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Make a test fail to show the bug #269

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Merged
merged 3 commits into from
Apr 20, 2020
Merged

Make a test fail to show the bug #269

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d4314db
Make a test fail to show the bug
jonc125 Apr 20, 2020
6db7477
Transfer cmeta:id when connecting variables
jonc125 Apr 20, 2020
3c344a8
Merge branch 'develop' into 267-fix-connections
jonc125 Apr 20, 2020
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5 changes: 5 additions & 0 deletions cellmlmanip/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -280,6 +280,11 @@ def connect_variables(self, source_name: str, target_name: str):
if target in self._ode_definition_map:
self._ode_definition_map[source.assigned_to] = self._ode_definition_map[target]
del self._ode_definition_map[target]
# Migrate the cmeta:id too so annotations work as expected
# Really modellers should annotate the source variable, but they don't always!
if target.cmeta_id is not None:
# Note that this method considers source as the variable with the cmeta:id already.
self.transfer_cmeta_id(source=target, target=source)

# Otherwise, this connection requires a conversion
else:
Expand Down
13 changes: 7 additions & 6 deletions tests/cellml_files/test_simple_odes.cellml
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Expand Up @@ -24,6 +24,7 @@ For annotations, we check:
* RDF within <variable> elements
* RDF within a <component> but not inside a <variable>
* RDF directly within <model>
* An annotation on a non-source variable (checks the cmeta:id is moved when connections resolved)

-->
<model name="test_simple_odes" cmeta:id="test_simple_odes"
Expand Down Expand Up @@ -92,7 +93,7 @@ For annotations, we check:
</units>

<component name="environment">
<variable name="time" public_interface="out" units="ms" cmeta:id="time">
<variable name="time" public_interface="out" units="ms">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#time">
<bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#time"/>
Expand All @@ -103,7 +104,7 @@ For annotations, we check:

<component name="single_independent_ode">
<!-- d(sv1)/d(time) = 1, sv1(0) = 1 -->
<variable name="time" public_interface="in" units="ms"/>
<variable name="time" public_interface="in" units="ms" cmeta:id="time"/>
<variable name="sv1" units="mV" cmeta:id="sv11" initial_value="1">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#sv11">
Expand Down Expand Up @@ -137,13 +138,13 @@ For annotations, we check:
</rdf:RDF>
</variable>
<variable name="a" units="mV_per_ms" initial_value="1" cmeta:id="a1">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#a1">
<modifiable-parameter xmlns="https://chaste.comlab.ox.ac.uk/cellml/ns/pycml#">yes</modifiable-parameter>
</rdf:Description>
</rdf:RDF>
</variable>
</variable>

<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
Expand Down Expand Up @@ -706,5 +707,5 @@ For annotations, we check:
<bqbiol:is rdf:resource="urn:test-ns#parameter_a1"/>
</rdf:Description>
</rdf:RDF>

</model>