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REDCap-ETL Installation Guide

REDCap-ETL System Components

The main components of an installed REDCap-ETL system are shown in the diagram below, and described in the text below.

ETL Process

  • Configuration File. This file contains the configuration information for a REDCap-ETL process. A single REDCap-ETL instance can have multiple configuration files that describe different ETL processes.
  • REDCap Project. The REDCap project that contains the data to be extracted.
  • REDCap-ETL. The software that actually does the Extract, Transform and Load.
  • Database. REDCap-ETL needs a place where the extracted and transformed data can be loaded. You can specify a database or, for CSV file output, a directory where the CSV files are to be stored. REDCap-ETL can also log information about its processes to a database.
  • E-mail Server. This is optional, and if set up, is used for e-mailing error notifications and logging summaries to designated users.
  • Log File. An optional log file can be set up where REDCap-ETL will log the results of its ETL processes.

Installation Steps

Step 1 - Set up the Server

Install the System Requirements:

  • PHP 7.1+ or 8+, with:
    • curl extension
    • openssl extension
  • Subversion or Git, for retrieving the REDCap-ETL code
  • In addition, you need to be using REDCap version 7+

Example commands for setting up an Ubuntu 16 system:

sudo apt install php php-curl
sudo apt install git

Step 2 (Optional) - Set up a Database

If you want to store the extracted and transformed data in a database, instead of CSV files, you will need to have a database set up that can be accessed by REDCap-ETL. And, you need to have a user account for the database that supports at least the following permissions:

  • ALTER
  • CREATE
  • CREATE VIEW
  • DROP
  • INSERT
  • SELECT

The following database systems are currently supported:

  • MySQL
  • PostgreSQL
  • SQL Server
  • SQLite

Note: By default, REDCap-ETL requires databases to support SSL (secure) communication. This is set by the db_ssl configuration property, which defaults to true. If your database does not support SSL communication, you will get a database error when you run REDCap-ETL. You can set the db_ssl property to 0 to turn off the database SSL requirement, but this is not generally recommended for security reasons.

MySQL Database Setup Example

Example commands for setting up MySQL on Ubuntu 16:

sudo apt install php-mysql
sudo phpenmod mysqli    # enable mysqli extension
sudo phpenmod pdo_mysql # enable PDO extension for PHP 

sudo apt install mysql-server
sudo mysql_secure_installation

systemctl status mysql.service   # check status

Create a database and database user that will be used as the place to store the REDCap data, for example, in MySQL use:

CREATE DATABASE `etl`;
CREATE USER 'etl_user'@'localhost' IDENTIFIED BY 'etlPassword';
GRANT ALL ON `etl`.* TO 'etl_user'@'localhost';

SQLite Setup Example

Example commands for setting up SQLite on Ubuntu 16:

sudo apt install php-sqlite3  # add PHP support for SQLite
sudo apt install sqlite3
sudo apt install sqlitebrowser   # optional

To create a database, in the directory where you want the database, execute, for example:

sqlite3 etl-data.db
# then enter ".q" to exit SQLite

Step 3 - Get the REDCap-ETL Software

The basic Git command to get the code is:

git clone https://github.com/IUREDCap/redcap-etl

To install the code to the /opt/redcap-etl directory, the following command could be used:

sudo git clone https://github.com/IUREDCap/redcap-etl /opt/redcap-etl

Set the permissions for the new directory as desired. For example, if the process was being run as user etl in group etl, the following command might be used on a Linux system:

sudo chown -R etl:etl /opt/redcap-etl

Step 4 - Create a Configuration File

The configuration file can be used to specify your entire configuration, or it can be used in conjunction with a configuration project.

The standard place to store configuration files is in the config/ directory of the REDCap-ETL installation. However, they could be stored in any directory where REDCap-ETL has read access.

To create a new configuration file, the file config/config-example.ini can be copied and then modified. See this file, and the Configuration Guide for more information about the configuration properties.

Step 5 (Optional) - Set up an E-mail Server

You can optionally set up an e-mail server that will be used for logging errors using e-mail to a specified list of users.

On Ubuntu 16, for example, you can set up an e-mail server using the following command:

    sudo apt install sendmail

The script bin/email_test.php can be used to test if e-mail logging works.

Running the ETL Process

There are 2 ways to run REDCap-ETL:

  1. Manual. Execute the bin/redcap_etl.php command manually on the server
  2. Scheduled. Set up a cron job to run the ETL process at specific recurring times

Running ETL Manually

To run the ETL process manually, you need to run the redcap_etl.php script and specify the configuration file to use, for example:

    /opt/redcap-etl/bin/redcap_etl.php -c /opt/redcap-etl/config/visits.ini

In the example above:

  • /opt/redcap-etl is the directory where REDCap-ETL was installed on the server
  • /opt/redcap-etl/config/visits.ini is a configuration file set up by a user that specifies an ETL process

Depending on how your server is set up, you may need to use php /opt/redcap-etl/bin/redcap_etl.php ... to run the command.

Running ETL at Regularly Scheduled Times

On Linux systems, you should be able to set up a cron job to run ETL processes on a regularly scheduled basis.

Here is an example crontab entry for a cron job to run the ETL process:

0 2 * * * cd /opt/redcap-etl/bin; php ./redcap_etl.php \
    -c /opt/redcap-etl/config/visits.ini

For this example:

  • 0 2 * * * indicates that the ETL process will be run at 2:00am every day. See cron documentation for more details.
  • /opt/redcap-etl is the directory where REDCap-ETL has been installed in this case
  • redcap_etl.php is the standard REDCap-ETL script for running the ETL process
  • /opt/redcap-etl/config/visits.ini is the configuration file for the ETL process that has been set up by the user