Some errors using Atlas after installation

[alicesaw (alice)]

Hi @pavgra,

used the following command:

git clone https://github.com/OHDSI/WebAPI.git

[pavgra (Pavel Grafkin)]

@alicesaw, this command is pulling the latest development version. To get 2.6.0 you need to:

git clone --branch v2.6.0 https://github.com/OHDSI/WebAPI.git

[alicesaw (alice)]

Thank you. I will give it a try. Does Atlas 2.6.0 and WebAPI 2.6.0 work with CDM v5?

[Chris_Knoll]

Yes.

[alicesaw (alice)]

Thanks much to all for help.
I managed to build the .war file for WebAPI 2.6.0
Deployed WebAPI 2.6.0 and Atlas 2.6.0 to Tomcat and it is running now, can do vocab search, view profiles and view data sources reports.

In addition I have these issues/queries still unresolved, if anyone has advice I would be most grateful:

@alicesaw

Under the Data Sources > Death, some of the charts are not showing

image.png1632x866 405 KB

@alicesaw

But I am not sure how to test if the rest of the sections (concept Sets, cohort Definitions, characterisations, cohort pathways, incidence rates, estimation, prediction) are correctly set up and would be grateful for advice on how to go about checking.

Thank you so much for all your help

[Chris_Knoll]

For #1, hard to tell exactly what the issue is here: looks like the data returned didn’t have any of the required fields in it, so the errors are saying ‘I’m looking for a Y_PREVALENCE_1000PP field, but it’s not here!’ and then throws an error. I don’t know if that means your DEATH table has no values in it, there was a problem running Achilles, etc.

I’ll try to track down the query that’s returning the death report data, and maybe you can execute it manually on your environment and we can see about what the real issue is.

For #2: first step is to create a cohort. Go to cohort Definitions, click ‘New Cohort’ and off you go. If you’re not familiar with the cohort definition UI, you’re not alone! I believe there are videos that demonstrate usage, I can find them if you need them. If you already know how cohort definitions work, then just create a cohort definition, click the generate button, and look for non-zero counts in the summary. Happy to walk you through it in more detail if you need.

[alicesaw (alice)]

Thanks @Chris_Knoll

I’ll try to track down the query that’s returning the death report data, and maybe you can execute it manually on your environment and we can see about what the real issue is.

Sure, I can run the query.

For #2: first step is to create a cohort. Go to cohort Definitions, click ‘New Cohort’ and off you go. If you’re not familiar with the cohort definition UI, you’re not alone! I believe there are videos that demonstrate usage, I can find them if you need them. If you already know how cohort definitions work, then just create a cohort definition, click the generate button, and look for non-zero counts in the summary. Happy to walk you through it in more detail if you need.

Yes, the videos to show how to create cohort will be helpful as we are starting from scratch (not familiar with the UI)

Best regards,
-Alice

[SELVA_MUTHU_KUMARAN (Selva)]

Hello Guys,

Just restarting this thread as I was facing some issues after Atlas installaton. FYI, we were able to generate the cohort successfully in Atlas and have imported the same cohort and feature paramters under “Characterization” tab of atlas

However, Am facing some issue while generating reports under “Characterization” tab of Atlas. As you can see from the below screenshot that “Executions” are complete but when I click on “View latest results” or “reports”, I don’t see anything. It just keeps loading. Can you please help?

In addition, under what circumstances can the generation status be “Failed”? Because, it fails at times as well. So would like to understand that.

Thanks
Selva