Unarchive a list of compressed tsv files into a database

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,
  ...
)

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.

Value

the database connection (invisibly)

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)
#> Warning: overwriting airlines.tsv.bz2
#> Exporting airlines in 50000 line chunks:
#> 	...Done! (in 0.001766443 secs)
#> Warning: overwriting airports.tsv.bz2
#> Exporting airports in 50000 line chunks:
#> 	...Done! (in 0.01085544 secs)
#> Warning: overwriting flights.tsv.bz2
#> Exporting flights in 50000 line chunks:
#> 	...Done! (in 5.796999 secs)
#> Warning: overwriting planes.tsv.bz2
#> Exporting planes in 50000 line chunks:
#> 	...Done! (in 0.01606011 secs)
#> Warning: overwriting weather.tsv.bz2
#> Exporting weather in 50000 line chunks:
#> 	...Done! (in 0.4103391 secs)

## 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)
#> Importing /tmp/RtmpkL3rOO/airlines.tsv.bz2 in 50000 line chunks:
#> 	...Done! (in 0.00699544 secs)
#> Importing /tmp/RtmpkL3rOO/airports.tsv.bz2 in 50000 line chunks:
#> 	...Done! (in 0.01344156 secs)
#> Importing /tmp/RtmpkL3rOO/flights.tsv.bz2 in 50000 line chunks:
#> 	...Done! (in 3.539262 secs)
#> Importing /tmp/RtmpkL3rOO/planes.tsv.bz2 in 50000 line chunks:
#> 	...Done! (in 0.01919818 secs)
#> Importing /tmp/RtmpkL3rOO/weather.tsv.bz2 in 50000 line chunks:
#> 	...Done! (in 0.1175041 secs)

## Prove table is returned successfully.
tbl(new_db, "flights")
#> # Source:   table<flights> [?? x 19]
#> # Database: sqlite 3.45.0 []
#>     year month   day dep_time sched_dep_time dep_delay arr_time sched_arr_time
#>    <int> <int> <int>    <int>          <int>     <int>    <int>          <int>
#>  1  2013     1     1      517            515         2      830            819
#>  2  2013     1     1      533            529         4      850            830
#>  3  2013     1     1      542            540         2      923            850
#>  4  2013     1     1      544            545        -1     1004           1022
#>  5  2013     1     1      554            600        -6      812            837
#>  6  2013     1     1      554            558        -4      740            728
#>  7  2013     1     1      555            600        -5      913            854
#>  8  2013     1     1      557            600        -3      709            723
#>  9  2013     1     1      557            600        -3      838            846
#> 10  2013     1     1      558            600        -2      753            745
#> # ℹ more rows
#> # ℹ 11 more variables: arr_delay <int>, carrier <chr>, flight <int>,
#> #   tailnum <chr>, origin <chr>, dest <chr>, air_time <int>, distance <int>,
#> #   hour <int>, minute <int>, time_hour <dbl>
# }