jps-test-artifact-python-utils

Utilities for creating, verifying, and managing test artifact directories used to support functional testing of command-line executables. Includes CLI tools for setting up test directories, generating MD5 manifests, and validating test data integrity.

🧩 Installation

pip install jps-test-artifact-python-utils

or install in editable mode for local development:

git clone git@github.com:jai-python3/jps-test-artifact-python-utils.git  
cd jps-test-artifact-python-utils  
pip install -e .

🧩 setup-test-artifacts

Sets up a new test artifact instance directory by copying representative input, output, and script files into a new workspace.

Usage

setup-test-artifacts --indir <test-case-dir> [--script-dir <scripts-dir>]

Example

setup-test-artifacts --indir synthentic-genomics-pipeline/v1.2.0/comp_analysis/test-case-001/

This generates a fully configured test workspace with expected structure and a runnable shell script.

🧩 create-md5-manifest

Generates an md5_manifest.txt file listing all files under a given directory with their MD5 checksums, sizes, and timestamps.

Usage

create-md5-manifest --test-case-dir <path> --manifest-file <path>

Example Output

## method-created: /scripts/create_md5_manifest.py
## date-created: 2025-10-28 13:22:01
## created-by: jsundaram
## Columns:
## 1: relative file path
## 2: md5sum
## 3: number of bytes
## 4: date/time md5sum was derived

inputs/sample_input.vcf  3d883acf1a3db79c3390b8a96570a2ec  2145  2025-10-28-13:22:03
outputs/expected_output.tsv  53754d366f5676075a00e4c979f85cae  907  2025-10-28-13:22:04

🧩 verify-md5-manifest

Compares the current MD5 checksums of files in a test artifact directory with a saved manifest, reporting any mismatches or missing files.

Usage

verify-md5-manifest --test-case-dir <path> --manifest-file <path>

Example Output

✔ inputs/sample_input.vcf
✔ outputs/expected_output.tsv
✘ outputs/altered_output.tsv

2 of 3 files passed
Files with mismatched MD5 sums:
File: outputs/altered_output.tsv
Current MD5: 25a89f...
Previous MD5: 53754d...

🗂 Example Test Artifact Directory Layout

synthentic-genomics-pipeline/v1.2.0/comp_analysis/test-case-001/
├── inputs/
│   ├── sample_input.bam
│   ├── sample_input.vcf
│   └── genes.fasta
├── outputs/
│   └── expected_output.tsv
└── scripts/
    ├── requirements.txt
    └── run_test_case.sh.tmpl

🧾 Logging

Logs follow this format:

LOG_FORMAT = "%(levelname)s : %(asctime)s : %(pathname)s : %(lineno)d : %(message)s"

• Only WARNING and above are printed to STDERR.
• INFO, WARNING, ERROR, and FATAL are all written to the log file.

🧪 Development and Testing

Install dependencies for linting, formatting, and testing:

pip install -e '.[dev]'

Run all lint and test checks:

make lint  
make test

🧾 License

MIT License
© 2025 Jaideep Sundaram