That makes sense. And works:). I had put my i2b2 data schema name in that field, instead of the sid.
If anyone else wants to try to install databuilder in an existing environment, it’s doable. Phillip From: Dan Connolly <[email protected]<mailto:[email protected]>> Date: Friday, January 9, 2015 at 1:10 PM To: Phillip Reeder <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: Installing DataBuilder That's the database = line in the config file. -- Dan ________________________________ From: Phillip Reeder [[email protected]<mailto:[email protected]>] Sent: Friday, January 09, 2015 12:07 PM To: Phillip Reeder; Dan Connolly Cc: [email protected]<mailto:[email protected]> Subject: Re: Installing DataBuilder How do I set the SID for the connection? sqlalchemy.exc.DatabaseError: (DatabaseError) ORA-12505: TNS:listener does not currently know of SID given in connect descriptor Phillip From: Phillip Reeder <[email protected]<mailto:[email protected]>> Date: Friday, January 9, 2015 at 11:16 AM To: Dan Connolly <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: Installing DataBuilder Ok. I’ve got the cgi and python all installed and it’s writing json files for me now. SELinux was enabled on the server which was not allowing the webserver to write the files. For cx_Oracle, I had to run ‘yum install python-devel’ to be able use pip to install cx_Oracle. Next step will be to configure my database and see if I can produce sqlite files. Phillip From: Dan Connolly <[email protected]<mailto:[email protected]>> Date: Tuesday, January 6, 2015 at 2:15 PM To: Phillip Reeder <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: Installing DataBuilder On a good day, installing the oracle driver for python goes like: $ ORACLE_HOME=/opt/oracle/wherever-your-libocci-lives/ pip install cx_Oracle Such good days are sufficiently rare that I'm looking into jython<https://informatics.gpcnetwork.org/trac/Project/wiki/BuilderSaga#Appendix:ConsiderJython> so we can just use the JDBC driver. I know a lot more than I really want to about installing cx_Oracle on various linux distributions, so if you can supply specific diagnostics, I can probably help you get past any issues. Our oracle config (currently) looks like: [deid] username = data_builder database = BHeronB2 host = localhost drivername = oracle+cx_oracle password = %(EXTRACT_PASSWORD)s port = 1521 and when we run dfbuilder.py, we set the EXTRACT_PASSWORD environment variable appropriately (using Jenkins). I expect BHeronB2 isn't portable to your site; salt to taste. The host = localhost because we use ssh tunnels to connect to the Oracle database server; again, salt to taste. -- Dan ________________________________ From: Phillip Reeder [[email protected]<mailto:[email protected]>] Sent: Tuesday, January 06, 2015 1:53 PM To: Dan Connolly Cc: [email protected]<mailto:[email protected]> Subject: Re: Installing DataBuilder Do you have a mk file with the oracle driver for Python? It looks like the vm install downloads the pg driver. I’m planning to sit down with our sysadmin on that server tomorrow and attempt the install. If it works, I’ll document the changes and make sure the gpc-dev group gets them. Also, if you have a dfbuild-extract.conf.example with an oracle driver info in it, I’ll probably need that too. Thanks, Phillip From: Dan Connolly <[email protected]<mailto:[email protected]>> Date: Tuesday, January 6, 2015 at 1:31 PM To: Phillip Reeder <[email protected]<mailto:[email protected]>> Subject: RE: Installing DataBuilder It was developed for Oracle; that's how we normally run it. I'm not sure what to tell you beyond the installation documentation in the source code. I'm willing to help with any specific problems that come up; copy the gpc-dev list if you can, please, so that we all learn together. -- Dan ________________________________ From: Phillip Reeder [[email protected]<mailto:[email protected]>] Sent: Tuesday, January 06, 2015 1:23 PM To: Dan Connolly Subject: Installing DataBuilder What is required to install DataBuilder on a non-i2b2 VM machine, and one running oracle, not postgress? I’m looking at installing it on our dev machine and trying to figure out the best path to take, without killing our dev i2b2 server:). If I change the paths to my webclient & i2b2 url’s etc in the i2b2_vm_deploy.mk file, do you think it will get me close enough that with a little help debugging, we could make it work? Thanks, Phillip ________________________________ UT Southwestern Medical Center The future of medicine, today.
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