openbis-parser-example

Example parser for openBIS using the bam-masterdata parser interface.

This repository can be used as a template for creating new parsers that can be used with the openbis-upload-helper.

1. Create a new parser repository

You can either fork this repository or use it as a template.

Click Use this template and choose Create a new repository:

Choose:

• the organization or profile where the repository will be created;
• a repository name;
• a short description;
• the desired visibility.

At BAM, parsers are typically hosted under the BAMresearch organization.

2. Define your parser

Clone your new repository:

git clone https://github.com/BAMresearch/<repository-name>.git

Note: The examples below use this repository's current package name, openbis_parser_example. Replace it with your own repository name where needed.

The repository has the following structure:

openbis-parser-example
├── LICENSE
├── pyproject.toml
├── README.md
├── src
│   ├── openbis_parser_example
│       ├── __init__.py
│       ├── parser.py
│       └── _version.py
└── tests
    ├── __init__.py
    ├── conftest.py
    └── test_parser.py

To create your parser:

1. Define your parser class in src/<package-name>/parser.py. The class must inherit from the bam-masterdata parser interface, AbstractParser.
2. Expose the parser in src/<package-name>/__init__.py:

from .parser import MyParser

my_parser_entry_point = {
    "name": "My Parser",
    "description": "Description of the parser.",
    "parser_class": MyParser,
}

3. Register the parser in pyproject.toml:

[project.entry-points."bam.parsers"]
my_parser = "<package-name>:my_parser_entry_point"

4. Update the remaining package-specific values in pyproject.toml, such as the project name, package paths, URLs, and setuptools-scm configuration.

3. Implement and test the parser

Implement the parsing logic in:

src/<package-name>/parser.py

Add or update tests in:

tests/test_parser.py

The parser should transform the source files into bam-masterdata objects that can later be written to openBIS.

4. Use the parser with openbis-upload-helper

Once the parser is developed, tested, and released as a Python package, it can be included as a dependency of the openbis-upload-helper.

openbis-upload-helper automatically discovers installed parsers registered under the bam.parsers entry-point group.

If the parser should be included in the distributed application, contact the openbis-upload-helper maintainers and provide the parser repository and released package version.