connector

Overview

connector provides a seamless and consistent interface for connecting to different data sources, such as as simple file storage systems and databases.

It also gives the option to use a central configuration file to manage your connections in your project, which ensures a consistent reference to the same data source across different scripts in your project, and enables you to easily switch between different data sources.

The connector package comes with the possibilities of creating connections to file system folders using connector_fs() and general databases using connector_dbi(), which is built on top of the {DBI} package.

connector also has a series of expansion packages that allows you to easily connect to more specific data sources:

• {connector.databricks}: Connect to Databricks
• {connector.sharepoint}: Connect to SharePoint sites

Installation

# Install the released version from CRAN:
install.packages("connector")
# Install the development version from GitHub:
pak::pak("NovoNordisk-OpenSource/connector")

Usage

The recommended way of using connector is to specify a common yaml configuration file in your project that contains the connection details to all your data sources.

A simple example creating connectors to both a folder and a database is shown below:

_connector.yml:

metadata:
  path: !expr withr::local_tempdir()

datasources:
  - name: "folder"
    backend:
        type: "connector::connector_fs"
        path: "{metadata.path}"
  - name: "database"
    backend:
        type: "connector::connector_dbi"
        drv: "RSQLite::SQLite()"
        dbname: ":memory:"

It is easy to initialize this file with:

connector::use_connector()

First we specify common metadata for the connectors, which here is a temporary folder that we want to use. Afterwards we specify the datasources needed in the project, and their specifications.

The first we name “folder”, specify the type to be connector_fs(), and the path to the folder. The second is a database connector to an in memory SQLite database, that we specify using the connector_dbi() type, which uses DBI::dbConnect() to initalize the connection. Therefore we also give the DBI driver to use, and arguments to it.

To connect and create the conenctors we use connect() with the configuration file as input:

library(connector)

db <- connect("_connector.yml")
#> ───────────────────────────────────────────────────
#> Connection to:
#> → folder
#> • connector::connector_fs
#> • /var/folders/kv/q2rqqp3s0s5f9rxn_854l2lm0000gp/T//RtmpMlcjzV/file151272fbf7ccb
#> [1] "ConnectorFS" "Connector"   "R6"
#> ───────────────────────────────────────────────────
#> Connection to:
#> → database
#> • connector::connector_dbi
#> • RSQLite::SQLite() and :memory:

print(db)
#> <connectors>
#>   $folder <ConnectorFS>
#>   $database <ConnectorDBI>

This creates a connectors objects that contains each connector. When printing the individual connector you get the some general information on their methods and specifications.

print(db$database)
#> <ConnectorDBI>
#> Inherits from: <Connector>
#> Registered methods:
#> • `disconnect_cnt.ConnectorDBI()`
#> • `list_content_cnt.ConnectorDBI()`
#> • `log_read_connector.ConnectorDBI()`
#> • `log_remove_connector.ConnectorDBI()`
#> • `log_write_connector.ConnectorDBI()`
#> • `read_cnt.ConnectorDBI()`
#> • `remove_cnt.ConnectorDBI()`
#> • `tbl_cnt.ConnectorDBI()`
#> • `write_cnt.ConnectorDBI()`
#> Specifications:
#> • conn: <SQLiteConnection>

We are now ready to use the connectors, so we can start by writing some data to the folder one:

# Initially it is empty
db$folder |>
  list_content_cnt()
#> character(0)

# Create some data
cars <- mtcars |>
  tibble::as_tibble(rownames = "car")

# Write to folder as a parquet file
db$folder |>
  write_cnt(x = cars, name = "cars.parquet")

# Now the folder contains the file
db$folder |>
  list_content_cnt()
#> [1] "cars.parquet"

# And we can read it back in
db$folder |>
  read_cnt(name = "cars.parquet")
#> # A tibble: 32 × 12
#>    car           mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
#>    <chr>       <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#>  1 Mazda RX4    21       6  160    110  3.9   2.62  16.5     0     1     4     4
#>  2 Mazda RX4 …  21       6  160    110  3.9   2.88  17.0     0     1     4     4
#>  3 Datsun 710   22.8     4  108     93  3.85  2.32  18.6     1     1     4     1
#>  4 Hornet 4 D…  21.4     6  258    110  3.08  3.22  19.4     1     0     3     1
#>  5 Hornet Spo…  18.7     8  360    175  3.15  3.44  17.0     0     0     3     2
#>  6 Valiant      18.1     6  225    105  2.76  3.46  20.2     1     0     3     1
#>  7 Duster 360   14.3     8  360    245  3.21  3.57  15.8     0     0     3     4
#>  8 Merc 240D    24.4     4  147.    62  3.69  3.19  20       1     0     4     2
#>  9 Merc 230     22.8     4  141.    95  3.92  3.15  22.9     1     0     4     2
#> 10 Merc 280     19.2     6  168.   123  3.92  3.44  18.3     1     0     4     4
#> # ℹ 22 more rows

Here the parquet format has been used, but when using a connector_fs it is possible to read and write several different file types. See read_file() and write_file() for more information.

For the database connector it works in the same way:

# Initially no tables exists
db$database |>
  list_content_cnt()
#> character(0)

# Write cars to the database as a table
db$database |>
  write_cnt(x = cars, name = "cars")

# Now the cara table exists
db$database |>
  list_content_cnt()
#> [1] "cars"

# And we can read it back in
db$database |>
  read_cnt(name = "cars") |>
  dplyr::as_tibble()
#> # A tibble: 32 × 12
#>    car           mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
#>    <chr>       <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#>  1 Mazda RX4    21       6  160    110  3.9   2.62  16.5     0     1     4     4
#>  2 Mazda RX4 …  21       6  160    110  3.9   2.88  17.0     0     1     4     4
#>  3 Datsun 710   22.8     4  108     93  3.85  2.32  18.6     1     1     4     1
#>  4 Hornet 4 D…  21.4     6  258    110  3.08  3.22  19.4     1     0     3     1
#>  5 Hornet Spo…  18.7     8  360    175  3.15  3.44  17.0     0     0     3     2
#>  6 Valiant      18.1     6  225    105  2.76  3.46  20.2     1     0     3     1
#>  7 Duster 360   14.3     8  360    245  3.21  3.57  15.8     0     0     3     4
#>  8 Merc 240D    24.4     4  147.    62  3.69  3.19  20       1     0     4     2
#>  9 Merc 230     22.8     4  141.    95  3.92  3.15  22.9     1     0     4     2
#> 10 Merc 280     19.2     6  168.   123  3.92  3.44  18.3     1     0     4     4
#> # ℹ 22 more rows

Useful links

For more information on how to use the package, see the following links:

• connect() for more documentation and how to specify the configuration file
• vignette("connector") for more examples and how to use the package
• vignette("customize") on how to create your own connector and customize behavior
• help("connector-options") for all the options available to customize the behavior of connector
• NovoNordisk-OpenSource/R-packages for an overview of connector and other R packages published by Novo Nordisk