public void testParameterEdit() throws Exception {
ConfigurationContext configCtx = ConfigurationContextFactory.createEmptyConfigurationContext();
AxisConfiguration axisConfig = configCtx.getAxisConfiguration();
Parameter parameter = new Parameter();
parameter.setValue("true");
parameter.setName("enableMTOM");
axisConfig.addParameter(parameter);
parameter.setValue("true");
AxisServiceGroup serviceGroup = new AxisServiceGroupImpl();
serviceGroup.setName("testServiceGroup");
AxisService service = new AxisService();
service.setName("service");
serviceGroup.addService(service);
axisConfig.addServiceGroup(serviceGroup);
parameter = serviceGroup.getParameter("enableMTOM");
parameter.setValue("true");
Parameter para2 = serviceGroup.getParameter("enableMTOM");
assertEquals(para2.getValue(), "true");
Parameter test = new Parameter();
test.setName("test");
test.setValue("test");
serviceGroup.addParameter(test);
Parameter para = serviceGroup.getParameter("test");
assertNotNull(para);
assertEquals(para.getValue(), "test");
para.setValue("newValue");
para = serviceGroup.getParameter("test");
assertNotNull(para);
assertEquals(para.getValue(), "newValue");
}
public ParameterTable add(String pname, String pvalue, String desc) {
Parameter p = get(pname, false);
if (p != null) // update value
{
p.setValue(pvalue).setDesc(desc);
} else {
p = Parameter.by(pname);
p.setValue(pvalue).setDesc(desc);
synchronized (table) {
table.add(p);
}
}
return this;
}
public void testNodeAttributeEvent() {
TestAttributeListener l = new TestAttributeListener();
Node test = Node.ROOT_NODE.newInstance(testLibrary, "test");
test.addNodeAttributeListener(l);
// Setting the name to itself does not trigger an event.
test.setName("test");
assertEquals(0, l.nameCounter);
test.setName("newname");
assertEquals(1, l.nameCounter);
Parameter p1 = test.addParameter("p1", Parameter.Type.FLOAT);
assertEquals(1, l.parameterCounter);
p1.setName("parameter1");
assertEquals(2, l.parameterCounter);
// TODO: These trigger ParameterAttributeChanged
// p1.setBoundingMethod(Parameter.BoundingMethod.HARD);
// assertEquals(3, l.parameterCounter);
// p1.setMinimumValue(0F);
// assertEquals(4, l.parameterCounter);
// Changing the value does not trigger the event.
// The event only happens for metadata, not data.
// If you want to catch that, use DirtyListener.
p1.setValue(20F);
assertEquals(2, l.parameterCounter);
test.removeParameter("parameter1");
assertEquals(3, l.parameterCounter);
}
@Override
public Parameter getParameter(ParameterKey key) {
Connection connection = connectionDaoService.getRiceConnection();
try (PreparedStatement stmt =
setString(
4,
key.getApplicationId(),
setString(
3,
key.getName(),
setString(
2,
key.getComponentCode(),
setString(
1,
key.getNamespaceCode(),
connection.prepareStatement(
"SELECT VAL, PARM_DESC_TXT, PARM_TYP_CD, EVAL_OPRTR_CD "
+ " FROM KRCR_PARM_T WHERE NMSPC_CD = ? AND CMPNT_CD = ? AND PARM_NM = ? AND APPL_ID = ?")))));
ResultSet result = stmt.executeQuery()) {
if (result.next()) {
Parameter p = new Parameter();
p.setParameterKey(key);
p.setValue(result.getString(1));
p.setDescription(result.getString(2));
p.setParameterTypeCode(result.getString(3));
p.setEvaluationOperatorCode(result.getString(4));
return p;
}
return null;
} catch (SQLException e) {
throw new RuntimeException(e);
}
}
/* (non-Javadoc)
* @see java.lang.Object#clone()
*/
@Override
public Parameter clone() throws CloneNotSupportedException {
Parameter param = new Parameter(name);
param.setValue(value);
param.setHelp(help);
param.setReadOnly(readOnly);
return param;
}
@Test
public void testGettersAndSetters() {
Parameter p = new Parameter();
assertTrue(p.getName() == null);
assertTrue(p.getValue() == null);
p.setName("bob");
p.setValue("val");
assertTrue(p.getName().equals("bob"));
assertTrue(p.getValue().equals("val"));
}
private static List<Parameter> getParameters(ArrayList<CustomField> infos, Entry entry) {
List<Parameter> parameters = new ArrayList<>();
if (infos == null) return parameters;
for (CustomField info : infos) {
Parameter param = new Parameter();
param.setEntry(entry);
param.setKey(info.getName());
param.setValue(info.getValue());
parameters.add(param);
}
return parameters;
}
@Test
public void testAsString() {
Parameter p = new Parameter();
assertTrue(p.asString().equals("name=null,value=null"));
p.setName("bob");
assertTrue(p.asString().equals("name=bob,value=null"));
p.setValue("val");
assertTrue(p.asString().equals("name=bob,value=val"));
p.setName(null);
assertTrue(p.asString().equals("name=null,value=val"));
}
public Parameter clone() {
Parameter clone = null;
try {
clone = this.getClass().newInstance();
clone.setParameterList(parameterList);
clone.setName(getName());
clone.setValue(value);
} catch (InstantiationException exception) {
exception.printStackTrace();
} catch (IllegalAccessException exception) {
exception.printStackTrace();
}
return clone;
// Parameter clone = new DefaultParameter(this.processor, this.name);
}
/** @param args the command line arguments */
public static void main(String[] args) {
// TODO code application logic here
Model model;
String insertstmt;
String insertmodel = "",
insertspecies = "",
insertcompartment = "",
insertfunction = "",
insertunitdef = "",
insertunits = "",
insertreaction = "",
insertreactant = "",
insertproduct = "";
String insertmodifier = "",
insertklaw = "",
insertrules = "",
insertconstraint = "",
insertdelay = "",
inserttrigger = "",
insertevent = "",
inserteventassign = "",
insertparameter = "";
String insertstatement = "";
String server, user, password, dbname, filepath;
String Filedata = "";
String cwd = System.getProperty("user.dir");
if (args.length == 0) {
server = "localhost";
user = "******";
password = "******";
dbname = "sbmldb2";
/**
* Path to extract the SBML files from database, where cwd is
* "github\db2sbml\dbtosbml_standalone_Project\dbtosbml" so add a folder in this directory and
* mention folder name instead of extractedbm folder
*/
filepath = cwd + "\\extractedbm\\";
} else {
server = args[0];
user = args[1];
password = args[2];
dbname = args[3];
filepath = args[4];
}
try {
Filedata = readFileAsString(cwd + "\\sbmldbschema.sql");
} catch (Exception e) {
e.printStackTrace();
}
Mysqlconn sql = new Mysqlconn(server, user, password, dbname);
// String modelids.getId() = "MorrisonAllegra" ;
ASTNode math = null;
int level = 0, version = 0;
ArrayList<modellist> modelidlist = sql.getmodels();
insertstatement =
"LOCK TABLES `model` WRITE,`species` WRITE,`compartment` WRITE,`functiondefinition` WRITE,";
insertstatement =
insertstatement
+ "`listofunitdefinitions` WRITE,`listofunits` WRITE,`reaction` WRITE,`simplespeciesreference` WRITE,";
insertstatement =
insertstatement
+ "`modifierspeciesreference` WRITE,`kineticlaw` WRITE,`parameter` WRITE,`sbmlconstraint` WRITE,";
insertstatement =
insertstatement
+ "`event` WRITE,`sbmltrigger` WRITE,`delay` WRITE,`eventassignment` WRITE,`rules` WRITE"
+ ";";
for (modellist modelids : modelidlist) {
ArrayList<modellist> modellevel = sql.getmodeldetails(modelids.getId());
for (modellist modellv : modellevel) {
level = modellv.getlevel();
version = modellv.getversion();
}
SBMLDocument doc = new SBMLDocument(level, version);
ArrayList<modellist> modellists = sql.getmodeldetails(modelids.getId());
if (!modellists.isEmpty())
insertmodel =
insertmodel
+ "\nInsert Into model (id, name,SBML_level,version,notes,annotation) Values";
for (modellist models : modellists) {
insertmodel =
insertmodel
+ "(\'"
+ models.getId()
+ "\',\'"
+ models.getName()
+ "\',"
+ models.getlevel()
+ ","
+ models.getversion()
+ ",\'"
+ models.getnotes()
+ "\',\'"
+ models.getannotation().toString()
+ "\'),";
model = doc.createModel(models.getId());
model.setName(models.getName());
// System.out.println("model : " + models.getId());
// model.setNotes(models.getnotes()); // there is some null exception is command line run
// but run perfectly from netbeans so ommented out
if (!models.getannotation().equals("")) {
Annotation annot = new Annotation(models.getannotation().toString());
model.setAnnotation(annot);
}
doc.setModel(model);
}
if (!modellists.isEmpty()) {
insertmodel = insertmodel.substring(0, insertmodel.length() - 1);
insertmodel = insertmodel + ';';
}
// insertmodel = insertmodel + "\nUNLOCK TABLES;";
// System.out.println(insertmodel);
ArrayList<SpeciesList> specieslist = sql.getspecies(modelids.getId());
if (!specieslist.isEmpty())
insertspecies =
insertspecies
+ "\nInsert Into species (id, name, compartment, initialAmount, initialConcentration,substanceUnits,hasOnlySubstanceUnits,boundaryCondition,constant,conversionFactor,model_id,annotation) Values";
for (SpeciesList species : specieslist) {
insertspecies =
insertspecies
+ "(\'"
+ species.getId()
+ "\',\'"
+ species.getName()
+ "\',\'"
+ species.getcompartment()
+ "\',"
+ species.getia()
+ ","
+ species.getic()
+ ",\'"
+ species.getsu()
+ "\',"
+ species.gethosu()
+ ","
+ species.getbc()
+ ","
+ species.getconstant()
+ ","
+ species.getcf()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ species.getannotation()
+ "\'),";
Species sp = doc.getModel().createSpecies(species.getId());
sp.setName(species.getName());
sp.setCompartment(species.getcompartment());
sp.setConstant(species.getconstant());
sp.setInitialAmount(species.getia());
sp.setInitialConcentration(species.getic());
sp.setHasOnlySubstanceUnits(species.gethosu());
if (doc.getModel().getLevel() == 3) sp.setConversionFactor(species.getcf());
sp.setBoundaryCondition(species.getbc());
sp.setSubstanceUnits(species.getsu());
if (!species.getannotation().equals("")) {
Annotation annot = new Annotation(species.getannotation().toString());
sp.setAnnotation(annot);
}
// doc.getModel().addSpecies(sp) ;
}
if (!specieslist.isEmpty()) {
insertspecies = insertspecies.substring(0, insertspecies.length() - 1);
insertspecies = insertspecies + ';';
}
ArrayList<CompartmentList> complist = sql.getcompartments(modelids.getId());
if (!complist.isEmpty())
insertcompartment =
insertcompartment
+ "\nInsert Into compartment (id, name,constant,model_id,spacialDimensions,size,units) Values";
for (CompartmentList comp : complist) {
insertcompartment =
insertcompartment
+ "(\'"
+ comp.getId()
+ "\',\'"
+ comp.getName()
+ "\',"
+ comp.getconstant()
+ ",\'"
+ modelids.getId()
+ "\',"
+ comp.getspatialdimensions()
+ ","
+ comp.getsize()
+ ","
+ comp.getunits()
+ "\'),";
Compartment c = doc.getModel().createCompartment(comp.getId());
c.setName(comp.getName());
c.setConstant(comp.getconstant());
c.setSize(comp.getsize());
c.setSpatialDimensions(comp.getspatialdimensions());
if (comp.getspatialdimensions() != 0) c.setUnits(comp.getunits());
// doc.getModel().addSpecies(sp) ;
}
if (!complist.isEmpty()) {
insertcompartment = insertcompartment.substring(0, insertcompartment.length() - 1);
insertcompartment = insertcompartment + ';';
}
ArrayList<functionList> funclist = sql.getfunctions(modelids.getId());
if (!funclist.isEmpty())
insertfunction =
insertfunction + "\nInsert Into functiondefinition (id, xmlns,model_id) Values";
for (functionList func : funclist) {
insertfunction =
insertfunction
+ "(\'"
+ func.getId()
+ "\',\'"
+ func.getxmlns()
+ "\',\'"
+ modelids.getId()
+ "\'),";
FunctionDefinition fd = doc.getModel().createFunctionDefinition(func.getId());
try {
math = ASTNode.parseFormula(func.getxmlns());
fd.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!funclist.isEmpty()) {
insertfunction = insertfunction.substring(0, insertfunction.length() - 1);
insertfunction = insertfunction + ';';
}
ArrayList<unitList> unitlist = sql.getunitlist(modelids.getId());
if (!unitlist.isEmpty())
insertunitdef =
insertunitdef + "\nInsert Into listofunitdefinitions (id,name,model_id) Values";
for (unitList units : unitlist) {
insertunitdef =
insertunitdef
+ "(\'"
+ units.getId()
+ "\',\'"
+ units.getName()
+ "\',\'"
+ modelids.getId()
+ "\'),";
UnitDefinition ud = doc.getModel().createUnitDefinition(units.getId());
ud.setName(units.getName());
ArrayList<unitList> unitdeflist = sql.getunitdef(units.getId());
if (!unitdeflist.isEmpty())
insertunits =
insertunits
+ "\nInsert Into listofunits (listofunitdefinitions_id,kind, scale,exponent,multiplier) Values";
for (unitList unitdef : unitdeflist) {
insertunits =
insertunits
+ "(\'"
+ units.getId()
+ "\',\'"
+ unitdef.getkind()
+ "\',"
+ unitdef.getscale()
+ ","
+ unitdef.getexponent()
+ ","
+ unitdef.getmultiplier()
+ "),";
Unit u = ud.createUnit(Unit.Kind.valueOf(unitdef.getkind()));
u.setScale(unitdef.getscale());
u.setExponent(unitdef.getexponent());
u.setMultiplier(unitdef.getmultiplier());
}
// doc.getModel().addSpecies(sp) ;
if (!unitdeflist.isEmpty()) {
insertunits = insertunits.substring(0, insertunits.length() - 1);
insertunits = insertunits + ';';
}
}
if (!unitlist.isEmpty()) {
insertunitdef = insertunitdef.substring(0, insertunitdef.length() - 1);
insertunitdef = insertunitdef + ';';
}
ArrayList<reactionList> reactionlist = sql.getreactons(modelids.getId());
if (!reactionlist.isEmpty())
insertreaction =
insertreaction
+ "\nInsert Into reaction (id,name, reversible,fast,model_id,compartment,annotation) Values";
for (reactionList reaction : reactionlist) {
insertreaction =
insertreaction
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reaction.getName()
+ "\',"
+ reaction.getreversible()
+ ","
+ reaction.getfast()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ reaction.getcompartment()
+ "\',\'"
+ reaction.getannotation()
+ "\'),";
Reaction rn = doc.getModel().createReaction(reaction.getId());
rn.setName(reaction.getName());
if (doc.getModel().getLevel() == 3) rn.setCompartment(reaction.getcompartment());
rn.setFast(reaction.getfast());
rn.setReversible(reaction.getreversible());
if (!reaction.getannotation().equals("")) {
Annotation annot = new Annotation(reaction.getannotation().toString());
rn.setAnnotation(annot);
}
ArrayList<reactionList> reactantlist = sql.getreactants(reaction.getId());
if (!reactantlist.isEmpty())
insertreactant =
insertreactant
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,speciestype,constant) Values";
for (reactionList reactant : reactantlist) {
insertreactant =
insertreactant
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reactant.getspecies()
+ "\',\'"
+ reactant.getsboTerm()
+ "\',"
+ reactant.getstoichometry()
+ ","
+ reactant.getconstant()
+ ",\'reactants\'),";
SpeciesReference rt = new SpeciesReference();
rt.setName(reactant.getspecies());
rt.setSpecies(reactant.getspecies());
// rt.setSBOTerm(reactant.getsboTerm());
rt.setStoichiometry(reactant.getstoichometry());
// rt.setConstant(reactant.getconstant());
rn.addReactant(rt);
}
if (!reactantlist.isEmpty()) {
insertreactant = insertreactant.substring(0, insertreactant.length() - 1);
insertreactant = insertreactant + ';';
}
ArrayList<reactionList> productlist = sql.getproducts(reaction.getId());
if (!productlist.isEmpty())
insertproduct =
insertproduct
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,constant,speciestype) Values";
for (reactionList product : productlist) {
insertproduct =
insertproduct
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ product.getspecies()
+ "\',\'"
+ product.getsboTerm()
+ "\',"
+ product.getstoichometry()
+ ","
+ product.getconstant()
+ ",\'products\'),";
SpeciesReference pr = new SpeciesReference();
pr.setName(product.getspecies());
pr.setSpecies(product.getspecies());
// pr.setSBOTerm(product.getsboTerm());
pr.setStoichiometry(product.getstoichometry());
// pr.setConstant(product.getconstant());
rn.addProduct(pr);
}
if (!productlist.isEmpty()) {
insertproduct = insertproduct.substring(0, insertproduct.length() - 1);
insertproduct = insertproduct + ';';
}
ArrayList<reactionList> modifierlist = sql.getmodifiers(reaction.getId());
if (!modifierlist.isEmpty())
insertmodifier =
insertmodifier
+ "\nInsert Into modifierspeciesreference (reaction_id,species, sboTerm,speciestype) Values";
for (reactionList modifier : modifierlist) {
insertmodifier =
insertmodifier
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ modifier.getspecies()
+ "\',\'"
+ modifier.getsboTerm()
+ "\',\'modifiers\'),";
ModifierSpeciesReference m = new ModifierSpeciesReference();
m.setName(modifier.getspecies());
m.setSpecies(modifier.getspecies());
// m.setSBOTerm(modifier.getsboTerm());
rn.addModifier(m);
}
if (!modifierlist.isEmpty()) {
insertmodifier = insertmodifier.substring(0, insertmodifier.length() - 1);
insertmodifier = insertmodifier + ';';
}
ArrayList<reactionList> klawlist = sql.getkineticlaws(reaction.getId());
if (!klawlist.isEmpty())
insertklaw =
insertklaw + "\nInsert Into kineticlaw (reaction_id,kid, math,annotation) Values";
for (reactionList klaw : klawlist) {
insertklaw =
insertklaw
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ klaw.getId()
+ "\',\'"
+ klaw.getmath()
+ "\',\'"
+ klaw.getannotation()
+ "\'),";
KineticLaw kl = rn.createKineticLaw();
try {
math = ASTNode.parseFormula(klaw.getmath());
kl.setMath(math);
if (!klaw.getannotation().equals("")) {
Annotation annot = new Annotation(klaw.getannotation().toString());
kl.setAnnotation(annot);
}
} catch (Exception e) {
e.printStackTrace();
}
}
if (!klawlist.isEmpty()) {
insertklaw = insertklaw.substring(0, insertklaw.length() - 1);
insertklaw = insertklaw + ';';
}
}
if (!reactionlist.isEmpty()) {
insertreaction = insertreaction.substring(0, insertreaction.length() - 1);
insertreaction = insertreaction + ';';
}
ArrayList<parameterList> paralist = sql.getparameters(modelids.getId());
if (!paralist.isEmpty())
insertparameter =
insertparameter
+ "\nInsert Into parameter (id,name,value,units,constant,model_id) Values";
for (parameterList para : paralist) {
insertparameter =
insertparameter
+ "(\'"
+ para.getId()
+ "\',\'"
+ para.getName()
+ "\',"
+ para.getvalue()
+ ","
+ para.getunits()
+ ","
+ para.getconstant()
+ ",\'"
+ modelids.getId()
+ "\'),";
Parameter par = doc.getModel().createParameter(para.getId());
par.setName(para.getId());
par.setConstant(para.getconstant());
par.setUnits(para.getunits());
par.setValue(para.getvalue());
}
if (!paralist.isEmpty()) {
insertparameter = insertparameter.substring(0, insertparameter.length() - 1);
insertparameter = insertparameter + ';';
}
ArrayList<constraintList> conslist = sql.getconstraints(modelids.getId());
if (!conslist.isEmpty())
insertconstraint =
insertconstraint + "\nInsert Into sbmlconstraint (math,message,model_id) Values";
for (constraintList constraint : conslist) {
insertconstraint =
insertconstraint
+ "(\'"
+ constraint.getmath()
+ "\',\'"
+ constraint.getmessage()
+ "\',\'"
+ modelids.getId()
+ "\'),";
Constraint cons = doc.getModel().createConstraint();
try {
math = ASTNode.parseFormula(constraint.getmath());
cons.setMath(math);
cons.setMessage(constraint.getmessage());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!conslist.isEmpty()) {
insertconstraint = insertconstraint.substring(0, insertconstraint.length() - 1);
insertconstraint = insertconstraint + ';';
}
ArrayList<eventsList> eventlist = sql.getevents(modelids.getId());
if (!eventlist.isEmpty())
insertevent =
insertevent + "\nInsert Into event (id,name,UseValuesFromTriggerTime,model_id) Values";
for (eventsList events : eventlist) {
insertevent =
insertevent
+ "(\'"
+ events.getId()
+ "\',\'"
+ events.getName()
+ "\',"
+ events.getuservalues()
+ ",\'"
+ modelids.getId()
+ "\'),";
Event ev = doc.getModel().createEvent(events.getId());
ev.setName(events.getName());
// ev.setUseValuesFromTriggerTime(events.getuservalues());
ArrayList<eventsList> triggerlist = sql.gettriggers(events.getId());
if (!triggerlist.isEmpty())
inserttrigger =
inserttrigger
+ "\nInsert Into sbmltrigger (event_id,initialvalue,persisent,math) Values";
for (eventsList triggers : triggerlist) {
Trigger tr = doc.getModel().createTrigger();
try {
math = ASTNode.parseFormula(triggers.getmath());
tr.setMath(math);
tr.setInitialValue(triggers.getinitialval());
tr.setPersistent(triggers.getpersistent());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!triggerlist.isEmpty()) {
inserttrigger = inserttrigger.substring(0, insertmodel.length() - 1);
inserttrigger = inserttrigger + ';';
}
ArrayList<eventsList> delaylist = sql.getdelays(events.getId());
if (!delaylist.isEmpty())
insertdelay = insertdelay + "\nInsert Into delay (event_id,math) Values";
for (eventsList delays : delaylist) {
Delay d = doc.getModel().createDelay();
try {
math = ASTNode.parseFormula(delays.getmath());
d.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!delaylist.isEmpty()) {
insertdelay = insertdelay.substring(0, insertdelay.length() - 1);
insertdelay = insertdelay + ';';
}
ArrayList<eventsList> evasslist = sql.geteventassignments(events.getId());
if (!evasslist.isEmpty())
inserteventassign =
inserteventassign + "\nInsert Into eventassignment (event_id,variable,math) Values";
for (eventsList evassign : evasslist) {
EventAssignment ea = doc.getModel().createEventAssignment();
try {
math = ASTNode.parseFormula(evassign.getmath());
ea.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!evasslist.isEmpty()) {
inserteventassign = inserteventassign.substring(0, inserteventassign.length() - 1);
inserteventassign = inserteventassign + ';';
}
}
if (!eventlist.isEmpty()) {
insertevent = insertevent.substring(0, insertevent.length() - 1);
insertevent = insertevent + ';';
}
ArrayList<ruleslist> rulelist = sql.getrules(modelids.getId());
if (!rulelist.isEmpty())
insertrules = insertrules + "\nInsert Into rules (id,math,ruletype,model_id) Values";
for (ruleslist rules : rulelist) {
insertrules =
insertrules
+ "(\'"
+ rules.getId()
+ "\',\'"
+ rules.getmath()
+ "\',\'"
+ rules.getruletype()
+ "\',\'"
+ modelids.getId()
+ "\'),";
if (rules.getruletype().equals("assignmentrule")) {
Rule r = doc.getModel().createAssignmentRule();
r.setMetaId(rules.getId());
try {
math = ASTNode.parseFormula(rules.getmath());
r.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
}
if (!rulelist.isEmpty()) {
insertrules = insertrules.substring(0, insertrules.length() - 1);
insertrules = insertrules + ';';
}
SBMLWriter writer = new SBMLWriter();
try {
String Path = filepath + modelids.getId() + ".xml";
writer.write(doc, Path);
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(Path);
Element root = document.getDocumentElement();
Element newdataset = document.createElement("dataset");
root.appendChild(newdataset);
ArrayList<dataset> datasetlist = sql.getdataset(modelids.getId());
for (dataset ds : datasetlist) {
// System.out.println(ds.getexpcond());
Element name = document.createElement("experimentalcondition");
name.setAttribute("bioelement", ds.getbioel());
name.setAttribute("name", ds.getName());
name.setAttribute("descr", ds.getdescr());
name.setAttribute("expcond", ds.getexpcond());
name.setAttribute("value", String.valueOf(ds.getvalue()));
name.setAttribute("type", ds.gettype());
name.setAttribute("uri", ds.geturi());
newdataset.appendChild(name);
}
root.appendChild(newdataset);
DOMSource source = new DOMSource(document);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
StreamResult result = new StreamResult(filepath + modelids.getId() + "d.xml");
transformer.transform(source, result);
System.out.println(
"Files : "
+ modelids.getId()
+ ".xml and "
+ modelids.getId()
+ "d.xml have been generated successfully !!!");
} catch (Exception e) {
e.printStackTrace();
}
insertstatement =
insertstatement
+ "\n\n"
+ insertmodel
+ "\n"
+ insertspecies
+ "\n"
+ insertcompartment
+ "\n"
+ insertfunction;
insertstatement =
insertstatement
+ "\n"
+ insertparameter
+ "\n"
+ insertreaction
+ "\n"
+ insertreactant
+ "\n"
+ insertproduct;
insertstatement =
insertstatement
+ "\n"
+ insertmodifier
+ "\n"
+ insertklaw
+ "\n"
+ insertunitdef
+ "\n"
+ insertunits;
insertstatement =
insertstatement
+ "\n"
+ insertrules
+ "\n"
+ insertconstraint
+ "\n"
+ insertevent
+ "\n"
+ inserttrigger
+ "\n"
+ insertdelay
+ "\n"
+ inserteventassign;
insertcompartment = "";
insertmodel = "";
insertspecies = "";
// System.out.println("document : " + doc);
}
insertstatement = insertstatement + "\nUNLOCK TABLES;";
Filedata = Filedata + "\n\n\n" + insertstatement;
try {
wrtireStringToFile(Filedata, filepath + "sbmldb.sql");
} catch (IOException e) {
e.printStackTrace();
}
// System.out.println(insertstatement);
}
private static void parseConfiguration(String stringUrl, Product product) {
try {
URL url = new URL(stringUrl);
URLConnection connection = url.openConnection();
int fileLength = connection.getContentLength();
if (fileLength == -1) {
System.out.println("Invalide URL or file.");
return;
}
CommandClass currentCC = null;
Parameter currentParameter = null;
Association currentAssociation = null;
XMLInputFactory inputFactory = XMLInputFactory.newInstance();
InputStream input = connection.getInputStream();
final XMLEventReader eventReader = inputFactory.createXMLEventReader(input);
while (eventReader.hasNext()) {
XMLEvent event = eventReader.nextEvent();
if (event.isStartElement()) {
StartElement startElt = event.asStartElement();
if (startElt.getName().getLocalPart().equals("CommandClass")) {
CommandClass cc = product.view().createCommandClass();
Iterator<Attribute> attributes = startElt.getAttributes();
while (attributes.hasNext()) {
Attribute next = attributes.next();
String attrName = next.getName().toString();
if (attrName.equals("id")) {
cc.setId(Integer.parseInt(next.getValue(), 16));
}
}
product.addCommandClasses(cc);
currentCC = cc;
} else if (startElt.getName().getLocalPart().equals("Value")) {
Parameter param = product.view().createParameter();
Iterator<Attribute> attributes = startElt.getAttributes();
while (attributes.hasNext()) {
Attribute next = attributes.next();
String attrName = next.getName().toString();
if (!next.getValue().equals("")) {
if (attrName.equals("type")) {
param.setType(ParameterType.valueOf(next.getValue().toUpperCase()));
} else if (attrName.equals("genre")) {
param.setGenre(next.getValue());
} else if (attrName.equals("instance")) {
param.setInstance(Integer.valueOf(next.getValue()));
} else if (attrName.equals("index")) {
param.setIndex(Integer.valueOf(next.getValue()));
} else if (attrName.equals("label")) {
param.setLabel(next.getValue());
} else if (attrName.equals("value")) {
param.setValue(next.getValue());
} else if (attrName.equals("min")) {
param.setMin(Integer.valueOf(next.getValue()));
} else if (attrName.equals("max")) {
param.setMax(Integer.valueOf(next.getValue()));
} else if (attrName.equals("size")) {
param.setSize(Integer.valueOf(next.getValue()));
}
}
}
currentCC.addParameters(param);
currentParameter = param;
} else if (startElt.getName().getLocalPart().equals("Help")) {
// help
} else if (startElt.getName().getLocalPart().equals("Item")) {
ParameterItem item = product.view().createParameterItem();
Iterator<Attribute> attributes = startElt.getAttributes();
while (attributes.hasNext()) {
Attribute next = attributes.next();
String attrName = next.getName().toString();
if (attrName.equals("label")) {
item.setLabel(next.getValue());
} else if (attrName.equals("value")) {
item.setValue(Integer.valueOf(next.getValue()));
}
}
currentParameter.addItems(item);
} else if (startElt.getName().getLocalPart().equals("Associations")) {
Association assoc = product.view().createAssociation();
Iterator<Attribute> attributes = startElt.getAttributes();
while (attributes.hasNext()) {
Attribute next = attributes.next();
String attrName = next.getName().toString();
if (attrName.equals("num_groups")) {
assoc.setNumGroups(Integer.valueOf(next.getValue()));
}
}
currentCC.addAssociations(assoc);
currentAssociation = assoc;
} else if (startElt.getName().getLocalPart().equals("Group")) {
AssociationGroup group = product.view().createAssociationGroup();
Iterator<Attribute> attributes = startElt.getAttributes();
while (attributes.hasNext()) {
Attribute next = attributes.next();
String attrName = next.getName().toString();
if (attrName.equals("label")) {
group.setLabel(next.getValue());
} else if (attrName.equals("index")) {
group.setIndex(Integer.valueOf(next.getValue()));
} else if (attrName.equals("max_associations")) {
group.setMaxAssociations(Integer.valueOf(next.getValue()));
} else if (attrName.equals("auto")) {
group.setAuto(Boolean.valueOf(next.getValue()));
}
currentAssociation.addGroups(group);
}
}
}
}
} catch (MalformedURLException e) {
e.printStackTrace();
} catch (XMLStreamException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
}
public void setValue(T value) {
baseParam.setValue(value);
}
public PresentationObject getChooser(IWContext iwc, IWBundle bundle) {
if (useOldLogic) { // Old chooser
Table table = new Table(2, 1);
table.setCellpadding(0);
table.setCellspacing(0);
Parameter value = new Parameter(getChooserParameter(), "");
if (this._stringValue != null) {
value.setValue(this._stringValue);
}
table.add(value);
PresentationObject object = getPresentationObject(iwc);
table.add(new Parameter(VALUE_PARAMETER_NAME, value.getName()));
// GenericButton button = new
// GenericButton("chooserbutton",bundle.getResourceBundle(iwc).getLocalizedString(chooserText,"Choose"));
if (this._addForm) {
SubmitButton button = new SubmitButton(this._iwrb.getLocalizedString("choose", "Choose"));
table.add(button, 2, 1);
this._form.addParameter(CHOOSER_SELECTION_PARAMETER, getChooserParameter());
this._form.addParameter(
FORM_ID_PARAMETER,
"window.opener.document.getElementById(\"" + this._form.getID() + "\").");
this._form.addParameter(SCRIPT_SUFFIX_PARAMETER, "value");
if (this.filter != null) {
if (this.filter.length() > 0) {
this._form.addParameter(FILTER_PARAMETER, this.filter);
}
}
addParametersToForm(this._form);
} else {
getLink(this._iwrb);
if (getUsePublicWindowOpener()) {
this.link.setPublicWindowToOpen(getChooserWindowClass());
} else {
this.link.setWindowToOpen(getChooserWindowClass());
}
this.link.addParameter(CHOOSER_SELECTION_PARAMETER, getChooserParameter());
this.link.addParameter(FORM_ID_PARAMETER, getParentFormID());
// TODO Make the javascript work for other objects than form elements,
// e.g. a Link
/*
* if(object instanceof Layer){
* link.addParameter(SCRIPT_SUFFIX_PARAMETER,"title"); }
*/
this.link.addParameter(SCRIPT_SUFFIX_PARAMETER, "value");
// }
// this was object.getID() but the id could change if this object was kept in session but
// the form changed
// by using getName() the reference is not lost, however we might need to add extra steps
// for handling more than one
// chooser of the same type in the same form.
this.link.addParameter(DISPLAYSTRING_PARAMETER_NAME, object.getName());
this.link.addParameter(VALUE_PARAMETER_NAME, value.getName());
if (this._attributeName != null && this._attributeValue != null) {
this.link.addParameter(this._attributeName, this._attributeValue);
}
if (this.filter != null) {
if (this.filter.length() > 0) {
this.link.addParameter(FILTER_PARAMETER, this.filter);
}
}
addParametersToLink(this.link);
table.add(this.link, 2, 1);
}
table.add(object, 1, 1);
table.add(new Parameter(DISPLAYSTRING_PARAMETER_NAME, "151324213"));
return (table);
} else { // New chooser
Layer container = new Layer();
String chooserObject = getChooserHelperVarName();
if (chooserObject == null) {
chooserObject = AbstractChooserBlock.GLOBAL_HELPER_NAME;
} else {
add(
PresentationUtil.getJavaScriptAction(
PresentationUtil.getJavaScriptLinesLoadedLazily(
CoreUtil.getResourcesForChooser(iwc),
new StringBuilder("if (!")
.append(chooserObject)
.append(") var ")
.append(chooserObject)
.append(" = new ChooserHelper();")
.toString())));
}
PresentationObject object = getPresentationObject(iwc);
container.add(object);
Image chooser = getChooser(bundle);
chooser.setStyleClass("chooserStyle");
chooser.setMarkupAttribute("choosername", chooserObject);
// OnClick action
StringBuffer action =
new StringBuffer("addChooserObject('").append(chooser.getId()).append("', '");
action.append(getChooserWindowClass().getName());
if (getHiddenInputAttribute() == null) {
action.append("', null, '");
} else {
action.append("', '").append(getHiddenInputAttribute()).append("', '");
}
action.append(ICBuilderConstants.CHOOSER_VALUE_VIEWER_ID_ATTRIBUTE).append("', '");
action
.append(getResourceBundle().getLocalizedString("loading", "Loading..."))
.append("', ")
.append(
_stringValue == null
? "null"
: new StringBuilder("'").append(_stringValue).append("'").toString())
.append(", ")
.append(
_stringDisplay == null
? "null"
: new StringBuilder("'").append(_stringDisplay).append("'").toString())
.append(");");
chooser.setOnClick(action.toString());
container.add(chooser);
return container;
}
}
