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 <[email protected]>
Sent: Thursday, August 27, 2020 9:52 AM
To: Dan Connolly <[email protected]>; Mandhadi, Vasanthi (Medical Research
Office) <[email protected]>; [email protected]
<[email protected]>
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 <[email protected]>
Date: Wednesday, August 26, 2020 at 11:04 AM
To: "Mandhadi, Vasanthi (Medical Research Office)"
<[email protected]>, "[email protected]"
<[email protected]>
Cc: mrkfw <[email protected]>
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 <[email protected]> on behalf of Mandhadi,
Vasanthi (Medical Research Office) <[email protected]>
Sent: Wednesday, August 26, 2020 10:12 AM
To: [email protected] <[email protected]>
Cc: mrkfw <[email protected]>
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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