Atlas - Unable to view characterisation results

SELVA_MUTHU_KUMARAN · October 27, 2020, 9:31am

Hello Everyone,

We are trying to run a cohort characterization analysis. Though the execution is successful, when we try to view the results, it keeps loading forever. This is similar to this post but a different error message

Upon pressing CTRL+SHIFT+I, shows the below

@vineet_jain - Apologies I just saw your post. I also experience something similar. Have you found a solution to this?

Chris_Knoll · October 27, 2020, 2:44pm

I can’t tell, but there does seem to be a problem with the concept name when it is embedded into the HTML as a tooltip. Can you identify the full concept name or concept ID that has the title that looks like ALLEVYN DRESSING 4?

SELVA_MUTHU_KUMARAN · October 28, 2020, 4:04am

Hi @Chris_Knoll,

I am not sure whether i understood you correctly. Are you askibg me for concepts which are similar to Allevyn dressing?

This is what I found in Athena. Not sure whether it helps

https://athena.ohdsi.org/search-terms/terms?query=Allevyn+dressing+4&boosts&page=1

Chris_Knoll · October 28, 2020, 4:37am

I mean something in the concept name is causing some HTML error. Do you see the part in your screenshot where it says ‘invalid token’? And then it shows the value of the toltip binding…something in the HTML is malformed. You could use the chrome DOM inspector to see what the actual HTML element is.

But, looking at your search results, it looks like there are concept names with quotes in them., so looksl ike the problem could be the " in things like" ALLEVYN DRESSING 4"X4".

Chris_Knoll · October 28, 2020, 5:04am

Looks like the fix for this was applied to the 2.8 branch, but possibly not applied back to a hotfix branch: https://github.com/OHDSI/Atlas/pull/2058/files. You can either wait for the 2.8 release to fix this, or the hotfix maintainers can look into making a hotfix release for this.

SELVA_MUTHU_KUMARAN · October 28, 2020, 5:39am

Thanks for your response @Chris_Knoll . Unfortunately am not a developer/don’t have expertise with javascript, Html, etc, so can I seek your help with the below?

When you mean “hotfix maintainers”, should I reach out to anyone in the OHDSI community or should I find help from someone at our side who can address/resolve this specific issue? Should we just make changes to our Atlas prevalencestatconverter.js, conceptset.js and commonutil.js files as shown in this link and restart our ATLAS/WebAPI etc?
from a non developer perspective, do you think just removing the double quotes from my concept names can also help in fixing the issue?

Chris_Knoll · October 28, 2020, 5:50am

If you can make those small edits in the Atlas javascript files, then that’s the simplest approach. You won’t need to restart WebAPI, just refresh your browser. I don’t recommend making any edits to the vocabulary.

SELVA_MUTHU_KUMARAN · October 28, 2020, 5:52am

Fantastic. Thanks @Chris_Knoll

hui_xing_tan · November 6, 2020, 4:13am

Hi,

We are facing similar issues in viewing both characterisation and cohort pathway results. While the execution is successful, the counts returned are ‘0’, as shown below:

However, when running a separate query via sql it shows that there is a set of people who fulfil the criteria for the cohorts in the analysis.

Upon pressing CTRL+SHIFT+I, the error message given is as follows:

Sreemanee · November 9, 2020, 4:11am

Hi @Chris_Knoll,

I work with Hui Xing who has a follow up question on this topic. We would be most grateful if you had some advice for us with regards to the errors we are seeing please.

Thank you very much!

Best wishes,
Sreemanee

Chris_Knoll · November 9, 2020, 4:15am

I’m sorry, but I can’t tell from your errors. I know this is unrelated, but why are you getting a 500 response when going to: /WebAPI/notifications?

hui_xing_tan · November 9, 2020, 10:55am

Thanks @Chris_Knoll for the reply

I’m not too sure about the 500 Error response, however, it seems to appear no matter which page of our local Atlas we open, and is always referring to this webpage: http://localhost:8080/WebAPI/notifications

Typical error messages we encounter when opening an atlas webpage (or clicking refresh):

Typical%20error%20msg

If we type http://localhost:8080/WebAPI/notifications into the url bar, this is what we see:

Currently the version that we’ve installed is Atlas v2.7.0 and webapi 2.7.0 - could this be something in previous versions of Atlas and will it help if we installed a later version? Sorry that we are not too sure how to debug or interpret the message as we do not have experience with http.

Going back to the characterisation and cohort pathways result, one thing is that while the cohort definitions tables are populated after running the execution, the concept sets are empty. Is this expected?

Cohort Definitions (cohorts are there)

Concept Sets (concept sets are absent)

Previously we also had issues creating concept sets which we are still not able to resolve (see here), so I am not too sure if this could be related and it might help in the debugging of this issue. Any ideas?

Thanks again!

Best Regards,
Hui Xing

Konstantin_Yaroshove · November 9, 2020, 1:57pm

I recommend to share here stack trace for error from Tomcat logs. It’s not clear what happens. But the problem happens on WebAPI side.

hui_xing_tan · November 10, 2020, 3:00pm

Thank you, @Konstantin_Yaroshove.

Could you advise how we could get the stack trace for error from Tomcat logs? I found a couple of files on Tomcat 9.0/logs folder.

Thanks

Best regards,
Hui Xing

hui_xing_tan · November 16, 2020, 7:36am

Hi all,

Just to update that we had resolved this issue by first fixing another issue with the concept sets mentioned in this post.

Thanks for the help!

Regards,
Hui Xing