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No Data in Atlas and Vocab Version missing


(Ambuj) #1

Hello,

I was able to run Achilles successfully in my environment, I am on CentOS, postgresql db, nginx as a webserver.

But when I deployed Atlas, I do not see any data or Achilles reports showing up, its showing all the boxes as NO DATA and the configuration part do not show with vocabulary version.
I tried to run http://localhost:8080/WebAPI/vocabulary/vocab/info and I get the following
{“payload”:{“cause”:null,“stackTrace”:[{“methodName”:“getInfo”,“fileName”:“VocabularyService.java”,“lineNumber”:848,“className”:“org.ohdsi.webapi.service.VocabularyService”,“nativeMethod”:false},{“methodName”:“invoke0”,“fileName”:“NativeMethodAccessorImpl.java”,“lineNumber”:-2,“className”:“sun.reflect.NativeMethodAccessorImpl”,“nativeMethod”:true},{“methodName”:“invoke”,“fileName”:“NativeMethodAccessorImpl.java”,“lineNumber”:62,“className”:“sun.reflect.NativeMethodAccessorImpl”,“nativeMethod”:false},{“methodName”:“invoke”,“fileName”:“DelegatingMethodAccessorImpl.java”,“lineNumber”:43,“className”:“sun.reflect.DelegatingMethodAccessorImpl”,“nativeMethod”:false},{“methodName”:“invoke”,“fileName”:“Method.java”,“lineNumber”:498,“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},{“methodName”:“process”,“fileName”:“ServerRuntime.java”,“lineNumber”:305,“className”:“org.glassfish.jersey.server.ServerRuntime”,“nativeMethod”:false},{“methodName”:“handle”,“fileName”:“ApplicationHandler.java”,“lineNumber”:1154,“className”:“org.glassfish.jersey.server.ApplicationHandler”,“nativeMethod”:false},{“methodName”:“serviceImpl”,“fileName”:“WebComponent.java”,“lineNumber”:473,“className”:“org.glassfish.jersey.servlet.WebComponent”,“nativeMethod”:false},{“methodName”:“service”,“fileName”:“WebComponent.java”,“lineNumber”:427,“className”:“org.glassfish.jersey.servlet.WebComponent”,“nativeMethod”:false},{“methodName”:“service”,“fileName”:“ServletContainer.java”,“lineNumber”:388,“className”:“org.glassfish.jersey.servlet.ServletContainer”,“nativeMethod”:false},{“methodName”:“service”,“fileName”:“ServletContainer.java”,“lineNumber”:341,“className”:“org.glassfish.jersey.servlet.ServletContainer”,“nativeMethod”:false},{“methodName”:“service”,“fileName”:“ServletContainer.java”,“lineNumber”:228,“className”:“org.glassfish.jersey.servlet.ServletContainer”,“nativeMethod”:false},{“methodName”:“internalDoFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:303,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:208,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“WsFilter.java”,“lineNumber”:52,“className”:“org.apache.tomcat.websocket.server.WsFilter”,“nativeMethod”:false},{“methodName”:“internalDoFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:241,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:208,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“ProxiedFilterChain.java”,“lineNumber”:61,“className”:“org.apache.shiro.web.servlet.ProxiedFilterChain”,“nativeMethod”:false},{“methodName”:“executeChain”,“fileName”:“AdviceFilter.java”,“lineNumber”:108,“className”:“org.apache.shiro.web.servlet.AdviceFilter”,“nativeMethod”:false},{“methodName”:“doFilterInternal”,“fileName”:“AdviceFilter.java”,“lineNumber”:137,“className”:“org.apache.shiro.web.servlet.AdviceFilter”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“OncePerRequestFilter.java”,“lineNumber”:125,“className”:“org.apache.shiro.web.servlet.OncePerRequestFilter”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“ProxiedFilterChain.java”,“lineNumber”:66,“className”:“org.apache.shiro.web.servlet.ProxiedFilterChain”,“nativeMethod”:false},{“methodName”:“executeChain”,“fileName”:“AbstractShiroFilter.java”,“lineNumber”:449,“className”:“org.apache.shiro.web.servlet.AbstractShiroFilter”,“nativeMethod”:false},{“methodName”:“call”,“fileName”:“AbstractShiroFilter.java”,“lineNumber”:365,“className”:“org.apache.shiro.web.servlet.AbstractShiroFilter$1”,“nativeMethod”:false},{“methodName”:“doCall”,“fileName”:“SubjectCallable.java”,“lineNumber”:90,“className”:“org.apache.shiro.subject.support.SubjectCallable”,“nativeMethod”:false},{“methodName”:“call”,“fileName”:“SubjectCallable.java”,“lineNumber”:83,“className”:“org.apache.shiro.subject.support.SubjectCallable”,“nativeMethod”:false},{“methodName”:“execute”,“fileName”:“DelegatingSubject.java”,“lineNumber”:383,“className”:“org.apache.shiro.subject.support.DelegatingSubject”,“nativeMethod”:false},{“methodName”:“doFilterInternal”,“fileName”:“AbstractShiroFilter.java”,“lineNumber”:362,“className”:“org.apache.shiro.web.servlet.AbstractShiroFilter”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“OncePerRequestFilter.java”,“lineNumber”:125,“className”:“org.apache.shiro.web.servlet.OncePerRequestFilter”,“nativeMethod”:false},{“methodName”:“internalDoFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:241,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:208,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“executeChain”,“fileName”:“AdviceFilter.java”,“lineNumber”:108,“className”:“org.apache.shiro.web.servlet.AdviceFilter”,“nativeMethod”:false},{“methodName”:“doFilterInternal”,“fileName”:“AdviceFilter.java”,“lineNumber”:137,“className”:“org.apache.shiro.web.servlet.AdviceFilter”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“OncePerRequestFilter.java”,“lineNumber”:125,“className”:“org.apache.shiro.web.servlet.OncePerRequestFilter”,“nativeMethod”:false},{“methodName”:“internalDoFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:241,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:208,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilterInternal”,“fileName”:“RequestContextFilter.java”,“lineNumber”:99,“className”:“org.springframework.web.filter.RequestContextFilter”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“OncePerRequestFilter.java”,“lineNumber”:107,“className”:“org.springframework.web.filter.OncePerRequestFilter”,“nativeMethod”:false},{“methodName”:“internalDoFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:241,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:208,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilterInternal”,“fileName”:“HttpPutFormContentFilter.java”,“lineNumber”:105,“className”:“org.springframework.web.filter.HttpPutFormContentFilter”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“OncePerRequestFilter.java”,“lineNumber”:107,“className”:“org.springframework.web.filter.OncePerRequestFilter”,“nativeMethod”:false},{“methodName”:“internalDoFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:241,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilter”,“fileName”:“ApplicationFilterChain.java”,“lineNumber”:208,“className”:“org.apache.catalina.core.ApplicationFilterChain”,“nativeMethod”:false},{“methodName”:“doFilterInternal”,“fileName”:“HiddenHttpMethodFilter.java”,“lineNumber”:81,“className”:“org.springframework.web.filter.HiddenHttpMethodFilter”,“nativeMethod”:false},{“me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Need help so it shows correct version of it.
Source and Source Daimon configuration are as follows:
1 “OHDSI” “omop_cdm” “jdbc:postgresql://localhost:5432/omop_cdm?user=omopuser&password=omopuser” “postgresql”

Source_Daimon:
3 1 2 “results” 2
1 1 0 “omop_cdm” 1
2 1 1 “omop_cdm” 0

Also attached are the screenshot for Atlas window.

I am really stuck here, I tried removing all the results table and rebuilding them.Restarting webserver too. Not able to identify where the problem is, however Achilles worked fine.

Need urgent help.

Thank you for reading the long post, I believe this will help other users to figure out the solution if they get stuck somewhere.


(Daniel Lima) #2

Hi, what is there in your omop_cdm.omop_cdm schema?

$ psql omop_cdm postgres
omop_cdm=# SELECT * FROM omop_cdm.vocabulary LIMIT 5;

For instance, my database is:

incor_cdm=# select * from cdm5.vocabulary limit 5;
    vocabulary_id     |   vocabulary_name    |                              vocabulary_reference                               | vocabulary_version | vocabulary_concept_id
----------------------+----------------------+---------------------------------------------------------------------------------+--------------------+----------------------
 Cohort Type          | OMOP Cohort Type     | OMOP generated                                                                  |                    |              44819234
 Cost Type            | OMOP Cost Type       | OMOP generated                                                                  |                    |                  5029
 Death Type           | OMOP Death Type      | OMOP generated                                                                  |                    |              44819135
 UB04 Typ bill        | UB04 Typ bill        | https://ushik.ahrq.gov/ViewItemDetails?&system=apcd&itemKey=196987000           |                    |                 32044
 UB04 Point of Origin | UB04 Point of Origin | https://www.resdac.org/cms-data/variables/Claim-Source-Inpatient-Admission-Code |                    |                 32045
(5 rows)

(Ambuj) #3

@limadm
yes, I have the same entries in vocabulary.


(Sarath Manikonda) #4

@ambuj
Were you able to resolve the issues related to Vocabulary data?

In the source_daimon table, have the priority of all the 3 entries as 0. That’s the only thing I am able to see. Update the records and try again.


(Ambuj) #5

Yes, the issue got resolved, I actually had a wrong entry in source table.

Thanks


(Sarath Manikonda) #6

@ambuj
I think I am having similar issues with my accessing my vocabulary information. Can you share the exact issue you had so that I can check on my side if its the same issue for me also.


(Ambuj) #7

I want to know few things -

  1. Do you have a single schema for CDM and Vocabularies?
  2. Have you created results schema?
  3. Send me the entries you made in source and source_daimon tables.
  4. In google chrome, go to developer options, reload the atlas and send me the error.

May be I can help with above details.


(Sarath Manikonda) #8

@ambuj

Thank you for helping me. Here is the information from my end:

  1. Yes, we have one schema for CDM and Vocabulary. I created all the Vocabulary tables in to the CDM Schema and populated them with data from zip file (downloaded from Athena)
  2. Yes the Results schema is created separately and I created all the tables in this schema using the DDL from the path : /WebAPI/target/classes/ddl/results
    Here I have run all the table creation scripts and ignored the files that are loading data and the names of these files are initTables.sql, init_heracles_periods.sql, init_heracles_analysis.sql, init_concept_hierarchy.sql (i did not run these files). Let me know if this is ok?
  3. The entries from source and source_daimon are attached
  4. Error attached.

(Ambuj) #9

The entries looks good to me except the schema names which have ## in it. Are you using Apache tomcat as a webservice? and are you able to open localhost:8080/WebAPI/source/sources ?
Also, please share the scrrenshot of database and schema from GUI you are using to query the database.


(Sarath Manikonda) #10

@ambuj,

The ## in our schema names is a policy in our institution and we cannot change that.
Yes I am able to see the sources by calling the localhost:8080/WebAPI/source/sources
“please share the scrrenshot of database and schema from GUI you are using to query the database.” - I did not get this point. Out DB is Oracle, so do you mean the UI of SQL plus.
Also, which DB, like we have CDM and RESULTS on oracle. OHDSI DB is on PostGres.


(Ambuj) #11

Well, I am not sure on how postgres will query the result tables in oracle. I am blank here, please see if this link will help you out.


(Chris Knoll) #12

That is going to be a conflict with our queries. the ## represents a temp table name in MSSQL, which is the root dialect that we translate our queries across oracle, pdw, redshift, bigquery, postgresql, and impala.

Unless you get some sort of exception, you won’t be able to execute the queries.


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