forked from enviPath/enviPy
[Feature] Minimal IUCLID export (#338)
This is an initial implementation that creates a working minimal .i6z document. It passes schema validation and can be imported into IUCLID. Caveat: IUCLID files target individual compounds. Pathway is not actually covered by the format. It can be added in either soil or water and soil OECD endpoints. **I currently only implemented the soil endpoint for all data.** This sort of works, and I can report all degradation products in a pathway (not a nice view, but we can report many transformation products and add a diagram attachment in the future). Adding additional information is an absolute pain, as we need to explicitly map each type of information to the relevant OECD field. I use the XSD scheme for validation, but unfortunately the IUCLID parser is not fully compliant and requires a specific order, etc. The workflow is: finding the AI structure from the XSD scheme -> make the scheme validation pass -> upload to IUCLID to get obscure error messages -> guess what could be wrong -> repeat 💣 New specifications get released once per year, so we will have to update accordingly. I believe that this should be a more expensive feature, as it requires significant effort to uphold. Currently implemented for root compound only in SOIL: - Soil Texture 2 - Soil Texture 1 - pH value - Half-life per soil sample / scenario (mapped to disappearance; not sure about that). - CEC - Organic Matter (only Carbon) - Moisture content - Humidity <img width="2123" alt="image.png" src="attachments/d29830e1-65ef-4136-8939-1825e0959c62"> <img width="2124" alt="image.png" src="attachments/ac9de2ac-bf68-4ba4-b40b-82f810a9de93"> <img width="2139" alt="image.png" src="attachments/5674c7e6-865e-420e-974a-6b825b331e6c"> Reviewed-on: enviPath/enviPy#338 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
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231
epiuclid/schemas/v10/xlink.xsd
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231
epiuclid/schemas/v10/xlink.xsd
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<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
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xmlns:xlink="http://www.w3.org/1999/xlink" targetNamespace="http://www.w3.org/1999/xlink">
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<xs:annotation>
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<xs:documentation>
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This schema document provides attribute declarations and attribute
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group, complex type and simple type definitions which can be used in
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the construction of user schemas to define the structure of
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particular linking constructs, e.g.
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<![CDATA[
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<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
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xmlns:xl="http://www.w3.org/1999/xlink">
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<xs:import namespace="http://www.w3.org/1999/xlink"
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location="http://www.w3.org/1999/xlink.xsd">
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<xs:element name="mySimple">
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<xs:complexType>
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...
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<xs:attributeGroup ref="xl:simpleAttrs"/>
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...
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</xs:complexType>
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</xs:element>
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...
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</xs:schema>
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]]>
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</xs:documentation>
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</xs:annotation>
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<xs:import namespace="http://www.w3.org/XML/1998/namespace"
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schemaLocation="xml.xsd" />
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<xs:attribute name="type" type="xlink:typeType" />
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<xs:simpleType name="typeType">
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<xs:restriction base="xs:token">
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<xs:enumeration value="simple" />
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<xs:enumeration value="extended" />
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<xs:enumeration value="title" />
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<xs:enumeration value="resource" />
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<xs:enumeration value="locator" />
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<xs:enumeration value="arc" />
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</xs:restriction>
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</xs:simpleType>
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<xs:attribute name="href" type="xlink:hrefType" />
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<xs:simpleType name="hrefType">
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<xs:restriction base="xs:anyURI" />
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</xs:simpleType>
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<xs:attribute name="role" type="xlink:roleType" />
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<xs:simpleType name="roleType">
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<xs:restriction base="xs:anyURI">
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<xs:minLength value="1" />
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</xs:restriction>
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</xs:simpleType>
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<xs:attribute name="arcrole" type="xlink:arcroleType" />
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<xs:simpleType name="arcroleType">
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<xs:restriction base="xs:anyURI">
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<xs:minLength value="1" />
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</xs:restriction>
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</xs:simpleType>
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<xs:attribute name="title" type="xlink:titleAttrType" />
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<xs:simpleType name="titleAttrType">
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<xs:restriction base="xs:string" />
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</xs:simpleType>
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<xs:attribute name="show" type="xlink:showType" />
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<xs:simpleType name="showType">
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<xs:restriction base="xs:token">
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<xs:enumeration value="new" />
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<xs:enumeration value="replace" />
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<xs:enumeration value="embed" />
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<xs:enumeration value="other" />
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<xs:enumeration value="none" />
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</xs:restriction>
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</xs:simpleType>
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<xs:attribute name="actuate" type="xlink:actuateType" />
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<xs:simpleType name="actuateType">
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<xs:restriction base="xs:token">
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<xs:enumeration value="onLoad" />
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<xs:enumeration value="onRequest" />
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<xs:enumeration value="other" />
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<xs:enumeration value="none" />
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</xs:restriction>
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</xs:simpleType>
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<xs:attribute name="label" type="xlink:labelType" />
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<xs:simpleType name="labelType">
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<xs:restriction base="xs:NCName" />
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</xs:simpleType>
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<xs:attribute name="from" type="xlink:fromType" />
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<xs:simpleType name="fromType">
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<xs:restriction base="xs:NCName" />
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</xs:simpleType>
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<xs:attribute name="to" type="xlink:toType" />
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<xs:simpleType name="toType">
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<xs:restriction base="xs:NCName" />
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</xs:simpleType>
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<xs:attributeGroup name="simpleAttrs">
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<xs:attribute ref="xlink:type" fixed="simple" />
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<xs:attribute ref="xlink:href" />
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<xs:attribute ref="xlink:role" />
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<xs:attribute ref="xlink:arcrole" />
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<xs:attribute ref="xlink:title" />
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<xs:attribute ref="xlink:show" />
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<xs:attribute ref="xlink:actuate" />
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</xs:attributeGroup>
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<xs:group name="simpleModel">
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<xs:sequence>
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<xs:any processContents="lax" minOccurs="0" maxOccurs="unbounded" />
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</xs:sequence>
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</xs:group>
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<xs:complexType mixed="true" name="simple">
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<xs:annotation>
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<xs:documentation>
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Intended for use as the type of user-declared elements to make them simple
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links.
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</xs:documentation>
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</xs:annotation>
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<xs:group ref="xlink:simpleModel" />
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<xs:attributeGroup ref="xlink:simpleAttrs" />
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</xs:complexType>
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<xs:attributeGroup name="extendedAttrs">
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<xs:attribute ref="xlink:type" fixed="extended" use="required" />
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<xs:attribute ref="xlink:role" />
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<xs:attribute ref="xlink:title" />
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</xs:attributeGroup>
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<xs:group name="extendedModel">
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<xs:choice>
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<xs:element ref="xlink:title" />
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<xs:element ref="xlink:resource" />
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<xs:element ref="xlink:locator" />
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<xs:element ref="xlink:arc" />
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</xs:choice>
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</xs:group>
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<xs:complexType name="extended">
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<xs:annotation>
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<xs:documentation>
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Intended for use as the type of user-declared elements to make them extended
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links. Note that the elements referenced in the content model are
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all abstract. The intention is that by simply declaring elements
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with these as their substitutionGroup, all the right things will
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happen.
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</xs:documentation>
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</xs:annotation>
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<xs:group ref="xlink:extendedModel" minOccurs="0" maxOccurs="unbounded" />
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<xs:attributeGroup ref="xlink:extendedAttrs" />
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</xs:complexType>
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<xs:element name="title" type="xlink:titleEltType" abstract="true" />
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<xs:attributeGroup name="titleAttrs">
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<xs:attribute ref="xlink:type" fixed="title" use="required" />
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<xs:attribute ref="xml:lang">
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<xs:annotation>
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<xs:documentation>
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xml:lang is not required, but provides much of the motivation for title
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elements in addition to attributes, and so is provided here for
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convenience.
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</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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</xs:attributeGroup>
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<xs:group name="titleModel">
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<xs:sequence>
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<xs:any processContents="lax" minOccurs="0" maxOccurs="unbounded" />
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</xs:sequence>
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</xs:group>
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<xs:complexType mixed="true" name="titleEltType">
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<xs:group ref="xlink:titleModel" />
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<xs:attributeGroup ref="xlink:titleAttrs" />
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</xs:complexType>
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<xs:element name="resource" type="xlink:resourceType"
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abstract="true" />
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<xs:attributeGroup name="resourceAttrs">
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<xs:attribute ref="xlink:type" fixed="resource" use="required" />
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<xs:attribute ref="xlink:role" />
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<xs:attribute ref="xlink:title" />
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<xs:attribute ref="xlink:label" />
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</xs:attributeGroup>
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<xs:group name="resourceModel">
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<xs:sequence>
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<xs:any processContents="lax" minOccurs="0" maxOccurs="unbounded" />
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</xs:sequence>
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</xs:group>
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<xs:complexType mixed="true" name="resourceType">
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<xs:group ref="xlink:resourceModel" />
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<xs:attributeGroup ref="xlink:resourceAttrs" />
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</xs:complexType>
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<xs:element name="locator" type="xlink:locatorType"
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abstract="true" />
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<xs:attributeGroup name="locatorAttrs">
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<xs:attribute ref="xlink:type" fixed="locator" use="required" />
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<xs:attribute ref="xlink:href" use="required" />
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<xs:attribute ref="xlink:role" />
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<xs:attribute ref="xlink:title" />
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<xs:attribute ref="xlink:label">
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<xs:annotation>
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<xs:documentation>
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label is not required, but locators have no particular XLink function if
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they are not labeled.
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</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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</xs:attributeGroup>
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<xs:group name="locatorModel">
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<xs:sequence>
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<xs:element ref="xlink:title" minOccurs="0" maxOccurs="unbounded" />
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</xs:sequence>
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</xs:group>
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<xs:complexType name="locatorType">
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<xs:group ref="xlink:locatorModel" />
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<xs:attributeGroup ref="xlink:locatorAttrs" />
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</xs:complexType>
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<xs:element name="arc" type="xlink:arcType" abstract="true" />
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<xs:attributeGroup name="arcAttrs">
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<xs:attribute ref="xlink:type" fixed="arc" use="required" />
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<xs:attribute ref="xlink:arcrole" />
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<xs:attribute ref="xlink:title" />
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<xs:attribute ref="xlink:show" />
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<xs:attribute ref="xlink:actuate" />
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<xs:attribute ref="xlink:from" />
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<xs:attribute ref="xlink:to">
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<xs:annotation>
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<xs:documentation>
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from and to have default behavior when values are missing
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</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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</xs:attributeGroup>
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<xs:group name="arcModel">
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<xs:sequence>
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<xs:element ref="xlink:title" minOccurs="0" maxOccurs="unbounded" />
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</xs:sequence>
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</xs:group>
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<xs:complexType name="arcType">
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<xs:group ref="xlink:arcModel" />
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<xs:attributeGroup ref="xlink:arcAttrs" />
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</xs:complexType>
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</xs:schema>
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