feat(cellml): add validation for cellML 1.1

biosimulators · Apr 13, 2022 · f6adda9 · f6adda9
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diff --git a/biosimulators_utils/model_lang/cellml/cellml_1_1.xsd b/biosimulators_utils/model_lang/cellml/cellml_1_1.xsd
diff --git a/biosimulators_utils/model_lang/cellml/common/common-attribs.xsd b/biosimulators_utils/model_lang/cellml/common/common-attribs.xsd
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<xs:schema 
+  xmlns:xs="http://www.w3.org/2001/XMLSchema"
+  xmlns="http://www.w3.org/1998/Math/MathML"
+  xmlns:xlink="http://www.w3.org/1999/xlink"
+  targetNamespace="http://www.w3.org/1998/Math/MathML"
+  elementFormDefault="qualified"
+>
+
+<xs:annotation>
+  <xs:documentation>
+  This is the common attributes module for MathML.
+  Author: St&#233;phane Dalmas, INRIA.
+  </xs:documentation>
+</xs:annotation>
+
+
+<xs:import namespace="http://www.w3.org/1999/xlink" schemaLocation="xlink-href.xsd"/>
+<xs:import/> <!-- import any foreign namespace -->
+
+
+<!-- The type of "class" is from the XHTML modularization with Schema
+     document -->
+<xs:attributeGroup name="Common.attrib">
+  <xs:attribute name="class" type="xs:NMTOKENS"/>
+  <xs:attribute name="style" type="xs:string"/>
+  <xs:attribute name="xref" type="xs:IDREF"/>
+  <xs:attribute name="id" type="xs:ID"/>
+  <xs:attribute ref="xlink:href"/>
+  <!-- allow attributes from foreign namespaces, and don't check them -->
+  <xs:anyAttribute namespace="##other" processContents="skip"/>
+</xs:attributeGroup>
+
+</xs:schema>
+<!--
+  Copyright &#251; 2002 World Wide Web Consortium, (Massachusetts Institute
+  of Technology, Institut National de Recherche en Informatique et en
+  Automatique, Keio University). All Rights Reserved. See
+  http://www.w3.org/Consortium/Legal/.
+  -->
diff --git a/biosimulators_utils/model_lang/cellml/common/math.xsd b/biosimulators_utils/model_lang/cellml/common/math.xsd
@@ -0,0 +1,130 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<xs:schema
+  xmlns:xs="http://www.w3.org/2001/XMLSchema"
+  xmlns="http://www.w3.org/1998/Math/MathML"
+  targetNamespace="http://www.w3.org/1998/Math/MathML"
+  elementFormDefault="qualified"
+ >
+
+<xs:annotation>
+  <xs:documentation>
+  This is an XML Schema module defining the "math" element of MathML.
+  Author: St&#233;phane Dalmas, INRIA.
+  </xs:documentation>
+</xs:annotation>
+
+<!-- The four groups that govern a lot of things -->
+
+<!-- currently very lax. Should be tightened from Chapter 5 -->
+
+<xs:group name="Presentation-expr.class">
+  <xs:choice>
+    <xs:group ref="PresExpr.class"/>
+    <xs:group ref="ContExpr.class"/>
+  </xs:choice>
+</xs:group>
+
+<xs:group name="Content-expr.class">
+  <xs:choice>
+    <xs:group ref="ContExpr.class"/>
+    <xs:group ref="PresExpr.class"/>
+  </xs:choice>
+</xs:group>
+
+<xs:group name="PresExpr.class">
+  <xs:choice>
+    <xs:group ref="Presentation-token.class"/>
+    <xs:group ref="Presentation-layout.class"/>
+    <xs:group ref="Presentation-script.class"/>
+    <xs:group ref="Presentation-table.class"/>
+    <xs:element ref="mspace"/>
+    <xs:element ref="maction"/>
+    <xs:element ref="merror"/>
+    <xs:element ref="mstyle"/>
+  </xs:choice>
+</xs:group>
+
+<xs:group name="ContExpr.class">
+  <xs:choice>
+    <xs:group ref="Content-tokens.class"/>
+    <xs:group ref="Content-arith.class"/>
+    <xs:group ref="Content-functions.class"/>
+    <xs:group ref="Content-logic.class"/>
+    <xs:group ref="Content-constants.class"/>
+    <xs:group ref="Content-sets.class"/>
+    <xs:group ref="Content-relations.class"/>
+    <xs:group ref="Content-elementary-functions.class"/>
+    <xs:group ref="Content-calculus.class"/>
+    <xs:group ref="Content-linear-algebra.class"/>
+    <xs:group ref="Content-vector-calculus.class"/>
+    <xs:group ref="Content-statistics.class"/>
+    <xs:group ref="Content-constructs.class"/>
+    <xs:element ref="semantics"/>
+  </xs:choice>
+</xs:group>
+
+<!-- "math" -->
+
+<xs:attributeGroup name="Browser-interface.attrib">
+  <xs:attribute name="baseline" type="xs:string"/>
+  <xs:attribute name="overflow" default="scroll">
+    <xs:simpleType>
+      <xs:restriction base="xs:string">
+        <xs:enumeration value="scroll"/>
+        <xs:enumeration value="elide"/>
+        <xs:enumeration value="truncate"/>
+        <xs:enumeration value="scale"/>
+      </xs:restriction>
+    </xs:simpleType>
+  </xs:attribute>
+  <xs:attribute name="altimg" type="xs:anyURI"/>
+  <xs:attribute name="alttext" type="xs:string"/>
+  <xs:attribute name="type" type="xs:string"/>
+  <xs:attribute name="name" type="xs:string"/>
+  <xs:attribute name="height" type="xs:string"/>
+  <xs:attribute name="width" type="xs:string"/>
+</xs:attributeGroup>
+
+<xs:attributeGroup name="math.attlist">
+  <xs:attributeGroup ref="Browser-interface.attrib"/>
+  <xs:attribute name="macros" type="xs:string"/>
+<!-- deprecated
+  <xs:attribute name="mode" type="xs:string"/>
+-->
+  <xs:attribute name="display" default="inline">
+    <xs:simpleType>
+      <xs:restriction base="xs:string">
+        <xs:enumeration value="block"/>
+        <xs:enumeration value="inline"/>
+      </xs:restriction>
+    </xs:simpleType>
+  </xs:attribute>
+  <xs:attributeGroup ref="Common.attrib"/>
+</xs:attributeGroup>
+
+<xs:group name="math.content">
+  <xs:choice>
+<!-- *** This region was not commented out in the original W3C version,
+         but has been commented out as the mathml:math element in
+         CellML does not allow presentation MathML elements.
+    <xs:group ref="PresExpr.class"/>
+*** End of region commented out for CellML *** -->
+    <xs:group ref="ContExpr.class"/>
+  </xs:choice>
+</xs:group>
+
+<xs:complexType name="math.type">
+  <xs:group ref="math.content" minOccurs="0" maxOccurs="unbounded"/>
+  <xs:attributeGroup ref="math.attlist"/>
+</xs:complexType>
+
+<xs:element name="math" type="math.type"/>
+
+</xs:schema>
+<!--
+  Copyright &#251; 2002 World Wide Web Consortium, (Massachusetts Institute
+  of Technology, Institut National de Recherche en Informatique et en
+  Automatique, Keio University). All Rights Reserved. See
+  http://www.w3.org/Consortium/Legal/.
+  -->
diff --git a/biosimulators_utils/model_lang/cellml/common/xlink-href.xsd b/biosimulators_utils/model_lang/cellml/common/xlink-href.xsd
@@ -0,0 +1,20 @@
+<schema targetNamespace="http://www.w3.org/1999/xlink" 
+        xmlns:xlink="http://www.w3.org/1999/xlink" 
+        xmlns="http://www.w3.org/2001/XMLSchema">
+  <annotation>
+    <documentation xml:lang="en">
+      This schema provides the XLink href attribute for use in the MathML2 
+      schema. Written by Max Froumentin, W3C.
+    </documentation>
+  </annotation>
+
+  <attribute name="href" type="anyURI"/>
+</schema>
+
+
+<!--
+  Copyright &#251; 2002 World Wide Web Consortium, (Massachusetts Institute
+  of Technology, Institut National de Recherche en Informatique et en
+  Automatique, Keio University). All Rights Reserved. See
+  http://www.w3.org/Consortium/Legal/.
+  -->
diff --git a/biosimulators_utils/model_lang/cellml/content/arith.xsd b/biosimulators_utils/model_lang/cellml/content/arith.xsd
@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<xs:schema
+  xmlns:xs="http://www.w3.org/2001/XMLSchema"
+  xmlns="http://www.w3.org/1998/Math/MathML"
+  targetNamespace="http://www.w3.org/1998/Math/MathML"
+  elementFormDefault="qualified"
+>
+
+<xs:annotation>
+  <xs:documentation>
+  This is an XML Schema module for the "arithmetic" operators of content
+  MathML.
+  Author: St&#233;phane Dalmas, INRIA.
+  </xs:documentation>
+</xs:annotation>
+
+<!-- a common type for all this -->
+
+<xs:complexType name="Arith.type">
+  <xs:attributeGroup ref="Definition.attrib"/>
+  <xs:attributeGroup ref="Common.attrib"/>
+</xs:complexType>
+
+<!-- The elements -->
+
+<xs:element name="abs" type="Arith.type"/>
+<xs:element name="conjugate" type="Arith.type"/>
+<xs:element name="arg" type="Arith.type"/>
+<xs:element name="real" type="Arith.type"/>
+<xs:element name="imaginary" type="Arith.type"/>
+
+<xs:element name="floor" type="Arith.type"/>
+<xs:element name="ceiling" type="Arith.type"/>
+
+<xs:element name="power" type="Arith.type"/>
+<xs:element name="root" type="Arith.type"/>
+
+<xs:element name="minus" type="Arith.type"/>
+<xs:element name="plus" type="Arith.type"/>
+<xs:element name="sum" type="Arith.type"/>
+<xs:element name="times" type="Arith.type"/>
+<xs:element name="product" type="Arith.type"/>
+
+<xs:element name="max" type="Arith.type"/>
+<xs:element name="min" type="Arith.type"/>
+
+<xs:element name="factorial" type="Arith.type"/>
+<xs:element name="quotient" type="Arith.type"/>
+<xs:element name="divide" type="Arith.type"/>
+<xs:element name="rem" type="Arith.type"/>
+<xs:element name="gcd" type="Arith.type"/>
+<xs:element name="lcm" type="Arith.type"/>
+
+<!-- And the group of everything -->
+
+<xs:group name="Content-arith.class">
+  <xs:choice>
+    <xs:element ref="abs"/>
+    <xs:element ref="conjugate"/>
+    <xs:element ref="factorial"/>
+    <xs:element ref="arg"/>
+    <xs:element ref="real"/>
+    <xs:element ref="imaginary"/>
+    <xs:element ref="floor"/>
+    <xs:element ref="ceiling"/>
+    <xs:element ref="quotient"/>
+    <xs:element ref="divide"/>
+    <xs:element ref="rem"/>
+    <xs:element ref="minus"/>
+    <xs:element ref="plus"/>
+    <xs:element ref="times"/>
+    <xs:element ref="power"/>
+    <xs:element ref="root"/>
+    <xs:element ref="max"/>
+    <xs:element ref="min"/>
+    <xs:element ref="gcd"/>
+    <xs:element ref="lcm"/>
+    <xs:element ref="sum"/>
+    <xs:element ref="product"/>
+  </xs:choice>
+</xs:group>
+
+</xs:schema>
+<!--
+  Copyright &#251; 2002 World Wide Web Consortium, (Massachusetts Institute
+  of Technology, Institut National de Recherche en Informatique et en
+  Automatique, Keio University). All Rights Reserved. See
+  http://www.w3.org/Consortium/Legal/.
+  -->