When I do an upgrade form my exisiting Plus v3 database, all of the Clinical Diagnosis values show up in the drop down when adding Events to a Collection Protocol. However, on a fresh install that I did locally, those values are missing. I checked the catissue_permissible_value table and the upgraded database has over twice as many rows (64,581) versus the fresh install (32,738). Is there something else I have to load to get these values?
Hi Bob,
I am having the same issue. Clinical Diagnosis drop-down list is empty. How did you fix the issue?
Thanks!
I actually have not fixed it. On our test server, we upgraded from Plus v3.0 and did not have this issue. On my local install on my workstation which was from scratch (fresh database), I have the empty dropdown. I copied the database from test to my local MySQL instance and redeployed the app poiting to it. Now I have the clinical diagnosis list in the dropdown (over 4000 of them). So, the fresh install is not building that list in the permissable values table. I was hoping Krishagni could shed some light on why that is.
Hi @bob_lange/@diya_any ,
We haven’t faced this issue. It seems like something went wrong in the deployment. It would be very helpful if you can share the deployment log. That will help us to know the exact cause.
~Nitesh
@nitesh_marwaha, where does the deployment log get written? Or do I have to do a deploy again and redirect the output to a file?
Sorry @bob_lange , I forgot to mention. Yes you need to run deploy_all again and redirect it to a output file as mentioned below:
For Linux: nohup ant deploy_all (this will redirect the log to nohup.out)
For Windows: ant deploy_all > nohup.out 2 > &1
~Nitesh
@bob_lange, Could you please check that whether the Clinical Diagnosis values are inserted in the catissue_permissible_value table or not. To check please execute the below SQL:
select count () from catissue_permissible_value where public_id like ‘Clinical_Diagnosis_PID’*
~Nitesh
The query returns 63683, so it looks like there are plenty of rows. That makes up the vast majority of values in that table as the total count is 64581. I’ll try to redeploy and post the results.
nohup.out (143.7 KB)
I have attached the deployment log. In looking at it, there are a number of errors. Many seem to be related to liquibase being unable to create indexes, etc. There was also an error related to writing log4j messages (including in the clinical diagnosis step of the deploy).
@nitesh_marwaha, is this what you need?
Yes, Thanks for the log. The error is related to the logger file. But that should not interrupt the clinical diagnosis export.
Could you please let me know the count returned by the below query:
select count (*) from catissue_permissible_value where public_id like ‘Clinical_Diagnosis_PID’
~Nitesh
Yes @diya_any, the count is correct. All the Clinical Diagnosis values got inserted in the database. Also checked the deployment log didn’t find any issue with the deployment.
Regarding the Clinical Diagnosis DropDown, you need to type to get the values. As the count is more that 60K, so these values are not loaded by default on the UI. When the user types it gets the matching values from the database and display on the UI.
Please try this and let us know if you are still facing the issue. It will very helpful if you can share some video or screenshots of the UI where its not loading the values.
BTW which browser version you are using ?
OpenSpecimen supports IE-9, latest version of Safari and FireFox.
~Nitesh
Bob and Nitesh,
I get count as 0.
Thanks,
Diya
In my case it is a fresh install. Do i need to re-deploy the app to get clinical diagnosis values?
We will not be able to comment much if you do not have the deployment log. Since the count is 0 for you, looks like the diagnosis did not get inserted.
Please run deploy_all again and redirect it to a output file as mentioned below:
For Linux: nohup ant deploy_all -Dusername=replace_with_login_name (this will redirect the log to nohup.out)
For Windows: ant deploy_all -Dusername=replace_with_login_name > nohup.out 2 > &1
Please note you will lose your data when you do this, hope this is a test server.
Thanks,
Poornima
Poornima,
I did tried redeploying how ever build failed.
Error: java.sql.SQLException: ORA-00955: name is already used by an existing object. Do i need to drop the objects before re-deploying?
Thanks!
Yes @diya_any, Please drop the existing database and re create it. Then run the deploy_all as specified by Poornima in the previous reply.
~Nitesh
Hi Nitesh,
I have redeployed the application. Still the count is 0. I am attaching log file.
nohup.out (171.6 KB)
Thanks,
Diya
Hi @diya_any,
For oracle, OS uses sqlldr utility to load the clinical diagnosis values. So it seems like the command genereated by OS is not working. Could you please try to run the below command on your OS server:
sqlldr “userName”/“password”@“tnsName” control=’${OS_HOME}\SQL\Permissible_values\CATISSUE_PERMISSIBLE_VALUE.ctl’
Here:
userName: database username
password: database password
tnsName: TNS name
${OS_HOME}: the path where you have decompressed the OS installable.
CATISSUE_PERMISSIBLE_VALUE.ctl file is generated while deployment. So I hope this file will be present in you installable @${OS_HOME}/SQL/Permissible_values/
~Nitesh
Hi Nitesh,
After running the command here is the error message
SQLLoader-500: Unable to open file (${D:\OpenSpecimen_v1.1_Installable_RC
\Permissible_values\CATISSUE_PERMISSIBLE_VALUE.ctl)
SQLLoader-554: error opening file
SQL*Loader-509: System error: The device does not recognize the command.
Thank,
Diya