END_TEST
START_TEST ( test_ModelHistory_copyConstructor )
{
ModelHistory * mh = new ModelHistory();
ModelCreator *mc = new ModelCreator();
mc->setFamilyName("Keating");
mc->setGivenName("Sarah");
mc->setEmail("*****@*****.**");
mh->addCreator(mc);
delete mc;
Date * date = new Date(2005, 12, 30, 12, 15, 45, 1, 2, 0);
mh->setCreatedDate(date);
delete date;
fail_unless(mh->getCreatedDate()->getMonth() == 12);
fail_unless(mh->getCreatedDate()->getSecond() == 45);
fail_unless(static_cast <ModelCreator*>
(mh->getListCreators()->get(0))->getFamilyName() == "Keating");
ModelHistory* mh2=new ModelHistory(*mh);
fail_unless(mh2->getCreatedDate()->getMonth() == 12);
fail_unless(mh2->getCreatedDate()->getSecond() == 45);
fail_unless(static_cast <ModelCreator*>(mh2->getListCreators()->get(0))->getFamilyName() == "Keating");
delete mh2;
delete mh;
}
END_TEST
START_TEST (test_Validation_ModelHistory3)
{
ModelHistory * mh = new ModelHistory();
fail_unless(mh != NULL);
fail_unless (!(mh->hasRequiredAttributes()));
Date * date = new Date(2007, 12, 30, 12, 15, 45, 1, 2, 0);
mh->setCreatedDate(date);
fail_unless (!(mh->hasRequiredAttributes()));
mh->setModifiedDate(date);
fail_unless (!(mh->hasRequiredAttributes()));
ModelCreator * mc = new ModelCreator();
mc->setFamilyName("Keating");
mh->addCreator(mc);
fail_unless (!(mh->hasRequiredAttributes()));
delete mh;
}
int
main (int argc, char *argv[])
{
SBMLDocument* d;
unsigned int errors;
if (argc != 3)
{
cout << endl
<< " usage: addModelHistory <input-filename> <output-filename>" << endl
<< endl;
return 2;
}
d = readSBML(argv[1]);
errors = d->getNumErrors();
if (errors > 0)
{
cout << "Read Error(s):" << endl;
d->printErrors(cout);
cout << "Correct the above and re-run." << endl;
}
else
{
ModelHistory * h = new ModelHistory();
ModelCreator *c = new ModelCreator();
c->setFamilyName("Keating");
c->setGivenName("Sarah");
c->setEmail("*****@*****.**");
c->setOrganization("University of Hertfordshire");
int status = h->addCreator(c);
printStatus("Status for addCreator: ", status);
Date * date = new Date("1999-11-13T06:54:32");
Date * date2 = new Date("2007-11-30T06:54:00-02:00");
status = h->setCreatedDate(date);
printStatus("Set created date: ", status);
status = h->setModifiedDate(date2);
printStatus("Set modified date: ", status);
status = d->getModel()->setModelHistory(h);
printStatus("Set model history: ", status);
writeSBML(d, argv[2]);
}
delete d;
return errors;
}
END_TEST
START_TEST (test_RDFAnnotation2_modelWithHistoryAndMultipleModifiedDates)
{
ModelHistory * h = new ModelHistory();
ModelCreator *c = new ModelCreator();
c->setFamilyName("Keating");
c->setGivenName("Sarah");
h->addCreator(c);
Date * d = new Date(2005, 2, 2, 14, 56, 11);
h->setCreatedDate(d);
h->addModifiedDate(d);
h->addModifiedDate(d);
m2->unsetModelHistory();
m2->setModelHistory(h);
XMLNode *ann = RDFAnnotationParser::parseModelHistory(m2);
const char * expected =
"<annotation>\n"
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
" <rdf:Description rdf:about=\"#_000001\">\n"
" <dc:creator rdf:parseType=\"Resource\">\n"
" <rdf:Bag>\n"
" <rdf:li rdf:parseType=\"Resource\">\n"
" <vCard:N rdf:parseType=\"Resource\">\n"
" <vCard:Family>Keating</vCard:Family>\n"
" <vCard:Given>Sarah</vCard:Given>\n"
" </vCard:N>\n"
" </rdf:li>\n"
" </rdf:Bag>\n"
" </dc:creator>\n"
" <dcterms:created rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n"
" </dcterms:created>\n"
" <dcterms:modified rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n"
" </dcterms:modified>\n"
" <dcterms:modified rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n"
" </dcterms:modified>\n"
" </rdf:Description>\n"
" </rdf:RDF>\n"
"</annotation>";
fail_unless( equals(expected, ann->toXMLString().c_str()) );
delete c;
delete d;
delete h;
delete ann;
}
END_TEST
START_TEST ( test_ModelCreator_copyConstructor )
{
ModelCreator * mc = new ModelCreator();
mc->setFamilyName("Keating");
mc->setEmail("*****@*****.**");
fail_unless(mc->getFamilyName() == "Keating");
fail_unless(mc->getEmail() == "*****@*****.**");
ModelCreator* mc2=new ModelCreator(*mc);
fail_unless(mc2->getFamilyName() == "Keating");
fail_unless(mc2->getEmail() == "*****@*****.**");
delete mc2;
delete mc;
}
END_TEST
START_TEST ( test_ModelCreator_assignmentOperator )
{
ModelCreator * mc = new ModelCreator();
mc->setFamilyName("Keating");
mc->setEmail("*****@*****.**");
fail_unless(mc->getFamilyName() == "Keating");
fail_unless(mc->getEmail() == "*****@*****.**");
ModelCreator* mc2=new ModelCreator();
(*mc2) = *mc;
fail_unless(mc2->getFamilyName() == "Keating");
fail_unless(mc2->getEmail() == "*****@*****.**");
delete mc2;
delete mc;
}
void Billboard_Test::Init(Scene * scene)
{
BillboardPtr ptr = scene->AddBillboard();
Billboard * b = ptr.Get();
b->SetSize(20.0f, 20.0f);
b->UseDiffuseTexture(true);
b->SetDiffuseTexture("assets/fire.png");
StaticVert verts[4];
verts[0].pos = Vector3(-1.0f, -1.0f, 0.0f);
verts[1].pos = Vector3(-1.0f, 1.0f, 0.0f);
verts[2].pos = Vector3(1.0f, 1.0f, 0.0f);
verts[3].pos = Vector3(1.0f, -1.0f, 0.0f);
verts[0].u = 0.0f;
verts[0].v = 1.0f;
verts[1].u = 0.0f;
verts[1].v = 0.0f;
verts[2].u = 1.0f;
verts[2].v = 0.0f;
verts[3].u = 1.0f;
verts[3].v = 1.0f;
unsigned int ind[] = { 0, 1, 3, 1, 3, 2 };
ModelCreator<StaticVert> creator;
creator.StartMesh();
creator.SetTopology(D3D11_PRIMITIVE_TOPOLOGY_TRIANGLELIST);
creator.SetDrawMethod(DM_DRAW_INDEXED);
creator.SetVertexBuffer(verts, sizeof(verts), sizeof(StaticVert));
creator.SetIndexBuffer(ind, 6);
creator.EndMesh();
StaticEntityPtr triPtr = scene->AddStaticEntity(creator, "tri");
StaticEntity * tri = triPtr.Get();
tri->Illuminate(false);
tri->SetPosition(50.0f, 0.0f, 0.0f);
tri->SetScale(20.0f, 20.0f, 2.0f);
Material * mat = tri->GetMaterial(0);
mat->UseDiffuseMap(true);
mat->SetDiffuseMap("assets/fire.png");
mat->SetEmmisivePower(1);
}
END_TEST
START_TEST (test_Validation_ModelCreator)
{
ModelCreator * mc = new ModelCreator();
fail_unless(mc != NULL);
fail_unless (!(mc->hasRequiredAttributes()));
mc->setEmail("k123");
fail_unless (!(mc->hasRequiredAttributes()));
mc->setFamilyName("Keating");
fail_unless (!(mc->hasRequiredAttributes()));
mc->setGivenName("Sarah");
fail_unless (mc->hasRequiredAttributes());
delete mc;
}
END_TEST
START_TEST ( test_ModelCreator_clone )
{
ModelCreator * mc = new ModelCreator();
mc->setFamilyName("Keating");
mc->setEmail("*****@*****.**");
fail_unless(mc->getFamilyName() == "Keating");
fail_unless(mc->getEmail() == "*****@*****.**");
ModelCreator* mc2 = static_cast<ModelCreator*>(mc->clone());
fail_unless(mc2->getFamilyName() == "Keating");
fail_unless(mc2->getEmail() == "*****@*****.**");
delete mc2;
delete mc;
}
void Object_Picking_Test::CreateLine(Vector3 begin, Vector3 end)
{
StaticVert verts[2];
verts[0].pos = begin;
verts[1].pos = end;
ModelCreator<StaticVert> modelCreator;
modelCreator.StartMesh();
modelCreator.SetDrawMethod(DM_DRAW);
modelCreator.SetTopology(D3D10_PRIMITIVE_TOPOLOGY_LINELIST);
modelCreator.SetVertexBuffer(verts, sizeof(verts), sizeof(StaticVert));
modelCreator.EndMesh();
StaticEntityPtr linePtr = scene->AddStaticEntity(modelCreator, "line " + std::to_string(currentBox));
StaticEntity * line = linePtr.Get();
line->Illuminate(false);
Material * mat = line->GetMaterial(0);
mat->UseDiffuseMap(false);
mat->SetDiffuseColor(Color::Red());
currentBox++;
}
/*
* takes a Model creator information
* and creates the RDF annotation
*/
XMLNode *
RDFAnnotationParser::parseModelHistory(const SBase *object)
{
if (object->getLevel() < 3 && object->getTypeCode() != SBML_MODEL)
{
return NULL;
}
ModelHistory * history = object->getModelHistory();
if (history == NULL)
{
return NULL;
}
XMLNode *description = createRDFDescription(object);
/* create the basic triples */
XMLTriple li_triple = XMLTriple("li",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLTriple bag_triple = XMLTriple("Bag",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLTriple creator_triple = XMLTriple("creator",
"http://purl.org/dc/elements/1.1/",
"dc");
XMLTriple N_triple = XMLTriple("N",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Family_triple = XMLTriple("Family",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Given_triple = XMLTriple("Given",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Email_triple = XMLTriple("EMAIL",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Org_triple = XMLTriple("ORG",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple Orgname_triple = XMLTriple("Orgname",
"http://www.w3.org/2001/vcard-rdf/3.0#",
"vCard");
XMLTriple created_triple = XMLTriple("created",
"http://purl.org/dc/terms/",
"dcterms");
XMLTriple modified_triple = XMLTriple("modified",
"http://purl.org/dc/terms/",
"dcterms");
XMLTriple W3CDTF_triple = XMLTriple("W3CDTF",
"http://purl.org/dc/terms/",
"dcterms");
XMLTriple empty_triple = XMLTriple( "", "", "");
/* attributes */
XMLAttributes blank_att = XMLAttributes();
XMLAttributes parseType_att = XMLAttributes();
parseType_att.add("rdf:parseType", "Resource");
/* tokens */
XMLToken bag_token = XMLToken(bag_triple, blank_att);
XMLToken li_token = XMLToken(li_triple, parseType_att);
// for L2V4 it was realised that it was invalid for the creator
// to have a parseType attribute
XMLToken creator_token;
if (object->getLevel() > 2 ||
(object->getLevel() == 2 && object->getVersion() > 3))
{
creator_token = XMLToken(creator_triple, blank_att);
}
else
{
creator_token = XMLToken(creator_triple, parseType_att);
}
XMLToken N_token = XMLToken(N_triple, parseType_att);
XMLToken created_token = XMLToken(created_triple, parseType_att);
XMLToken modified_token = XMLToken(modified_triple, parseType_att);
XMLToken Family_token = XMLToken(Family_triple, blank_att);
XMLToken Given_token = XMLToken(Given_triple, blank_att);
XMLToken Email_token = XMLToken(Email_triple, blank_att);
// for L2V4 it was realised that the VCard:ORG
// should have a parseType attribute
XMLToken Org_token;
if (object->getLevel() > 2 ||
(object->getLevel() == 2 && object->getVersion() > 3))
{
Org_token = XMLToken(Org_triple, parseType_att);
}
else
{
Org_token = XMLToken(Org_triple, blank_att);
}
XMLToken Orgname_token = XMLToken(Orgname_triple, blank_att);
XMLToken W3CDTF1_token = XMLToken(W3CDTF_triple, blank_att);
XMLToken W3CDTF2_token = XMLToken(W3CDTF_triple, blank_att);
XMLToken empty_token = XMLToken("");
/* nodes */
XMLNode bag = XMLNode(bag_token);
XMLNode created = XMLNode(created_token);
XMLNode modified= XMLNode(modified_token);
XMLNode W3CDTF1 = XMLNode(W3CDTF1_token);
XMLNode W3CDTF2 = XMLNode(W3CDTF2_token);
//
// The following XMLNode objects are used only
// in the for loop below (for each ModelCreator object
// in ModelHistory object) and reset in each step.
// Thus, they are defined only in the block in which
// they are used to avoid a memory leak.
//
// XMLNode * N
// XMLNode * Email
// XMLNode * Org
// XMLNode Family;
// XMLNode Given
// XMLNode Orgname
// XMLNode li
//
/* now add the data from the ModelHistory */
for (unsigned int n = 0; n < history->getNumCreators(); n++)
{
XMLNode * N = 0;
XMLNode * Email = 0;
XMLNode * Org = 0;
ModelCreator* c = history->getCreator(n);
if (c->isSetFamilyName())
{
XMLNode empty(empty_token);
empty.append(c->getFamilyName());
XMLNode Family(Family_token);
Family.addChild(empty);
N = new XMLNode(N_token);
N->addChild(Family);
}
if (c->isSetGivenName())
{
XMLNode empty(empty_token);
empty.append(c->getGivenName());
XMLNode Given(Given_token);
Given.addChild(empty);
if (!N)
{
N = new XMLNode(N_token);
}
N->addChild(Given);
}
if (c->isSetEmail())
{
XMLNode empty(empty_token);
empty.append(c->getEmail());
Email = new XMLNode(Email_token);
Email->addChild(empty);
}
if (c->isSetOrganisation())
{
XMLNode empty(empty_token);
empty.append(c->getOrganisation());
XMLNode Orgname(Orgname_token);
Orgname.addChild(empty);
Org = new XMLNode(Org_token);
Org->addChild(Orgname);
}
XMLNode li(li_token);
if (N)
{
li.addChild(*N);
delete N;
}
if (Email)
{
li.addChild(*Email);
delete Email;
}
if (Org)
{
li.addChild(*Org);
delete Org;
}
if (c->getAdditionalRDF())
{
li.addChild(*(c->getAdditionalRDF()));
}
bag.addChild(li);
}
XMLNode creator(creator_token);
creator.addChild(bag);
description->addChild(creator);
/* created date */
if (history->isSetCreatedDate())
{
XMLNode empty(empty_token);
empty.append(history->getCreatedDate()->getDateAsString());
W3CDTF1.addChild(empty);
created.addChild(W3CDTF1);
description->addChild(created);
}
/* modified date */
if (history->isSetModifiedDate())
{
XMLNode empty(empty_token);
empty.append(history->getModifiedDate(0)->getDateAsString());
W3CDTF2.addChild(empty);
modified.addChild(W3CDTF2);
description->addChild(modified);
for (unsigned int n = 1; n < history->getNumModifiedDates(); n++)
{
XMLNode empty(empty_token);
W3CDTF2.removeChildren();
modified.removeChildren();
empty.append(history->getModifiedDate(n)->getDateAsString());
W3CDTF2.addChild(empty);
modified.addChild(W3CDTF2);
description->addChild(modified);
}
}
// add CVTerms here
XMLNode *CVTerms = createCVTerms(object);
if (CVTerms)
{
for (unsigned int i = 0; i < CVTerms->getNumChildren(); i++)
{
description->addChild(CVTerms->getChild(i));
}
delete CVTerms;
}
XMLNode * RDF = createRDFAnnotation();
RDF->addChild(*description);
delete description;
XMLNode *ann = createAnnotation();
ann->addChild(*RDF);
delete RDF;
return ann;
}
END_TEST
START_TEST (test_RDFAnnotation2_modelWithHistoryAndCVTerms)
{
ModelHistory * h = new ModelHistory();
ModelCreator *c = new ModelCreator();
c->setFamilyName("Keating");
c->setGivenName("Sarah");
h->addCreator(c);
Date *d = new Date(2008, 11, 17, 18, 37, 0, 0, 0, 0);
h->setCreatedDate(d);
h->setModifiedDate(d);
m2->unsetModelHistory();
m2->setModelHistory(h);
CVTerm *cv = new CVTerm();
cv->setQualifierType(BIOLOGICAL_QUALIFIER);
cv->setBiologicalQualifierType(BQB_IS_VERSION_OF);
cv->addResource("http://www.geneontology.org/#GO:0005892");
m2->addCVTerm(cv);
XMLNode *ann = RDFAnnotationParser::parseModelHistory(m2);
const char * expected =
"<annotation>\n"
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
" <rdf:Description rdf:about=\"#_000001\">\n"
" <dc:creator rdf:parseType=\"Resource\">\n"
" <rdf:Bag>\n"
" <rdf:li rdf:parseType=\"Resource\">\n"
" <vCard:N rdf:parseType=\"Resource\">\n"
" <vCard:Family>Keating</vCard:Family>\n"
" <vCard:Given>Sarah</vCard:Given>\n"
" </vCard:N>\n"
" </rdf:li>\n"
" </rdf:Bag>\n"
" </dc:creator>\n"
" <dcterms:created rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n"
" </dcterms:created>\n"
" <dcterms:modified rdf:parseType=\"Resource\">\n"
" <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n"
" </dcterms:modified>\n"
" <bqbiol:isVersionOf>\n"
" <rdf:Bag>\n"
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005892\"/>\n"
" </rdf:Bag>\n"
" </bqbiol:isVersionOf>\n"
" </rdf:Description>\n"
" </rdf:RDF>\n"
"</annotation>";
if (ann != NULL)
{
fail_unless( equals(expected, ann->toXMLString().c_str()) );
}
else
{
fail("parseModelHistory failed");
}
}
StaticEntityPtr Object_Picking_Test::CreateBBox(StaticEntityPtr ptr)
{
AABB bbox = ptr.Get()->GetAABB();
Vector3 min = bbox.min;
Vector3 max = bbox.max;
StaticVert box[32];
box[0].pos = Vector3(min.x, max.y, min.z);
box[1].pos = Vector3(max.x, max.y, min.z);
box[2].pos = Vector3(max.x, max.y, min.z);
box[3].pos = Vector3(max.x, min.y, min.z);
box[4].pos = Vector3(max.x, min.y, min.z);
box[5].pos = Vector3(min.x,min.y,min.z);
box[6].pos = Vector3(min.x, min.y, min.z);
box[7].pos = Vector3(min.x, max.y, min.z);
box[8].pos = Vector3(min.x, max.y, max.z);
box[9].pos = Vector3(max.x, max.y, max.z);
box[10].pos = Vector3(max.x, max.y, max.z);
box[11].pos = Vector3(max.x, min.y, max.z);
box[12].pos = Vector3(max.x, min.y, max.z);
box[13].pos = Vector3(min.x, min.y, max.z);
box[14].pos = Vector3(min.x, min.y, max.z);
box[15].pos = Vector3(min.x, max.y, max.z);
box[16].pos = Vector3(max.x, max.y, min.z);
box[17].pos = Vector3(max.x, max.y, max.z);
box[18].pos = Vector3(max.x, max.y, max.z);
box[19].pos = Vector3(max.x, min.y, max.z);
box[20].pos = Vector3(max.x, min.y, max.z);
box[21].pos = Vector3(max.x, min.y, min.z);
box[22].pos = Vector3(max.x, min.y, min.z);
box[23].pos = Vector3(max.x, max.y, min.z);
box[24].pos = Vector3(min.x, max.y, min.z);
box[25].pos = Vector3(min.x, max.y, max.z);
box[26].pos = Vector3(min.x, max.y, max.z);
box[27].pos = Vector3(min.x, min.y, max.z);
box[28].pos = Vector3(min.x, min.y, max.z);
box[29].pos = Vector3(min.x, min.y, min.z);
box[30].pos = Vector3(min.x, min.y, min.z);
box[31].pos = Vector3(min.x, max.y, min.z);
ModelCreator<StaticVert> cr;
cr.StartMesh();
cr.SetTopology(D3D11_PRIMITIVE_TOPOLOGY_LINELIST);
cr.SetDrawMethod(DM_DRAW);
cr.SetVertexBuffer(box, sizeof(box), sizeof(StaticVert));
cr.EndMesh();
StaticEntityPtr boxPtr = scene->AddStaticEntity(cr, "box" + std::to_string(currentBox));
StaticEntity * ent = boxPtr.Get();
Material * mat = ent->GetMaterial(0);
mat->SetDiffuseColor(Color::Blue());
currentBox++;
return boxPtr;
}
