Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update Fbc V3 package #350

Merged
merged 8 commits into from
Sep 19, 2023
Merged

Update Fbc V3 package #350

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
b3eb9c3
Update Fbc V3 package
fbergmann Sep 15, 2023
9816eb7
- update matlab test file
fbergmann Sep 15, 2023
5a54f15
- updated matlab test file
fbergmann Sep 15, 2023
876212b
- fix validation of coefficient
fbergmann Sep 15, 2023
c2e1656
- fix another test file
fbergmann Sep 15, 2023
45ab62e
- the default should not be nan for a string
fbergmann Sep 15, 2023
7013ab7
- change value type
fbergmann Sep 15, 2023
aee04c3
adding validation
skeating Sep 19, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 10 additions & 0 deletions NEWS.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,11 @@ and converting models.
- Attributes of the ModelHistory can now be accessed from
const objects.

- The FBC V3 package has been updated to reflect the latest
specification. There are now optional attributes `fbc:reaction2`
on the FluxObjective and `fbc:variable2` on the
UserDefinedConstraintComponent.

* Bug fixes

- A bug converting / validating models with the 'comp' package
Expand All @@ -23,6 +28,11 @@ and converting models.

- A fix to the CMake Build system ensures that check for dependencies
is more robust. Thanks to first time contributor @adelhpour

- The type of the FBC V3 `coefficient` attribute on the
UserDefinedConstraintComponent has been corrected, it was mistakenly
a double before, now it has been corrected to be a SIdRef as
described in the specification.


====================================================================
Expand Down
4 changes: 3 additions & 1 deletion dev/packages/deviser-fbc_v3.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,7 @@
<attribute name="id" required="false" type="SId" abstract="false"/>
<attribute name="name" required="false" type="string" abstract="false"/>
<attribute name="reaction" required="true" type="SIdRef" element="Reaction" abstract="false"/>
<attribute name="reaction2" required="false" type="SIdRef" element="Reaction" abstract="false"/>
<attribute name="coefficient" required="true" type="double" abstract="false"/>
<attribute name="variableType" required="true" type="enum" element="FbcVariableType" abstract="false"/>
</attributes>
Expand Down Expand Up @@ -226,8 +227,9 @@
<attributes>
<attribute name="id" required="false" type="SId" abstract="false"/>
<attribute name="name" required="false" type="string" abstract="false"/>
<attribute name="coefficient" required="true" type="double" abstract="false"/>
<attribute name="coefficient" required="true" type="SIdRef" element="Parameter" abstract="false"/>
<attribute name="variable" required="true" type="SIdRef" element="Reaction,Parameter" abstract="false"/>
<attribute name="variable2" required="false" type="SIdRef" element="Reaction,Parameter" abstract="false"/>
<attribute name="variableType" required="true" type="enum" element="FbcVariableType" abstract="false"/>
</attributes>
</element>
Expand Down
2 changes: 1 addition & 1 deletion src/bindings/matlab/getDefaultValues.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3565,7 +3565,7 @@
int32(-1), ...
'', ...
'', ...
0/0, ...
'', ...
int32(0), ...
'', ...
'', ...
Expand Down
2 changes: 1 addition & 1 deletion src/bindings/matlab/getValueType.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3568,7 +3568,7 @@
'int', ...
'char', ...
'char', ...
'double', ...
'char', ...
'bool', ...
'char', ...
'char', ...
Expand Down
2 changes: 1 addition & 1 deletion src/bindings/matlab/test/test-data/fbcV3.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@
<fbc:listOfUserDefinedConstraints>
<fbc:userDefinedConstraint sboTerm="SBO:0000001" fbc:id="uc2" fbc:lowerBound="uc2lb" fbc:upperBound="uc2ub">
<fbc:listOfUserDefinedConstraintComponents>
<fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:id="dd" fbc:name="string" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
<fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:id="dd" fbc:name="string" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
</fbc:listOfUserDefinedConstraintComponents>
</fbc:userDefinedConstraint>
</fbc:listOfUserDefinedConstraints>
Expand Down
2 changes: 1 addition & 1 deletion src/bindings/matlab/test/testReadFromFileFbc3.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -77,8 +77,8 @@

Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).typecode, 'SBML_FBC_USERDEFINEDCONSTRAINTCOMPONENT'));
Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_id, 'dd'));
Totalfail = Totalfail + fail_unless( m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_coefficient == 2);
Totalfail = Totalfail + fail_unless( m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).isSetfbc_coefficient == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_coefficient, 'uc2ub'));
Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_variable, 'R2'));
Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_variableType, 'linear'));

Expand Down
8 changes: 5 additions & 3 deletions src/sbml/packages/fbc/extension/test/TestWriteFbcExtension.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -415,17 +415,19 @@ START_TEST(test_FbcExtension_create_and_write_L3V1V3)
FluxObjective* fluxObjective = objective->createFluxObjective();
fluxObjective->setReaction("J0");
fluxObjective->setCoefficient(1);
fluxObjective->setVariableType("linear");
fluxObjective->setReaction2("J0");
fluxObjective->setVariableType("quadratic");

UserDefinedConstraint* userconstraint = mplugin->createUserDefinedConstraint();
userconstraint->setId("uc2");
userconstraint->setLowerBound("uc2lb");
userconstraint->setUpperBound("uc2ub");

UserDefinedConstraintComponent * udcc = userconstraint->createUserDefinedConstraintComponent();
udcc->setCoefficient(2);
udcc->setCoefficient("ucc1");
udcc->setVariable("Avar");
udcc->setVariableType("linear");
udcc->setVariableType("quadratic");
udcc->setVariable2("Avar2");

// check annotations on several types
FbcSBasePlugin* sbaseplugin = dynamic_cast<FbcSBasePlugin*>(compartment->getPlugin("fbc"));
Expand Down
4 changes: 2 additions & 2 deletions src/sbml/packages/fbc/extension/test/test-data/fbc_example2_v3.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,14 +32,14 @@
</listOfKeyValuePairs>
</annotation>
<fbc:listOfFluxObjectives>
<fbc:fluxObjective fbc:reaction="J0" fbc:coefficient="1" fbc:variableType="linear"/>
<fbc:fluxObjective fbc:reaction="J0" fbc:coefficient="1" fbc:variableType="quadratic" fbc:reaction2="J0"/>
</fbc:listOfFluxObjectives>
</fbc:objective>
</fbc:listOfObjectives>
<fbc:listOfUserDefinedConstraints>
<fbc:userDefinedConstraint fbc:id="uc2" fbc:lowerBound="uc2lb" fbc:upperBound="uc2ub">
<fbc:listOfUserDefinedConstraintComponents>
<fbc:userDefinedConstraintComponent fbc:coefficient="2" fbc:variable="Avar" fbc:variableType="linear"/>
<fbc:userDefinedConstraintComponent fbc:coefficient="ucc1" fbc:variable="Avar" fbc:variableType="quadratic" fbc:variable2="Avar2"/>
</fbc:listOfUserDefinedConstraintComponents>
</fbc:userDefinedConstraint>
</fbc:listOfUserDefinedConstraints>
Expand Down
4 changes: 2 additions & 2 deletions src/sbml/packages/fbc/extension/test/test-data/fbc_examplev3.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,14 +21,14 @@

<fbc:listOfUserDefinedConstraintComponents>

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