diff --git a/README.md b/README.md index f826e33..0017d8d 100644 --- a/README.md +++ b/README.md @@ -305,6 +305,7 @@ See [tests/test_mapper/test_schema_mapper.py](tests/test_schema_mapper/test_sche ## Not supported - Aggregation +- ... ## Why another framework? @@ -337,6 +338,7 @@ precise mappings between *entities* (e.g. schema.org Person is the same as DBPed that many people wanted to extend the language to perform more complex mappings. To address this, we help a workshop at the Biocuration conference in Padua, Italy in 2022. +- [Discussion](https://github.com/orgs/linkml/discussions/1829) - [SSSOM paper](https://academic.oup.com/database/article/doi/10.1093/database/baac035/6591806) - [SSSOM Update 2023](https://ceur-ws.org/Vol-3591/om2023_STpaper3.pdf) - [SSSOM Complex Mappings Workshop 2023](https://www.youtube.com/playlist?list=PLqu_J7ADQtKyX55F7RqZtaSS7TwGd3MoR) diff --git a/notebooks/Tutorial.ipynb b/notebooks/Tutorial.ipynb index 84008af..73a00a9 100644 --- a/notebooks/Tutorial.ipynb +++ b/notebooks/Tutorial.ipynb @@ -24,8 +24,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:05.802136Z", - "start_time": "2024-01-03T02:07:05.768310Z" + "end_time": "2024-01-17T22:29:59.302402Z", + "start_time": "2024-01-17T22:29:58.965289Z" } }, "id": "63a064b31f623bdd" @@ -97,8 +97,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:06.074890Z", - "start_time": "2024-01-03T02:07:05.802747Z" + "end_time": "2024-01-17T22:29:59.378265Z", + "start_time": "2024-01-17T22:29:58.988218Z" } }, "id": "ef2c60ef7fbcbe20" @@ -136,8 +136,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:06.134479Z", - "start_time": "2024-01-03T02:07:06.074052Z" + "end_time": "2024-01-17T22:30:01.239725Z", + "start_time": "2024-01-17T22:29:59.312872Z" } }, "id": "a6257aa9e6ab021e" @@ -166,8 +166,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:06.368605Z", - "start_time": "2024-01-03T02:07:06.138171Z" + "end_time": "2024-01-17T22:30:01.484509Z", + "start_time": "2024-01-17T22:30:01.238874Z" } }, "id": "47b95e209790b423" @@ -191,7 +191,7 @@ { "data": { "image/svg+xml": "\n\n\n\n\n\n\n\n\nsourcePerson\n\nPerson\n\nfamily_name : string\n\ngiven_name : string\n\nage_in_years : integer\n\nheight_in_cm : float\n\n\n\ntargetIndividual\n\nIndividual\n\nfamily_name : string\n\ngiven_name : string\n\nage : integer\n\nheight : float\n\n\n\nsourcePerson:family_name->targetIndividual:family_name\n\n\n\n\n\nsourcePerson:given_name->targetIndividual:given_name\n\n\n\n\n\nsourcePerson:age_in_years->targetIndividual:age\n\n\n\n\n\nsourcePerson:height_in_cm->targetIndividual:height\n\n\n\n\n\n", - "text/plain": "" + "text/plain": "" }, "execution_count": 5, "metadata": {}, @@ -204,8 +204,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:06.816125Z", - "start_time": "2024-01-03T02:07:06.369496Z" + "end_time": "2024-01-17T22:30:02.244818Z", + "start_time": "2024-01-17T22:30:01.486984Z" } }, "id": "1c623cdc3c1cfbca" @@ -249,8 +249,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:06.829871Z", - "start_time": "2024-01-03T02:07:06.823308Z" + "end_time": "2024-01-17T22:30:02.251017Z", + "start_time": "2024-01-17T22:30:02.241183Z" } }, "id": "9f4d1fc4ca97f80c" @@ -336,8 +336,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:06.853312Z", - "start_time": "2024-01-03T02:07:06.832158Z" + "end_time": "2024-01-17T22:30:02.260147Z", + "start_time": "2024-01-17T22:30:02.253561Z" } }, "id": "687912c18bf6752" @@ -398,8 +398,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:06.903169Z", - "start_time": "2024-01-03T02:07:06.848243Z" + "end_time": "2024-01-17T22:30:02.326085Z", + "start_time": "2024-01-17T22:30:02.258015Z" } }, "id": "789a7b6535ab410f" @@ -422,7 +422,7 @@ { "data": { "image/svg+xml": "\n\n\n\n\n\n\n\n\nsourcePerson\n\nPerson\n\nfamily_name : string\n\ngiven_name : string\n\nage_in_years : integer\n\nheight_in_cm : float\n\n\n\ntargetIndividual\n\nIndividual\n\nname : string\n\nage_in_months : string\n\nheight_in_meters : string\n\n\n\nsourcePerson:given_name->targetIndividual:name\n\n\n\n\n\nsourcePerson:family_name->targetIndividual:name\n\n\n\n\n\nsourcePerson:age_in_years->targetIndividual:age_in_months\n\n\n\n\n\nsourcePerson:height_in_cm->targetIndividual:height_in_meters\n\n\n\n\n\n", - "text/plain": "" + "text/plain": "" }, "execution_count": 9, "metadata": {}, @@ -435,8 +435,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.250708Z", - "start_time": "2024-01-03T02:07:06.913474Z" + "end_time": "2024-01-17T22:30:03.283023Z", + "start_time": "2024-01-17T22:30:02.345894Z" } }, "id": "2a18ccb5d7dc469b" @@ -470,8 +470,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.250930Z", - "start_time": "2024-01-03T02:07:07.244685Z" + "end_time": "2024-01-17T22:30:03.283868Z", + "start_time": "2024-01-17T22:30:03.278695Z" } }, "id": "5e20e98e2b23751f" @@ -528,8 +528,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.256503Z", - "start_time": "2024-01-03T02:07:07.252109Z" + "end_time": "2024-01-17T22:30:03.290589Z", + "start_time": "2024-01-17T22:30:03.286701Z" } }, "id": "7c1f7efef1836364" @@ -608,8 +608,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.271763Z", - "start_time": "2024-01-03T02:07:07.266055Z" + "end_time": "2024-01-17T22:30:03.323328Z", + "start_time": "2024-01-17T22:30:03.300567Z" } }, "id": "65a5ce5d97e27f76" @@ -649,8 +649,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.329627Z", - "start_time": "2024-01-03T02:07:07.293054Z" + "end_time": "2024-01-17T22:30:03.365363Z", + "start_time": "2024-01-17T22:30:03.321298Z" } }, "id": "bc99bad97970b1b7" @@ -674,8 +674,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.635126Z", - "start_time": "2024-01-03T02:07:07.330891Z" + "end_time": "2024-01-17T22:30:03.622621Z", + "start_time": "2024-01-17T22:30:03.370531Z" } }, "id": "831b444d9c47e0ea" @@ -734,8 +734,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.640576Z", - "start_time": "2024-01-03T02:07:07.635834Z" + "end_time": "2024-01-17T22:30:03.629604Z", + "start_time": "2024-01-17T22:30:03.624546Z" } }, "id": "b589e0e95550962d" @@ -760,8 +760,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.645267Z", - "start_time": "2024-01-03T02:07:07.640190Z" + "end_time": "2024-01-17T22:30:03.630816Z", + "start_time": "2024-01-17T22:30:03.629262Z" } }, "id": "f492b27c0f0fbf88" @@ -776,8 +776,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.648640Z", - "start_time": "2024-01-03T02:07:07.643720Z" + "end_time": "2024-01-17T22:30:03.661717Z", + "start_time": "2024-01-17T22:30:03.635358Z" } }, "id": "3ac3f93ab8561300" @@ -792,8 +792,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.683985Z", - "start_time": "2024-01-03T02:07:07.654269Z" + "end_time": "2024-01-17T22:30:03.662631Z", + "start_time": "2024-01-17T22:30:03.646582Z" } }, "id": "84262d357323f76e" @@ -825,8 +825,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.715300Z", - "start_time": "2024-01-03T02:07:07.674231Z" + "end_time": "2024-01-17T22:30:03.709283Z", + "start_time": "2024-01-17T22:30:03.667849Z" } }, "id": "2f282430f48e13c0" @@ -858,8 +858,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.747368Z", - "start_time": "2024-01-03T02:07:07.716444Z" + "end_time": "2024-01-17T22:30:03.739195Z", + "start_time": "2024-01-17T22:30:03.711288Z" } }, "id": "fdd23ae82909770e" @@ -909,8 +909,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.789903Z", - "start_time": "2024-01-03T02:07:07.759627Z" + "end_time": "2024-01-17T22:30:03.781498Z", + "start_time": "2024-01-17T22:30:03.754420Z" } }, "id": "e8c1c3f98081d38" @@ -923,8 +923,8 @@ "metadata": { "collapsed": false, "ExecuteTime": { - "end_time": "2024-01-03T02:07:07.793832Z", - "start_time": "2024-01-03T02:07:07.788230Z" + "end_time": "2024-01-17T22:30:03.785065Z", + "start_time": "2024-01-17T22:30:03.782845Z" } }, "id": "ee14ace4b1c7d256" diff --git a/poetry.lock b/poetry.lock index a5de47e..16c3dca 100644 --- a/poetry.lock +++ b/poetry.lock @@ -25,24 +25,26 @@ files = [ [[package]] name = "anyio" -version = "3.6.2" +version = "4.2.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" category = "dev" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.8" files = [ - {file = "anyio-3.6.2-py3-none-any.whl", hash = "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"}, - {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"}, + {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"}, + {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"}, ] [package.dependencies] +exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] -trio = ["trio (>=0.16,<0.22)"] +doc = ["Sphinx (>=7)", "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)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] [[package]] name = "appnope" @@ -58,23 +60,24 @@ files = [ [[package]] name = "argon2-cffi" -version = "21.3.0" -description = "The secure Argon2 password hashing algorithm." +version = "23.1.0" +description = "Argon2 for Python" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "argon2-cffi-21.3.0.tar.gz", hash = "sha256:d384164d944190a7dd7ef22c6aa3ff197da12962bd04b17f64d4e93d934dba5b"}, - {file = "argon2_cffi-21.3.0-py3-none-any.whl", hash = "sha256:8c976986f2c5c0e5000919e6de187906cfd81fb1c72bf9d88c01177e77da7f80"}, + {file = "argon2_cffi-23.1.0-py3-none-any.whl", hash = "sha256:c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea"}, + {file = "argon2_cffi-23.1.0.tar.gz", hash = "sha256:879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08"}, ] [package.dependencies] argon2-cffi-bindings = "*" [package.extras] -dev = ["cogapp", 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1da5e61..05e85f5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,7 @@ linkml-runtime = ">=1.5.2" asteval = "^0.9.29" deepdiff = "^6.7.1" pydantic = "^2.5.3" -pyoxigraph = "^0.3.22" +ucumvert = "^0.1.1" [tool.poetry.dev-dependencies] pytest = "^7.3.1" diff --git a/src/linkml_transformer/functions/unit_conversion.py b/src/linkml_transformer/functions/unit_conversion.py index 28af916..49f771d 100644 --- a/src/linkml_transformer/functions/unit_conversion.py +++ b/src/linkml_transformer/functions/unit_conversion.py @@ -1,29 +1,30 @@ """ Basic unit conversion functions. -Currently uses pint, which is an optional dependency. But -note that pint may not work well with UCUM, see: +Currently only native pint units or UCUM units are supported. -- https://github.com/hgrecco/pint/issues/1769 +For UCUM, the ucumvert library is used to convert UCUM units to pint units, +see ``_. """ -import re from enum import Enum from functools import lru_cache from typing import Any, Optional +import lark +import pint +from ucumvert import PintUcumRegistry + class UnitSystem(str, Enum): + """Enumeration of supported unit systems.""" + UCUM = "ucum" IEC61360 = "iec61360" - SI = "si" + SI = "SI" -# TODO: this is currently highly incomplete; consider deriving from established mappings -MAPPINGS = { - UnitSystem.UCUM: { - "mo": "month", - "Cel": "degC", - }, +REGISTRIES = { + UnitSystem.UCUM: PintUcumRegistry(), } @@ -36,6 +37,12 @@ class UndefinedUnitError(Exception): """ +class QuantitySyntaxError(Exception): + """ + Raised when a quantity cannot be parsed. + """ + + class DimensionalityError(Exception): """ Raised when a unit conversion cannot be performed. @@ -51,10 +58,25 @@ def convert_units( """ Convert a quantity between units. + >>> convert_units(1, "m", "cm") + 100.0 + >>> convert_units(1, "m", "cm", system=UnitSystem.UCUM) + 100.0 + >>> convert_units(1, "m", "cm", system=UnitSystem.SI) + 100.0 + >>> convert_units(1.0, "hectare", "m^2", system=UnitSystem.SI) + 10000.0 + >>> convert_units(1.0, "hectare", "m ** 2", system=UnitSystem.SI) + 10000.0 + >>> convert_units(1.0, "hectare", "m ** 2", system=None) + 10000.0 + >>> convert_units(1.0, "km2", "m2", system=UnitSystem.UCUM) + 1000000.0 + :param magnitude: :param from_unit: :param to_unit: - :return: + :return: converted magnitude """ import pint @@ -63,6 +85,8 @@ def convert_units( to_unit = normalize_unit(to_unit, system) try: from_unit_q = ureg.parse_units(from_unit) + except lark.exceptions.UnexpectedCharacters: + raise UndefinedUnitError(f"Cannot parse unit: {from_unit}") except pint.errors.UndefinedUnitError: raise UndefinedUnitError(f"Unknown source unit: {from_unit}") quantity = magnitude * from_unit_q @@ -79,7 +103,30 @@ def get_unit_registry(system: Optional[UnitSystem] = None) -> Any: """ Get a unit registry. - :param system: + >>> ureg = get_unit_registry(UnitSystem.UCUM) + >>> ureg.from_ucum("m/s2.kg") + + >>> str(_) + '1.0 kilogram * meter / second ** 2' + >>> ureg.from_ucum("m[H2O]{35Cel}") # UCUM code with annotation + + >>> _.to("mbar") + + >>> ureg("degC") # a standard pint unit + + >>> ureg.from_ucum("g/m2") + + >>> _.to(ureg.from_ucum("kg/m2")) + + >>> ureg.from_ucum("nmol/mmol{Cre}") + + >>> sireg = get_unit_registry(UnitSystem.SI) + >>> sireg("degC") + + >>> sireg("ha") + + + :param system: currently only supported values are None or UnitSystem.UCUM :return: """ import pint @@ -87,54 +134,23 @@ def get_unit_registry(system: Optional[UnitSystem] = None) -> Any: ureg = pint.UnitRegistry() if not system: return ureg - if system not in MAPPINGS: - raise NotImplementedError(f"Unknown unit system: {system}") - for k, v in MAPPINGS[system].items(): - ureg.define(f"{k} = {v}") - return ureg + if system in REGISTRIES: + return REGISTRIES[system] + if system.value in dir(ureg.sys): + ureg.default_system = system.value + return ureg + raise NotImplementedError(f"Unknown unit system: {system}") def normalize_unit(unit: str, system: Optional[UnitSystem] = None) -> str: if system is None: return unit if system == UnitSystem.UCUM: - return remove_ucum_annotations(convert_to_exponential_format(convert_dot_to_slash(unit))) + try: + return str(get_unit_registry(system).from_ucum(unit)) + except pint.errors.UndefinedUnitError: + raise UndefinedUnitError(f"Unknown unit: {unit}") + except lark.exceptions.UnexpectedCharacters: + raise UndefinedUnitError(f"Cannot parse unit: {unit}") else: return unit - - -def remove_ucum_annotations(code: str) -> str: - """ - Remove UCUM annotations from text. - - >>> remove_ucum_annotations("nmol/mmol{Cre}") - 'nmol/mmol' - - :param text: - :return: - """ - # Regular expression to find and replace UCUM annotations - return re.sub(r"\{.*?\}", "", code) - - -def convert_to_exponential_format(code: str) -> str: - """ - Convert units like g/m2 to g/m^2 in the given text. - - >>> convert_to_exponential_format("g/m2") - 'g/m^2' - - """ - # Regular expression to find and replace units like g/m2 to g/m^2 - return re.sub(r"(\w+)/(\w+)(\d+)", r"\1/\2^\3", code) - - -def convert_dot_to_slash(text): - """ - Convert units from forms like pmol.umol-1 to pmol/umol in the given text. - - >>> convert_dot_to_slash("pmol.umol-1") - 'pmol/umol' - """ - # Regular expression to find and replace units like pmol.umol-1 to pmol/umol - return re.sub(r"(\w+)\.(\w+)-1", r"\1/\2", text) diff --git a/tests/test_compliance/test_compliance_suite.py b/tests/test_compliance/test_compliance_suite.py index bad8e4f..3160d56 100644 --- a/tests/test_compliance/test_compliance_suite.py +++ b/tests/test_compliance/test_compliance_suite.py @@ -515,8 +515,19 @@ def infer_range(v: Any, typ: Optional[str] = None): ("s1", "s1", "pinknoodles", "m", "ucum_code", 1.0, None, UndefinedUnitError, None), ("s1", "s1", "m/s", "cm/s", "ucum_code", 1.0, 100.0, None, None), ("s1", "s1", "m.s-1", "cm.s-1", "ucum_code", 1.0, 100.0, None, None), - ("s1", "s1", "g.m2-1", "kg.m2-1", "ucum_code", 1.0, 0.001, None, None), + ( + "s1", + "s1", + "g.m2-1", + "kg.m2-1", + "ucum_code", + 1.0, + 0.001, + None, + "https://github.com/dalito/ucumvert/issues/8", + ), ("height_in_m", "height_in_cm", "m", "cm", "ucum_code", 1.0, 100.0, None, None), + ("s1", "s1", "m[H2O]{35Cel}", "m[H2O]{35Cel}", "ucum_code", 1.0, 1.0, None, None), ], ) def test_simple_unit_conversion(