29379954731
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Ran 15 Jul 2026 12:48AM UTC

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Committed 15 Jul 2026 12:46AM UTC coverage: 99.671%. Remained the same

Build # 29379954731

Build Type

Pull #2

github

Committed by

clintval

Commit Message

feat: hand the JVM a .jar-named handle so reflections-based tools work

Tools like GATK discover classes (e.g. -T walkers) via libraries such as
reflections, which only scan classpath entries whose filename ends in .jar.
A magicked file with a bare name (./gatk3) reaches the JVM as java -jar $0,
gets skipped, and the tool finds nothing ("Could not find walker").

When $0 lacks a .jar suffix, the preamble now materializes a .jar-named handle
in a temp dir and runs the JVM against it; names already ending in .jar exec
directly. A staged symlink (e.g. a workflow engine's task-dir link) is copied
so the JVM sees a real .jar rather than a hardlink-to-symlink that resolves
back to a bare name; a real file uses a cheap hardlink, falling back to a copy
across filesystems. An EXIT trap removes the temp dir (fires on normal exit and
SIGINT/TERM/HUP; only SIGKILL leaks it, which /tmp reaps); removing the handle
never touches the original jar.

Adds a unit test for the generated preamble plus integration tests for a
bare-named real file and a symlink-staged file.

Pull Request Pull Request #2: feat: hand the JVM a .jar-named handle so reflections-based tools work

Coverage Stats

303 of 304 relevant lines covered (99.67%)

8.87 hits per line

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ID	Job ID	Ran	Files	Coverage
1	29379954731.1	15 Jul 2026 12:48AM UTC	2	99.67	GitHub Action Run

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