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Building Athena in a local system


#1

I went through the following steps to install Athena on my local system.

  1. download Athena 1.10.0 from github
  2. preparing Windows System (with 8GB main memory)
  3. install apache-maven 3.6.2
  4. install JDK 8u231
  5. install postgresql 12
  6. create new Database ID, ohdsi
  7. make Databases(“athena_db_test”, “athena_cdm_v5_test”, “athena_db”, “athena_cdm_v4_5”, “athena_cdm_v5”). This is required during the mvn build process.
  8. build (mvn package )
  9. import vocabulary csv files to tables
    (https://github.com/OHDSI/CommonDataModel/tree/master/PostgreSQL/VocabImport)

9-1. "REFRESH MATERIALIZED VIEW concepts_view " in postgresql query tool (by Sergey )
10. execute solr (7.7.2) ( 3 steps )
(solr create -c concepts / copy resources/solr files to solr folder / solr start -p 8984)

  1. run athena.jar (java -jar Athena.jar)

I have two problems in the process.

  1. When solr is run, no data is collected. The query in configuration is :
    select c.concept_id,
    c.concept_code,
    c.concept_name,
    c.concept_class_id,
    c.domain_id,
    c.vocabulary_id,
    c.standard_concept,
    c.invalid_reason,
    d.domain_name,
    v.vocabulary_name,
    c.concept_synonym_name
    from concepts_view as c
    join domain as d on c.domain_id = d.domain_id
    join vocabulary as v on c.vocabulary_id = v.vocabulary_id

concepts_view has the same scheme as concept, can I change to concept for the solr’s operation? Or should I construct concepts_view separately?

  1. Running athena gives the following error: (java -jar athena.jar)
    “org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘CDMFlywayConfig’: Invocation of init method failed; nested exception is org.flywaydb.core.api.FlywayException: Validate failed. Detected resolved migration not applied to database: 20170928131000”

It’s an error from flyway initialization. How can I fix it?

Thanks.


(Sergey Suvorov) #2

Hello

  1. You should not change concepts_view to concept, concepts_view will be constructed when you run athena first time. After importing vocabularies refresh it with command
    REFRESH MATERIALIZED VIEW concepts_view;
  2. Did you run athena between steps 8 and 9? Were there any errors?

#3

Thank you. concepts_view was refreshed and solr was running correctly. I also copied the postgresql.jar file so that solr can connect to DB.

Running between steps 8 and 9 results in the above error. The same error occurs when I run it now in step 11.

The only thing that affects the result seems to be the DB. I created a DB account (ohdsi / ohdsi) and uploaded the SNOMED voca to the athena_cdm_v5 database.

error message is
2019-12-25 13:01:23.474 ERROR 1140 — [ main] o.s.boot.SpringApplication : Application startup failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘CDMFlywayConfig’: Invocation of init method failed; nested exception is org.flywaydb.core.api.FlywayException: Validate failed. Detected resolved migration not applied to database: 20170928131000


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