Improve test coverage

[ctmay4]

Summary

Improve test coverage across the staging APIs, decision engine, data providers, and algorithm-specific data wrappers. Add enforceable coverage thresholds and separate the slow CS comparison suite from regular builds.

Changes

Expanded test coverage

• Add coverage for public Staging.getInputs and getOutputs APIs:
  • Table paths and mappings
  • Input/output mappings
  • Inclusion and exclusion contexts
  • Excluded inputs
  • Context-key removal
  • Explicit and inferred schema outputs
• Expand SchemaLookup tests:
  • Site and histology mutation
  • Equality and hash-code contracts
  • Allowed-key validation
  • Clearing inputs
  • Discriminator edge cases
• Add contract tests for CS, TNM, and EOD staging data:
  • Constructors
  • Typed input/output accessors
  • SSF boundaries and validation
  • Builder methods
  • EOD discriminators
• Add meaningful DecisionEngine branch scenarios:
  • Missing and malformed data
  • Mapping inclusion and exclusion
  • Defaults and validation
  • Null table paths and mappings
  • Input/output key interactions
• Expand provider coverage:
  • In-memory provider contracts and unsupported glossary operations
  • Missing tables and schemas
  • Valid-value range expansion and zero padding
  • Invalid table input definitions
  • External glossary loading and matching
  • Malformed and inconsistent algorithm ZIP files

Coverage enforcement

• Upgrade JaCoCo from 0.8.12 to 0.8.15 for Java 25 compatibility.
• Add bundle-level coverage checks during Maven verify:
  • Minimum line coverage: 95%
  • Minimum branch coverage: 89%
• Upload the generated JaCoCo report as a GitHub Actions artifact.

Current coverage:

Metric	Coverage
Lines	97.70%
Branches	92.31%
Methods	98.96%
Instructions	97.71%

CS comparison separation

• Move the slow manual CS comparison into a dedicated source set:
  • src/cs-comparison/java
  • src/cs-comparison/resources
• Rename the runner to CsComparisonRunner.
• Add a disabled-by-default cs-comparison Maven profile.
• Pin the supporting Maven plugins:
  • build-helper-maven-plugin 3.6.1
  • exec-maven-plugin 3.6.3
• Make comparison mismatches fail the Maven execution instead of only being logged.
• Update the manual workflow to run:

./mvnw -B -Pcs-comparison verify

Regular builds no longer compile the comparison runner or copy its 115 large resource files.

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud