Is concept_hierarchy table mandatory

,
1
  • I am trying to setup Atlas for my OMOP CDM database.
  • The script for results schema setup is running for almost a week.
  • URL I used to get the script -
http://<server:port>/WebAPI/ddl/results?dialect=<your_cdm_database_dialect>&schema=<your_results_schema>&vocabSchema=<your_vocab_schema>&tempSchema=<your_temp_schema>&initConceptHierarchy=true
  • After some analysis I found that the creation of concept_hierarchy is the reason for script taking so much time to complete the run.
  • What will be the effect on functionality of Atals if I remove concept_hierarchy part by setting initConceptHierarchy = false?
  • Is there any way to find the progress %.

@Chris_Knoll @gregk

2

You won’t be able to use any of the data-sources functions because the concept_hiearchy is used to provide the hierarchy of concepts on the domain type reports.

Otherwise, if you don’t use DataSources you should be able to start WebAPI without those tables.

However, I have found that the achilles tables do need to be populated due to the ‘record count’ functionality that is provided in the vocabulary search functions, so you should try to at least create the achilles tables in the CDM source your WebAPI references.

3

Can you please tell me the sql code used for concept_hirarchy?

4

With WebAPI running, you can go to:

WebAPI base URL/ddl/results?vocabSchema=<vocabSchema>&schema=<resultsSchema>&dialect=<dialect>&tempSchema=<tempSchema (if using Oracle or Spark, otherwise, remove)>

This script would be used for creating all needed results schemas in Atlas for that source, including the concept_hierarchy table.

5

@Ajit_Londhe @Chris_Knoll
I can get the script from the WebAPI endpoint you refer to.

The script creates a set of tables in results schema and populate following tables:

  • results.concept_hierarchy
  • results.heracles_analysis
  • results.heracles_periods

These are the tables in cdm, not in the postgresql database, correct? or should I create and populate these table in postgresql too?

Thanks
Jack

6

The endpoint gives you DDL for the results schema (that exists along side your cdm schema in your CDM database). Don’t create the results schema in your WebAPI (postgres) database.

7

@Chris_Knoll

There are some overlap in the table names between results schema in CDM database and the WebAPI Postgresql database, which confuses me.

heracles_analysis
heracles_results
heracles_results_dist

Particularly, heracles_analysis in CDM is empty but has rows in WebAPI db. I am sure what this table’s role is in Atlas.

Some of the domain-type reports show “No Data” in Atlas at our site. Investigating the issue leads me to this thread of empty concept_hierarchy table in CDM. That is what happened at our end.

After populating this table in CDM database, will its data cache in WebAPI database? in achilles_cache table?

Thanks
Jack

8

This is a old implementation that we thought would be helpful: we added tables to the WebAPI schema to model the results table in the CDM for easy reference, but this was before we introduced the notion of the /ddl that you could fetch the results schema DDL from.

You can ignore those 3 tables from the WEBAPI schema (and you shouldn’t point your CDM data source to the WEBAPI database at all…your CDM database should be separeate from your WebAPI database).

In 3.0, we’ll be cleaning up those tables so we can remove that confusion. You’re not the first person who’s raised that question, and I agree it’s confusing and distracting.