R Package - `dbr`¶

Source: daroczig/dbr: Secure database connections and convenient queries from R on the top of DBI (github.com)

Convenient database connections and queries from R.

Vignette coming, until then, please check the talk presented at the useR! 2018 conference:

slides
video

Contents¶

Setting up a config file for the database connections¶

To be able to connect to a database, the connection parameters are to be specified in a YAML file, for example for a SQLite database to be created in a temp file:

sqlite:
  drv: !expr RSQLite::SQLite()
  dbname: !expr tempfile()

By default, dbr will look for a file named db_config.yaml in the current working directory, that can be override via the dbr.db_config_path global option, eg to the example config bundled in this package:

options(dbr.db_config_path = system.file('example_db_config.yaml', package = 'dbr'))

A more complex example from the demo YAML file describing a MySQL connection to a database hosted by RStudio (with public username and password):

shinydemo:
  drv: !expr RMySQL::MySQL()
  host: shiny-demo.csa7qlmguqrf.us-east-1.rds.amazonaws.com
  username: guest
  password: guest
  dbname: shinydemo

Note, that instead of simple strings, you can also specify KMS-encrypted passwords, other secrets and parameters as well, eg:

redshift:
  host: !aws_kms |
    KMSencryptedciphertext...
  port: 5439
  dbname: dbname
  user: username
  drv: !expr RPostgreSQL::PostgreSQL()
  password: !aws_kms |
    KMSencryptedciphertext...
  s3_copy_bucket: !attr |-
    's3://openmail-model/temp'
  s3_copy_iam_role: !attr |-
    arn:aws:iam::accountid:role/redshift_role

Querying databases¶

Once the connection parameters are loaded from a config file, making SQL queries are as easy as specifying the SQL statement and the name of the connection:

db_query('show tables', 'shinydemo')
#> INFO [2019-01-06 01:06:18] Connecting to shinydemo
#> INFO [2019-01-06 01:06:19] Executing:**********
#> INFO [2019-01-06 01:06:19] show tables
#> INFO [2019-01-06 01:06:19] ********************
#> INFO [2019-01-06 01:06:19] Finished in 0.1336 secs returning 3 rows
#> INFO [2019-01-06 01:06:19] Closing connection to shinydemo
#>   Tables_in_shinydemo
#> 1                City
#> 2             Country
#> 3     CountryLanguage

For more advanced usage, eg caching database connections, check ?db_connect and the above mentioned vignette.

SQL templating¶

To reuse SQL chunks, you may list your SQL queries (or parts of it) in a structured YAML file, like in the bundled example config at example_sql_chunks.yaml

Use sql_chunk_files to list or update the currently used SQL template YAML file(s), eg via

sql_chunk_files(system.file('example_sql_chunks.yaml', package = 'dbr'))

Then you may refer to any key in that definition by a string that consist of the keys in hierarchy separated by a dot, so looking at the below definition (part of example_sql_chunks.yaml):

dbr:
  shinydemo:
    countries:
      count: SELECT COUNT(*) FROM Country

Getting the count key from for the countries item in dbr‘s shinydemo section, you could do something like:

sql_chunk('dbr.shinydemo.countries.count')
#> SELECT COUNT(*) FROM Country

And pass it right away to db_query:

countries <- db_query(sql_chunk('dbr.shinydemo.countries.count'), 'shinydemo')
#> INFO [2019-01-06 01:33:33] Connecting to shinydemo
#> INFO [2019-01-06 01:33:34] Executing:**********
#> INFO [2019-01-06 01:33:34] SELECT COUNT(*) FROM Country
#> INFO [2019-01-06 01:33:34] ********************
#> INFO [2019-01-06 01:33:34] Finished in 0.1291 secs returning 1 rows
#> INFO [2019-01-06 01:33:34] Closing connection to shinydemo

SQL chunks can be also defined in files outside of the YAML with the sql file extensions, and referenced with the !include tag in the YAML file, eg:

dbr:
  shinydemo:
    countries:
      europe: !include europe.sql

This will read the content of europe.sql and make it available as sql_chunk('dbr.shinydemo.countries.count').

Besides files, a folder with sql files can be also included – in that case, the base filename (without the sql file extension) will become the key under the given key. For example, consider this YAML definition:

cities: !include cities.sql

Will load all the files from the cities.sql folder and make those available under europe, so resulting in an intermediate YAML as:

cities: !include cities.sql
  europe: |-
    SELECT Name
    FROM City
    WHERE CountryCode IN (
      {sql_chunk('dbr.shinydemo.countries.europe', indent_after_linebreak = 2)})
  europe_large: |-
    SELECT Name
    FROM City
    WHERE
      Population > 1000000 AND
      Name IN (
        {sql_chunk('dbr.shinydemo.cities.europe', indent_after_linebreak = 4)}))

If the key of a directory !include is ~!, then the keys are made available in the parent node, so eg

cities:
  ~!: !include cities.sql

Would not actually create the cities key, but only the europe and europe_large keys in the root node.

As you can see from the above, the main power of this templating approach is that you can easily reuse SQL chunks, eg for the list of European countries in:

cities <- db_query(sql_chunk('dbr.shinydemo.cities.europe'), 'shinydemo')
#> INFO [2019-01-06 01:32:02] Connecting to shinydemo
#> INFO [2019-01-06 01:32:02] Executing:**********
#> INFO [2019-01-06 01:32:02] SELECT Name
#> FROM City
#> WHERE CountryCode IN (
#>   SELECT Code
#>   FROM Country
#>   WHERE Continent = 'Europe')
#> INFO [2019-01-06 01:32:02] ********************
#> INFO [2019-01-06 01:32:02] Finished in 0.1225 secs returning 643 rows
#> INFO [2019-01-06 01:32:02] Closing connection to shinydemo

Where the Country-related subquery was specified in the dbr.shinydemo.countries.europe key as per:

SELECT Name
FROM City
WHERE CountryCode IN (
  {sql_chunk('dbr.shinydemo.countries.europe', indent_after_linebreak = 2)})

The indent_after_linebreak parameter is just for cosmetic updates in the query to align FROM and WHERE on the same character in the SQL statement.

Even more complex / nested example:

sql_chunk('dbr.shinydemo.cities.europe_large')
#> SELECT Name
#> FROM City
#> WHERE
#>   Population > 1000000 AND
#>   Name IN (
#>     SELECT Name
#>     FROM City
#>     WHERE CountryCode IN (
#>       SELECT Code
#>       FROM Country
#>       WHERE Continent = 'Europe')))

Appendix: Links¶

Tools
Development \<\<\<\<\<\<\< HEAD:3-Resources/Tools/R/R Packages/Database R Packages/R Package - dbr.md
R
R Database Packages =======
2-Areas/MOCs/R
R - Database Packages List >>>>>>> develop:3-Resources/Tools/Developer Tools/Languages/R/R Packages/Database R Packages/R Package - dbr.md

Backlinks:

list from [[R Package - dbr]] AND -"Changelog"

R Package - dbr¶