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From: <mh...@us...> - 2013-01-31 22:52:40
|
Revision: 17015
http://sbml.svn.sourceforge.net/sbml/?rev=17015&view=rev
Author: mhucka
Date: 2013-01-31 22:52:33 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
Need to create the Canvas object as double-buffered to avoid flickering seen on Windows.
Modified Paths:
--------------
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultMap.java
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultMap.java
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultMap.java 2013-01-31 21:16:43 UTC (rev 17014)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultMap.java 2013-01-31 22:52:33 UTC (rev 17015)
@@ -160,7 +160,7 @@
shell.addListener(SWT.Close, UIUtils.createShellCloseListener(shell));
shell.addListener(SWT.Traverse, UIUtils.createEscapeKeyListener(shell));
- canvas = new Canvas(shell, SWT.NONE);
+ canvas = new Canvas(shell, SWT.DOUBLE_BUFFERED);
canvas.addMouseListener(new MouseAdapter() {
@Override
public void mouseUp(MouseEvent arg0)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <luc...@us...> - 2013-01-31 21:16:49
|
Revision: 17014
http://sbml.svn.sourceforge.net/sbml/?rev=17014&view=rev
Author: luciansmith
Date: 2013-01-31 21:16:43 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
Missed a 'j'.
Modified Paths:
--------------
trunk/libsbml/src/sbml/Model.cpp
Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp 2013-01-31 18:54:34 UTC (rev 17013)
+++ trunk/libsbml/src/sbml/Model.cpp 2013-01-31 21:16:43 UTC (rev 17014)
@@ -5700,7 +5700,7 @@
u->setKind(getUnitDefinition(unitNo)->getUnit(pp)->getKind());
u->setMultiplier(getUnitDefinition(unitNo)->getUnit(pp)
->getMultiplier());
- u->setScale(getUnitDefinition(j)->getUnit(pp)->getScale());
+ u->setScale(getUnitDefinition(unitNo)->getUnit(pp)->getScale());
u->setExponent(-1 * (getUnitDefinition(unitNo)->getUnit(pp)
->getExponent()));
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|
|
From: <sar...@us...> - 2013-01-31 18:54:40
|
Revision: 17013
http://sbml.svn.sourceforge.net/sbml/?rev=17013&view=rev
Author: sarahkeating
Date: 2013-01-31 18:54:34 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
made some adjustments so that unknown attributes on a package element can be caught later on and more specific errors reported
Modified Paths:
--------------
trunk/libsbml/src/sbml/SBMLError.h
trunk/libsbml/src/sbml/SBMLErrorTable.h
trunk/libsbml/src/sbml/SBase.cpp
trunk/libsbml/src/sbml/SBase.h
Modified: trunk/libsbml/src/sbml/SBMLError.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLError.h 2013-01-31 18:52:35 UTC (rev 17012)
+++ trunk/libsbml/src/sbml/SBMLError.h 2013-01-31 18:54:34 UTC (rev 17013)
@@ -847,6 +847,8 @@
, MultiplierNotValidAttribute = 99924 /*!< Attribute 'multiplier' on Unit objects is not supported in SBML Level 1. */
, OffsetNotValidAttribute = 99925 /*!< Attribute 'offset' on Unit objects is only available in SBML Level 2 Version 1. */
, L3SpatialDimensionsUnset = 99926 /*!< No value given for 'spatialDimensions' attribute; assuming a value of 3. */
+, UnknownCoreAttribute = 99994 /*!< Encountered an unknow attribute in core ns */
+, UnknownPackageAttribute = 99995 /*!< Encountered an unknow attribute in package ns */
, PackageConversionNotSupported = 99996 /*!< Conversion of SBML Level 3 package constructs is not yet supported. */
, InvalidTargetLevelVersion = 99997 /*!< The requested SBML Level/Version combination is not known to exist. */
, L3NotSupported = 99998 /*!< SBML Level 3 is not yet supported. */
Modified: trunk/libsbml/src/sbml/SBMLErrorTable.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorTable.h 2013-01-31 18:52:35 UTC (rev 17012)
+++ trunk/libsbml/src/sbml/SBMLErrorTable.h 2013-01-31 18:54:34 UTC (rev 17013)
@@ -9106,8 +9106,40 @@
// "L3V1 Section 4.2.6"}
//},
+ //99994
+ {
+ UnknownCoreAttribute,
+ "",
+ LIBSBML_CAT_INTERNAL,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ ""
+ },
+
//99996
{
+ UnknownPackageAttribute,
+ "",
+ LIBSBML_CAT_INTERNAL,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ LIBSBML_SEV_ERROR,
+ ""
+ },
+
+
+
+ //99996
+ {
PackageConversionNotSupported,
"Conversion of SBML Level 3 package constructs is not yet supported",
LIBSBML_CAT_INTERNAL_CONSISTENCY,
Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp 2013-01-31 18:52:35 UTC (rev 17012)
+++ trunk/libsbml/src/sbml/SBase.cpp 2013-01-31 18:54:34 UTC (rev 17013)
@@ -4219,22 +4219,38 @@
SBase::logUnknownAttribute( const string& attribute,
const unsigned int level,
const unsigned int version,
- const string& element )
+ const string& element,
+ const string& prefix)
{
ostringstream msg;
if (getPackageName() != "core")
{
- msg << "Attribute '" << attribute << "' is not part of the "
- << "definition of an SBML Level " << level
- << " Version " << version << " Package "
- << getPackageName() << " Version " << getPackageVersion() << " "
- << element << " element.";
- if (mSBML != NULL)
+ if (prefix.empty() == false)
{
- getErrorLog()->logError(NotSchemaConformant,
- level, version, msg.str(), getLine(), getColumn());
+ msg << "Attribute '" << attribute << "' is not part of the "
+ << "definition of an SBML Level " << level
+ << " Version " << version << " Package "
+ << getPackageName() << " Version " << getPackageVersion() << " "
+ << element << " element.";
+ if (mSBML != NULL)
+ {
+ getErrorLog()->logError(UnknownPackageAttribute,
+ level, version, msg.str(), getLine(), getColumn());
+ }
}
+ else
+ {
+ msg << "Attribute '" << attribute << "' is not part of the "
+ << "definition of an SBML Level " << level
+ << " Version " << version << " "
+ << element << " element.";
+ if (mSBML != NULL)
+ {
+ getErrorLog()->logError(UnknownCoreAttribute,
+ level, version, msg.str(), getLine(), getColumn());
+ }
+ }
return;
}
else
@@ -4756,7 +4772,7 @@
}
else if (!expectedAttributes.hasAttribute(name))
{
- logUnknownAttribute(name, level, version, getElementName());
+ logUnknownAttribute(name, level, version, getElementName(), prefix);
}
}
@@ -5539,10 +5555,23 @@
// for now log the empty list
if (static_cast <ListOf*> (object)->size() == 0)
{
- ostringstream errMsg;
- errMsg << object->getElementName() << " cannot be empty.";
-
- logError(NotSchemaConformant, getLevel(), getVersion(), errMsg.str());
+ /* hack to stop an empty listOfFunctionTerms that has
+ * a defaultTerm object being logged as empty
+ */
+ if (object->getPackageName() == "qual" &&
+ object->getElementName() == "listOfFunctionTerms")
+ {
+ // do nothing
+ // will need to check for defaultTerm but will
+ // have to pass that to the qual extension
+ }
+ else
+ {
+ ostringstream errMsg;
+ errMsg << object->getElementName() << " cannot be empty.";
+
+ logError(NotSchemaConformant, getLevel(), getVersion(), errMsg.str());
+ }
}
return;
}
Modified: trunk/libsbml/src/sbml/SBase.h
===================================================================
--- trunk/libsbml/src/sbml/SBase.h 2013-01-31 18:52:35 UTC (rev 17012)
+++ trunk/libsbml/src/sbml/SBase.h 2013-01-31 18:54:34 UTC (rev 17013)
@@ -3240,7 +3240,8 @@
void logUnknownAttribute( const std::string& attribute,
const unsigned int level,
const unsigned int version,
- const std::string& element );
+ const std::string& element,
+ const std::string& prefix="");
/**
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2013-01-31 18:52:42
|
Revision: 17012
http://sbml.svn.sourceforge.net/sbml/?rev=17012&view=rev
Author: sarahkeating
Date: 2013-01-31 18:52:35 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
more validation
Modified Paths:
--------------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-pass-00-01.xml
Added Paths:
-----------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-fail-01-01.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020403-fail-01-01.xml
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.cpp 2013-01-31 18:26:52 UTC (rev 17011)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.cpp 2013-01-31 18:52:35 UTC (rev 17012)
@@ -203,7 +203,8 @@
if ( mSBMLExt->getLevel(mURI) > 2 )
{
XMLTriple tripleCharge("charge", mURI, mPrefix);
- mIsSetCharge = attributes.readInto(tripleCharge, mCharge, getErrorLog(), false, getLine(), getColumn());
+ mIsSetCharge = attributes.readInto(tripleCharge, mCharge, getErrorLog(),
+ false, getLine(), getColumn());
XMLTriple tripleChemicalFormula("chemicalFormula", mURI, mPrefix);
attributes.readInto(tripleChemicalFormula, mChemicalFormula, getErrorLog(), false, getLine(), getColumn());
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.cpp 2013-01-31 18:26:52 UTC (rev 17011)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.cpp 2013-01-31 18:52:35 UTC (rev 17012)
@@ -29,6 +29,7 @@
#include <sbml/packages/fbc/sbml/FluxBound.h>
#include <sbml/packages/fbc/extension//FbcExtension.h>
#include <sbml/packages/fbc/validator/FbcVisitor.h>
+#include <sbml/packages/fbc/validator/FbcSBMLError.h>
#if defined(WIN32) && !defined(CYGWIN)
#define isnan _isnan
@@ -454,6 +455,31 @@
{
SBase::readAttributes(attributes,expectedAttributes);
+ // look to see whether an unknown attribute error was logged
+ if (getErrorLog() != NULL)
+ {
+ unsigned int numErrs = getErrorLog()->getNumErrors();
+ for (int n = numErrs-1; n >= 0; n--)
+ {
+ if (getErrorLog()->getError(n)->getErrorId() == UnknownPackageAttribute)
+ {
+ const std::string details =
+ getErrorLog()->getError(n)->getMessage();
+ getErrorLog()->remove(UnknownPackageAttribute);
+ getErrorLog()->logPackageError("fbc", FbcFluxBoundRequiredAttributes,
+ getPackageVersion(), getLevel(), getVersion(), details);
+ }
+ else if (getErrorLog()->getError(n)->getErrorId() == UnknownCoreAttribute)
+ {
+ const std::string details =
+ getErrorLog()->getError(n)->getMessage();
+ getErrorLog()->remove(UnknownCoreAttribute);
+ getErrorLog()->logPackageError("fbc", FbcFluxBoundAllowedL3Attributes,
+ getPackageVersion(), getLevel(), getVersion(), details);
+ }
+ }
+ }
+
const unsigned int sbmlLevel = getLevel ();
const unsigned int sbmlVersion = getVersion();
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp 2013-01-31 18:26:52 UTC (rev 17011)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp 2013-01-31 18:52:35 UTC (rev 17012)
@@ -59,7 +59,7 @@
END_CONSTRAINT
// 20301 - caught at read
-// 20302 - caught at read
+// 20302 - TO DO
// 20303 - TO DO
/** @endcond */
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-fail-01-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-fail-01-01.xml (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-fail-01-01.xml 2013-01-31 18:52:35 UTC (rev 17012)
@@ -0,0 +1,78 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound constant="true" metaid="_gg" sboTerm="SBO:0000001" fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxObjectives>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxObjectives>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-pass-00-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-pass-00-01.xml 2013-01-31 18:26:52 UTC (rev 17011)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-pass-00-01.xml 2013-01-31 18:52:35 UTC (rev 17012)
@@ -68,10 +68,10 @@
<fbc:listOfObjectives fbc:activeObjective="c">
<fbc:objective fbc:id="c" fbc:type="maximize">
- <fbc:listOfFluxes>
+ <fbc:listOfFluxObjectives>
<fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
<fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
- </fbc:listOfFluxes>
+ </fbc:listOfFluxObjectives>
</fbc:objective>
</fbc:listOfObjectives>
</model>
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020403-fail-01-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020403-fail-01-01.xml (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020403-fail-01-01.xml 2013-01-31 18:52:35 UTC (rev 17012)
@@ -0,0 +1,121 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model>
+ <listOfCompartments>
+ <compartment id="compartment" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="Node1" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="Node2" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="Node3" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="Node4" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="Node5" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="Node6" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="Node7" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="Node8" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="Node0" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
+ <species id="Node9" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node0" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node1" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node1" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node2" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node2" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node3" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J3" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node1" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node4" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J4" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node4" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node3" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J5" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node3" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node5" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J6" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node5" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node6" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J7" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node6" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node7" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J8" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node5" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node8" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J9" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node8" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node7" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J10" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="Node7" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="Node9" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:coefficient="2" fbc:reaction="J0" fbc:operation="greaterEqual" fbc:value="0"/>
+ <fbc:fluxBound fbc:id="bound2" fbc:reaction="J0" fbc:operation="lessEqual" fbc:value="10"/>
+ </fbc:listOfFluxBounds>
+ <fbc:listOfObjectives fbc:activeObjective="obj1">
+ <fbc:objective fbc:id="obj1" fbc:type="maximize">
+ <fbc:listOfFluxObjectives>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxObjectives>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
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|
|
From: <fbe...@us...> - 2013-01-31 18:26:58
|
Revision: 17011
http://sbml.svn.sourceforge.net/sbml/?rev=17011&view=rev
Author: fbergmann
Date: 2013-01-31 18:26:52 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
- noticed a couple of typos while going through the validation rules
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-validation.tex
Modified: trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-validation.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-validation.tex 2013-01-31 18:25:40 UTC (rev 17010)
+++ trunk/specifications/sbml-level-3/version-1/fbc/spec/apdx-validation.tex 2013-01-31 18:26:52 UTC (rev 17011)
@@ -133,9 +133,9 @@
\sec{model-class}.) }
\validRule{fbc-20205}{A \ListOfFluxBounds object may have the optional
-\token{meta\-id} and \token{sboTerm} defined by SBML Level~3 Core. No
-other attributes from the SBML Level~3 Core namespace or the Flux
-Balance Constraints namespace are permitted on a \ListOfFluxBounds
+attributes \token{meta\-id} and \token{sboTerm} defined by SBML Level~3
+Core. No other attributes from the SBML Level~3 Core namespace or the
+Flux Balance Constraints namespace are permitted on a \ListOfFluxBounds
object. (References: SBML Level~3 Package Specification for Flux Balance
Constraints, Version~1, \sec{model-class}.) }
@@ -185,12 +185,12 @@
\validRule{fbc-20401}{A \FluxBound object may have the optional SBML
Level 3 Core attributes \token{metaid} and \token{sboTerm}. No other
-attributes from the SBML Level 3 Core namespaces are permitted on a
+attributes from the SBML Level 3 Core namespace are permitted on a
\FluxBound. (References: SBML Level~3 Version~1 Core, Section~3.2.) }
\validRule{fbc-20402}{A \FluxBound object may have the optional SBML
Level 3 Core subobjects for notes and annotations. No other elements
-from the SBML Level 3 Core namespaces are permitted on a \FluxBound.
+from the SBML Level 3 Core namespace are permitted on a \FluxBound.
(References: SBML Level~3 Version~1 Core, Section~3.2.) }
\validRule{fbc-20403}{A \FluxBound object must have the required
@@ -201,34 +201,34 @@
\FluxBound object. (References: SBML Level~3 Package Specification for
Flux Balance Constraints, Version~1, \sec{fluxbound-class}.) }
-\validRule{fbc-20404}{The attribute \token{fbc:\-reaction} in \FluxBound
+\validRule{fbc-20404}{The attribute \token{fbc:\-reaction} of a \FluxBound
must be of the data type \token{SIdRef}. (References: SBML Level~3
Package Specification for Flux Balance Constraints, Version~1,
\sec{fluxbound-class}.) }
-\validRule{fbc-20405}{The attribute \token{fbc:\-name} in \FluxBound
+\validRule{fbc-20405}{The attribute \token{fbc:\-name} of a \FluxBound
must be of the data type \token{string}. (References: SBML Level~3
Package Specification for Flux Balance Constraints, Version~1,
\sec{fluxbound-class}.) }
-\validRule{fbc-20406}{The attribute \token{fbc:\-operation} in
+\validRule{fbc-20406}{The attribute \token{fbc:\-operation} of a
\FluxBound must be of the data type \token{FbcOperation}. (References:
SBML Level~3 Package Specification for Flux Balance Constraints,
Version~1, \sec{fluxbound-class}.) }
-\validRule{fbc-20407}{The attribute \token{fbc:\-value} in \FluxBound
+\validRule{fbc-20407}{The attribute \token{fbc:\-value} of a \FluxBound
must be of the data type \token{double}. (References: SBML Level~3
Package Specification for Flux Balance Constraints, Version~1,
\sec{fluxbound-class}.) }
\validRule{fbc-20408}{The value of the attribute \token{fbc:\-reaction}
-in a \FluxBound object must be the identifier of an existing \Reaction
+of a \FluxBound object must be the identifier of an existing \Reaction
object defined in the enclosing \Model object. (References: SBML Level~3
Package Specification for Flux Balance Constraints, Version~1,
\sec{fluxbound-class}.) }
\validRule{fbc-20409}{The value of the attribute \token{fbc:\-operation}
-in a \FluxBound object must be one of \val{lessEqual},
+of a \FluxBound object must be one of \val{lessEqual},
\val{greaterEqual} or \val{equal}. (References: SBML Level~3 Package
Specification for Flux Balance Constraints, Version~1,
\sec{fluxbound-class}.) }
@@ -244,12 +244,12 @@
\validRule{fbc-20501}{A \Objective object may have the optional SBML
Level 3 Core attributes \token{metaid} and \token{sboTerm}. No other
-attributes from the SBML Level 3 Core namespaces are permitted on a
+attributes from the SBML Level 3 Core namespace are permitted on a
\Objective. (References: SBML Level~3 Version~1 Core, Section~3.2.) }
\validRule{fbc-20502}{A \Objective object may have the optional SBML
Level 3 Core subobjects for notes and annotations. No other elements
-from the SBML Level 3 Core namespaces are permitted on a \Objective.
+from the SBML Level 3 Core namespace are permitted on a \Objective.
(References: SBML Level~3 Version~1 Core, Section~3.2.) }
\validRule{fbc-20503}{A \Objective object must have the required
@@ -259,34 +259,34 @@
object. (References: SBML Level~3 Package Specification for Flux Balance
Constraints, Version~1, \sec{objective-class}.) }
-\validRule{fbc-20504}{The attribute \token{fbc:\-name} in \Objective
+\validRule{fbc-20504}{The attribute \token{fbc:\-name} on a \Objective
must be of the data type \token{string}. (References: SBML Level~3
Package Specification for Flux Balance Constraints, Version~1,
\sec{objective-class}.) }
-\validRule{fbc-20505}{The attribute \token{fbc:\-type} in \Objective
+\validRule{fbc-20505}{The attribute \token{fbc:\-type} on a \Objective
must be of the data type \token{FbcType}. (References: SBML Level~3
Package Specification for Flux Balance Constraints, Version~1,
\sec{objective-class}.) }
-\validRule{fbc-20506}{The value of the attribute \token{fbc:\-type} in a
+\validRule{fbc-20506}{The value of the attribute \token{fbc:\-type} on a
\Objective object must be one of \val{minimize} or \val{maximize}.
(References: SBML Level~3 Package Specification for Flux Balance
Constraints, Version~1, \sec{objective-class}.) }
-\validRule{fbc-20507}{A \Objective must have one and only one instance
-of the \ListOfFluxObjectives object. (References: SBML Level~3 Package
-Specification for Flux Balance Constraints, Version~1,
+\validRule{fbc-20507}{A \Objective object must have one and only one
+instance of the \ListOfFluxObjectives object. (References: SBML Level~3
+Package Specification for Flux Balance Constraints, Version~1,
\sec{objective-class}.) }
-\validRule{fbc-20508}{The \ListOfFluxObjectives subobject with a
+\validRule{fbc-20508}{The \ListOfFluxObjectives subobject within a
\Objective object must not be empty. (References: SBML Level~3 Package
Specification for Flux Balance Constraints, Version~1,
\sec{objective-class}.) }
\validRule{fbc-20509}{Apart from the general notes and annotation
subobjects permitted on all SBML objects, a \ListOfFluxObjectives
-container object may only contain \Objective objects. (References: SBML
+container object may only contain \FluxObjective objects. (References: SBML
Level~3 Package Specification for Flux Balance Constraints, Version~1,
\sec{objective-class}.) }
@@ -302,13 +302,13 @@
\validRule{fbc-20601}{A \FluxObjective object may have the optional SBML
Level 3 Core attributes \token{metaid} and \token{sboTerm}. No other
-attributes from the SBML Level 3 Core namespaces are permitted on a
+attributes from the SBML Level 3 Core namespace are permitted on a
\FluxObjective. (References: SBML Level~3 Version~1 Core, Section~3.2.)
}
\validRule{fbc-20602}{A \FluxObjective object may have the optional SBML
Level 3 Core subobjects for notes and annotations. No other elements
-from the SBML Level 3 Core namespaces are permitted on a \FluxObjective.
+from the SBML Level 3 Core namespace are permitted on a \FluxObjective.
(References: SBML Level~3 Version~1 Core, Section~3.2.) }
\validRule{fbc-20603}{A \FluxObjective object must have the required
@@ -319,7 +319,7 @@
Level~3 Package Specification for Flux Balance Constraints, Version~1,
\sec{fluxobjective-class}.) }
-\validRule{fbc-20604}{The attribute \token{fbc:\-name} in \FluxObjective
+\validRule{fbc-20604}{The attribute \token{fbc:\-name} on a \FluxObjective
must be of the data type \token{string}. (References: SBML Level~3
Package Specification for Flux Balance Constraints, Version~1,
\sec{fluxobjective-class}.) }
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|
|
From: <fbe...@us...> - 2013-01-31 18:25:47
|
Revision: 17010
http://sbml.svn.sourceforge.net/sbml/?rev=17010&view=rev
Author: fbergmann
Date: 2013-01-31 18:25:40 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
correct example
Modified Paths:
--------------
branches/libsbml-packages/fbc/examples/xml/fbc_example1.xml
Modified: branches/libsbml-packages/fbc/examples/xml/fbc_example1.xml
===================================================================
--- branches/libsbml-packages/fbc/examples/xml/fbc_example1.xml 2013-01-31 17:51:41 UTC (rev 17009)
+++ branches/libsbml-packages/fbc/examples/xml/fbc_example1.xml 2013-01-31 18:25:40 UTC (rev 17010)
@@ -111,9 +111,9 @@
</fbc:listOfFluxBounds>
<fbc:listOfObjectives activeObjective="obj1">
<fbc:objective fbc:id="obj1" fbc:type="maximize">
- <fbc:listOfFluxes>
+ <fbc:listOfFluxObjectives>
<fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
- </fbc:listOfFluxes>
+ </fbc:listOfFluxObjectives>
</fbc:objective>
</fbc:listOfObjectives>
</model>
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|
|
From: <luc...@us...> - 2013-01-31 17:51:48
|
Revision: 17009
http://sbml.svn.sourceforge.net/sbml/?rev=17009&view=rev
Author: luciansmith
Date: 2013-01-31 17:51:41 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
Removed duplicate validation rules.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex
Modified: trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex 2013-01-31 17:29:54 UTC (rev 17008)
+++ trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex 2013-01-31 17:51:41 UTC (rev 17009)
@@ -851,24 +851,14 @@
(References: SBML Level~3 Package Specification for Hierarchical Model
Composition, Version~1, \sec{replacedelement-conversionfactor}.) }
-\validRule{comp-21007}{The value of a \token{comp:submodelRef}
- attribute on a \ReplacedElement object must always conform to the
- syntax of the SBML data type \primtype{SId}. (References: SBML
- Level~3 Package Specification for Hierarchical Model Composition,
- Version~1, \sec{replacedelement-submodelref}.) }
+\validRule{comp-21007}{\begin{blockChanged}(Rule removed because it was
+ a duplicate of 10308.)\end{blockChanged}}
-\validRule{comp-21008}{The value of a \token{comp:deletion} attribute
- on a \ReplacedElement object must always conform to the syntax of the
- SBML data type \primtype{SId}. (References: SBML Level~3 Package
- Specification for Hierarchical Model Composition, Version~1,
- \sec{replacedelement-deletion}.) }
+\validRule{comp-21008}{\begin{blockChanged}(Rule removed because it was
+ a duplicate of 10309.)\end{blockChanged} }
-\validRule{comp-21009}{The value of a
- \token{comp:conversionFactor} attribute on a \ReplacedElement
- object must always conform to the syntax of the SBML data type
- \primtype{SId}. (References: SBML Level~3 Package Specification for
- Hierarchical Model Composition, Version~1,
- \sec{replacedelement-conversionfactor}.) }
+\validRule{comp-21009}{\begin{blockChanged}(Rule removed because it was
+ a duplicate of 10310.)\end{blockChanged} }
\validRule{comp-21010}{No two \ReplacedElement objects in the same
\Model may reference the \begin{blockChanged}same\end{blockChanged} object unless that object is a \Deletion.
@@ -908,8 +898,5 @@
(References: SBML Level~3 Package Specification for Hierarchical Model
Composition, Version~1, \sec{replacedby-submodelref}.) }
-\validRule{comp-21105}{The value of a \token{comp:submodelRef}
- attribute on a \ReplacedBy object must always conform to the
- syntax of the SBML data type \primtype{SId}. (References: SBML
- Level~3 Package Specification for Hierarchical Model Composition,
- Version~1, \sec{replacedby-submodelref}.) }
+\validRule{comp-21105}{\begin{blockChanged}(Rule removed because it was
+ a duplicate of 10308.)\end{blockChanged} }
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|
|
From: <fbe...@us...> - 2013-01-31 17:30:05
|
Revision: 17008
http://sbml.svn.sourceforge.net/sbml/?rev=17008&view=rev
Author: fbergmann
Date: 2013-01-31 17:29:54 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
- added basic command line version that allows to run a configured wrapper from command line
Modified Paths:
--------------
trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/Main.java
trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/WrapperConfig.java
trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/commandline/TestSuiteArguments.java
trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/data/ResultSet.java
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/Main.java
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/Main.java 2013-01-31 16:47:34 UTC (rev 17007)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/Main.java 2013-01-31 17:29:54 UTC (rev 17008)
@@ -30,6 +30,7 @@
package org.sbml.testsuite.core;
+import org.sbml.testsuite.core.RunOutcome.Code;
import org.sbml.testsuite.core.commandline.TestSuiteArguments;
/**
@@ -48,11 +49,111 @@
public static void main(String[] rawArgs)
{
TestSuiteArguments args = new TestSuiteArguments(rawArgs);
- if (args.isValid())
+ if (!args.isValid())
{
args.printArguments(System.err);
System.exit(1);
}
+
+ if (args.isShouldRun())
+ {
+ runWrapper(args);
+ }
+
}
+
+ /**
+ * Runs the specified wrapper for over the given range.
+ *
+ * @param args
+ * the parsed arguments
+ */
+ public static void runWrapper(TestSuiteArguments args)
+ {
+ TestSuiteSettings settings = TestSuiteSettings.loadDefault();
+ WrapperConfig wrapper = settings.getWrapper(args.getWrapperName());
+ if (wrapper == null)
+ {
+ System.out.println(String.format("The wrapper '%s' does not exist.",
+ args.getWrapperName()));
+ System.exit(1);
+ }
+
+ if (!wrapper.canRun())
+ {
+ System.out.println(String.format("The wrapper '%s' cannot be executed.",
+ args.getWrapperName()));
+ System.exit(1);
+ }
+
+ TestCase test = settings.getSuite().get(args.getTestOrTestRange());
+ if (test != null)
+ {
+ System.out.println(String.format("Starting Wrapper %s for case %s",
+ wrapper.getName(), test.getId()));
+ RunOutcome result = wrapper.run(test, settings.getSuite()
+ .getCasesDirectory()
+ .getAbsolutePath());
+
+ if (result.getCode() == Code.success)
+ {
+ System.out.println(String.format("... run succeeded, result is: "
+ + wrapper.getResultType(test).toString()));
+ }
+ else
+ {
+ System.out.println(result.getMessage());
+ }
+
+ }
+ else
+ {
+ String[] range = args.getTestOrTestRange().split("-");
+ if (range == null || range.length != 2)
+ {
+ System.out.println(String.format("Invalid test range '%s' specified",
+ args.getTestOrTestRange()));
+ System.exit(1);
+ }
+ try
+ {
+
+ int lower = Integer.parseInt(range[0]);
+ int end = Integer.parseInt(range[1]);
+
+ for (int i = lower; i >= 0 && i <= end
+ && i < settings.getSuite().getNumCases(); i++)
+ {
+ test = settings.getSuite().get(i - 1);
+ System.out.println(String.format("Starting Wrapper %s for case %s",
+ wrapper.getName(),
+ test.getId()));
+ RunOutcome result = wrapper.run(test,
+ settings.getSuite()
+ .getCasesDirectory()
+ .getAbsolutePath());
+ if (result.getCode() == Code.success)
+ {
+ System.out.println(String.format("... run succeeded, result is: "
+ + wrapper.getResultType(test).toString()));
+ }
+ else
+ {
+ System.out.println(result.getMessage());
+ }
+ }
+ }
+ catch (NumberFormatException ex)
+ {
+ System.out.println(String.format("Invalid test range '%s' specified",
+ args.getTestOrTestRange()));
+ System.exit(1);
+ }
+
+ }
+ System.out.println();
+ System.out.println("done ...");
+ System.exit(0);
+ }
}
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/WrapperConfig.java
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/WrapperConfig.java 2013-01-31 16:47:34 UTC (rev 17007)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/WrapperConfig.java 2013-01-31 17:29:54 UTC (rev 17008)
@@ -30,11 +30,8 @@
package org.sbml.testsuite.core;
-import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
import java.util.TreeMap;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
@@ -56,534 +53,534 @@
*/
@Default
public class WrapperConfig
- {
- /**
- * Load a wrapper configuration from file
- *
- * @param file
- * the filename
- * @return the wrapper object
- * @throws Exception
- * IO / Deserialization exceptions
- */
- public static WrapperConfig fromFile(File file)
- throws Exception
- {
- Serializer serializer = new Persister();
- WrapperConfig config = serializer.read(WrapperConfig.class, file);
- if (config.unsupportedTags == null)
- config.unsupportedTags = new Vector<String>();
- return config;
- }
+{
+ /**
+ * Load a wrapper configuration from file
+ *
+ * @param file
+ * the filename
+ * @return the wrapper object
+ * @throws Exception
+ * IO / Deserialization exceptions
+ */
+ public static WrapperConfig fromFile(File file)
+ throws Exception
+ {
+ Serializer serializer = new Persister();
+ WrapperConfig config = serializer.read(WrapperConfig.class, file);
+ if (config.unsupportedTags == null)
+ config.unsupportedTags = new Vector<String>();
+ return config;
+ }
- /**
- * Simple test that checks whether a given process is running
- *
- * @param p
- * the process
- *
- * @return true, if process is running, false otherwise.
- */
- public static boolean isRunning(Process p)
- {
- if (p == null) return false;
+ /**
+ * Simple test that checks whether a given process is running
+ *
+ * @param p
+ * the process
+ *
+ * @return true, if process is running, false otherwise.
+ */
+ public static boolean isRunning(Process p)
+ {
+ if (p == null) return false;
- boolean isRunning = false;
+ boolean isRunning = false;
- try
- {
- p.exitValue();
- }
- catch (IllegalThreadStateException e)
- {
- isRunning = true;
- }
- return isRunning;
- }
+ try
+ {
+ p.exitValue();
+ }
+ catch (IllegalThreadStateException e)
+ {
+ isRunning = true;
+ }
+ return isRunning;
+ }
- private String name;
- @Element(required = false)
- private String program;
- private String outputPath;
- @Element(required = false)
- private String arguments;
+ private String name;
+ @Element(required = false)
+ private String program;
+ private String outputPath;
+ @Element(required = false)
+ private String arguments;
- private Vector<String> unsupportedTags;
+ private Vector<String> unsupportedTags;
- @Element(required = false)
- private boolean supportsAllVersions;
+ @Element(required = false)
+ private boolean supportsAllVersions;
- @Transient
- private TreeMap<String, DelayedResult> resultCache;
+ @Transient
+ private TreeMap<String, DelayedResult> resultCache;
- static ExecutorService executor = Executors.newFixedThreadPool(20);
+ static ExecutorService executor = Executors.newFixedThreadPool(20);
+ /**
+ * Default Constructor
+ */
+ public WrapperConfig()
+ {
+ super();
+ this.name = "";
+ this.program = "";
+ this.outputPath = "";
+ this.arguments = "";
+ supportsAllVersions = false;
+ unsupportedTags = new Vector<String>();
+ }
- /**
- * Default Constructor
- */
- public WrapperConfig()
- {
- super();
- this.name = "";
- this.program = "";
- this.outputPath = "";
- this.arguments = "";
- supportsAllVersions = false;
- unsupportedTags = new Vector<String>();
- }
+ /**
+ * Constructs a new config with name
+ *
+ * @param name
+ * the name for the configuration
+ */
+ public WrapperConfig(String name)
+ {
+ this();
+ this.name = name;
+ }
- /**
- * Constructs a new config with name
- *
- * @param name
- * the name for the configuration
- */
- public WrapperConfig(String name)
- {
- this();
- this.name = name;
- }
+ /**
+ * Constructs a new config with name, program, outputPath and arguments
+ *
+ * @param name
+ * the name of the simulator
+ * @param program
+ * the wrapper executable
+ * @param outputPath
+ * the output path of the wrapper
+ * @param arguments
+ * additional arguments
+ */
+ public WrapperConfig(String name, String program, String outputPath,
+ String arguments)
+ {
+ this(name);
+ this.program = program;
+ this.outputPath = outputPath;
+ this.arguments = arguments;
+ }
- /**
- * Constructs a new config with name, program, outputPath and arguments
- *
- * @param name
- * the name of the simulator
- * @param program
- * the wrapper executable
- * @param outputPath
- * the output path of the wrapper
- * @param arguments
- * additional arguments
- */
- public WrapperConfig(String name, String program, String outputPath,
- String arguments)
- {
- this(name);
- this.program = program;
- this.outputPath = outputPath;
- this.arguments = arguments;
- }
+ /**
+ * Constructs a new config with name, program, outputPath, arguments as well
+ * as a list
+ * of unsupported test flags and a boolean indicating whether the wrapper
+ * can run all levels / versions of SBML
+ *
+ * @param name
+ * the name of the simulator
+ * @param program
+ * the wrapper executable
+ * @param outputPath
+ * the output path of the wrapper
+ * @param arguments
+ * additional arguments
+ * @param unsupportedTags
+ * a comma separated list of test / component tags not supported
+ * by this simulator
+ * @param supportsAllVersions
+ * boolean indicating whether this simulator supports *all*
+ * levels / versions of SBML
+ */
+ public WrapperConfig(String name, String program, String outputPath,
+ String arguments, String unsupportedTags,
+ boolean supportsAllVersions)
+ {
+ this(name, program, outputPath, arguments);
+ this.unsupportedTags = new Vector<String>(Util.split(unsupportedTags));
+ this.supportsAllVersions = supportsAllVersions;
+ }
- /**
- * Constructs a new config with name, program, outputPath, arguments as well
- * as a list
- * of unsupported test flags and a boolean indicating whether the wrapper
- * can run all levels / versions of SBML
- *
- * @param name
- * the name of the simulator
- * @param program
- * the wrapper executable
- * @param outputPath
- * the output path of the wrapper
- * @param arguments
- * additional arguments
- * @param unsupportedTags
- * a comma separated list of test / component tags not supported
- * by this simulator
- * @param supportsAllVersions
- * boolean indicating whether this simulator supports *all*
- * levels / versions of SBML
- */
- public WrapperConfig(String name, String program, String outputPath,
- String arguments, String unsupportedTags,
- boolean supportsAllVersions)
- {
- this(name, program, outputPath, arguments);
- this.unsupportedTags = new Vector<String>(Util.split(unsupportedTags));
- this.supportsAllVersions = supportsAllVersions;
- }
+ /**
+ * Constructs a new config with name, program, outputPath, arguments as well
+ * as a list
+ * of unsupported test flags and a boolean indicating whether the wrapper
+ * can run all levels / versions of SBML
+ *
+ * @param name
+ * the name of the simulator
+ * @param program
+ * the wrapper executable
+ * @param outputPath
+ * the output path of the wrapper
+ * @param arguments
+ * additional arguments
+ * @param unsupportedTags
+ * a string vector of test / component tags not supported by this
+ * simulator
+ * @param supportsAllVersions
+ * boolean indicating whether this simulator supports *all*
+ * levels / versions of SBML
+ */
+ public WrapperConfig(String name, String program, String outputPath,
+ String arguments, Vector<String> unsupportedTags,
+ boolean supportsAllVersions)
+ {
+ this(name, program, outputPath, arguments);
+ this.unsupportedTags = unsupportedTags;
+ this.supportsAllVersions = supportsAllVersions;
+ }
- /**
- * Constructs a new config with name, program, outputPath, arguments as well
- * as a list
- * of unsupported test flags and a boolean indicating whether the wrapper
- * can run all levels / versions of SBML
- *
- * @param name
- * the name of the simulator
- * @param program
- * the wrapper executable
- * @param outputPath
- * the output path of the wrapper
- * @param arguments
- * additional arguments
- * @param unsupportedTags
- * a string vector of test / component tags not supported by this
- * simulator
- * @param supportsAllVersions
- * boolean indicating whether this simulator supports *all*
- * levels / versions of SBML
- */
- public WrapperConfig(String name, String program, String outputPath,
- String arguments, Vector<String> unsupportedTags,
- boolean supportsAllVersions)
- {
- this(name, program, outputPath, arguments);
- this.unsupportedTags = unsupportedTags;
- this.supportsAllVersions = supportsAllVersions;
- }
+ /**
+ * Starts the calculation of all results.
+ *
+ * @param suite
+ * the tests to compare against
+ */
+ public void beginUpdate(TestSuite suite)
+ {
+ resultCache = new TreeMap<String, DelayedResult>();
+ for (final TestCase test : suite.getCases())
+ {
- /**
- * Starts the calculation of all results.
- *
- * @param suite
- * the tests to compare against
- */
- public void beginUpdate(TestSuite suite)
- {
- resultCache = new TreeMap<String, DelayedResult>();
- for (final TestCase test : suite.getCases())
- {
+ resultCache.put(test.getId(), new DelayedResult(WrapperConfig.this,
+ test));
- resultCache.put(test.getId(), new DelayedResult(WrapperConfig.this,
- test));
+ }
+ }
- }
- }
+ /**
+ * @return boolean indicating whether this wrapepr is executable. This is
+ * the case when the wrapper executable exists as well as teh output
+ * tag.
+ */
+ public boolean canRun()
+ {
+ if (program == null || program.length() == 0) return false;
+ if (outputPath == null || outputPath.length() == 0) return false;
- /**
- * @return boolean indicating whether this wrapepr is executable. This is
- * the case when the wrapper executable exists as well as teh output
- * tag.
- */
- public boolean canRun()
- {
- if (program == null || program.length() == 0) return false;
- if (outputPath == null || outputPath.length() == 0) return false;
+ File outPath = new File(outputPath);
+ File fileProg = new File(program);
+ if (fileProg.exists() && fileProg.isFile() && outPath.exists()
+ && outPath.isDirectory()) return true;
- File outPath = new File(outputPath);
- File fileProg = new File(program);
- if (fileProg.exists() && fileProg.isFile() && outPath.exists()
- && outPath.isDirectory()) return true;
+ return false;
+ }
- return false;
- }
+ /**
+ * Deletes the result for the given test
+ *
+ * @param test
+ * the test
+ */
+ public void deleteResult(TestCase test)
+ {
+ File testFile = getResultFile(test);
+ if (testFile.exists()) testFile.delete();
+ resultCache.put(test.getId(), new DelayedResult(ResultType.Unknown));
+ }
- /**
- * Deletes the result for the given test
- *
- * @param test
- * the test
- */
- public void deleteResult(TestCase test)
- {
- File testFile = getResultFile(test);
- if (testFile.exists()) testFile.delete();
- resultCache.put(test.getId(), new DelayedResult(ResultType.Unknown));
- }
+ /**
+ * @return the wrapper arguments
+ */
+ public String getArguments()
+ {
+ return arguments;
+ }
- /**
- * @return the wrapper arguments
- */
- public String getArguments()
- {
- return arguments;
- }
+ /**
+ * @return the cache of all computed results
+ */
+ public TreeMap<String, DelayedResult> getCache()
+ {
+ return resultCache;
+ }
- /**
- * @return the cache of all computed results
- */
- public TreeMap<String, DelayedResult> getCache()
- {
- return resultCache;
- }
+ /**
+ * returns the cached result for the test with given id
+ *
+ * @param id
+ * the test id
+ * @return the result type
+ */
+ public ResultType getCachedResult(String id)
+ {
+ TreeMap<String, DelayedResult> cache = resultCache;
- /**
- * returns the cached result for the test with given id
- *
- * @param id
- * the test id
- * @return the result type
- */
- public ResultType getCachedResult(String id)
- {
- TreeMap<String, DelayedResult> cache = resultCache;
+ return cache.get(id).getResult();
- return cache.get(id).getResult();
+ }
- }
+ /**
+ * Expands variables within the argument string
+ *
+ * @param test
+ * the test case
+ * @param testSuiteDir
+ * the test suite directory
+ * @return expanded argument string
+ */
+ private String getExpandedArguments(TestCase test, String testSuiteDir)
+ {
+ String arguments = getArguments();
+ arguments = arguments.replace("%d", testSuiteDir);
+ arguments = arguments.replace("%o", getOutputPath());
+ arguments = arguments.replace("%n", test.getId());
+ arguments = arguments.replace("%l", test.getHighestSupportedLevel()
+ + "");
+ arguments = arguments.replace("%v", test.getHighestSupportedVersion()
+ + "");
+ return arguments;
+ }
- /**
- * Expands variables within the argument string
- *
- * @param test
- * the test case
- * @param testSuiteDir
- * the test suite directory
- * @return expanded argument string
- */
- private String getExpandedArguments(TestCase test, String testSuiteDir)
- {
- String arguments = getArguments();
- arguments = arguments.replace("%d", testSuiteDir);
- arguments = arguments.replace("%o", getOutputPath());
- arguments = arguments.replace("%n", test.getId());
- arguments = arguments.replace("%l", test.getHighestSupportedLevel()
- + "");
- arguments = arguments.replace("%v", test.getHighestSupportedVersion()
- + "");
- return arguments;
- }
+ /**
+ * @return the name of this configuration
+ */
+ public String getName()
+ {
+ return name;
+ }
- /**
- * @return the name of this configuration
- */
- public String getName()
- {
- return name;
- }
+ /**
+ * @return the wrapper output path / the folder containing the simulator
+ * results
+ */
+ public String getOutputPath()
+ {
+ return outputPath;
+ }
- /**
- * @return the wrapper output path / the folder containing the simulator
- * results
- */
- public String getOutputPath()
- {
- return outputPath;
- }
+ /**
+ * @return the wrapper executable
+ */
+ public String getProgram()
+ {
+ return program;
+ }
- /**
- * @return the wrapper executable
- */
- public String getProgram()
- {
- return program;
- }
+ /**
+ * Returns the file for the simulator result file for the given test
+ *
+ * @param test
+ * the test
+ * @return simulator result file
+ */
+ public File getResultFile(TestCase test)
+ {
+ return new File(getOutputPath() + File.separator + test.getId()
+ + ".csv");
- /**
- * Returns the file for the simulator result file for the given test
- *
- * @param test
- * the test
- * @return simulator result file
- */
- public File getResultFile(TestCase test)
- {
- return new File(getOutputPath() + File.separator + test.getId()
- + ".csv");
+ }
- }
+ /**
+ * Get the result set for the given test
+ *
+ * @param test
+ * the test to get the result for
+ * @return the simulator result for the test
+ */
+ public ResultSet getResultSet(TestCase test)
+ {
+ File testFile = getResultFile(test);
+ if (!testFile.exists()) return null;
+ return ResultSet.fromFile(testFile);
- /**
- * Get the result set for the given test
- *
- * @param test
- * the test to get the result for
- * @return the simulator result for the test
- */
- public ResultSet getResultSet(TestCase test)
- {
- File testFile = getResultFile(test);
- if (!testFile.exists()) return null;
- return ResultSet.fromFile(testFile);
+ }
- }
+ /**
+ * Gets the result type for the given test (computes it immidiately)
+ *
+ * @param test
+ * the test to get the result type for
+ * @return the result type
+ */
+ public ResultType getResultType(TestCase test)
+ {
+ ResultType result = getResultTypeInternal(test);
+ if (resultCache != null)
+ {
+ resultCache.put(test.getId(), new DelayedResult(result));
+ }
+ return result;
- /**
- * Gets the result type for the given test (computes it immidiately)
- *
- * @param test
- * the test to get the result type for
- * @return the result type
- */
- public ResultType getResultType(TestCase test)
- {
- ResultType result = getResultTypeInternal(test);
- if (resultCache != null)
- {
- resultCache.put(test.getId(), new DelayedResult(result));
- }
- return result;
+ }
- }
+ /**
+ * Computes the result type for the given test
+ *
+ * @param test
+ * the test
+ * @return the result type
+ */
+ public ResultType getResultTypeInternal(TestCase test)
+ {
+ if (test.matches(getUnsupportedTags())) return ResultType.CannotSolve;
- /**
- * Computes the result type for the given test
- *
- * @param test
- * the test
- * @return the result type
- */
- public ResultType getResultTypeInternal(TestCase test)
- {
- if (test.matches(getUnsupportedTags())) return ResultType.CannotSolve;
+ ResultSet deliveredResult = getResultSet(test);
+ if (deliveredResult == null) return ResultType.Unknown;
- ResultSet deliveredResult = getResultSet(test);
- if (deliveredResult == null) return ResultType.Unknown;
+ ResultSet expectedResult = test.getExpectedResult();
- ResultSet expectedResult = test.getExpectedResult();
+ CompareResultSet set = new CompareResultSet(expectedResult,
+ deliveredResult);
+ if (set.compareUsingTestSuite(test.getSettings().getAbsoluteError(),
+ test.getSettings().getRelativeError()))
+ return ResultType.Match;
+ else
+ return ResultType.NoMatch;
+ }
- CompareResultSet set = new CompareResultSet(expectedResult,
- deliveredResult);
- if (set.compareUsingTestSuite(test.getSettings().getAbsoluteError(),
- test.getSettings().getRelativeError()))
- return ResultType.Match;
- else
- return ResultType.NoMatch;
- }
+ /**
+ * @return the list of unsupported test / component tags
+ */
+ public Vector<String> getUnsupportedTags()
+ {
+ return unsupportedTags;
+ }
- /**
- * @return the list of unsupported test / component tags
- */
- public Vector<String> getUnsupportedTags()
- {
- return unsupportedTags;
- }
+ /**
+ * @return a string containing a comma separated list of unsupported test /
+ * component tags
+ */
+ public String getUnsupportedTagsString()
+ {
+ return Util.toString(unsupportedTags);
+ }
- /**
- * @return a string containing a comma separated list of unsupported test /
- * component tags
- */
- public String getUnsupportedTagsString()
- {
- return Util.toString(unsupportedTags);
- }
+ /**
+ * @return boolean indicating whether this wrapper supports all levels /
+ * versions of SBML
+ */
+ public boolean isSupportsAllVersions()
+ {
+ return supportsAllVersions;
+ }
- /**
- * @return boolean indicating whether this wrapper supports all levels /
- * versions of SBML
- */
- public boolean isSupportsAllVersions()
- {
- return supportsAllVersions;
- }
+ /**
+ * Executed the given test
+ *
+ * @param test
+ * the test to execute
+ * @param testSuiteDir
+ * the test cases directory
+ */
+ public RunOutcome run(TestCase test, String testSuiteDir)
+ {
+ return run(test, testSuiteDir, null);
+ }
- /**
- * Executed the given test
- *
- * @param test
- * the test to execute
- * @param testSuiteDir
- * the test cases directory
- */
- public void run(TestCase test, String testSuiteDir)
- {
- run(test, testSuiteDir, null);
- }
+ /**
+ * Executed the given test
+ *
+ * @param test
+ * the test to execute
+ * @param testSuiteDir
+ * the test cases directory
+ * @param callback
+ * a cancellation callback allowing to interrupt the execution
+ */
+ public RunOutcome run(TestCase test, String testSuiteDir,
+ CancelCallback callback)
+ {
+ return run(test, testSuiteDir, 250, callback);
+ }
- /**
- * Executed the given test
- *
- * @param test
- * the test to execute
- * @param testSuiteDir
- * the test cases directory
- * @param callback
- * a cancellation callback allowing to interrupt the execution
- */
- public void run(TestCase test, String testSuiteDir,
- CancelCallback callback)
- {
- run(test, testSuiteDir, 250, callback);
- }
+ /**
+ * Executed the given test
+ *
+ * @param test
+ * the test to execute
+ * @param testSuiteDir
+ * the test cases directory
+ * @param milli
+ * milliseconds to wait between calling the callback
+ * @param callback
+ * a cancellation callback allowing to interrupt the execution
+ */
+ public RunOutcome run(TestCase test, String testSuiteDir, int milli,
+ CancelCallback callback)
+ {
+ Runtime rt = Runtime.getRuntime();
+ String cmd = getProgram() + " "
+ + getExpandedArguments(test, testSuiteDir);
+ Process process;
- /**
- * Executed the given test
- *
- * @param test
- * the test to execute
- * @param testSuiteDir
- * the test cases directory
- * @param milli
- * milliseconds to wait between calling the callback
- * @param callback
- * a cancellation callback allowing to interrupt the execution
- */
- public RunOutcome run(TestCase test, String testSuiteDir,
- int milli, CancelCallback callback)
- {
- Runtime rt = Runtime.getRuntime();
- String cmd = getProgram() + " " + getExpandedArguments(test, testSuiteDir);
- Process process;
+ // ProcessBuilder builder = new ProcessBuilder(getProgram(),
+ // getExpandedArguments(test, testSuiteDir));
+ try
+ {
+ // Process p = builder.start();
+ process = rt.exec(cmd);
+ if (callback == null || milli < 0)
+ process.waitFor();
+ else
+ {
+ if (isRunning(process))
+ {
+ if (callback != null && callback.cancellationRequested())
+ return new RunOutcome(RunOutcome.Code.success, cmd);
+ Thread.sleep(milli);
+ }
+ }
- // ProcessBuilder builder = new ProcessBuilder(getProgram(),
- // getExpandedArguments(test, testSuiteDir));
- try
- {
- // Process p = builder.start();
- process = rt.exec(cmd);
- if (callback == null || milli < 0)
- process.waitFor();
- else
- {
- if (isRunning(process))
- {
- if (callback != null && callback.cancellationRequested())
- return new RunOutcome(RunOutcome.Code.success, cmd);
- Thread.sleep(milli);
- }
- }
+ process.destroy();
+ }
+ catch (IOException ex)
+ {
+ resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
+ return new RunOutcome(RunOutcome.Code.ioError,
+ "IO exception running command: " + cmd);
+ }
+ catch (SecurityException ex)
+ {
+ resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
+ return new RunOutcome(RunOutcome.Code.securityError,
+ "Security exception running command: " + cmd);
+ }
+ catch (IllegalArgumentException ex)
+ {
+ resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
+ return new RunOutcome(RunOutcome.Code.argumentError,
+ "Badly formed command line: " + cmd);
+ }
+ catch (InterruptedException ex)
+ {
+ resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
+ return new RunOutcome(RunOutcome.Code.interrupted,
+ "Process interrupted: " + cmd);
+ }
+ catch (Exception e)
+ {
+ resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
+ return new RunOutcome(RunOutcome.Code.unknownError,
+ "Unexpected error running: " + cmd);
+ // TODO Auto-generated catch block
+ // e.printStackTrace();
+ }
- process.destroy();
- }
- catch (IOException ex)
- {
- resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
- return new RunOutcome(RunOutcome.Code.ioError,
- "IO exception running command: " + cmd);
- }
- catch (SecurityException ex)
- {
- resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
- return new RunOutcome(RunOutcome.Code.securityError,
- "Security exception running command: " + cmd);
- }
- catch (IllegalArgumentException ex)
- {
- resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
- return new RunOutcome(RunOutcome.Code.argumentError,
- "Badly formed command line: " + cmd);
- }
- catch (InterruptedException ex)
- {
- resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
- return new RunOutcome(RunOutcome.Code.interrupted,
- "Process interrupted: " + cmd);
- }
- catch (Exception e)
- {
- resultCache.put(test.getId(), new DelayedResult(ResultType.Error));
- return new RunOutcome(RunOutcome.Code.unknownError,
- "Unexpected error running: " + cmd);
- // TODO Auto-generated catch block
- // e.printStackTrace();
- }
+ resultCache.put(test.getId(),
+ new DelayedResult(getResultTypeInternal(test)));
+ return new RunOutcome(RunOutcome.Code.success, cmd);
+ }
- resultCache.put(test.getId(),
- new DelayedResult(getResultTypeInternal(test)));
- return new RunOutcome(RunOutcome.Code.success, cmd);
- }
-
/**
* Sets the wrapper arguments
*
@@ -732,7 +729,8 @@
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
@@ -741,77 +739,62 @@
final int prime = 31;
int result = 1;
result = prime * result
- + ((arguments == null) ? 0 : arguments.hashCode());
+ + ((arguments == null) ? 0 : arguments.hashCode());
result = prime * result + ((name == null) ? 0 : name.hashCode());
result = prime * result
- + ((outputPath == null) ? 0 : outputPath.hashCode());
+ + ((outputPath == null) ? 0 : outputPath.hashCode());
result = prime * result + ((program == null) ? 0 : program.hashCode());
result = prime * result
- + ((resultCache == null) ? 0 : resultCache.hashCode());
+ + ((resultCache == null) ? 0 : resultCache.hashCode());
result = prime * result + (supportsAllVersions ? 1231 : 1237);
result = prime * result
- + ((unsupportedTags == null) ? 0 : unsupportedTags.hashCode());
+ + ((unsupportedTags == null) ? 0 : unsupportedTags.hashCode());
return result;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
* @see java.lang.Object#equals(java.lang.Object)
*/
@Override
public boolean equals(Object obj)
{
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (!(obj instanceof WrapperConfig))
- return false;
+ if (this == obj) return true;
+ if (obj == null) return false;
+ if (!(obj instanceof WrapperConfig)) return false;
WrapperConfig other = (WrapperConfig) obj;
if (arguments == null)
{
- if (other.arguments != null)
- return false;
+ if (other.arguments != null) return false;
}
- else if (!arguments.equals(other.arguments))
- return false;
+ else if (!arguments.equals(other.arguments)) return false;
if (name == null)
{
- if (other.name != null)
- return false;
+ if (other.name != null) return false;
}
- else if (!name.equals(other.name))
- return false;
+ else if (!name.equals(other.name)) return false;
if (outputPath == null)
{
- if (other.outputPath != null)
- return false;
+ if (other.outputPath != null) return false;
}
- else if (!outputPath.equals(other.outputPath))
- return false;
+ else if (!outputPath.equals(other.outputPath)) return false;
if (program == null)
{
- if (other.program != null)
- return false;
+ if (other.program != null) return false;
}
- else if (!program.equals(other.program))
- return false;
+ else if (!program.equals(other.program)) return false;
if (resultCache == null)
{
- if (other.resultCache != null)
- return false;
+ if (other.resultCache != null) return false;
}
- else if (!resultCache.equals(other.resultCache))
- return false;
- if (supportsAllVersions != other.supportsAllVersions)
- return false;
+ else if (!resultCache.equals(other.resultCache)) return false;
+ if (supportsAllVersions != other.supportsAllVersions) return false;
if (unsupportedTags == null)
{
- if (other.unsupportedTags != null)
- return false;
+ if (other.unsupportedTags != null) return false;
}
- else if (!unsupportedTags.equals(other.unsupportedTags))
- return false;
+ else if (!unsupportedTags.equals(other.unsupportedTags)) return false;
return true;
}
}
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/commandline/TestSuiteArguments.java
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/commandline/TestSuiteArguments.java 2013-01-31 16:47:34 UTC (rev 17007)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/commandline/TestSuiteArguments.java 2013-01-31 17:29:54 UTC (rev 17008)
@@ -31,12 +31,18 @@
package org.sbml.testsuite.core.commandline;
import java.io.PrintStream;
+import org.sbml.testsuite.core.TestSuiteSettings;
/**
* TestSuiteArguments is a parser for command line arguments (unused)
*/
public class TestSuiteArguments
{
+ private boolean shouldRun;
+ private String wrapperName;
+ private String testOrTestRange;
+
+
/**
* Constructor parsing arguments
*
@@ -46,15 +52,39 @@
public TestSuiteArguments(String args[])
{
+ parseArgs(args);
+
}
+ public void parseArgs(String[] args)
+ {
+ for (int i = 0; i < args.length; i++)
+ {
+ String current = args[i].toLowerCase();
+ String first = (i + 1 < args.length ? args[i + 1] : null);
+ String second = (i + 2 < args.length ? args[i + 2] : null);
+
+ if ((current.equals("-r") || current.equals("--run"))
+ && first != null && second != null)
+ {
+ shouldRun = true;
+ wrapperName = first;
+ testOrTestRange = second;
+ i += 2;
+ }
+
+ }
+ }
+
+
/**
* @return flag indicating whether valid arguments were provided
*/
public boolean isValid()
{
- return false;
+ return (shouldRun && (wrapperName != null && TestSuiteSettings.loadDefault()
+ .getWrapper(wrapperName) != null));
}
@@ -83,11 +113,86 @@
stream.println("SBML TestSuite (core)");
stream.println("=====================");
stream.println();
- if (message == null || message.length() == 0)
+ if (message != null && message.length() > 0)
{
stream.println(message);
stream.println();
}
stream.println("Usage: ");
+ stream.println();
+ stream.println(" -r | --run <wrapperName> <test-range>");
+ stream.println();
+
}
+
+
+ /**
+ * If true the given wrapper and test range should be run.
+ *
+ * @return the shouldRun
+ */
+ public boolean isShouldRun()
+ {
+ return shouldRun;
+ }
+
+
+ /**
+ * Specifies whether the given wrapper should be run
+ *
+ * @param shouldRun
+ * the shouldRun to set
+ */
+ public void setShouldRun(boolean shouldRun)
+ {
+ this.shouldRun = shouldRun;
+ }
+
+
+ /**
+ * Returns the selected wrapper
+ *
+ * @return the wrapperName
+ */
+ public String getWrapperName()
+ {
+ return wrapperName;
+ }
+
+
+ /**
+ * Sets the wrapper for command line operations.
+ *
+ * @param wrapperName
+ * the wrapperName to set
+ */
+ public void setWrapperName(String wrapperName)
+ {
+ this.wrapperName = wrapperName;
+ }
+
+
+ /**
+ * Gets either a single test (by specifying a number), or a test range in
+ * the format: start-end (with start and end included).
+ *
+ * @return the testOrTestRange
+ */
+ public String getTestOrTestRange()
+ {
+ return testOrTestRange;
+ }
+
+
+ /**
+ * Sets either a single test (by specifying a number), or a test range in
+ * the format: start-end (with start and end included).
+ *
+ * @param testOrTestRange
+ * the testOrTestRange to set
+ */
+ public void setTestOrTestRange(String testOrTestRange)
+ {
+ this.testOrTestRange = testOrTestRange;
+ }
}
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/data/ResultSet.java
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/data/ResultSet.java 2013-01-31 16:47:34 UTC (rev 17007)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-core/src/org/sbml/testsuite/core/data/ResultSet.java 2013-01-31 17:29:54 UTC (rev 17008)
@@ -71,6 +71,8 @@
// nevermind
}
}
+
+
/**
* Computes a result set with absolute differences between two results
*
@@ -155,10 +157,8 @@
}
}
-
private Vector<String> headers;
-
private double[][] data;
@@ -333,6 +333,16 @@
{
BufferedReader reader = new BufferedReader(new FileReader(file));
String line = reader.readLine();
+ if (line == null)
+ {
+
+ // if this happens we have an empty file present, this is not
+ // good! The best we can do at this point is to close the reader
+ // and return.
+ // that will flag the file as invalid later on.
+ reader.close();
+ return;
+ }
String[] values = line.split(",");
headers = new Vector<String>();
for (int i = 0; i < values.length; i++)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2013-01-31 16:47:42
|
Revision: 17007
http://sbml.svn.sourceforge.net/sbml/?rev=17007&view=rev
Author: sarahkeating
Date: 2013-01-31 16:47:34 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
more validation
Modified Paths:
--------------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp
Added Paths:
-----------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020301-fail-01-01.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-pass-00-01.xml
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.cpp 2013-01-31 15:51:23 UTC (rev 17006)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.cpp 2013-01-31 16:47:34 UTC (rev 17007)
@@ -22,7 +22,7 @@
*/
#include <sbml/packages/fbc/extension/FbcSpeciesPlugin.h>
-
+#include <sbml/packages/fbc/validator/FbcSBMLError.h>
#include <iostream>
using namespace std;
@@ -184,7 +184,21 @@
FbcSpeciesPlugin::readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes)
{
- SBasePlugin::readAttributes(attributes, expectedAttributes);
+ // dont call this as all it does it log unknown attributes
+// SBasePlugin::readAttributes(attributes, expectedAttributes);
+ for (int i = 0; i < attributes.getLength(); i++)
+ {
+ std::string name = attributes.getName(i);
+ std::string uri = attributes.getURI(i);
+
+ if (uri != mURI) continue;
+
+ if (!expectedAttributes.hasAttribute(name))
+ {
+ getErrorLog()->logPackageError("fbc", FbcSpeciesAllowedL3Attributes,
+ getPackageVersion(), getLevel(), getVersion());
+ }
+ }
if ( mSBMLExt->getLevel(mURI) > 2 )
{
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h 2013-01-31 15:51:23 UTC (rev 17006)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h 2013-01-31 16:47:34 UTC (rev 17007)
@@ -134,8 +134,8 @@
"One of each list of allowed",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "There may be at most one instance of each of the "
- "following kinds of objects within a <model> object using Flux Balance "
+ "There may be at most one instance of each of the "
+ "following kinds of objects within a <model> object using Flux Balance "
"Constraints: <listOfFluxBounds> and <listOfObjectives>.",
{ "L3V1 Fbc V1 Section 3.3"
}
@@ -146,9 +146,9 @@
"ListOf elements cannot be empty",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "The various ListOf subobjects with a <model> object are optional, "
- "but if present, these container object must not be empty. Specifically, "
- "if any of the following classes of objects are present on the <model>, "
+ "The various ListOf subobjects with a <model> object are optional, "
+ "but if present, these container object must not be empty. Specifically, "
+ "if any of the following classes of objects are present on the <model>, "
"it must not be empty: <listOfFluxBounds> and <listOfObjectives>.",
{ "L3V1 Fbc V1 Section 3.3"
}
@@ -159,7 +159,7 @@
"Allowed elements on ListOfFluxBounds",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "Apart from the general notes and annotation subobjects permitted on "
+ "Apart from the general notes and annotation subobjects permitted on "
"all SBML objects, a <listOfFluxBounds> container object may only "
"contain <fluxBound> objects.",
{ "L3V1 Fbc V1 Section 3.3"
@@ -171,7 +171,7 @@
"Allowed elements on ListOfObjectives",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "Apart from the general notes and annotation subobjects permitted on "
+ "Apart from the general notes and annotation subobjects permitted on "
"all SBML objects, a <listOfObjectives> container object may only "
"contain <objective> objects.",
{ "L3V1 Fbc V1 Section 3.3"
@@ -183,9 +183,9 @@
"Allowed attributes on ListOfFluxBounds",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "A <listOfFluxBounds> object may have the optional attributes 'metaid' "
- "and 'sboTerm' defined by SBML Level~3 Core. No other attributes from "
- "the SBML Level 3 Core namespace or the Flux Balance Constraints "
+ "A <listOfFluxBounds> object may have the optional attributes 'metaid' "
+ "and 'sboTerm' defined by SBML Level~3 Core. No other attributes from "
+ "the SBML Level 3 Core namespace or the Flux Balance Constraints "
"namespace are permitted on a <listOfFluxBounds> object. ",
{ "L3V1 Fbc V1 Section 3.3"
}
@@ -196,10 +196,10 @@
"Allowed attributes on ListOfObjectives",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "A <listOfFluxBounds> object may have the optional attributes 'metaid' "
- "and 'sboTerm' defined by SBML Level~3 Core. Additionally the "
- "<listOfObjectives> must contain the attribute 'activeObjective'. "
- "No other attributes from the SBML Level 3 Core namespace or the Flux "
+ "A <listOfFluxBounds> object may have the optional attributes 'metaid' "
+ "and 'sboTerm' defined by SBML Level~3 Core. Additionally the "
+ "<listOfObjectives> must contain the attribute 'activeObjective'. "
+ "No other attributes from the SBML Level 3 Core namespace or the Flux "
"Balance Constraints namespace are permitted on a "
"<listOfFluxBounds> object. ",
{ "L3V1 Fbc V1 Section 3.3"
@@ -211,7 +211,7 @@
"Type of activeObjective attribute",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "The value of attribute 'fbc:activeObjective' on the <listOfObjectives> "
+ "The value of attribute 'fbc:activeObjective' on the <listOfObjectives> "
"object must be of the data type SIdRef.",
{ "L3V1 Fbc V1 Section 3.2.2"
}
@@ -222,7 +222,7 @@
"ActiveObjective must reference Objective",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "The value of attribute 'fbc:activeObjective' on the <listOfObjectives> "
+ "The value of attribute 'fbc:activeObjective' on the <listOfObjectives> "
"object must be the identifier of an existing <objective>.",
{ "L3V1 Fbc V1 Section 3.2.2"
}
@@ -233,8 +233,8 @@
"Species allowed attributes",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "A SBML <species> object may have the optional attributes 'fbc:charge' "
- "and 'fbc:chemicalFormula'. No other attributes from the Flux Balance "
+ "A SBML <species> object may have the optional attributes 'fbc:charge' "
+ "and 'fbc:chemicalFormula'. No other attributes from the Flux Balance "
"Constraints namespaces are permitted on a <species>. ",
{ "L3V1 Fbc V1 Section 3.4"
}
@@ -245,7 +245,7 @@
"Charge must be integer",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "The value of attribute 'fbc:charge' on SBML <species> object "
+ "The value of attribute 'fbc:charge' on SBML <species> object "
"must be of the data type integer.",
{ "L3V1 Fbc V1 Section 3.4"
}
@@ -256,8 +256,8 @@
"Chemical formula must be string",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "The value of attribute 'fbc:chemicalFormula' on the SBML <species> "
- "object must be set to a string consisting only of atomic names or user "
+ "The value of attribute 'fbc:chemicalFormula' on the SBML <species> "
+ "object must be set to a string consisting only of atomic names or user "
"defined compounds and their occurance.",
{ "L3V1 Fbc V1 Section 3.4"
}
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp 2013-01-31 15:51:23 UTC (rev 17006)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp 2013-01-31 16:47:34 UTC (rev 17007)
@@ -30,6 +30,9 @@
#ifndef AddingConstraintsToValidator
#include <sbml/validator/VConstraint.h>
+#include <sbml/packages/fbc/sbml/Objective.h>
+
+#include <sbml/packages/fbc/validator/FbcSBMLError.h>
#endif
#include <sbml/validator/ConstraintMacros.h>
@@ -37,7 +40,28 @@
/** @cond doxygen-ignored */
using namespace std;
+// 20101 - caught at read
+// 20102 - caught at read
+// 20103 - caught at read
+// 20201 - caught at read
+// 20202 - caught at read
+// 20203 - caught at read
+// 20204 - caught at read
+// 20205 - caught at read
+// 20206 - caught at read
+// 20207 - caught at read
+
+// 20208 - TO DO
+START_CONSTRAINT (FbcActiveObjectiveRefersObjective, ListOfObjectives, loObj)
+{
+}
+END_CONSTRAINT
+
+// 20301 - caught at read
+// 20302 - caught at read
+// 20303 - TO DO
+
/** @endcond */
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020301-fail-01-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020301-fail-01-01.xml (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020301-fail-01-01.xml 2013-01-31 16:47:34 UTC (rev 17007)
@@ -0,0 +1,78 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20" fbc:spatialDimensions="d"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-pass-00-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-pass-00-01.xml (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020401-pass-00-01.xml 2013-01-31 16:47:34 UTC (rev 17007)
@@ -0,0 +1,78 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound metaid="_gg" sboTerm="SBO:0000001" fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
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|
|
From: <fbe...@us...> - 2013-01-31 15:51:30
|
Revision: 17006
http://sbml.svn.sourceforge.net/sbml/?rev=17006&view=rev
Author: fbergmann
Date: 2013-01-31 15:51:23 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
- filled in remaining error messages
Modified Paths:
--------------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h 2013-01-31 15:12:49 UTC (rev 17005)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h 2013-01-31 15:51:23 UTC (rev 17006)
@@ -93,7 +93,7 @@
, FbcObjectiveOneListOfObjectives = 2020507
, FbcObjectiveLOFluxObjMustNotBeEmpty = 2020508
, FbcObjectiveLOFluxObjOnlyFluxObj = 2020509
-, FbcObjectiveLOFluxObjAllowedElements = 2020510
+, FbcObjectiveLOFluxObjAllowedAttribs = 2020510
, FbcFluxObjectAllowedL3Attributes = 2020601
, FbcFluxObjectAllowedElements = 2020602
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h 2013-01-31 15:12:49 UTC (rev 17005)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h 2013-01-31 15:51:23 UTC (rev 17006)
@@ -265,12 +265,12 @@
// 2020401
{ FbcFluxBoundAllowedL3Attributes,
- "<fluxBound> may only have metaId and sboTerm from L3 namespace",
+ "<fluxBound> may only have 'metaId' and 'sboTerm' from L3 namespace",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
"A <fluxBound> object may have the optional SBML Level 3 Core "
- "attributes metaid and sboTerm. No other attributes from the "
- "SBML Level 3 Core namespaces are permitted on a <fluxBound>.",
+ "attributes 'metaid' and 'sboTerm'. No other attributes from the "
+ "SBML Level 3 Core namespace are permitted on a <fluxBound>.",
{ "L3V1 Core, Section 3.2."
}
},
@@ -282,7 +282,7 @@
LIBSBML_SEV_ERROR,
"A <fluxBound> object may have the optional SBML Level 3 Core "
"subobjects for notes and annotations. No other elements from the "
- "SBML Level 3 Core namespaces are permitted on a <fluxBound>.",
+ "SBML Level 3 Core namespace are permitted on a <fluxBound>.",
{ "L3V1 Core, Section 3.2."
}
},
@@ -358,7 +358,7 @@
// 2020409
{ FbcFluxBoundOperationValueRange,
- "Invalid value of 'fbc:operation'",
+ "Invalid value for 'fbc:operation'",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
"The valueof the attribute 'fbc:operation' of a <fluxBound> object "
@@ -382,171 +382,201 @@
// 2020501
{ FbcObjectiveAllowedL3Attributes,
- "",
+ "<objective> may only have 'metaId' and 'sboTerm' from L3 namespace",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <objective> object may have the optional SBML Level 3 Core "
+ "attributes 'metaid' and 'sboTerm'. No other attributes from the SBML "
+ "Level 3 Core namespace are permitted on a <objective>. ",
+ { "L3V1 Core, Section 3.2"
}
},
// 2020502
{ FbcObjectiveAllowedElements,
- "",
+ "<objective> may only have <notes> and <annotations> from L3 Core",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <objective> object may have the optional SBML Level 3 Core subobjects "
+ "for notes and annotations. No other elements from the SBML Level 3 Core "
+ "namespace are permitted on a <objective>.",
+ { "L3V1 Core, Section 3.2"
}
},
// 2020503
{ FbcObjectiveRequiredAttributes,
- "",
+ "Invalid attribute found on <objective> object",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <objective> object must have the required attributes 'fbc:id' and "
+ "'fbc:type' and may have the optional attribute 'fbc:name'. No other "
+ "attributes from the SBML Level 3 Flux Balance Constraints namespace "
+ "are permitted on a <objective> object.",
+ { "L3V1 Fbc V1, Section 3.6"
}
},
// 2020504
{ FbcObjectiveNameMustBeString,
- "",
+ "The attribute 'fbc:name' must be of the data type string",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The attribute 'fbc:name' on a <objective> must be of the data type "
+ "'string'. ",
+ { "L3V1 Fbc V1, Section 3.6"
}
},
// 2020505
{ FbcObjectiveTypeMustBeEnum,
- "",
+ "The attribute 'fbc:type' must be of data type FbcType.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The attribute 'fbc:type' on a <objective> must be of the data type "
+ "FbcType.",
+ { "L3V1 Fbc V1, Section 3.6"
}
},
// 2020506
{ FbcObjectiveTypeValueRange,
- "",
+ "Invalid value for 'fbc:type'",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The value of the attribute 'fbc:type' on a <objective> object must be "
+ "one of 'minimize' or 'maximize.",
+ { "L3V1 Fbc V1, Section 3.6"
}
},
// 2020507
{ FbcObjectiveOneListOfObjectives,
- "",
+ "An <objective> must have one <listOfFluxObjectives>.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <objective> object must have one and only one instance of the "
+ "<listOfFluxObjectives> object. ",
+ { "L3V1 Fbc V1, Section 3.6"
}
},
// 2020508
{ FbcObjectiveLOFluxObjMustNotBeEmpty,
- "",
+ "<listOfFluxObjectives> subobject must not be empty",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The <listOfFluxObjectives> subobject within a <objective> object must "
+ "not be empty.",
+ { "L3V1 Fbc V1, Section 3.6"
}
},
// 2020509
{ FbcObjectiveLOFluxObjOnlyFluxObj,
- "",
+ "Invalid element found in <listOfFluxObjectives>",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "Apart from the general notes and annotation subobjects permitted on all "
+ "SBML objects, a <listOfFluxObjectives> container object may only contain "
+ "<fluxObjective> objects.",
+ { "L3V1 Fbc V1, Section 3.6"
}
},
// 2020510
- { FbcObjectiveLOFluxObjAllowedElements,
- "",
+ { FbcObjectiveLOFluxObjAllowedAttribs,
+ "<listOfFluxObjectives> may only have 'metaId' and 'sboTerm' from L3 core",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <listOfFluxObjectives> object may have the optional 'metaid' and "
+ "'sboTerm' defined by SBML Level 3 Core. No other attributes from the "
+ "SBML Level 3 Core namespace or the Flux Balance Constraints namespace "
+ "are permitted on a <listOfFluxObjectives> object",
+ { "L3V1 Fbc V1, Section 3.6"
}
},
// 2020601
{ FbcFluxObjectAllowedL3Attributes,
- "",
+ "<fluxObjective> may only have 'metaId' and 'sboTerm' from L3 namespace",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <fluxObjective> object may have the optional SBML Level 3 Core "
+ "attributes 'metaid' and 'sboTerm'. No other attributes from the SBML "
+ "Level 3 Core namespace are permitted on a <fluxObjective>. ",
+ { "L3V1 Core, Section 3.2"
}
},
// 2020602
{ FbcFluxObjectAllowedElements,
- "",
+ "<fluxObjective> may only have <notes> and <annotations> from L3 Core",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <fluxObjective> object may have the optional SBML Level 3 Core "
+ "subobjects for notes and annotations. No other elements from the "
+ "SBML Level 3 Core namespace are permitted on a <fluxObjective>.",
+ { "L3V1 Core, Section 3.2"
}
},
// 2020603
{ FbcFluxObjectRequiredAttributes,
- "",
+ "Invalid attribute found on <fluxObjective> object",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <fluxObjective> object must have the required attributes "
+ "'fbc:reaction' and 'fbc:coefficient', and may have the optional "
+ "attributes 'fbc:id' and 'fbc:name'. No other attributes from the "
+ "SBML Level 3 Flux Balance Constraints namespace are permitted on "
+ "a <fluxObjective> object.",
+ { "L3V1 Fbc V1, Section 3.7"
}
},
// 2020604
{ FbcFluxObjectNameMustBeString,
- "",
+ "The attribute 'fbc:name' must be of the data type string",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The attribute 'fbc:name' on a <fluxObjective> must be of the data "
+ "type 'string'.",
+ { "L3V1 Fbc V1, Section 3.7"
}
},
// 2020605
{ FbcFluxObjectReactionMustBeSIdRef,
- "",
+ "Datatype for 'fbc:reaction' must be SIdRef",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The value of the attribute 'fbc:reaction' of a <fluxObjective> object "
+ "must conform to the syntax of the SBML data type 'SIdRef'.",
+ { "L3V1 Fbc V1, Section 3.7"
}
},
// 2020606
{ FbcFluxObjectReactionMustExist,
- "",
+ "'fbc:reaction' must refer to valid reaction",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The value of the attribute 'fbc:reaction' of a "
+ "<fluxObjective> object must be the identifier of an existing <reaction> "
+ "object defined in the enclosing <model> object.",
+ { "L3V1 Fbc V1, Section 3.7"
}
},
// 2020607
{ FbcFluxObjectCoefficientMustBeDouble,
- "",
+ "The attribute 'fbc:coefficient' must be of the data type double",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The value of the attribute 'fbc:coefficient' of a <fluxObjective> "
+ "object must conform to the syntax of the SBML data type 'double'.",
+ { "L3V1 Fbc V1, Section 3.7"
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2013-01-31 15:12:58
|
Revision: 17005
http://sbml.svn.sourceforge.net/sbml/?rev=17005&view=rev
Author: sarahkeating
Date: 2013-01-31 15:12:49 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
adding validation to fbc
Modified Paths:
--------------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020101-fail-01-01.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020102-fail-01-01-01016.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-fail-01-01.xml
Added Paths:
-----------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-pass-00-01.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020201-fail-01-01.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020201-fail-01-02.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020205-pass-00-01.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020207-fail-01-01.xml
Property Changed:
----------------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020101-fail-01-01.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020102-fail-01-01-01016.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-fail-01-01.xml
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp 2013-01-31 15:04:10 UTC (rev 17004)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp 2013-01-31 15:12:49 UTC (rev 17005)
@@ -24,8 +24,10 @@
#include <sbml/packages/fbc/extension/FbcModelPlugin.h>
#include <sbml/packages/fbc/extension/FbcExtension.h>
#include <sbml/packages/fbc/validator/FbcVisitor.h>
+#include <sbml/packages/fbc/validator/FbcSBMLError.h>
+
#include <iostream>
using namespace std;
@@ -112,6 +114,12 @@
{
if ( name == "listOfFluxBounds" )
{
+ if (mBounds.size() != 0)
+ {
+ getErrorLog()->logPackageError("fbc", FbcOnlyOneEachListOf,
+ getPackageVersion(), getLevel(), getVersion());
+ }
+
object = &mBounds;
if (targetPrefix.empty())
@@ -121,6 +129,12 @@
}
else if ( name == "listOfObjectives" )
{
+ if (mObjectives.size() != 0)
+ {
+ getErrorLog()->logPackageError("fbc", FbcOnlyOneEachListOf,
+ getPackageVersion(), getLevel(), getVersion());
+ }
+
object = &mObjectives;
if (targetPrefix.empty())
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.cpp 2013-01-31 15:04:10 UTC (rev 17004)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.cpp 2013-01-31 15:12:49 UTC (rev 17005)
@@ -30,6 +30,7 @@
#include <sbml/packages/fbc/sbml/Objective.h>
#include <sbml/packages/fbc/extension/FbcExtension.h>
#include <sbml/packages/fbc/validator/FbcVisitor.h>
+#include <sbml/packages/fbc/validator/FbcSBMLError.h>
using namespace std;
@@ -865,6 +866,7 @@
void
ListOfObjectives::addExpectedAttributes(ExpectedAttributes& attributes)
{
+ SBase::addExpectedAttributes(attributes);
//
// required attribute is not defined for SBML Level 2 or lesser.
//
@@ -885,7 +887,18 @@
if ( getLevel() > 2 )
{
- attributes.readInto("activeObjective", mActiveObjective, getErrorLog(), true, getLine(), getColumn());
+ bool assigned = attributes.readInto("activeObjective", mActiveObjective,
+ getErrorLog(), false, getLine(), getColumn());
+ if (assigned && mActiveObjective.empty())
+ {
+ logEmptyString(mActiveObjective, getLevel(), getVersion(),
+ "<listOfObjectives>");
+ }
+ if (!SyntaxChecker::isValidSBMLSId(mActiveObjective))
+ {
+ getErrorLog()->logPackageError("fbc", FbcActiveObjectiveSyntax,
+ getPackageVersion(), getLevel(), getVersion());
+ }
}
}
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020101-fail-01-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020101-fail-01-01.xml 2013-01-31 15:04:10 UTC (rev 17004)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020101-fail-01-01.xml 2013-01-31 15:12:49 UTC (rev 17005)
@@ -1,77 +1,77 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1">
- <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
- <listOfUnitDefinitions>
- <unitDefinition id="vol_per_time">
- <listOfUnits>
- <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
- <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
- </listOfUnits>
- </unitDefinition>
- </listOfUnitDefinitions>
- <listOfCompartments>
- <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
- <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- </listOfSpecies>
- <listOfReactions>
- <reaction id="R1" reversible="false" fast="false">
- <listOfReactants>
- <speciesReference species="S1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S2" constant="true"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci> k </ci>
- <ci> S1 </ci>
- </apply>
- </math>
- <listOfLocalParameters>
- <localParameter id="k" value="0.1" units="vol_per_time"/>
- </listOfLocalParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R2" reversible="false" fast="false">
- <listOfReactants>
- <speciesReference species="S2" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S4" constant="true"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci> k </ci>
- <ci> S2 </ci>
- </apply>
- </math>
- <listOfLocalParameters>
- <localParameter id="k" value="0.1" units="vol_per_time"/>
- </listOfLocalParameters>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- <fbc:listOfFluxBounds>
- <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
- <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
- </fbc:listOfFluxBounds>
- <fbc:listOfObjectives fbc:activeObjective="obj1">
- <fbc:objective fbc:id="c" fbc:type="maximize">
- <fbc:listOfFluxes>
- <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
- <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
- </fbc:listOfFluxes>
- </fbc:objective>
- </fbc:listOfObjectives>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
Property changes on: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020101-fail-01-01.xml
___________________________________________________________________
Added: svn:eol-style
+ native
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020102-fail-01-01-01016.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020102-fail-01-01-01016.xml 2013-01-31 15:04:10 UTC (rev 17004)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020102-fail-01-01-01016.xml 2013-01-31 15:12:49 UTC (rev 17005)
@@ -1,77 +1,77 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="2">
- <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
- <listOfUnitDefinitions>
- <unitDefinition id="vol_per_time">
- <listOfUnits>
- <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
- <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
- </listOfUnits>
- </unitDefinition>
- </listOfUnitDefinitions>
- <listOfCompartments>
- <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
- <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- </listOfSpecies>
- <listOfReactions>
- <reaction id="R1" reversible="false" fast="false">
- <listOfReactants>
- <speciesReference species="S1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S2" constant="true"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci> k </ci>
- <ci> S1 </ci>
- </apply>
- </math>
- <listOfLocalParameters>
- <localParameter id="k" value="0.1" units="vol_per_time"/>
- </listOfLocalParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R2" reversible="false" fast="false">
- <listOfReactants>
- <speciesReference species="S2" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S4" constant="true"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci> k </ci>
- <ci> S2 </ci>
- </apply>
- </math>
- <listOfLocalParameters>
- <localParameter id="k" value="0.1" units="vol_per_time"/>
- </listOfLocalParameters>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- <fbc:listOfFluxBounds>
- <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
- <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
- </fbc:listOfFluxBounds>
- <fbc:listOfObjectives fbc:activeObjective="obj1">
- <fbc:objective fbc:id="c" fbc:type="maximize">
- <fbc:listOfFluxes>
- <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
- <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
- </fbc:listOfFluxes>
- </fbc:objective>
- </fbc:listOfObjectives>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="2">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
Property changes on: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020102-fail-01-01-01016.xml
___________________________________________________________________
Added: svn:eol-style
+ native
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-fail-01-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-fail-01-01.xml 2013-01-31 15:04:10 UTC (rev 17004)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-fail-01-01.xml 2013-01-31 15:12:49 UTC (rev 17005)
@@ -1,77 +1,77 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="true">
- <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
- <listOfUnitDefinitions>
- <unitDefinition id="vol_per_time">
- <listOfUnits>
- <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
- <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
- </listOfUnits>
- </unitDefinition>
- </listOfUnitDefinitions>
- <listOfCompartments>
- <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
- <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
- </listOfSpecies>
- <listOfReactions>
- <reaction id="R1" reversible="false" fast="false">
- <listOfReactants>
- <speciesReference species="S1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S2" constant="true"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci> k </ci>
- <ci> S1 </ci>
- </apply>
- </math>
- <listOfLocalParameters>
- <localParameter id="k" value="0.1" units="vol_per_time"/>
- </listOfLocalParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R2" reversible="false" fast="false">
- <listOfReactants>
- <speciesReference species="S2" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="S4" constant="true"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <apply>
- <times/>
- <ci> k </ci>
- <ci> S2 </ci>
- </apply>
- </math>
- <listOfLocalParameters>
- <localParameter id="k" value="0.1" units="vol_per_time"/>
- </listOfLocalParameters>
- </kineticLaw>
- </reaction>
- </listOfReactions>
- <fbc:listOfFluxBounds>
- <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
- <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
- </fbc:listOfFluxBounds>
- <fbc:listOfObjectives fbc:activeObjective="obj1">
- <fbc:objective fbc:id="c" fbc:type="maximize">
- <fbc:listOfFluxes>
- <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
- <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
- </fbc:listOfFluxes>
- </fbc:objective>
- </fbc:listOfObjectives>
- </model>
-</sbml>
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="true">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
Property changes on: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-fail-01-01.xml
___________________________________________________________________
Added: svn:eol-style
+ native
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-pass-00-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-pass-00-01.xml (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-pass-00-01.xml 2013-01-31 15:12:49 UTC (rev 17005)
@@ -0,0 +1,78 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020201-fail-01-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020201-fail-01-01.xml (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020201-fail-01-01.xml 2013-01-31 15:12:49 UTC (rev 17005)
@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020201-fail-01-02.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020201-fail-01-02.xml (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020201-fail-01-02.xml 2013-01-31 15:12:49 UTC (rev 17005)
@@ -0,0 +1,87 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+
+ <fbc:listOfObjectives fbc:activeObjective="c">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020205-pass-00-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020205-pass-00-01.xml (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020205-pass-00-01.xml 2013-01-31 15:12:49 UTC (rev 17005)
@@ -0,0 +1,78 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds metaid="_fff" sboTerm="SBO:0000001">
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+
+ <fbc:listOfObjectives fbc:activeObjective="c" metaid="_ggg" sboTerm="SBO:0000001">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020207-fail-01-01.xml
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020207-fail-01-01.xml (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020207-fail-01-01.xml 2013-01-31 15:12:49 UTC (rev 17005)
@@ -0,0 +1,78 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model id="m" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="vol_per_time">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S1" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S2" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S3" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ <species id="S4" compartment="c" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="s20"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R2" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S2" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S4" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <ci> S2 </ci>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="k" value="0.1" units="vol_per_time"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds metaid="_fff" sboTerm="SBO:0000001">
+ <fbc:fluxBound fbc:id="s" fbc:reaction="J0" fbc:operation="equal" fbc:value="10"/>
+ <fbc:fluxBound fbc:reaction="J0" fbc:id="s1" fbc:operation="equal" fbc:value="23"/>
+ </fbc:listOfFluxBounds>
+
+ <fbc:listOfObjectives fbc:activeObjective="1obj1" metaid="_ggg" sboTerm="SBO:0000001">
+ <fbc:objective fbc:id="c" fbc:type="maximize">
+ <fbc:listOfFluxes>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="J8" fbc:coefficient="1"/>
+ </fbc:listOfFluxes>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fbe...@us...> - 2013-01-31 15:04:16
|
Revision: 17004
http://sbml.svn.sourceforge.net/sbml/?rev=17004&view=rev
Author: fbergmann
Date: 2013-01-31 15:04:10 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
- getNumXXX ought to return unsigned int rather than int
Modified Paths:
--------------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.h
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp 2013-01-31 14:21:39 UTC (rev 17003)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp 2013-01-31 15:04:10 UTC (rev 17004)
@@ -704,7 +704,7 @@
*
* @return the number of FluxBound object in this plugin object.
*/
-int
+unsigned int
FbcModelPlugin::getNumFluxBounds() const
{
return mBounds.size();
@@ -925,7 +925,7 @@
*
* @return the number of Objective object in this plugin object.
*/
-int
+unsigned int
FbcModelPlugin::getNumObjectives() const
{
return mObjectives.size();
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.h 2013-01-31 14:21:39 UTC (rev 17003)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.h 2013-01-31 15:04:10 UTC (rev 17004)
@@ -298,7 +298,7 @@
*
* @return the number of FluxBound object in this plugin object.
*/
- int getNumFluxBounds() const;
+ unsigned int getNumFluxBounds() const;
@@ -429,7 +429,7 @@
*
* @return the number of Objective object in this plugin object.
*/
- int getNumObjectives() const;
+ unsigned int getNumObjectives() const;
/**
* Returns the current active objective.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2013-01-31 14:21:47
|
Revision: 17003
http://sbml.svn.sourceforge.net/sbml/?rev=17003&view=rev
Author: sarahkeating
Date: 2013-01-31 14:21:39 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
adding more error entries
Modified Paths:
--------------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h 2013-01-31 13:06:41 UTC (rev 17002)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h 2013-01-31 14:21:39 UTC (rev 17003)
@@ -69,6 +69,9 @@
, FbcActiveObjectiveSyntax = 2020207
, FbcActiveObjectiveRefersObjective = 2020208
+, FbcSpeciesAllowedL3Attributes = 2020301
+, FbcSpeciesChargeMustBeInteger = 2020302
+, FbcSpeciesFormulaMustBeString = 2020303
, FbcFluxBoundAllowedL3Attributes = 2020401
, FbcFluxBoundAllowedElements = 2020402
@@ -100,53 +103,6 @@
, FbcFluxObjectReactionMustExist = 2020606
, FbcFluxObjectCoefficientMustBeDouble = 2020607
-
-
-// NOT YET DONE
-//, FbcExtModDefAllowedAttributes = 2020303
-//, FbcReferenceMustBeL3 = 2020304
-//, FbcModReferenceMustIdOfModel = 2020305
-//, FbcExtModMd5DoesNotMatch = 2020306
-//, FbcInvalidSourceSyntax = 2020307
-//, FbcInvalidModelRefSyntax = 2020308
-//, FbcCircularExternalModelReference = 2020310
-//, FbcOneListOfOnModel = 2020501
-//, FbcOneListOfDeletionOnSubmodel = 2020603
-//, FbcModReferenceSyntax = 2020608
-//, FbcSubmodelMustReferenceModel = 2020615
-//, FbcSubmodelCannotReferenceSelf = 2020616
-//, FbcModCannotCircularlyReferenceSelf = 2020617
-//, FbcTimeConversionMustBeParameter = 2020622
-//, FbcExtentConversionMustBeParameter = 2020623
-//, FbcPortRefMustReferencePort = 2020701
-//, FbcIdRefMustReferenceObject = 2020702
-//, FbcUnitRefMustReferenceUnitDef = 2020703
-//, FbcMetaIdRefMustReferenceObject = 2020704
-//, FbcParentOfSBRefChildMustBeSubmodel = 2020705
-//, FbcInvalidMetaIdRefSyntax = 2020709
-//, FbcOneSBaseRefOnly = 2020710
-//, FbcDeprecatedSBaseRefSpelling = 2020711
-//, FbcPortMustReferenceObject = 2020801
-//, FbcPortMustReferenceOnlyOneObject = 2020802
-//, FbcPortAllowedAttributes = 2020803
-//, FbcPortReferencesUnique = 2020804
-//, FbcDeletionMustReferenceObject = 2020901
-//, FbcDeletionMustReferOnlyOneObject = 2020902
-//, FbcDeletionAllowedAttributes = 2020903
-//, FbcReplacedElementMustRefObject = 2021001
-//, FbcReplacedElementMustRefOnlyOne = 2021002
-//, FbcReplacedElementAllowedAttributes = 2021003
-//, FbcReplacedElementSubModelRef = 2021004
-//, FbcReplacedElementDeletionRef = 2021005
-//, FbcReplacedElementConvFactorRef = 2021006
-//, FbcReplacedElementSameReference = 2021010
-//, FbcReplacedByMustRefObject = 2021101
-//, FbcReplacedByMustRefOnlyOne = 2021102
-//, FbcReplacedByAllowedAttributes = 2021103
-//, FbcReplacedBySubModelRef = 2021104
-//, FbcUnresolvedReference = 2090101
-//, FbcNoModelInReference = 2090102
-//, FbcExtModDefBad = 2090103
} FbcSBMLErrorCode_t;
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h 2013-01-31 13:06:41 UTC (rev 17002)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h 2013-01-31 14:21:39 UTC (rev 17003)
@@ -131,84 +131,138 @@
// 2020201
{ FbcOnlyOneEachListOf,
- "",
+ "One of each list of allowed",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "There may be at most one instance of each of the "
+ "following kinds of objects within a <model> object using Flux Balance "
+ "Constraints: <listOfFluxBounds> and <listOfObjectives>.",
+ { "L3V1 Fbc V1 Section 3.3"
}
},
// 2020202
{ FbcNoEmptyListOfs,
- "",
+ "ListOf elements cannot be empty",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The various ListOf subobjects with a <model> object are optional, "
+ "but if present, these container object must not be empty. Specifically, "
+ "if any of the following classes of objects are present on the <model>, "
+ "it must not be empty: <listOfFluxBounds> and <listOfObjectives>.",
+ { "L3V1 Fbc V1 Section 3.3"
}
},
// 2020203
{ FbcLOFluxBoundsAllowedElements,
- "",
+ "Allowed elements on ListOfFluxBounds",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "Apart from the general notes and annotation subobjects permitted on "
+ "all SBML objects, a <listOfFluxBounds> container object may only "
+ "contain <fluxBound> objects.",
+ { "L3V1 Fbc V1 Section 3.3"
}
},
// 2020204
{ FbcLOObjectivesAllowedElements,
- "",
+ "Allowed elements on ListOfObjectives",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "Apart from the general notes and annotation subobjects permitted on "
+ "all SBML objects, a <listOfObjectives> container object may only "
+ "contain <objective> objects.",
+ { "L3V1 Fbc V1 Section 3.3"
}
},
// 2020205
{ FbcLOFluxBoundsAllowedAttributes,
- "",
+ "Allowed attributes on ListOfFluxBounds",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <listOfFluxBounds> object may have the optional attributes 'metaid' "
+ "and 'sboTerm' defined by SBML Level~3 Core. No other attributes from "
+ "the SBML Level 3 Core namespace or the Flux Balance Constraints "
+ "namespace are permitted on a <listOfFluxBounds> object. ",
+ { "L3V1 Fbc V1 Section 3.3"
}
},
// 2020206
{ FbcLOObjectivesAllowedAttributes,
- "",
+ "Allowed attributes on ListOfObjectives",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "A <listOfFluxBounds> object may have the optional attributes 'metaid' "
+ "and 'sboTerm' defined by SBML Level~3 Core. Additionally the "
+ "<listOfObjectives> must contain the attribute 'activeObjective'. "
+ "No other attributes from the SBML Level 3 Core namespace or the Flux "
+ "Balance Constraints namespace are permitted on a "
+ "<listOfFluxBounds> object. ",
+ { "L3V1 Fbc V1 Section 3.3"
}
},
// 2020207
{ FbcActiveObjectiveSyntax,
- "",
+ "Type of activeObjective attribute",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The value of attribute 'fbc:activeObjective' on the <listOfObjectives> "
+ "object must be of the data type SIdRef.",
+ { "L3V1 Fbc V1 Section 3.2.2"
}
},
// 2020208
{ FbcActiveObjectiveRefersObjective,
- "",
+ "ActiveObjective must reference Objective",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "",
- { ""
+ "The value of attribute 'fbc:activeObjective' on the <listOfObjectives> "
+ "object must be the identifier of an existing <objective>.",
+ { "L3V1 Fbc V1 Section 3.2.2"
}
},
+ // 2020301
+ { FbcSpeciesAllowedL3Attributes,
+ "Species allowed attributes",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "A SBML <species> object may have the optional attributes 'fbc:charge' "
+ "and 'fbc:chemicalFormula'. No other attributes from the Flux Balance "
+ "Constraints namespaces are permitted on a <species>. ",
+ { "L3V1 Fbc V1 Section 3.4"
+ }
+ },
+
+ // 2020302
+ { FbcSpeciesChargeMustBeInteger,
+ "Charge must be integer",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The value of attribute 'fbc:charge' on SBML <species> object "
+ "must be of the data type integer.",
+ { "L3V1 Fbc V1 Section 3.4"
+ }
+ },
+
+ // 2020303
+ { FbcSpeciesFormulaMustBeString,
+ "Chemical formula must be string",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The value of attribute 'fbc:chemicalFormula' on the SBML <species> "
+ "object must be set to a string consisting only of atomic names or user "
+ "defined compounds and their occurance.",
+ { "L3V1 Fbc V1 Section 3.4"
+ }
+ },
+
// 2020401
{ FbcFluxBoundAllowedL3Attributes,
"<fluxBound> may only have metaId and sboTerm from L3 namespace",
@@ -494,556 +548,8 @@
"",
{ ""
}
- },
-
-
-// TO DO - NOT YET DONE
- // // 2020303
- // { FbcExtModDefAllowedAttributes,
- // "Allowed <externalModelDefinitions> attributes",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "An <externalModelDefinition> object must have the attributes "
- // "'fbc:id' and 'fbc:source', and may have the optional attributes "
- // "'fbc:name', 'fbc:modelRef', and 'fbc:md5'. No other attributes "
- // "from the Flux Balance Constraints namespace are permitted on "
- // "an <externalModelDefinition> object.",
- // { "L3V1 Fbc V1 Section 3.3.2"
- // }
- // },
+ }
- // // 2020304
- // { FbcReferenceMustBeL3,
- // "External models must be L3",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of the 'fbc:source' attribute on an <externalModelDefinition> "
- // "object must reference an SBML Level 3 Version 1 document.",
- // { "L3V1 Fbc V1 Section 3.3.2"
- // }
- // },
-
- // // 2020305
- // { FbcModReferenceMustIdOfModel,
- // "'modelRef' must be the 'id' of a model in the 'source' document",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of the 'fbc:modelRef' attribute on an <externalModelDefinit"
- // "ion> object must be the value of an id attribute on a <model>, "
- // "<modelDefinition>, or <externalModelDefinition> object in the SBML "
- // "document referenced by the 'fbc:source' attribute.",
- // { "L3V1 Fbc V1 Section 3.3.2"
- // }
- // },
-
- // // 2020306
- // { FbcExtModMd5DoesNotMatch,
- // "MD5 checksum does not match the 'source' document",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_WARNING,
- // "The value of the 'fbc:md5' attribute, if present on an "
- //"<externalModelDefinition> object, should match the calculated MD5 "
- //"checksum of the SBML document referenced by the 'fbc:source' "
- //"attribute. ",
- // { "L3V1 Fbc V1 Section 3.3.2"
- // }
- // },
-
- // // 2020307
- // { FbcInvalidSourceSyntax,
- // "The 'fbc:source' attribute must be of type 'anyURI'",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:source' attribute on an <externalModelDefinition> "
- // "object must always conform to the syntax of the XML Schema 1.0 data "
- // "type 'anyURI'.",
- // { "L3V1 Fbc V1 Section 3.3.2"
- // }
- // },
-
- // // 2020308
- // { FbcInvalidModelRefSyntax,
- // "The 'fbc:modelRef' attribute must have the syntax of 'SId'",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a fbc:modelRef attribute on an <externalModelDefinition> "
- // "object must always conform to the syntax of the SBML data type SId.",
- // { "L3V1 Fbc V1 Section 3.3.2"
- // }
- // },
-
- // // 2020310
- // { FbcCircularExternalModelReference,
- // "Circular reference in <externalModelDefinition>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "An <externalModelDefinition> object must not reference an "
- // "<externalModelDefinition> in a different SBML document that, in turn, "
- // "refers back to the original <externalModelDefinition object, "
- // "whether directly or indirectly through a chain of "
- //"<externalModelDefinition> objects. ",
- // { "L3V1 Fbc V1 Section 3.3.2"
- // }
- // },
-
- // // 2020501
- // { FbcOneListOfOnModel,
- // "Only one <listOfSubmodels> and one <listOfPorts> allowed",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "There may be at most one instance of each of the following kinds of "
- // "objects within a <model> or <modelDefinition> object using "
- // "Flux Balance Constraints: <listOfSubmodels> and <listOfPorts>.",
- // { "L3V1 Fbc V1 Section 3.4"
- // }
- // },
-
- // // 2020603
- // { FbcOneListOfDeletionOnSubmodel,
- // "Only one <listOfDeletions> on a <submodel> allowed",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "There may be at most one <listOfDeletions> container object within a "
- //"<submodel> object.",
- // { "L3V1 Fbc V1 Section 3.5"
- // }
- // },
-
- // // 2020608
- // { FbcModReferenceSyntax,
- // "'fbc:modelRef' must conform to SId syntax",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:modelRef' attribute on a <submodel> object must "
- //"always conform to the syntax of the SBML data type SId. ",
- // { "L3V1 Fbc V1 Section 3.5.1"
- // }
- // },
-
- // // 2020615
- // { FbcSubmodelMustReferenceModel,
- // "The 'fbc:modelRef' attribute must reference a model",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:modelRef' attribute on a <submodel> must be the "
- // "identifier of a <model>, <modelDefinition>, or "
- // "<externalModelDefinition> object in the same SBML object as the "
- // "<submodel>.",
- // { "L3V1 Fbc V1 Section 3.5.1"
- // }
- // },
-
- // // 2020616
- // { FbcSubmodelCannotReferenceSelf,
- // "The 'fbc:modelRef' attribute cannot reference own model",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <model> or <modelDefinition> object must not contain a <submodel> "
- // "which references that model object itself. That is, the value of a "
- // "'fbc:modelRef' attribute on a <submodel> must not be the value of "
- // "the parent <model> or <modelDefinition>'s 'id' attribute.",
- // { "L3V1 Fbc V1 Section 3.5.1"
- // }
- // },
-
- // // 2020617
- // { FbcModCannotCircularlyReferenceSelf,
- // "<model> may not reference <submodel> that references itself.",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <model> object must not contain a <submodel> which references that "
- //"<model> indirectly. That is, the 'fbc:modelRef' attribute of a "
- //"<submodel> may not point to the 'id' of a <model> containing a "
- //"<submodel> object that references the original <model> directly or "
- //"indirectly through a chain of <model>/<submodel> pairs.",
- // { "L3V1 Fbc V1 Section 3.5.1"
- // }
- // },
-
- // // 2020622
- // { FbcTimeConversionMustBeParameter,
- // "The 'fbc:timeConversionFactor' must reference a parameter",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:timeConversionFactor' attribute on a given "
- // "<submodel> object must be the identifier of a <parameter> object "
- // "defined in the same Model containing the <submodel>.",
- // { "L3V1 Fbc V1 Section 3.5.1"
- // }
- // },
-
- // // 2020623
- // { FbcExtentConversionMustBeParameter,
- // "The 'fbc:extentConversionFactor' must reference a parameter",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:extentConversionFactor' attribute on a given "
- // "<submodel> object must be the identifier of a <parameter> object "
- // "defined in the same Model containing the <submodel>.",
- // { "L3V1 Fbc V1 Section 3.5.1"
- // }
- // },
- //
- // // 2020701
- // { FbcPortRefMustReferencePort,
- // "The 'fbc:portRef' attribute must be the 'id' of a <port>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:portRef' attribute on an <sBaseRef> object "
- //"must be the identifier of a <port> object in the <model> referenced "
- //"by that <sBaseRef>.",
- // { "L3V1 Fbc V1 Section 3.7.1"
- // }
- // },
-
- // // 2020702
- // { FbcIdRefMustReferenceObject,
- // "The 'fbc:idRef' attribute must be the 'id' of a model element",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:idRef' attribute on an <sBaseRef> object must "
- //"be the identifier of an object contained in (that is, within the "
- //"SId namespace of) the <model> referenced by that <sBaseRef>. This "
- //"includes objects with 'id' attributes defined in packages other "
- //"than SBML Level 3 Core or the Flux Balance Constraints "
- //"package.",
- // { "L3V1 Fbc V1 Section 3.7.1"
- // }
- // },
-
- // // 2020703
- // { FbcUnitRefMustReferenceUnitDef,
- // "The 'fbc:unitRef' attribute must be the 'id' of a UnitDefinition",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:unitRef' attribute on an <sBaseRef> object must "
- //"be the identifier of a <unitDefinition< object contained in the "
- //"<model> referenced by that <sBaseRef>.",
- // { "L3V1 Fbc V1 Section 3.7.1"
- // }
- // },
-
- // // 2020704
- // { FbcMetaIdRefMustReferenceObject,
- // "The 'fbc:metaIdRef' attribute must be the 'metaid' of an object",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:metaIdRef' attribute on an <sBaseRef> object "
- //"must be the value of a 'fbc:metaid' attribute on an element contained "
- //"in the <model> referenced by that <sBaseRef>.",
- // { "L3V1 Fbc V1 Section 3.7.1"
- // }
- // },
-
- // // 2020705
- // { FbcParentOfSBRefChildMustBeSubmodel,
- // "If <sBaseRef> has a child <sBaseRef> its parent must be a <submodel>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "If an <sBaseRef> object contains an <sBaseRef> child, the parent "
- //"<sBaseRef> must point to a <submodel> object. ",
- // { "L3V1 Fbc V1 Section 3.7.2"
- // }
- // },
-
- // // 2020709
- // { FbcInvalidMetaIdRefSyntax,
- // "The 'fbc:metaIdRef' attribute must have the syntax of an XML ID",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:metaIdRef' attribute on an SBaseRef object must "
- // "always conform to the syntax of the XML data type ID.",
- // { "L3V1 Fbc V1 Section 3.7.1"
- // }
- // },
-
-
- // // 2020710
- // { FbcOneSBaseRefOnly,
- // "Only one <sbaseRef>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "Apart from the general notes and annotation subobjects permitted on "
- // "all SBML objects, an SBaseRef object may only contain a single "
- // "<sBaseRef> child.",
- // { "L3V1 Fbc V1 Section 3.7.2"
- // }
- // },
-
- // // 2020711
- // { FbcDeprecatedSBaseRefSpelling,
- // "The spelling 'sbaseRef' is deprecated",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_WARNING,
- // "The 'sbaseRef' spelling of an SBaseRef child of an SBaseRef object "
- // "is considered deprecated, and 'sBaseRef' should be used instead.",
- // { "L3V1 Fbc V1 Section 3.7.2"
- // }
- // },
-
- // // 2020801
- // { FbcPortMustReferenceObject,
- // "Port must reference an object",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <port> object must point to another object; that "
- // "is, a <port> object must always have a value for one of the attributes "
- // "'fbc:idRef', 'fbc:unitRef', or 'fbc:metaIdRef'",
- // { "L3V1 Fbc V1 Section 3.4.3"
- // }
- // },
-
- // // 2020802
- // { FbcPortMustReferenceOnlyOneObject,
- // "Port must reference only one other object.",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <port> object can only point to one other "
- // "object; that is, a given <port> object can only have a value for one of "
- // "the attributes 'fbc:idRef', 'fbc:unitRef', or 'fbc:metaIdRef'",
- // { "L3V1 Fbc V1 Section 3.4.3"
- // }
- // },
-
- // // 2020803
- // { FbcPortAllowedAttributes,
- // "Allowed attributes on a Port",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <port> object must have a value for the required "
- // "attribute 'fbc:id', and one, and only one, of the "
- // "attributes 'fbc:idRef', 'fbc:unitRef', or "
- // "'fbc:metaIdRef'. No other attributes from the Hierarchical "
- // "Model Fbcosition namespace are permitted on a <port> object.",
- // { "L3V1 Fbc V1 Section 3.4.3"
- // }
- // },
-
- // // 2020804
- // { FbcPortReferencesUnique,
- // "Port definitions must be unique.",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "Port definitions must be unique; that is, no two "
- // "<port> objects in a given Model may reference the same object in that "
- // "Model.",
- // { "L3V1 Fbc V1 Section 3.4.3"
- // }
- // },
-
- // // 2020901
- // { FbcDeletionMustReferenceObject,
- // "Deletion must reference an object",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <deletion> object must point to another object; that "
- // "is, a <deletion> object must always have a value for one of the attributes "
- // "'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', or 'fbc:metaIdRef'",
- // { "L3V1 Fbc V1 Section 3.5.3"
- // }
- // },
-
- // // 2020902
- // { FbcDeletionMustReferOnlyOneObject,
- // "Deletion must reference only one other object.",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <deletion> object can only point to one other "
- // "object; that is, a given <deletion> object can only have a value for one of "
- // "the attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', or "
- // "'fbc:metaIdRef'",
- // { "L3V1 Fbc V1 Section 3.5.3"
- // }
- // },
-
- // // 2020903
- // { FbcDeletionAllowedAttributes,
- // "Allowed attributes on a Deletion",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <deletion> object must have a value for one, and only one, of the "
- // "attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', and "
- // "'fbc:metaIdRef'. It may also have the optional attributes 'fbc:id' "
- // "and 'fbc:name'. No other attributes from the Hierarchical "
- // "Model Fbcosition namespace are permitted on a <deletion> object.",
- // { "L3V1 Fbc V1 Section 3.5.3"
- // }
- // },
-
- // // 2021001
- // { FbcReplacedElementMustRefObject,
- // "ReplacedElement must reference an object",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <replacedElement> object must point to another object; that "
- // "is, a <replacedElement> object must always have a value for one of the "
- // "attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', "
- // "'fbc:metaIdRef' or 'fbc:deletion'.",
- // { "L3V1 Fbc V1 Section 3.6.2"
- // }
- // },
-
- // // 2021002
- // { FbcReplacedElementMustRefOnlyOne,
- // "ReplacedElement must reference only one other object.",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <replacedElement> object can only point to one other "
- // "object; that is, a given <replacedElement> object can only have a value "
- // "for one of the attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', "
- // "'fbc:metaIdRef' or 'fbc:deletion'.",
- // { "L3V1 Fbc V1 Section 3.6.2"
- // }
- // },
-
- // // 2021003
- // { FbcReplacedElementAllowedAttributes,
- // "Allowed attributes on <replacedElement>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <replacedElement> object must have a value for the required attribute "
- // "'fbc:submodelRef', and a value for one, and only one, of the following "
- // "attributes: 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', "
- // "'fbc:metaIdRef', or 'fbc:deletion'. It may also have a value for the "
- // "optional attribute 'fbc:conversionFactor'. No other attributes from "
- // "the HierarchicalModel Fbcosition namespace are permitted on a "
- // "<replacedElement> object.",
- // { "L3V1 Fbc V1 Section 3.6.2"
- // }
- // },
-
- // // 2021004
- // { FbcReplacedElementSubModelRef,
- // "The 'fbc:submodelRef' attribute must point to a <submodel>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:submodelRef' attribute on a <replacedElement> "
- // "object must be the identifier of a <submodel> present in the "
- // "<replacedElement> object\x92s parent Model.",
- // { "L3V1 Fbc V1 Section 3.6.2"
- // }
- // },
-
- // // 2021005
- // { FbcReplacedElementDeletionRef,
- // "The 'fbc:deletion' attribute must point to a <deletion>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:deletion' attribute on a <replacedElement> "
- // "object must be the identifier of a <deletion> present in the "
- // "<replacedElement> object\x92s parent Model.",
- // { "L3V1 Fbc V1 Section 3.6.2"
- // }
- // },
-
- // // 2021006
- // { FbcReplacedElementConvFactorRef,
- // "The 'fbc:conversionFactor attribute must point to a <parameter>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:conversionFactor' attribute on a "
- // "<replacedElement> object must be the identifier of a <parameter> "
- // "present in the <replacedElement> object\x92s parent Model",
- // { "L3V1 Fbc V1 Section 3.6.2"
- // }
- // },
-
- // // 2021010
- // { FbcReplacedElementSameReference,
- // "No <replacedElement> refer to same object",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "No two <replacedElement> objects in the same Model may reference the same "
- // "object unless that object is a <deletion>",
- // { "L3V1 Fbc V1 Section 3.6.2"
- // }
- // },
-
- // // 2021101
- // { FbcReplacedByMustRefObject,
- // "ReplacedBy must reference an object",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <replacedBy> object must point to another object; that "
- // "is, a <replacedBy> object must always have a value for one of the "
- // "attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef' or "
- // "'fbc:metaIdRef'.",
- // { "L3V1 Fbc V1 Section 3.6.4"
- // }
- // },
-
- // // 2021102
- // { FbcReplacedByMustRefOnlyOne,
- // "ReplacedBy must reference only one other object.",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <replacedBy> object can only point to one other "
- // "object; that is, a given <replacedBy> object can only have a value "
- // "for one of the attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', "
- // "or 'fbc:metaIdRef'.",
- // { "L3V1 Fbc V1 Section 3.6.4"
- // }
- // },
-
- // // 2021103
- // { FbcReplacedByAllowedAttributes,
- // "Allowed attributes on <replacedBy>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "A <replacedBy> object must have a value for the required attribute "
- // "'fbc:submodelRef', and a value for one, and only one, of the following "
- // "attributes: 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef' "
- // "or 'fbc:metaIdRef'. No other attributes from "
- // "the HierarchicalModel Fbcosition namespace are permitted on a "
- // "<replacedElement> object.",
- // { "L3V1 Fbc V1 Section 3.6.4"
- // }
- // },
-
- // // 2021104
- // { FbcReplacedBySubModelRef,
- // "The 'fbc:submodelRef' attribute must point to a <submodel>",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The value of a 'fbc:submodelRef' attribute on a <replacedBy> "
- // "object must be the identifier of a <submodel> present in the "
- // "<replacedBy> object\x92s parent Model.",
- // { "L3V1 Fbc V1 Section 3.6.4"
- // }
- // },
-
- // // 2090101
- // { FbcUnresolvedReference,
- // "Unresolved reference.",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The external model referenced in this model could not be "
- // "resolved. ",
- // { ""
- // }
- // },
-
- // // 2090102
- // { FbcNoModelInReference,
- // "No model in referenced document.",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "The external model referenced in this model did not contain any models.",
- // { ""
- // }
- // },
-
- // // 2090103
- // { FbcExtModDefBad,
- // "Referenced <externalModelDefinition> unresolvable.",
- // LIBSBML_CAT_GENERAL_CONSISTENCY,
- // LIBSBML_SEV_ERROR,
- // "An external model definition referenced by an external model "
- // "definition in this model was itself unresolvable.",
- // { ""
- // }
- // }
-
};
LIBSBML_CPP_NAMESPACE_END
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|
|
From: <sar...@us...> - 2013-01-31 13:06:47
|
Revision: 17002
http://sbml.svn.sourceforge.net/sbml/?rev=17002&view=rev
Author: sarahkeating
Date: 2013-01-31 13:06:41 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
if indexing in reactant was wrong - it was also probably wrong in product
which it was
Modified Paths:
--------------
trunk/libsbml/src/sbml/Model.cpp
Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp 2013-01-31 12:49:57 UTC (rev 17001)
+++ trunk/libsbml/src/sbml/Model.cpp 2013-01-31 13:06:41 UTC (rev 17002)
@@ -5315,7 +5315,9 @@
{
ud = new UnitDefinition(getSBMLNamespaces());
for (j = 0; j < fud->getUnitDefinition()->getNumUnits(); j++)
+ {
ud->addUnit(fud->getUnitDefinition()->getUnit(j));
+ }
// unless time has been overridden
if (getUnitDefinition("time") != NULL)
{
@@ -5687,19 +5689,19 @@
}
else
{
- for (j = 0; j < getNumUnitDefinitions(); j++)
+ for (unsigned int unitNo = 0; unitNo < getNumUnitDefinitions(); unitNo++)
{
- if (!strcmp(units.c_str(), getUnitDefinition(j)->getId().c_str()))
+ if (!strcmp(units.c_str(), getUnitDefinition(unitNo)->getId().c_str()))
{
for (unsigned int pp = 0;
- pp < getUnitDefinition(j)->getNumUnits(); pp++)
+ pp < getUnitDefinition(unitNo)->getNumUnits(); pp++)
{
u = new Unit(getSBMLNamespaces());
- u->setKind(getUnitDefinition(j)->getUnit(pp)->getKind());
- u->setMultiplier(getUnitDefinition(j)->getUnit(pp)
+ u->setKind(getUnitDefinition(unitNo)->getUnit(pp)->getKind());
+ u->setMultiplier(getUnitDefinition(unitNo)->getUnit(pp)
->getMultiplier());
u->setScale(getUnitDefinition(j)->getUnit(pp)->getScale());
- u->setExponent(-1 * (getUnitDefinition(j)->getUnit(pp)
+ u->setExponent(-1 * (getUnitDefinition(unitNo)->getUnit(pp)
->getExponent()));
ud->addUnit(u);
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|
|
From: <fbe...@us...> - 2013-01-31 12:50:04
|
Revision: 17001
http://sbml.svn.sourceforge.net/sbml/?rev=17001&view=rev
Author: fbergmann
Date: 2013-01-31 12:49:57 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
- added placeholders for further error messages
Modified Paths:
--------------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h 2013-01-31 07:07:35 UTC (rev 17000)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h 2013-01-31 12:49:57 UTC (rev 17001)
@@ -69,6 +69,39 @@
, FbcActiveObjectiveSyntax = 2020207
, FbcActiveObjectiveRefersObjective = 2020208
+
+, FbcFluxBoundAllowedL3Attributes = 2020401
+, FbcFluxBoundAllowedElements = 2020402
+, FbcFluxBoundRequiredAttributes = 2020403
+, FbcFluxBoundRectionMustBeSIdRef = 2020404
+, FbcFluxBoundNameMustBeString = 2020405
+, FbcFluxBoundOperationMustBeEnum = 2020406
+, FbcFluxBoundValueMustBeDouble = 2020407
+, FbcFluxBoundReactionMustExist = 2020408
+, FbcFluxBoundOperationValueRange = 2020409
+, FbcFluxBoundsForReactionConflict = 2020410
+
+, FbcObjectiveAllowedL3Attributes = 2020501
+, FbcObjectiveAllowedElements = 2020502
+, FbcObjectiveRequiredAttributes = 2020503
+, FbcObjectiveNameMustBeString = 2020504
+, FbcObjectiveTypeMustBeEnum = 2020505
+, FbcObjectiveTypeValueRange = 2020506
+, FbcObjectiveOneListOfObjectives = 2020507
+, FbcObjectiveLOFluxObjMustNotBeEmpty = 2020508
+, FbcObjectiveLOFluxObjOnlyFluxObj = 2020509
+, FbcObjectiveLOFluxObjAllowedElements = 2020510
+
+, FbcFluxObjectAllowedL3Attributes = 2020601
+, FbcFluxObjectAllowedElements = 2020602
+, FbcFluxObjectRequiredAttributes = 2020603
+, FbcFluxObjectNameMustBeString = 2020604
+, FbcFluxObjectReactionMustBeSIdRef = 2020605
+, FbcFluxObjectReactionMustExist = 2020606
+, FbcFluxObjectCoefficientMustBeDouble = 2020607
+
+
+
// NOT YET DONE
//, FbcExtModDefAllowedAttributes = 2020303
//, FbcReferenceMustBeL3 = 2020304
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h 2013-01-31 07:07:35 UTC (rev 17000)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h 2013-01-31 12:49:57 UTC (rev 17001)
@@ -209,6 +209,294 @@
}
},
+ // 2020401
+ { FbcFluxBoundAllowedL3Attributes,
+ "<fluxBound> may only have metaId and sboTerm from L3 namespace",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "A <fluxBound> object may have the optional SBML Level 3 Core "
+ "attributes metaid and sboTerm. No other attributes from the "
+ "SBML Level 3 Core namespaces are permitted on a <fluxBound>.",
+ { "L3V1 Core, Section 3.2."
+ }
+ },
+
+ // 2020402
+ { FbcFluxBoundAllowedElements,
+ "<fluxBound> may only have <notes> and <annotations> from L3 Core",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "A <fluxBound> object may have the optional SBML Level 3 Core "
+ "subobjects for notes and annotations. No other elements from the "
+ "SBML Level 3 Core namespaces are permitted on a <fluxBound>.",
+ { "L3V1 Core, Section 3.2."
+ }
+ },
+
+ // 2020403
+ { FbcFluxBoundRequiredAttributes,
+ "Invalid attribute found on <fluxBound> object",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "A <fluxBound> object must have the required attributes 'fbc:reaction', "
+ "'fbc:operation' and 'fbc:value', and may have the optional attributes "
+ "'fbc:id' and 'fbc:name'. No other attributes from the SBML Level 3 Flux "
+ "Balance Constraints namespace are permitted on a <fluxBound> object.",
+ { "L3V1 Fbc V1 Section 3.5"
+ }
+ },
+
+ // 2020404
+ { FbcFluxBoundRectionMustBeSIdRef,
+ "Datatype for 'fbc:reaction' must be SIdRef",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The attribute 'fbc:reaction' of a <fluxBound> must be of the data "
+ "type SIdRef.",
+ { "L3V1 Fbc V1 Section 3.5"
+ }
+ },
+
+ // 2020405
+ { FbcFluxBoundNameMustBeString,
+ "The attribute 'fbc:name' must be of the data type string",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The attribute 'fbc:name' of a <fluxBound> must be of the data type "
+ "string.",
+ { "L3V1 Fbc V1 Section 3.5"
+ }
+ },
+
+ // 2020406
+ { FbcFluxBoundOperationMustBeEnum,
+ "The attribute 'fbc:operation' must be of data type FbcOperation",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The attribute 'fbc:operation' of a <fluxBound> must be of the data "
+ "type FbcOperation.",
+ { "L3V1 Fbc V1 Section 3.5"
+ }
+ },
+
+ // 2020407
+ { FbcFluxBoundValueMustBeDouble,
+ "The attribute 'fbc:value' must be of the data type double",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The attribute 'fbc:value' of a <fluxBound> must be of the "
+ "data type double.",
+ { "L3V1 Fbc V1 Section 3.5"
+ }
+ },
+
+ // 2020408
+ { FbcFluxBoundReactionMustExist,
+ "'fbc:reaction' must refer to valid reaction",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The value of the attribute 'fbc:reaction' of a <fluxBound> object "
+ "must be the identifier of an existing <reaction> object defined in "
+ "the enclosing <model> object.",
+ { "L3V1 Fbc V1 Section 3.5"
+ }
+ },
+
+ // 2020409
+ { FbcFluxBoundOperationValueRange,
+ "Invalid value of 'fbc:operation'",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The valueof the attribute 'fbc:operation' of a <fluxBound> object "
+ "must be one of 'lessEqual', 'greaterEqual' or 'equal'.",
+ { "L3V1 Fbc V1 Section 3.5"
+ }
+ },
+
+ // 2020410
+ { FbcFluxBoundsForReactionConflict,
+ "Conflicting set of FluxBounds for a reaction",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The combined set of all <fluxBound>'s with identical values for "
+ "'fbc:reaction' must be consistent. That is while it is possible "
+ "to define a lower and an upper bound for a reaction, it is not "
+ "possible to define multiple lower or upper bounds.",
+ { "L3V1 Fbc V1 Section 3.5"
+ }
+ },
+
+ // 2020501
+ { FbcObjectiveAllowedL3Attributes,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020502
+ { FbcObjectiveAllowedElements,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020503
+ { FbcObjectiveRequiredAttributes,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020504
+ { FbcObjectiveNameMustBeString,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020505
+ { FbcObjectiveTypeMustBeEnum,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020506
+ { FbcObjectiveTypeValueRange,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020507
+ { FbcObjectiveOneListOfObjectives,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020508
+ { FbcObjectiveLOFluxObjMustNotBeEmpty,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020509
+ { FbcObjectiveLOFluxObjOnlyFluxObj,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020510
+ { FbcObjectiveLOFluxObjAllowedElements,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020601
+ { FbcFluxObjectAllowedL3Attributes,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020602
+ { FbcFluxObjectAllowedElements,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020603
+ { FbcFluxObjectRequiredAttributes,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020604
+ { FbcFluxObjectNameMustBeString,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020605
+ { FbcFluxObjectReactionMustBeSIdRef,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020606
+ { FbcFluxObjectReactionMustExist,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020607
+ { FbcFluxObjectCoefficientMustBeDouble,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+
// TO DO - NOT YET DONE
// // 2020303
// { FbcExtModDefAllowedAttributes,
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|
|
From: <luc...@us...> - 2013-01-31 07:07:46
|
Revision: 17000
http://sbml.svn.sourceforge.net/sbml/?rev=17000&view=rev
Author: luciansmith
Date: 2013-01-31 07:07:35 +0000 (Thu, 31 Jan 2013)
Log Message:
-----------
Fixed a bug that would send the program into an infinite loop any time it tried to validate a file with a reaction with more reactants in a reaction than there were unit definitions. This was due to the variable 'j' being re-used as a loop variable inside a 'j' loop.
Modified Paths:
--------------
trunk/libsbml/src/sbml/Model.cpp
Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp 2013-01-30 17:03:34 UTC (rev 16999)
+++ trunk/libsbml/src/sbml/Model.cpp 2013-01-31 07:07:35 UTC (rev 17000)
@@ -5593,19 +5593,19 @@
}
else
{
- for (j = 0; j < getNumUnitDefinitions(); j++)
+ for (unsigned int unitdef = 0; unitdef < getNumUnitDefinitions(); unitdef++)
{
- if (!strcmp(units.c_str(), getUnitDefinition(j)->getId().c_str()))
+ if (!strcmp(units.c_str(), getUnitDefinition(unitdef)->getId().c_str()))
{
for (unsigned int pp = 0;
- pp < getUnitDefinition(j)->getNumUnits(); pp++)
+ pp < getUnitDefinition(unitdef)->getNumUnits(); pp++)
{
u = new Unit(getSBMLNamespaces());
- u->setKind(getUnitDefinition(j)->getUnit(pp)->getKind());
- u->setMultiplier(getUnitDefinition(j)->getUnit(pp)
+ u->setKind(getUnitDefinition(unitdef)->getUnit(pp)->getKind());
+ u->setMultiplier(getUnitDefinition(unitdef)->getUnit(pp)
->getMultiplier());
- u->setScale(getUnitDefinition(j)->getUnit(pp)->getScale());
- u->setExponent(-1 * (getUnitDefinition(j)->getUnit(pp)
+ u->setScale(getUnitDefinition(unitdef)->getUnit(pp)->getScale());
+ u->setExponent(-1 * (getUnitDefinition(unitdef)->getUnit(pp)
->getExponent()));
ud->addUnit(u);
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|
|
From: <luc...@us...> - 2013-01-30 17:03:42
|
Revision: 16999
http://sbml.svn.sourceforge.net/sbml/?rev=16999&view=rev
Author: luciansmith
Date: 2013-01-30 17:03:34 +0000 (Wed, 30 Jan 2013)
Log Message:
-----------
* Changed the settings files for fbc tests to clear 'dummy' variables.
* Removed the 'initial conditions' sections of the fbc .m files, since fbc tests don't use initial conditions.
* Changed the absolute and relative tolerances to be 0.001 instead of 0.0001 since COBRA only outputs four digits of precision.
Modified Paths:
--------------
trunk/test-suite/cases/semantic/01186/01186-model.m
trunk/test-suite/cases/semantic/01186/01186-settings.txt
trunk/test-suite/cases/semantic/01187/01187-model.m
trunk/test-suite/cases/semantic/01187/01187-settings.txt
trunk/test-suite/cases/semantic/01188/01188-model.m
trunk/test-suite/cases/semantic/01188/01188-settings.txt
trunk/test-suite/cases/semantic/01189/01189-model.m
trunk/test-suite/cases/semantic/01189/01189-settings.txt
trunk/test-suite/cases/semantic/01190/01190-model.m
trunk/test-suite/cases/semantic/01190/01190-settings.txt
trunk/test-suite/cases/semantic/01191/01191-model.m
trunk/test-suite/cases/semantic/01191/01191-settings.txt
trunk/test-suite/cases/semantic/01192/01192-model.m
trunk/test-suite/cases/semantic/01192/01192-settings.txt
trunk/test-suite/cases/semantic/01193/01193-model.m
trunk/test-suite/cases/semantic/01193/01193-settings.txt
trunk/test-suite/cases/semantic/01194/01194-model.m
trunk/test-suite/cases/semantic/01194/01194-settings.txt
trunk/test-suite/cases/semantic/01195/01195-model.m
trunk/test-suite/cases/semantic/01195/01195-settings.txt
trunk/test-suite/cases/semantic/01196/01196-model.m
trunk/test-suite/cases/semantic/01196/01196-settings.txt
Modified: trunk/test-suite/cases/semantic/01186/01186-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01186/01186-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01186/01186-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -16,9 +16,8 @@
* 1 compartment (Cell)
* 1 objective (OBJF)
-
The active objective is OBJF, which is to be maximized:
- + 1 R26
+ + 1 R26
There are 26 reactions, and 52 flux bounds:
@@ -50,32 +49,5 @@
| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ |
| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |]
-The initial conditions are as follows:
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01186/01186-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01186/01186-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01186/01186-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R26,OBJF
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01187/01187-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01187/01187-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01187/01187-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -49,32 +49,4 @@
| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ |
| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01187/01187-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01187/01187-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01187/01187-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R26,OBJF
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01188/01188-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01188/01188-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01188/01188-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -49,32 +49,4 @@
| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= INF$ |
| R26: S -> Y | $R26 >= 0 && R26 <= INF$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01188/01188-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01188/01188-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01188/01188-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R26,OBJF
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01189/01189-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01189/01189-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01189/01189-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -49,32 +49,4 @@
| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= INF$ |
| R26: S -> Y | $R26 >= 0 && R26 <= INF$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01189/01189-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01189/01189-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01189/01189-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R26,OBJF
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01190/01190-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01190/01190-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01190/01190-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -49,32 +49,4 @@
| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ |
| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01190/01190-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01190/01190-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01190/01190-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R26,OBJF
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01191/01191-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01191/01191-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01191/01191-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -49,32 +49,4 @@
| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ |
| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01191/01191-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01191/01191-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01191/01191-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R26,OBJF2
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01192/01192-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01192/01192-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01192/01192-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -50,32 +50,4 @@
| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ |
| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01192/01192-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01192/01192-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01192/01192-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R26,R10,R07,OBJF
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01193/01193-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01193/01193-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01193/01193-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -49,32 +49,4 @@
| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ |
| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01193/01193-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01193/01193-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01193/01193-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R26,R10,R07,OBJF
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01194/01194-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01194/01194-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01194/01194-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -49,32 +49,4 @@
| R25: A + T -> 0.5S + U | $R25 >= 0 && R25 <= 1000$ |
| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01194/01194-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01194/01194-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01194/01194-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R07,R10,OBJF,R26,R25
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01195/01195-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01195/01195-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01195/01195-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -49,32 +49,4 @@
| R25: A + T -> 0.5S + U | $R25 == 0.4$ |
| R26: S -> Y | $R26 >= 0 && R26 <= 1000$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01195/01195-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01195/01195-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01195/01195-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: R01,R07,R10,OBJF,R26,R25
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
Modified: trunk/test-suite/cases/semantic/01196/01196-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01196/01196-model.m 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01196/01196-model.m 2013-01-30 17:03:34 UTC (rev 16999)
@@ -49,32 +49,4 @@
| R21: P -> L | $R21 >= -1000 && R21 <= 1000$ |
| R20: O -> P | $R20 >= -1000 && R20 <= 1000$ |]
-The initial conditions are as follows:
-
-[{width:35em,margin: 1em auto}| | *Value* | *Constant* |
-| Initial concentration of species A | $0$ | variable |
-| Initial concentration of species B | $0$ | variable |
-| Initial concentration of species C | $0$ | variable |
-| Initial concentration of species D | $0$ | variable |
-| Initial concentration of species E | $0$ | variable |
-| Initial concentration of species F | $0$ | variable |
-| Initial concentration of species G | $0$ | variable |
-| Initial concentration of species H | $0$ | variable |
-| Initial concentration of species I | $0$ | variable |
-| Initial concentration of species J | $0$ | variable |
-| Initial concentration of species K | $0$ | variable |
-| Initial concentration of species L | $0$ | variable |
-| Initial concentration of species M | $0$ | variable |
-| Initial concentration of species N | $0$ | variable |
-| Initial concentration of species O | $0$ | variable |
-| Initial concentration of species P | $0$ | variable |
-| Initial concentration of species Q | $0$ | variable |
-| Initial concentration of species R | $0$ | variable |
-| Initial concentration of species S | $0$ | variable |
-| Initial concentration of species T | $0$ | variable |
-| Initial concentration of species U | $0$ | variable |
-| Initial concentration of species X | $0$ | variable |
-| Initial concentration of species Y | $0$ | variable |
-| Initial volume of compartment 'Cell' | $1$ | variable |]
-
*)
Modified: trunk/test-suite/cases/semantic/01196/01196-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/01196/01196-settings.txt 2013-01-30 16:51:59 UTC (rev 16998)
+++ trunk/test-suite/cases/semantic/01196/01196-settings.txt 2013-01-30 17:03:34 UTC (rev 16999)
@@ -1,8 +1,8 @@
-start: 0
-duration: 1
-steps: 1
+start:
+duration:
+steps:
variables: OBJF
-absolute: 0.0001
-relative: 0.0001
+absolute: 0.001
+relative: 0.001
amount:
concentration:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2013-01-30 16:52:05
|
Revision: 16998
http://sbml.svn.sourceforge.net/sbml/?rev=16998&view=rev
Author: sarahkeating
Date: 2013-01-30 16:51:59 +0000 (Wed, 30 Jan 2013)
Log Message:
-----------
updated with new dirs
Modified Paths:
--------------
branches/libsbml-packages/create-zip-fbc.bat
Modified: branches/libsbml-packages/create-zip-fbc.bat
===================================================================
--- branches/libsbml-packages/create-zip-fbc.bat 2013-01-30 16:51:17 UTC (rev 16997)
+++ branches/libsbml-packages/create-zip-fbc.bat 2013-01-30 16:51:59 UTC (rev 16998)
@@ -32,7 +32,13 @@
mkdir src\sbml\packages\%PACKAGE_NAME%\extension\test\test-data
mkdir src\sbml\packages\%PACKAGE_NAME%\sbml
mkdir src\sbml\packages\%PACKAGE_NAME%\util
+mkdir src\sbml\packages\%PACKAGE_NAME%\validator
+mkdir src\sbml\packages\%PACKAGE_NAME%\validator\constraints
+mkdir src\sbml\packages\%PACKAGE_NAME%\validator\test
+mkdir src\sbml\packages\%PACKAGE_NAME%\validator\test\test-data
+mkdir src\sbml\packages\%PACKAGE_NAME%\validator\test\test-data\general-constraints
+
copy /y %PACKAGE_DIR%\%PACKAGE_NAME%-package.cmake .
copy /y %PACKAGE_DIR%\src\%PACKAGE_NAME%-package.cmake src
@@ -44,6 +50,10 @@
copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\sbml\*.cpp src\sbml\packages\%PACKAGE_NAME%\sbml\
copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\util\*.h src\sbml\packages\%PACKAGE_NAME%\util\
copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\util\*.cpp src\sbml\packages\%PACKAGE_NAME%\util\
+copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\validator\*.h src\sbml\packages\%PACKAGE_NAME%\validator\
+copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\validator\*.cpp src\sbml\packages\%PACKAGE_NAME%\validator\
+copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\validator\constraints\*.h src\sbml\packages\%PACKAGE_NAME%\validator\constraints
+copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\validator\constraints\*.cpp src\sbml\packages\%PACKAGE_NAME%\validator\constraints
copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\extension\test\*.h src\sbml\packages\%PACKAGE_NAME%\extension\test\
copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\extension\test\*.c src\sbml\packages\%PACKAGE_NAME%\extension\test\
@@ -51,6 +61,12 @@
copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\extension\test\*.txt src\sbml\packages\%PACKAGE_NAME%\extension\test\
copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\extension\test\test-data\*.xml src\sbml\packages\%PACKAGE_NAME%\extension\test\test-data
+copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\validator\test\*.h src\sbml\packages\%PACKAGE_NAME%\validator\test\
+copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\validator\test\*.c src\sbml\packages\%PACKAGE_NAME%\validator\test\
+copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\validator\test\*.cpp src\sbml\packages\%PACKAGE_NAME%\validator\test\
+copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\validator\test\*.txt src\sbml\packages\%PACKAGE_NAME%\validator\test\
+copy /y %PACKAGE_DIR%\src\sbml\packages\%PACKAGE_NAME%\validator\test\test-data\general-constraints\*.xml src\sbml\packages\%PACKAGE_NAME%\validator\test\test-data\general-constraints
+
mkdir src\bindings
mkdir src\bindings\csharp
mkdir src\bindings\java
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2013-01-30 16:51:29
|
Revision: 16997
http://sbml.svn.sourceforge.net/sbml/?rev=16997&view=rev
Author: sarahkeating
Date: 2013-01-30 16:51:17 +0000 (Wed, 30 Jan 2013)
Log Message:
-----------
adding validation to fbc
Modified Paths:
--------------
branches/libsbml-packages/fbc/src/fbc-package.cmake
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcExtension.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcExtension.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/test/TestReadFbcExtension.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxObjective.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxObjective.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.h
Added Paths:
-----------
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcConsistencyValidator.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcConsistencyValidator.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcValidator.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcValidator.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcVisitor.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcVisitor.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/CMakeLists.txt
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/TestFbcConsistencyValidator.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/TestFile.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/TestFile.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/TestValidator.cpp
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/TestValidator.h
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020101-fail-01-01.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020102-fail-01-01-01016.xml
branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/test/test-data/general-constraints/2020103-fail-01-01.xml
Modified: branches/libsbml-packages/fbc/src/fbc-package.cmake
===================================================================
--- branches/libsbml-packages/fbc/src/fbc-package.cmake 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/fbc-package.cmake 2013-01-30 16:51:17 UTC (rev 16997)
@@ -15,7 +15,7 @@
set(FBC_SOURCES)
# go through all directtories: common, extension and sbml
-foreach(dir common extension sbml util)
+foreach(dir common extension sbml util validator validator/constraints)
# add to include directory
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/fbc/${dir})
@@ -46,6 +46,7 @@
if(WITH_CHECK)
add_subdirectory(sbml/packages/fbc/extension/test)
+ add_subdirectory(sbml/packages/fbc/validator/test)
endif()
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcExtension.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcExtension.cpp 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcExtension.cpp 2013-01-30 16:51:17 UTC (rev 16997)
@@ -21,7 +21,7 @@
#include <sbml/extension/SBMLExtensionRegister.h>
#include <sbml/extension/SBMLExtensionRegistry.h>
#include <sbml/extension/SBasePluginCreator.h>
-#include <sbml/extension/SBMLDocumentPlugin.h>
+#include <sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.h>
#include <sbml/conversion/SBMLConverterRegistry.h>
#include <sbml/packages/fbc/util/CobraToFbcConverter.h>
#include <sbml/packages/fbc/util/FbcToCobraConverter.h>
@@ -29,6 +29,7 @@
#include <sbml/packages/fbc/extension/FbcExtension.h>
#include <sbml/packages/fbc/extension/FbcModelPlugin.h>
#include <sbml/packages/fbc/extension/FbcSpeciesPlugin.h>
+#include <sbml/packages/fbc/validator/FbcSBMLErrorTable.h>
#ifdef __cplusplus
@@ -338,7 +339,7 @@
SBaseExtensionPoint modelExtPoint("core",SBML_MODEL);
SBaseExtensionPoint speciesExtPoint("core",SBML_SPECIES);
- SBasePluginCreator<SBMLDocumentPlugin, FbcExtension> sbmldocPluginCreator(sbmldocExtPoint,packageURIs);
+ SBasePluginCreator<FbcSBMLDocumentPlugin, FbcExtension> sbmldocPluginCreator(sbmldocExtPoint,packageURIs);
SBasePluginCreator<FbcModelPlugin, FbcExtension> modelPluginCreator(modelExtPoint,packageURIs);
SBasePluginCreator<FbcSpeciesPlugin, FbcExtension> speciesPluginCreator(speciesExtPoint,packageURIs);
@@ -373,6 +374,39 @@
}
+packageErrorTableEntry
+FbcExtension::getErrorTable(unsigned int index) const
+{
+ return fbcErrorTable[index];
+}
+
+unsigned int
+FbcExtension::getErrorTableIndex(unsigned int errorId) const
+{
+ unsigned int tableSize = sizeof(fbcErrorTable)/sizeof(fbcErrorTable[0]);
+ unsigned int index = 0;
+
+ for ( unsigned int i = 0; i < tableSize; i++ )
+ {
+ if ( errorId == fbcErrorTable[i].code )
+ {
+ index = i;
+ break;
+ }
+ }
+
+ return index;
+}
+
+
+unsigned int
+FbcExtension::getErrorIdOffset() const
+{
+ return 2000000;
+}
+
+
+
#endif /* __cplusplus */
LIBSBML_CPP_NAMESPACE_END
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcExtension.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcExtension.h 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcExtension.h 2013-01-30 16:51:17 UTC (rev 16997)
@@ -209,6 +209,12 @@
static void init();
+ virtual packageErrorTableEntry getErrorTable(unsigned int index) const;
+
+ virtual unsigned int getErrorTableIndex(unsigned int errorId) const;
+
+ virtual unsigned int getErrorIdOffset() const;
+
/** @endcond doxygen-libsbml-internal */
};
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp 2013-01-30 16:51:17 UTC (rev 16997)
@@ -23,6 +23,7 @@
#include <sbml/packages/fbc/extension/FbcModelPlugin.h>
#include <sbml/packages/fbc/extension/FbcExtension.h>
+#include <sbml/packages/fbc/validator/FbcVisitor.h>
#include <iostream>
@@ -1239,7 +1240,28 @@
mObjectives.enablePackageInternal(pkgURI,pkgPrefix,flag);
}
+bool
+FbcModelPlugin::acceptFbc(FbcVisitor& v) const
+{
+ const Model * model = static_cast<const Model * >(this->getParentSBMLObject());
+
+ v.visit(*model);
+ v.leave(*model);
+ for (unsigned int i = 0; i < getNumFluxBounds(); i++)
+ {
+ getFluxBound(i)->acceptFbc(v);
+ }
+ for (unsigned int i = 0; i < getNumObjectives(); i++)
+ {
+ getObjective(i)->acceptFbc(v);
+ }
+
+ return true;
+}
+
+
+
LIBSBML_EXTERN
int
FbcModelPlugin_addFluxBound(SBasePlugin_t * fbc, FluxBound_t * fb)
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.h 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcModelPlugin.h 2013-01-30 16:51:17 UTC (rev 16997)
@@ -43,6 +43,8 @@
LIBSBML_CPP_NAMESPACE_BEGIN
+class FbcVisitor;
+
class LIBSBML_EXTERN FbcModelPlugin : public SBasePlugin
{
public:
@@ -640,6 +642,14 @@
const std::string& pkgPrefix, bool flag);
/** @endcond doxygen-libsbml-internal */
+ /** @cond doxygen-libsbml-internal */
+
+ virtual bool acceptFbc(FbcVisitor& v) const;
+
+ /** @endcond */
+
+
+
protected:
/** @cond doxygen-libsbml-internal */
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.cpp (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.cpp 2013-01-30 16:51:17 UTC (rev 16997)
@@ -0,0 +1,190 @@
+/**
+ * @file FbcSBMLDocumentPlugin.cpp
+ * @brief Implementation of FbcSBMLDocumentPlugin, the plugin class of
+ * fbc package for the SBase element.
+ * @author Lucian Smith
+ *
+ *<!---------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright 2011 California Institute of Technology.
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *------------------------------------------------------------------------- -->
+ */
+
+#include <ostream>
+
+#include <sbml/common/libsbml-version.h>
+#include <sbml/packages/fbc/common/fbcfwd.h>
+#include <sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.h>
+#include <sbml/packages/fbc/validator/FbcConsistencyValidator.h>
+#include <sbml/packages/fbc/validator/FbcValidator.h>
+#include <sbml/packages/fbc/validator/FbcSBMLError.h>
+
+#include <iostream>
+
+#ifdef __cplusplus
+
+using namespace std;
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+FbcSBMLDocumentPlugin::FbcSBMLDocumentPlugin (const string &uri, const string &prefix, FbcPkgNamespaces *fbcns)
+ : SBMLDocumentPlugin(uri,prefix, fbcns)
+{
+}
+
+
+FbcSBMLDocumentPlugin::FbcSBMLDocumentPlugin(const FbcSBMLDocumentPlugin& orig)
+ : SBMLDocumentPlugin(orig)
+{
+}
+
+
+FbcSBMLDocumentPlugin&
+FbcSBMLDocumentPlugin::operator=(const FbcSBMLDocumentPlugin& orig)
+{
+ if(&orig!=this)
+ {
+ SBMLDocumentPlugin::operator =(orig);
+ }
+ return *this;
+}
+
+
+/*
+ * Creates and returns a deep copy of this FbcSBMLDocumentPlugin object.
+ */
+FbcSBMLDocumentPlugin*
+FbcSBMLDocumentPlugin::clone () const
+{
+ return new FbcSBMLDocumentPlugin(*this);
+}
+
+/*
+ * Destroy this object.
+ */
+FbcSBMLDocumentPlugin::~FbcSBMLDocumentPlugin ()
+{
+}
+
+
+void
+FbcSBMLDocumentPlugin::readAttributes (const XMLAttributes& attributes,
+ const ExpectedAttributes& expectedAttributes)
+{
+ // do not need to call this as we are going to read the required attribute here
+ //SBMLDocumentPlugin::readAttributes(attributes, expectedAttributes);
+ unsigned int numErrs = getErrorLog()->getNumErrors();
+ XMLTriple tripleRequired("required", mURI, getPrefix());
+ bool assigned = attributes.readInto(tripleRequired, mRequired,
+ getErrorLog(), false, getLine(), getColumn());
+ if (assigned == false)
+ {
+ if (getErrorLog()->getNumErrors() == numErrs + 1 &&
+ getErrorLog()->contains(XMLAttributeTypeMismatch))
+ {
+ getErrorLog()->logPackageError("fbc", FbcAttributeRequiredMustBeBoolean,
+ getPackageVersion(), getLevel(), getVersion());
+ }
+ else
+ {
+ getErrorLog()->logPackageError("fbc", FbcAttributeRequiredMissing,
+ getPackageVersion(), getLevel(), getVersion());
+ }
+ }
+ else
+ {
+ mIsSetRequired = true;
+ if (mRequired == true)
+ {
+ getErrorLog()->logPackageError("fbc", FbcRequiredFalse,
+ getPackageVersion(), getLevel(), getVersion());
+ }
+ }
+}
+
+
+bool
+FbcSBMLDocumentPlugin::isFlatteningImplemented() const
+{
+ return false;
+}
+
+
+unsigned int
+FbcSBMLDocumentPlugin::checkConsistency()
+{
+ unsigned int nerrors = 0;
+ unsigned int total_errors = 0;
+
+ SBMLDocument* doc = static_cast<SBMLDocument *>(this->getParentSBMLObject());
+ SBMLErrorLog *log = doc->getErrorLog();
+
+ unsigned char applicableValidators = doc->getApplicableValidators();
+
+ /* determine which validators to run */
+ bool id = false; //((applicableValidators & 0x01) == 0x01);
+ bool sbml = ((applicableValidators & 0x02) == 0x02);
+
+ //FbcIdentifierConsistencyValidator id_validator;
+ FbcConsistencyValidator validator;
+
+ //if (id)
+ //{
+ // id_validator.init();
+ // nerrors = id_validator.validate(*doc);
+ // total_errors += nerrors;
+ // if (nerrors > 0)
+ // {
+ // log->add(id_validator.getFailures() );
+ // /* only want to bail if errors not warnings */
+ // if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0)
+ // {
+ // return total_errors;
+ // }
+ // }
+ //}
+
+ if (sbml)
+ {
+ validator.init();
+ nerrors = validator.validate(*doc);
+ total_errors += nerrors;
+ if (nerrors > 0)
+ {
+ log->add( validator.getFailures() );
+ /* only want to bail if errors not warnings */
+ // TO DO note 1 for debugging
+ if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0)
+ {
+ return total_errors;
+ }
+ }
+ }
+
+ return 0;
+}
+
+bool
+FbcSBMLDocumentPlugin::acceptFbc(FbcVisitor& v) const
+{
+ const SBMLDocument *doc = static_cast<const SBMLDocument *>(this->getParentSBMLObject());
+ v.visit(*doc);
+
+ v.leave(*doc);
+
+ return true;
+}
+
+
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif /* __cplusplus */
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.h (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.h 2013-01-30 16:51:17 UTC (rev 16997)
@@ -0,0 +1,123 @@
+/**
+ * @file FbcSBMLDocumentPlugin.h
+ * @brief Definition of FbcSBMLDocumentPlugin, the plugin class of
+ * Fbc package for the Model element.
+ * @author Lucian Smith
+ *
+ *<!---------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *------------------------------------------------------------------------- -->
+ */
+
+#ifndef FbcSBMLDocumentPlugin_h
+#define FbcSBMLDocumentPlugin_h
+
+
+#ifdef __cplusplus
+
+#include <sbml/common/extern.h>
+#include <sbml/extension/SBMLDocumentPlugin.h>
+
+#include <iostream>
+#include <string>
+#include <map>
+
+#include <sbml/packages/fbc/extension/FbcExtension.h>
+#include <sbml/packages/fbc/validator/FbcValidator.h>
+#include <sbml/packages/fbc/validator/FbcVisitor.h>
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+class FbcValidator;
+class FbcVisitor;
+
+class LIBSBML_EXTERN FbcSBMLDocumentPlugin : public SBMLDocumentPlugin
+{
+public:
+
+ /**
+ * Constructor
+ */
+ FbcSBMLDocumentPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns);
+
+
+ /**
+ * Copy constructor. Creates a copy of this SBase object.
+ */
+ FbcSBMLDocumentPlugin(const FbcSBMLDocumentPlugin& orig);
+
+
+ /**
+ * Destroy this object.
+ */
+ virtual ~FbcSBMLDocumentPlugin ();
+
+
+ /**
+ * Assignment operator for FbcSBMLDocumentPlugin.
+ */
+ FbcSBMLDocumentPlugin& operator=(const FbcSBMLDocumentPlugin& orig);
+
+
+ /**
+ * Creates and returns a deep copy of this FbcSBMLDocumentPlugin object.
+ *
+ * @return a (deep) copy of this SBase object
+ */
+ virtual FbcSBMLDocumentPlugin* clone () const;
+
+
+#ifndef SWIG
+
+ /** @cond doxygen-libsbml-internal */
+ /**
+ * Reads the attributes of corresponding package in SBMLDocument element.
+ */
+ virtual void readAttributes (const XMLAttributes& attributes,
+ const ExpectedAttributes& expectedAttributes);
+ /** @endcond */
+
+
+#endif //SWIG
+
+ virtual bool isFlatteningImplemented() const;
+
+
+ virtual unsigned int checkConsistency();
+
+
+ /** @cond doxygen-libsbml-internal */
+
+ virtual bool acceptFbc(FbcVisitor& v) const;
+
+ /** @endcond */
+
+
+
+
+
+
+};
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif /* __cplusplus */
+#endif /* FbcSBMLDocumentPlugin_h */
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/test/TestReadFbcExtension.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/test/TestReadFbcExtension.cpp 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/extension/test/TestReadFbcExtension.cpp 2013-01-30 16:51:17 UTC (rev 16997)
@@ -30,22 +30,6 @@
extern char *TestDataDirectory;
-
-START_TEST (test_FbcExtension_read_ga_L3V1V1)
-{
- char *filename = safe_strcat(TestDataDirectory, "fbc_ga_example.xml");
- SBMLDocument *document = readSBMLFromFile(filename);
- Model *model = document->getModel();
- fail_unless(model != NULL);
- FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
- fail_unless(mplugin != NULL);
- fail_unless(mplugin->getNumGeneAssociations() == 1);
- fail_unless(mplugin->getGeneAssociation(0)->getAssociation()->toInfix() == "(b111 or b112)");
-
-
-}
-END_TEST
-
START_TEST (test_FbcExtension_read_L3V1V1)
{
char *filename = safe_strcat(TestDataDirectory, "fbc_example1.xml");
@@ -210,7 +194,6 @@
TCase *tcase = tcase_create("ReadFbcExtension");
tcase_add_test( tcase, test_FbcExtension_OpertationTypes);
- tcase_add_test( tcase, test_FbcExtension_read_ga_L3V1V1);
tcase_add_test( tcase, test_FbcExtension_read_L3V1V1);
tcase_add_test( tcase, test_FbcExtension_read_L3V1V1_defaultNS);
tcase_add_test( tcase, test_FbcExtension_read_L3V1V1_unknown_elements);
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.cpp 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.cpp 2013-01-30 16:51:17 UTC (rev 16997)
@@ -28,6 +28,7 @@
#include <sbml/packages/fbc/sbml/FluxBound.h>
#include <sbml/packages/fbc/extension//FbcExtension.h>
+#include <sbml/packages/fbc/validator/FbcVisitor.h>
#if defined(WIN32) && !defined(CYGWIN)
#define isnan _isnan
@@ -800,6 +801,13 @@
}
+bool
+FluxBound::acceptFbc(FbcVisitor& v) const
+{
+ return v.visit(*this);
+}
+
+
LIBSBML_EXTERN
FluxBound_t *
FluxBound_create(unsigned int level, unsigned int version, unsigned int pkgversion)
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.h 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxBound.h 2013-01-30 16:51:17 UTC (rev 16997)
@@ -51,6 +51,7 @@
LIBSBML_CPP_NAMESPACE_BEGIN
+class FbcVisitor;
class LIBSBML_EXTERN FluxBound : public SBase
{
@@ -429,6 +430,11 @@
virtual bool hasRequiredElements() const ;
/** @endcond doxygen-libsbml-internal */
+ /** @cond doxygen-libsbml-internal */
+
+ virtual bool acceptFbc(FbcVisitor& v) const;
+
+ /** @endcond */
protected:
/**
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxObjective.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxObjective.cpp 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxObjective.cpp 2013-01-30 16:51:17 UTC (rev 16997)
@@ -29,6 +29,7 @@
#include <sbml/packages/fbc/sbml/FluxObjective.h>
#include <sbml/packages/fbc/extension/FbcExtension.h>
+#include <sbml/packages/fbc/validator/FbcVisitor.h>
#if defined(WIN32) && !defined(CYGWIN)
#define isnan _isnan
@@ -597,6 +598,13 @@
}
+bool
+FluxObjective::acceptFbc(FbcVisitor& v) const
+{
+ return v.visit(*this);
+}
+
+
LIBSBML_EXTERN
FluxObjective_t *
FluxObjective_create(unsigned int level, unsigned int version, unsigned int pkgversion)
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxObjective.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxObjective.h 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/FluxObjective.h 2013-01-30 16:51:17 UTC (rev 16997)
@@ -38,7 +38,9 @@
LIBSBML_CPP_NAMESPACE_BEGIN
+class FbcVisitor;
+
class LIBSBML_EXTERN FluxObjective : public SBase
{
protected:
@@ -307,7 +309,14 @@
*/
virtual bool accept (SBMLVisitor& v) const;
/** @endcond doxygen-libsbml-internal */
-
+
+ /** @cond doxygen-libsbml-internal */
+
+ virtual bool acceptFbc(FbcVisitor& v) const;
+
+ /** @endcond */
+
+
protected:
/**
* @return the SBML object corresponding to next XMLToken in the
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.cpp 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.cpp 2013-01-30 16:51:17 UTC (rev 16997)
@@ -29,6 +29,7 @@
#include <sbml/packages/fbc/sbml/Objective.h>
#include <sbml/packages/fbc/extension/FbcExtension.h>
+#include <sbml/packages/fbc/validator/FbcVisitor.h>
using namespace std;
@@ -694,8 +695,22 @@
/** @endcond doxygen-libsbml-internal */
+bool
+Objective::acceptFbc(FbcVisitor& v) const
+{
+ v.visit(*this);
+ for (unsigned int n = 0; n < getNumFluxObjectives(); n++)
+ {
+ getFluxObjective(n)->acceptFbc(v);
+ }
+ v.leave(*this);
+ return true;
+}
+
+
+
/*
* Ctor.
*/
Modified: branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.h 2013-01-30 02:07:19 UTC (rev 16996)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/sbml/Objective.h 2013-01-30 16:51:17 UTC (rev 16997)
@@ -51,6 +51,7 @@
LIBSBML_CPP_NAMESPACE_BEGIN
+class FbcVisitor;
class LIBSBML_EXTERN Objective : public SBase
{
@@ -491,6 +492,11 @@
virtual bool hasRequiredElements() const ;
/** @endcond doxygen-libsbml-internal */
+ /** @cond doxygen-libsbml-internal */
+
+ virtual bool acceptFbc(FbcVisitor& v) const;
+
+ /** @endcond */
protected:
/**
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcConsistencyValidator.cpp
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcConsistencyValidator.cpp (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcConsistencyValidator.cpp 2013-01-30 16:51:17 UTC (rev 16997)
@@ -0,0 +1,56 @@
+/**
+ * @cond doxygen-libsbml-internal
+ *
+ * @file FbcConsistencyValidator.cpp
+ * @brief Checks an SBML model for structural consistency
+ * @author Sarah Keating
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2012 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution and
+ * also available online as http://sbml.org/software/libsbml/license.html
+ * ---------------------------------------------------------------------- -->*/
+
+#ifndef doxygen_ignore
+
+#include <sbml/packages/fbc/validator/FbcConsistencyValidator.h>
+
+
+/*
+ * Compile ConsistencyConstraints
+ */
+#include "constraints/FbcConsistencyConstraints.cpp"
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+/*
+ * Initializes this Validator with a set of Constraints.
+ */
+void
+FbcConsistencyValidator::init ()
+{
+#define AddingConstraintsToValidator 1
+#include "constraints/FbcConsistencyConstraints.cpp"
+}
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif
+
+/** @endcond */
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcConsistencyValidator.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcConsistencyValidator.h (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcConsistencyValidator.h 2013-01-30 16:51:17 UTC (rev 16997)
@@ -0,0 +1,64 @@
+/**
+ * @cond doxygen-libsbml-internal
+ *
+ * @file FbcConsistencyValidator.h
+ * @brief Performs consistency checks on an SBML model
+ * @author Sarah Keating
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2012 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution and
+ * also available online as http://sbml.org/software/libsbml/license.html
+ * ---------------------------------------------------------------------- -->*/
+
+#ifndef FbcConsistencyValidator_h
+#define FbcConsistencyValidator_h
+
+
+#ifdef __cplusplus
+
+
+#include <sbml/packages/fbc/validator/FbcValidator.h>
+
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+class FbcConsistencyValidator: public FbcValidator
+{
+public:
+
+ FbcConsistencyValidator () :
+ FbcValidator( LIBSBML_CAT_GENERAL_CONSISTENCY ) { }
+
+ virtual ~FbcConsistencyValidator () { }
+
+ /**
+ * Initializes this Validator with a set of Constraints.
+ */
+ virtual void init ();
+};
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif /* __cplusplus */
+#endif /* ConsistencyValidator_h */
+
+
+/** @endcond */
+
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLError.h 2013-01-30 16:51:17 UTC (rev 16997)
@@ -0,0 +1,125 @@
+/**
+ * @file FbcSBMLError.h
+ * @brief Represents SBML errors and other diagnostics
+ * @author Michael Hucka
+ * @author Sarah Keating
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2012 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ------------------------------------------------------------------------ -->
+ *
+ */
+
+#ifndef FbcSBMLError_h
+#define FbcSBMLError_h
+
+#include <sbml/common/extern.h>
+#include <sbml/SBMLError.h>
+#include <sbml/SBMLNamespaces.h>
+
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+BEGIN_C_DECLS
+
+/**
+ * Codes for all SBML-level errors and warnings.
+ *
+ * These are distinguished from the XML layer (LIBLAX) error codes by being
+ * numbered > 10000, while the XML layer's codes are < 9999. Calling
+ * programs may wish to check whether a given SBMLError object's error
+ * identifier is actually from SBMLErrorCode_t or XMLError::XMLErrorCode_t.
+ * This distinction corresponds to whether a given error represents a
+ * low-level XML problem or an SBML problem.
+ */
+typedef enum
+{
+ FbcUnknown = 2010100
+, FbcNSUndeclared = 2010101
+, FbcElementNotInNs = 2010102
+, FbcDuplicateComponentId = 2010301
+
+, FbcAttributeRequiredMissing = 2020101
+, FbcAttributeRequiredMustBeBoolean = 2020102
+, FbcRequiredFalse = 2020103
+
+, FbcOnlyOneEachListOf = 2020201
+, FbcNoEmptyListOfs = 2020202
+, FbcLOFluxBoundsAllowedElements = 2020203
+, FbcLOObjectivesAllowedElements = 2020204
+, FbcLOFluxBoundsAllowedAttributes = 2020205
+, FbcLOObjectivesAllowedAttributes = 2020206
+, FbcActiveObjectiveSyntax = 2020207
+, FbcActiveObjectiveRefersObjective = 2020208
+
+// NOT YET DONE
+//, FbcExtModDefAllowedAttributes = 2020303
+//, FbcReferenceMustBeL3 = 2020304
+//, FbcModReferenceMustIdOfModel = 2020305
+//, FbcExtModMd5DoesNotMatch = 2020306
+//, FbcInvalidSourceSyntax = 2020307
+//, FbcInvalidModelRefSyntax = 2020308
+//, FbcCircularExternalModelReference = 2020310
+//, FbcOneListOfOnModel = 2020501
+//, FbcOneListOfDeletionOnSubmodel = 2020603
+//, FbcModReferenceSyntax = 2020608
+//, FbcSubmodelMustReferenceModel = 2020615
+//, FbcSubmodelCannotReferenceSelf = 2020616
+//, FbcModCannotCircularlyReferenceSelf = 2020617
+//, FbcTimeConversionMustBeParameter = 2020622
+//, FbcExtentConversionMustBeParameter = 2020623
+//, FbcPortRefMustReferencePort = 2020701
+//, FbcIdRefMustReferenceObject = 2020702
+//, FbcUnitRefMustReferenceUnitDef = 2020703
+//, FbcMetaIdRefMustReferenceObject = 2020704
+//, FbcParentOfSBRefChildMustBeSubmodel = 2020705
+//, FbcInvalidMetaIdRefSyntax = 2020709
+//, FbcOneSBaseRefOnly = 2020710
+//, FbcDeprecatedSBaseRefSpelling = 2020711
+//, FbcPortMustReferenceObject = 2020801
+//, FbcPortMustReferenceOnlyOneObject = 2020802
+//, FbcPortAllowedAttributes = 2020803
+//, FbcPortReferencesUnique = 2020804
+//, FbcDeletionMustReferenceObject = 2020901
+//, FbcDeletionMustReferOnlyOneObject = 2020902
+//, FbcDeletionAllowedAttributes = 2020903
+//, FbcReplacedElementMustRefObject = 2021001
+//, FbcReplacedElementMustRefOnlyOne = 2021002
+//, FbcReplacedElementAllowedAttributes = 2021003
+//, FbcReplacedElementSubModelRef = 2021004
+//, FbcReplacedElementDeletionRef = 2021005
+//, FbcReplacedElementConvFactorRef = 2021006
+//, FbcReplacedElementSameReference = 2021010
+//, FbcReplacedByMustRefObject = 2021101
+//, FbcReplacedByMustRefOnlyOne = 2021102
+//, FbcReplacedByAllowedAttributes = 2021103
+//, FbcReplacedBySubModelRef = 2021104
+//, FbcUnresolvedReference = 2090101
+//, FbcNoModelInReference = 2090102
+//, FbcExtModDefBad = 2090103
+} FbcSBMLErrorCode_t;
+
+
+END_C_DECLS
+LIBSBML_CPP_NAMESPACE_END
+
+
+
+#endif /* SBMLError_h */
Added: branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h
===================================================================
--- branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h (rev 0)
+++ branches/libsbml-packages/fbc/src/sbml/packages/fbc/validator/FbcSBMLErrorTable.h 2013-01-30 16:51:17 UTC (rev 16997)
@@ -0,0 +1,764 @@
+/**
+ * @file FbcSBMLErrorTable.h
+ * @brief Represents SBML errors and other diagnostics
+ * @author Sarah Keating
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2012 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ---------------------------------------------------------------------- -->*/
+
+#include <string>
+#include <iostream>
+#include <sstream>
+
+#include <sbml/packages/fbc/validator/FbcSBMLError.h>
+
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+/** @cond doxygen-libsbml-internal */
+
+
+
+static const packageErrorTableEntry fbcErrorTable[] =
+{
+ // 2010100
+ { FbcUnknown,
+ "Unknown error from fbc",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "Unknown error from fbc",
+ { ""
+ }
+ },
+
+ // 2010101
+ { FbcNSUndeclared,
+ "The fbc ns is not correctly declared",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "To conform to Version 1 of the Flux Balance Constraints "
+ "package specification for SBML Level 3, an "
+ "SBML document must declare the use of the following XML Namespace: "
+ "'http://www.sbml.org/sbml/level3/version1/fbc/version1'",
+ { "L3V1 Fbc V1 Section 3.1"
+ }
+ },
+
+ // 2010102
+ { FbcElementNotInNs,
+ "Element not in fbc namespace",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "Wherever they appear in an SBML document, "
+ "elements and attributes from the Flux Balance Constraints "
+ "package must be declared either implicitly or explicitly to be in the "
+ "XML namespace 'http://www.sbml.org/sbml/level3/version1/fbc/version1'",
+ { "L3V1 Fbc V1 Section 3.1"
+ }
+ },
+
+ // 2010301
+ { FbcDuplicateComponentId,
+ "Duplicate 'id' attribute value",
+ LIBSBML_CAT_IDENTIFIER_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "(Extends validation rule #10301 in the SBML Level 3 Version 1 Core "
+ "specification.) Within a <model> object"
+ "the values of the attributes id and fbc:id on every instance of the "
+ "following classes of objects must be unique across the set of all id "
+ "and fbc:id attribute values of all such objects in a model: the "
+ "model itself, plus all contained <functionDefinition>, <compartment>,"
+ "<species>, <reaction>, <speciesReference>, <modifierSpeciesReference>, "
+ "<event>, and <parameter> objects, plus the <fluxBound>, <objective> "
+ "and <fluxObjective> "
+ "objects defined by the Flux Balance Constraints package.",
+ { "L3V1 Fbc V1 Section 3.2"
+ }
+ },
+
+ // 2020101
+ { FbcAttributeRequiredMissing,
+ "Required fbc:required attribute on <sbml>",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "In all SBML documents using the Flux Balance Constraints "
+ "package, the SBML object must include a value for the attribute "
+ "'fbc:required.",
+ { "L3V1 Core Section 4.1.2"
+ }
+ },
+
+ // 2020102
+ { FbcAttributeRequiredMustBeBoolean,
+ "The fbc:required attribute must be Boolean",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The value of attribute 'fbc:required' on the SBML object must "
+ "be of the data type Boolean.",
+ { "L3V1 Core Section 4.1.2"
+ }
+ },
+
+ // 2020103
+ { FbcRequiredFalse,
+ "The fbc:required attribute must be 'false'",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The value of attribute 'fbc:required' on the SBML object must "
+ "be set to 'false'.",
+ { "L3V1 Fbc V1 Section 3.1"
+ }
+ },
+
+ // 2020201
+ { FbcOnlyOneEachListOf,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020202
+ { FbcNoEmptyListOfs,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020203
+ { FbcLOFluxBoundsAllowedElements,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020204
+ { FbcLOObjectivesAllowedElements,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020205
+ { FbcLOFluxBoundsAllowedAttributes,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020206
+ { FbcLOObjectivesAllowedAttributes,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020207
+ { FbcActiveObjectiveSyntax,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+ // 2020208
+ { FbcActiveObjectiveRefersObjective,
+ "",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "",
+ { ""
+ }
+ },
+
+// TO DO - NOT YET DONE
+ // // 2020303
+ // { FbcExtModDefAllowedAttributes,
+ // "Allowed <externalModelDefinitions> attributes",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "An <externalModelDefinition> object must have the attributes "
+ // "'fbc:id' and 'fbc:source', and may have the optional attributes "
+ // "'fbc:name', 'fbc:modelRef', and 'fbc:md5'. No other attributes "
+ // "from the Flux Balance Constraints namespace are permitted on "
+ // "an <externalModelDefinition> object.",
+ // { "L3V1 Fbc V1 Section 3.3.2"
+ // }
+ // },
+
+ // // 2020304
+ // { FbcReferenceMustBeL3,
+ // "External models must be L3",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of the 'fbc:source' attribute on an <externalModelDefinition> "
+ // "object must reference an SBML Level 3 Version 1 document.",
+ // { "L3V1 Fbc V1 Section 3.3.2"
+ // }
+ // },
+
+ // // 2020305
+ // { FbcModReferenceMustIdOfModel,
+ // "'modelRef' must be the 'id' of a model in the 'source' document",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of the 'fbc:modelRef' attribute on an <externalModelDefinit"
+ // "ion> object must be the value of an id attribute on a <model>, "
+ // "<modelDefinition>, or <externalModelDefinition> object in the SBML "
+ // "document referenced by the 'fbc:source' attribute.",
+ // { "L3V1 Fbc V1 Section 3.3.2"
+ // }
+ // },
+
+ // // 2020306
+ // { FbcExtModMd5DoesNotMatch,
+ // "MD5 checksum does not match the 'source' document",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_WARNING,
+ // "The value of the 'fbc:md5' attribute, if present on an "
+ //"<externalModelDefinition> object, should match the calculated MD5 "
+ //"checksum of the SBML document referenced by the 'fbc:source' "
+ //"attribute. ",
+ // { "L3V1 Fbc V1 Section 3.3.2"
+ // }
+ // },
+
+ // // 2020307
+ // { FbcInvalidSourceSyntax,
+ // "The 'fbc:source' attribute must be of type 'anyURI'",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:source' attribute on an <externalModelDefinition> "
+ // "object must always conform to the syntax of the XML Schema 1.0 data "
+ // "type 'anyURI'.",
+ // { "L3V1 Fbc V1 Section 3.3.2"
+ // }
+ // },
+
+ // // 2020308
+ // { FbcInvalidModelRefSyntax,
+ // "The 'fbc:modelRef' attribute must have the syntax of 'SId'",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a fbc:modelRef attribute on an <externalModelDefinition> "
+ // "object must always conform to the syntax of the SBML data type SId.",
+ // { "L3V1 Fbc V1 Section 3.3.2"
+ // }
+ // },
+
+ // // 2020310
+ // { FbcCircularExternalModelReference,
+ // "Circular reference in <externalModelDefinition>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "An <externalModelDefinition> object must not reference an "
+ // "<externalModelDefinition> in a different SBML document that, in turn, "
+ // "refers back to the original <externalModelDefinition object, "
+ // "whether directly or indirectly through a chain of "
+ //"<externalModelDefinition> objects. ",
+ // { "L3V1 Fbc V1 Section 3.3.2"
+ // }
+ // },
+
+ // // 2020501
+ // { FbcOneListOfOnModel,
+ // "Only one <listOfSubmodels> and one <listOfPorts> allowed",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "There may be at most one instance of each of the following kinds of "
+ // "objects within a <model> or <modelDefinition> object using "
+ // "Flux Balance Constraints: <listOfSubmodels> and <listOfPorts>.",
+ // { "L3V1 Fbc V1 Section 3.4"
+ // }
+ // },
+
+ // // 2020603
+ // { FbcOneListOfDeletionOnSubmodel,
+ // "Only one <listOfDeletions> on a <submodel> allowed",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "There may be at most one <listOfDeletions> container object within a "
+ //"<submodel> object.",
+ // { "L3V1 Fbc V1 Section 3.5"
+ // }
+ // },
+
+ // // 2020608
+ // { FbcModReferenceSyntax,
+ // "'fbc:modelRef' must conform to SId syntax",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:modelRef' attribute on a <submodel> object must "
+ //"always conform to the syntax of the SBML data type SId. ",
+ // { "L3V1 Fbc V1 Section 3.5.1"
+ // }
+ // },
+
+ // // 2020615
+ // { FbcSubmodelMustReferenceModel,
+ // "The 'fbc:modelRef' attribute must reference a model",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:modelRef' attribute on a <submodel> must be the "
+ // "identifier of a <model>, <modelDefinition>, or "
+ // "<externalModelDefinition> object in the same SBML object as the "
+ // "<submodel>.",
+ // { "L3V1 Fbc V1 Section 3.5.1"
+ // }
+ // },
+
+ // // 2020616
+ // { FbcSubmodelCannotReferenceSelf,
+ // "The 'fbc:modelRef' attribute cannot reference own model",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <model> or <modelDefinition> object must not contain a <submodel> "
+ // "which references that model object itself. That is, the value of a "
+ // "'fbc:modelRef' attribute on a <submodel> must not be the value of "
+ // "the parent <model> or <modelDefinition>'s 'id' attribute.",
+ // { "L3V1 Fbc V1 Section 3.5.1"
+ // }
+ // },
+
+ // // 2020617
+ // { FbcModCannotCircularlyReferenceSelf,
+ // "<model> may not reference <submodel> that references itself.",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <model> object must not contain a <submodel> which references that "
+ //"<model> indirectly. That is, the 'fbc:modelRef' attribute of a "
+ //"<submodel> may not point to the 'id' of a <model> containing a "
+ //"<submodel> object that references the original <model> directly or "
+ //"indirectly through a chain of <model>/<submodel> pairs.",
+ // { "L3V1 Fbc V1 Section 3.5.1"
+ // }
+ // },
+
+ // // 2020622
+ // { FbcTimeConversionMustBeParameter,
+ // "The 'fbc:timeConversionFactor' must reference a parameter",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:timeConversionFactor' attribute on a given "
+ // "<submodel> object must be the identifier of a <parameter> object "
+ // "defined in the same Model containing the <submodel>.",
+ // { "L3V1 Fbc V1 Section 3.5.1"
+ // }
+ // },
+
+ // // 2020623
+ // { FbcExtentConversionMustBeParameter,
+ // "The 'fbc:extentConversionFactor' must reference a parameter",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:extentConversionFactor' attribute on a given "
+ // "<submodel> object must be the identifier of a <parameter> object "
+ // "defined in the same Model containing the <submodel>.",
+ // { "L3V1 Fbc V1 Section 3.5.1"
+ // }
+ // },
+ //
+ // // 2020701
+ // { FbcPortRefMustReferencePort,
+ // "The 'fbc:portRef' attribute must be the 'id' of a <port>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:portRef' attribute on an <sBaseRef> object "
+ //"must be the identifier of a <port> object in the <model> referenced "
+ //"by that <sBaseRef>.",
+ // { "L3V1 Fbc V1 Section 3.7.1"
+ // }
+ // },
+
+ // // 2020702
+ // { FbcIdRefMustReferenceObject,
+ // "The 'fbc:idRef' attribute must be the 'id' of a model element",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:idRef' attribute on an <sBaseRef> object must "
+ //"be the identifier of an object contained in (that is, within the "
+ //"SId namespace of) the <model> referenced by that <sBaseRef>. This "
+ //"includes objects with 'id' attributes defined in packages other "
+ //"than SBML Level 3 Core or the Flux Balance Constraints "
+ //"package.",
+ // { "L3V1 Fbc V1 Section 3.7.1"
+ // }
+ // },
+
+ // // 2020703
+ // { FbcUnitRefMustReferenceUnitDef,
+ // "The 'fbc:unitRef' attribute must be the 'id' of a UnitDefinition",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:unitRef' attribute on an <sBaseRef> object must "
+ //"be the identifier of a <unitDefinition< object contained in the "
+ //"<model> referenced by that <sBaseRef>.",
+ // { "L3V1 Fbc V1 Section 3.7.1"
+ // }
+ // },
+
+ // // 2020704
+ // { FbcMetaIdRefMustReferenceObject,
+ // "The 'fbc:metaIdRef' attribute must be the 'metaid' of an object",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:metaIdRef' attribute on an <sBaseRef> object "
+ //"must be the value of a 'fbc:metaid' attribute on an element contained "
+ //"in the <model> referenced by that <sBaseRef>.",
+ // { "L3V1 Fbc V1 Section 3.7.1"
+ // }
+ // },
+
+ // // 2020705
+ // { FbcParentOfSBRefChildMustBeSubmodel,
+ // "If <sBaseRef> has a child <sBaseRef> its parent must be a <submodel>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "If an <sBaseRef> object contains an <sBaseRef> child, the parent "
+ //"<sBaseRef> must point to a <submodel> object. ",
+ // { "L3V1 Fbc V1 Section 3.7.2"
+ // }
+ // },
+
+ // // 2020709
+ // { FbcInvalidMetaIdRefSyntax,
+ // "The 'fbc:metaIdRef' attribute must have the syntax of an XML ID",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:metaIdRef' attribute on an SBaseRef object must "
+ // "always conform to the syntax of the XML data type ID.",
+ // { "L3V1 Fbc V1 Section 3.7.1"
+ // }
+ // },
+
+
+ // // 2020710
+ // { FbcOneSBaseRefOnly,
+ // "Only one <sbaseRef>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "Apart from the general notes and annotation subobjects permitted on "
+ // "all SBML objects, an SBaseRef object may only contain a single "
+ // "<sBaseRef> child.",
+ // { "L3V1 Fbc V1 Section 3.7.2"
+ // }
+ // },
+
+ // // 2020711
+ // { FbcDeprecatedSBaseRefSpelling,
+ // "The spelling 'sbaseRef' is deprecated",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_WARNING,
+ // "The 'sbaseRef' spelling of an SBaseRef child of an SBaseRef object "
+ // "is considered deprecated, and 'sBaseRef' should be used instead.",
+ // { "L3V1 Fbc V1 Section 3.7.2"
+ // }
+ // },
+
+ // // 2020801
+ // { FbcPortMustReferenceObject,
+ // "Port must reference an object",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <port> object must point to another object; that "
+ // "is, a <port> object must always have a value for one of the attributes "
+ // "'fbc:idRef', 'fbc:unitRef', or 'fbc:metaIdRef'",
+ // { "L3V1 Fbc V1 Section 3.4.3"
+ // }
+ // },
+
+ // // 2020802
+ // { FbcPortMustReferenceOnlyOneObject,
+ // "Port must reference only one other object.",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <port> object can only point to one other "
+ // "object; that is, a given <port> object can only have a value for one of "
+ // "the attributes 'fbc:idRef', 'fbc:unitRef', or 'fbc:metaIdRef'",
+ // { "L3V1 Fbc V1 Section 3.4.3"
+ // }
+ // },
+
+ // // 2020803
+ // { FbcPortAllowedAttributes,
+ // "Allowed attributes on a Port",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <port> object must have a value for the required "
+ // "attribute 'fbc:id', and one, and only one, of the "
+ // "attributes 'fbc:idRef', 'fbc:unitRef', or "
+ // "'fbc:metaIdRef'. No other attributes from the Hierarchical "
+ // "Model Fbcosition namespace are permitted on a <port> object.",
+ // { "L3V1 Fbc V1 Section 3.4.3"
+ // }
+ // },
+
+ // // 2020804
+ // { FbcPortReferencesUnique,
+ // "Port definitions must be unique.",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "Port definitions must be unique; that is, no two "
+ // "<port> objects in a given Model may reference the same object in that "
+ // "Model.",
+ // { "L3V1 Fbc V1 Section 3.4.3"
+ // }
+ // },
+
+ // // 2020901
+ // { FbcDeletionMustReferenceObject,
+ // "Deletion must reference an object",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <deletion> object must point to another object; that "
+ // "is, a <deletion> object must always have a value for one of the attributes "
+ // "'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', or 'fbc:metaIdRef'",
+ // { "L3V1 Fbc V1 Section 3.5.3"
+ // }
+ // },
+
+ // // 2020902
+ // { FbcDeletionMustReferOnlyOneObject,
+ // "Deletion must reference only one other object.",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <deletion> object can only point to one other "
+ // "object; that is, a given <deletion> object can only have a value for one of "
+ // "the attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', or "
+ // "'fbc:metaIdRef'",
+ // { "L3V1 Fbc V1 Section 3.5.3"
+ // }
+ // },
+
+ // // 2020903
+ // { FbcDeletionAllowedAttributes,
+ // "Allowed attributes on a Deletion",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <deletion> object must have a value for one, and only one, of the "
+ // "attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', and "
+ // "'fbc:metaIdRef'. It may also have the optional attributes 'fbc:id' "
+ // "and 'fbc:name'. No other attributes from the Hierarchical "
+ // "Model Fbcosition namespace are permitted on a <deletion> object.",
+ // { "L3V1 Fbc V1 Section 3.5.3"
+ // }
+ // },
+
+ // // 2021001
+ // { FbcReplacedElementMustRefObject,
+ // "ReplacedElement must reference an object",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <replacedElement> object must point to another object; that "
+ // "is, a <replacedElement> object must always have a value for one of the "
+ // "attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', "
+ // "'fbc:metaIdRef' or 'fbc:deletion'.",
+ // { "L3V1 Fbc V1 Section 3.6.2"
+ // }
+ // },
+
+ // // 2021002
+ // { FbcReplacedElementMustRefOnlyOne,
+ // "ReplacedElement must reference only one other object.",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <replacedElement> object can only point to one other "
+ // "object; that is, a given <replacedElement> object can only have a value "
+ // "for one of the attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', "
+ // "'fbc:metaIdRef' or 'fbc:deletion'.",
+ // { "L3V1 Fbc V1 Section 3.6.2"
+ // }
+ // },
+
+ // // 2021003
+ // { FbcReplacedElementAllowedAttributes,
+ // "Allowed attributes on <replacedElement>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <replacedElement> object must have a value for the required attribute "
+ // "'fbc:submodelRef', and a value for one, and only one, of the following "
+ // "attributes: 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', "
+ // "'fbc:metaIdRef', or 'fbc:deletion'. It may also have a value for the "
+ // "optional attribute 'fbc:conversionFactor'. No other attributes from "
+ // "the HierarchicalModel Fbcosition namespace are permitted on a "
+ // "<replacedElement> object.",
+ // { "L3V1 Fbc V1 Section 3.6.2"
+ // }
+ // },
+
+ // // 2021004
+ // { FbcReplacedElementSubModelRef,
+ // "The 'fbc:submodelRef' attribute must point to a <submodel>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:submodelRef' attribute on a <replacedElement> "
+ // "object must be the identifier of a <submodel> present in the "
+ // "<replacedElement> object\x92s parent Model.",
+ // { "L3V1 Fbc V1 Section 3.6.2"
+ // }
+ // },
+
+ // // 2021005
+ // { FbcReplacedElementDeletionRef,
+ // "The 'fbc:deletion' attribute must point to a <deletion>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:deletion' attribute on a <replacedElement> "
+ // "object must be the identifier of a <deletion> present in the "
+ // "<replacedElement> object\x92s parent Model.",
+ // { "L3V1 Fbc V1 Section 3.6.2"
+ // }
+ // },
+
+ // // 2021006
+ // { FbcReplacedElementConvFactorRef,
+ // "The 'fbc:conversionFactor attribute must point to a <parameter>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "The value of a 'fbc:conversionFactor' attribute on a "
+ // "<replacedElement> object must be the identifier of a <parameter> "
+ // "present in the <replacedElement> object\x92s parent Model",
+ // { "L3V1 Fbc V1 Section 3.6.2"
+ // }
+ // },
+
+ // // 2021010
+ // { FbcReplacedElementSameReference,
+ // "No <replacedElement> refer to same object",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "No two <replacedElement> objects in the same Model may reference the same "
+ // "object unless that object is a <deletion>",
+ // { "L3V1 Fbc V1 Section 3.6.2"
+ // }
+ // },
+
+ // // 2021101
+ // { FbcReplacedByMustRefObject,
+ // "ReplacedBy must reference an object",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <replacedBy> object must point to another object; that "
+ // "is, a <replacedBy> object must always have a value for one of the "
+ // "attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef' or "
+ // "'fbc:metaIdRef'.",
+ // { "L3V1 Fbc V1 Section 3.6.4"
+ // }
+ // },
+
+ // // 2021102
+ // { FbcReplacedByMustRefOnlyOne,
+ // "ReplacedBy must reference only one other object.",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <replacedBy> object can only point to one other "
+ // "object; that is, a given <replacedBy> object can only have a value "
+ // "for one of the attributes 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef', "
+ // "or 'fbc:metaIdRef'.",
+ // { "L3V1 Fbc V1 Section 3.6.4"
+ // }
+ // },
+
+ // // 2021103
+ // { FbcReplacedByAllowedAttributes,
+ // "Allowed attributes on <replacedBy>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // LIBSBML_SEV_ERROR,
+ // "A <replacedBy> object must have a value for the required attribute "
+ // "'fbc:submodelRef', and a value for one, and only one, of the following "
+ // "attributes: 'fbc:portRef', 'fbc:idRef', 'fbc:unitRef' "
+ // "or 'fbc:metaIdRef'. No other attributes from "
+ // "the HierarchicalModel Fbcosition namespace are permitted on a "
+ // "<replacedElement> object.",
+ // { "L3V1 Fbc V1 Section 3.6.4"
+ // }
+ // },
+
+ // // 2021104
+ // { FbcReplacedBySubModelRef,
+ // "The 'fbc:submodelRef' attribute must point to a <submodel>",
+ // LIBSBML_CAT_GENERAL_CONSISTENCY,
+ // ...
[truncated message content] |
|
From: <mh...@us...> - 2013-01-30 02:07:26
|
Revision: 16996
http://sbml.svn.sourceforge.net/sbml/?rev=16996&view=rev
Author: mhucka
Date: 2013-01-30 02:07:19 +0000 (Wed, 30 Jan 2013)
Log Message:
-----------
Antialiasing isn't turned on by default on non-Mac platforms, so we have to turn it on deliberately to get smooth round squares.
Modified Paths:
--------------
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ListToolItem.java
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultColor.java
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultMap.java
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ListToolItem.java
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ListToolItem.java 2013-01-29 21:28:34 UTC (rev 16995)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ListToolItem.java 2013-01-30 02:07:19 UTC (rev 16996)
@@ -219,6 +219,7 @@
if (DEFAULT_PIXEL_HEIGHT < r.height)
topOffset = (r.height - DEFAULT_PIXEL_HEIGHT)/2 - 2 + topIndent;
+ e.gc.setAntialias(SWT.ON);
e.gc.fillGradientRectangle(r.x - 10 , r.y + topOffset,
r.width + 9, DEFAULT_PIXEL_HEIGHT, true);
e.gc.setForeground(borderColor);
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultColor.java
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultColor.java 2013-01-29 21:28:34 UTC (rev 16995)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultColor.java 2013-01-30 02:07:19 UTC (rev 16996)
@@ -28,6 +28,7 @@
package org.sbml.testsuite.ui;
+import org.eclipse.swt.SWT;
import org.eclipse.swt.graphics.Color;
import org.eclipse.swt.graphics.Device;
import org.eclipse.swt.graphics.GC;
@@ -103,6 +104,7 @@
{
Image image = new Image(Display.getDefault(), imageSize, imageSize);
GC gc = new GC(image);
+ gc.setAntialias(SWT.ON);
gc.setBackground(getColor());
gc.setForeground(getColor());
gc.fillRoundRectangle(0, 0, imageSize, imageSize, 5, 5);
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultMap.java
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultMap.java 2013-01-29 21:28:34 UTC (rev 16995)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/src/org/sbml/testsuite/ui/ResultMap.java 2013-01-30 02:07:19 UTC (rev 16996)
@@ -495,6 +495,7 @@
protected void paintCanvas(GC gc)
{
+ gc.setAntialias(SWT.ON);
if (keySets == null || keySets.length == 0)
{
gc.drawString("No Data ...", 10, 10);
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From: <fbe...@us...> - 2013-01-29 21:28:40
|
Revision: 16995
http://sbml.svn.sourceforge.net/sbml/?rev=16995&view=rev
Author: fbergmann
Date: 2013-01-29 21:28:34 +0000 (Tue, 29 Jan 2013)
Log Message:
-----------
- need to reference opal in the class path to show the dialog
Modified Paths:
--------------
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml 2013-01-29 21:05:05 UTC (rev 16994)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml 2013-01-29 21:28:34 UTC (rev 16995)
@@ -17,6 +17,7 @@
<mainClass>org.sbml.testsuite.ui.MainWindow</mainClass>
<cp>swt.jar</cp>
<cp>org.swtchart_0.7.0.v20110128.jar</cp>
+ <cp>opal-0.9.5.1.jar</cp>
<cp>simple-xml-2.6.4.jar</cp>
<cp>testsuite-core.jar</cp>
</classPath>
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|
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From: <fbe...@us...> - 2013-01-29 21:05:12
|
Revision: 16994
http://sbml.svn.sourceforge.net/sbml/?rev=16994&view=rev
Author: fbergmann
Date: 2013-01-29 21:05:05 +0000 (Tue, 29 Jan 2013)
Log Message:
-----------
- updated script for linux 64
Modified Paths:
--------------
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/ICON_CompareResults.png
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/sbmltestsuite.xml
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/ICON_CompareResults.png
===================================================================
(Binary files differ)
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml 2013-01-29 20:15:57 UTC (rev 16993)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml 2013-01-29 21:05:05 UTC (rev 16994)
@@ -52,6 +52,7 @@
<target name="jar" depends="build">
<manifestclasspath property="manifest.cp" jarfile="testsuite-ui.jar">
<classpath>
+ <pathelement location="opal-0.9.5.1.jar" />
<pathelement location="swt.jar" />
<pathelement location="org.swtchart_0.7.0.v20110128.jar" />
<pathelement location="testsuite-core.jar" />
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/sbmltestsuite.xml
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/sbmltestsuite.xml 2013-01-29 20:15:57 UTC (rev 16993)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/sbmltestsuite.xml 2013-01-29 21:05:05 UTC (rev 16994)
@@ -1,7 +1,7 @@
<project>
- <shortName>sbmltestsuite</shortName>
- <fullName>SBML Testsuite </fullName>
- <version>2.0</version>
+ <shortName>sbmltestrunner</shortName>
+ <fullName>SBML Test Runner</fullName>
+ <version>3.0</version>
<componentList>
<component>
<name>default</name>
@@ -12,9 +12,9 @@
<desktopShortcutList>
<shortcut>
<comment>Starts the SBML Test Suite</comment>
- <exec>${installdir}/launcher/SBMLTestSuite</exec>
+ <exec>${installdir}/launcher/SBMLTestRunner</exec>
<icon>${installdir}/ICON_CompareResults.png</icon>
- <name>SBML Testsuite</name>
+ <name>SBML Test Runner</name>
<path>${installdir}</path>
<platforms>all</platforms>
<runAsAdmin>0</runAsAdmin>
@@ -39,13 +39,16 @@
<origin>stage/simple-xml-2.6.4.jar</origin>
</distributionFile>
<distributionFile>
+ <origin>stage/opal-0.9.5.1.jar</origin>
+ </distributionFile>
+ <distributionFile>
<origin>stage/swt.jar</origin>
</distributionFile>
<distributionFile>
<origin>stage/testsuite-core.jar</origin>
</distributionFile>
<distributionFile>
- <origin>stage/testsuite_ui.jar</origin>
+ <origin>stage/testsuite-ui.jar</origin>
</distributionFile>
<distributionFile>
<origin>ICON_CompareResults.png</origin>
@@ -113,14 +116,14 @@
<javaLauncher>
<allowCommandLineArguments>1</allowCommandLineArguments>
<arguments></arguments>
- <binaryName>SBMLTestSuite</binaryName>
- <classpath>org.swtchart_0.7.0.v20110128.jar;simple-xml-2.6.4.jar;swt.jar;testsuite-core.jar;</classpath>
- <jarFile>${installdir}/testsuite_ui.jar</jarFile>
+ <binaryName>SBMLTestRunner</binaryName>
+ <classpath>org.swtchart_0.7.0.v20110128.jar;opal-0.9.5.1.jar;simple-xml-2.6.4.jar;swt.jar;testsuite-core.jar;</classpath>
+ <jarFile>${installdir}/testsuite-ui.jar</jarFile>
<mainClass>org.sbml.testsuite.ui.Program</mainClass>
<preferredJavaBinary></preferredJavaBinary>
<runInConsole>0</runInConsole>
<vmParameters></vmParameters>
- <windowsResourceFileVersion>1.0.0.0</windowsResourceFileVersion>
+ <windowsResourceFileVersion>3.0.0.0</windowsResourceFileVersion>
<workingDirectory>${installdir}</workingDirectory>
</javaLauncher>
</javaLauncherList>
@@ -131,10 +134,10 @@
<showMessageOnError>0</showMessageOnError>
<shortcutList>
<shortcut>
- <comment>Launch the SBML Testsuite</comment>
- <exec>${installdir}/launcher/SBMLTestSuite</exec>
+ <comment>Launch the SBML Test Runner</comment>
+ <exec>${installdir}/launcher/SBMLTestRunner</exec>
<icon>${installdir}/ICON_CompareResults.png</icon>
- <name>SBML Testsuite 2.0</name>
+ <name>SBML Testsuite 3.0</name>
<path>${installdir}</path>
<platforms>all</platforms>
<runAsAdmin>0</runAsAdmin>
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|
|
From: <fbe...@us...> - 2013-01-29 20:16:04
|
Revision: 16993
http://sbml.svn.sourceforge.net/sbml/?rev=16993&view=rev
Author: fbergmann
Date: 2013-01-29 20:15:57 +0000 (Tue, 29 Jan 2013)
Log Message:
-----------
- updated build script for OSX
Modified Paths:
--------------
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/GenericApp.icns
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/Info.plist
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/createAppBundle.sh
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/GenericApp.icns
===================================================================
(Binary files differ)
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/Info.plist
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/Info.plist 2013-01-29 20:01:20 UTC (rev 16992)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/Info.plist 2013-01-29 20:15:57 UTC (rev 16993)
@@ -3,7 +3,7 @@
<plist version="1.0">
<dict>
<key>CFBundleName</key>
- <string>SBML Testsuite</string>
+ <string>SBML Test Runner</string>
<key>CFBundleIdentifier</key>
<string>org.sbml.testsuite.ui.Program</string>
<key>CFBundleVersion</key>
@@ -34,7 +34,8 @@
<array>
<string>$JAVAROOT/testsuite-core.jar</string>
<string>$JAVAROOT/swt.jar</string>
- <string>$JAVAROOT/testsuite_ui.jar</string>
+ <string>$JAVAROOT/testsuite-ui.jar</string>
+ <string>$JAVAROOT/opal-0.9.5.1.jar</string>
<string>$JAVAROOT/simple-xml-2.6.4.jar</string>
<string>$JAVAROOT/org.swtchart_0.7.0.v20110128.jar</string>
</array>
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml 2013-01-29 20:01:20 UTC (rev 16992)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml 2013-01-29 20:15:57 UTC (rev 16993)
@@ -16,12 +16,13 @@
<path refid="core.classpath" />
<pathelement location="./libs/swt.jar" />
<pathelement location="./libs/org.swtchart_0.7.0.v20110128.jar" />
+ <pathelement location="./libs/opal-0.9.5.1.jar" />
<pathelement location="${core.location}/libs/simple-xml-2.6.4.jar" />
</path>
<target name="init">
<tstamp>
<format property="timestamp" pattern="yyyy-MM-dd HH:mm zzz"/>
- </tstamp>
+ </tstamp>
<mkdir dir="bin" />
<copy includeemptydirs="false" todir="bin">
<fileset dir="src">
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/createAppBundle.sh
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/createAppBundle.sh 2013-01-29 20:01:20 UTC (rev 16992)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/createAppBundle.sh 2013-01-29 20:15:57 UTC (rev 16993)
@@ -1,8 +1,8 @@
#!/bin/bash
DIRECTORY=$(cd `dirname $0` && pwd)
STAGE_DIR="$DIRECTORY/stage"
-DMG="$DIRECTORY/SBML_Testsuite.dmg"
-APP_DIR="$STAGE_DIR/SBML Testsuite.app"
+DMG="$DIRECTORY/SBML_Test_Runner.dmg"
+APP_DIR="$STAGE_DIR/SBML Test Runner.app"
STUB="/usr/share/java/Tools/Jar Bundler.app/Contents/MacOS/JavaApplicationStub"
cd $DIRECTORY
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From: <fbe...@us...> - 2013-01-29 20:01:27
|
Revision: 16992
http://sbml.svn.sourceforge.net/sbml/?rev=16992&view=rev
Author: fbergmann
Date: 2013-01-29 20:01:20 +0000 (Tue, 29 Jan 2013)
Log Message:
-----------
- update file info for the testrunner
Modified Paths:
--------------
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/NSIS_SBMLTestsuite.nsi
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/NSIS_SBMLTestsuite.nsi
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/NSIS_SBMLTestsuite.nsi 2013-01-29 19:53:25 UTC (rev 16991)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/NSIS_SBMLTestsuite.nsi 2013-01-29 20:01:20 UTC (rev 16992)
@@ -1,11 +1,11 @@
; Script generated by the HM NIS Edit Script Wizard.
; HM NIS Edit Wizard helper defines
-!define PRODUCT_NAME "SBML Testsuite"
+!define PRODUCT_NAME "SBML Test Runner"
!define PRODUCT_VERSION "3.0"
!define PRODUCT_PUBLISHER "SBML Team"
!define PRODUCT_WEB_SITE "http://sbml.org/Software/SBML_Test_Suite"
-!define PRODUCT_DIR_REGKEY "Software\Microsoft\Windows\CurrentVersion\App Paths\SBMLTestSuite.exe"
+!define PRODUCT_DIR_REGKEY "Software\Microsoft\Windows\CurrentVersion\App Paths\SBMLTestRunner.exe"
!define PRODUCT_UNINST_KEY "Software\Microsoft\Windows\CurrentVersion\Uninstall\${PRODUCT_NAME}"
!define PRODUCT_UNINST_ROOT_KEY "HKLM"
@@ -24,7 +24,7 @@
; Instfiles page
!insertmacro MUI_PAGE_INSTFILES
; Finish page
-!define MUI_FINISHPAGE_RUN "$INSTDIR\SBMLTestSuite.exe"
+!define MUI_FINISHPAGE_RUN "$INSTDIR\SBMLTestRunner.exe"
!insertmacro MUI_PAGE_FINISH
; Uninstaller pages
@@ -36,8 +36,8 @@
; MUI end ------
Name "${PRODUCT_NAME} ${PRODUCT_VERSION}"
-OutFile "Setup_SBMLTestSuite-${PRODUCT_VERSION}.exe"
-InstallDir "$PROGRAMFILES\SBML Testsuite"
+OutFile "Setup_SBMLTestRunner-${PRODUCT_VERSION}.exe"
+InstallDir "$PROGRAMFILES\SBML\SBML Test Runner"
InstallDirRegKey HKLM "${PRODUCT_DIR_REGKEY}" ""
ShowInstDetails show
ShowUnInstDetails show
@@ -45,29 +45,31 @@
Section "MainSection" SEC01
SetOutPath "$INSTDIR"
SetOverwrite try
+
+ File "stage\SBMLTestRunner.exe"
File "stage\org.swtchart_0.7.0.v20110128.jar"
- File "stage\SBMLTestSuite.exe"
- CreateDirectory "$SMPROGRAMS\SBML Testsuite"
- CreateShortCut "$SMPROGRAMS\SBML Testsuite\SBML Testsuite.lnk" "$INSTDIR\SBMLTestSuite.exe"
- CreateShortCut "$DESKTOP\SBML Testsuite.lnk" "$INSTDIR\SBMLTestSuite.exe"
File "stage\simple-xml-2.6.4.jar"
File "stage\swt.jar"
File "stage\testsuite-core.jar"
File "stage\opal-0.9.5.1.jar"
+
+ CreateDirectory "$SMPROGRAMS\SBML Test Runner"
+ CreateShortCut "$SMPROGRAMS\SBML Test Runner\SBML Test Runner.lnk" "$INSTDIR\SBMLTestRunner.exe"
+ CreateShortCut "$DESKTOP\SBML Test Runner.lnk" "$INSTDIR\SBMLTestRunner.exe"
SectionEnd
Section -AdditionalIcons
WriteIniStr "$INSTDIR\${PRODUCT_NAME}.url" "InternetShortcut" "URL" "${PRODUCT_WEB_SITE}"
- CreateShortCut "$SMPROGRAMS\SBML Testsuite\Website.lnk" "$INSTDIR\${PRODUCT_NAME}.url"
- CreateShortCut "$SMPROGRAMS\SBML Testsuite\Uninstall.lnk" "$INSTDIR\uninst.exe"
+ CreateShortCut "$SMPROGRAMS\SBML Test Runner\Website.lnk" "$INSTDIR\${PRODUCT_NAME}.url"
+ CreateShortCut "$SMPROGRAMS\SBML Test Runner\Uninstall.lnk" "$INSTDIR\uninst.exe"
SectionEnd
Section -Post
WriteUninstaller "$INSTDIR\uninst.exe"
- WriteRegStr HKLM "${PRODUCT_DIR_REGKEY}" "" "$INSTDIR\SBMLTestSuite.exe"
+ WriteRegStr HKLM "${PRODUCT_DIR_REGKEY}" "" "$INSTDIR\SBMLTestRunner.exe"
WriteRegStr ${PRODUCT_UNINST_ROOT_KEY} "${PRODUCT_UNINST_KEY}" "DisplayName" "$(^Name)"
WriteRegStr ${PRODUCT_UNINST_ROOT_KEY} "${PRODUCT_UNINST_KEY}" "UninstallString" "$INSTDIR\uninst.exe"
- WriteRegStr ${PRODUCT_UNINST_ROOT_KEY} "${PRODUCT_UNINST_KEY}" "DisplayIcon" "$INSTDIR\SBMLTestSuite.exe"
+ WriteRegStr ${PRODUCT_UNINST_ROOT_KEY} "${PRODUCT_UNINST_KEY}" "DisplayIcon" "$INSTDIR\SBMLTestRunner.exe"
WriteRegStr ${PRODUCT_UNINST_ROOT_KEY} "${PRODUCT_UNINST_KEY}" "DisplayVersion" "${PRODUCT_VERSION}"
WriteRegStr ${PRODUCT_UNINST_ROOT_KEY} "${PRODUCT_UNINST_KEY}" "URLInfoAbout" "${PRODUCT_WEB_SITE}"
WriteRegStr ${PRODUCT_UNINST_ROOT_KEY} "${PRODUCT_UNINST_KEY}" "Publisher" "${PRODUCT_PUBLISHER}"
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml 2013-01-29 19:53:25 UTC (rev 16991)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml 2013-01-29 20:01:20 UTC (rev 16992)
@@ -2,7 +2,7 @@
<dontWrapJar>false</dontWrapJar>
<headerType>gui</headerType>
<jar>stage\testsuite-ui.jar</jar>
- <outfile>.\stage\SBMLTestSuite.exe</outfile>
+ <outfile>.\stage\SBMLTestRunner.exe</outfile>
<errTitle></errTitle>
<cmdLine></cmdLine>
<chdir></chdir>
@@ -29,15 +29,15 @@
<opt>-D32 -Djava.library.path="%EXEDIR%"</opt>
</jre>
<versionInfo>
- <fileVersion>1.0.0.0</fileVersion>
- <txtFileVersion>1.0</txtFileVersion>
- <fileDescription>SBML TestSuite Runner</fileDescription>
- <copyright>(c) 2012 Frank T. Bergmann</copyright>
- <productVersion>1.0.0.0</productVersion>
- <txtProductVersion>1.0</txtProductVersion>
+ <fileVersion>3.0.0.0</fileVersion>
+ <txtFileVersion>3.0</txtFileVersion>
+ <fileDescription>SBML Test Runner</fileDescription>
+ <copyright>(c) 2013 Frank T. Bergmann and Michael Hucka</copyright>
+ <productVersion>3.0.0.0</productVersion>
+ <txtProductVersion>3.0</txtProductVersion>
<productName>testsuite</productName>
<companyName>Caltech</companyName>
<internalName>testsuite</internalName>
- <originalFilename>SBMLTestSuite.exe</originalFilename>
+ <originalFilename>SBMLTestRunner.exe</originalFilename>
</versionInfo>
</launch4jConfig>
\ No newline at end of file
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|
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From: <fbe...@us...> - 2013-01-29 19:53:32
|
Revision: 16991
http://sbml.svn.sourceforge.net/sbml/?rev=16991&view=rev
Author: fbergmann
Date: 2013-01-29 19:53:25 +0000 (Tue, 29 Jan 2013)
Log Message:
-----------
- update ant script, windows installer script, and icon
Modified Paths:
--------------
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/ICON_CompareResults.ico
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/NSIS_SBMLTestsuite.nsi
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/createInstaller.bat
trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/ICON_CompareResults.ico
===================================================================
(Binary files differ)
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/NSIS_SBMLTestsuite.nsi
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/NSIS_SBMLTestsuite.nsi 2013-01-29 17:35:44 UTC (rev 16990)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/NSIS_SBMLTestsuite.nsi 2013-01-29 19:53:25 UTC (rev 16991)
@@ -2,7 +2,7 @@
; HM NIS Edit Wizard helper defines
!define PRODUCT_NAME "SBML Testsuite"
-!define PRODUCT_VERSION "1.0"
+!define PRODUCT_VERSION "3.0"
!define PRODUCT_PUBLISHER "SBML Team"
!define PRODUCT_WEB_SITE "http://sbml.org/Software/SBML_Test_Suite"
!define PRODUCT_DIR_REGKEY "Software\Microsoft\Windows\CurrentVersion\App Paths\SBMLTestSuite.exe"
@@ -53,6 +53,7 @@
File "stage\simple-xml-2.6.4.jar"
File "stage\swt.jar"
File "stage\testsuite-core.jar"
+ File "stage\opal-0.9.5.1.jar"
SectionEnd
Section -AdditionalIcons
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml 2013-01-29 17:35:44 UTC (rev 16990)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/build.xml 2013-01-29 19:53:25 UTC (rev 16991)
@@ -67,6 +67,7 @@
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="src" includes="data/**/*" />
+ <fileset dir="src" includes="org/sbml/testsuite/ui/resources/*" />
</jar>
</target>
<target name="stage-common" depends="jar">
@@ -74,6 +75,7 @@
<copy file="../testsuite-ui.jar" todir="stage" />
<copy file="../testsuite-core.jar" todir="stage" />
<copy file="libs/swt.jar" todir="stage" />
+ <copy file="libs/opal-0.9.5.1.jar" todir="stage" />
<copy file="libs/org.swtchart_0.7.0.v20110128.jar" todir="stage" />
<copy file="libs/simple-xml-2.6.4.jar" todir="stage" />
</target>
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/createInstaller.bat
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/createInstaller.bat 2013-01-29 17:35:44 UTC (rev 16990)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/createInstaller.bat 2013-01-29 19:53:25 UTC (rev 16991)
@@ -1,6 +1,6 @@
@echo off
REM ADJUST THE FOLLOWING TO MEET YOUR ENVIRONMENT
-SET JAVA_HOME=C:\Program Files (x86)\Java\jdk1.7.0_04
+SET JAVA_HOME=C:\Program Files (x86)\Java\jdk1.7.0_09
SET L4J=C:\Program Files (x86)\Launch4j\launch4jc.exe
SET ANT=C:\Program Files\apache-ant-1.8.4\bin\ant.bat
SET NSIS=C:\Program Files (x86)\NSIS\makensis.exe
Modified: trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml
===================================================================
--- trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml 2013-01-29 17:35:44 UTC (rev 16990)
+++ trunk/test-suite/src/front-ends/new-standalone/testsuite-ui/testsuite-l4j.xml 2013-01-29 19:53:25 UTC (rev 16991)
@@ -1,7 +1,7 @@
<launch4jConfig>
<dontWrapJar>false</dontWrapJar>
<headerType>gui</headerType>
- <jar>stage\testsuite_ui.jar</jar>
+ <jar>stage\testsuite-ui.jar</jar>
<outfile>.\stage\SBMLTestSuite.exe</outfile>
<errTitle></errTitle>
<cmdLine></cmdLine>
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