i2b2 1.7 demo project - gender and vital status breakdowns return zero

[Saj]

Hi All

I have successfully installed i2b2 1.7.

Fresh New-install :
---------------------
Ubuntu 12.10 64bit
Postgresql 9.1
Java 1.7.0_17
JBOSS 7.1.1 Final

I can't seem to get the Gender patient breakdown and Vital Status patient breakdown to work for the demo project, if you try to create a cohort on Gender, I get 133 patients, but no breakdown.

Patient Set for "Gender@15:14:57"
Number of patients for "Gender@15:14:57"
patient_count: 133

Vital Status patient breakdown for "Gender@15:14:57"
Deceased: 0
Deferred: 0
Living: 0
Not recorded: 0

Gender patient breakdown for "Gender@15:14:57"
Female: 0
Male: 0
Unknown: 0

My QT_QUERY_RESULT_TYPE table is populated as normal. So are QT_BREAKDOWN_PATH and TABLE_ACCESS. After all it is the demo data, unchanged.

Can I just ask, if the breakdowns work for anyone else after a fresh install ?

Attached is my server.log

My install is available at http://i2b2pg.cloudapp.net/i2b2/webclient/

Thanks

Saj

[Saj]

Hi Guys, did another reinstall of i2b2 1.7 postgres and its the same.

Can anyone confirm that the gender patient breakdown and vital status patient breakdown work for the demo data after a fresh install of i2b2 postgres ?

Thanks

Saj

[Natus]

Hello Saj,

I have exactly the same behavior on ubuntu 12.04 / pgsql 9.3

With oracle they are no problem. (https://www.i2b2.org/webclient/)

Looking at it, and post here if I solve it. 

Thanks

[Natus]

Hello Saj,

Works know  :

just add to ./src/server/edu/harvard/i2b2/crc/dao/setfinder/QueryResultGenerator.java 

line 141 (after String dimCode = this.getDimCodeInSqlFormat(conceptType);)

                if(serverType.equalsIgnoreCase("postgresql")){

                                        dimCode = dimCode.replace("\\","\\\\");

                                }

and re-run ant-compile

--------------------------------------------

Explaination : (Could you please explain me how you enter in debug mode from jboss 7.x ? would help me to debug)

From your log, line 13122 : query  select count(distinct PATIENT_NUM) as item_count  from i2b2demodata.observation_fact where  patient_num in (select patient_num from DX )  and concept_cd IN (select concept_cd from i2b2demodata.concept_dimension   where concept_path LIKE '\i2b2\Demographics\Vital Status\Deceased\%')  FAILS

when double "\\" works   

select count(distinct PATIENT_NUM) as item_count  from i2b2demodata.observation_fact where  patient_num in (select patient_num from DX )  and concept_cd IN (select concept_cd from i2b2demodata.concept_dimension   where concept_path LIKE '\\i2b2\\Demographics\\Vital Status\\Deceased\\%')

[melek somai]

Hey all,

Thanks Saj for the code. I have actually had the same issue. I solved the issue using a similar code. In order to get yours working, you have to reverse the replace statement as following:

line 141     if(serverType.equalsIgnoreCase("postgresql")){

                                        dimCode = dimCode.replace("\\\\","\\");

                                }   

I hope that this will be helpful for other users in the community.

regards,

Melek