Updated publisher to use the latest CQL translator, 3.20.0

[brynrhodes]

Tested with sample-ig, cql-ig, and ecqm-content-qicore-2025

[dotasek]

This introduces new errors when building the following IG:

https://github.com/FHIR/sample-ig.git

Original

Translating CQL source                                                                               (00:00.037 / 00:28.064, 359Mb)
Translating CQL source in folder /Users/david.otasek/IdeaFhirCoreLibraries/sample-ig-testing/sample-ig/input/cql (00:00.000 / 00:28.064, 359Mb)
Translating CQL source in file /Users/david.otasek/IdeaFhirCoreLibraries/sample-ig-testing/sample-ig/input/cql/notincluded.cql (00:00.026 / 00:28.090, 361Mb)
CQL translation completed successfully.                                                              (00:00.591 / 00:28.682, 463Mb)
Translating CQL source in file /Users/david.otasek/IdeaFhirCoreLibraries/sample-ig-testing/sample-ig/input/cql/example.cql (00:00.000 / 00:28.683, 463Mb)
CQL translation completed successfully.                                                              (00:00.468 / 00:29.151, 401Mb)
...
Errors: 23, Warnings: 23, Info: 7, Broken Links: 0 (00:00.913 / 02:16.979, 1Gb)

Updated

Translating CQL source                                                                               (00:00.030 / 00:24.265, 419Mb)
Translating CQL source in folder /Users/david.otasek/IdeaFhirCoreLibraries/sample-ig-testing/sample-ig/input/cql (00:00.000 / 00:24.265, 419Mb)
Translating CQL source in file /Users/david.otasek/IdeaFhirCoreLibraries/sample-ig-testing/sample-ig/input/cql/notincluded.cql (00:00.025 / 00:24.291, 420Mb)
Translation failed with (1) errors; see the error log for more information.                          (00:00.253 / 00:24.544, 454Mb)
Translating CQL source in file /Users/david.otasek/IdeaFhirCoreLibraries/sample-ig-testing/sample-ig/input/cql/example.cql (00:00.000 / 00:24.545, 454Mb)
Translation failed with (605) errors; see the error log for more information.                        (00:00.310 / 00:24.855, 375Mb)
...
Errors: 627, Warnings: 20, Info: 7, Broken Links: 0 (00:03.194 / 02:15.616, 993Mb)

I think this indicates that the update would break some existing IGs. Are the errors here because sample-ig has bad CQL, or because it relies on the previous version?

[dotasek]

Some additional details regarding the failure above.

There is a simple command-line based replication.

1. First, build the project: mvn clean install -DskipTests (fast and thorough enough)
2. Then, run the jar with the built-in exec goal: mvn org.codehaus.mojo:exec-maven-plugin:exec@target-ig-cli -pl org.hl7.fhir.publisher.cli -Dpublisher.cli.exec.target-ig=/path/to/the/sample-ig

This will run, but the command line log will show errors involving CQL:

...
Translating CQL source in file /Users/david.otasek/IdeaFhirCoreLibraries/sample-ig-testing/sample-ig/input/cql/example.cql (00:00.000 / 00:24.545, 454Mb)
Translation failed with (605) errors; see the error log for more information.
...

There will also be details in sample-ig/output/qa.txt regarding these errors, which indicate a classpath issue:

...
ERROR: jakarta.xml.bind.JAXBException: ClassCastException: attempting to cast jar:file:/Users/david.otasek/IdeaFhirCoreLibraries/fhir-ig-publisher/org.hl7.fhir.publisher.cli/target/org.hl7.fhir.publisher.cli-1.8.9-SNAPSHOT.jar!/jakarta/xml/bind/JAXBContext.class to jar:file:/Users/david.otasek/IdeaFhirCoreLibraries/fhir-ig-publisher/org.hl7.fhir.publisher.cli/target/org.hl7.fhir.publisher.cli-1.8.9-SNAPSHOT.jar!/jakarta/xml/bind/JAXBContext.class.  Please make sure that you are specifying the proper ClassLoader.    
ERROR: jakarta.xml.bind.JAXBException: ClassCastException: attempting to cast jar:file:/Users/david.otasek/IdeaFhirCoreLibraries/fhir-ig-publisher/org.hl7.fhir.publisher.cli/target/org.hl7.fhir.publisher.cli-1.8.9-SNAPSHOT.jar!/jakarta/xml/bind/JAXBContext.class to jar:file:/Users/david.otasek/IdeaFhirCoreLibraries/fhir-ig-publisher/org.hl7.fhir.publisher.cli/target/org.hl7.fhir.publisher.cli-1.8.9-SNAPSHOT.jar!/jakarta/xml/bind/JAXBContext.class.  Please make sure that you are specifying the proper ClassLoader.    
ERROR: FHIRHelpers: Could not resolve model with namespace http://hl7.org/fhir
ERROR: FHIRHelpers: class org.hl7.elm.r1.Null cannot be cast to class org.hl7.elm.r1.TypeSpecifier (org.hl7.elm.r1.Null and org.hl7.elm.r1.TypeSpecifier are in unnamed module of loader 'app')
ERROR: FHIRHelpers: Could not resolve model name System
...

Dependency analysis seems to find version conflicts involving jakarta.xml.bind in a number of dependencies, such as archie and even the org.hl7.fhir.core libraries, but I can't find a combination of exclusions and explicit dependency inclusions that allows the above to complete without error.

I am experimenting with updated versions of the maven-dependency-plugin and maven-shade-plugin, on the theory that maybe these are more aware of jaxb, but no success to report yet.