Achilles - CDM v5.4 compatibility and HEEL retirement

Implementers
1

Hello Achilles community,

Two announcements!

First, the latest version of Achilles on the MASTER branch incorporates support for CDM v5.4.

As in previous versions of Achilles, you have the option to pass in a string value for the parameter, cdmVersion, when invoking Achilles::achilles. If you would like to explicitly use the cdmVersion parameter for your v5.4 CDM, you can do so via: cdmVersion = “5.4”.

However, cdmVersion has been and continues to be an optional parameter as Achilles determines a CDM’s version using CDM_SOURCE.CDM_VERSION.
If you previously did not specify cdmVersion when calling Achilles::achilles, you can continue this practice.

Among the changes made for CDM v5.4, (Changes by Table), was the addition of the
CDM_VERSION_CONCEPT_ID column to the CDM_SOURCE table. In future Achilles releases, we will be using this column rather than relying on a string to determine a CDM’s version. The correct CONCEPT_ID for CDM_SOURCE.CDM_VERSION_CONCEPT_ID for a v5.4 CDM is 756265 (Athena).

To be clear, we are not making this change now. However, this will be a best practice for a future release of Achilles, so please ensure CDM_SOURCE.CDM_VERSION_CONCEPT_ID is properly populated once you move to v5.4.

Second, Achilles HEEL (Achilles::achillesHeel) is being retired and will be removed from the Achilles package on 11/17/2021. While HEEL has been with us for some time, it has been replaced by the Data Quality Dashboard (https://github.com/OHDSI/DataQualityDashboard).

Any and all feedback is welcome. Feel free to respond at: https://github.com/OHDSI/Achilles/discussions

2

@AnthonyMolinaro
I am new to OHDSI stuff. i am facing issue in generating the sql script that needs to be created for redhsift. i am follwing the steps mentioned in the doc CDM Configuration · OHDSI/WebAPI Wiki (github.com) . to generate the result schema.
when I run the this statement going to web page

http://localhost:8080/WebAPI/ddl/results?dialect=redshift&schema=results_redshift&vocabSchema=vocabulary&tempSchema=temp&initConceptHierarchy=true

i am getting the error.

could you tell me waht needs to be local host and port here if we are using redshift. also where this command needs to be executed

3

I think there are still few checks in Heel that are not fully integrated into DQD.
We were working on this here: https://github.com/OHDSI/DataQualityDashboard/issues/60

4

Can you guys post the database schema for the input database (cdmDatabaseSchema)? I need to be able to verify that the database I will use to be analysed by Achilles will be “Achilles compliant”. Is this dependent on the cdmVersion parameter?

Thanks

5

When you run Achilles the cdmDatabaseSchema variable should refer to the schema of your CDM.

6

Hi Team,

I have a datasource. with in datasource there are 3 CDM schemas which needs to be processed and show the data in ATLAS. I tried processing source schema 1 one it worked fine. when i process source schema 2 it gets processed but when i go and see in ATLAS both 1 and 2 has same records. Here my result schema remain the same only the source schema will change.

could you tell me if it works. or should I create separate result schema for separate source schema.

7

There needs to be a separate result schema for each CDM.