orderly_db: Connect to orderly databases

In orderly: Lightweight Reproducible Reporting

Description

Connect to the orderly databases. These should be treated as as read-only.

Usage

orderly_db(type, root = NULL, locate = TRUE, validate = TRUE, instance = NULL)

Arguments

type	The type of connection to make (source, destination, csv or rds).
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.
validate	Logical, indicating if the database schema should be validated on open (currently only applicable with type = "destination"). This is primarily intended for internal use.
instance	Used only by type = "source", and used to select the instance, 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.

Details

Orderly has several databases:

• source: All of the databases named in the database section of the orderly_config.yml

• destination: The orderly index database (typically a SQLite database stored at the orderly root)

• csv: The cache of database query results, in csv format

• rds: The cache of database query results, in rds format

Value

A database connection, or list of connections in the case of source.

Examples

# Create an orderly that has a single commited report:
path <- orderly::orderly_example("minimal")
id <- orderly::orderly_run("example", root = path)
orderly::orderly_commit(id, root = path)

# The source database holds the data that might be accessible via
# the 'data' entry in orderly.yml:
db <- orderly::orderly_db("source", root = path)
# This is a list, with one connection per database listed in the
# orderly_config.yml (an empty list if none are specified):
db
DBI::dbListTables(db$source)
head(DBI::dbReadTable(db$source, "data"))
DBI::dbDisconnect(db$source)

# The destination database holds information about the archived
# reports:
db <- orderly::orderly_db("destination", root = path)
DBI::dbListTables(db)

# These tables are documented online:
# https://vimc.github.io/orderly/schema
DBI::dbReadTable(db, "report_version")

orderly documentation built on Sept. 22, 2021, 5:09 p.m.