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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/resources/chebi_webservice_wsdl.xml ADDED Viewed

@@ -0,0 +1,509 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Published by JAX-WS RI (http://jax-ws.java.net). RI's version is JAX-WS RI 2.3.0.2 svn-revision#b53771461f7d15f7842d8b88fd794780f6b9c4b4. -->
+<definitions xmlns:tns="https://www.ebi.ac.uk/webservices/chebi" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/" name="ChebiWebServices" targetNamespace="https://www.ebi.ac.uk/webservices/chebi">
+   <types>
+      <xsd:schema xmlns="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" targetNamespace="https://www.ebi.ac.uk/webservices/chebi">
+         <xsd:complexType name="LiteEntity">
+            <xsd:sequence>
+               <xsd:element maxOccurs="1" minOccurs="1" name="chebiId" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="chebiAsciiName" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="searchScore" type="xsd:float"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="entityStar" type="xsd:int"/>
+            </xsd:sequence>
+         </xsd:complexType>
+         <xsd:complexType name="LiteEntityList">
+            <xsd:sequence>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="ListElement" type="tns:LiteEntity"/>
+            </xsd:sequence>
+         </xsd:complexType>
+         <xsd:complexType name="OntologyDataItemList">
+            <xsd:sequence>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="ListElement" type="tns:OntologyDataItem"/>
+            </xsd:sequence>
+         </xsd:complexType>
+         <xsd:complexType name="CommentDataItem">
+            <xsd:sequence>
+               <xsd:element maxOccurs="1" minOccurs="1" name="text" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="date" type="xsd:string"/>
+            </xsd:sequence>
+         </xsd:complexType>
+         <xsd:complexType name="DataItem">
+            <xsd:sequence>
+               <xsd:element maxOccurs="1" minOccurs="1" name="data" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="type" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="source" type="xsd:string"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="Comments" type="tns:CommentDataItem"/>
+            </xsd:sequence>
+         </xsd:complexType>
+         <xsd:complexType name="StructureDataItem">
+            <xsd:sequence>
+               <xsd:element maxOccurs="1" minOccurs="1" name="structure" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="type" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="dimension" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="defaultStructure" type="xsd:boolean"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="Comments" type="tns:CommentDataItem"/>
+            </xsd:sequence>
+         </xsd:complexType>
+         <xsd:complexType name="OntologyDataItem">
+            <xsd:sequence>
+               <xsd:element maxOccurs="1" minOccurs="1" name="chebiName" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="chebiId" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="type" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="status" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="cyclicRelationship" type="xsd:boolean"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="Comments" type="tns:CommentDataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="OntologyElement" type="tns:OntologyDataItem"/>
+            </xsd:sequence>
+         </xsd:complexType>
+          <xsd:complexType name="CompoundOriginDataItem">
+              <xsd:sequence>
+                  <xsd:element maxOccurs="1" minOccurs="1" name="speciesText" type="xsd:string"/>
+                  <xsd:element maxOccurs="1" minOccurs="0" name="speciesAccession" type="xsd:string"/>
+                  <xsd:element maxOccurs="1" minOccurs="0" name="componentText" type="xsd:string"/>
+                  <xsd:element maxOccurs="1" minOccurs="0" name="componentAccession" type="xsd:string"/>
+                  <xsd:element maxOccurs="1" minOccurs="0" name="strainText" type="xsd:string"/>
+                  <xsd:element maxOccurs="1" minOccurs="0" name="strainAccession" type="xsd:string"/>
+                  <xsd:element maxOccurs="1" minOccurs="1" name="SourceType" type="xsd:string"/>
+                  <xsd:element maxOccurs="1" minOccurs="1" name="SourceAccession" type="xsd:string"/>
+              </xsd:sequence>
+          </xsd:complexType>
+         <xsd:complexType name="Entity">
+            <xsd:sequence>
+               <xsd:element maxOccurs="1" minOccurs="1" name="chebiId" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="chebiAsciiName" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="definition" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="status" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="smiles" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="inchi" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="inchiKey" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="charge" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="mass" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="monoisotopicMass" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="0" name="entityStar" type="xsd:int"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="SecondaryChEBIIds" type="xsd:string"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="Synonyms" type="tns:DataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="IupacNames" type="tns:DataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="Formulae" type="tns:DataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="RegistryNumbers" type="tns:DataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="Citations" type="tns:DataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="ChemicalStructures" type="tns:StructureDataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="DatabaseLinks" type="tns:DataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="OntologyParents" type="tns:OntologyDataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="OntologyChildren" type="tns:OntologyDataItem"/>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="GeneralComments" type="tns:CommentDataItem"/>
+                <xsd:element maxOccurs="unbounded" minOccurs="0" name="CompoundOrigins" type="tns:CompoundOriginDataItem"/>
+            </xsd:sequence>
+         </xsd:complexType>
+         <xsd:complexType name="UpdatedPolymer">
+            <xsd:sequence>
+               <xsd:element maxOccurs="1" minOccurs="1" name="updatedStructure" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="globalFormula" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="globalCharge" type="xsd:string"/>
+               <xsd:element maxOccurs="1" minOccurs="1" name="chebiId" type="xsd:string"/>
+            </xsd:sequence>
+         </xsd:complexType>
+         <complexType name="getLiteEntityResponse">
+            <sequence>
+               <element name="return" type="tns:LiteEntityList"/>
+            </sequence>
+         </complexType>
+         <element name="getLiteEntityResponse" type="tns:getLiteEntityResponse"/>
+         <simpleType name="SearchCategory">
+            <restriction base="xsd:string">
+               <enumeration value="ALL"/>
+               <enumeration value="CHEBI ID"/>
+               <enumeration value="CHEBI NAME"/>
+                <enumeration value="DEFINITION"/>
+               <enumeration value="ALL NAMES"/>
+               <enumeration value="IUPAC NAME"/>
+               <enumeration value="CITATIONS"/>
+               <enumeration value="REGISTRY NUMBERS"/>
+               <enumeration value="MANUAL XREFS"/>
+               <enumeration value="AUTOMATIC XREFS"/>
+               <enumeration value="FORMULA"/>
+               <enumeration value="MASS"/>
+               <enumeration value="MONOISOTOPIC MASS"/>
+               <enumeration value="CHARGE"/>
+               <enumeration value="INCHI/INCHI KEY"/>
+               <enumeration value="SMILES"/>
+               <enumeration value="SPECIES"/>
+            </restriction>
+         </simpleType>
+         <simpleType name="StructureSearchCategory">
+            <restriction base="xsd:string">
+               <enumeration value="IDENTITY"/>
+               <enumeration value="SUBSTRUCTURE"/>
+               <enumeration value="SIMILARITY"/>
+            </restriction>
+         </simpleType>
+         <simpleType name="StructureType">
+            <restriction base="xsd:string">
+               <enumeration value="MOLFILE"/>
+               <enumeration value="CML"/>
+               <enumeration value="SMILES"/>
+               <!--<enumeration value="INCHI"/>-->
+            </restriction>
+         </simpleType>
+         <simpleType name="RelationshipType">
+            <restriction base="xsd:string">
+               <enumeration value="is a"/>
+               <enumeration value="has part"/>
+               <enumeration value="is conjugate base of"/>
+               <enumeration value="is conjugate acid of"/>
+               <enumeration value="is tautomer of"/>
+               <enumeration value="is enantiomer of"/>
+               <enumeration value="has functional parent"/>
+               <enumeration value="has parent hydride"/>
+               <enumeration value="is substituent group from"/>
+               <enumeration value="has role"/>
+            </restriction>
+         </simpleType>
+         <simpleType name="StarsCategory">
+            <restriction base="xsd:string">
+               <enumeration value="ALL"/>
+               <enumeration value="TWO ONLY"/>
+               <enumeration value="THREE ONLY"/>
+            </restriction>
+         </simpleType>
+         <complexType name="getLiteEntity">
+            <sequence>
+               <element name="search" type="xsd:string"/>
+               <element name="searchCategory" type="tns:SearchCategory"/>
+               <element name="maximumResults" type="xsd:int"/>
+               <element name="stars" type="tns:StarsCategory"/>
+            </sequence>
+         </complexType>
+         <element name="getLiteEntity" type="tns:getLiteEntity"/>
+         <complexType name="getCompleteEntityResponse">
+            <sequence>
+               <element name="return" type="tns:Entity"/>
+            </sequence>
+         </complexType>
+         <element name="getCompleteEntityResponse" type="tns:getCompleteEntityResponse"/>
+         <complexType name="getCompleteEntity">
+            <sequence>
+               <element name="chebiId" type="xsd:string"/>
+            </sequence>
+         </complexType>
+         <element name="getCompleteEntity" type="tns:getCompleteEntity"/>
+          <!--Returns a the complete entity's using a list of LiteEntities. The maximum list passed is 50-->
+         <complexType name="getCompleteEntityByListResponse">
+            <sequence>
+               <xsd:element maxOccurs="unbounded" minOccurs="0" name="return" type="tns:Entity"/>
+            </sequence>
+         </complexType>
+         <element name="getCompleteEntityByListResponse" type="tns:getCompleteEntityByListResponse"/>
+         <complexType name="getCompleteEntityByList">
+            <sequence>
+               <xsd:element maxOccurs="50" minOccurs="0" name="ListOfChEBIIds" type="xsd:string"/>
+            </sequence>
+         </complexType>
+         <element name="getCompleteEntityByList" type="tns:getCompleteEntityByList"/>
+         <complexType name="getOntologyParentsResponse">
+            <sequence>
+               <element name="return" type="tns:OntologyDataItemList"/>
+            </sequence>
+         </complexType>
+         <element name="getOntologyParentsResponse" type="tns:getOntologyParentsResponse"/>
+         <complexType name="getOntologyParents">
+            <sequence>
+               <element name="chebiId" type="xsd:string"/>
+            </sequence>
+         </complexType>
+         <element name="getOntologyParents" type="tns:getOntologyParents"/>
+         <complexType name="getOntologyChildrenResponse">
+            <sequence>
+               <element name="return" type="tns:OntologyDataItemList"/>
+            </sequence>
+         </complexType>
+         <element name="getOntologyChildrenResponse" type="tns:getOntologyChildrenResponse"/>
+         <complexType name="getOntologyChildren">
+            <sequence>
+               <element name="chebiId" type="xsd:string"/>
+            </sequence>
+         </complexType>
+         <element name="getOntologyChildren" type="tns:getOntologyChildren"/>
+         <complexType name="getAllOntologyChildrenInPathResponse">
+            <sequence>
+               <element name="return" type="tns:OntologyDataItemList"/>
+            </sequence>
+         </complexType>
+         <element name="getAllOntologyChildrenInPathResponse" type="tns:getAllOntologyChildrenInPathResponse"/>
+         <complexType name="getAllOntologyChildrenInPath">
+            <sequence>
+               <element name="chebiId" type="xsd:string"/>
+               <element name="relationshipType" type="tns:RelationshipType"/>
+               <element name="structureOnly" type="xsd:boolean"/>
+            </sequence>
+         </complexType>
+         <element name="getAllOntologyChildrenInPath" type="tns:getAllOntologyChildrenInPath"/>
+         <complexType name="getStructureSearchResponse">
+            <sequence>
+               <element name="return" type="tns:LiteEntityList"/>
+            </sequence>
+         </complexType>
+         <element name="getStructureSearchResponse" type="tns:getLiteEntityResponse"/>
+         <complexType name="getStructureSearch">
+            <sequence>
+               <element name="structure" type="xsd:string"/>
+               <element name="type" type="tns:StructureType"/>
+               <element name="structureSearchCategory" type="tns:StructureSearchCategory"/>
+               <element name="totalResults" type="xsd:int"/>
+               <element name="tanimotoCutoff" type="xsd:float"/>
+            </sequence>
+         </complexType>
+         <element name="getStructureSearch" type="tns:getStructureSearch"/>
+          <complexType name="getUpdatedPolymer">
+              <sequence>
+                  <element name="chebiId" type="xsd:string"/>
+                  <xsd:element maxOccurs="unbounded" minOccurs="1" name="polymerisationIndex" type="xsd:string"/>
+              </sequence>
+          </complexType>
+         <element name="getUpdatedPolymer" type="tns:getUpdatedPolymer"/>
+         <complexType name="getUpdatedPolymerResponse">
+            <sequence>
+               <element name="return" type="tns:UpdatedPolymer"/>
+            </sequence>
+         </complexType>
+         <element name="getUpdatedPolymerResponse" type="tns:getUpdatedPolymerResponse"/>
+         <element name="ChebiWebServiceFault" type="tns:ChebiWebServiceFault"/>
+         <complexType name="ChebiWebServiceFault">
+            <sequence>
+               <element name="faultInfo" type="xsd:string"/>
+               <element name="message" type="xsd:string"/>
+            </sequence>
+         </complexType>
+      </xsd:schema>
+   </types>
+   <message name="getLiteEntity">
+      <part name="parameters" element="tns:getLiteEntity"/>
+   </message>
+   <message name="getLiteEntityResponse">
+      <part name="result" element="tns:getLiteEntityResponse"/>
+   </message>
+   <message name="getCompleteEntity">
+      <part name="parameters" element="tns:getCompleteEntity"/>
+   </message>
+   <message name="getCompleteEntityResponse">
+      <part name="result" element="tns:getCompleteEntityResponse"/>
+   </message>
+   <message name="getCompleteEntityByList">
+      <part name="parameters" element="tns:getCompleteEntityByList"/>
+   </message>
+   <message name="getCompleteEntityByListResponse">
+      <part name="result" element="tns:getCompleteEntityByListResponse"/>
+   </message>
+   <message name="getOntologyParents">
+      <part name="parameters" element="tns:getOntologyParents"/>
+   </message>
+   <message name="getOntologyParentsResponse">
+      <part name="result" element="tns:getOntologyParentsResponse"/>
+   </message>
+   <message name="getOntologyChildren">
+      <part name="parameters" element="tns:getOntologyChildren"/>
+   </message>
+   <message name="getOntologyChildrenResponse">
+      <part name="result" element="tns:getOntologyChildrenResponse"/>
+   </message>
+   <message name="getAllOntologyChildrenInPath">
+      <part name="parameters" element="tns:getAllOntologyChildrenInPath"/>
+   </message>
+   <message name="getAllOntologyChildrenInPathResponse">
+      <part name="result" element="tns:getAllOntologyChildrenInPathResponse"/>
+   </message>
+   <message name="getStructureSearch">
+      <part name="parameters" element="tns:getStructureSearch"/>
+   </message>
+   <message name="getStructureSearchResponse">
+      <part name="result" element="tns:getStructureSearchResponse"/>
+   </message>
+   <message name="getUpdatedPolymer">
+      <part name="parameters" element="tns:getUpdatedPolymer"/>
+   </message>
+   <message name="getUpdatedPolymerResponse">
+      <part name="result" element="tns:getUpdatedPolymerResponse"/>
+   </message>
+   <message name="chebiWebServiceFault">
+      <part name="ChebiWebServiceFault" element="tns:ChebiWebServiceFault"/>
+   </message>
+   <portType name="ChebiWebServicePortType">
+      <operation name="getLiteEntity">
+         <input message="tns:getLiteEntity"/>
+         <output message="tns:getLiteEntityResponse"/>
+         <fault name="chebiWebServiceFault" message="tns:chebiWebServiceFault"/>
+      </operation>
+      <operation name="getCompleteEntity">
+         <input message="tns:getCompleteEntity"/>
+         <output message="tns:getCompleteEntityResponse"/>
+         <fault name="chebiWebServiceFault" message="tns:chebiWebServiceFault"/>
+      </operation>
+      <operation name="getCompleteEntityByList">
+         <input message="tns:getCompleteEntityByList"/>
+         <output message="tns:getCompleteEntityByListResponse"/>
+         <fault name="chebiWebServiceFault" message="tns:chebiWebServiceFault"/>
+      </operation>
+      <operation name="getOntologyParents">
+         <input message="tns:getOntologyParents"/>
+         <output message="tns:getOntologyParentsResponse"/>
+         <fault name="chebiWebServiceFault" message="tns:chebiWebServiceFault"/>
+      </operation>
+      <operation name="getOntologyChildren">
+         <input message="tns:getOntologyChildren"/>
+         <output message="tns:getOntologyChildrenResponse"/>
+         <fault name="chebiWebServiceFault" message="tns:chebiWebServiceFault"/>
+      </operation>
+      <operation name="getAllOntologyChildrenInPath">
+         <input message="tns:getAllOntologyChildrenInPath"/>
+         <output message="tns:getLiteEntityResponse"/>
+         <fault name="chebiWebServiceFault" message="tns:chebiWebServiceFault"/>
+      </operation>
+      <operation name="getStructureSearch">
+         <input message="tns:getStructureSearch"/>
+         <output message="tns:getStructureSearchResponse"/>
+         <fault name="chebiWebServiceFault" message="tns:chebiWebServiceFault"/>
+      </operation>
+      <operation name="getUpdatedPolymer">
+         <input message="tns:getUpdatedPolymer"/>
+         <output message="tns:getUpdatedPolymerResponse"/>
+         <fault name="chebiWebServiceFault" message="tns:chebiWebServiceFault"/>
+      </operation>
+   </portType>
+   <binding name="ChebiWebServiceBinding" type="tns:ChebiWebServicePortType">
+      <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
+      <operation name="getCompleteEntity">
+         <soap:operation soapAction=""/>
+         <input>
+            <soap:body use="literal"/>
+         </input>
+         <output>
+            <soap:body use="literal"/>
+         </output>
+         <fault name="chebiWebServiceFault">
+            <soap:fault name="chebiWebServiceFault" use="literal"/>
+         </fault>
+      </operation>
+      <operation name="getCompleteEntityByList">
+         <soap:operation soapAction=""/>
+         <input>
+            <soap:body use="literal"/>
+         </input>
+         <output>
+            <soap:body use="literal"/>
+         </output>
+         <fault name="chebiWebServiceFault">
+            <soap:fault name="chebiWebServiceFault" use="literal"/>
+         </fault>
+      </operation>
+      <operation name="getLiteEntity">
+         <soap:operation soapAction=""/>
+         <input>
+            <soap:body use="literal"/>
+         </input>
+         <output>
+            <soap:body use="literal"/>
+         </output>
+         <fault name="chebiWebServiceFault">
+            <soap:fault name="chebiWebServiceFault" use="literal"/>
+         </fault>
+      </operation>
+      <operation name="getOntologyParents">
+         <soap:operation soapAction=""/>
+         <input>
+            <soap:body use="literal"/>
+         </input>
+         <output>
+            <soap:body use="literal"/>
+         </output>
+         <fault name="chebiWebServiceFault">
+            <soap:fault name="chebiWebServiceFault" use="literal"/>
+         </fault>
+      </operation>
+      <operation name="getOntologyChildren">
+         <soap:operation soapAction=""/>
+         <input>
+            <soap:body use="literal"/>
+         </input>
+         <output>
+            <soap:body use="literal"/>
+         </output>
+         <fault name="chebiWebServiceFault">
+            <soap:fault name="chebiWebServiceFault" use="literal"/>
+         </fault>
+      </operation>
+      <operation name="getAllOntologyChildrenInPath">
+         <soap:operation soapAction=""/>
+         <input>
+            <soap:body use="literal"/>
+         </input>
+         <output>
+            <soap:body use="literal"/>
+         </output>
+         <fault name="chebiWebServiceFault">
+            <soap:fault name="chebiWebServiceFault" use="literal"/>
+         </fault>
+      </operation>
+      <operation name="getStructureSearch">
+         <soap:operation soapAction=""/>
+         <input>
+            <soap:body use="literal"/>
+         </input>
+         <output>
+            <soap:body use="literal"/>
+         </output>
+         <fault name="chebiWebServiceFault">
+            <soap:fault name="chebiWebServiceFault" use="literal"/>
+         </fault>
+      </operation>
+      <operation name="getUpdatedPolymer">
+         <soap:operation soapAction=""/>
+         <input>
+            <soap:body use="literal"/>
+         </input>
+         <output>
+            <soap:body use="literal"/>
+         </output>
+         <fault name="chebiWebServiceFault">
+            <soap:fault name="chebiWebServiceFault" use="literal"/>
+         </fault>
+      </operation>
+   </binding>
+   <service name="ChebiWebServiceService">
+      <port name="ChebiWebServicePort" binding="tns:ChebiWebServiceBinding">
+         <soap:address location="http://www.ebi.ac.uk:80/webservices/chebi/2.0/webservice"/>
+      </port>
+   </service>
+</definitions>

pymetadata/resources/ontologies/README.md ADDED Viewed

@@ -0,0 +1,4 @@
+# Ontologies
+Ontologies have been downloaded from bioportal and other resources as OWL files.
+See `ontologies/ontology.py` for information on the download links.

pymetadata/resources/templates/ontology_enum.pytemplate ADDED Viewed

@@ -0,0 +1,61 @@
+"""{{ontology_id}} ontology."""
+from typing import Union, Optional
+from enum import Enum
+{{ontology_id}}Type = Union[str, '{{ontology_id}}']
+_terms = {
+    {% for tid in terms %}
+    {% if tid.startswith(ontology_id) %}
+    "{{tid}}": "{{terms[tid].name}}",
+    {% endif %}
+    {% endfor %}
+}
+pattern = r"{{pattern}}"
+class {{ontology_id}}(str, Enum):
+    """Enum for {{ontology_id}} ontology."""
+    {% for t in terms.values() %}
+    # {{t.name}}
+    {{t.id}} = "{{t.id}}"
+    {{t.var_name}} = "{{t.id}}"
+    {% endfor %}
+    @staticmethod
+    def get_name({{ontology_id.lower()}}: '{{ontology_id}}') -> Optional[str]:
+        """Get name for term.
+        :returns: None if term does not exist in ontology.
+        """
+        return _terms.get({{ontology_id.lower()}}.value, None)
+    @classmethod
+    def validate(cls, {{ontology_id.lower()}}: '{{ontology_id}}Type') -> '{{ontology_id}}':
+        """Validate and normalize {{ontology_id.lower()}}."""
+        term: '{{ontology_id}}'
+        if isinstance({{ontology_id.lower()}}, str):
+            if not {{ontology_id.lower()}}.startswith("{{ontology_id}}"):
+                raise ValueError({{ontology_id.lower()}} + " is not a {{ontology_id}} id.")
+            if {{ontology_id.lower()}}.startswith("{{ontology_id}}:"):
+                {{ontology_id.lower()}} = {{ontology_id.lower()}}.replace(":", "_")
+            term = getattr(cls, {{ontology_id.lower()}})
+        elif isinstance({{ontology_id.lower()}}, '{{ontology_id}}'):
+            term = {{ontology_id.lower()}}
+        else:
+            raise ValueError
+        return term
+__all__ = [
+    "{{ontology_id}}",
+    "{{ontology_id}}Type",
+]