Error seen trying to run search in Atlas

greshje.gmail · October 11, 2023, 2:57am

I’m getting an the error shown below trying to do a concept search in a new Atlas installation. I’m not sure what is different about this instance (it should be the same as other instances I’ve created). I am able to query the concept and vocabulary tables using the information in the source_daimon tables.

I’m running WebApi and Atlas v2.12.0

2023-10-11 02:36:39.911 ERROR http-nio-8080-exec-4 org.ohdsi.webapi.util.GenericExceptionMapper - [] - java.lang.NullPointerException
        at org.ohdsi.webapi.service.VocabularyService.getVocabularies(VocabularyService.java:1105)

Subsequently I get the following errors:

2023-10-11 02:37:12.022 WARN taskExecutor-1 org.ohdsi.webapi.achilles.service.AchillesCacheService - [] - Cannot cache drilldown reports for DATABRICKS_COVID_OHDSI_PROD, domain condition. Check if result schema contains achilles results tables.
2023-10-11 02:37:32.939 WARN taskExecutor-1 org.ohdsi.webapi.achilles.service.AchillesCacheService - [] - Cannot cache drilldown reports for DATABRICKS_COVID_OHDSI_PROD, domain observation. Check if result schema contains achilles results tables.
2023-10-11 02:37:36.546 WARN taskExecutor-1 org.ohdsi.webapi.achilles.service.AchillesCacheService - [] - Cannot cache drilldown reports for DATABRICKS_COVID_OHDSI_PROD, domain conditionera. Check if result schema contains achilles results tables.

The entire Tomcat output is attached.
errors.txt (81.2 KB)

greshje.gmail · October 11, 2023, 6:09am

I believe this might be due to there not being any records in cdm_source. I cannot connect to the host of my test system right now but will do so and confirm if this is the cause or not when I can.
— EDIT --------
I populated the cdm_source table, rebuilt webapi and atlas, and re-ran Achilles. Now I’m getting this error:

2023-10-11 06:02:58.660 INFO Finalizer com.simba.spark.jdbc42.internal.apache.commons.logging.impl.Jdk14Logger - [] - I/O exception (java.net.SocketException) caught when processing request to {s}->https://nachc-databricks.cloud.databricks.com:443: Socket closed
2023-10-11 06:02:58.661 INFO Finalizer com.simba.spark.jdbc42.internal.apache.commons.logging.impl.Jdk14Logger - [] - Retrying request to {s}->https://nachc-databricks.cloud.databricks.com:443
2023-10-11 06:03:29.249 WARN taskExecutor-1 org.ohdsi.webapi.achilles.service.AchillesCacheService - [] - Cannot cache drilldown reports for DATABRICKS_COVID_OHDSI_PROD, domain condition. Check if result schema contains achilles results tables.
2023-10-11 06:03:56.804 ERROR http-nio-8080-exec-7 org.ohdsi.webapi.util.GenericExceptionMapper - [] - java.lang.NullPointerException
        at org.ohdsi.webapi.service.VocabularyService.getVocabularies(VocabularyService.java:1105)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

Full output is attached:
errors2.txt (64.6 KB)

greshje.gmail · October 11, 2023, 4:35pm

Huzzah,

It looks like this was due to a bad value for the vocabulary version in the cdm_source table. I was able to fix using the Configuration tab in atlas and selecting the available vocabulary version.