pymetadata 0.5.0__py3-none-any.whl
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- pymetadata/__init__.py +14 -0
- pymetadata/cache.py +52 -0
- pymetadata/chebi.py +92 -0
- pymetadata/console.py +18 -0
- pymetadata/core/__init__.py +1 -0
- pymetadata/core/annotation.py +396 -0
- pymetadata/core/creator.py +46 -0
- pymetadata/core/synonym.py +12 -0
- pymetadata/core/xref.py +66 -0
- pymetadata/examples/__init__.py +1 -0
- pymetadata/examples/cache_path_example.py +15 -0
- pymetadata/examples/omex_example.py +46 -0
- pymetadata/examples/results/test_from_files.omex +0 -0
- pymetadata/examples/results/test_from_omex.omex +0 -0
- pymetadata/examples/results/testomex/README.md +3 -0
- pymetadata/examples/results/testomex/manifest.xml +9 -0
- pymetadata/examples/results/testomex/models/omex_comp.xml +174 -0
- pymetadata/examples/results/testomex/models/omex_comp_flat.xml +215 -0
- pymetadata/examples/results/testomex/models/omex_minimal.xml +99 -0
- pymetadata/examples/test.omex +0 -0
- pymetadata/identifiers/__init__.py +1 -0
- pymetadata/identifiers/miriam.py +43 -0
- pymetadata/identifiers/registry.py +397 -0
- pymetadata/log.py +29 -0
- pymetadata/metadata/__init__.py +6 -0
- pymetadata/metadata/eco.py +15918 -0
- pymetadata/metadata/kisao.py +2731 -0
- pymetadata/metadata/sbo.py +3754 -0
- pymetadata/omex.py +771 -0
- pymetadata/omex_v2.py +30 -0
- pymetadata/ontologies/__init__.py +1 -0
- pymetadata/ontologies/ols.py +214 -0
- pymetadata/ontologies/ontology.py +312 -0
- pymetadata/py.typed +0 -0
- pymetadata/resources/chebi_webservice_wsdl.xml +509 -0
- pymetadata/resources/ontologies/README.md +4 -0
- pymetadata/resources/templates/ontology_enum.pytemplate +61 -0
- pymetadata/unichem.py +190 -0
- pymetadata-0.5.0.dist-info/METADATA +154 -0
- pymetadata-0.5.0.dist-info/RECORD +42 -0
- pymetadata-0.5.0.dist-info/WHEEL +4 -0
- pymetadata-0.5.0.dist-info/licenses/LICENSE +7 -0
pymetadata/core/xref.py
ADDED
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"""Module for crossreferences (xref)."""
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import re
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from dataclasses import dataclass
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from typing import Dict
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from urllib.parse import urlparse
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from pymetadata import log
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logger = log.get_logger(__name__)
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url_regex = re.compile(
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r"^(?:http|ftp)s?://" # http:// or https://
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r"(?:(?:[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\.)+(?:[A-Z]{2,6}\.?|[A-Z0-9-]{2,}\.?)|" # domain...
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r"localhost|" # localhost...
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r"\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3})" # ...or ip
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r"(?::\d+)?" # optional port
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r"(?:/?|[/?]\S+)$",
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re.IGNORECASE,
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)
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def is_url(url: str) -> bool:
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"""Check if string is valid url."""
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try:
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result = urlparse(url)
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if not all([result.scheme, result.netloc]):
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return False
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if re.match(url_regex, url) is None:
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return False
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except ValueError:
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return False
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return True
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@dataclass()
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class CrossReference:
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"""Handling database cross references."""
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name: str
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accession: str
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url: str
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def __post_init__(self) -> None:
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"""Validate."""
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self.validate()
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def to_dict(self) -> Dict:
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"""Convert to dict."""
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return self.__dict__
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def validate(self, warnings: bool = True) -> bool:
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"""Validate the cross reference.
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:return:
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"""
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if not is_url(self.url):
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if warnings:
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logger.warning(
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f"{self.__class__.__name__} <{self.name}|{self.accession}> "
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f"has invalid url: '{self.url}'"
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)
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return False
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return True
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"""Examples for pymetadata."""
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"""Example for customizing the cache path."""
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from pathlib import Path
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import pymetadata
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from pymetadata.chebi import ChebiQuery
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pymetadata.CACHE_PATH = Path.home() / ".cache" / "pymetadata"
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if __name__ == "__main__":
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chebis = ["CHEBI:2668", "CHEBI:138366", "CHEBI:9637", "CHEBI:155897"]
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for chebi in chebis:
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d = ChebiQuery.query(chebi=chebi, cache=True)
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"""Example for reading and writing omex archives."""
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from pathlib import Path
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from pymetadata import RESOURCES_DIR
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from pymetadata.console import console
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from pymetadata.omex import EntryFormat, ManifestEntry, Omex
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"""
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# COMBINE archives in `pymetadata`
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COMBINE archives are a convenient method to exchange files and resources relevant
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for modeling studies. `pymetadata` provides functionality for reading, writing
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and validating archives.
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## Read archive from OMEX
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To read a COMBINE archive use the `Omex` helper methods which can either read from
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a given directory or
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"""
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omex_example: Path = RESOURCES_DIR / "data" / "omex" / "CompModels.omex"
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omex = Omex.from_omex(omex_example)
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console.print(omex)
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"""
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## Write archive to directory or archive
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"""
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omex.to_directory(Path("./results/testomex"))
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omex.to_omex(Path("./results/test_from_omex.omex"))
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"""
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## Create archive from files
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In the following a new archive is created by adding entries to the archive.
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"""
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omex = Omex()
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omex.add_entry(
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entry_path=Path("results/testomex/models/omex_comp_flat.xml"),
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entry=ManifestEntry(location="./model.xml", format=EntryFormat.SBML, master=False),
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)
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omex.add_entry(
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entry_path=Path("results/testomex/README.md"),
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entry=ManifestEntry(
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location="./README.md", format=EntryFormat.MARKDOWN, master=False
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),
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)
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omex.to_omex(Path("results/test_from_files.omex"))
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console.print(omex)
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Binary file
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Binary file
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<?xml version="1.0" encoding="UTF-8"?>
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<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">
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<content location="." format="http://identifiers.org/combine.specifications/omex" />
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<content location="./manifest.xml" format="http://identifiers.org/combine.specifications/omex-manifest" />
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<content location="./README.md" format="http://purl.org/NET/mediatypes/text/x-markdown" />
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<content location="./models/omex_comp_flat.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-1" />
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<content location="./models/omex_minimal.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-1" />
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<content location="./models/omex_comp.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-1" />
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</omexManifest>
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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
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<notes>
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<body xmlns="http://www.w3.org/1999/xhtml" style="background-color: white;padding: 30px;padding-bottom: 10px;font-size: 14px;padding-top: 10px;color: #333;font-family: Helvetica, arial, sans-serif;line-height: 1.6;">
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<p style="margin: 15px 0;margin-bottom: 0 !important;margin-top: 0 !important;">Created with <a href="https://github.com/matthiaskoenig/sbmlutils" style="text-decoration: none;color: #4183C4;">https://github.com/matthiaskoenig/sbmlutils</a>.
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<a href="https://doi.org/10.5281/zenodo.5525390" style="color: #4183C4;text-decoration: none;">
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<img alt="DOI" src="https://zenodo.org/badge/DOI/10.5281/zenodo.5525390.svg" style="max-width: 100%;"/></a></p>
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</body>
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</notes>
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<model id="omex_comp">
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<notes>
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<body xmlns="http://www.w3.org/1999/xhtml" style="padding-top: 10px;font-size: 14px;padding: 30px;color: #333;padding-bottom: 10px;background-color: white;font-family: Helvetica, arial, sans-serif;line-height: 1.6;">
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<p style="margin: 15px 0;margin-top: 0 !important;margin-bottom: 0 !important;">Hierarchical model reusing the minimal model in composite model coupling.</p>
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</body>
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</notes>
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<listOfCompartments>
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<compartment id="cell0" spatialDimensions="3" size="1" constant="true">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="cell0_RE" comp:portRef="cell_port" comp:submodelRef="submodel0"/>
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</comp:listOfReplacedElements>
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</compartment>
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<compartment id="cell1" spatialDimensions="3" size="1" constant="true">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="cell1_RE" comp:portRef="cell_port" comp:submodelRef="submodel1"/>
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</comp:listOfReplacedElements>
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</compartment>
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<compartment id="cell2" spatialDimensions="3" size="1" constant="true">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="cell2_RE" comp:portRef="cell_port" comp:submodelRef="submodel2"/>
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</comp:listOfReplacedElements>
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</compartment>
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<compartment id="cell3" spatialDimensions="3" size="1" constant="true">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="cell3_RE" comp:portRef="cell_port" comp:submodelRef="submodel3"/>
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</comp:listOfReplacedElements>
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</compartment>
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<compartment id="cell4" spatialDimensions="3" size="1" constant="true">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="cell4_RE" comp:portRef="cell_port" comp:submodelRef="submodel4"/>
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</comp:listOfReplacedElements>
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</compartment>
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</listOfCompartments>
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<listOfSpecies>
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<species id="S0" compartment="cell0" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="S0_RE" comp:portRef="S1_port" comp:submodelRef="submodel0"/>
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</comp:listOfReplacedElements>
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</species>
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<species id="S1" compartment="cell1" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="S1_RE" comp:portRef="S1_port" comp:submodelRef="submodel1"/>
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</comp:listOfReplacedElements>
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</species>
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<species id="S2" compartment="cell2" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="S2_RE" comp:portRef="S1_port" comp:submodelRef="submodel2"/>
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</comp:listOfReplacedElements>
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</species>
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<species id="S3" compartment="cell3" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="S3_RE" comp:portRef="S1_port" comp:submodelRef="submodel3"/>
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</comp:listOfReplacedElements>
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</species>
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<species id="S4" compartment="cell4" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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<comp:listOfReplacedElements>
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<comp:replacedElement metaid="S4_RE" comp:portRef="S1_port" comp:submodelRef="submodel4"/>
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</comp:listOfReplacedElements>
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</species>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="D" value="0.01" constant="true"/>
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</listOfParameters>
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<listOfReactions>
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<reaction id="J0" reversible="true" fast="false">
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<listOfReactants>
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<speciesReference species="S0" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="S1" stoichiometry="1" constant="true"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> D </ci>
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<apply>
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<minus/>
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<ci> S0 </ci>
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<ci> S1 </ci>
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</apply>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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<reaction id="J1" reversible="true" fast="false">
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<listOfReactants>
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<speciesReference species="S1" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="S2" stoichiometry="1" constant="true"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> D </ci>
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<apply>
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<minus/>
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<ci> S1 </ci>
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<ci> S2 </ci>
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</apply>
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</apply>
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<p style="margin: 15px 0;margin-bottom: 0 !important;margin-top: 0 !important;">Created with <a href="https://github.com/matthiaskoenig/sbmlutils" style="text-decoration: none;color: #4183C4;">https://github.com/matthiaskoenig/sbmlutils</a>.
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<body xmlns="http://www.w3.org/1999/xhtml" style="font-size: 14px;font-family: Helvetica, arial, sans-serif;line-height: 1.6;background-color: white;color: #333;padding-top: 10px;padding-bottom: 10px;padding: 30px;">
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<p style="margin-top: 0 !important;margin-bottom: 0 !important;margin: 15px 0;">Created with <a href="https://github.com/matthiaskoenig/sbmlutils" style="text-decoration: none;color: #4183C4;">https://github.com/matthiaskoenig/sbmlutils</a>.
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<a href="https://doi.org/10.5281/zenodo.5525390" style="color: #4183C4;text-decoration: none;">
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<img alt="DOI" src="https://zenodo.org/badge/DOI/10.5281/zenodo.5525390.svg" style="max-width: 100%;"/></a></p>
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</body>
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</notes>
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<model metaid="meta_omex_minimal" id="omex_minimal" fbc:strict="false">
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<notes>
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<body xmlns="http://www.w3.org/1999/xhtml" style="color: #333;background-color: white;line-height: 1.6;padding-bottom: 10px;padding: 30px;font-family: Helvetica, arial, sans-serif;font-size: 14px;padding-top: 10px;">
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<h2 style="position: relative;font-size: 24px;border-bottom: 1px solid #cccccc;margin-top: 0;margin: 20px 0 10px;cursor: text;padding-top: 0;color: black;padding: 0;font-weight: bold;-webkit-font-smoothing: antialiased;">Terms of use</h2>
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<p style="margin: 15px 0;">The content of this model has been carefully created in a manual research effort.
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This file has been created by <a href="https://livermetabolism.com" style="text-decoration: none;color: #4183C4;">Matthias König</a>
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using <a style="text-decoration: none;color: #4183C4;"/>
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<a href="https://github.com/matthiaskoenig/sbmlutils" style="color: #4183C4;text-decoration: none;">sbmlutils</a>.
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For questions contact koenigmx@hu-berlin.de.</p>
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<a href="https://livermetabolism.com" style="text-decoration: none;color: #4183C4;">
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<img src="https://livermetabolism.com/img/people/koenig.png" style="max-width: 100%;" width="80"/>
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</a>
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Copyright © 2021 Matthias König.
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<a href="http://creativecommons.org/licenses/by/4.0/" rel="license" style="color: #4183C4;text-decoration: none;">
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<img alt="Creative Commons License" src="https://i.creativecommons.org/l/by/4.0/88x31.png" style="border-width:0;max-width: 100%;"/></a>
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<br/>This work is licensed under a <a href="http://creativecommons.org/licenses/by/4.0/" rel="license" style="text-decoration: none;color: #4183C4;">Creative Commons Attribution 4.0 International License</a>.
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<p style="margin: 15px 0;">Redistribution and use of any part of this model, with or without modification,
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are permitted provided that the following conditions are met:</p>
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<ol style="margin: 15px 0;padding-left: 30px;">
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<li style="margin-top: 0;margin: 15px 0;">Redistributions of this SBML file must retain the above copyright notice, this
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list of conditions and the following disclaimer.</li>
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<li style="margin-bottom: 0;margin: 15px 0;">Redistributions in a different form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation and/or
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other materials provided with the distribution.</li>
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</ol>
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<p style="margin-bottom: 0 !important;margin: 15px 0;">This model is distributed in the hope that it will be useful, but WITHOUT ANY
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WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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FOR A PARTICULAR PURPOSE.</p></body>
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</notes>
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Description rdf:about="#meta_omex_minimal">
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<dcterms:creator>
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<rdf:Bag>
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<rdf:li rdf:parseType="Resource">
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<vCard:N rdf:parseType="Resource">
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<vCard:Family>König</vCard:Family>
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<vCard:Given>Matthias</vCard:Given>
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</vCard:N>
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<vCard:EMAIL>koenigmx@hu-berlin.de</vCard:EMAIL>
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<vCard:ORG rdf:parseType="Resource">
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<vCard:Orgname>Humboldt-University Berlin, Institute for Theoretical Biology</vCard:Orgname>
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</vCard:ORG>
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</rdf:li>
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</rdf:Bag>
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</dcterms:creator>
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<dcterms:created rdf:parseType="Resource">
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<dcterms:W3CDTF>1900-01-01T00:00:00Z</dcterms:W3CDTF>
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</dcterms:created>
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<dcterms:modified rdf:parseType="Resource">
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<dcterms:W3CDTF>1900-01-01T00:00:00Z</dcterms:W3CDTF>
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</dcterms:modified>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfCompartments>
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<compartment id="cell" spatialDimensions="3" size="1" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species id="S1" compartment="cell" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="S2" compartment="cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="k1" value="0.1" constant="true"/>
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</listOfParameters>
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<listOfReactions>
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<reaction id="J0" reversible="false" fast="false">
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<listOfReactants>
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<speciesReference species="S1" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="S2" stoichiometry="1" constant="true"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> k1 </ci>
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<ci> S2 </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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</listOfReactions>
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<comp:listOfPorts>
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<comp:port metaid="cell_port" sboTerm="SBO:0000599" comp:idRef="cell" comp:id="cell_port" comp:name="Port of cell"/>
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<comp:port metaid="S1_port" sboTerm="SBO:0000599" comp:idRef="S1" comp:id="S1_port" comp:name="Port of S1"/>
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</comp:listOfPorts>
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</model>
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</sbml>
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Binary file
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"""Identifiers.org and MIRIAM."""
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