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ATLAS Migration from 2.7.0 to 2.7.8

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(Chidam) #1

Hi All,

Currently i am doing migration from version ATLAS 2.7.0 to 2.7.8, also migrating WebAPI to latest 2.7.8.

Is there any option to transfer conceptsets, cohorts characterization, pathways definitions from atlas version 2.7.0 to atlas 2.7.8? How to do that? Actually I want to copy all the created definitions from old version to new version.

Please advise.

thanks
regards
Chidam


(Chris Knoll) #2

We try to remain backwards compatable as much as possible, so you should be able to deploy the new 2.7.8 WAR into the same instance, and it will automatically manage any database updates in WebAPi (but you may need to look at your individual results schemas on your CDMs for updates, check the release notes). You should make a backup of your current WebAPI database, just in case you need to roll back to the 2.7.0 version.


(Chidam) #3

Thanks Chris.

I will try to use the same webAPI database. Thanks

regards
Chidam


(Chidam) #4

Hi Chris,

Thanks for your advise, For WebAPI 2.7.8, I use version 2.7.0 WebAPI database. During webAPI deployment, it updates some tables in the WebAPI database.

Want to check, is there any schema changes in the webAPI results? So can i use 2.7.0 webAPI results schema? means, can i use same CDM database for webAPI 2.7.0 and 2.7.8?

please advise

thanks
regards
Chidam


(Chris Knoll) #5

I believe there’s changes to the results schema (note: not webAPI database, but your CDM’s results schema which you had to manually create yourself via the WebAPI’s /ddl/results script that you can download from WebAPI).

I suggest you go to the releases page: https://github.com/OHDSI/WebAPI/releases and scroll through the release notes for 2.7.0 -> 2.7.8 and look for ‘migration notes’. I believe there was a note under 2.7.2, but you should look for the others. Or, you can get the DDL script from WebAPI/ddl/results and do a schema comparison between what you have in your results schema and what the latest /ddl/results script builds.


(Chidam) #6

Hi Chris,

Thanks a lot. I will try to compare both 2.7.0 CDM results schema with 2.7.8 CDM results schema.
If i found any changes, just alter 2.7.0 CDM result schema accordingly based on 2.7.8
correct?

Please correct me, example, the cohort definitions stored in webapi database? and the results are stored in the CDM results?

thanks
regards
Chidam


(Chris Knoll) #7

Yes cohort definitions are stored in the webAPI database (and those tables are automatically migrated for you when you install new WebAPI, so you don’t need to worry). But, those tables in the results schema of each CDM you have need to be manually maintained. An example of a manual change you’ll find in release notes is from v2.7.3:

ALTER TABLE @results_schema.pathway_analysis_stats
  ALTER COLUMN target_cohort_count BIGINT NOT NULL;
ALTER TABLE @results_schema.pathway_analysis_stats
  ALTER COLUMN pathways_count BIGINT NOT NULL;

Remember, you’ll need to adjust the syntax to your own SQL dialect (oracle, sql server, postgresql) and replace the placeholder @results_schema with your results schema name.


(Chidam) #8

Thanks Chris.


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