Onyx HowTo Data Export

Tags: Onyx HowTo Data Integration Tomcat

Notes

The Onyx export only exports completed questionnaires that have not previously been export. This can be changed in the Onyx configuration.

Process

DO NOT FOLLOW THESE INSTRUCTIONS IF YOU ARE REBUILDING THE ONTOLOGY. SEE i2b2 Onyx Importer.

1. Check in the Tomcat application manager that nobody is logged onto the server.
2. In Onyx click on the Participants tab.
3. Click on the Export button. It will tell you where it will export the files, but this should be in /var/lib/tomcat6//target/.
4. FTP the file onto the Hospital BRICCS drive into the /Data Export from Live Onyx/ folder.
5. FTP the files to the uhlbriccsapp03.xuhl-tr.nhs.uk server in the /home/nick/onyx data for importing directory.
6. Then refer to the instructions i2b2 Onyx Importer.
7. sudo su
8. cd /usr/local/i2b2-procedures-1.1-production
9. export I2B2_PROCEDURES_HOME=$PWD
10. ./bin/data-prep/1-namespace-update.sh {jobname} /home/nick/onyx-data-for-importing/{zipfile name}
11. ./bin/data-prep/2-clean-onyx-variables.sh {jobname}
12. ./bin/data-prep/3-onyx2metadata.sh {jobname}
13. ./bin/data-prep/5-refine-metadata.sh {jobname}
14. ./bin/data-prep/A-onyx2pdo-SQL.sh {jobname} -pid={next pid} -eid={next eid}
15. ./bin/data-prep/B-xslt-pdo2crc.sh {jobname}
16. ./bin/participant-upload/participant-upload-sql.sh {jobname}

How to reload All the Data into i2b2

1. Log onto uhlbriccsapp03.xuhl-tr.nhs.uk
2. sudo su
3. cd /usr/local/i2b2-procedures-1.1-production
4. export I2B2_PROCEDURES_HOME=$PWD
5. For each jobname in ls -1tr /usr/local/i2b2-procedures-1.1-production/work
6. ./bin/participant-upload/participant-upload-sql.sh {jobname}
7. Alternatively, run the command ls -1tr /usr/local/i2b2-procedures-1.1-production/work | xargs -i ./bin/participant-upload/participant-upload-sql.sh {}

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