Linux Install Failing in setting up umls_aui_fword table

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Create UMLS MySql DB
2. Install ytex 0.5 per instructions
3. Script hangs at the setting up umls_aui_fword table. I have given it >2 days 
to run. When looking at mysql process list, the ytex user account only logs in 
once to create the table and doesn't login again. So the mysql settings are 
correct as the script can access the db but I can't seem to get it to progress.

What version of the product are you using? On what operating system?
0.5 on RedHat Enterprise Linux 6.2

Please provide any additional information below.

Of Note, I sucessfully installed this on Win7 machine without issue but I need 
this on the Linux server for further testing.

Any help would be greatly appreciated.

Original issue reported on code.google.com by snuf...@snuffy2.com on 13 Jan 2012 at 3:48

[GoogleCodeExporter]

Hello,

Can you please obtain a thread dump on the ytex java process that is launched 
in the umls_aui_fword setup?  Try ps -ef | grep java to get the list of java 
processes, and then to a kill -quit <pid>.  This will cause the jvm to spit out 
a thread dump.  Then post the thread dump.

Additional debugging: 
* see if anything is being added to umls_aui_fword:
select count(*) from umls_aui_fword
* turn up debugging for SetupAuiFirstWord, in ytex\config\desc\log4j.properties 
make following change
log4j.logger.ytex.tools.SetupAuiFirstWord=DEBUG

Original comment by vnga...@gmail.com on 18 Jan 2012 at 9:31

[GoogleCodeExporter]

Sorry, for the belated reply. Got sidetracked and then could not really figure 
out how to get a thread dump as kill -quit with the PID did not work.
Used jstack for a thread dump and I hope that's  ok. File is attached.
Added the line to log4j.properties
There are 0 rows in the umls_aui_fword table, BUT it is being created by the 
script each time.

Original comment by snuf...@snuffy2.com on 10 Feb 2012 at 6:40

Attachments:

• ytex_trace.txt

[GoogleCodeExporter]

The thread dump is unfortunately for the ant java process, not for the 
SetupAuiFirstWord java process, so there is no useful information there.

In v0.5 we used the mysql command line client to run sql scripts, and jdbc to 
load the umls_aui_fword table.  There is most probably a problem with the jdbc 
url - this is why running the scripts works, but running SetupAuiFirstWord 
fails.

In v0.6 we use jdbc for the entire setup, and we check the jdbc connection 
before attempting setup, so this problem will be caught much earlier.

Original comment by vnga...@gmail.com on 28 Mar 2012 at 7:53

• Changed state: Fixed