Command-line data file processing in Rust https://git.guillemborrell.es/guillem/dr
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
Go to file
Guillem Borrell Nogueras f4b3a525bb
ci/woodpecker/push/woodpecker Pipeline was successful Details
Fixed bash string quotes
2 months ago
src Added more documentation in the cli 2 months ago
.gitignore Improved documentation 4 months ago
.woodpecker.yml exe for windows 4 months ago
Cargo.toml Version bump 2 months ago
LICENSE Initial commit 4 months ago
README.md Fixed bash string quotes 2 months ago
wine.csv Got to read from stdin, write to stdoutgit 4 months ago

README.md

dr.rs

status-badge | Download | Source | Bugs

A toolkit to process data files (csv and parquet) using the command line, inspired by csvkit, with blazing speed, and powered by Rust.

You may wonder why I'm implementing this, since there's already xsv. There are two reasons for that:

  1. This what I'm implementing to learn Rust.
  2. The Rust data ecosystem has evolved immensely since xsv was sarted. Now we can add things like SQL commands to filter csv files, or translate results to parquet files.

TL;DR

You can install dr the rust way with cargo install dr but downloading a binary from here may be all you need.

$ dr --help
dr is a handy command line tool to handle csv and parquet files.
It is designed to integrate nicely with other command line tools
like cat, sed, awk and database clients cli. You can find more
information an a short tutorial https://git.guillemborrell.es/guillem/dr
            

Usage: dr [COMMAND]

Commands:
  csv
          Read csv, output arrow stream
  schema
          Several table schema related utilities
  sql
          Runs a sql statement on the file
  print
          Pretty prints the table
  rpq
          Read parquet file
  wpq
          Write to a paquet file
  help
          Print this message or the help of the given subcommand(s)

Options:
  -h, --help
          Print help information (use `-h` for a summary)

  -V, --version
          Print version information

Howto

dr is convenience command to explore, transform, and analyze csv and parquet files to save you from writing throwaway python scripts or create a custom container image for verys simple tasks. It's designed to make the life of a data engineer a little easier.

Assume you have a very large csv file, and you just want to translate it to parquet with some type inference and sane defaults. With dr this is as easy as:

$ dr csv wine.csv -P wine.pq

Parquet files are binary, and you may want to check that you've not written nonsense by printing the header on your terminal.

$ dr rpq wine.pq -a
shape: (5, 14)
┌──────┬─────────┬────────────┬──────┬─────┬───────────┬──────┬──────┬─────────┐
│ Wine ┆ Alcohol ┆ Malic.acid ┆ Ash  ┆ ... ┆ Color.int ┆ Hue  ┆ OD   ┆ Proline │
│ ---  ┆ ---     ┆ ---        ┆ ---  ┆     ┆ ---       ┆ ---  ┆ ---  ┆ ---     │
│ i64  ┆ f64     ┆ f64        ┆ f64  ┆     ┆ f64       ┆ f64  ┆ f64  ┆ i64     │
╞══════╪═════════╪════════════╪══════╪═════╪═══════════╪══════╪══════╪═════════╡
│ 1    ┆ 14.23   ┆ 1.71       ┆ 2.43 ┆ ... ┆ 5.64      ┆ 1.04 ┆ 3.92 ┆ 1065    │
├╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┤
│ 1    ┆ 13.2    ┆ 1.78       ┆ 2.14 ┆ ... ┆ 4.38      ┆ 1.05 ┆ 3.4  ┆ 1050    │
├╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┤
│ 1    ┆ 13.16   ┆ 2.36       ┆ 2.67 ┆ ... ┆ 5.68      ┆ 1.03 ┆ 3.17 ┆ 1185    │
├╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┤
│ 1    ┆ 14.37   ┆ 1.95       ┆ 2.5  ┆ ... ┆ 7.8       ┆ 0.86 ┆ 3.45 ┆ 1480    │
├╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┤
│ 1    ┆ 13.24   ┆ 2.59       ┆ 2.87 ┆ ... ┆ 4.32      ┆ 1.04 ┆ 2.93 ┆ 735     │
└──────┴─────────┴────────────┴──────┴─────┴───────────┴──────┴──────┴─────────┘

Maybe the most interesing feature of dr is the ability to process csv and parquet files using SQL, while solutions like xsv and csvkit rely on a rich set of subcommands and options. If you already know SQL, there's no need to read any more documentation to select, filter, or group data. The only thing you need to remember is that the table will be called this. The following command outputs a csv of the wine with the highest concentration of alcohol in the popular wine dataset:

 dr csv wine.csv -q "select * from this where Alcohol = max(Alcohol)" | dr print
shape: (1, 14)
┌──────┬─────────┬────────────┬──────┬─────┬───────────┬──────┬──────┬─────────┐
│ Wine ┆ Alcohol ┆ Malic.acid ┆ Ash  ┆ ... ┆ Color.int ┆ Hue  ┆ OD   ┆ Proline │
│ ---  ┆ ---     ┆ ---        ┆ ---  ┆     ┆ ---       ┆ ---  ┆ ---  ┆ ---     │
│ i64  ┆ f64     ┆ f64        ┆ f64  ┆     ┆ f64       ┆ f64  ┆ f64  ┆ i64     │
╞══════╪═════════╪════════════╪══════╪═════╪═══════════╪══════╪══════╪═════════╡
│ 1    ┆ 14.83   ┆ 1.64       ┆ 2.17 ┆ ... ┆ 5.2       ┆ 1.08 ┆ 2.85 ┆ 1045    │
└──────┴─────────┴────────────┴──────┴─────┴───────────┴──────┴──────┴─────────┘

If you don't use any option that formats the output of the results, dr outputs Arrow's IPC format, meaning that multiple dr calls can be efficiently chained with very low overhead. The following script loads one month of NY taxi data and executes two sql queries on the data.

$ dr rpq data/yellow_tripdata_2014-01.parquet \
    -q "select count(1) as cnt, passenger_count from this group by passenger_count" \
    | dr sql "select * from this order by cnt desc" \
    | dr print
┌─────────┬─────────────────┐
│ cnt     ┆ passenger_count │
│ ---     ┆ ---             │
│ u32     ┆ i64             │
╞═════════╪═════════════════╡
│ 9727321 ┆ 1               │
├╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤
│ 1891588 ┆ 2               │
├╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤
│ 789070  ┆ 5               │
├╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤
│ 566248  ┆ 3               │
├╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤
│ ...     ┆ ...             │
├╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤
│ 19      ┆ 208             │
├╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤
│ 16      ┆ 9               │
├╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤
│ 7       ┆ 7               │
├╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤
│ 5       ┆ 8               │
└─────────┴─────────────────┘

Operate with SQL databases

How many times did you have to insert a csv file (sometimes larger than memory) to a database? Tens of times? Hundreds? You've probably used Pandas for that, since it can infer the table's datatypes. So a simple data operation becomes a python script with Pandas and a driver for PostgreSQL as dependencies.

Now dr can provide the table creation statement with a handful of columns:

$ head wine.csv | dr schema -i -p -n wine
CREATE TABLE IF NOT EXISTS "wine" (  );
ALTER TABLE "wine" ADD COLUMN "Wine" integer;
ALTER TABLE "wine" ADD COLUMN "Alcohol" real;
ALTER TABLE "wine" ADD COLUMN "Malic.acid" real;
ALTER TABLE "wine" ADD COLUMN "Ash" real;
ALTER TABLE "wine" ADD COLUMN "Acl" real;
ALTER TABLE "wine" ADD COLUMN "Mg" integer;
ALTER TABLE "wine" ADD COLUMN "Phenols" real;
ALTER TABLE "wine" ADD COLUMN "Flavanoids" real;
ALTER TABLE "wine" ADD COLUMN "Nonflavanoid.phenols" real;
ALTER TABLE "wine" ADD COLUMN "Proanth" real;
ALTER TABLE "wine" ADD COLUMN "Color.int" real;
ALTER TABLE "wine" ADD COLUMN "Hue" real;
ALTER TABLE "wine" ADD COLUMN "OD" real;
ALTER TABLE "wine" ADD COLUMN "Proline" integer;

More about this in the Examples section

Since most databases can ingest and spit CSV files, some simple operations can be enhanced with dr, like storing the results of a query in a parquet file

$ psql -c "copy (select * from wine) to stdout with (FORMAT 'csv', HEADER)" | dr csv -i -P wine.pq

Reference

Some commands that generate raw output in ipc format.

  • Read a csv or parquet file and print the header: dr {csv, rpq} [file] -a
  • Read a csv or parquet file, execute a SQL statement, and output the results in stdout using Arrow's ipc format dr {csv, rpq} [file] -q "statement"
  • Read a csv or parquet file and print a summary of each column: dr {csv, rpq} [file] -s "[query]"
  • Read a csv or parquet file, execute a query, and output the results in stdout using the csv format dr {csv, rpq} [file] -s "[query]" -t
  • Read a csv and write a parquet file with the same contents: dr csv [file.csv] -P [file.pq]

Some commands that convert raw input in ipc format

  • Read from stdin in ipc and pretty print the table: dr print
  • Read from stdin in csv and pretty print the table: dr print -t
  • Read from stdin in ipc and write the data in parquet: dr wpq [file.pq]

Some commands that read csv data from stdin

  • Read csv from stdin and print the schema as it would be inserted in a postgresql database: dr schema -i -p -n tablename
  • Reas csv from stdin and save as parquet, inferring types: dr csv -i -P filename.pq

Examples

Inserting CSV into postgres

Assume that you were given a large (several GiB) with a weird (latin1) encoding, and you want to insert it into postgres. This dataset may be too large to store it in memory in one go, so you'd like to stream it into the database. You need to

  • Read the csv file
  • Infer the schema, and create a table
  • Change the encoding of the file to the same as the database

You can use dr to turn this into a two-step process, and pipe the encoding conversion in one go. The first step would be to infer the schema of the resulting table and creating the table

$ head large_csv_file.csv | iconv -f latin1 -t utf-8 | dr schema -i -p -n tablename | pgsql -U username -h hostname database

The second step would be leveraging the pgsql command to write the contents of the file into the database

$ cat large_csv_file.csv | iconv -f latin1 -t UTF-8 | psql -U username -h hostname -c "\copy tablename from stdin with (FORMAT 'csv', HEADER)" database

The ingestion process is atomic, meaning that if pgsql fails to insert any record, no insertions will be made at all. If the insertion fails, probably because some column of type varchar can't fit the inferred type, you can change the type with:

$ psql -U username -h hostname -c 'alter table tablename alter column "LongDescription" type varchar(1024);' database

And try inserting again

Performance

This command runs two dr processes. The first one makes an aggregation on a compressed parquet file of 144MB of size, and the second one just orders the result:

$ dr rpq data/yellow_tripdata_2014-01.parquet \
    -q "select count(1) as cnt, passenger_count from this group by passenger_count" \
    | dr sql "select * from this order by cnt desc" \
    > /dev/null

On a very very old machine (Intel(R) Core(TM) i5-6500T CPU @ 2.50GHz), this takes around half a second, which is roughly the time needed to read and decompress the parquet file. Polar's csv and parquet readers have some decent performance, so you can count on dr to be one of the fastest in the block.

Caveats

  1. dr uses Polars to build and transform dataframes in Rust, and the entire table may be loaded in memory. At the time when dr was created, streaming support didn't get along very well with SQL contexts.

  2. dr uses Polars' SQLContext to execute the query which supports a small subset of the SQL language.

Built standing on the shoulders of giants

None of this would be possible without Polars