Onyx Export and Purge

Sources of Info

The Onyx User Guide has a useful Chapter 12 "Topics for System Administrators" with details of the export and purge functions.

• The User Guide can be found here ​http://wiki.obiba.org/confluence/display/ONYX/Onyx+User+Guide

Other useful links to the obiba wiki

• Configuring export and purge ​http://wiki.obiba.org/confluence/display/ONYX16x/Configuring+Data+Export+and+Purge
• Data Exportation from Onyx. Interesting, but don't know how up to date: ​http://wiki.obiba.org/confluence/display/ONYX/Data+Exportation+from+Onyx
• Onyx Variables: ​http://wiki.obiba.org/confluence/display/ONYX/Onyx+Variables

Overview

Exporting data from Onyx means reading data from the Onyx database and writing it to one or more export destinations. Exporting does not delete any data from the Onyx database. Deleting data from the database is done by the purge function. An export destination is a compressed zip file. Participant data and experimental conditions data can be exported. Configuration of data export is done entirely in configuration files, not through the Onyx user interface. Some things that can be configured:

• Which data is selected for export
• Directory to which export files are written
• How many export destinations are defined

NB: Only system administrators can execute a data export from the Onyx user interface. My understanding is that this means an export is triggered from the user interface.

Purging data means deleting data from the Onyx database. Only participant data can be purged — not experimental conditions data. Configuration of data purging is done entirely in configuration files, not through the Onyx user interface. As per data export, only a system administrator can execute a purge of data by a function from within the user interface.

Sample Config Export File and resulting Export Zip File

The following represent an export of only four participants. The zip file contains a lot of xml. It's worth opening and just pondering how we might approach this. Virtually everything is captured regarding a participant and the interview process. How much of this do we want in i2b2?

Export destinations file
Resulting export zip file

How much do we want to export and purge?

It looks as if the export config file attached results in almost all data being exported for those participants whose interview status is closed, completed or cancelled.

Some aspects are excluded which I (Jeff) do not fully comprehend:

1. Notably to do with the variable 'Participants:Admin.Interview.exportLog.destination'.
2. Some aspects of the Consent table are not exported.

The question of how much we purge is an open question. Remember that this may affect the reporting tool. I mention this here because I believe the purge config file that we have as a default will result in almost everything going.

On the whole it seems sensible to export as much as we can and then archive export files; ie: retain them forever. We may wish to consider encryption given the idea of retaining in perpetuity.

Why export everything? Because it gives us more than one bite of the cherry for the import into i2b2 (or any other piece of software). The detail shown in the export file is quite daunting. It is conceivable that if we filtered during the export we might get this wrong, or change our minds later.

Filtering the exported data