pyjaniml

A package to serialize and deserialize janiml json documents using marshmallow.

Based on

https://docs.google.com/document/d/1vpPbkAqPFc22efJ0IXvGGSzAn_4VFNG_OiaEfn42zx4/edit?usp=sharing

https://github.com/AnIML/schemas/blob/master/animl-core.xsd

Installation

Install directly from the GitLab repository $ pip install pyjaniml

Usage

Example usage

Not yet implemented

• Nested categories
• Signature Set
• Audit Trail

Contributing

The project uses black and isort for formatting its code. flake8 is used for linting. mypy is used for type checking. All these are combined into pre-commit to run before each commit and push. To set it up:

(env)$ python -m pip install pre-commit
(env)$ pre-commit install -t pre-commit -t pre-push --install-hooks

To run the unit tests you need some additional utilities that need to be installed before you can run the tests.

(env)$ python -m pip install -r requirements/tests.txt .
(env)$ python -m pip install -e .
(env)$ pytest --cov

Issuing a new Release

1. Determine the next version you want to release. For that, check the CHANGELOG and the chances made since the last release. Let's call it $VERSION.

2. Start a new branch release/$VERSION.

console (env)$ git checkout main (env)$ git pull (env)$ git checkout -b "release/$VERSION"

1. Update the CHANGELOG with the new desired version. Also ensure the notes for the new release make sense and are coherant. Remember, the target audience for this changelog.

2. Commit the changes an push them. Then open a merge request.

console (env)$ git add CHANGELOG.md (env)$ git commit -m "Release $VERSION" (env)$ git push -o merge_request.create -u origin "release/$VERSION"

1. Once the merge request has been approved and merged, pull the changes, add a git tag and push it:

console (env)$ git checkout main (env)$ git pull (env)$ # If you have a GPG key, please sign the tag: (env)$ git tag -s -m "Release $VERSION" "$VERSION" (env)$ # If you do not have a GPG key: (env)$ git tag -m "Release $VERSION" "$VERSION" (env)$ git push --tags

1. Check the build pipeline

Converting Bruker OPUS Files

Bruker OPUS Files can be converted into json using the following snippet:

file_path=/Path/To/Files
import pyjaniml
 converter = Converter()
_ = converter.convert_folder_and_zip(file_path)

or directly via the console

python3 pyjaniml /Path/To/Files