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[sbml-svn] SF.net SVN: sbml:[8162] trunk/libsbml/src/sbml
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From: <sar...@us...> - 2008-09-11 22:56:35
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Revision: 8162
http://sbml.svn.sourceforge.net/sbml/?rev=8162&view=rev
Author: sarahkeating
Date: 2008-09-11 22:56:32 +0000 (Thu, 11 Sep 2008)
Log Message:
-----------
Two things happening:
1) future proofing the code that reads and writes attributes
2) adding tests for read/write of l2v2 and l2v3 components/attributes that have never been tested
Modified Paths:
--------------
trunk/libsbml/src/sbml/CompartmentType.cpp
trunk/libsbml/src/sbml/Constraint.cpp
trunk/libsbml/src/sbml/Delay.cpp
trunk/libsbml/src/sbml/Event.cpp
trunk/libsbml/src/sbml/test/TestReadFromFile6.cpp
trunk/libsbml/src/sbml/test/TestReadFromFile7.cpp
trunk/libsbml/src/sbml/test/TestWriteSBML.cpp
trunk/libsbml/src/sbml/test/test-data/l2v2-newComponents.xml
trunk/libsbml/src/sbml/test/test-data/l2v3-all.xml
Modified: trunk/libsbml/src/sbml/CompartmentType.cpp
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.cpp 2008-09-11 18:22:18 UTC (rev 8161)
+++ trunk/libsbml/src/sbml/CompartmentType.cpp 2008-09-11 22:56:32 UTC (rev 8162)
@@ -139,6 +139,12 @@
const unsigned int level = getLevel();
const unsigned int version = getVersion();
+ if (level < 2 || (level == 2 && version == 1))
+ {
+ logError(NotSchemaConformant, getLevel(), getVersion(),
+ "CompartmentType is not a valid component for this level/version.");
+ }
+
std::vector<std::string> expectedAttributes;
expectedAttributes.clear();
@@ -202,6 +208,12 @@
const unsigned int level = getLevel();
const unsigned int version = getVersion();
+ /* invalid level/version */
+ if (level < 2 || (level == 2 && version == 1))
+ {
+ return;
+ }
+
//
// id: SId { use="required" } (L2v2 ->)
//
Modified: trunk/libsbml/src/sbml/Constraint.cpp
===================================================================
--- trunk/libsbml/src/sbml/Constraint.cpp 2008-09-11 18:22:18 UTC (rev 8161)
+++ trunk/libsbml/src/sbml/Constraint.cpp 2008-09-11 22:56:32 UTC (rev 8162)
@@ -344,14 +344,18 @@
const unsigned int level = getLevel();
const unsigned int version = getVersion();
- std::vector<std::string> expectedAttributes;
- expectedAttributes.clear();
- if (level == 2 && version > 1)
+ if (level < 2 || (level == 2 && version == 1))
{
- expectedAttributes.push_back("metaid");
- expectedAttributes.push_back("sboTerm");
+ logError(NotSchemaConformant, getLevel(), getVersion(),
+ "Constraint is not a valid component for this level/version.");
+ return;
}
+ std::vector<std::string> expectedAttributes;
+ expectedAttributes.clear();
+ expectedAttributes.push_back("metaid");
+ expectedAttributes.push_back("sboTerm");
+
// check that all attributes are expected
for (int i = 0; i < attributes.getLength(); i++)
{
@@ -365,10 +369,9 @@
}
//
- // sboTerm: SBOTerm { use="optional" } (L2v2)
+ // sboTerm: SBOTerm { use="optional" } (L2v2 -> )
//
- if (level == 2 && version > 1)
- mSBOTerm = SBO::readTerm(attributes, this->getErrorLog());
+ mSBOTerm = SBO::readTerm(attributes, this->getErrorLog());
}
/** @endcond doxygen-libsbml-internal */
@@ -387,11 +390,16 @@
const unsigned int level = getLevel();
const unsigned int version = getVersion();
+ /* invalid level/version */
+ if (level < 2 || (level == 2 && version == 1))
+ {
+ return;
+ }
+
//
- // sboTerm: SBOTerm { use="optional" } (L2v2)
+ // sboTerm: SBOTerm { use="optional" } (L2v2 ->)
//
- if (level == 2 && version > 1)
- SBO::writeTerm(stream, mSBOTerm);
+ SBO::writeTerm(stream, mSBOTerm);
}
/** @endcond doxygen-libsbml-internal */
Modified: trunk/libsbml/src/sbml/Delay.cpp
===================================================================
--- trunk/libsbml/src/sbml/Delay.cpp 2008-09-11 18:22:18 UTC (rev 8161)
+++ trunk/libsbml/src/sbml/Delay.cpp 2008-09-11 22:56:32 UTC (rev 8162)
@@ -347,14 +347,18 @@
const unsigned int level = getLevel();
const unsigned int version = getVersion();
+ if (level < 2)
+ {
+ logError(NotSchemaConformant, getLevel(), getVersion(),
+ "Delay is not a valid component for this level/version.");
+ }
std::vector<std::string> expectedAttributes;
expectedAttributes.clear();
- if (level == 2)
+
+ expectedAttributes.push_back("metaid");
+ if (!(level == 2 && version < 3))
{
- if (version > 1)
- expectedAttributes.push_back("metaid");
- if (version > 2)
- expectedAttributes.push_back("sboTerm");
+ expectedAttributes.push_back("sboTerm");
}
// check that all attributes are expected
@@ -370,9 +374,9 @@
}
//
- // sboTerm: SBOTerm { use="optional" } (L2v2)
+ // sboTerm: SBOTerm { use="optional" } (L2v3 ->)
//
- if (level == 2 && version > 1)
+ if (!(level == 2 && version < 3))
mSBOTerm = SBO::readTerm(attributes, this->getErrorLog());
}
/** @endcond doxygen-libsbml-internal */
@@ -392,10 +396,15 @@
const unsigned int level = getLevel();
const unsigned int version = getVersion();
+ if (level < 2)
+ {
+ return;
+ }
+
//
- // sboTerm: SBOTerm { use="optional" } (L2v2)
+ // sboTerm: SBOTerm { use="optional" } (L2v3 ->)
//
- if (level == 2 && version > 1)
+ if (!(level == 2 && version < 3))
SBO::writeTerm(stream, mSBOTerm);
}
/** @endcond doxygen-libsbml-internal */
Modified: trunk/libsbml/src/sbml/Event.cpp
===================================================================
--- trunk/libsbml/src/sbml/Event.cpp 2008-09-11 18:22:18 UTC (rev 8161)
+++ trunk/libsbml/src/sbml/Event.cpp 2008-09-11 22:56:32 UTC (rev 8162)
@@ -533,23 +533,25 @@
const unsigned int level = getLevel();
const unsigned int version = getVersion();
+ if (level < 2)
+ {
+ logError(NotSchemaConformant, getLevel(), getVersion(),
+ "Event is not a valid component for this level/version.");
+ }
std::vector<std::string> expectedAttributes;
expectedAttributes.clear();
- if (level == 2)
+ expectedAttributes.push_back("metaid");
+ expectedAttributes.push_back("name");
+ expectedAttributes.push_back("id");
+
+ if (level == 2 && version < 3)
{
- expectedAttributes.push_back("metaid");
- expectedAttributes.push_back("name");
- expectedAttributes.push_back("id");
+ expectedAttributes.push_back("timeUnits");
+ }
- if (version < 3)
- {
- expectedAttributes.push_back("timeUnits");
- }
-
- if (version != 1)
- {
- expectedAttributes.push_back("sboTerm");
- }
+ if (!(level == 2 && version == 1))
+ {
+ expectedAttributes.push_back("sboTerm");
}
// check that all attributes are expected
@@ -565,7 +567,7 @@
}
//
- // id: SId { use="optional" } (L2v1, L2v2)
+ // id: SId { use="optional" } (L2v1 ->)
//
bool assigned = attributes.readInto("id", mId, getErrorLog(), false);
if (assigned && mId.size() == 0)
@@ -575,7 +577,7 @@
SBase::checkIdSyntax();
//
- // name: string { use="optional" } (L2v1, L2v2)
+ // name: string { use="optional" } (L2v1 ->)
//
attributes.readInto("name", mName);
@@ -583,14 +585,16 @@
// timeUnits: SId { use="optional" } (L2v1, L2v2)
// removed in l2v3
//
- attributes.readInto("timeUnits", mTimeUnits);
- SBase::checkUnitSyntax();
+ if (level == 2 && version < 3)
+ {
+ attributes.readInto("timeUnits", mTimeUnits);
+ SBase::checkUnitSyntax();
+ }
-
//
- // sboTerm: SBOTerm { use="optional" } (L2v2)
+ // sboTerm: SBOTerm { use="optional" } (L2v2 ->)
//
- if (level == 2 && version > 1)
+ if (!(level == 2 && version == 1))
mSBOTerm = SBO::readTerm(attributes, this->getErrorLog());
}
/** @endcond doxygen-libsbml-internal */
@@ -610,18 +614,23 @@
const unsigned int level = getLevel();
const unsigned int version = getVersion();
+ if (level < 2)
+ {
+ return;
+ }
+
//
- // id: SId { use="optional" } (L2v1, L2v2)
+ // id: SId { use="optional" } (L2v1 ->)
//
if (!mInternalIdOnly)
stream.writeAttribute("id", mId);
//
- // name: string { use="optional" } (L2v1, L2v2)
+ // name: string { use="optional" } (L2v1->)
//
stream.writeAttribute("name", mName);
- if (version < 3)
+ if (level == 2 && version < 3)
{
//
// timeUnits: SId { use="optional" } (L2v1, L2v2)
@@ -632,9 +641,9 @@
//
- // sboTerm: SBOTerm { use="optional" } (L2v2)
+ // sboTerm: SBOTerm { use="optional" } (L2v2 ->)
//
- if (level == 2 && version > 1)
+ if (!(level == 2 && version == 1))
SBO::writeTerm(stream, mSBOTerm);
}
/** @endcond doxygen-libsbml-internal */
Modified: trunk/libsbml/src/sbml/test/TestReadFromFile6.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestReadFromFile6.cpp 2008-09-11 18:22:18 UTC (rev 8161)
+++ trunk/libsbml/src/sbml/test/TestReadFromFile6.cpp 2008-09-11 22:56:32 UTC (rev 8162)
@@ -81,6 +81,9 @@
KineticLaw* kl;
UnitDefinition* ud;
Reaction* r1;
+ Constraint* con;
+
+ const ASTNode* ast;
std::string filename(TestDataDirectory);
filename += "l2v2-newComponents.xml";
@@ -135,6 +138,28 @@
fail_unless( ct != NULL , NULL );
fail_unless( ct->getId() == "mitochondria", NULL );
+ //<listOfConstraints>
+ // <constraint sboTerm="SBO:0000064">
+ // <math xmlns="http://www.w3.org/1998/Math/MathML">
+ // <apply>
+ // <lt/>
+ // <cn type="integer"> 1 </cn>
+ // <ci> cell </ci>
+ // </apply>
+ // </math>
+ // </constraint>
+ //</listOfConstraints>
+ fail_unless( m->getNumConstraints() == 1, NULL );
+
+ con = m->getConstraint(0);
+ fail_unless( con != NULL , NULL );
+ fail_unless(con->getSBOTerm() == 64, NULL);
+ fail_unless(con->getSBOTermID() == "SBO:0000064", NULL);
+
+ ast = con->getMath();
+ fail_unless(!strcmp(SBML_formulaToString(ast), "lt(1, cell)"), NULL);
+
+
///**
// * tests for the unit API functions
// */
Modified: trunk/libsbml/src/sbml/test/TestReadFromFile7.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestReadFromFile7.cpp 2008-09-11 18:22:18 UTC (rev 8161)
+++ trunk/libsbml/src/sbml/test/TestReadFromFile7.cpp 2008-09-11 22:56:32 UTC (rev 8162)
@@ -81,6 +81,12 @@
KineticLaw* kl;
UnitDefinition* ud;
Reaction* r1;
+ Constraint* con;
+ Event* e;
+ Delay* delay;
+ Trigger* t;
+
+ const ASTNode* ast;
std::string filename(TestDataDirectory);
filename += "l2v3-all.xml";
@@ -133,8 +139,78 @@
fail_unless( ct->getSBOTerm() == 236, NULL );
fail_unless( ct->getSBOTermID() == "SBO:0000236", NULL );
+ //<listOfConstraints>
+ // <constraint>
+ // <math xmlns="http://www.w3.org/1998/Math/MathML">
+ // <apply>
+ // <lt/>
+ // <ci> x </ci>
+ // <cn type="integer"> 3 </cn>
+ // </apply>
+ // </math>
+ // </constraint>
+ //</listOfConstraints>
+ fail_unless( m->getNumConstraints() == 1, NULL );
+ con = m->getConstraint(0);
+ fail_unless( con != NULL , NULL );
+ ast = con->getMath();
+ fail_unless(!strcmp(SBML_formulaToString(ast), "lt(x, 3)"), NULL);
+
+ //<event id="e1" sboTerm="SBO:0000231">
+ // <trigger>
+ // <math xmlns="http://www.w3.org/1998/Math/MathML">
+ // <apply>
+ // <lt/>
+ // <ci> x </ci>
+ // <cn type="integer"> 3 </cn>
+ // </apply>
+ // </math>
+ // </trigger>
+ // <delay sboTerm="SBO:0000064">
+ // <math xmlns="http://www.w3.org/1998/Math/MathML">
+ // <apply>
+ // <plus/>
+ // <ci> x </ci>
+ // <cn type="integer"> 3 </cn>
+ // </apply>
+ // </math>
+ // </delay>
+ // <listOfEventAssignments>
+ // <eventAssignment variable="a">
+ // <math xmlns="http://www.w3.org/1998/Math/MathML">
+ // <apply>
+ // <times/>
+ // <ci> x </ci>
+ // <ci> p3 </ci>
+ // </apply>
+ // </math>
+ // </eventAssignment>
+ // </listOfEventAssignments>
+ //</event>
+ fail_unless( m->getNumEvents() == 1, NULL );
+
+ e = m->getEvent(0);
+ fail_unless(e != NULL, NULL);
+
+ fail_unless(e->getId() == "e1", NULL);
+
+ fail_unless(e->getSBOTerm() == 231, NULL);
+ fail_unless(e->getSBOTermID() == "SBO:0000231");
+
+ fail_unless(e->isSetDelay(), NULL);
+
+ delay = e->getDelay();
+ fail_unless(delay != NULL, NULL);
+
+ fail_unless(delay->getSBOTerm() == 64, NULL);
+ fail_unless(delay->getSBOTermID() == "SBO:0000064");
+
+ ast = delay->getMath();
+ fail_unless(!strcmp(SBML_formulaToString(ast), "p + 3"), NULL);
+
+
///**
// * tests for the unit API functions
// */
Modified: trunk/libsbml/src/sbml/test/TestWriteSBML.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestWriteSBML.cpp 2008-09-11 18:22:18 UTC (rev 8161)
+++ trunk/libsbml/src/sbml/test/TestWriteSBML.cpp 2008-09-11 22:56:32 UTC (rev 8162)
@@ -26,6 +26,7 @@
#include <sstream>
#include <sbml/xml/XMLOutputStream.h>
+#include <sbml/xml/XMLNode.h>
#include <sbml/util/util.h>
#include <sbml/SBMLTypes.h>
@@ -1577,7 +1578,22 @@
END_TEST
+START_TEST (test_WriteSBML_Event_WithSBO)
+{
+ const char* expected = wrapXML("<event id=\"e\" sboTerm=\"SBO:0000076\"/>");
+
+ Event e;
+ e.setId("e");
+ e.setSBOTerm(76);
+
+ e.write(*XOS);
+
+ fail_unless( equals(expected) );
+}
+END_TEST
+
+
START_TEST (test_WriteSBML_Event_trigger)
{
const char* expected = wrapXML
@@ -1633,6 +1649,32 @@
END_TEST
+START_TEST (test_WriteSBML_Event_delayWithSBO)
+{
+ const char* expected = wrapXML
+ (
+ "<event id=\"e\">\n"
+ " <delay sboTerm=\"SBO:0000064\">\n"
+ " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
+ " <cn type=\"integer\"> 5 </cn>\n"
+ " </math>\n"
+ " </delay>\n"
+ "</event>"
+ );
+
+ Event e("e");
+ ASTNode *node = SBML_parseFormula("5");
+ Delay d(node);
+ d.setSBOTerm(64);
+ e.setDelay(&d);
+
+ e.write(*XOS);
+
+ fail_unless( equals(expected) );
+}
+END_TEST
+
+
START_TEST (test_WriteSBML_Event_both)
{
const char* expected = wrapXML
@@ -1749,7 +1791,96 @@
END_TEST
+START_TEST (test_WriteSBML_Constraint)
+{
+ D->setLevelAndVersion(2, 2);
+ const char* expected = wrapXML("<constraint sboTerm=\"SBO:0000064\"/>");
+
+
+ Constraint ct;
+ ct.setSBOTerm(64);
+ ct.setSBMLDocument(D);
+
+ ct.write(*XOS);
+
+ fail_unless( equals(expected) );
+}
+END_TEST
+
+
+START_TEST (test_WriteSBML_Constraint_math)
+{
+ const char* expected = wrapXML
+ (
+ "<constraint>\n"
+ " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
+ " <apply>\n"
+ " <leq/>\n"
+ " <ci> P1 </ci>\n"
+ " <ci> t </ci>\n"
+ " </apply>\n"
+ " </math>\n"
+ "</constraint>"
+ );
+
+ Constraint c;
+ ASTNode *node = SBML_parseFormula("leq(P1,t)");
+ c.setMath(node);
+
+ c.write(*XOS);
+
+ fail_unless( equals(expected) );
+}
+END_TEST
+
+
+START_TEST (test_WriteSBML_Constraint_full)
+{
+ const char* expected = wrapXML
+ (
+ "<constraint sboTerm=\"SBO:0000064\">\n"
+ " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
+ " <apply>\n"
+ " <leq/>\n"
+ " <ci> P1 </ci>\n"
+ " <ci> t </ci>\n"
+ " </apply>\n"
+ " </math>\n"
+ " <message>\n"
+ " <p xmlns=\"http://www.w3.org/1999/xhtml\"> Species P1 is out of range </p>\n"
+ " </message>\n"
+ "</constraint>"
+ );
+
+ Constraint c;
+ ASTNode *node = SBML_parseFormula("leq(P1,t)");
+ c.setMath(node);
+ c.setSBOTerm(64);
+
+ const XMLNode *text = XMLNode::convertStringToXMLNode(" Species P1 is out of range ");
+ XMLTriple triple = XMLTriple("p", "http://www.w3.org/1999/xhtml", "");
+ XMLAttributes att = XMLAttributes();
+ att.add("xmlns", "http://www.w3.org/1999/xhtml");
+
+ XMLNode *p = new XMLNode(triple, att);
+ p->addChild(*(text));
+
+ XMLTriple triple1 = XMLTriple("message", "", "");
+ XMLAttributes att1 = XMLAttributes();
+ XMLNode *message = new XMLNode(triple1, att1);
+
+ message->addChild(*(p));
+
+ c.setMessage(message);
+
+ c.write(*XOS);
+
+ fail_unless( equals(expected) );
+}
+END_TEST
+
+
START_TEST (test_WriteSBML_NaN)
{
const char* expected = wrapXML("<parameter id=\"p\" value=\"NaN\"/>");
@@ -2057,8 +2188,10 @@
// Event
tcase_add_test( tcase, test_WriteSBML_Event );
+ tcase_add_test( tcase, test_WriteSBML_Event_WithSBO );
tcase_add_test( tcase, test_WriteSBML_Event_trigger );
tcase_add_test( tcase, test_WriteSBML_Event_delay );
+ tcase_add_test( tcase, test_WriteSBML_Event_delayWithSBO );
tcase_add_test( tcase, test_WriteSBML_Event_both );
tcase_add_test( tcase, test_WriteSBML_Event_full );
@@ -2066,6 +2199,11 @@
tcase_add_test( tcase, test_WriteSBML_CompartmentType );
tcase_add_test( tcase, test_WriteSBML_CompartmentType_withSBO );
+ //Constraint
+ tcase_add_test( tcase, test_WriteSBML_Constraint );
+ tcase_add_test( tcase, test_WriteSBML_Constraint_math );
+ tcase_add_test( tcase, test_WriteSBML_Constraint_full );
+
// Miscellaneous
tcase_add_test( tcase, test_WriteSBML_NaN );
tcase_add_test( tcase, test_WriteSBML_INF );
Modified: trunk/libsbml/src/sbml/test/test-data/l2v2-newComponents.xml
===================================================================
--- trunk/libsbml/src/sbml/test/test-data/l2v2-newComponents.xml 2008-09-11 18:22:18 UTC (rev 8161)
+++ trunk/libsbml/src/sbml/test/test-data/l2v2-newComponents.xml 2008-09-11 22:56:32 UTC (rev 8162)
@@ -30,7 +30,7 @@
</initialAssignment>
</listOfInitialAssignments>
<listOfConstraints>
- <constraint>
+ <constraint sboTerm="SBO:0000064">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<lt/>
Modified: trunk/libsbml/src/sbml/test/test-data/l2v3-all.xml
===================================================================
--- trunk/libsbml/src/sbml/test/test-data/l2v3-all.xml 2008-09-11 18:22:18 UTC (rev 8161)
+++ trunk/libsbml/src/sbml/test/test-data/l2v3-all.xml 2008-09-11 22:56:32 UTC (rev 8162)
@@ -31,7 +31,7 @@
<speciesType id="gg"/>
</listOfSpeciesTypes>
<listOfCompartments>
- <compartment id="a" size="2.3" compartmentType="hh" sboTerm="SBO:0000236"/>
+ <compartment id="a" size="2.3" compartmentType="hh" sboTerm="SBO:0000236" constant="false"/>
</listOfCompartments>
<listOfSpecies>
<species id="s" compartment="a" initialAmount="0"/>
@@ -128,7 +128,7 @@
</reaction>
</listOfReactions>
<listOfEvents>
- <event>
+ <event id="e1" sboTerm="SBO:0000231">
<trigger>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
@@ -138,6 +138,15 @@
</apply>
</math>
</trigger>
+ <delay sboTerm="SBO:0000064">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <plus/>
+ <ci> p </ci>
+ <cn type="integer"> 3 </cn>
+ </apply>
+ </math>
+ </delay>
<listOfEventAssignments>
<eventAssignment variable="a">
<math xmlns="http://www.w3.org/1998/Math/MathML">
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