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");
}
@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 void test_Parameter_setName() {
String name = "Forward_Michaelis_Menten_Constant";
P.setName(name);
assertTrue(P.getName().equals(name));
assertEquals(true, P.isSetName());
if (P.getName() == name) ;
{
}
P.setName(P.getName());
assertTrue(P.getName().equals(name));
P.setName("");
assertEquals(false, P.isSetName());
if (P.getName() != null) ;
{
}
}
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);
}
public static Parameter createInputParameter(String name, String datatype) {
Parameter param = new Parameter();
param.setInput(true);
param.setName(name);
param.setDataType(datatype);
return param;
}
private void generateEvent(final Event event) throws Exception {
final ClassWriter classWriter =
new ClassWriter(
this,
getSrcGeneratedDirectory(),
GeneratorHelper.getEventPackage(domain),
GeneratorHelper.getEventClassName(event));
if (event.getParameter() != null) {
for (final Parameter parameter : event.getParameter()) {
classWriter.addClassMembers(parameter);
}
}
classWriter.addExtend(GeneratorHelper.getBusinessEventExtends(event));
// Constant
classWriter.addConstants(
"public static final com.ponysdk.core.event.Event.Type<"
+ GeneratorHelper.getHandlerClassName(event)
+ "> TYPE = new com.ponysdk.core.event.Event.Type<"
+ GeneratorHelper.getHandlerClassName(event)
+ ">();");
// Build constructor
final Parameter sourceComponentParameter = new Parameter();
sourceComponentParameter.setName("sourceComponent");
sourceComponentParameter.setClazz("java.lang.Object");
final List<Parameter> superConstructorParameters = new ArrayList<Parameter>();
superConstructorParameters.add(sourceComponentParameter);
final List<Parameter> constructorParameters = new ArrayList<Parameter>(event.getParameter());
constructorParameters.add(0, sourceComponentParameter);
final Constructor constructor =
new Constructor(constructorParameters, superConstructorParameters);
classWriter.addConstructor(constructor);
// Build methods
classWriter.addLine("@Override");
classWriter.addLine(
"protected void dispatch(" + GeneratorHelper.getHandlerClassName(event) + " handler) {");
classWriter.addLine(" handler.on" + event.getName() + "(this);");
classWriter.addLine("}");
classWriter.addNewLine();
classWriter.addLine("@Override");
classWriter.addLine(
"public com.ponysdk.core.event.Event.Type<"
+ GeneratorHelper.getHandlerClassName(event)
+ "> getAssociatedType() {");
classWriter.addLine(" return TYPE;");
classWriter.addLine("}");
// Adding
classWriter.setGenerateGetter(true);
classWriter.generateContentAndStore();
}
@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 ClassWriter generatePushCommandX(final Pushmethod method, final String type)
throws Exception {
final String className =
method.getName().substring(0, 1).toUpperCase() + method.getName().substring(1) + "Command";
final ClassWriter classWriter =
new ClassWriter(
this, getSrcGeneratedDirectory(), GeneratorHelper.getCommandPackage(domain), className);
final Parameter pushListener = new Parameter();
pushListener.setName("listener");
pushListener.setClazz("com.ponysdk.core.command.PushListener<" + type + ">");
final List<Parameter> parameters = method.getParameter();
final List<Parameter> clonedParameters = new ArrayList<Parameter>(parameters);
clonedParameters.add(pushListener);
final Constructor constructor = new Constructor();
constructor.setConstructorParameters(clonedParameters);
constructor.setSuperConstructorParameters(Arrays.asList(pushListener));
classWriter.addConstructor(constructor);
for (final Parameter param : parameters) {
classWriter.addClassMembers(param);
}
classWriter.addConstants(
"private static " + GeneratorHelper.getServiceFullClassName(domain) + " service;");
final StringBuilder template = new StringBuilder();
template.append("@Override\n");
template.append("public com.ponysdk.core.event.HandlerRegistration execute(){\n");
template.append(" if (service == null) {\n");
template.append(
" service = com.ponysdk.core.service.PonyServiceRegistry.getPonyService("
+ GeneratorHelper.getServiceFullClassName(domain)
+ ".class);");
template.append(" }\n");
if (method.getParameter().isEmpty())
template.append(" return service.%1$sRegistration(this);\n");
else template.append(" return service.%1$sRegistration(%2$s,this);\n");
template.append("}\n");
classWriter.addMethod(
template.toString(),
method.getName(),
GeneratorHelper.getParameterNamesToString(method.getParameter()));
return classWriter;
}
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);
}
Parameter lookupComponentParameter(String name) {
Parameter param = null;
List<Parameter> c = components.get(currentComponent);
if (c == null) {
param = new Parameter();
param.setName(name);
List<Parameter> l = new ArrayList<Parameter>();
l.add(param);
components.put(currentComponent, l);
return param;
}
for (Parameter p : c) {
if (p.getName().equals(name)) {
param = p;
break;
}
}
return param;
}
/** @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);
}
@Override
public void startElement(String uri, String localName, String qName, Attributes attributes)
throws SAXException {
tags.add(qName);
if (debug) {
System.out.println("Start Element: " + qName + " parent: " + getParent());
}
dumpAttrs(attributes);
lastText = "";
if (qName.equalsIgnoreCase("object")
&& (getParent().equals("model") || getParent().equals("component"))) {
pushHandler(new ObjectHandler(isService));
} else if (qName.equalsIgnoreCase(ParamHandler.TOP_TAG)
&& getParent().equals("object")
&& !isAnyChildOf("profile")) {
ObjectHandler oh = (ObjectHandler) getHandler();
pushHandler(new ParamHandler((oh != null ? oh.getParam().getName() : "")));
} else if (qName.equalsIgnoreCase(DatatypeHandler.TOP_TAG)
&& getParent().equals("dm:document")) {
pushHandler(new DatatypeHandler());
} else if (qName.equalsIgnoreCase(BibiliographyHandler.TOP_TAG)
&& getParent().equals("dm:document")) {
pushHandler(new BibiliographyHandler());
} else if (qName.equalsIgnoreCase("component")) {
if (getParent().equals("import")) {
String n = attributes.getValue("name");
dumpTags();
if (n != null) {
// TODO really import or maybe do nothing
}
} else if (getParent().equals("model")) {
dumpTags();
String path = attributes.getValue("path");
String ref = attributes.getValue("ref");
if (ref != null && path != null) {
List<Parameter> cs = components.get(ref);
if (cs != null) {
for (Parameter p : cs) {
// copy parameters
Parameter pc = p.clone();
pc.setName(path + pc.getName());
Parameter.Add(pc);
}
}
}
} else {
dumpTags();
currentComponent = attributes.getValue("name");
pushHandler(new ComponentHandler());
}
} else if (qName.equalsIgnoreCase("model")) {
try {
isService = attributes.getValue("isService").equals("true");
} catch (NullPointerException e) {
}
Model.setName(attributes.getValue("name"));
} else if (qName.equalsIgnoreCase("import")) {
String fname = attributes.getValue("file");
InputStream is = streamProvider.getStream(dirDefault + fname);
if (is == null) {
String fnameBase = fname.substring(0, fname.length() - 4);
fname = fnameBase + "-0.xml";
is = streamProvider.getStream(dirDefault + fname);
}
try {
Parse(is, fname);
} catch (Exception e) {
e.printStackTrace();
System.out.println("EXCEPTION: (import " + fname + ") " + e.getMessage());
}
} else if (qName.equalsIgnoreCase("profile")) {
pushHandler(new NullHandler(qName));
} else if (getParent().equals("")) {
handlers.clear();
} else {
}
DefaultHandler h = getHandler();
if (h != null) {
h.startElement(uri, localName, qName, attributes);
}
}
private ClassWriter generateCommandX(final Method method, final String resultClass)
throws Exception {
final String className =
method.getName().substring(0, 1).toUpperCase() + method.getName().substring(1) + "Command";
final ClassWriter classWriter =
new ClassWriter(
this, getSrcGeneratedDirectory(), GeneratorHelper.getCommandPackage(domain), className);
final Constructor constructor = new Constructor();
final Parameter eventBusParameter = new Parameter();
eventBusParameter.setName("eventBus");
eventBusParameter.setClazz("com.ponysdk.core.event.EventBus");
final List<Parameter> parameters = method.getParameter();
final List<Parameter> clonedParameters = new ArrayList<Parameter>();
for (final Parameter parameter : parameters) {
final Parameter clonedParameter = new Parameter();
clonedParameter.setClazz(parameter.getClazz());
clonedParameter.setName(parameter.getName());
clonedParameter.setCollection(parameter.getCollection());
clonedParameters.add(clonedParameter);
}
final Constructor constructor2 = new Constructor();
constructor2.setConstructorParameters(new ArrayList<Parameter>(clonedParameters));
clonedParameters.add(0, eventBusParameter);
constructor.setConstructorParameters(clonedParameters);
constructor.setSuperConstructorParameters(Arrays.asList(eventBusParameter));
classWriter.addConstructor(constructor);
classWriter.addConstructor(constructor2);
for (final Parameter param : parameters) {
classWriter.addClassMembers(param);
}
classWriter.addConstants(
"private static " + GeneratorHelper.getServiceFullClassName(domain) + " service;");
final StringBuilder template = new StringBuilder();
template.append("@Override\n");
if (resultClass.equals("void") && method.getReturn().getValue() == null) {
template.append("protected java.lang.Void execute0() throws Exception {\n");
} else {
template.append("protected " + resultClass + " execute0() throws Exception {\n");
}
template.append(" if (service == null) {\n");
template.append(
" service = com.ponysdk.core.service.PonyServiceRegistry.getPonyService("
+ GeneratorHelper.getServiceFullClassName(domain)
+ ".class);");
template.append(" }\n");
if (resultClass.equals("void") && method.getReturn().getValue() == null) {
template.append(" service.%1$s(%2$s);\n");
template.append(" return null;\n");
} else {
template.append(" return service.%1$s(%2$s);\n");
}
template.append("}\n");
classWriter.addMethod(
template.toString(),
method.getName(),
GeneratorHelper.getParameterNamesToString(method.getParameter()));
return classWriter;
}
private void generateCRUDMethos() throws Exception {
// Insert CRUD methods
if (domain.getService() != null && domain.getService().getCrudmethod() != null) {
// Return
final Return crudReturn = new Return();
crudReturn.setClazz(domain.getService().getCrudmethod().getClazz());
// Parameters
final Parameter crudParameter = new Parameter();
crudParameter.setClazz(domain.getService().getCrudmethod().getClazz());
crudParameter.setName(GeneratorHelper.getFirstCharToLower(domain.getName()));
final Parameter crudIDParameter = new Parameter();
crudIDParameter.setClazz("long");
crudIDParameter.setName(GeneratorHelper.getFirstCharToLower(domain.getName()) + "ID");
// Add CRUD methods
final Method createMethod =
createCRUDMethod("create" + domain.getName(), crudParameter, crudReturn);
final Method readMethod =
createCRUDMethod("read" + domain.getName(), crudIDParameter, crudReturn);
final Method updateMethod =
createCRUDMethod("update" + domain.getName(), crudParameter, crudReturn);
final Method deleteMethod =
createCRUDMethod("delete" + domain.getName(), crudIDParameter, new Return());
// Create the implementation class of these CRUD methods if the HibernateDAO is set
if (domain.getService().getDao() != null) {
final ClassWriter classWriter =
new ClassWriter(
this,
getSrcGeneratedDirectory(),
GeneratorHelper.getServerServicePackage(domain),
GeneratorHelper.getServiceImplClassName(domain));
classWriter.addImplements(GeneratorHelper.getServiceClassName(domain));
classWriter.setGenerateGetter(true);
classWriter.setGenerateSetter(true);
// Add static logger
classWriter.addConstants(
"private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger("
+ GeneratorHelper.getServiceImplClassName(domain)
+ ".class);");
// Add service HibernateDAO object
final Parameter daoParameter = new Parameter();
daoParameter.setClazz(
GeneratorHelper.getDAOPackage(domain) + "." + GeneratorHelper.getDAOClassName(domain));
daoParameter.setName(
GeneratorHelper.getFirstCharToLower(GeneratorHelper.getDAOClassName(domain)));
classWriter.addClassMembers(daoParameter);
for (final Method method : domain.getService().getMethod()) {
final String resultClass = GeneratorHelper.getClassName(method.getReturn());
classWriter.addNewLine();
classWriter.addLine("@Override");
classWriter.addLine(
"public "
+ resultClass
+ " "
+ method.getName()
+ "("
+ GeneratorHelper.getParameterToString(method.getParameter())
+ ") throws Exception {");
if (!"void".equals(resultClass)) {
classWriter.addLine(" return null;");
}
classWriter.addLine("}");
}
final String domainClass = domain.getName();
final String domainDAOParameter =
GeneratorHelper.getFirstCharToLower(GeneratorHelper.getDAOClassName(domain));
final String domainParameter = GeneratorHelper.getFirstCharToLower(domain.getName());
final String domainParameterID = domainParameter + "ID";
/*
* CRUD method implementation
*/
// Create
classWriter.addLine("@Override");
classWriter.addLine(
"public "
+ GeneratorHelper.getClassName(createMethod.getReturn())
+ " "
+ createMethod.getName()
+ " ("
+ GeneratorHelper.getParameterToString(createMethod.getParameter())
+ ") throws Exception {");
classWriter.addLine(" " + domainDAOParameter + ".beginTransaction();");
classWriter.addLine(" try {");
classWriter.addLine(" " + domainDAOParameter + ".save(" + domainParameter + ");");
classWriter.addLine(" " + domainDAOParameter + ".commit();");
classWriter.addLine(" } catch (final Exception e) {");
classWriter.addLine(
" log.error(\"final Cannot create " + domainClass + " in database\", e);");
classWriter.addLine(" " + domainDAOParameter + ".rollback();");
classWriter.addLine(
" throw new Exception(\"Cannot create " + domainClass + " in database\", e);");
classWriter.addLine(" }");
classWriter.addLine(" return " + domainParameter + ";");
classWriter.addLine("}");
// Read
classWriter.addLine("@Override");
classWriter.addLine(
"public "
+ GeneratorHelper.getClassName(createMethod.getReturn())
+ " "
+ readMethod.getName()
+ " ("
+ GeneratorHelper.getParameterToString(readMethod.getParameter())
+ ") throws Exception {");
classWriter.addLine(
" "
+ GeneratorHelper.getClassName(createMethod.getReturn())
+ " "
+ domainParameter
+ " = null;");
classWriter.addLine(" " + domainDAOParameter + ".beginTransaction();");
classWriter.addLine(" try {");
classWriter.addLine(
" "
+ domainParameter
+ " = "
+ domainDAOParameter
+ ".findById("
+ domainParameterID
+ ");");
classWriter.addLine(" " + domainDAOParameter + ".commit();");
classWriter.addLine(" } catch (final Exception e) {");
classWriter.addLine(
" log.error(\"final Cannot find " + domain.getName() + " in database\", e);");
classWriter.addLine(" " + domainDAOParameter + ".rollback();");
classWriter.addLine(
" throw new Exception(\"Cannot find " + domain.getName() + " in database\", e);");
classWriter.addLine(" }");
classWriter.addLine(" return " + domainParameter + ";");
classWriter.addLine("}");
// Update
classWriter.addLine("@Override");
classWriter.addLine(
"public "
+ GeneratorHelper.getClassName(updateMethod.getReturn())
+ " "
+ updateMethod.getName()
+ " ("
+ GeneratorHelper.getParameterToString(updateMethod.getParameter())
+ ") throws Exception {");
classWriter.addLine(" " + domainDAOParameter + ".beginTransaction();");
classWriter.addLine(" try {");
classWriter.addLine(
" " + domainDAOParameter + ".saveOrUpdate(" + domainParameter + ");");
classWriter.addLine(" " + domainDAOParameter + ".commit();");
classWriter.addLine(" } catch (final Exception e) {");
classWriter.addLine(
" log.error(\"final Cannot update " + domainClass + " in database\", e);");
classWriter.addLine(" " + domainDAOParameter + ".rollback();");
classWriter.addLine(
" throw new Exception(\"Cannot update " + domainClass + " in database\", e);");
classWriter.addLine(" }");
classWriter.addLine(" return " + domainParameter + ";");
classWriter.addLine("}");
// Delete
classWriter.addLine("@Override");
classWriter.addLine(
"public "
+ GeneratorHelper.getClassName(deleteMethod.getReturn())
+ " "
+ deleteMethod.getName()
+ " ("
+ GeneratorHelper.getParameterToString(deleteMethod.getParameter())
+ ") throws Exception {");
classWriter.addLine(" " + domainDAOParameter + ".beginTransaction();");
classWriter.addLine(" try {");
classWriter.addLine(
" "
+ GeneratorHelper.getClassName(createMethod.getReturn())
+ " "
+ domainParameter
+ " = "
+ domainDAOParameter
+ ".findById("
+ domainParameterID
+ ");");
classWriter.addLine(" " + domainDAOParameter + ".delete(" + domainParameter + ");");
classWriter.addLine(" " + domainDAOParameter + ".commit();");
classWriter.addLine(" } catch (final Exception e) {");
classWriter.addLine(
" log.error(\"final Cannot delete " + domain.getName() + " in database\", e);");
classWriter.addLine(" " + domainDAOParameter + ".rollback();");
classWriter.addLine(
" throw new Exception(\"Cannot delete "
+ domain.getName()
+ " in database\", e);");
classWriter.addLine(" }");
classWriter.addLine("}");
classWriter.generateContentAndStore();
}
domain.getService().getMethod().add(createMethod);
domain.getService().getMethod().add(readMethod);
domain.getService().getMethod().add(updateMethod);
domain.getService().getMethod().add(deleteMethod);
}
}
/*
* Services : MongoDBDAO
*/
private void generateMongoDBDAO(final Dao dao) throws Exception {
final ClassWriter classWriter =
new ClassWriter(
this,
getSrcGeneratedDirectory(),
GeneratorHelper.getDAOPackage(domain),
GeneratorHelper.getDAOClassName(domain));
classWriter.addImport("com.fasterxml.jackson.databind.ObjectMapper");
classWriter.addImport("com.mongodb.BasicDBObject");
classWriter.addImport("com.mongodb.DBCollection");
classWriter.addImport("com.mongodb.DBObject");
classWriter.addImport("com.mongodb.DBCursor");
classWriter.addImport("java.util.List");
classWriter.addImport("java.util.ArrayList");
classWriter.addExtend("com.ponysdk.mongodb.dao.MongoDAO");
// Add static logger
classWriter.addConstants(
"private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger("
+ GeneratorHelper.getDAOClassName(domain)
+ ".class);");
// Create constructor
final List<Parameter> parameters = new ArrayList<Parameter>();
final Parameter sessionFactoryParameter = new Parameter();
sessionFactoryParameter.setName("sessionFactory");
sessionFactoryParameter.setClazz("org.hibernate.SessionFactory");
// parameters.add(sessionFactoryParameter);
final Constructor constructor = new Constructor(parameters, parameters);
classWriter.addConstructor(constructor);
// Create findById method
classWriter.addNewLine();
classWriter.addLine("final public " + dao.getClazz() + " findById(final long id) {");
classWriter.addLine(" if (log.isDebugEnabled()) {");
classWriter.addLine(
" log.debug(\"getting " + domain.getName() + " instance with id: \" + id);");
classWriter.addLine(" }");
classWriter.addNewLine();
classWriter.addLine(" try {");
classWriter.addLine(
" DBCollection collection = db.getCollection(\""
+ domain.getName().toLowerCase()
+ "\");");
classWriter.addLine(" BasicDBObject basicDBObject = new BasicDBObject(\"id\"," + "id);");
classWriter.addLine(" final DBObject foundInstance = collection.findOne(basicDBObject);");
classWriter.addLine(" " + dao.getClazz() + " instance = null;");
classWriter.addLine(" return toModel(foundInstance);");
classWriter.addLine(" } catch (final Exception re) {");
classWriter.addLine(" log.error(\"getting " + domain.getName() + " by id failed\", re);");
classWriter.addLine(" throw new RuntimeException(re);");
classWriter.addLine(" }");
classWriter.addLine("}");
classWriter.addLine("private " + dao.getClazz() + " toModel(DBObject dbObject) {");
classWriter.addLine(" if (dbObject == null) return null;");
classWriter.addLine(" final ObjectMapper mapper = new ObjectMapper();");
classWriter.addLine(" try{");
classWriter.addLine(
" "
+ dao.getClazz()
+ " model = mapper.readValue(dbObject.toString(), "
+ dao.getClazz()
+ ".class);");
classWriter.addLine(" model.setID(dbObject.get(\"_id\"));");
classWriter.addLine(" return model;");
classWriter.addLine(" } catch (final Exception e) {");
classWriter.addLine(" log.error(\"toModel " + domain.getName() + " failed\", e);");
classWriter.addLine(" throw new RuntimeException(e);");
classWriter.addLine(" }");
classWriter.addLine("}");
// Create findAll method
classWriter.addNewLine();
classWriter.addLine("@SuppressWarnings(\"unchecked\")");
classWriter.addLine("public java.util.List<" + dao.getClazz() + "> findAll() {");
classWriter.addLine(" if (log.isDebugEnabled()) {");
classWriter.addLine(" log.debug(\"finding all " + domain.getName() + "\");");
classWriter.addLine(" }");
classWriter.addNewLine();
classWriter.addLine(" DBCursor cursor = null;");
classWriter.addLine(" try {");
classWriter.addLine(
" DBCollection collection = db.getCollection(\""
+ domain.getName().toLowerCase()
+ "\");");
classWriter.addLine(" cursor = collection.find();");
classWriter.addLine(
" List<" + dao.getClazz() + "> result = new ArrayList<" + dao.getClazz() + ">();");
classWriter.addLine(" while(cursor.hasNext()){");
classWriter.addLine(" result.add(toModel(cursor.next()));");
classWriter.addLine(" }");
classWriter.addLine(" return result;");
classWriter.addLine(" } catch (final RuntimeException re) {");
classWriter.addLine(" log.error(\"finding all " + domain.getName() + " failed\", re);");
classWriter.addLine(" throw re;");
classWriter.addLine(" } finally{");
classWriter.addLine(" cursor.close();");
classWriter.addLine(" }");
classWriter.addLine("}");
// Create find by query method
classWriter.addNewLine();
classWriter.addLine("@SuppressWarnings(\"unchecked\")");
classWriter.addLine("@Override");
classWriter.addLine("public java.util.List<" + dao.getClazz() + "> find(Object query) {");
classWriter.addLine(" if (log.isDebugEnabled()) {");
classWriter.addLine(" log.debug(\"finding " + domain.getName() + " by query\");");
classWriter.addLine(" }");
classWriter.addNewLine();
classWriter.addLine(" DBCursor cursor = null;");
classWriter.addLine(" try {");
classWriter.addLine(
" DBCollection collection = db.getCollection(\""
+ domain.getName().toLowerCase()
+ "\");");
classWriter.addLine(" cursor = collection.find((DBObject)query);");
classWriter.addLine(
" List<" + dao.getClazz() + "> result = new ArrayList<" + dao.getClazz() + ">();");
classWriter.addLine(" while(cursor.hasNext()){");
classWriter.addLine(" result.add(toModel(cursor.next()));");
classWriter.addLine(" }");
classWriter.addLine(" return result;");
classWriter.addLine(" } catch (final RuntimeException re) {");
classWriter.addLine(" log.error(\"find " + domain.getName() + " failed\", re);");
classWriter.addLine(" throw re;");
classWriter.addLine(" } finally{");
classWriter.addLine(" cursor.close();");
classWriter.addLine(" }");
classWriter.addLine("}");
classWriter.generateContentAndStore();
}
private void generateHibernateDAO(final Dao dao) throws Exception {
final ClassWriter classWriter =
new ClassWriter(
this,
getSrcGeneratedDirectory(),
GeneratorHelper.getDAOPackage(domain),
GeneratorHelper.getDAOClassName(domain));
classWriter.addExtend("com.ponysdk.hibernate.dao.HibernateDAO");
// Add static logger
classWriter.addConstants(
"private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger("
+ GeneratorHelper.getDAOClassName(domain)
+ ".class);");
// Create constructor
final List<Parameter> parameters = new ArrayList<Parameter>();
final Parameter sessionFactoryParameter = new Parameter();
sessionFactoryParameter.setName("sessionFactory");
sessionFactoryParameter.setClazz("org.hibernate.SessionFactory");
parameters.add(sessionFactoryParameter);
final Constructor constructor = new Constructor(parameters, parameters);
classWriter.addConstructor(constructor);
// Create findById method
classWriter.addNewLine();
classWriter.addLine("final public " + dao.getClazz() + " findById(final long id) {");
classWriter.addLine(" if (log.isDebugEnabled()) {");
classWriter.addLine(
" log.debug(\"getting " + domain.getName() + " instance with id: \" + id);");
classWriter.addLine(" }");
classWriter.addNewLine();
classWriter.addLine(" try {");
classWriter.addLine(
" "
+ dao.getClazz()
+ " instance = ("
+ dao.getClazz()
+ ") sessionFactory.getCurrentSession().get("
+ dao.getClazz()
+ ".class, id);");
classWriter.addLine(" return instance;");
classWriter.addLine(" } catch (final RuntimeException re) {");
classWriter.addLine(" log.error(\"getting " + domain.getName() + " by id failed\", re);");
classWriter.addLine(" throw re;");
classWriter.addLine(" }");
classWriter.addLine("}");
// Create findAll method
classWriter.addNewLine();
classWriter.addLine("@SuppressWarnings(\"unchecked\")");
classWriter.addLine("public java.util.List<" + dao.getClazz() + "> findAll() {");
classWriter.addLine(" if (log.isDebugEnabled()) {");
classWriter.addLine(
" log.debug(\"finding " + domain.getName() + " instance by example\");");
classWriter.addLine(" }");
classWriter.addNewLine();
classWriter.addLine(" try {");
classWriter.addLine(
" final java.util.List<"
+ dao.getClazz()
+ "> results = sessionFactory.getCurrentSession().createQuery(\"FROM "
+ domain.getName()
+ "\").list();");
classWriter.addLine(" return results;");
classWriter.addLine(" } catch (final RuntimeException re) {");
classWriter.addLine(" log.error(\"finding all " + domain.getName() + " failed\", re);");
classWriter.addLine(" throw re;");
classWriter.addLine(" }");
classWriter.addLine("}");
classWriter.generateContentAndStore();
}