All the configuration goes in the db.properties file, just like with i2b2 ("in section 3.4.2 Set Database Properties<https://community.i2b2.org/wiki/display/getstarted/3.4.2+Set+Database+Properties> of the i2b2 installation guide<https://community.i2b2.org/wiki/display/getstarted/i2b2+Installation+Guide>")
You shouldn't need to change any of the .groovy files. Oh... the README probably should talk about db.properties by name in that section, shouldn't it? Sorry. It's documented down in the reference section, but that's pretty obscure: --db=PROPS database properties file [default: db.properties] -- Dan ________________________________ From: mrkfw <mr...@mail.missouri.edu> Sent: Thursday, August 27, 2020 9:52 AM To: Dan Connolly <dconno...@kumc.edu>; Mandhadi, Vasanthi (Medical Research Office) <mandha...@health.missouri.edu>; gpc-dev@listserv.kumc.edu <gpc-dev@listserv.kumc.edu> Subject: Re: PCORNet Tumor table Hi, According to the “Getting Started” section of README, we need to modify/provide the Database configuration, naccr.flat-file and, i2b2.patient-mapping-query and then generate the jar file. In “DBConfig.groovy” file, we could modify the Database configuration, but we are not sure where to modify or provide the naccr.flat-file and i2b2.patient-mapping-query. This is my understanding so far, please correct me if I am wrong and provide a guidance accordingly. Thank you, Rana From: Dan Connolly <dconno...@kumc.edu> Date: Wednesday, August 26, 2020 at 11:04 AM To: "Mandhadi, Vasanthi (Medical Research Office)" <mandha...@health.missouri.edu>, "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu> Cc: mrkfw <mr...@mail.missouri.edu> Subject: Re: PCORNet Tumor table Yes, that's the right documentation and jar file*. Does the "Getting Started" section of the README make sense? *for the jar file, the commit hash is not part of its URL: https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.7.4/naaccr-tumor-data.jar<https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.7.4/naaccr-tumor-data.jar> -- Dan ________________________________ From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu> on behalf of Mandhadi, Vasanthi (Medical Research Office) <mandha...@health.missouri.edu> Sent: Wednesday, August 26, 2020 10:12 AM To: gpc-dev@listserv.kumc.edu <gpc-dev@listserv.kumc.edu> Cc: mrkfw <mr...@mail.missouri.edu> Subject: PCORNet Tumor table Hi GPC-dev, We are starting to look into implementing the pcornet tumor table from NAACCR tumor data. I am not sure if I am looking at the latest readme file and jar file that other sites used. If not can anyone share the correct jar file and instructions. ReadMe: https://github.com/kumc-bmi/naaccr-tumor-data#readme<https://github.com/kumc-bmi/naaccr-tumor-data#readme> Jar file: https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.4-pcornet-1/naaccr-tumor-data.jar<https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.4-pcornet-1/naaccr-tumor-data.jar>1342e39 Any suggestions or guidance on how to get started would be helpful. Thank you, Vasanthi Mandhadi Sr. Research Design Engineer University of Missouri School of Medicine Office: (573) 882-6273 Cell: (573) 529-8151
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