{"id":35926679,"url":"https://github.com/BAMresearch/sigmabam2openbis","last_synced_at":"2026-01-16T15:00:55.179Z","repository":{"id":320379536,"uuid":"1037292943","full_name":"BAMresearch/sigmabam2openbis","owner":"BAMresearch","description":"Mapper script to convert SigmaBAM chemical inventory exports into openBIS-compatible format.","archived":false,"fork":false,"pushed_at":"2025-12-16T15:50:14.000Z","size":343,"stargazers_count":2,"open_issues_count":1,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-20T02:56:30.850Z","etag":null,"topics":["bam-data-store","mapper","openbis","parser"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BAMresearch.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-08-13T10:59:43.000Z","updated_at":"2025-12-16T15:50:18.000Z","dependencies_parsed_at":"2025-12-31T15:06:27.215Z","dependency_job_id":null,"html_url":"https://github.com/BAMresearch/sigmabam2openbis","commit_stats":null,"previous_names":["bamresearch/sigmabam2openbis"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BAMresearch/sigmabam2openbis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BAMresearch%2Fsigmabam2openbis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BAMresearch%2Fsigmabam2openbis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BAMresearch%2Fsigmabam2openbis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BAMresearch%2Fsigmabam2openbis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BAMresearch","download_url":"https://codeload.github.com/BAMresearch/sigmabam2openbis/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BAMresearch%2Fsigmabam2openbis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28479406,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bam-data-store","mapper","openbis","parser"],"created_at":"2026-01-10T06:00:38.491Z","updated_at":"2026-01-16T15:00:55.146Z","avatar_url":"https://github.com/BAMresearch.png","language":"Jupyter Notebook","funding_links":[],"categories":["Research Data Management"],"sub_categories":[],"readme":"\nYou can use this package to parse SigmaBAM files in openBIS. There are two resources used for automating the parsing of such files:\n\n1. Using the Python script in  `tutorials/parser_tutorial.py`. This script uses the parser class defined in `src/sigmabam2openbis/parser.py` and the [`bam-masterdata`](https://github.com/BAMresearch/bam-masterdata) parser infrastructure. **We recommend using this tutorial**. To run it, after setting up your environment (see below), run in the terminal `python tutorials/parser_script.py`.\n2. Using the _Jupyter notebook_ from `tutorials/chemical_data_inventory_openbis_mapper_1_0.ipynb`. This tutorial uses [PyBIS](https://pypi.org/project/pybis/).\n\n\n## Development\n\nIf you want to develop locally this package, clone the project and enter in the workspace folder:\n\n```bash\ngit clone https://github.com/BAMresearch/sigmabam2openbis.git\ncd sigmabam2openbis\n```\n\nCreate a virtual environment (you can use Python\u003e=3.10) in your workspace:\n\n- **Using venv**:\n  ```bash\n  python3 -m venv .venv\n  source .venv/bin/activate  # in Windows (cmd): source .venv\\Scripts\\activate\n  ```\n- **Using conda**:\n  ```bash\n  conda create --name .venv pip\n  conda activate .venv\n  ```\n\nInstall the package in editable mode (with the flag `-e`):\n```bash\npip install --upgrade pip\npip install -e '.[dev]'\n```\n\n**Note**: In order to install faster the package, you can use [`uv`](https://docs.astral.sh/uv/) for pip installing Python packages:\n```bash\npip install --upgrade pip\npip install uv\nuv pip install -e '.[dev]'\n```\n\n\n### Run the tests\n\nYou can locally run the tests by doing:\n\n```bash\npython -m pytest -sv tests\n```\n\nwhere the `-s` and `-v` options toggle the output verbosity.\n\nYou can also generate a local coverage report:\n\n```bash\npython -m pytest --cov=src tests\n```\n\n### Run auto-formatting and linting\n\nWe use [Ruff](https://docs.astral.sh/ruff/) for formatting and linting the code following the rules specified in the `pyproject.toml`. You can run locally:\n\n```bash\nruff check .\n```\n\nThis will produce an output with the specific issues found. In order to auto-fix them, run:\n\n```bash\nruff format .\n```\n\nIf some issues are not possible to fix automatically, you will need to visit the file and fix them by hand.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBAMresearch%2Fsigmabam2openbis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FBAMresearch%2Fsigmabam2openbis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBAMresearch%2Fsigmabam2openbis/lists"}