sdrf_convert

SDRF -> sdrf_convert -> CLI||config

Usage

python -m sdrf_convert some.sdrf <tool> <additional_params_depending_on_tool>

Development

Getting started

Just enter

conda env create -f environment.yaml
conda activate sdrf_convert

and you are good to go.

Receiving updates

Make sure to check if someone else altered environment.yaml or pyproject.toml after you pull the repository. You might need to update

# conda environment
conda activate sdrf_convert
conda update -f environment.yaml
# python
pip install -e '.[dev]

Need additional dependencies

• Binary dependencies (OpenMS, Comet, Yarn, NodeJS ...) will go into environment.yaml
• Python dependencies (pyopenms, pandas, ...) will go into pyproject.toml

This ensures conda does not mess up our python environment AND all python packages are in one place once we want to publish.

Implementing a new converter

1. Add a new python file for the converter ending with _converter.py
2. Import the abstract converter: from sdrf_convert import AbstractConverter
3. Add a class definition for the new converter, inheriting the AbstractConverter: class MyToolConverer(AbstractConverter):
4. Call the super constructor in the new converters constructor

   def __init__(self):
       super().__init__()

5. Implement the convert()-function which calls init_converter()

Example:

# comet_converter.py
from sdrf_convert.abstract_converter import AbstractConverter

class CometConverter(AbstractConverter):
    # Implement the stuff used to convert the 
    # SDRF for the specific software.
    # E.g. constructor, conversions, lookups, ...
    def __init__(self):
        super().__init__()

    def convert(self, sdrf: Union[pd.DataFrame, IOBase, Path]) -> Tuple[str, str]:
        """
        Convert SDRF file to Comet CLI string and corresponding input file.

        Returns
        -------
        Any
            The converted SDRF file
        """
        self.init_converter(sdrf)
        # Do stuff
        return (cli, config)

Code styling

1. Make sure to use typed python. It is a bit more difficult to write but much easier to maintain and understand
2. Before submitting a pull request make sure to run pylint (pylint sdrf_convert) and fix your code styling