diff --git a/poetry.lock b/poetry.lock index 78aa02d..f7b2d17 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. [[package]] name = "airium" @@ -6,6 +6,7 @@ version = "0.2.6" description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies." optional = false python-versions = "*" +groups = ["main"] files = [ {file = "airium-0.2.6-py3-none-any.whl", hash = "sha256:50af5cf491e084f27909e29a93550b4170e587cde01334d58c6249644ee8c6c2"}, {file = "airium-0.2.6.tar.gz", hash = "sha256:ccab36b798b6cce3d0c5074e52ce8059f6e82991caae4985f42cadfad80b1de4"}, @@ -21,17 +22,33 @@ version = "0.7.16" description = "A light, configurable Sphinx theme" optional = false python-versions = ">=3.9" +groups = ["dev"] +markers = "python_version < \"3.11\"" files = [ {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] +[[package]] +name = "alabaster" +version = "1.0.0" +description = "A light, configurable Sphinx theme" +optional = false +python-versions = ">=3.10" +groups = ["dev"] +markers = "python_version >= \"3.11\"" +files = [ + {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"}, + {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"}, +] + [[package]] name = "annotated-types" version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" +groups = ["main", "llm"] files = [ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, @@ -43,19 +60,21 @@ version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, ] [[package]] name = "anyio" -version = "4.8.0" +version = "4.9.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.9" +groups = ["main", "dev", "llm"] files = [ - {file = "anyio-4.8.0-py3-none-any.whl", hash = "sha256:b5011f270ab5eb0abf13385f851315585cc37ef330dd88e27ec3d34d651fd47a"}, - {file = "anyio-4.8.0.tar.gz", hash = "sha256:1d9fe889df5212298c0c0723fa20479d1b94883a2df44bd3897aa91083316f7a"}, + {file = "anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c"}, + {file = "anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028"}, ] [package.dependencies] @@ -65,8 +84,8 @@ sniffio = ">=1.1" typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] -doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21)"] +doc = ["Sphinx (>=8.2,<9.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"] +test = ["anyio[trio]", "blockbuster (>=1.5.23)", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1) ; python_version >= \"3.10\"", "uvloop (>=0.21) ; platform_python_implementation == \"CPython\" and platform_system != \"Windows\" and python_version < \"3.14\""] trio = ["trio (>=0.26.1)"] [[package]] @@ -75,6 +94,7 @@ version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." optional = false python-versions = "*" +groups = ["main"] files = [ {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, @@ -86,6 +106,8 @@ version = "0.1.4" description = "Disable App Nap on macOS >= 10.9" optional = false python-versions = ">=3.6" +groups = ["dev"] +markers = "platform_system == \"Darwin\"" files = [ {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"}, {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"}, @@ -97,6 +119,7 @@ version = "23.1.0" description = "Argon2 for Python" optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "argon2_cffi-23.1.0-py3-none-any.whl", hash = "sha256:c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea"}, {file = "argon2_cffi-23.1.0.tar.gz", hash = "sha256:879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08"}, @@ -117,6 +140,7 @@ version = "21.2.0" description = "Low-level CFFI bindings for Argon2" optional = false python-versions = ">=3.6" +groups = ["dev"] files = [ {file = "argon2-cffi-bindings-21.2.0.tar.gz", hash = "sha256:bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3"}, {file = "argon2_cffi_bindings-21.2.0-cp36-abi3-macosx_10_9_x86_64.whl", hash = "sha256:ccb949252cb2ab3a08c02024acb77cfb179492d5701c7cbdbfd776124d4d2367"}, @@ -154,6 +178,7 @@ version = "1.3.0" description = "Better dates & times for Python" optional = false python-versions = ">=3.8" +groups = ["main", "dev"] files = [ {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, @@ -173,6 +198,7 @@ version = "3.0.0" description = "Annotate AST trees with source code positions" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"}, {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"}, @@ -184,36 +210,38 @@ test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"] [[package]] name = "async-lru" -version = "2.0.4" +version = "2.0.5" description = "Simple LRU cache for asyncio" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" +groups = ["dev"] files = [ - 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{file = "attrs-25.1.0.tar.gz", hash = "sha256:1c97078a80c814273a76b2a298a932eb681c87415c11dee0a6921de7f1b02c3e"}, + {file = "attrs-25.3.0-py3-none-any.whl", hash = "sha256:427318ce031701fea540783410126f03899a97ffc6f61596ad581ac2e40e3bc3"}, + {file = "attrs-25.3.0.tar.gz", hash = "sha256:75d7cefc7fb576747b2c81b4442d4d4a1ce0900973527c011d1030fd3bf4af1b"}, ] [package.extras] -benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"] -tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] +benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"] +cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"] +dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"] +docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier"] +tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"] +tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\""] [[package]] name = "babel" @@ -221,13 +249,14 @@ version = "2.17.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"}, {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"}, ] [package.extras] -dev = ["backports.zoneinfo", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata"] +dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata ; sys_platform == \"win32\""] [[package]] name = "bcp47" @@ -235,6 +264,7 @@ version = "0.1.0" description = "Language tags made easy" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "bcp47-0.1.0-py3-none-any.whl", hash = "sha256:a567b7fe881c900916a9db62ac8f792370c7ddf2664e601b74eeed35d8758aa5"}, {file = "bcp47-0.1.0.tar.gz", hash = "sha256:37cc7a03fd696149ebfe7de785c5bad473f911eddac8415cf479584049cf03d5"}, @@ -242,13 +272,14 @@ files = [ [[package]] name = "beautifulsoup4" -version = "4.13.3" +version = "4.13.4" description = "Screen-scraping library" optional = false python-versions = ">=3.7.0" +groups = ["main", "dev"] files = [ - 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Easily extensible." optional = false python-versions = "*" +groups = ["main"] files = [ {file = "num2words-0.5.14-py3-none-any.whl", hash = "sha256:1c8e5b00142fc2966fd8d685001e36c4a9911e070d1b120e1beb721fa1edb33d"}, {file = "num2words-0.5.14.tar.gz", hash = "sha256:b066ec18e56b6616a3b38086b5747daafbaa8868b226a36127e0451c0cf379c6"}, @@ -3052,6 +3339,7 @@ version = "1.26.4" description = "Fundamental package for array computing in Python" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "numpy-1.26.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:9ff0f4f29c51e2803569d7a51c2304de5554655a60c5d776e35b4a41413830d0"}, {file = "numpy-1.26.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2e4ee3380d6de9c9ec04745830fd9e2eccb3e6cf790d39d7b98ffd19b0dd754a"}, @@ -3093,13 +3381,14 @@ files = [ [[package]] name = "oaklib" -version = "0.6.19" +version = "0.6.22" description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends" optional = false python-versions = "<4.0.0,>=3.9" +groups = ["main"] files = [ - {file = "oaklib-0.6.19-py3-none-any.whl", hash = "sha256:8b31cacfc525d00b66bf5953a7b3dfbae000b3d115ec9c4e4aad51b49a577840"}, - {file = "oaklib-0.6.19.tar.gz", hash = "sha256:6ce85ddc5076e1a5f5e2a56a80e85eb712817052d61eb174cabc2bffe05561a2"}, + {file = "oaklib-0.6.22-py3-none-any.whl", hash = "sha256:c945538c071da6682ca5ebc04eb02d4e85b770aea94f4540fd6dcc6e3ce9becc"}, + {file = "oaklib-0.6.22.tar.gz", hash = "sha256:bd557aeab6d8aca7ef8840f8e68da66110e33447f946107dc9f463a500a27674"}, ] [package.dependencies] @@ -3134,6 +3423,7 @@ sssom = ">=0.4.4,<0.5.0" tenacity = ">=8.2.3" [package.extras] +bioservices = ["bioservices"] gilda = ["gilda (>=1.0.0)", "urllib3 (<2)"] llm = ["aiohttp", "html2text", "llm (>=0.14,<0.15)"] semsimian = ["semsimian (>=0.2.18)"] @@ -3144,6 +3434,7 @@ version = "3.2.2" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "oauthlib-3.2.2-py3-none-any.whl", hash = "sha256:8139f29aac13e25d502680e9e19963e83f16838d48a0d71c287fe40e7067fbca"}, {file = "oauthlib-3.2.2.tar.gz", hash = "sha256:9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918"}, @@ -3160,6 +3451,7 @@ version = "0.1.4" description = "A client to the EBI Ontology Lookup Service" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "ols_client-0.1.4-py3-none-any.whl", hash = "sha256:7bdca0590042e07cc7ee3ef3fba99c3b6862cde6c8835afb129de31284b3e010"}, {file = "ols_client-0.1.4.tar.gz", hash = "sha256:cd2a0f39107f39eaf0f40b9098f12d442cf3d43e28228e63feb407d0aeb44470"}, @@ -3182,6 +3474,7 @@ version = "0.3.3" description = "COGS Operates Google Sheets" optional = false python-versions = ">=3.6, <4" +groups = ["main"] files = [ {file = "ontodev-cogs-0.3.3.tar.gz", hash = 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"sha256:e8c947097eae7892cb3d26868d637f79f47b4a0554bc6b80065dfe5aac3705dd"}, + {file = "validators-0.35.0.tar.gz", hash = "sha256:992d6c48a4e77c81f1b4daba10d16c3a9bb0dbb79b3a19ea847ff0928e70497a"}, ] [package.extras] @@ -5841,6 +6308,7 @@ version = "6.0.0" description = "Filesystem events monitoring" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "watchdog-6.0.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d1cdb490583ebd691c012b3d6dae011000fe42edb7a82ece80965b42abd61f26"}, {file = "watchdog-6.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:bc64ab3bdb6a04d69d4023b29422170b74681784ffb9463ed4870cf2f3e66112"}, @@ -5883,6 +6351,7 @@ version = "0.2.13" description = "Measures the displayed width of unicode strings in a terminal" optional = false python-versions = "*" +groups = ["dev"] files = [ {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, @@ -5894,6 +6363,7 @@ version = "24.11.1" description = "A library for working with the color formats defined by HTML and CSS." optional = false python-versions = ">=3.9" +groups = ["main", "dev"] files = [ {file = "webcolors-24.11.1-py3-none-any.whl", hash = "sha256:515291393b4cdf0eb19c155749a096f779f7d909f7cceea072791cb9095b92e9"}, {file = "webcolors-24.11.1.tar.gz", hash = "sha256:ecb3d768f32202af770477b8b65f318fa4f566c22948673a977b00d589dd80f6"}, @@ -5905,6 +6375,7 @@ version = "0.5.1" description = "Character encoding aliases for legacy web content" optional = false python-versions = "*" +groups = ["dev"] files = [ {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, @@ -5916,6 +6387,7 @@ version = "1.8.0" description = "WebSocket client for Python with low level API options" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"}, {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"}, @@ -5928,13 +6400,14 @@ test = ["websockets"] [[package]] name = "widgetsnbextension" -version = "4.0.13" +version = "4.0.14" description = "Jupyter interactive widgets for Jupyter Notebook" optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ - {file = "widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71"}, - {file = "widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6"}, + {file = "widgetsnbextension-4.0.14-py3-none-any.whl", hash = "sha256:4875a9eaf72fbf5079dc372a51a9f268fc38d46f767cbf85c43a36da5cb9b575"}, + {file = "widgetsnbextension-4.0.14.tar.gz", hash = "sha256:a3629b04e3edb893212df862038c7232f62973373869db5084aed739b437b5af"}, ] [[package]] @@ -5943,6 +6416,7 @@ version = "1.17.2" description = "Module for decorators, wrappers and monkey patching." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "wrapt-1.17.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3d57c572081fed831ad2d26fd430d565b76aa277ed1d30ff4d40670b1c0dd984"}, {file = "wrapt-1.17.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b5e251054542ae57ac7f3fba5d10bfff615b6c2fb09abeb37d2f1463f841ae22"}, @@ -6031,17 +6505,19 @@ version = "3.21.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.9" +groups = ["main", "dev"] +markers = "python_version < \"3.10\"" files = [ {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"}, {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] [extras] @@ -6052,6 +6528,6 @@ mariadb = ["mariadb"] postgres = ["psycopg2-binary"] [metadata] -lock-version = "2.0" +lock-version = "2.1" python-versions = "^3.9" -content-hash = "c9060878d6892edca9c7fb46a0fcebed9cec12d9d3a2aa5e4f2fe5f9dca810fb" +content-hash = "9de9061acbb2fd17b14c25052603b113f4f8a41a7a6176f6a05ae3125cd6d3ef" diff --git a/pyproject.toml b/pyproject.toml index e53db50..f47ffd3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -56,6 +56,7 @@ rdflib = "^7.1.1" jsonasobj2 = "^1.0.4" deprecation = "^2.1.0" numpy = "<2.0" +lxml = "^5.3.0" pydbml = "^1.1.2" pyyaml = "^6.0.2" llm = {version = "^0.21", optional = true} @@ -68,6 +69,10 @@ sphinx-click = ">=3.1.0" sphinxcontrib-mermaid = ">=0.9.2" myst-parser = "*" jupyter = ">=1.0.0" +lxml-stubs = "^0.5.1" + +[tool.poetry.group.llm.dependencies] +llm = ">=0.12" lxml = ">=4.9.1" deptry = "^0.23.0" diff --git a/schema_automator/cli.py b/schema_automator/cli.py index 780d0b3..641abd8 100644 --- a/schema_automator/cli.py +++ b/schema_automator/cli.py @@ -32,6 +32,7 @@ from schema_automator.importers.rdfs_import_engine import RdfsImportEngine from schema_automator.importers.sql_import_engine import SqlImportEngine from schema_automator.importers.tabular_import_engine import TableImportEngine +from schema_automator.importers.xsd_import_engine import XsdImportEngine from schema_automator.utils.schemautils import write_schema from schema_automator import __version__ @@ -497,6 +498,23 @@ def import_rdfs(rdfsfile: str, output: str, metamodel_mappings: str, schema_name schema = sie.convert(rdfsfile, name=schema_name, **args) write_schema(schema, output) +@main.command() +@click.argument('xsd') +@output_option +@schema_name_option +@click.option('--output', '-o', help="Path to saved yaml schema") +def import_xsd(xsd: str, output: str, **kwargs): + """ + Import an XML Schema Definition Language (XSD) schema to LinkML + + Example: + + schemauto import-xsd schema.xml -o prov.yaml + """ + engine = XsdImportEngine() + schema = engine.convert(xsd, **kwargs) + write_schema(schema, output) + @main.command() @click.argument('rdffile') @output_option diff --git a/schema_automator/importers/__init__.py b/schema_automator/importers/__init__.py index 2011d25..21d1c8f 100644 --- a/schema_automator/importers/__init__.py +++ b/schema_automator/importers/__init__.py @@ -3,3 +3,13 @@ from schema_automator.importers.dosdp_import_engine import DOSDPImportEngine from schema_automator.importers.frictionless_import_engine import FrictionlessImportEngine from schema_automator.importers.cadsr_import_engine import CADSRImportEngine +from schema_automator.importers.xsd_import_engine import XsdImportEngine + +__all__ = [ + 'JsonSchemaImportEngine', + 'OwlImportEngine', + 'DOSDPImportEngine', + 'FrictionlessImportEngine', + 'CADSRImportEngine', + 'XsdImportEngine' +] diff --git a/schema_automator/importers/xsd_import_engine.py b/schema_automator/importers/xsd_import_engine.py new file mode 100644 index 0000000..fc2410e --- /dev/null +++ b/schema_automator/importers/xsd_import_engine.py @@ -0,0 +1,611 @@ +from __future__ import annotations +from dataclasses import dataclass, field +import re +from types import GenericAlias +from typing import Any, Iterable, Type, cast, TypeVar +from urllib.parse import urljoin +from linkml.utils.schema_builder import SchemaBuilder +from linkml_runtime.linkml_model import ( + SchemaDefinition, + SlotDefinition, + ClassDefinition, +) +from linkml_runtime.linkml_model.meta import AnonymousSlotExpression +from linkml_runtime.utils import formatutils +from lxml import etree + + +from linkml_runtime.linkml_model import SchemaDefinition +from schema_automator.importers.import_engine import ImportEngine + +# Mapping between https://www.w3.org/TR/2012/REC-xmlschema11-2-20120405/datatypes.html#built-in-primitive-datatypes and https://linkml.io/linkml-model/latest/docs/#types +TYPE_MAP = { + "anyURI": "Uri", + "boolean": "Boolean", + "date": "Date", + "dateTime": "DateTime", + "decimal": "Decimal", + "double": "Double", + "float": "Float", + "string": "String", + "time": "Time", + "int": "Integer", + "integer": "Integer", + # NMTOKEN is basically just a string inside an attribute + "NMTOKEN": "String", +} +PLACEHOLDER_NAME = "PLACEHOLDER" +Attributes = dict[str, SlotDefinition] +MISSING_TYPES = { + "base64Binary", + "duration", + "hexBinary", + "gDay", + "gMonth", + "gMonthDay", + "gYear", + "gYearMonth", + "NOTATION", + "QName", + "normalizedString", + "token", + "language", + "NMTOKEN", + "NMTOKENS", + "Name", + "NCName", + "ID", + "IDREF", + "IDREFS", + "ENTITY", + "ENTITIES", + "nonPositiveInteger", + "negativeInteger", + "long", + "short", + "byte", + "nonNegativeInteger", + "unsignedLong", + "unsignedInt", + "unsignedShort", + "unsignedByte", + "positiveInteger", +} +XSD = "http://www.w3.org/2001/XMLSchema" +NAMESPACES = {"xsd": "http://www.w3.org/2001/XMLSchema"} + +T = TypeVar("T") +def assert_type(x: Any, t: Type[T]) -> T: + """ + Utility function to assert that a value is of a certain type. + Useful when we know that, say, `element.text` is a string and not bytes. + Unlike `cast`, this function will raise an error if the type is incorrect to avoid silent failures. + """ + # Allow generics such as list[t] to be passed in, but only check the base type such as list + if isinstance(t, GenericAlias): + base_type = t.__origin__ + else: + base_type = t + if not isinstance(x, base_type): + raise TypeError(f"Expected {t}, got {type(x)}") + return x + +def xsd_to_linkml_type(xsd_type: etree.QName) -> str: + """ + Returns the LinkML type from an XSD type + """ + if xsd_type.namespace == XSD: + if xsd_type.localname in TYPE_MAP: + # Atomic XSD types can be looked up + return TYPE_MAP[xsd_type.localname] + elif xsd_type.localname in MISSING_TYPES: + raise ValueError( + f"Atomic type {xsd_type} does not have a corresponding LinkML type" + ) + else: + raise ValueError(f"Atomic type {xsd_type} is not defined in the standard") + else: + # Assume any remaining type is a complex type that we have or will define separately + return xsd_type.localname + + +def resolve_type(el: etree._Element, attribute: str) -> etree.QName: + """ + Returns the fully resolved type of an XSD element + + Params: + el: the element to resolve the type of. Must be either an or , with a 'type' attribute. + attribute: the attribute that holds the type information, e.g. "type" or "base" + """ + typ: str = el.attrib.get(attribute, "string") + if typ.count(":") == 1: + # Hacky fallback for when a custom namespace is used + prefix, name = typ.split(":") + return etree.QName(el.nsmap[prefix], name) + else: + return etree.QName(typ) + + +def element_to_linkml_type(el: etree._Element, attribute: str) -> str: + """ + Returns the LinkML type of an XSD element + + Params: + el: the element to resolve the type of. Must be either an or , with a 'type' attribute. + attribute: the attribute that holds the type information, e.g. "type" or "base" + """ + return xsd_to_linkml_type(resolve_type(el, attribute)) + + +def find_class_name(el: etree._Element, root_name: str = "Root") -> str: + """ + Returns the name of the class that this element is a slot for + + Params: + el: the element that will be a slot for the class whose name we want to find + root_name: class name to assign to the schema's root + """ + for parent in el.iterancestors(): + if "name" in parent.attrib: + return assert_type(parent.attrib["name"], str) + elif parent.tag == f"{{{XSD}}}schema": + return root_name + raise ValueError("Could not find class name for element") + +def get_value_element(cls: ClassDefinition) -> SlotDefinition: + if not isinstance(cls.attributes, dict): + raise ValueError("cls.attributes should be a dictionary at this point") + if "value" not in cls.attributes: + raise ValueError("Value element should have been added by this stage") + return cast(SlotDefinition, cls.attributes["value"]) + +@dataclass +class XsdImportEngine(ImportEngine): + sb: SchemaBuilder = field(default_factory=lambda: SchemaBuilder()) + target_ns: str | None = None + + def __post_init__(self): + self.sb.add_defaults() + self.sb.add_prefix("xsd", XSD) + + def visit_element(self, el: etree._Element) -> SlotDefinition: + """ + Converts an `` into a SlotDefinition + + See 3.3.2 XML Representation of Element Declaration Schema Components: https://www.w3.org/TR/2012/REC-xmlschema11-1-20120405/structures.html#declare-element + """ + + slot_name = formatutils.lcamelcase(assert_type(el.attrib["name"], str)) if "name" in el.attrib else PLACEHOLDER_NAME + slot = SlotDefinition( + name=formatutils.lcamelcase(slot_name) if "name" in el.attrib else PLACEHOLDER_NAME, + slot_uri=urljoin(self.target_ns, slot_name) if self.target_ns else None, + instantiates=["xsd:element"], + range = "boolean" + ) + """ + XML supports empty elements, which we can represent as booleans. + For example this XML data: + ```xml + + + + ``` + Can be represented as: + ```yaml + parent: + some_flag: true + ``` + """ + + # First pass, to determine if this is simple or complex + for child in el: + if child.tag == f"{{{XSD}}}complexType": + # If we find a complex type, we need to create a class + cls_name: str = el.attrib.get("name", PLACEHOLDER_NAME) + cls = ClassDefinition( + name=cls_name, + class_uri=urljoin(self.target_ns, cls_name) if self.target_ns else None + ) + self.sb.add_class(cls) + slot.range = cls_name + self.visit_complex_type(child, cls) + elif child.tag == f"{{{XSD}}}simpleType": + # If we find a simple type, the range is a restriction of a primitive type + self.visit_simple_type(child, slot) + + + if "type" in el.attrib: + slot.range = element_to_linkml_type(el, "type") + + if "ref" in el.attrib: + # If we find a ref, we're creating a slot. Also, that slot's range is a reference to another class. + # We can make up a name for the slot using the referenced class, although the slot doesn't actually have a name in XSD + slot.range = assert_type(el.attrib["ref"], str) + + if slot.name == PLACEHOLDER_NAME: + slot.name = formatutils.lcamelcase(assert_type(el.attrib["ref"], str)) + + # Second pass, to add annotations + for child in el: + if child.tag == f"{{{XSD}}}annotation": + # If we find an annotation, we can use it as documentation + slot.description = self.visit_annotation(child, slot.description) + + return slot + + def visit_documentation(self, el: etree._Element) -> str: + """ + Converts an `` into a string + """ + return re.sub(r"\s+", " ", assert_type(el.text, str)).strip() + + def visit_annotation(self, el: etree._Element, existing: str | None = None) -> str: + """ + Converts an annotation into a string to be used for documentation + + See 3.15.2 XML Representation of Annotation Schema Components: https://www.w3.org/TR/2012/REC-xmlschema11-1-20120405/structures.html#declare-annotation + + Params: + el: the `` element + existing: any existing documentation to append to + """ + # Note: This only supports xsd:documentation, other annotation types are ignored + text = [] + if existing is not None: + text.append(existing) + for child in el: + if child.tag == f"{{{XSD}}}documentation": + text.append(self.visit_documentation(child)) + return "\n".join(text) + + def visit_simple_type_restriction(self, el: etree._Element, slot: SlotDefinition | AnonymousSlotExpression) -> None: + """" + Visits an and applies type restrictions to a slot. + + Despite the name, this can be used for both simple types: + ```xml + + + ... + + + ``` + and complex types: + ```xml + + + + ... + + + + ``` + Since there are a subset of elements that can be used inside both. + """ + slot.range = element_to_linkml_type(el, "base") + for child in el: + value = assert_type(child.attrib["value"], str) + if child.tag == f"{{{XSD}}}minInclusive": + slot.minimum_value = value + elif child.tag == f"{{{XSD}}}maxInclusive": + slot.maximum_value = value + elif child.tag == f"{{{XSD}}}pattern": + slot.pattern = value + elif child.tag == f"{{{XSD}}}minLength": + slot.minimum_cardinality = int(value) + elif child.tag == f"{{{XSD}}}maxLength": + slot.maximum_cardinality = int(value) + + def visit_simple_content_restriction(self, el: etree._Element, cls: ClassDefinition) -> None: + """ + Visit a restriction inside a simple content element: + ```xml + + + + ... + + + + ``` + """ + value = get_value_element(cls) + self.visit_simple_type_restriction(el, value) + for child in el: + if child.tag == f"{{{XSD}}}attribute": + if cls.attributes is None: + cls.attributes = {} + attributes = assert_type(cls.attributes, Attributes) + name = assert_type(child.attrib["name"], str) + attributes[name] = self.visit_attribute(child) + + def visit_simple_content_extension(self, el: etree._Element, cls: ClassDefinition) -> None: + """ + Visit a: + ```xml + + + + ... + + + + ``` + """ + cls.is_a = element_to_linkml_type(el, "base") + for child in el: + if child.tag == f"{{{XSD}}}attribute": + name = assert_type(child.attrib["name"], str) + attributes = assert_type(cls.attributes, dict[str, SlotDefinition]) + attributes[name] = self.visit_attribute(child) + + def visit_simple_content(self, el: etree._Element, cls: ClassDefinition) -> None: + """ + Visit a: + ```xml + + + ... + + + ``` + See 3.4.2.2 Mapping Rules for Complex Types with Simple Content: https://www.w3.org/TR/2012/REC-xmlschema11-2-20120405/datatypes.html#xr-defn + + simpleContent maps to a ClassDefinition as it can have multiple values due to XML attributes. + It must also have a main value which is the content inside the XML element. Therefore: + ```xml + + + + + + + + ``` + Would be represented as: + ```yaml + SomeClass: + attributes: + someAttr: + range: integer + value: + range: string + ``` + """ + value_slot = SlotDefinition( + name="value", + comments=["Mapped from the main content of the element"], + ) + + attributes = assert_type(cls.attributes, Attributes) + attributes["value"] = value_slot + for child in el: + if child.tag == f"{{{XSD}}}restriction": + self.visit_simple_content_restriction(child, cls) + elif child.tag == f"{{{XSD}}}extension": + self.visit_simple_content_extension(child, cls) + elif child.tag == f"{{{XSD}}}annotation": + # Annotations inside simple content are applied to the value slot, not the class + value_slot.description = self.visit_annotation(child, value_slot.description) + + def visit_simple_type(self, el: etree._Element, slot: SlotDefinition | AnonymousSlotExpression) -> None: + """ + Converts an `` into a LinkML type + + A simple type always maps to a slot in LinkML since it cannot have attributes or children. + e.g. + ```xml + + + ... + + + ``` + + See 3.16.2 XML Representation of Simple Type Definition Schema Components: https://www.w3.org/TR/xmlschema11-1/#declare-datatype + + Params: + el: a element + slot: the slot to annotate + """ + for child in el: + if child.tag == f"{{{XSD}}}annotation": + slot.description = self.visit_annotation(child, slot.description) + elif child.tag == f"{{{XSD}}}restriction": + self.visit_simple_type_restriction(child, slot) + elif child.tag == f"{{{XSD}}}list": + slot.multivalued = True + if "itemType" in child.attrib: + slot.range = assert_type(child.attrib["itemType"], str) + else: + slot.range = AnonymousSlotExpression() + for list_child in child: + if list_child.tag == f"{{{XSD}}}simpleType": + self.visit_simple_type(list_child, slot.range) + else: + raise ValueError("Only xsd:simpleType is allowed inside xsd:list") + raise ValueError("xsd:list must have an itemType attribute or an xsd:simpleType child element") + elif child.tag == f"{{{XSD}}}union": + slot.any_of = [] + for union_child in child: + union_slot = AnonymousSlotExpression() + self.visit_simple_type(union_child, union_slot) + slot.any_of.append(union_slot) + + def visit_attribute(self, el: etree._Element) -> SlotDefinition: + """ + Converts an `` into a SlotDefinition + """ + description: str | None = None + + for child in el: + if child.tag == f"{{{XSD}}}annotation": + description = self.visit_annotation(child) + + return SlotDefinition( + name=formatutils.lcamelcase(assert_type(el.attrib["name"], str)), + slot_uri=( + urljoin(self.target_ns, assert_type(el.attrib["name"], str)) if self.target_ns else None + ), + range=element_to_linkml_type(el, "type"), + required=el.attrib.get("use") == "required", + instantiates=["xsd:attribute"], + description=description + ) + + def visit_complex_content_child(self, el: etree._Element, cls: ClassDefinition) -> None: + """ + Visit any of the following children of an xsd:complexContent element. + We can reuse the functionality since each of these elements can contain sequence, group, choice etc + + ```xml + + + + ... + + + , + ```, or + + ```xml + + + + ... + + + + ``` + """ + if "base" in el.attrib: + cls.is_a = element_to_linkml_type(el, "base") + + attributes = assert_type(cls.attributes, Attributes) + if el.tag == f"{{{XSD}}}sequence": + attributes |= { + slot.name: slot for slot in self.visit_sequence(el) + } + elif el.tag == f"{{{XSD}}}group": + raise NotImplementedError("xsd:group is not yet supported") + elif el.tag == f"{{{XSD}}}all": + raise NotImplementedError("xsd:all is not yet supported") + elif el.tag == f"{{{XSD}}}choice": + attributes |= { + slot.name: slot for slot in self.visit_choice(el) + } + elif el.tag == f"{{{XSD}}}attribute": + slot = self.visit_attribute(el) + attributes[slot.name] = slot + elif el.tag == f"{{{XSD}}}annotation": + cls.description = self.visit_annotation(el, cls.description) + + def visit_complex_content(self, el: etree._Element, cls: ClassDefinition) -> None: + """ + Visit a: + ```xml + + + ... + + + ``` + + See 3.4.2.3 Mapping Rules for Complex Types with Complex Content: https://www.w3.org/TR/xmlschema11-1/#dcl.ctd.ctcc + + Params: + el: the element + cls: the class to annotate, derived from the enclosing element + """ + #: If we have found an extension or restriction + for child in el: + if child.tag == f"{{{XSD}}}extension": + self.visit_complex_content_child(child, cls) + elif child.tag == f"{{{XSD}}}restriction": + self.visit_complex_content_child(child, cls) + elif child.tag == f"{{{XSD}}}annotation": + cls.description = self.visit_annotation(child, cls.description) + + def visit_complex_type(self, el: etree._Element, cls: ClassDefinition) -> None: + """ + Adds information from a `` onto a ClassDefinition + + See 3.4 Complex Type Definitions: https://www.w3.org/TR/xmlschema11-1/#Complex_Type_Definitions + """ + # Update the class name using the complex type's name, if we don't already have one + if cls.name == PLACEHOLDER_NAME and "name" in el.attrib: + cls.name = assert_type(el.attrib["name"], str) + cls.class_uri = urljoin(self.target_ns, cls.name) if self.target_ns else None + + found_content = False + for child in el: + if child.tag == f"{{{XSD}}}complexContent": + self.visit_complex_content(child, cls) + found_content = True + elif child.tag == f"{{{XSD}}}simpleContent": + self.visit_simple_content(child, cls) + found_content = True + + if not found_content: + """ + 3.4.2.3.2 Mapping Rules for Complex Types with Implicit Complex Content: + > When the source declaration has neither nor as a child, it is taken as shorthand for complex content restricting ·xs:anyType·. + """ + for child in el: + self.visit_complex_content_child(child, cls) + + def visit_choice(self, el: etree._Element) -> Iterable[SlotDefinition]: + """ + Converts an xsd:choice into a list of SlotDefinitions + """ + # TODO: indicate that not all slots can be used at the same time + return self.visit_sequence(el) + + def visit_sequence(self, el: etree._Element) -> Iterable[SlotDefinition]: + """ + Converts an xsd:sequence into a list of SlotDefinitions + """ + for child in el: + if child.tag == f"{{{XSD}}}element": + yield self.visit_element(child) + elif child.tag == f"{{{XSD}}}choice": + yield from self.visit_choice(child) + elif child.tag == f"{{{XSD}}}sequence": + yield from self.visit_sequence(child) + elif isinstance(child, etree._Comment): + pass + else: + print(f"Skipping unknown tag {child.tag}") + + def visit_schema(self, schema: etree._Element) -> None: + """ + Converts an xsd:schema into a SchemaDefinition + """ + self.target_ns = schema.attrib.get("targetNamespace") + if self.target_ns is not None and not self.target_ns.endswith("/"): + # Ensure that the target namespace ends with a slash + self.target_ns += "/" + + attributes: dict[str, SlotDefinition] = {} + for child in schema: + if child.tag == f"{{{XSD}}}element": + definition = self.visit_element(child) + attributes[definition.name] = definition + elif child.tag == f"{{{XSD}}}complexType": + # complexType can be at the top level + cls = ClassDefinition(name=PLACEHOLDER_NAME) + self.visit_complex_type(child, cls) + self.sb.add_class(cls) + schema_root = ClassDefinition( + name="SchemaRoot", + class_uri=urljoin(self.target_ns, "SchemaRoot") if self.target_ns else None, + attributes=attributes, + description="Entry point of the schema, treated as a class", + ) + self.sb.add_class(schema_root) + + def convert(self, file: str, **kwargs: Any) -> SchemaDefinition: + parser = etree.XMLParser(remove_blank_text=True) + tree = etree.parse(file, parser=parser) + self.visit_schema(tree.getroot()) + return self.sb.schema diff --git a/tests/test_importers/test_xsd_importer.py b/tests/test_importers/test_xsd_importer.py new file mode 100644 index 0000000..8dc8c2d --- /dev/null +++ b/tests/test_importers/test_xsd_importer.py @@ -0,0 +1,59 @@ +from linkml_runtime import SchemaView +from schema_automator.importers import XsdImportEngine +import tempfile + +def parse_string(xsd: str) -> SchemaView: + engine = XsdImportEngine() + with tempfile.NamedTemporaryFile(mode='w', delete=False) as f: + f.write(''' + ''') + f.write(xsd) + f.write("") + schema = engine.convert(f.name) + return SchemaView(schema) + +def test_embedded_type(): + schema = parse_string('') + assert len(schema.all_classes()) == 1 + root = schema.get_class("SchemaRoot") + assert len(root.attributes) == 1 + assert root.attributes["acquisitionDate"].range == "DateTime" + assert "xsd:element" in root.attributes["acquisitionDate"].instantiates + assert "xsd" in schema.schema.prefixes + +def test_complex_type(): + schema = parse_string(''' + + + + Some docs + + + + + + + + + + + ''') + assert len(schema.all_classes()) == 2 + my_class = schema.get_class("MyClass") + assert len(my_class.attributes) == 3 + assert my_class.attributes["elementSlotA"].range == "Float" + assert my_class.attributes["elementSlotB"].range == "Integer" + assert my_class.attributes["attributeSlot"].range == "Boolean" + # The annotation should be applied to the slot and not the class + assert my_class.description is None + + root = schema.get_class("SchemaRoot") + assert len(root.attributes) == 1 + assert root.attributes["myClass"].range == "MyClass" + assert root.attributes["myClass"].description == "Some docs"