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update tests
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@JR-1991
JR-1991 committed Aug 19, 2024
1 parent 958b321 commit a57a732
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415 changes: 157 additions & 258 deletions tests/fixtures/sbml/ode_example_enzml.json
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46 changes: 16 additions & 30 deletions tests/fixtures/sbml/ode_example_sbml.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,22 +2,22 @@
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model name="Test">
<annotation>
<enzymeml:data xmlns:enzymeml="https://www.enzymeml.org/v2" file="data.csv">
<enzymeml:data xmlns:enzymeml="https://www.enzymeml.org/v2" file="data.tsv">
<enzymeml:measurement id="m0" name="m0" timeUnit="u1">
<enzymeml:conditions>
<enzymeml:ph value="7.0"/>
<enzymeml:temperature value="298.15" unit="u3"/>
</enzymeml:conditions>
<enzymeml:initConc species="s0" unit="u2"/>
<enzymeml:initConc species="s1" value="10.0" unit="u2"/>
<enzymeml:speciesData species="s0" unit="u2" type="CONCENTRATION"/>
<enzymeml:speciesData species="s1" value="10.0" unit="u2" type="CONCENTRATION"/>
</enzymeml:measurement>
<enzymeml:measurement id="m1" name="m1" timeUnit="u1">
<enzymeml:conditions>
<enzymeml:ph value="7.0"/>
<enzymeml:temperature value="298.15" unit="u3"/>
</enzymeml:conditions>
<enzymeml:initConc species="s0" unit="u2"/>
<enzymeml:initConc species="s1" value="10.0" unit="u2"/>
<enzymeml:speciesData species="s0" unit="u2" type="CONCENTRATION"/>
<enzymeml:speciesData species="s1" value="10.0" unit="u2" type="CONCENTRATION"/>
</enzymeml:measurement>
</enzymeml:data>
</annotation>
Expand Down Expand Up @@ -56,7 +56,7 @@
</rdf:RDF>
</annotation>
<listOfUnits>
<unit kind="second" exponent="-1" scale="1"/>
<unit kind="second" exponent="1" scale="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="u3" name="K">
Expand All @@ -71,21 +71,7 @@
<unit kind="kelvin" exponent="1" scale="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="u4" name="mmol / l s">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UO_0000063">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/UO_0000000"/>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfUnits>
<unit kind="mole" exponent="1" scale="-3"/>
<unit kind="litre" exponent="-1" scale="1"/>
<unit kind="second" exponent="-1" scale="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="u5" name="1 / s">
<unitDefinition id="u4" name="1 / s">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UO_0000010">
Expand All @@ -104,7 +90,7 @@
<rdf:RDF xmlns:OBO="http://purl.obolibrary.org/obo/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description
rdf:about="http://www.enzymeml.org/v2/Vessel/02063116-73f1-4ba1-b166-8fe835e55659">
rdf:about="http://www.enzymeml.org/v2/Vessel/abc02182-675a-4fd7-b067-9f376f17b874">
<schema:name>Vessel 1</schema:name>
<OBO:OBI_0002139 rdf:datatype="http://www.w3.org/2001/XMLSchema#double">10.0
</OBO:OBI_0002139>
Expand All @@ -121,7 +107,7 @@
<rdf:RDF xmlns:OBO="http://purl.obolibrary.org/obo/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description
rdf:about="http://www.enzymeml.org/v2/Protein/cf3097ad-5833-4ff8-99f1-784cd5f673ca">
rdf:about="http://www.enzymeml.org/v2/Protein/487be0d2-e325-4f0b-857b-3bd8d54c4003">
<schema:name>Enzyme</schema:name>
<OBO:GSSO_007262>MTEY</OBO:GSSO_007262>
<OBO:OBI_0100026>E.coli</OBO:OBI_0100026>
Expand All @@ -141,7 +127,7 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description
rdf:about="http://www.enzymeml.org/v2/Complex/fa79ccd6-acbe-47e4-a8d1-795eb18346db">
rdf:about="http://www.enzymeml.org/v2/Complex/2f52086d-d7a8-4a2d-870b-bd6bafd91504">
<schema:name>Enzyme-Substrate Complex</schema:name>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Complex"/>
</rdf:Description>
Expand All @@ -157,7 +143,7 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description
rdf:about="http://www.enzymeml.org/v2/SmallMolecule/5375d6fb-6246-43b0-bc81-d47e3e72493f">
rdf:about="http://www.enzymeml.org/v2/SmallMolecule/551e35d3-ae18-490d-b4a7-003fcd28f446">
<schema:name>Substrate</schema:name>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/SmallMolecule"/>
</rdf:Description>
Expand All @@ -173,7 +159,7 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description
rdf:about="http://www.enzymeml.org/v2/SmallMolecule/c7318d93-2a0f-44c0-9ebe-a79fc27bf01e">
rdf:about="http://www.enzymeml.org/v2/SmallMolecule/1a93b3f8-ce94-429d-975b-ff6a837b0424">
<schema:name>Product</schema:name>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/SmallMolecule"/>
</rdf:Description>
Expand All @@ -186,11 +172,11 @@
</species>
</listOfSpecies>
<listOfParameters>
<parameter id="kcat" name="kcat" units="u5" constant="true">
<parameter id="kcat" name="kcat" units="u4" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description
rdf:about="http://www.enzymeml.org/v2/Parameter/404206dc-7e11-432e-b1a8-871b822325ef">
rdf:about="http://www.enzymeml.org/v2/Parameter/2872b6d6-191f-4bc4-a36a-130eb4534837">
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
</rdf:Description>
</rdf:RDF>
Expand All @@ -205,7 +191,7 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description
rdf:about="http://www.enzymeml.org/v2/Parameter/a5b7ca60-4945-4cfe-9eb9-6c97dfdaa770">
rdf:about="http://www.enzymeml.org/v2/Parameter/31e315d7-8e87-4ef9-9ca4-1e9e08f2ded7">
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
</rdf:Description>
</rdf:RDF>
Expand All @@ -220,7 +206,7 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description
rdf:about="http://www.enzymeml.org/v2/Parameter/26b501d3-7200-4813-ac11-b62f0f665054">
rdf:about="http://www.enzymeml.org/v2/Parameter/d49325e0-8483-469a-9d6d-1bcadac2bb98">
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
</rdf:Description>
</rdf:RDF>
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