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MDACA 3.0.1 - #2378

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chrisknoll merged 155 commits into
OHDSI:mdaca-3.0.1from
mdaca:mdaca-3.0.1
May 5, 2025
Merged

chrisknoll merged 155 commits into
OHDSI:mdaca-3.0.1from
mdaca:mdaca-3.0.1

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@mdaca

@mdaca mdaca commented Jun 25, 2024

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Requested by Anthony Sena for upgrade to Spring Boot 3 and JDK 17.

  • Starts using Tomcat embedded 10.1.20
  • Also have tested deploying to Tomcat server 11
  • Background jobs have not been fully validated
  • Spring Batch upgrade has been implemented as a Flyway script (Postgres only)
  • Only validated with a Redshift CDM so far
  • Database authentication and OIDC (via Keylcoak) have been validated
  • Requires modified ArachneCommons to be built first ( https://github.com/mdaca/OHDSI-ArachneCommons)

chrisknoll and others added 30 commits December 11, 2023 16:54
Bump to version 2.15.0
Updated Milestones for Atlas and WebAPI
* Implemented permission lookup to bypass hibernate.
* Moved PermissionsDTO to PermissionManager
* Removed GSON to use the app-wide ObjectMapper from Jackson
* Removed unused imports to GSON.
* Create new webapi-databricks profile
* Check for spark and databricks connection string info
spinsysmpeterson and others added 21 commits December 20, 2024 19:07
… for only run when specific folder/files are updated as well updated 4th octet from .2 to .3
@chrisknoll

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I'd like to consider bumping this up to JDK 21. From what I've read, there's improved light-weight threads for heavily threaded applications (as our webservices are very multi-threaded, this seems like it would benefit us), memory usage, the record structures, etc. I'm not requesting anything from you guys about this PR being pushed to JDK 21, but I was considering using this as a basis to bump it to JDK 21.

Did you guys do any research on 19 vs. 21 where you identified potential challenges?

spring.jpa.properties.hibernate.jdbc.batch_size=${spring.jpa.properties.hibernate.jdbc.batch_size}
spring.jpa.properties.hibernate.order_inserts=${spring.jpa.properties.hibernate.order_inserts}
# Hibernate configuration
spring.jpa.hibernate.ddl-auto=validate

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I don't think we should haev this here. We use Flyway to manage db migrations, and it's unclear how hibernate DDL validation will interact with this. I don't htink we should enable it.

@chrisknoll

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@mdaca : I'm trying to start to build and run this branch locally, and Maven is having issues resolving a few dependencies:

Failed to execute goal on project WebAPI: Could not collect dependencies for project org.ohdsi:WebAPI:war:3.0.0
Failed to read artifact descriptor for com.odysseusinc.arachne:arachne-common-utils:jar:3.x-MDACA
	Caused by: The following artifacts could not be resolved: com.odysseusinc.arachne:arachne-common-utils:pom:3.x-MDACA (absent): Could not transfer artifact com.odysseusinc.arachne:arachne-common-utils:pom:3.x-MDACA from/to jitpack.io (https://jitpack.io): PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
Failed to read artifact descriptor for com.odysseusinc.arachne:execution-engine-commons:jar:3.x-MDACA
	Caused by: The following artifacts could not be resolved: com.odysseusinc.arachne:execution-engine-commons:pom:3.x-MDACA (absent): Could not transfer artifact com.odysseusinc.arachne:execution-engine-commons:pom:3.x-MDACA from/to jitpack.io (https://jitpack.io): PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
Failed to read artifact descriptor for com.odysseusinc:logging:jar:3.x-MDACA
	Caused by: The following artifacts could not be resolved: com.odysseusinc:logging:pom:3.x-MDACA (absent): Could not transfer artifact com.odysseusinc:logging:pom:3.x-MDACA from/to jitpack.io (https://jitpack.io): PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
Failed to read artifact descriptor for com.odysseusinc.arachne:arachne-scheduler:jar:3.x-MDACA
	Caused by: The following artifacts could not be resolved: com.odysseusinc.arachne:arachne-scheduler:pom:3.x-MDACA (absent): Could not transfer artifact com.odysseusinc.arachne:arachne-scheduler:pom:3.x-MDACA from/to jitpack.io (https://jitpack.io): PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
Failed to read artifact descriptor for com.odysseusinc:data-source-manager:jar:3.x-MDACA
	Caused by: The following artifacts could not be resolved: com.odysseusinc:data-source-manager:pom:3.x-MDACA (absent): Could not transfer artifact com.odysseusinc:data-source-manager:pom:3.x-MDACA from/to jitpack.io (https://jitpack.io): PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target

It seems there are a few MDACA-specific jars related to odysseusinc. Can you provide information as to how to resolve these dependencies? Are they published to a private nexus repository?

Flyway fw = Flyway.configure().dataSource(secondaryDataSource())
.locations("classpath:db/migration/postgresql")
.placeholders(Map.of("ohdsiSchema", "webapi")).load();
return fw;

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Hello @mdaca :

I don't believe this is correct. These configurations are based on application properties, In addition, the newer versions of Flyway change the default name of the schema_version table, so existing applications will need a way to set the tablename (and schema).

@chrisknoll

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I'm going to pull this into our OHDSI branch so that I'm able to push some commits to address some issutes.

@chrisknoll
chrisknoll merged commit b1798dc into OHDSI:mdaca-3.0.1 May 5, 2025
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Upgrade to Spring Boot 2.3

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