{"id":32176425,"url":"https://github.com/livmats/dtool-lookup-api","last_synced_at":"2026-04-06T06:31:50.243Z","repository":{"id":37957044,"uuid":"311799093","full_name":"livMatS/dtool-lookup-api","owner":"livMatS","description":"Python client API for communicating with 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|dtool| image:: https://github.com/livMatS/dtool-lookup-api/blob/main/icons/22x22/dtool_logo.png?raw=True\n    :height: 20px\n    :target: https://github.com/livMatS/dtool-lookup-api\n\n.. |pypi| image:: https://img.shields.io/pypi/v/dtool-lookup-api\n    :alt: PyPI\n    :target: https://pypi.org/project/dtool-lookup-api/\n\n.. |tag| image:: https://img.shields.io/github/v/tag/livMatS/dtool-lookup-api\n    :alt: GitHub tag (latest by date)\n    :target: https://github.com/livMatS/dtool-lookup-api/tags\n\n.. |tests| image:: https://img.shields.io/github/actions/workflow/status/livMatS/dtool-lookup-api/test.yml?branch=main\u0026label=tests\n    :alt: GitHub Workflow Status\n    :target: https://github.com/livMatS/dtool-lookup-api/actions/workflows/test.yml\n\n.. |docs| image:: https://readthedocs.org/projects/dtool-lookup-api/badge/?version=latest\n    :alt: Documentation Status\n    :target: https://readthedocs.org/projects/dtool-lookup-api?badge=latest\n\n.. |zenodo| image:: https://zenodo.org/badge/311799093.svg\n    :alt: Zenodo Archive\n    :target: https://doi.org/10.5281/zenodo.14811473\n\n|dtool| |pypi| |tag| |tests| |docs| |zenodo|\n\nPython API for interacting with dserver.\n\nThis package offers a class-based asynchronous lookup API within ``dtool_lookup_api.core.LookupClient``,\na simple class-less wrapper around it at ``dtool_lookup_api.asynchronous``,\nand a synchronous interface on top at ``dtool_lookup_api.synchronous``.\n\nDirect imports of utility functions from `dtool_lookup_api` in the examples below forward to the synchronous API variant.\n\n\nInstallation\n------------\n\nTo install the dtool_lookup_api package.\n\n.. code-block:: bash\n\n    pip install dtool_lookup_api\n\nThis package depends on a `dserver\n\u003chttps://github.com/jic-dtool/dserver\u003e`_ instance to talk to.\n\nConfiguration\n-------------\n\nThe API needs to know the URL of the lookup server\n\n.. code-block:: bash\n\n    export DSERVER_URL=https://localhost:5000\n\nYou may also need specify an access token generated on the server\n\n.. code-block:: bash\n\n    export DSERVER_TOKEN=$(flask user token testuser)\n\n\nInstead of specifying the access token directly, it is also possible to provide\n\n.. code-block:: bash\n\n    export DSERVER_TOKEN_GENERATOR_URL=https://localhost:5001\n    export DSERVER_USERNAME=my-username\n    export DSERVER_PASSWORD=my-password\n\nfor the API to request a token. This, however, is intended only for testing\npurposes and strongly discouraged in a production environment, as your password\nwould reside within environment variables or the dtool config file as clear text.\n\nOur recommended setup is a combination of\n\n.. code-block:: bash\n\n    export DSERVER_URL=https://localhost:5000\n    export DSERVER_TOKEN_GENERATOR_URL=https://localhost:5001\n\nin the config. If used interactively, the API will then ask for your\ncredentials at the first interaction and cache the provided values for this\nsession, i.e.\n\n.. code-block::\n\n    In [1]: from dtool_lookup_api import query\n       ...: res = query(\n       ...:     {\n       ...:         'readme.owners.name': {'$regex': '^Testing User$'},\n       ...:     }\n       ...: )\n    Authentication URL https://localhost:5001/token username:my-username\n    Authentication URL https://localhost:5001/token password:\n\n    In [2]: res\n    Out[2]:\n    [{'base_uri': 'smb://test-share',\n      'created_at': 'Sun, 08 Nov 2020 18:38:40 GMT',\n      'creator_username': 'jotelha',\n      'dtoolcore_version': '3.17.0',\n      'frozen_at': 'Wed, 11 Nov 2020 17:20:30 GMT',\n      'name': 'simple_test_dataset',\n      'tags': [],\n      'type': 'dataset',\n      'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',\n      'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]\n\n    In [3]: from dtool_lookup_api import all\n       ...: all()\n    Out[4]:\n    [{'base_uri': 'smb://test-share',\n      'created_at': 1604860720.736269,\n      'creator_username': 'jotelha',\n      'frozen_at': 1604921621.719575,\n      'name': 'simple_test_dataset',\n      'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',\n      'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]\n\nCredentials caching and interactive prompting are turned off with\n\n.. code-block::\n\n  In [1]: import dtool_lookup_api.core.config\n     ...: dtool_lookup_api.core.config.Config.interactive = False\n     ...: dtool_lookup_api.core.config.Config.cache = False\n\n  In [2]: from dtool_lookup_api import all\n     ...: all()\n  ...\n  RuntimeError: Authentication failed\n\nFor testing purposes, it is possible to disable SSL certificates validation with\n\n.. code-block:: bash\n\n    export DSERVER_VERIFY_SSL=false\n\nAs usual, these settings may be specified within the default dtool configuration\nfile as well, i.e. at ``~/.config/dtool/dtool.json``\n\n.. code-block:: bash\n\n    {\n        \"DSERVER_TOKEN_GENERATOR_URL\": \"https://localhost:5001/token\",\n        \"DSERVER_URL\": \"https://localhost:5000\"\n    }\n\n\nList all datasets\n-----------------\n\nTo list all registered datasets\n\n.. code-block::\n\n    In [1]: from dtool_lookup_api import get_datasets\n       ...: res = get_datasets()\n\n    In [2]: res\n    Out[2]:\n    [{'base_uri': 'smb://test-share',\n    'created_at': 1604860720.736269,\n    'creator_username': 'jotelha',\n    'frozen_at': 1604921621.719575,\n    'name': 'simple_test_dataset',\n    'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',\n    'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]\n\n\n\nLooking up datasets by UUID\n---------------------------\n\nTo lookup URIs from a dataset UUID within Python\n\n.. code-block::\n\n    In [1]: from dtool_lookup_api import get_datasets_by_uuid\n       ...: uuid = \"1a1f9fad-8589-413e-9602-5bbd66bfe675\"\n       ...: res = get_datasets_by_uuid(uuid)\n\n    In [2]: res\n    Out[2]:\n    [{'base_uri': 'smb://test-share',\n      'created_at': 1604860720.736269,\n      'creator_username': 'jotelha',\n      'frozen_at': 1604921621.719575,\n      'name': 'simple_test_dataset',\n      'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',\n      'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]\n\n\nFull text searching\n-------------------\n\nFull text search for the word \"test\"\n\n.. code-block::\n\n    In [1]: from dtool_lookup_api import get_datasets\n        ...: res = get_datasets(free_text=\"test\")\n\n    In [2]: res\n    Out[2]:\n    [{'base_uri': 'smb://test-share',\n      'created_at': 1604860720.736,\n      'creator_username': 'jotelha',\n      'dtoolcore_version': '3.17.0',\n      'frozen_at': 1605027357.308,\n      'name': 'simple_test_dataset',\n      'tags': [],\n      'type': 'dataset',\n      'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',\n      'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]\n\n\nManifest\n--------\n\nRequest the manifest of a particular dataset by URI\n\n.. code-block::\n\n    In [1]: from dtool_lookup_api import get_manifest\n       ...: uri = 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675'\n       ...: res = get_manifest(uri)\n\n    In [2]: res\n    Out[2]:\n    {'dtoolcore_version': '3.17.0',\n     'hash_function': 'md5sum_hexdigest',\n     'items': {'eb58eb70ebcddf630feeea28834f5256c207edfd': {'hash': '2f7d9c3e0cfd47e8fcab0c12447b2bf0',\n       'relpath': 'simple_text_file.txt',\n       'size_in_bytes': 17,\n       'utc_timestamp': 1605027357.284966}}}\n\n\nReadme\n------\n\nRequest the readme content of a particular dataset by URI\n\n.. code-block::\n\n    In [1]: from dtool_lookup_api import get_readme\n        ..: res = get_readme('smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675')\n\n    In [2]: import yaml\n        ..: yaml.safe_load(res)\n    Out[2]:\n    {'creation_date': '2020-11-08',\n    'description': 'testing description',\n    'expiration_date': '2022-11-08',\n    'funders': [{'code': 'testing_code',\n     'organization': 'testing_organization',\n     'program': 'testing_program'}],\n    'owners': [{'email': 'testing@test.edu',\n     'name': 'Testing User',\n     'orcid': 'testing_orcid',\n     'username': 'testing_user'}],\n    'project': 'testing project'}\n\n\n\nDirect mongo language queries\n-----------------------------\n\nTo list all datasets at a certain base URI with their name matching some regular\nexpression pattern, send a direct mongo language query to the server with\n\n.. code-block::\n\n    In [15]: from dtool_lookup_api import query\n        ...: res = query(\n        ...:     {\n        ...:         'base_uri': 'smb://test-share',\n        ...:         'name': {'$regex': 'test'},\n        ...:     }\n        ...: )\n\n    In [16]: res\n    Out[16]:\n    [{'base_uri': 'smb://test-share',\n    'created_at': 'Sun, 08 Nov 2020 18:38:40 GMT',\n    'creator_username': 'jotelha',\n    'dtoolcore_version': '3.17.0',\n    'frozen_at': 'Tue, 10 Nov 2020 16:55:57 GMT',\n    'name': 'simple_test_dataset',\n    'tags': [],\n    'type': 'dataset',\n    'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',\n    'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]\n\n\nIt is possible to search readme content via\n\n.. code-block::\n\n    In [21]: from dtool_lookup_api import query\n        ...: res = query(\n        ...:     {\n        ...:         'readme.owners.name': {'$regex': '^Testing User$'},\n        ...:     }\n        ...: )\n\n    In [22]: res\n    Out[22]:\n    [{'base_uri': 'smb://test-share',\n      'created_at': 'Sun, 08 Nov 2020 18:38:40 GMT',\n      'creator_username': 'jotelha',\n      'dtoolcore_version': '3.17.0',\n      'frozen_at': 'Tue, 10 Nov 2020 16:55:57 GMT',\n      'name': 'simple_test_dataset',\n      'tags': [],\n      'type': 'dataset',\n      'uri': 'smb://test-share/1a1f9fad-8589-413e-9602-5bbd66bfe675',\n      'uuid': '1a1f9fad-8589-413e-9602-5bbd66bfe675'}]\n\nThis requires the server-side `dserver-direct-mongo-plugin\n\u003chttps://github.com/livMatS/dserver-direct-mongo-plugin\u003e`_.\n\nTODO: Response from server-side direct mongo plugin still yields dates as strings.\nFix within https://github.com/IMTEK-Simulation/dserver-direct-mongo-plugin.\n\n\nUsage on Jupyter notebook\n--------------------------\n\nThe current implementation via ``asgiref.async_to_sync`` (https://github.com/django/asgiref)\nhinders the use of the synchronous interface within Jupyter notebooks.\nDirectly use the asynchronous api instead\n\n.. code-block:: python\n\n    import dtool_lookup_api.asynchronous as dl\n    res = await dl.query({\n        'base_uri': 'smb://test-share',\n        'name': {'$regex': 'test'},\n    })\n\nThe drawback of the above approach is that the same code doesn't work in python and in jupyter (`await` outsite of a function is a syntax error in non-interactive python context).\nThe code below can be executed in both contexts:\n\n.. code-block:: python\n\n    import dtool_lookup_api.asynchronous as dl\n    if asyncio.get_event_loop().is_running():\n        # then we are in jupyter notebook\n        # this allows nested event loops, i.e. calls to asyncio.run inside the notebook as well\n        # This way, the same code works in notebook and python\n        import nest_asyncio\n        nest_asyncio.apply()\n\n    def query(query_dict):\n        return asyncio.run(dl.query(query_dict))\n\n    query({\n        'base_uri': 'smb://test-share',\n        'name': {'$regex': 'test'},\n    })\n\nSee https://github.com/jupyter/notebook/issues/3397#issuecomment-419386811, https://ipython.readthedocs.io/en/stable/interactive/autoawait.html\n\n\nTesting\n-------\n\nInstall editable with testing requirements with\n\n.. code-block:: bash\n\n    pip install -e .[test]\n\nBy default, tests rely on the `demo.dtool.dev` demonstrator instance.\n\nThis can be changed by configuring\n\n.. code-block:: python\n\n    DSERVER_ADDRESS_AND_CREDENTIALS = {\n        \"DSERVER_URL\": \"https://demo.dtool.dev/lookup\",\n        \"DSERVER_TOKEN_GENERATOR_URL\": \"https://demo.dtool.dev/token\",\n        \"DSERVER_USERNAME\": \"testuser\",\n        \"DSERVER_PASSWORD\": \"test_password\",\n        \"DSERVER_VERIFY_SSL\": False,\n    }\n\nwithin ``tests/conftest.py``.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flivmats%2Fdtool-lookup-api","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flivmats%2Fdtool-lookup-api","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flivmats%2Fdtool-lookup-api/lists"}