Changes between Version 2 and Version 3 of Onyx HowTo Data Export

Timestamp:

05/20/15 17:51:17 (10 years ago)

Author:

Richard Bramley

Comment:

--

Onyx HowTo Data Export

@@ -9 +9 @@
 == 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.
@@ -15 +17 @@
 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. Unzip the file using the instruction
-{{{
-sudo unzip {filename} /usr/local/i2b2-procedures-1.1-production/unprocessed/
-}}}
-
+7. {{{sudo su -u}}}
+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} }}}
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