Creating projects in I2B2
Albaruthenia
let me briefly introduce myself to the community. My name is Alexander
Saip, and I work at Vanderbilt University. We have just started our
pilot project that involves installing and configuring the I2B2 server
to work with our clinical research data. The installation process was
a breeze, and we even switched from the local Oracle XE instance to a
remote RAC cluster. Unfortunately, the next step of setting up a
separate project for our data wasn't completely successful, as I
described in a Google document at
https://docs.google.com/document/d/1NIktzULNMnaYlhURdQUO0dbIMcXY82uFpgTBR2cIgaU/edit?hl=en_US#.
I would appreciate any help on that.
Thank you in advance.
Albaruthenia
I2B2HIVE.CRC_DB_LOOKUP table, setting the C_DB_DATASOURCE column to
java:QueryToolRDDS for both Demo and Demo2 projects. But when I opened
the Workbench and selected the I2B2 Demo2 project, to my surprise, the
log showed:
2011-07-23 22:12:15,896 INFO
[edu.harvard.i2b2.crc.dao.OracleDAOFactory] Using datasource
java:QueryToolDemoDS
As a result, the application used the data from the I2B2DEMODATA
schema. I went one step further: commented out the QueryToolDemoDS
entry in crc-ds.xml, and restarted JBoss, making sure that
java:QueryToolDemoDS didn't show up in the log any longer. But now the
Workbench opens up with the following error:
2011-07-23 22:22:13,896 INFO
[edu.harvard.i2b2.crc.dao.OracleDAOFactory] Using datasource
java:QueryToolDemoDS
2011-07-23 22:22:13,897 ERROR [STDERR]
javax.naming.NameNotFoundException: QueryToolDemoDS not bound
I wonder why JBoss still tries to use the datasource that doesn't
exist in CRC_DB_LOOKUP? Does it use a cache or something instead of
actually querying the table? That would explain why it doesn't see the
new project (RD) that I added...
Has anybody ever tried to create a new project and point it to a
different Oracle schema rather than I2B2DEMODATA?
Thank you in advance.
On Jul 19, 9:58 am, Albaruthenia <solu...@gmail.com> wrote:
> Good Morning Everybody,
>
> let me briefly introduce myself to the community. My name is Alexander
> Saip, and I work at Vanderbilt University. We have just started our
> pilot project that involves installing and configuring the I2B2 server
> to work with our clinical research data. The installation process was
> a breeze, and we even switched from the local Oracle XE instance to a
> remote RAC cluster. Unfortunately, the next step of setting up a
> separate project for our data wasn't completely successful, as I
Phillips, Lori C.
There is an early step that tells the CRC where the CRC_DB_LOOKUP table
resides.
The jboss conf/crcapp/crc.properties file identifies the DS for the
CRC_DB_LOOKUP table
see queryprocessor.ds.lookup.datasource property.
I am guessing that in your case it is pointing to QueryToolDemoDS.
Rename this to something generic like: CRCBootstrapDS.
Next, the conf/crcapp/CRCApplicationContext.xml file provides a place to define
the dataSource
for the CRCBootstrapDS... Is this entry pointing to the correct
CRC_DB_LOOKUP table (db , uname, password, etc) ?
There are similar files in conf/crcloaderapp/ that you will want to verify
also.
If you are adding a project to the "demo" hive:
For starters I am a little confused why you are reusing the 'Demo' and 'Demo2'
projects as
opposed to creating a new one.
1.You said you created a new datasource QueryToolRDDS, but did you also change
the C_DB_Fullschema
entry for this data source to point to something other than i2b2demodata?
2. Are the original entries for Demo/Demo2 projects still in the CRC_DB_LOOKUP
table?
There should be only one entry in the CRC_DB_LOOKUP for a given domain/project
pair.
Thank you in advance.
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Albaruthenia
datasource to I2B2HIVE.CRC_DB_LOOKUP in the Oracle XE instance on the
I2B2 server, the workbench opens without any errors. Could anybody
kindly explain to me why the application is going to the local Oracle
database instead of the remote one for that specific record, when all
*-ds.xml files in the JBoss 'deploy' directory point to the remote
Oracle instance? Do I have to re-build the CRC and CRC Loader JARs to
fix that?
>
>
> - Show quoted text -
Albaruthenia
I could read yours. Editing the 'HIVE_DS' entity in conf/crcapp/
CRCApplicationContext.xml and 'TestDataSource' and 'LoaderLookupDS' in
conf/crcloaderapp/CRCLoaderApplicationContext.xml apparently did the
trick. There is no 'CRCBootstrapDS' entity in
CRCApplicationContext.xml. I don't see the
queryprocessor.ds.lookup.datasource property in the conf/crcapp/
crc.properties file either and anything of that kind in conf/
crcloaderapp/edu.harvard.i2b2.crc.loader.properties. It looks what I
didn't find is not as important for the application, or is it? I
wonder if there is any documentation on configuring I2B2 that would
explain which files and entries can be customized to reflect the
actual setup?
As for the Demo projects, I decided to migrate them to our Oracle
instance to (1) make sure the I2B2 application can work the same way
it does with the local XE database and (2) let our stakeholders to
play with the application before we get our real data in.
Thanks again.
On Jul 25, 8:51 am, "Phillips, Lori C." <LCPHILL...@PARTNERS.ORG>
wrote:
>
> > Thank you in advance.
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
Phillips, Lori C.
Did you install the hive yourself or are you using the VM image?
Documents can be found on https://www.i2b2.org/software/#documents
Albaruthenia
to Hyper-V). I did read the CRC Installation guide, but since I wasn't
rebuilding the cell, I overlooked the files in the 'conf' directory. I
guess a "Configuration guide" could be helpful for folks like me who
deal with the packaged server.
On Jul 25, 10:12 am, "Phillips, Lori C." <LCPHILL...@PARTNERS.ORG>
wrote:
>
Gul Shahzad Sarwar
I am also trying to make a second project apart from Demo, but no success. Can anyone list step by step procedure to make an i2b2 project or post a document on how to make a project?
Thanks
Gul
Peter Beninato
Hi,
There might be some information in the Install documentation regarding this but at a high level.
The HIVE and PM cells will be shared between your projects.
You need to make some entries in the hive db tables for the cells and each project, so like crc_db_lookup, im_db_lookup, ont_db_lookup, work_db_lookup.
The xml datasource files in …/etc/jboss for these cells, also need to be edited for the new Projects datasources. The datasource name needs to correspond to the c_db_datasource column in these tables.
And then redeployed via running the ANT targets.
This is at a very high level, but I think if you examine the xml datasource files, the tables, and the install documentation, it might be enough to go on.
FYI.
-Peter
From: i2b2-ins...@googlegroups.com [mailto:i2b2-ins...@googlegroups.com]
On Behalf Of Gul Shahzad Sarwar
Sent: Thursday, October 01, 2015 8:22 AM
To: i2b2 Install Help
Cc: mme...@partners.org; sol...@gmail.com
Subject: Re: Creating projects in I2B2
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