Update SBML version in test models

sybila · Mar 4, 2024 · 29cdfa6 · 29cdfa6
1 parent 24e7458
commit 29cdfa6
Show file tree

Hide file tree

Showing 3 changed files with 21 additions and 21 deletions.
diff --git a/test-inputs/Mukandavire2020.xml b/test-inputs/Mukandavire2020.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" render:required="false"
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" layout:required="false" level="3" render:required="false"
       version="1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
       xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
     <model areaUnits="area" extentUnits="substance"
@@ -26,7 +26,7 @@
                 </p>
             </body>
         </notes>
-        <annotation xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <annotation xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/"
                      xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#"
                      xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
@@ -123,7 +123,7 @@
                 </rdf:RDF>
             </COPASI>
         </annotation>
-        <listOfFunctionDefinitions xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfFunctionDefinitions xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <functionDefinition id="Rate_Law_for_reaction" metaid="COPASI17" name="Rate Law for reaction">
                 <annotation>
                     <COPASI xmlns="http://www.copasi.org/static/sbml">
@@ -175,7 +175,7 @@
                 </math>
             </functionDefinition>
         </listOfFunctionDefinitions>
-        <listOfUnitDefinitions xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfUnitDefinitions xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <unitDefinition id="length" name="length">
                 <listOfUnits>
                     <unit exponent="1" kind="metre" multiplier="1" scale="0"/>
@@ -202,7 +202,7 @@
                 </listOfUnits>
             </unitDefinition>
         </listOfUnitDefinitions>
-        <listOfCompartments xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfCompartments xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <compartment constant="true" id="South_Africa" metaid="COPASI1" name="South_Africa" size="1"
                          spatialDimensions="3" units="volume">
                 <annotation>
@@ -239,7 +239,7 @@
                 </annotation>
             </compartment>
         </listOfCompartments>
-        <listOfSpecies xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfSpecies xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <species boundaryCondition="false" compartment="South_Africa" constant="false" hasOnlySubstanceUnits="false"
                      id="Susceptible" initialConcentration="36196938" metaid="COPASI2" name="Susceptible"
                      substanceUnits="substance">
@@ -403,7 +403,7 @@
                 </annotation>
             </species>
         </listOfSpecies>
-        <listOfParameters xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfParameters xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <parameter constant="true" id="beta" metaid="COPASI6" name="beta" value="1.3">
                 <annotation>
                     <COPASI xmlns="http://www.copasi.org/static/sbml">
@@ -517,14 +517,14 @@
                 </annotation>
             </parameter>
         </listOfParameters>
-        <listOfInitialAssignments xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfInitialAssignments xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <initialAssignment symbol="Susceptible">
                 <math xmlns="http://www.w3.org/1998/Math/MathML">
                     <ci>N</ci>
                 </math>
             </initialAssignment>
         </listOfInitialAssignments>
-        <listOfRules xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfRules xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <assignmentRule variable="Cumulative_cases">
                 <math xmlns="http://www.w3.org/1998/Math/MathML">
                     <apply>
@@ -535,7 +535,7 @@
                 </math>
             </assignmentRule>
         </listOfRules>
-        <listOfReactions xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfReactions xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <reaction fast="false" id="Susceptible_to_Exposed" metaid="COPASI14" name="Susceptible_to_Exposed"
                       reversible="false">
                 <annotation>
@@ -706,7 +706,7 @@
                 </kineticLaw>
             </reaction>
         </listOfReactions>
-        <listOfEvents xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfEvents xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <event id="Lockdown" metaid="COPASI13" name="Lockdown" useValuesFromTriggerTime="false">
                 <annotation>
                     <COPASI xmlns="http://www.copasi.org/static/sbml">

diff --git a/test-inputs/cholesterol_metabolism_and_atherosclerosis.xml b/test-inputs/cholesterol_metabolism_and_atherosclerosis.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="2" version="4">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="2" version="4">
     <model id="McAuley2012___Whole_body_Cholesterol_Metabolism" metaid="COPASI0"
            name="Davies2023 - Cholesterol Metabolism and Atherosclerosis Model">
         <notes>
@@ -9,7 +9,7 @@
                 </p>
             </body>
         </notes>
-        <annotation xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <annotation xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <copasi:COPASI xmlns:copasi="http://www.copasi.org/static/sbml">
                 <rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#"
                          xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
@@ -182,7 +182,7 @@
 
             </rdf:RDF>
         </annotation>
-        <listOfFunctionDefinitions xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfFunctionDefinitions xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <functionDefinition id="Rate_Law_for_Cholesterol_Absorption_1__1" metaid="COPASI114"
                                 name="Rate Law for Cholesterol Absorption_1 [1]">
                 <annotation>
@@ -2516,7 +2516,7 @@
                 </math>
             </functionDefinition>
         </listOfFunctionDefinitions>
-        <listOfUnitDefinitions xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfUnitDefinitions xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <unitDefinition id="length" name="length">
                 <listOfUnits>
                     <unit exponent="1" kind="metre" multiplier="1" scale="0"/>
@@ -2543,7 +2543,7 @@
                 </listOfUnits>
             </unitDefinition>
         </listOfUnitDefinitions>
-        <listOfCompartments xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfCompartments xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <compartment constant="true" id="Intake" metaid="COPASI1" name="Intake" size="1" spatialDimensions="3">
                 <annotation>
                     <copasi:COPASI xmlns:copasi="http://www.copasi.org/static/sbml">
@@ -2705,7 +2705,7 @@
             </compartment>
             <compartment constant="true" id="Endothelium" name="Endothelium" size="1" spatialDimensions="3"/>
         </listOfCompartments>
-        <listOfSpecies xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfSpecies xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <species boundaryCondition="true" compartment="Intake" constant="true" id="species_1"
                      initialConcentration="1051" metaid="COPASI7" name="DC">
                 <annotation>
@@ -3844,7 +3844,7 @@
             <species boundaryCondition="false" compartment="Endothelium" constant="false" id="HDL"
                      initialConcentration="0" name="HDL"/>
         </listOfSpecies>
-        <listOfParameters xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfParameters xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <parameter constant="true" id="alfa7" name="alfa7" value="2.8067"/>
             <parameter constant="true" id="ActEndstim_a" name="ActEndstim_a" value="0"/>
             <parameter constant="true" id="ActEndstim_b" name="ActEndstim_b" value="3.51949"/>
@@ -3911,7 +3911,7 @@
             <parameter constant="true" id="MCblood" name="MCblood" value="1"/>
             <parameter constant="true" id="M" name="M" value="0.0155561"/>
         </listOfParameters>
-        <listOfRules xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfRules xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <assignmentRule variable="SUMRecTAINF">
                 <math xmlns="http://www.w3.org/1998/Math/MathML">
                     <apply>
@@ -4142,7 +4142,7 @@
                 </math>
             </assignmentRule>
         </listOfRules>
-        <listOfReactions xmlns="http://www.sbml.org/sbml/level3/version1/core">
+        <listOfReactions xmlns="http://www.sbml.org/sbml/level3/version2/core">
             <reaction id="reaction_1" metaid="COPASI41" name="Ingestion" reversible="false">
                 <annotation>
                     <copasi:COPASI xmlns:copasi="http://www.copasi.org/static/sbml">

diff --git a/test-inputs/model.sbml b/test-inputs/model.sbml
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" level="3" qual:required="true"
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" layout:required="false" level="3" qual:required="true"
   xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" version="1"
   xmlns:qual="http://www.sbml.org/sbml/level3/version1/qual/version1">
   <model metaid="_174907b7-8e1c-47f3-9a50-bb8e4c6ebd0d" id="model_id">