Hello everyone. I would like to get some assistance related to setting up ATLAS as I am not sure what would be the issue occurring now, i.e. I am stuck!
Below you can see that ATLAS is running and calling most of its functionalities fine, but it does not recognize the vocabulary, therefore it won’t run Achilles to populate the results schema and allow ATLAS to show the data.
When I try to run Achilles to populate the results schema I am getting the error below, I am quite sure that the connection is correct as I could create the ddls using Achilles with the same connection, although I doubt what is the correct user to set for the connection, the one that has access to the whole DB, or the ohdsi_admin(that also goes to the URL JDBC, I mean which one is the correct one please?).
This is how I populated the source table, the source_ID is populated using the SEQUENCE that if my understanding is right works with other tables in the webapi schema allowing to create users and define their privileges to access ATLAS.
The CDM_SOURCE is populated with the CDM OMOP v6.0 with a constrain with vocabulary schema
ALTER TABLE webapi.CDM_SOURCE ADD CONSTRAINT fpk_CDM_SOURCE_cdm_version_concept_id FOREIGN KEY (cdm_version_concept_id) REFERENCES vocab.CONCEPT (CONCEPT_ID);
The SOURCE_DAIMON below:
Considering that the model is not finding the vocabulary, I have gathered as much information as possible to help anyone understand what the issue could be.
The vocabulary table has the CDM v6.0 and its concept in the concept table too, in fact, all the constraints are in place, as the indexes and all the concepts were mapped. The ETL was done with Python and I have a decent function that will collect all the concepts and create the vocabulary tables, including source_to_concept_map.
The tomcat log seems that everything works fine, except when it comes to finding the vocabulary and subsequently the OMOP tables(person, observation_period,…)
Error from the browser’s console
After reading a few similar questions in the forum I believe that it could be that I need to deploy a new war file where the datasource.schema is set to “cdm”, as I just did to the webapi, could it be the solution?