Skip to content

Latest commit

 

History

History
111 lines (85 loc) · 7.45 KB

README.md

File metadata and controls

111 lines (85 loc) · 7.45 KB
Raw

WR logo White Rabbit

RiaH logo Rabbit in a Hat

Introduction

WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.

Features

  • Can scan databases in SQL Server, Oracle, PostgreSQL, MySQL, MS Access, Amazon RedShift, Google BigQuery, SAS files and CSV files
  • The scan report contains information on tables, fields, and frequency distributions of values
  • Cutoff on the minimum frequency of values to protect patient privacy
  • WhiteRabbit can be run with a graphical user interface or from the command prompt
  • Interactive tool (Rabbit in a Hat) for designing the ETL using the scan report as basis
  • Rabbit in a Hat generates ETL specification document according to OMOP template

Screenshots

White Rabbit Rabbit in a Hat
White RabbitRabbit in a Hat

Technology

White Rabbit and Rabbit in a Hat are pure Java applications. Both applications use Apache's POI Java libraries to read and write Word and Excel files. White Rabbit uses JDBC to connect to the respective databases.

System Requirements

Requires Java 1.8 or higher, and read access to the database to be scanned. Java can be downloaded from http://www.java.com.

Dependencies

For the distributable packages, the only requirement is Java 8. For building the package, also Maven is needed.

Getting Started

WhiteRabbit

  1. Under the Releases tab, download WhiteRabbit*.zip
  2. Unzip the download
  3. Double-click on bin/whiteRabbit.bat on Windows to start White Rabbit, and bin/whiteRabbit on macOS and Linux.

(See the documentation for details on how to run from the command prompt instead)

Rabbit-In-A-Hat

  1. Using the files downloaded for WhiteRabbit, double-click on bin/rabbitInAHat.bat to start Rabbit-In-A-Hat on Windows, and bin/rabbitInAHat on macOS and Linux.

Note: on releases earlier than version 0.8.0, open the respective WhiteRabbit.jar or RabbitInAHat.jar files instead.

Example in- and output

The file examples.zip contains a set of input and output examples for White Rabbit and Rabbit in a Hat. These are used for testing of the main White Rabbit and Rabbit in a Hat features. An overview is given in below table.

Folder Description
wr_input_csv csv files to test scanning on different data types and long table names.
wr_input_sas sas7bdat files to test sas input
wr_output Scan reports created from files in wr_input_csv, wr_input_sas and native a Synthea database loaded in Postgres. All with default scan options.
This folder also includes fake data generated from the csv scan report. The csv scan report is used to test the opening a Scan Report in Rabbit in a Hat.
riah_input An example mapping file used to create the Rabbit in a Hat outputs.
riah_output All export formats created by Rabbit in a Hat: as word, html, markdown, sql skeleton and the R TestFramework.
These are all generated from riah_input/riah_mapping_example.gz.

Getting Involved

  • User guide and Help: WhiteRabbit documentation
  • Developer questions/comments/feedback: OHDSI Forum
  • We use the GitHub issue tracker for all bugs/issues/enhancements
  • Historically, all files have CRLF line endings. Please configure your IDE and local git to keep line endings as is. This avoids merge conflicts.

License

WhiteRabbit is licensed under Apache License 2.0

Development

White Rabbit and Rabbit in a Hat are structured as a Maven package and can be developed in Eclipse. Contributions are welcome.

To generate the files ready for distribution, run mvn install.

Testing

Some newer code has unit and/or integration tests. Tests that depend on external resources being available, such as a database, should be excluded from executing automatically. You can use the @Tag annotation to combine such tests in a group with the same tag, and exclude that tag from being run automatically by maven (this should be done in the configuration of the surefire plugin in pom.xml of the module involved).

An exception to the above are tests that depend on Docker. Currently, these tests are implemented with the TestContainers library, and are configured to check for Docker being present. If not, these tests will not be run, but the tests as a whole will still succeed. However, it is recommended that these tests are run since these tests verify essential functionality for WhiteRabbit, like the database interface.

Also, GitHub actions have been configured to run the test suite automatically.

Development status

Production. This program is being used by many people.