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CDM Upload Script

This repo contains a single R script for uploading data from local CSV files to a database, using the OMOP Common Data Model (CDM). It assumes the data has already been converted to the CDM, and is just for the uploading part. The script will

  • Automatically skip CSV files that do not correspond to a table in the CDM.
  • Automatically skip columns that do not correspond to a field in the CDM.
  • Automatically add missing datetime fields (by copying date fields).
  • Populates the drug_exposure.drug_exposure_end_date field based on the drug_exposure_start_date and days_supply, if not already populated.
  • Populates the cdm_source table.

The script was designed specifically to upload Synpuf data to a PostgreSQL database, but could easily be adapted for other data and database platforms.

Required packages

Use this to install the required packages:

install.packages("SqlRender")
install.packages("DatabaseConnector")
install.packages("readr")

It is also recommended to keep your database credentials secure, and not put them in your code. The keyring package can help with that:

install.packages("keyring")

Setting credentials in keyring

The script by default uses credentials stored in keytring. To set these credentials, use this code, changing the credentials to the correct ones:

keyring::key_set_with_value("postgresServer", password = "mydb.server.com")
keyring::key_set_with_value("postgresDatabase", password = "ohdsi")
keyring::key_set_with_value("postgresUser", password = "john")
keyring::key_set_with_value("postgresPassword", password = "secret!")
keyring::key_set_with_value("postgresPort", password = "5432")

This will need to be done only once, after which the credentials will be stored in your system's credential manager.

Using bulk loading

When using PostgreSQL, it is highly recommended to use bulk loading. This requires:

  1. Installing pgAdmin on your local system. You can download pgAdmin from https://www.pgadmin.org/download/.
  2. Setting the POSTGRES_PATH environmental variable to the folder containing pg.exe, e.g.:
Sys.setenv(POSTGRES_PATH = "D:/PostgreSQL/13/bin")

CDM SQL

This repo currently contains SQL for CDM 5.2.2. This can be updated by replacing the SQL files with newer ones from https://github.com/OHDSI/CommonDataModel

Vocabulary data

The vocabulary data is assumed to have been downloaded from Athena.

CDM data

The CDM data is assumed to be in CSV files, one or several per CDM table. Number prefixes will be ignored. E.g. care_site_1.csv will be loaded into the case_site table.

PostgreSQL server optimization

We highly recommend using PGTune to optimize the performance of your PostgreSQL database. Choose 'Data warehouse' as DB type. Once you've selected your system specifications, PGTune provides two ways to update your configuration: by manually editing your postgresql.conf file, or by issuing ALTER SYSTEM commands via a SQL client (like pgAdmin). I personally find the latter easier to use. Don't forget to restart your server for the changes to take effect.