This repository uses unittest (Python standard library) to isolate orchestration logic and shell script behavior without calling real external tools (Docker daemon, RMLStreamer, Brotli, HDT).

• test/test_vcf_rdfizer_unit.py

  • Verifies wrapper control flow for the 5-step pipeline.
  • Verifies image/version resolution behavior and error handling.
  • Verifies CLI compression option propagation into compression.sh.

• test/test_vcf_rdfizer_cross_platform_unit.py

  • Runs a Windows/macOS/Linux-safe subset of wrapper tests.
  • Focuses on CLI parsing, image resolution, compression method parsing, and mocked compress mode execution.

• test/test_vcf_as_tsv_unit.py

  • Verifies .vcf and .vcf.gz input handling.
  • Verifies header extraction and per-VCF TSV generation (<sample>.records.tsv, <sample>.header_lines.tsv, <sample>.file_metadata.tsv).
  • Verifies header normalization (#CHROM -> CHROM) and data row retention.
  • Verifies error path for empty input directories.

• test/test_run_conversion_unit.py

  • Replaces java with a fake executable to avoid real RMLStreamer.
  • Verifies output normalization to .nt.
  • Verifies unified metrics CSV row creation and schema consistency.

• test/test_compression_unit.py

  • Replaces gzip, brotli, and rdf2hdt with fake executables.
  • Verifies compression artifact generation and metrics row update.
  • Verifies -m none behavior (no compression outputs, metrics still updated).

• Windows runners execute:
  • test/test_vcf_rdfizer_cross_platform_unit.py
  • package smoke test (pip install + vcf-rdfizer --help)
• macOS/Linux runners execute the full suite, including shell-script unit tests.

• It tests the highest-risk logic in this codebase: orchestration, branching, path wiring, and metrics consistency.
• It catches regressions in command construction without requiring heavyweight dependencies.
• It validates that metrics remain comparable across runs by enforcing one shared CSV schema.

Run:

python -m unittest discover -s test -p "test_*_unit.py" -v

Success indicators:

• Each test prints a clear marker:
  • [TEST] <description>
  • [PASS] <description>
• unittest prints ok next to each test.
• Final summary ends with:
  • Ran <N> tests ...
  • OK

Example (truncated):

[TEST] Wrapper runs all pipeline steps and forwards compression arguments.
[PASS] Wrapper runs all pipeline steps and forwards compression arguments.
...
Ran 10 tests in 0.90s
OK