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Atlas not showing Person graph

Developers
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#1

Hey everyone,

Another issue on my end :slight_smile: So I have WebAPI and Atlas running locally. I ran the Synthea 3.0.0 to generate a test CDM dataset. It looks to have created only 1 record in my person table. In Atlas, I can go to ‘Profiles’ and search for this person using id of 1 and see this person and some of their data in a graph. I can also search and browse the vocabulary in Atlas for concepts.

However, whenever I go to Data Sources and select ‘My_CDM’ all of the dropdowns except for ‘Data Density’ appear to be empty and not showing any sort of graphs. In looking at the catalina.out for webAPI, I do not see any errors occurring when I try to visit these pages. Am I supposed to first create a Cohort Definition?

In running Achilles, I did run into this error/warning but thought it might have just been a disconnection error/warning. It appeared to execute a lot of SQL commands. However, I’m not 100% sure how to verify that Achilles ran successfully.

Executing SQL took 0.0294 secs
[Total Runtime] 21.074821 secs
[Total Runtime] 21.074821 secs
An error occurred while the ‘DatabaseConnector’ package was updating the RStudio Connections pane:
Error in NULL: host must be a single element of type ‘character’
If necessary, these warnings can be squelched by setting options(rstudio.connectionObserver.errorsSuppressed = TRUE)

Any idea what I’m missing? Thanks all!

#2

I found this issue being reported here:https://github.com/OHDSI/Achilles/issues/728

I was able to run the script without any error and was finally able to see the graph get populated. Although, I did try many things so not sure going to 1.7.0 was my sole issue here. With Synthea 3.0.0 I only got 1 person in my CDM Person table, and I believe I needed to add smallCellCount to account for this.

Anyways, I rolled back to Achilles 1.7.0 using this remotes::install_github("OHDSI/Achilles@v1.7.0") and I was able to run the script without the error occurring.

Another issue that I haven’t looked into yet is that in the webapi schema and achilles_cache schema. It was holding onto empty results from my failed Achilles attempts for all the records. Once I deleted the records from achilles_cache and visited the reports again in Atlas it created new records with data.

1 Like
#3

Thank you for coming back and describing your experience. It helps other people learn and possibly help people avoid similar issues in the future.

t