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[sbml-svn] SF.net SVN: sbml:[18331] trunk/libsbml/src/sbml/packages/comp/util
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From: <luc...@us...> - 2013-08-24 00:25:22
|
Revision: 18331
http://sourceforge.net/p/sbml/code/18331
Author: luciansmith
Date: 2013-08-24 00:25:19 +0000 (Sat, 24 Aug 2013)
Log Message:
-----------
* Many more tests for flattening models with unknown namespaces.
* Almost fixed a bug in flattening where if an unknown namespace/package came in, but flattening failed, the document would be changed. Stymied by the lack of ability to set the 'required' flag for unknown packages.
Modified Paths:
--------------
trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.h
trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp
trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningUnknownPackageRefs.cpp
Added Paths:
-----------
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9_flat.xml
Modified: trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp 2013-08-23 06:53:54 UTC (rev 18330)
+++ trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp 2013-08-24 00:25:19 UTC (rev 18331)
@@ -65,6 +65,7 @@
CompFlatteningConverter::CompFlatteningConverter() : SBMLConverter()
+ , mDisabledPackages()
{
}
@@ -73,6 +74,7 @@
CompFlatteningConverter::CompFlatteningConverter
(const CompFlatteningConverter& orig) :
SBMLConverter(orig)
+ , mDisabledPackages(orig.mDisabledPackages)
{
}
@@ -141,6 +143,7 @@
if (canFlatten == false)
{
+ restoreNamespaces();
return LIBSBML_OPERATION_FAILED;
}
@@ -179,6 +182,7 @@
if (errors > 0)
{
+ restoreNamespaces();
return LIBSBML_CONV_INVALID_SRC_DOCUMENT;
}
}
@@ -186,6 +190,7 @@
if (modelPlugin==NULL)
{
+ restoreNamespaces();
return LIBSBML_OPERATION_FAILED;
}
@@ -205,6 +210,7 @@
if (flatmodel == NULL)
{
//'flattenModel' sets its own error messages.
+ restoreNamespaces();
return LIBSBML_OPERATION_FAILED;
}
@@ -240,6 +246,7 @@
result = reconstructDocument(flatmodel, *(dummy) );
if (result != LIBSBML_OPERATION_SUCCESS)
{
+ restoreNamespaces();
return result;
}
@@ -280,6 +287,7 @@
}
}
delete dummy;
+ restoreNamespaces();
return LIBSBML_CONV_INVALID_SRC_DOCUMENT;
}
else
@@ -303,6 +311,7 @@
if (result != LIBSBML_OPERATION_SUCCESS)
{
+ restoreNamespaces();
return result;
}
@@ -473,7 +482,7 @@
}
bool
-CompFlatteningConverter::canBeFlattened() const
+CompFlatteningConverter::canBeFlattened()
{
bool canFlatten = true;
@@ -547,7 +556,8 @@
{
unsigned int warningnumber = CompFlatteningNotRecognisedNotReqd;
std::string message = "The ";
- if (mDocument->getPackageRequired(ns->getURI(i))) {
+ bool required = mDocument->getPackageRequired(ns->getURI(i));
+ if (required) {
message += "required ";
warningnumber = CompFlatteningNotRecognisedReqd;
}
@@ -556,8 +566,11 @@
if (getIgnorePackages())
{
//LS DEBUG: This will change the original document even if flattening fails for some other reason (BUG)
- mDocument->enablePackageInternal(ns->getURI(i),
- ns->getPrefix(i), false);
+ string nsURI = ns->getURI(i);
+ string nsPrefix = ns->getPrefix(i);
+ mDocument->enablePackageInternal(nsURI, nsPrefix, false);
+ mDisabledPackages.insert(make_pair(nsURI, nsPrefix));
+ mPackageRequired.insert(make_pair(nsURI, required));
}
mDocument->getErrorLog()->logPackageError("comp",
warningnumber,
@@ -572,8 +585,9 @@
{
unsigned int warningnumber = CompFlatteningNotImplementedNotReqd;
std::string message = "The ";
- if (static_cast<SBMLDocumentPlugin*>(mDocument->getPlugin(i))
- ->getRequired())
+ bool required = static_cast<SBMLDocumentPlugin*>(mDocument->getPlugin(i))
+ ->getRequired();
+ if (required)
{
message += "required ";
warningnumber = CompFlatteningNotImplementedReqd;
@@ -586,6 +600,8 @@
std::string pkgURI = mDocument->getPlugin(i)->getURI();
std::string prefix = mDocument->getPlugin(i)->getPrefix();
mDocument->disablePackage(pkgURI, prefix);
+ mDisabledPackages.insert(make_pair(pkgURI, prefix));
+ mPackageRequired.insert(make_pair(pkgURI, required));
}
mDocument->getErrorLog()->logPackageError("comp",
@@ -598,6 +614,21 @@
return canFlatten;
}
+void CompFlatteningConverter::restoreNamespaces()
+{
+ for (set<pair<string, string> >::iterator pkg = mDisabledPackages.begin();
+ pkg != mDisabledPackages.end(); pkg++)
+ {
+ mDocument->enablePackageInternal((*pkg).first, (*pkg).second, true);
+ }
+ for (set<pair<string, bool> >::iterator pkg = mPackageRequired.begin();
+ pkg != mPackageRequired.end(); pkg++)
+ {
+ //Note: the following does not work for unrecognized packages. LS DEBUG
+ mDocument->setPackageRequired((*pkg).first, (*pkg).second);
+ }
+}
+
/** @cond doxygenCOnly */
Modified: trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.h 2013-08-23 06:53:54 UTC (rev 18330)
+++ trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.h 2013-08-24 00:25:19 UTC (rev 18331)
@@ -130,8 +130,13 @@
bool getPerformValidation() const;
- bool canBeFlattened() const;
+ bool canBeFlattened();
+ void restoreNamespaces();
+
+ std::set<std::pair<std::string, std::string> > mDisabledPackages;
+ std::set<std::pair<std::string, bool > > mPackageRequired;
+
};
LIBSBML_CPP_NAMESPACE_END
Modified: trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp 2013-08-23 06:53:54 UTC (rev 18330)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp 2013-08-24 00:25:19 UTC (rev 18331)
@@ -3619,7 +3619,49 @@
}
END_TEST
+START_TEST(test_comp_flatten_invalid77)
+{
+ ConversionProperties* props = new ConversionProperties();
+
+ props->addOption("flatten comp");
+ props->addOption("perform validation", false);
+ SBMLConverter* converter =
+ SBMLConverterRegistry::getInstance().getConverterFor(*props);
+
+ // load document
+ string dir(TestDataDirectory);
+ string fileName = dir + "replacedby_unknown.xml";
+ SBMLDocument* doc = readSBMLFromFile(fileName.c_str());
+ string origdoc = writeSBMLToString(doc);
+
+ // fail if there is no model
+ //(readSBMLFromFile always returns a valid document)
+ fail_unless(doc->getModel() != NULL);
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(doc->getNumErrors() == 1);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+
+ converter->setDocument(doc);
+ int result = converter->convert();
+ string newdoc = writeSBMLToString(doc);
+
+ fail_unless( result == LIBSBML_OPERATION_FAILED);
+ //fail_unless(newdoc == origdoc); //Failing to convert should always leave the original document intact.
+
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompModelFlatteningFailed) == true);
+ fail_unless(errors->contains(CompIdRefMustReferenceObject) == true);
+
+ delete doc;
+ delete converter;
+}
+END_TEST
+
+
Suite *
create_suite_TestFlatteningErrorMessages (void)
{
@@ -3702,6 +3744,7 @@
tcase_add_test(tcase, test_comp_flatten_invalid74);
tcase_add_test(tcase, test_comp_flatten_invalid75);
tcase_add_test(tcase, test_comp_flatten_invalid76);
+ tcase_add_test(tcase, test_comp_flatten_invalid77);
tcase_add_test(tcase, test_comp_flatten_invalid_core);
suite_add_tcase(suite, tcase);
Modified: trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningUnknownPackageRefs.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningUnknownPackageRefs.cpp 2013-08-23 06:53:54 UTC (rev 18330)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningUnknownPackageRefs.cpp 2013-08-24 00:25:19 UTC (rev 18331)
@@ -87,8 +87,8 @@
*/
string newModel = writeSBMLToString(doc);
- string outfile = filename + "SOMETHING.flat.xml";
- writeSBMLToFile(doc, outfile.c_str());
+ //string outfile = filename + "unknown_flat.xml";
+ //writeSBMLToFile(doc, outfile.c_str());
string ffile = filename + file2;
SBMLDocument* fdoc = readSBMLFromFile(ffile.c_str());
string flatModel = writeSBMLToString(fdoc);
@@ -128,7 +128,259 @@
}
END_TEST
+START_TEST (test_comp_flatten_unknown_3)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown3.xml", "unknown3_flat.xml");
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_4)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown4.xml", "unknown4_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_5)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown5.xml", "unknown5_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_6)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown6.xml", "unknown6_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_7)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown7.xml", "unknown7_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_8)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown8.xml", "unknown8_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_9)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown9.xml", "unknown9_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_10)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown10.xml", "unknown10_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_11)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown11.xml", "unknown11_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_12)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown12.xml", "unknown12_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_13)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown13.xml", "unknown13_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_14)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown14.xml", "unknown14_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_15)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown15.xml", "unknown15_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_16)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown16.xml", "unknown16_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_17)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown17.xml", "unknown17_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_18)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown18.xml", "unknown18_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_19)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown19.xml", "unknown19_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_20)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown20.xml", "unknown20_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+
Suite *
create_suite_TestFlatteningUnknownPackageRefs (void)
{
@@ -137,6 +389,24 @@
tcase_add_test(tcase, test_comp_flatten_unknown_1);
tcase_add_test(tcase, test_comp_flatten_unknown_2);
+ tcase_add_test(tcase, test_comp_flatten_unknown_3);
+ tcase_add_test(tcase, test_comp_flatten_unknown_4);
+ tcase_add_test(tcase, test_comp_flatten_unknown_5);
+ tcase_add_test(tcase, test_comp_flatten_unknown_6);
+ tcase_add_test(tcase, test_comp_flatten_unknown_7);
+ tcase_add_test(tcase, test_comp_flatten_unknown_8);
+ tcase_add_test(tcase, test_comp_flatten_unknown_9);
+ tcase_add_test(tcase, test_comp_flatten_unknown_10);
+ tcase_add_test(tcase, test_comp_flatten_unknown_11);
+ tcase_add_test(tcase, test_comp_flatten_unknown_12);
+ tcase_add_test(tcase, test_comp_flatten_unknown_13);
+ tcase_add_test(tcase, test_comp_flatten_unknown_14);
+ tcase_add_test(tcase, test_comp_flatten_unknown_15);
+ tcase_add_test(tcase, test_comp_flatten_unknown_16);
+ tcase_add_test(tcase, test_comp_flatten_unknown_17);
+ tcase_add_test(tcase, test_comp_flatten_unknown_18);
+ tcase_add_test(tcase, test_comp_flatten_unknown_19);
+ tcase_add_test(tcase, test_comp_flatten_unknown_20);
suite_add_tcase(suite, tcase);
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:portRef="y_port" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:portRef="y_port"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:portRef="y_port"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="y" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="y" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:portRef="y_port" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:portRef="y_port" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:portRef="y_port"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:portRef="y_port"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="y" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="y" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:portRef="y_port" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
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