Atlas Profiles can't find person

dramacloak · January 29, 2019, 9:49pm

{“methodName”:“run”,“fileName”:null,“lineNumber”:-1,“className”:“java.lang.Thread”,“nativeMethod”:false}],“serverErrorMessage”:{“message”:“relation “cdm.concept” does not exist”,“file”:“parse_relation.c”,“table”:null,“schema”:null,“position”:88,“severity”:“ERROR”,“sqlstate”:“42P01”,“column”:null,“where”:null,“internalQuery”:null,“routine”:“parserOpenTable”,“constraint”:null,“detail”:null,“datatype”:null,“hint”:null,“internalPosition”:0,“line”:1159},“errorCode”:0,“nextException”:null,“sqlstate”:“42P01”,“localizedMessage”:“ERROR: relation “cdm.concept” does not exist\n Position: 88”,“message”:“ERROR: relation “cdm.concept” does not exist\n Position: 88”,“suppressed”:[]},“localizedMessage”:“PreparedStatementCallback; bad SQL grammar [select gender_concept_id, year_of_birth, concept_name as gender\nfrom cdm.person p\njoin cdm.concept c on p.gender_concept_id = c.concept_id\nwhere person_id = ?\n]; nested exception is org.postgresql.util.PSQLException: ERROR: relation “cdm.concept” does not exist\n Position: 88”,“suppressed”:[]},“headers”:{“id”:“d34c5c80-80fe-2bda-6159-785abb1c774f”,“timestamp”:1548798527367}}

For some reason, Atlas profiles appears to be looking for the concept table in the cdm schema instead of in the vocab schema. How do I fix this? Thanks.

Chris_Knoll · January 29, 2019, 11:59pm

The notion of having separate schemas for vocabulary and CDM tables is relatively recent, and introduces a bit of confusion when talking about the cdm schema.

Is there any reason you can’t put the vocabulary tables in the CDM schema? Failing that, I would create views in your cdm schema that point over to your separate vocabulary schema.

dramacloak · January 31, 2019, 8:08pm

Alright, I created some views for the vocabulary in the CDM schema but am still not seeing anyone in profiles. It’s still getting a "Failed to load resource: server responded with a status of 500 () message linked to: http://localhost:8080/WebAPI/OHDSI/person/1?cohort=0

{“payload”:{“cause”:null,“stackTrace”:[{“methodName”:“compareTo”,“fileName”:null,“lineNumber”:-1,“className”:“java.sql.Timestamp”,“nativeMethod”:false},{“methodName”:“compareTo”,“fileName”:null,“lineNumber”:-1,“className”:“java.sql.Timestamp”,“nativeMethod”:false},{“methodName”:“lambda$comparing$77a9974f$1”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.Comparator”,“nativeMethod”:false},{“methodName”:“lambda$minBy$0”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.function.BinaryOperator”,“nativeMethod”:false},{“methodName”:“accept”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.stream.ReduceOps$2ReducingSink”,“nativeMethod”:false},{“methodName”:“forEachRemaining”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.ArrayList$ArrayListSpliterator”,“nativeMethod”:false},{“methodName”:“copyInto”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.stream.AbstractPipeline”,“nativeMethod”:false},{“methodName”:“wrapAndCopyInto”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.stream.AbstractPipeline”,“nativeMethod”:false},{“methodName”:“evaluateSequential”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.stream.ReduceOps$ReduceOp”,“nativeMethod”:false},{“methodName”:“evaluate”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.stream.AbstractPipeline”,“nativeMethod”:false},{“methodName”:“reduce”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.stream.ReferencePipeline”,“nativeMethod”:false},{“methodName”:“min”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.stream.ReferencePipeline”,“nativeMethod”:false},{“methodName”:“lambda$getPersonProfile$4”,“fileName”:“PersonService.java”,“lineNumber”:138,“className”:“org.ohdsi.webapi.service.PersonService”,“nativeMethod”:false},{“methodName”:“orElseGet”,“fileName”:null,“lineNumber”:-1,“className”:“java.util.Optional”,“nativeMethod”:false},{“methodName”:“getPersonProfile”,“fileName”:“PersonService.java”,“lineNumber”:137,“className”:“org.ohdsi.webapi.service.PersonService”,“nativeMethod”:false},{“methodName”:“invoke”,“fileName”:null,“lineNumber”:-1,“className”:“sun.reflect.GeneratedMethodAccessor302”,“nativeMethod”:false},{“methodName”:“invoke”,“fileName”:null,“lineNumber”:-1,“className”:“sun.reflect.DelegatingMethodAccessorImpl”,“nativeMethod”:false},{“methodName”:“invoke”,“fileName”:null,“lineNumber”:-1,“className”:“java.lang.reflect.Method”,“nativeMethod”:false},{“methodName”:“invoke”,“fileName”:“ResourceMethodInvocationHandlerFactory.java”,“lineNumber”:81,“className”:“org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1”,“nativeMethod”:false},{“methodName”:“run”,“fileName”:“AbstractJavaResourceMethodDispatcher.java”,“lineNumber”:144,“className”:“org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1”,“nativeMethod”:false},{“methodName”:“invoke”,“fileName”:“AbstractJavaResourceMethodDispatcher.java”,“lineNumber”:161,“className”:“org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher”,“nativeMethod”:false},{“methodName”:“doDispatch”,“fileName”:“JavaResourceMethodDispatcherProvider.java”,“lineNumber”:205,“className”:“org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker”,“nativeMethod”:false},{“methodName”:“dispatch”,“fileName”:“AbstractJavaResourceMethodDispatcher.java”,“lineNumber”:99,“className”:“org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher”,“nativeMethod”:false},{“methodName”:“invoke”,“fileName”:“ResourceMethodInvoker.java”,“lineNumber”:389,“className”:“org.glassfish.jersey.server.model.ResourceMethodInvoker”,“nativeMethod”:false},{“methodName”:“apply”,“fileName”:“ResourceMethodInvoker.java”,“lineNumber”:347,“className”:“org.glassfish.jersey.server.model.ResourceMethodInvoker”,“nativeMethod”:false},{“methodName”:“apply”,“fileName”:“ResourceMethodInvoker.java”,“lineNumber”:102,“className”:“org.glassfish.jersey.server.model.ResourceMethodInvoker”,“nativeMethod”:false},{“methodName”:“run”,“fileName”:“ServerRuntime.java”,“lineNumber”:326,“className”:“org.glassfish.jersey.server.ServerRuntime$2”,“nativeMethod”:false},{“methodName”:“call”,“fileName”:“Errors.java”,“lineNumber”:271,“className”:“org.glassfish.jersey.internal.Errors$1”,“nativeMethod”:false},{“methodName”:“call”,“fileName”:“Errors.java”,“lineNumber”:267,“className”:“org.glassfish.jersey.internal.Errors$1”,“nativeMethod”:false},{“methodName”:“process”,“fileName”:“Errors.java”,“lineNumber”:315,“className”:“org.glassfish.jersey.internal.Errors”,“nativeMethod”:false},{“methodName”:“process”,“fileName”:“Errors.java”,“lineNumber”:297,“className”:“org.glassfish.jersey.internal.Errors”,“nativeMethod”:false},{“methodName”:“process”,“fileName”:“Errors.java”,“lineNumber”:267,“className”:“org.glassfish.jersey.internal.Errors”,“nativeMethod”:false},{“methodName”:“runInScope”,“fileName”:“RequestScope.java”,“lineNumber”:317,“className”:“org.glassfish.jersey.process.internal.RequestScope”,“nativeMethod”:false},{“method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Chris_Knoll · January 31, 2019, 11:29pm

I can’t quite tell where the problem actually happens, but this part of the stack trace is a hint:

This is where it’s trying to get the patient level data out of the PersonService, however, looking at the requested URL: a cohort_id of 0 seems a little strange (IDs should start at 1)

Are you certain that there is a cohort_id = 0 that contains a subject_id = 1 in it?

dramacloak · February 1, 2019, 10:07pm

There isn’t a cohort_id = 0. The only cohort_id I have is 5 at the moment. My subject_id’s in the person table start at 1. I’m not sure why it’s trying to pull from a non-existent cohort?

Chris_Knoll · February 1, 2019, 10:22pm

Do you get the same exception when you take the ?cohort_id param off of the url?

dramacloak · February 1, 2019, 10:30pm

Yes. I wouldn’t think cohort would have anything to do with the profiles page, as it is based on the source data set rather than a particular cohort definition. At least there is no functionality to change the cohort that you’re interested in on the profiles page.

Chris_Knoll · February 1, 2019, 11:08pm

So, based on the stack trace, the issue is around this line of code here (assuming you are running in version 2.6):

github.com

OHDSI/WebAPI/blob/master/src/main/java/org/ohdsi/webapi/service/PersonService.java#L135


    item.endDate = resultSet.getTimestamp("cohort_end_date");
    item.cohortDefinitionId = resultSet.getLong("cohort_definition_id");
    
    profile.cohorts.add(item);
    return null;
  }
});




LocalDateTime cohortStartDate = null;
Optional<CohortPerson> cohort = cohortId > 0 ? profile.cohorts.stream().filter(c -> c.cohortDefinitionId.equals(cohortId)).findFirst() :
        Optional.empty();
cohortStartDate = cohort.map(c -> c.startDate.toLocalDateTime()).orElseGet(() ->
  profile.records.stream().min(Comparator.comparing(c -> c.startDate))
    .map(r -> r.startDate.toLocalDateTime()).orElse(null));


		if (cohortStartDate != null && profile.yearOfBirth > 0) {
			profile.ageAtIndex = cohortStartDate.getYear() - profile.yearOfBirth;
		}
		
for(PersonRecord record : profile.records){

And, just FYI, you can open the patient profile int he context of a cohort, however it does check for a cohort_id > 0 so, for purposes of the URL you wen tto, it should ignore the cohort paramater.

Unfortunately, I’m not as familiar with the profile/PersonService as other parts of the code. I can tell you that this statement:

profile.records.stream().min(Comparator.comparing(c -> c.startDate))

something in there is NULL. I’m guessing it’s the profile.records field. What you can do is try to invoke the query directly on your database, starting with this one:

select gender_concept_id, year_of_birth, concept_name as gender from @tableQualifier.person p join @tableQualifier.concept c on p.gender_concept_id = c.concept_id where person_id = @personId

(found from: https://github.com/OHDSI/WebAPI/blob/master/src/main/resources/resources/person/sql/personInfo.sql)

start with that one, since that’s the starting point for all the additional fetches for the patient level data. Let us know the result.

Akshay · April 9, 2020, 2:52pm

Hi,

I was also facing similar issue (but not the same) during characterization where Atlas looks for cdm.concept table whereas my concept table is in vocab schema. Since the error message is clear as “cdm.concept” doesn’t exist, I resolved it by moving concept table. But may I kindly check with you on below items?

Can I have a copy of concept table only in cdm schema and leave the original in vocab schema as is (without deleting)?
Though I didn’t have any error messages about other tables (might be because the code is looking at vocab schema for other tables), do I still have to copy all vocabulary tables (concept_synonym, concept_relationship, relationship, etc) to cdm schema as well?
If I copy only concept table to cdm schema, can it result in any performance issues? Because I feel the query runs for a longer time. So thought of checking with you.

Can I kindly request you to help me with this?