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Merge pull request #350 from sbmlteam/fbcV3-update
Update Fbc V3 package
2 parents bee0af7 + aee04c3 commit 9faec63

39 files changed

+892
-197
lines changed

‎NEWS.txt

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@@ -14,6 +14,11 @@ and converting models.
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- Attributes of the ModelHistory can now be accessed from
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const objects.
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- The FBC V3 package has been updated to reflect the latest
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specification. There are now optional attributes `fbc:reaction2`
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on the FluxObjective and `fbc:variable2` on the
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UserDefinedConstraintComponent.
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* Bug fixes
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- A bug converting / validating models with the 'comp' package
@@ -23,6 +28,11 @@ and converting models.
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- A fix to the CMake Build system ensures that check for dependencies
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is more robust. Thanks to first time contributor @adelhpour
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- The type of the FBC V3 `coefficient` attribute on the
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UserDefinedConstraintComponent has been corrected, it was mistakenly
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a double before, now it has been corrected to be a SIdRef as
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described in the specification.
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====================================================================

‎dev/packages/deviser-fbc_v3.xml

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@@ -168,6 +168,7 @@
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<attribute name="id" required="false" type="SId" abstract="false"/>
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<attribute name="name" required="false" type="string" abstract="false"/>
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<attribute name="reaction" required="true" type="SIdRef" element="Reaction" abstract="false"/>
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<attribute name="reaction2" required="false" type="SIdRef" element="Reaction" abstract="false"/>
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<attribute name="coefficient" required="true" type="double" abstract="false"/>
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<attribute name="variableType" required="true" type="enum" element="FbcVariableType" abstract="false"/>
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</attributes>
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<attributes>
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<attribute name="id" required="false" type="SId" abstract="false"/>
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<attribute name="name" required="false" type="string" abstract="false"/>
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<attribute name="coefficient" required="true" type="double" abstract="false"/>
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<attribute name="coefficient" required="true" type="SIdRef" element="Parameter" abstract="false"/>
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<attribute name="variable" required="true" type="SIdRef" element="Reaction,Parameter" abstract="false"/>
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<attribute name="variable2" required="false" type="SIdRef" element="Reaction,Parameter" abstract="false"/>
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<attribute name="variableType" required="true" type="enum" element="FbcVariableType" abstract="false"/>
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</attributes>
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</element>

‎src/bindings/matlab/getDefaultValues.m

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@@ -3565,7 +3565,7 @@
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int32(-1), ...
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'', ...
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'', ...
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0/0, ...
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'', ...
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int32(0), ...
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'', ...
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'', ...

‎src/bindings/matlab/getValueType.m

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'int', ...
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'char', ...
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'char', ...
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'double', ...
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'char', ...
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'bool', ...
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'char', ...
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'char', ...

‎src/bindings/matlab/test/test-data/fbcV3.xml

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@@ -75,7 +75,7 @@
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<fbc:listOfUserDefinedConstraints>
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<fbc:userDefinedConstraint sboTerm="SBO:0000001" fbc:id="uc2" fbc:lowerBound="uc2lb" fbc:upperBound="uc2ub">
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<fbc:listOfUserDefinedConstraintComponents>
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<fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:id="dd" fbc:name="string" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
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<fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:id="dd" fbc:name="string" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
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</fbc:listOfUserDefinedConstraintComponents>
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</fbc:userDefinedConstraint>
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</fbc:listOfUserDefinedConstraints>

‎src/bindings/matlab/test/testReadFromFileFbc3.m

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Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).typecode, 'SBML_FBC_USERDEFINEDCONSTRAINTCOMPONENT'));
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Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_id, 'dd'));
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Totalfail = Totalfail + fail_unless( m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_coefficient == 2);
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Totalfail = Totalfail + fail_unless( m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).isSetfbc_coefficient == 1);
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Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_coefficient, 'uc2ub'));
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Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_variable, 'R2'));
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Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_variableType, 'linear'));
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‎src/sbml/packages/fbc/extension/test/TestWriteFbcExtension.cpp

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@@ -415,17 +415,19 @@ START_TEST(test_FbcExtension_create_and_write_L3V1V3)
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FluxObjective* fluxObjective = objective->createFluxObjective();
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fluxObjective->setReaction("J0");
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fluxObjective->setCoefficient(1);
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fluxObjective->setVariableType("linear");
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fluxObjective->setReaction2("J0");
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fluxObjective->setVariableType("quadratic");
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UserDefinedConstraint* userconstraint = mplugin->createUserDefinedConstraint();
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userconstraint->setId("uc2");
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userconstraint->setLowerBound("uc2lb");
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userconstraint->setUpperBound("uc2ub");
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UserDefinedConstraintComponent * udcc = userconstraint->createUserDefinedConstraintComponent();
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udcc->setCoefficient(2);
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udcc->setCoefficient("ucc1");
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udcc->setVariable("Avar");
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udcc->setVariableType("linear");
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udcc->setVariableType("quadratic");
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udcc->setVariable2("Avar2");
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// check annotations on several types
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FbcSBasePlugin* sbaseplugin = dynamic_cast<FbcSBasePlugin*>(compartment->getPlugin("fbc"));

‎src/sbml/packages/fbc/extension/test/test-data/fbc_example2_v3.xml

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</listOfKeyValuePairs>
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</annotation>
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<fbc:listOfFluxObjectives>
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<fbc:fluxObjective fbc:reaction="J0" fbc:coefficient="1" fbc:variableType="linear"/>
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<fbc:fluxObjective fbc:reaction="J0" fbc:coefficient="1" fbc:variableType="quadratic" fbc:reaction2="J0"/>
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</fbc:listOfFluxObjectives>
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</fbc:objective>
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</fbc:listOfObjectives>
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<fbc:listOfUserDefinedConstraints>
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<fbc:userDefinedConstraint fbc:id="uc2" fbc:lowerBound="uc2lb" fbc:upperBound="uc2ub">
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<fbc:listOfUserDefinedConstraintComponents>
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<fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="Avar" fbc:variableType="linear"/>
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<fbc:userDefinedConstraintComponent fbc:coefficient="ucc1" fbc:variable="Avar" fbc:variableType="quadratic" fbc:variable2="Avar2"/>
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</fbc:listOfUserDefinedConstraintComponents>
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</fbc:userDefinedConstraint>
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</fbc:listOfUserDefinedConstraints>

‎src/sbml/packages/fbc/extension/test/test-data/fbc_examplev3.xml

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<fbc:listOfUserDefinedConstraintComponents>
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<fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="Avar" fbc:variableType="linear"/>
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<fbc:userDefinedConstraintComponent fbc:coefficient="uc2ub" fbc:variable="Avar" fbc:variableType="linear"/>
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</fbc:listOfUserDefinedConstraintComponents>
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</fbc:userDefinedConstraint>
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</fbc:listOfUserDefinedConstraints>
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<fbc:listOfObjectives fbc:activeObjective="obj1">
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<fbc:objective fbc:id="obj1" fbc:type="maximize">
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<fbc:listOfFluxes>
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<fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1" fbc:variableType="linear"/>
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<fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1" fbc:variableType="quadratic" fbc:reaction2="J8"/>
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</fbc:listOfFluxes>
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</fbc:objective>
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</fbc:listOfObjectives>

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