[jcschaff]

Why

In compose-api's biomodels-curated-300 run 3, six models failed in sbml_to_vcml with this error:

MissingReflectionRegistrationError: The program tried to reflectively invoke method
   public boolean org.sbml.jsbml.Annotation.isSetAbout()

The models were BIOMD 56, 94, 150, 168, 169 and 192. The stack trace runs through SBMLReader → XMLNodeReader.processNamespace → MessageFormat.format → AbstractTreeNode.toString.

jsbml formats its debug messages eagerly, even when debug logging is off. When <annotation> declares a namespace, the message's context object is the Annotation. AbstractTreeNode.toString() then reflects over its isSet*/get*/set* methods and fields. The native image only registers what MainRecorder's run reaches, and its models never take that path.

What

• The config: vcell-native/src/main/native-image/jsbml/reachability-metadata.json registers allDeclaredMethods, allPublicMethods and allDeclaredFields for every jsbml tree node class, 127 of them, core and spatial.
• The generator: scripts/JsbmlReflection.java writes the file from the jsbml jar. Regenerate it when the jsbml version changes.
• The build: both native profiles read it with the recording (-H:ConfigurationFileDirectories=target/recording,src/main/native-image/jsbml).
• The test: test_sbml_to_vcml_with_an_annotation_namespace is a 10-line model with <annotation xmlns:jd=…>. It fails on 0.0.23 with the error above.
• Version: bumped to 0.0.24.

Checked (macOS arm64, GraalVM 23.0.2)

• The minimal model and BIOMD 56, 94, 150, 168, 169, 192: all failed on 0.0.23, and all import with the rebuilt library.
• pytest tests: 26 passed, 4 skipped.

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