arkdb (version 0.0.19)

unark: Unarchive a list of compressed tsv files into a database

Description

Unarchive a list of compressed tsv files into a database

Usage

unark(
  files,
  db_con,
  streamable_table = NULL,
  lines = 50000L,
  overwrite = "ask",
  encoding = Sys.getenv("encoding", "UTF-8"),
  tablenames = NULL,
  try_native = TRUE,
  ...
)

Value

the database connection (invisibly)

Arguments

files

vector of filenames to be read in. Must be tsv format, optionally compressed using bzip2, gzip, zip, or xz format at present.

db_con

a database src (src_dbi object from dplyr)

streamable_table

interface for serializing/deserializing in chunks

lines

number of lines to read in a chunk.

overwrite

should any existing text files of the same name be overwritten? default is "ask", which will ask for confirmation in an interactive session, and overwrite in a non-interactive script. TRUE will always overwrite, FALSE will always skip such tables.

encoding

encoding to be assumed for input files.

tablenames

vector of tablenames to be used for corresponding files. By default, tables will be named using lowercase names from file basename with special characters replaced with underscores (for SQL compatibility).

try_native

logical, default TRUE. Should we try to use a native bulk import method for the database connection? This can substantially speed up read times and will fall back on the DBI method for any table that fails to import. Currently only MonetDBLite connections support this.

...

additional arguments to streamable_table$read method.

Details

unark will read in a files in chunks and write them into a database. This is essential for processing large compressed tables which may be too large to read into memory before writing into a database. In general, increasing the lines parameter will result in a faster total transfer but require more free memory for working with these larger chunks.

If using readr-based streamable-table, you can suppress the progress bar by using options(readr.show_progress = FALSE) when reading in large files.

Examples

# \donttest{
## Setup: create an archive.
library(dplyr)
dir <- tempdir()
db <- dbplyr::nycflights13_sqlite(tempdir())

## database -> .tsv.bz2
ark(db, dir)

## list all files in archive (full paths)
files <- list.files(dir, "bz2$", full.names = TRUE)

## Read archived files into a new database (another sqlite in this case)
new_db <- DBI::dbConnect(RSQLite::SQLite())
unark(files, new_db)

## Prove table is returned successfully.
tbl(new_db, "flights")
# }