private QConClass classConstraint() {
if (i_constraints.size() != 1) {
return null;
}
Constraint constr = singleConstraint();
if (constr.getClass() != QConClass.class) {
return null;
}
return (QConClass) constr;
}
/* process the list of pending constraints */
protected void processWorklist() {
int iter = 0;
while (!w.isEmpty()) {
int size = w.size();
Constraint c = w.removeFirst();
c.accept(this);
size -= w.size();
iter++;
}
}
/**
* Helper function. Add a new state, if it does not already exist, and returns its index.
*
* @param loc1: Index of location of PTA 1
* @param loc2: Index of location of PTA 2
*/
private int addState(int loc1, int loc2) {
// See if this is a new state
IndexPair stateNew = new IndexPair(loc1, loc2);
if (states.add(stateNew)) {
// If so, add to the explore list
explore.add(stateNew);
// Get index of state in state set
int locNew = states.getIndexOfLastAdd();
// And add a location to the PTA
par.addLocation(
PTA.combineLocationNames(pta1.getLocationName(loc1), pta2.getLocationName(loc2)));
// Invariant is conjunction of two invariants
for (Constraint c : pta1.getInvariantConstraints(loc1))
par.addInvariantCondition(locNew, c.deepCopy().renameClocks(pta1, par));
for (Constraint c : pta2.getInvariantConstraints(loc2))
par.addInvariantCondition(locNew, c.deepCopy().renameClocks(pta2, par));
}
// Return index of state in state set
return states.getIndexOfLastAdd();
}
private static final SecurityHandler basicAuth(String realm) {
OpenfireLoginService l = new OpenfireLoginService();
l.setName(realm);
Constraint constraint = new Constraint();
constraint.setName(Constraint.__BASIC_AUTH);
constraint.setRoles(new String[] {"jmxweb"});
constraint.setAuthenticate(true);
ConstraintMapping cm = new ConstraintMapping();
cm.setConstraint(constraint);
cm.setPathSpec("/*");
ConstraintSecurityHandler csh = new ConstraintSecurityHandler();
csh.setAuthenticator(new BasicAuthenticator());
csh.setRealmName(realm);
csh.addConstraintMapping(cm);
csh.setLoginService(l);
return csh;
}
private Constraint addInterfaceConstraint(ReflectClass claxx) {
Collection4 classes = stream().classCollection().forInterface(claxx);
if (classes.size() == 0) {
QConClass qcc = new QConClass(_trans, null, null, claxx);
addConstraint(qcc);
return qcc;
}
Iterator4 i = classes.iterator();
Constraint constr = null;
while (i.moveNext()) {
ClassMetadata classMetadata = (ClassMetadata) i.current();
ReflectClass classMetadataClaxx = classMetadata.classReflector();
if (classMetadataClaxx != null) {
if (!classMetadataClaxx.isInterface()) {
if (constr == null) {
constr = constrain(classMetadataClaxx);
} else {
constr = constr.or(constrain(classMetadata.classReflector()));
}
}
}
}
return constr;
}
/** @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);
}
/**
* Get the decision from the database, given its name
*
* @param name the decision name
*/
public void fromDatabase(String name) {
String findQuery = "";
RationaleDB db = RationaleDB.getHandle();
Connection conn = db.getConnection();
this.name = name;
name = RationaleDBUtil.escape(name);
Statement stmt = null;
ResultSet rs = null;
try {
stmt = conn.createStatement();
findQuery = "SELECT * FROM " + "PATTERNDECISIONS where name = '" + name + "'";
// *** System.out.println(findQuery);
rs = stmt.executeQuery(findQuery);
if (rs.next()) {
id = rs.getInt("id");
description = RationaleDBUtil.decode(rs.getString("description"));
type = (DecisionType) DecisionType.fromString(rs.getString("type"));
devPhase = (Phase) Phase.fromString(rs.getString("phase"));
ptype = RationaleElementType.fromString(rs.getString("ptype"));
parent = rs.getInt("parent");
// artifact = rs.getString("artifact");
// enabled = rs.getBoolean("enabled");
status = (DecisionStatus) DecisionStatus.fromString(rs.getString("status"));
String subdecs = rs.getString("subdecreq");
if (subdecs.compareTo("Yes") == 0) {
alts = false;
} else {
alts = true;
}
try {
int desID = rs.getInt("designer");
designer = new Designer();
designer.fromDatabase(desID);
} catch (SQLException ex) {
designer = null; // nothing...
}
}
rs.close();
// need to read in the rest - recursive routines?
subDecisions.removeAllElements();
alternatives.removeAllElements();
if (!alts) {
Vector<String> decNames = new Vector<String>();
findQuery =
"SELECT name from PATTERNDECISIONS where "
+ "ptype = '"
+ RationaleElementType.DECISION.toString()
+ "' and parent = "
+ new Integer(id).toString();
// *** System.out.println(findQuery2);
rs = stmt.executeQuery(findQuery);
while (rs.next()) {
decNames.add(RationaleDBUtil.decode(rs.getString("name")));
}
Enumeration decs = decNames.elements();
while (decs.hasMoreElements()) {
PatternDecision subDec = new PatternDecision();
subDec.fromDatabase((String) decs.nextElement());
subDecisions.add(subDec);
}
} else {
Vector<String> altNames = new Vector<String>();
findQuery =
"SELECT name from ALTERNATIVES where "
+ "ptype = '"
+ RationaleElementType.DECISION.toString()
+ "' and parent = "
+ new Integer(id).toString();
// *** System.out.println(findQuery2);
rs = stmt.executeQuery(findQuery);
while (rs.next()) {
altNames.add(RationaleDBUtil.decode(rs.getString("name")));
}
Enumeration alts = altNames.elements();
while (alts.hasMoreElements()) {
Alternative alt = new Alternative();
alt.fromDatabase((String) alts.nextElement());
alternatives.add(alt);
}
}
// need to do questions too
Vector<String> questNames = new Vector<String>();
findQuery =
"SELECT name from QUESTIONS where "
+ "ptype = '"
+ RationaleElementType.DECISION.toString()
+ "' and parent = "
+ new Integer(id).toString();
// *** System.out.println(findQuery3);
rs = stmt.executeQuery(findQuery);
while (rs.next()) {
questNames.add(RationaleDBUtil.decode(rs.getString("name")));
}
Enumeration quests = questNames.elements();
questions.removeAllElements();
while (quests.hasMoreElements()) {
Question quest = new Question();
quest.fromDatabase((String) quests.nextElement());
questions.add(quest);
}
// no, not last - need history too
findQuery =
"SELECT * from HISTORY where ptype = 'Decision' and "
+ "parent = "
+ Integer.toString(id);
// *** System.out.println(findQuery5);
rs = stmt.executeQuery(findQuery);
history.removeAllElements();
while (rs.next()) {
History nextH = new History();
nextH.setStatus(rs.getString("status"));
nextH.setReason(RationaleDBUtil.decode(rs.getString("reason")));
nextH.dateStamp = rs.getTimestamp("date");
// nextH.dateStamp = rs.getDate("date");
history.add(nextH);
}
// now, get our constraints
findQuery =
"SELECT * from ConDecRelationships WHERE " + "decision = " + new Integer(id).toString();
rs = stmt.executeQuery(findQuery);
constraints.removeAllElements();
if (rs != null) {
while (rs.next()) {
int ontID = rs.getInt("constr");
Constraint cont = new Constraint();
cont.fromDatabase(ontID);
this.addConstraint(cont);
}
rs.close();
}
// now, candidate patterns
findQuery =
"SELECT * from pattern_decision WHERE parentType= 'Decision' and decisionID=" + this.id;
rs = stmt.executeQuery(findQuery);
if (rs != null) {
while (rs.next()) {
int patternID = rs.getInt("patternID");
Pattern p = new Pattern();
p.fromDatabase(patternID);
this.addCandidatePattern(p);
}
}
} catch (SQLException ex) {
// handle any errors
RationaleDB.reportError(ex, "Error in PatternDecision.fromDatabase", findQuery);
} finally {
RationaleDB.releaseResources(stmt, rs);
}
}
/**
* Save our decision to the database.
*
* @param parent - the parent of the decision
* @param ptype - the parent's type
* @return the unique ID
*/
public int toDatabase(int parent, RationaleElementType ptype) {
RationaleDB db = RationaleDB.getHandle();
Connection conn = db.getConnection();
String updateQuery = "";
int ourid = 0;
RationaleUpdateEvent l_updateEvent;
// find out if this requirement is already in the database
Statement stmt = null;
ResultSet rs = null;
String subsReq = "No";
if (!alts) subsReq = "Yes";
try {
stmt = conn.createStatement();
if (inDatabase(parent, ptype)) {
// set up Designer update string
String updateD;
if (designer == null) updateD = "D.designer = null";
else updateD = "D.designer = " + designer.getID();
updateQuery =
"UPDATE PATTERNDECISIONS D "
+ "SET D.parent = "
+ new Integer(parent).toString()
+ ", D.ptype = '"
+ ptype.toString()
+ "', D.phase = '"
+ devPhase.toString()
+ "', D.description = '"
+ RationaleDBUtil.escape(description)
+ "', D.type = '"
+ type.toString()
+ "', D.name = '"
+ RationaleDBUtil.escape(name)
+ "', D.status = '"
+ status.toString()
+ "', D.subdecreq = '"
+ subsReq
+ "', "
+ updateD
+ " WHERE "
+ "D.id = "
+ this.id
+ " ";
stmt.execute(updateQuery);
l_updateEvent = m_eventGenerator.MakeUpdated();
} else {
if (!fromXML) id = RationaleDB.findAvailableID("PATTERNDECISIONS");
String parentSt;
String parentTSt;
// now, we have determined that the decision is new
if ((this.parent < 0) || (ptype == null)) {
parentSt = "NULL";
parentTSt = "None";
} else {
parentSt = new Integer(this.parent).toString();
parentTSt = ptype.toString();
}
String updateD;
if (designer == null) updateD = "null";
else updateD = new Integer(designer.getID()).toString();
updateQuery =
"INSERT INTO PATTERNDECISIONS "
+ "(id, name, description, type, status, phase, subdecreq, parent, ptype, designer) "
+ "VALUES ("
+ id
+ ", '"
+ RationaleDBUtil.escape(this.name)
+ "', '"
+ RationaleDBUtil.escape(this.description)
+ "', '"
+ this.type.toString()
+ "', '"
+ this.status.toString()
+ "', '"
+ this.devPhase.toString()
+ "', '"
+ subsReq
+ "', "
+ parentSt
+ ", '"
+ parentTSt
+ "', "
+ updateD
+ ")";
stmt.execute(updateQuery);
/*
//Now, associate with pattern.
//Get id first
updateQuery = "SELECT id FROM patterndecisions where name='" +
RationaleDBUtil.escape(this.name) + "'";
rs = stmt.executeQuery(updateQuery);
if (rs.next())
{
ourid = rs.getInt("id");
rs.close();
//We have found out our ID and the insert is a success.
//get association set up.
updateQuery = "INSERT into pattern_decision values (" + parent +
"ourid" + "DECISION)";
}
//And now, we have patternID and patterndecisionID. We can insert into relationship entry
updateQuery = "INSERT INTO pattern_decision values (" + parentPattern + ", " +
ourid + ", " + "'Decision')";
stmt.execute(updateQuery);
*/
l_updateEvent = m_eventGenerator.MakeCreated();
}
// in either case, we want to update any sub-requirements in case
// they are new!
// now, we need to get our ID
updateQuery =
"SELECT id FROM PATTERNDECISIONS where name='" + RationaleDBUtil.escape(this.name) + "'";
rs = stmt.executeQuery(updateQuery);
if (rs.next()) {
ourid = rs.getInt("id");
rs.close();
} else {
ourid = -1;
}
this.id = ourid;
Enumeration alts = alternatives.elements();
while (alts.hasMoreElements()) {
Alternative alt = (Alternative) alts.nextElement();
// System.out.println("Saving alternative from decision");
alt.toDatabase(ourid, RationaleElementType.DECISION);
}
Enumeration decs = subDecisions.elements();
while (decs.hasMoreElements()) {
Decision dec = (Decision) decs.nextElement();
dec.toDatabase(ourid, RationaleElementType.DECISION);
}
Enumeration quests = questions.elements();
while (quests.hasMoreElements()) {
Question quest = (Question) quests.nextElement();
quest.toDatabase(ourid, RationaleElementType.DECISION);
}
// finally, the history
Enumeration hist = history.elements();
while (hist.hasMoreElements()) {
History his = (History) hist.nextElement();
his.toDatabase(ourid, RationaleElementType.DECISION);
}
// need to update our relationships with the constraints
Enumeration conkids = this.constraints.elements();
while (conkids.hasMoreElements()) {
Constraint kid = (Constraint) conkids.nextElement();
// if the parent ID is not zero, then update the parent-child relationship
updateQuery =
"SELECT * from ConDecRelationships WHERE "
+ "constr = "
+ new Integer(kid.getID()).toString()
+ " and decision = "
+ new Integer(ourid).toString();
rs = stmt.executeQuery(updateQuery.toUpperCase());
if (rs.next()) {
rs.close();
} else {
String insertRel =
"INSERT INTO ConDecRelationships (constr, decision) "
+ "VALUES ("
+ new Integer(kid.getID()).toString()
+ ", "
+ new Integer(ourid).toString()
+ ")";
System.out.println(insertRel.toUpperCase());
stmt.execute(insertRel);
}
kid.toDatabase(ourid);
} // checking parent
m_eventGenerator.Broadcast(l_updateEvent);
} catch (SQLException ex) {
// handle any errors
RationaleDB.reportError(ex, "Error in PatternDecision.toDatabase", updateQuery);
} finally {
RationaleDB.releaseResources(stmt, rs);
}
return ourid;
}
/** Construct the parallel composition of two PTAs. */
public PTA compose(PTA pta1, PTA pta2) {
Set<String> alpha1, alpha2, alpha1only, alpha2only, sync;
Transition transition;
Edge edge;
double prob;
IndexPair state;
int src, dest;
// Store PTAs locally and create new one to store parallel composition
this.pta1 = pta1;
this.pta2 = pta2;
par = new PTA();
// New set of clocks is union of sets for two PTAs
for (String s : pta1.clockNames) {
par.getOrAddClock(s);
}
for (String s : pta2.clockNames) {
par.getOrAddClock(s);
}
// Get alphabets, compute intersection etc.
alpha1 = pta1.getAlphabet();
alpha2 = pta2.getAlphabet();
// System.out.println("alpha1: " + alpha1);
// System.out.println("alpha2: " + alpha2);
sync = new LinkedHashSet<String>();
alpha1only = new LinkedHashSet<String>();
alpha2only = new LinkedHashSet<String>();
for (String a : alpha1) {
if (!("".equals(a)) && alpha2.contains(a)) {
sync.add(a);
} else {
alpha1only.add(a);
}
}
for (String a : alpha2) {
if (!alpha1.contains(a)) {
alpha2only.add(a);
}
}
// Explicitly add tau to action lists
alpha1only.add("");
alpha2only.add("");
// System.out.println("alpha1only: " + alpha1only);
// System.out.println("alpha2only: " + alpha2only);
// System.out.println("sync: " + sync);
// Initialise states storage
states = new IndexedSet<IndexPair>();
explore = new LinkedList<IndexPair>();
// Add initial location
addState(0, 0);
src = -1;
while (!explore.isEmpty()) {
// Pick next state to explore
// (they are stored in order found so know index is src+1)
state = explore.removeFirst();
src++;
// Go through asynchronous transitions of PTA 1
for (String a : alpha1only) {
for (Transition transition1 : pta1.getTransitionsByAction(state.i1, a)) {
// Create new transition
transition = par.addTransition(src, a);
// Copy guard
for (Constraint c : transition1.getGuardConstraints())
transition.addGuardConstraint(c.deepCopy().renameClocks(pta1, par));
// Combine edges
for (Edge edge1 : transition1.getEdges()) {
prob = edge1.getProbability();
dest = addState(edge1.getDestination(), state.i2);
edge = transition.addEdge(prob, dest);
// Copy resets
for (Map.Entry<Integer, Integer> e : edge1.getResets()) {
edge.addReset(PTA.renameClock(pta1, par, e.getKey()), e.getValue());
}
}
}
}
// Go through asynchronous transitions of PTA 2
for (String a : alpha2only) {
for (Transition transition2 : pta2.getTransitionsByAction(state.i2, a)) {
// Create new transition
transition = par.addTransition(src, a);
// Copy guard
for (Constraint c : transition2.getGuardConstraints())
transition.addGuardConstraint(c.deepCopy().renameClocks(pta2, par));
// Combine edges
for (Edge edge2 : transition2.getEdges()) {
prob = edge2.getProbability();
dest = addState(state.i1, edge2.getDestination());
edge = transition.addEdge(prob, dest);
// Copy resets
for (Map.Entry<Integer, Integer> e : edge2.getResets()) {
edge.addReset(PTA.renameClock(pta2, par, e.getKey()), e.getValue());
}
}
}
}
// Go through synchronous transitions
for (String a : sync) {
for (Transition transition1 : pta1.getTransitionsByAction(state.i1, a)) {
for (Transition transition2 : pta2.getTransitionsByAction(state.i2, a)) {
// Create new transition
transition = par.addTransition(src, a);
// Guard is conjunction of guards
for (Constraint c : transition1.getGuardConstraints())
transition.addGuardConstraint(c.deepCopy().renameClocks(pta1, par));
for (Constraint c : transition2.getGuardConstraints())
transition.addGuardConstraint(c.deepCopy().renameClocks(pta2, par));
// Combine edges
for (Edge edge1 : transition1.getEdges()) {
for (Edge edge2 : transition2.getEdges()) {
prob = edge1.getProbability() * edge2.getProbability();
dest = addState(edge1.getDestination(), edge2.getDestination());
edge = transition.addEdge(prob, dest);
// Reset set is union of reset sets
for (Map.Entry<Integer, Integer> e : edge1.getResets()) {
edge.addReset(PTA.renameClock(pta1, par, e.getKey()), e.getValue());
}
for (Map.Entry<Integer, Integer> e : edge2.getResets()) {
edge.addReset(PTA.renameClock(pta2, par, e.getKey()), e.getValue());
}
}
}
}
}
}
}
return par;
}
/** Build a time bounded reachability query into a PTA; return the new target location set. */
private BitSet buildTimeBoundIntoPta(
PTA pta, BitSet targetLocs, int timeBound, boolean timeBoundStrict) {
String timerClock = null;
int timerClockIndex, numLocs, newTargetLoc;
String newTargetLocString;
List<Transition> trNewList;
Transition trNew;
BitSet targetLocsNew;
boolean toTarget;
int i;
// Add a timer clock
timerClock = "time";
while (pta.getClockIndex(timerClock) != -1) timerClock += "_";
timerClockIndex = pta.addClock(timerClock);
// Add a new target location
numLocs = pta.getNumLocations();
newTargetLocString = "target";
while (pta.getLocationIndex(newTargetLocString) != -1) newTargetLocString += "_";
newTargetLoc = pta.addLocation(newTargetLocString);
// Go through old (on-target) locations
for (i = 0; i < numLocs; i++) {
trNewList = new ArrayList<Transition>();
for (Transition tr : pta.getTransitions(i)) {
// See if the transition can go to a target location
toTarget = false;
for (Edge e : tr.getEdges()) {
if (targetLocs.get(e.getDestination())) {
toTarget = true;
break;
}
}
// Copy transition, modify edges going to target and add guard
if (toTarget) {
trNew = new Transition(tr);
for (Edge e : trNew.getEdges()) {
if (targetLocs.get(e.getDestination())) {
e.setDestination(newTargetLoc);
}
}
if (timeBoundStrict)
trNew.addGuardConstraint(Constraint.buildLt(timerClockIndex, timeBound));
else trNew.addGuardConstraint(Constraint.buildLeq(timerClockIndex, timeBound));
trNewList.add(trNew);
// Modify guard of copied transition
if (timeBoundStrict)
tr.addGuardConstraint(Constraint.buildGeq(timerClockIndex, timeBound));
else tr.addGuardConstraint(Constraint.buildGt(timerClockIndex, timeBound));
}
}
// Add new transitions to PTA
for (Transition tr : trNewList) {
pta.addTransition(tr);
}
}
// Re-generate set of target locations
targetLocsNew = new BitSet(pta.getNumLocations());
targetLocsNew.set(newTargetLoc);
return targetLocsNew;
}