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Move Units children of Component to Model element. #8

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Move Units children of Component to Model element. #8

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91a92ae
Add a basic model with namespaces on MathML cn elements.
hsorby Jun 14, 2021
675bb8d
Move units that are children of components into the model element.
hsorby Jun 14, 2021
172b7dc
Add example Van der Pol model with units as a child of a component.
hsorby Jun 14, 2021
7c02254
Add new line to end of basic model.
hsorby Jun 14, 2021
5e7c466
Add .gitignore file and ignore tmp/ directory.
hsorby Aug 25, 2021
283821b
Add van der Pol model with Units defined in a Component.
hsorby Aug 25, 2021
fde1a48
Merge branch 'master' of github.com:cellml/cellml1to2 into main
hsorby Aug 25, 2021
b4973e4
Merge branch 'cn-units-namespace' into main
hsorby Aug 25, 2021
6d033e9
Remove duplicated test-models/van_der_pol_model_1928.txt model.
hsorby Aug 25, 2021
3753dc6
Copy over name attribute of Units when moving from Component to Model.
hsorby Aug 25, 2021
9f8f519
Add a simple testing regime using libCellML, Python, and saxon.
hsorby Aug 25, 2021
a263309
Simplify test_model.py script.
hsorby Aug 25, 2021
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9 changes: 9 additions & 0 deletions cellml1to2.xsl
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Original file line number Diff line number Diff line change
Expand Up @@ -52,10 +52,19 @@
<xsl:template match="cellml10:model | cellml11:model">
<model xmlns="http://www.cellml.org/cellml/2.0#" xmlns:cellml="http://www.cellml.org/cellml/2.0#">
<xsl:copy-of select="@name"/>
<!-- Units elements can only be declared as a child of the model element -->
<xsl:for-each select="cellml10:component/cellml10:units | cellml11:component/cellml11:units" >
<xsl:element name="{local-name()}" namespace="http://www.cellml.org/cellml/2.0#">
<xsl:apply-templates select="@* | node()"/>

@jonc125 jonc125 Aug 17, 2021

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I think this will result in attributes on the units elements being ignored, since the template for @* above does nothing. Have you checked this?

@hsorby hsorby Aug 25, 2021

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You're correct, now I have added a copy command to copy the name attribute. Testing with the van der pol model seems to give the correct result now.

</xsl:element>
</xsl:for-each>
<xsl:apply-templates select="@* | node()"/>
</model>
</xsl:template>

<!-- Don't do anything with units that are children of components -->
<xsl:template match="cellml10:component/cellml10:units | cellml11:component/cellml11:units"/>

<!-- Variable elements need special handling for their interface attributes -->
<xsl:template match="cellml10:variable | cellml11:variable">
<xsl:element name="variable" namespace="http://www.cellml.org/cellml/2.0#">
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16 changes: 16 additions & 0 deletions test-models/basic_model.cellml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink" name="basic_model" id="metaid0">
<component name="environment">
<variable id="environment.t" initial_value="0" name="t" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>t</ci>
<apply>
<plus/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1</cn>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">3</cn>
</apply>
</apply>
</math>
</component>
</model>
61 changes: 61 additions & 0 deletions test-models/van_der_pol_model.cellml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
<?xml version='1.0'?>
<model name="van_der_pol_model_1928" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
<component name="main">
<units name="per_second">
<unit exponent="-1" units="second"/>
</units>
<variable name="time" units="second"/>
<variable initial_value="-2" name="x" units="dimensionless"/>
<variable initial_value="0" name="y" units="dimensionless"/>
<variable initial_value="1" name="epsilon" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>x</ci>
</apply>
<apply>
<times/>
<ci>y</ci>
<cn cellml:units="per_second">1</cn>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>y</ci>
</apply>
<apply>
<times/>
<apply>
<minus/>
<apply>
<times/>
<ci>epsilon</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<power/>
<ci>x</ci>
<cn cellml:units="dimensionless">2</cn>
</apply>
</apply>
<ci>y</ci>
</apply>
<ci>x</ci>
</apply>
<cn cellml:units="per_second">1</cn>
</apply>
</apply>
</math>
</component>
</model>