= 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]]
1. {{{sudo su}}}
1. {{{cd /usr/local/i2b2-procedures-1.1-production}}}
1. {{{export I2B2_PROCEDURES_HOME=$PWD}}}
1. For each jobname in {{{ls -1tr /usr/local/i2b2-procedures-1.1-production/work}}}
1. {{{./bin/participant-upload/participant-upload-sql.sh {jobname} }}}
1. 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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