orderly_run: Run a report
In vimc/orderly: Lightweight Reproducible Reporting

orderly_run

R Documentation

Run a report

Description

Run a report. This will create a new directory in ⁠drafts/<reportname>⁠, copy your declared resources there, extract data from databases (if you are using them), run your script and check that all expected artefacts were created. Once successfully run you can use orderly_commit() to move it to the archive directory.

Usage

orderly_run(
  name = NULL,
  parameters = NULL,
  envir = NULL,
  root = NULL,
  locate = TRUE,
  echo = TRUE,
  message = NULL,
  instance = NULL,
  use_draft = FALSE,
  remote = NULL,
  tags = NULL
)

Arguments

`name`	Name of the report to run (see `orderly_list()`). A leading `⁠src/⁠` will be removed if provided, allowing easier use of autocomplete. Alternatively, the default of `NULL` is useful if you have already set the working directory to be the source directory.
`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.
`echo`	Print the result of running the R code to the console
`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.
`use_draft`	Should draft reports be used for dependencies? This should be used only in development. Valid values are logical (`TRUE`, `FALSE`) or use the string `newer` to use draft reports where they are newer than archive reports. For consistency, `always` and `never` are equivalent to `TRUE` and `FALSE`, respectively.
`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`.

Details

Parameters are passed to the report as a named list, for example

id <- orderly::orderly_run("other", list(nmin = 0.2), root = path)

(see the examples). The names of the parameters (here, nmin) must correspond to declared parameters in the orderly.yml. It is an error if parameters without a default are omitted, and it is an error if unknown parameters are provided.

Environment variables that are created in orderly_envir.yml will be available while the report runs. Those that begin with ORDERLY_ will be saved into the orderly_run.rds within the ⁠$env⁠ section (except for any that match the patterns "TOKEN", "PAT" or "PASS").

Value

The id of the newly created report

Examples

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

# To run most reports, provide the report name (and the path if
# not running in the working directory, as is the case here):
id <- orderly::orderly_run("minimal", root = path)

# Every report gets a unique identifier, based on the time (it is
# ISO 8601 time with random hex appended to end)
id

# After being run, a report is a "draft" and will exist in the
# drafts directory:
orderly::orderly_list_drafts(root = path)

# Draft reports are always stored in the path
# <root>/draft/<name>/<id>, so we have
dir(file.path(path, "draft", "minimal", id))

# which contains the files when the report was run.

# If a report has parameters, then these must be passed in as a
# named list.
id <- orderly::orderly_run("other", list(nmin = 0.2), root = path)

# These parameters can be used in SQL queries or in the report
# code.

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