ] 20221116-140024-ab48e1c3 #> [ start ] 2022-11-16 14:00:24 #> [ data ] source => dat: 20 x 2 #> [ bundle pack ] 20221116-140024-ab48e1c3 # The return value is a list with the id and the path to the zip # file created: res #> $id #>  "20221116-140024-ab48e1c3" #> #> $path #>  "/tmp/Rtmpj7MjPt/file461090b8e8/20221116-140024-ab48e1c3.zip" #> # A list of reports bundled in this directory and their status orderly::orderly_bundle_list(workdir) #> id name parameters status time #> 1 20221116-140024-ab48e1c3 example incomplete 2022-11-16 14:00:24 # Run the bundle (this would ordinarily be done on another computer) zip <- orderly::orderly_bundle_run(res$path, workdir) #> [ start ] 2022-11-16 14:00:24 #> #> > png("mygraph.png") #> #> > par(mar = c(15, 4, 0.5, 0.5)) #> #> > barplot(setNames(dat$number, dat$name), las = 2) #> #> > dev.off() #> agg_png #> 2 #> [ end ] 2022-11-16 14:00:24 #> [ elapsed ] Ran report in 0.01284194 secs #> [ artefact ] mygraph.png: 175369b2bcf4115f343c8ad746c0c072 zip #> $id #>  "20221116-140024-ab48e1c3" #> #> $path #>  "/tmp/Rtmpj7MjPt/file461090b8e8/20221116-140024-ab48e1c3.zip" #> #> $filename #>  "20221116-140024-ab48e1c3.zip" #> # The status has now been updated to reflect the status orderly::orderly_bundle_list(workdir) #> id name parameters status time #> 1 20221116-140024-ab48e1c3 example complete 2022-11-16 14:00:24 # We can import this into the orderly tree orderly::orderly_bundle_import(zip$path, root = path) #> [ import ] example:20221116-140024-ab48e1c3 # 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) #> name id #> 1 example 20221116-140024-ab48e1c3