{"id":20641826,"url":"https://github.com/informaticsmatters/squonk2-data-manager-metadata","last_synced_at":"2026-02-11T17:03:17.709Z","repository":{"id":40482680,"uuid":"366662844","full_name":"InformaticsMatters/squonk2-data-manager-metadata","owner":"InformaticsMatters","description":"A metadata package for the Data Tier Data Manager service","archived":false,"fork":false,"pushed_at":"2025-01-28T10:09:53.000Z","size":775,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-25T07:17:05.065Z","etag":null,"topics":["squonk2"],"latest_commit_sha":null,"homepage":"","language":"Python","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/InformaticsMatters.png","metadata":{"files":{"readme":"README.rst","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}},"created_at":"2021-05-12T09:30:46.000Z","updated_at":"2025-01-28T10:08:02.000Z","dependencies_parsed_at":"2025-01-17T08:45:53.640Z","dependency_job_id":"d889141b-a04f-406e-863f-ef450f320742","html_url":"https://github.com/InformaticsMatters/squonk2-data-manager-metadata","commit_stats":null,"previous_names":["informaticsmatters/data-manager-metadata"],"tags_count":39,"template":false,"template_full_name":null,"purl":"pkg:github/InformaticsMatters/squonk2-data-manager-metadata","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/InformaticsMatters%2Fsquonk2-data-manager-metadata","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/InformaticsMatters%2Fsquonk2-data-manager-metadata/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/InformaticsMatters%2Fsquonk2-data-manager-metadata/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/InformaticsMatters%2Fsquonk2-data-manager-metadata/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/InformaticsMatters","download_url":"https://codeload.github.com/InformaticsMatters/squonk2-data-manager-metadata/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/InformaticsMatters%2Fsquonk2-data-manager-metadata/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29338671,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-11T16:14:43.024Z","status":"ssl_error","status_checked_at":"2026-02-11T16:14:15.258Z","response_time":97,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["squonk2"],"created_at":"2024-11-16T16:06:46.262Z","updated_at":"2026-02-11T17:03:17.676Z","avatar_url":"https://github.com/InformaticsMatters.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Informatics Matters Data-Manager Metadata\n=========================================\n\nA metadata framework package for the Data Tier Data Manager service.\nThe ``im-data-manager-metadata`` package is a set of utilities\nemployed by the `Informatics Matters`_ Data-Manager service\nas a metadata framework for molecular datasets.\n\n.. image:: /docs/data-manager-metadata.png\n  :width: 800\n  :alt: Data Manager Metadata Classes\n\nDependencies\n************\n- PyYAML\u003e=6.0.1,\u003c7.0\n\n\nRunning the Unit Tests\n**********************\n\n    \u003e\u003e\u003e python -m venv venv\n    \u003e\u003e\u003e source venv/bin/activate\n    \u003e\u003e\u003e pip install --upgrade pip\n    \u003e\u003e\u003e pip install -r package-requirements.txt\n    \u003e\u003e\u003e python -m unittest test.test_metadata\n    \u003e\u003e\u003e python -m unittest test.test_api\n\nRunning the Command Line Interface *md-manage.py*\n*************************************************\n\nThe data manager metadata command line interface can be used by applications to\nadd annotations to the Metadata by means of an annotations.json files that can be\nuploaded.\n\n    - help functions. Note that the *annotation_type* (lb, fd or se) is required.\n\n    \u003e\u003e\u003e python md_manage.py -h\n    \u003e\u003e\u003e python md_manage.py lb -h\n    \u003e\u003e\u003e python md_manage.py fd -h\n    \u003e\u003e\u003e python md_manage.py se -h\n\n    - Creates a label annotation in an annotations.json file placed in test/output.\n      Note that the *label* is required. Running the command again will create a second annotation\n      in the same file (i.e. a list of two).\n\n    \u003e\u003e\u003e python md_manage.py lb test/output/results.sdf 'foo' -lv='bar'\n\n    - Creates a FieldsDescriptorAnnotation in an annotations.json file placed in test/output.\n      If the annotations.json file exists it will add it to the list of annotations in the file.\n\n    \u003e\u003e\u003e python md_manage.py fd test/output/results.sdf -fo='squonk2-job'\n                            -fp='minimizedAffinity,number,Binding affinity\n                            predicted by smina using the vinardo scoring function,true,true'\n                            -fd='Run smina docking'\n\n    - Creates a service execution annotation in an annotations.json file placed in test/output.\n\n    \u003e\u003e\u003e python md_manage.py se test/output/results.sdf -su=bob -sys='run-smina'\n                           -sy='test/input/virtual-screening.yaml'\n                           -sp param1=val1 param2=val2 -fo='squonk2-job'\n                           -fp='minimizedAffinity,number,Binding affinity predicted,true,true'\n                           -fd='Run smina docking'\n\nContributing\n************\n\nThe project uses: -\n\n- `pre-commit`_ to enforce linting of files prior to committing them to the\n  upstream repository\n- `Commitizen`_ to enforce a [Convention Commit] commit message format\n- `Black`_ as a code formatter\n\nYou **MUST** comply with these choices in order to  contribute to the project.\n\nTo get started review the pre-commit utility and the conventional commit style\nand then set-up your local clone by following the **Installation** and\n**Quick Start** sections: -\n\n    \u003e\u003e\u003e pip install -r package-requirements.txt\n    \u003e\u003e\u003e pre-commit install -t commit-msg -t pre-commit\n\nNow the project's rules will run on every commit, and you can check the\ncurrent health of your clone with: -\n\n    \u003e\u003e\u003e pre-commit run --all-files\n\n.. _Informatics Matters: http://www.informaticsmatters.com\n.. _black: https://black.readthedocs.io/en/stable\n.. _commitizen: https://commitizen-tools.github.io/commitizen/\n.. _pre-commit: https://pre-commit.com\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finformaticsmatters%2Fsquonk2-data-manager-metadata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finformaticsmatters%2Fsquonk2-data-manager-metadata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finformaticsmatters%2Fsquonk2-data-manager-metadata/lists"}