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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epiuclid/schemas/v10/xml.xsd
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145
epiuclid/schemas/v10/xml.xsd
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<?xml version='1.0'?>
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<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en">
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<xs:annotation>
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<xs:documentation>
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See http://www.w3.org/XML/1998/namespace.html and
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http://www.w3.org/TR/REC-xml for information about this namespace.
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This schema document describes the XML namespace, in a form
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suitable for import by other schema documents.
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Note that local names in this namespace are intended to be defined
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only by the World Wide Web Consortium or its subgroups. The
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following names are currently defined in this namespace and should
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not be used with conflicting semantics by any Working Group,
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specification, or document instance:
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base (as an attribute name): denotes an attribute whose value
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provides a URI to be used as the base for interpreting any
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relative URIs in the scope of the element on which it
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appears; its value is inherited. This name is reserved
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by virtue of its definition in the XML Base specification.
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id (as an attribute name): denotes an attribute whose value
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should be interpreted as if declared to be of type ID.
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This name is reserved by virtue of its definition in the
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xml:id specification.
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lang (as an attribute name): denotes an attribute whose value
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is a language code for the natural language of the content of
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any element; its value is inherited. This name is reserved
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by virtue of its definition in the XML specification.
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space (as an attribute name): denotes an attribute whose
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value is a keyword indicating what whitespace processing
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discipline is intended for the content of the element; its
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value is inherited. This name is reserved by virtue of its
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definition in the XML specification.
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Father (in any context at all): denotes Jon Bosak, the chair of
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the original XML Working Group. This name is reserved by
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the following decision of the W3C XML Plenary and
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XML Coordination groups:
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In appreciation for his vision, leadership and dedication
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the W3C XML Plenary on this 10th day of February, 2000
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reserves for Jon Bosak in perpetuity the XML name
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xml:Father
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</xs:documentation>
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</xs:annotation>
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<xs:annotation>
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<xs:documentation>This schema defines attributes and an attribute group
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suitable for use by
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schemas wishing to allow xml:base, xml:lang, xml:space or xml:id
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attributes on elements they define.
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To enable this, such a schema must import this schema
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for the XML namespace, e.g. as follows:
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<schema . . .>
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. . .
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<import namespace="http://www.w3.org/XML/1998/namespace"
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schemaLocation="http://www.w3.org/2001/xml.xsd"/>
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Subsequently, qualified reference to any of the attributes
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or the group defined below will have the desired effect, e.g.
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<type . . .>
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. . .
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<attributeGroup ref="xml:specialAttrs"/>
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will define a type which will schema-validate an instance
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element with any of those attributes</xs:documentation>
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</xs:annotation>
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<xs:annotation>
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<xs:documentation>In keeping with the XML Schema WG's standard versioning
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policy, this schema document will persist at
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http://www.w3.org/2007/08/xml.xsd.
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At the date of issue it can also be found at
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http://www.w3.org/2001/xml.xsd.
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The schema document at that URI may however change in the future,
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in order to remain compatible with the latest version of XML Schema
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itself, or with the XML namespace itself. In other words, if the XML
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Schema or XML namespaces change, the version of this document at
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http://www.w3.org/2001/xml.xsd will change
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accordingly; the version at
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http://www.w3.org/2007/08/xml.xsd will not change.
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</xs:documentation>
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</xs:annotation>
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<xs:attribute name="lang">
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<xs:annotation>
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<xs:documentation>Attempting to install the relevant ISO 2- and 3-letter
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codes as the enumerated possible values is probably never
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going to be a realistic possibility. See
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RFC 3066 at http://www.ietf.org/rfc/rfc3066.txt and the IANA registry
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at http://www.iana.org/assignments/lang-tag-apps.htm for
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further information.
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The union allows for the 'un-declaration' of xml:lang with
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the empty string.</xs:documentation>
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</xs:annotation>
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<xs:simpleType>
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<xs:union memberTypes="xs:language">
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<xs:simpleType>
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<xs:restriction base="xs:string">
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<xs:enumeration value=""/>
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</xs:restriction>
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</xs:simpleType>
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</xs:union>
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</xs:simpleType>
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</xs:attribute>
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<xs:attribute name="space">
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<xs:simpleType>
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<xs:restriction base="xs:NCName">
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<xs:enumeration value="default"/>
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<xs:enumeration value="preserve"/>
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</xs:restriction>
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</xs:simpleType>
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</xs:attribute>
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<xs:attribute name="base" type="xs:anyURI">
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<xs:annotation>
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<xs:documentation>See http://www.w3.org/TR/xmlbase/ for
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information about this attribute.</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="id" type="xs:ID">
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<xs:annotation>
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<xs:documentation>See http://www.w3.org/TR/xml-id/ for
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information about this attribute.</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attributeGroup name="specialAttrs">
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<xs:attribute ref="xml:base"/>
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<xs:attribute ref="xml:lang"/>
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<xs:attribute ref="xml:space"/>
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<xs:attribute ref="xml:id"/>
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</xs:attributeGroup>
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</xs:schema>
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