arkdb

The goal of arkdb is to provide a convienent way to move data from large compressed text files (tsv, csv, etc) into any DBI-compliant database connection (e.g. MYSQL, Postgres, SQLite; see DBI), and move tables out of such databases into text files. The key feature of arkdb is that files are moved between databases and text files in chunks of a fixed size, allowing the package functions to work with tables that would be much to large to read into memory all at once.

Links

• A more detailed introduction to package design and use can be found in the package Vignette
• Online versions of package documentation

Installation

You can install arkdb from GitHub with:

# install.packages("devtools")
devtools::install_github("cboettig/arkdb")

Basic use

library(arkdb)

# additional libraries just for this demo
library(dbplyr)
library(dplyr)
library(fs)

Creating an archive of a database

Consider the nycflights database in SQLite:

tmp <- tempdir() # Or can be your working directory, "."
db <- dbplyr::nycflights13_sqlite(tmp)
#> Caching nycflights db at /var/folders/y8/0wn724zs10jd79_srhxvy49r0000gn/T//Rtmp3oFbR8/nycflights13.sqlite
#> Creating table: airlines
#> Creating table: airports
#> Creating table: flights
#> Creating table: planes
#> Creating table: weather

Create an archive of the database:

dir <- fs::dir_create(fs::path(tmp, "nycflights"))
ark(db, dir, lines = 50000)
#> Exporting airlines in 50000 line chunks:
#>  ...Done! (in 0.00859499 secs)
#> Exporting airports in 50000 line chunks:
#>  ...Done! (in 0.03927302 secs)
#> Exporting flights in 50000 line chunks:
#>  ...Done! (in 27.67571 secs)
#> Exporting planes in 50000 line chunks:
#>  ...Done! (in 0.2452919 secs)
#> Exporting weather in 50000 line chunks:
#>  ...Done! (in 2.398423 secs)

Unarchive

Import a list of compressed tabular files (i.e. *.csv.bz2) into a local SQLite database:

files <- fs::dir_ls(dir)
new_db <- src_sqlite(fs::path(tmp, "local.sqlite"), create=TRUE)

unark(files, new_db, lines = 50000)
#> Importing airlines.tsv.bz2 in 50000 line chunks:
#>  ...Done! (in 0.04621601 secs)
#> Importing airports.tsv.bz2 in 50000 line chunks:
#>  ...Done! (in 0.146152 secs)
#> Importing flights.tsv.bz2 in 50000 line chunks:
#>  ...Done! (in 17.44235 secs)
#> Importing planes.tsv.bz2 in 50000 line chunks:
#>  ...Done! (in 0.06386805 secs)
#> Importing weather.tsv.bz2 in 50000 line chunks:
#>  ...Done! (in 1.224544 secs)

new_db
#> src:  sqlite 3.22.0 [/var/folders/y8/0wn724zs10jd79_srhxvy49r0000gn/T/Rtmp3oFbR8/local.sqlite]
#> tbls: airlines, airports, flights, planes, weather

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.