Set up your environment to contribute

Set up

In this vignette we explain how to set up your environment to be able to contribute to the package. OmopOnPostgres is an open-source package open for contributions, if you want to contribute you will need to be able to run the tests locally. To do so you need a local postgres instance with the following credentials:

POSTGRES_USER=omop_postgres_connector
POSTGRES_PASSWORD=omopverse
POSTGRES_DB=omop_test

The GitHub actions run on a container where these credentials have already been created, you can rely on the GitHub actions to run tests there.

There are several ways to have this:

Install Postgres and create manually a database

1. Download postgres
2. Set up your installer and install Postgre and pgAdmin 4. Please use PORT 5432, if port 5432 is not available create an environment variable OMOP_POSTGRES_CONNECTOR_PORT with the port that you are using:

OMOP_POSTGRES_CONNECTOR_PORT=5432

3. Create your a user. Please use USER: omop_postgres_connector and PASSWORD: omopverse; if this is not possible please create environment variables to provide the credentials:

OMOP_POSTGRES_CONNECTOR_USER=omop_postgres_connector
OMOP_POSTGRES_CONNECTOR_PASSWORD=omopverse

4. Create a database. Please use DATABASE: omop_test; if this is not possible please create environment variables to provide the credentials:

OMOP_POSTGRES_CONNECTOR_DB=omop_test

If you successfully completed the 4 steps please go to Check the set up.

Install Postgres via docker

1. Download docker desktop

2. Run the following code from the terminal:

docker run --name local-postgres \
  -e POSTGRES_USER=omop_postgres_connector \
  -e POSTGRES_PASSWORD=omopverse \
  -e POSTGRES_DB=omop_test \
  -p 5432:5432 \
  -d postgres:16

Check the set up

If your connection is successful you should be able to run the following lines of code without any error:

library(DBI)
library(RPostgres)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

# create connection
con <- dbConnect(
  drv = Postgres(),
  dbname = Sys.getenv("OMOP_POSTGRES_CONNECTOR_DB", "omop_test"),
  host = "localhost",
  port = Sys.getenv("OMOP_POSTGRES_CONNECTOR_PORT", "5432"),
  user = Sys.getenv("OMOP_POSTGRES_CONNECTOR_USER", "omop_postgres_connector"),
  password = Sys.getenv("OMOP_POSTGRES_CONNECTOR_PASSWORD", "omopverse")
)
con
#> <PqConnection> omop_test@localhost:5432

# create new schema
dbExecute(conn = con, statement = "CREATE SCHEMA opc_main;")
#> [1] 0
dbWriteTable(conn = con, name = Id(schema = "opc_main", table = "test"), value = cars)
tbl(con, I("opc_main.test"))
#> # Source:   table<opc_main.test> [?? x 2]
#> # Database: postgres  [omop_postgres_connector@localhost:5432/omop_test]
#>    speed  dist
#>    <dbl> <dbl>
#>  1     4     2
#>  2     4    10
#>  3     7     4
#>  4     7    22
#>  5     8    16
#>  6     9    10
#>  7    10    18
#>  8    10    26
#>  9    10    34
#> 10    11    17
#> # ℹ more rows
dbExecute(con, "DROP SCHEMA opc_main CASCADE;")
#> NOTICE:  drop cascades to table opc_main.test
#> [1] 0

# create new database
dbExecute(conn = con, statement = "CREATE DATABASE opc_test;")
#> [1] 0
dbDisconnect(conn = con)

# connect to new database
con <- dbConnect(
  drv = Postgres(),
  dbname = "opc_test",
  host = "localhost",
  port = Sys.getenv("OMOP_POSTGRES_CONNECTOR_PORT", "5432"),
  user = Sys.getenv("OMOP_POSTGRES_CONNECTOR_USER", "omop_postgres_connector"),
  password = Sys.getenv("OMOP_POSTGRES_CONNECTOR_PASSWORD", "omopverse")
)

dbExecute(conn = con, statement = "CREATE SCHEMA opc_main;")
#> [1] 0
dbWriteTable(conn = con, name = Id(schema = "opc_main", table = "test"), value = cars)
tbl(con, I("opc_main.test"))
#> # Source:   table<opc_main.test> [?? x 2]
#> # Database: postgres  [omop_postgres_connector@localhost:5432/opc_test]
#>    speed  dist
#>    <dbl> <dbl>
#>  1     4     2
#>  2     4    10
#>  3     7     4
#>  4     7    22
#>  5     8    16
#>  6     9    10
#>  7    10    18
#>  8    10    26
#>  9    10    34
#> 10    11    17
#> # ℹ more rows
dbDisconnect(conn = con)

# delete created database
con <- dbConnect(
  drv = Postgres(),
  dbname = Sys.getenv("OMOP_POSTGRES_CONNECTOR_DB", "omop_test"),
  host = "localhost",
  port = Sys.getenv("OMOP_POSTGRES_CONNECTOR_PORT", "5432"),
  user = Sys.getenv("OMOP_POSTGRES_CONNECTOR_USER", "omop_postgres_connector"),
  password = Sys.getenv("OMOP_POSTGRES_CONNECTOR_PASSWORD", "omopverse")
)
dbExecute(con, "DROP DATABASE opc_test;")
#> [1] 0
dbDisconnect(conn = con)

Now that you are ready try cloning the code locally and run devtools::check() if no error arises you are all set up.