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:

use-this-template

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.

create-new-template

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,
}
  1. Register the parser in pyproject.toml:
[project.entry-points."bam.parsers"]
my_parser = "<package-name>:my_parser_entry_point"
  1. 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.

Project links

Data verified by PyPI on Sep 11, 2026
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1 maintainer

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Avatar for JosePizarro3 from gravatar.com JosePizarro3

Credits

Author: BAM Data Store

Maintainer: Jose M. Pizarro

GitHub Statistics

Data verified by PyPI on Sep 11, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

Apache License

Requires

Python >=3.13

Provides Extra

dev

Classifiers

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