ATLAS on Impala

[tomwhite]

Umbrella issue to cover getting ATLAS running using Impala for data access.

[tomwhite]

With these changes I am able to run using Impala defined in the source/source_daimon tables, and PostgreSQL in the datasource.url env variable.

• Data sources work (except Achilles Heel): Dashboard, Data Density, etc.
• Vocabulary search works.
• Cohort generation does not work yet. The Impala query generated and displayed in the Export tab does work when run manually against Impala, but the Generate button causes an error due to the cohort_inclusion table not being found.

I'm a bit confused about the different schemas and the tables in them. E.g. the cohort_inclusion table is in the OHDSI schema (which I've stored in PostgreSQL), but GenerateCohortTasklet in WebAPI refers to it in the "results" schema, which is in Impala, and is where the Achilles results are found (I think)?

Can someone help explain which schemas the cohort tables (including cohort_inclusion) live in, and how they are managed by WebAPI? Thanks!

[chrisknoll]

the cohort_inclusion table should be manually crated on the CDM's results schema. There's a set of tables that should be translated from the PostgreSQL webapi schema into the target CDM's platform, this article will tell you which tables those are. There is an open issue for using an automated db migration onto the results schema of the CDM, but I think this is stalled.

http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:webapi:multiple_datasets_configuration

[tomwhite]

Thanks @chrisknoll, that has helped me make some progress.

[anthonysena]

I see that all of the open pull requests for this issue have been closed and presumably the work is complete. I'm going to close out this issue but feel free to re-open if there is still work happening here.