/**
* Creates a wrapper model class that contains all model classes as list of objects. This class is
* used for storing test data
*/
private void generateWrapperClassForTestData(
List<String> generatedClassNames, StringTemplateGroup templateGroup) {
Model model = new Model();
model.setName("TestData");
model.setDescription(
"Class used to store all the test data. This should not be used for any development");
List<ModelField> modelFields = new ArrayList<ModelField>();
model.setFields(modelFields);
for (String className : generatedClassNames) {
ModelField aParam = new ModelField();
aParam.setName(this.getNameGenerator().applyMethodNamingPolicy(className) + "List");
aParam.setParamType(this.getDataTypeMappingProvider().getListReturnTypeSignature(className));
modelFields.add(aParam);
}
List<String> imports = new ArrayList<String>();
imports.addAll(this.config.getDefaultModelImports());
imports.addAll(this.getDataTypeMappingProvider().getListIncludes());
for (ModelField param : model.getFields()) {
for (String importDef :
param
.getFieldDefinition(this.getDataTypeMappingProvider(), config, nameGenerator)
.getImportDefinitions()) {
if (!imports.contains(importDef)) {
imports.add(importDef);
}
}
}
StringTemplate template = templateGroup.getInstanceOf(MODEL_OBJECT_TEMPLATE);
template.setAttribute("fields", model.getFields());
template.setAttribute("imports", imports);
template.setAttribute("annotationPackageName", languageConfig.getAnnotationPackageName());
template.setAttribute("extends", config.getDefaultModelBaseClass());
template.setAttribute(PACKAGE_NAME, config.getModelPackageName());
template.setAttribute("className", model.getGenratedClassName());
File aFile =
new File(
languageConfig.getModelClassLocation()
+ model.getGenratedClassName()
+ languageConfig.getClassFileExtension());
writeFile(aFile, template.toString(), "Wrapper class for test data file");
}
/** @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);
}
}
public Model toMavenModel() {
Model model = new Model();
model.setBuild(new Build());
model.setDescription(description);
model.setUrl(url);
model.setName(projectId.getArtifact());
model.setGroupId(projectId.getGroup());
model.setVersion(projectId.getVersion());
model.setArtifactId(projectId.getArtifact());
model.setModelVersion("4.0.0");
// parent
if (parent != null) {
model.setParent(parent);
}
model.setPackaging(packaging);
if (properties != null) {
Properties modelProperties = new Properties();
for (Property p : properties) {
modelProperties.setProperty(p.getKey(), p.getValue());
}
model.setProperties(modelProperties);
}
// Add jar repository urls.
if (null != repositories) {
for (String repoUrl : repositories.getRepositories()) {
Repository repository = new Repository();
repository.setId(Integer.toString(repoUrl.hashCode()));
repository.setUrl(repoUrl);
model.addRepository(repository);
}
}
// Add dependency management
if (overrides != null) {
DependencyManagement depMan = new DependencyManagement();
for (Id dep : overrides) {
Dependency dependency = new Dependency();
dependency.setGroupId(dep.getGroup());
dependency.setArtifactId(dep.getArtifact());
dependency.setVersion(dep.getVersion());
// JVZ: We need to parse these
dependency.setType("jar");
if (null != dep.getClassifier()) {
dependency.setClassifier(dep.getClassifier());
}
depMan.addDependency(dependency);
}
model.setDependencyManagement(depMan);
}
// Add project dependencies.
if (deps != null) {
for (Id dep : deps) {
Dependency dependency = new Dependency();
dependency.setGroupId(dep.getGroup());
dependency.setArtifactId(dep.getArtifact());
dependency.setVersion(dep.getVersion());
// JVZ: We need to parse these
dependency.setType("jar");
if (null != dep.getClassifier()) {
dependency.setClassifier(dep.getClassifier());
}
model.addDependency(dependency);
}
}
if (modules != null) {
model.setModules(modules);
}
if (pluginOverrides != null) {
PluginManagement management = new PluginManagement();
management.setPlugins(pluginOverrides);
model.getBuild().setPluginManagement(management);
}
if (plugins != null) {
model.getBuild().setPlugins(plugins);
}
// Optional source dirs customization.
if (dirs != null) {
Build build = new Build();
String srcDir = dirs.get("src");
String testDir = dirs.get("test");
if (null != srcDir) build.setSourceDirectory(srcDir);
if (null != testDir) build.setTestSourceDirectory(testDir);
model.setBuild(build);
}
if (null != scm) {
Scm scm = new Scm();
scm.setConnection(this.scm.getConnection());
scm.setDeveloperConnection(this.scm.getDeveloperConnection());
scm.setUrl(this.scm.getUrl());
model.setScm(scm);
}
return model;
}
public ResourceMethod generateMethod(
Endpoint endPoint,
Resource resource,
DataTypeMappingProvider dataTypeMapper,
NamingPolicyProvider nameGenerator) {
if (method == null) {
method = new ResourceMethod();
// add method description
method.setTitle(this.getSummary());
method.setDescription(this.getNotes());
// add method name
// get resource path for making web service call
/**
* Logic for method names 1. remove all path parameters 2. Remove format path parameter 3. For
* POST add save 4. For PUT add update 5. For DELETE add delete 6. For GET add get 7.
* Concatenate rest of the path with init caps 8.
*/
String inputobjectName =
nameGenerator.getInputObjectName(
resource.generateClassName(nameGenerator), endPoint.getPath());
String[] pathElements = endPoint.getPath().split("/");
StringBuilder urlPath = new StringBuilder("");
if (pathElements != null) {
for (int i = 0; i < pathElements.length; i++) {
String pathElement = pathElements[i];
if (pathElement != null && pathElement.length() > 0) {
int position = pathElement.indexOf("{");
if (urlPath.length() > 0) {
urlPath.append("+");
}
if (position < 0) {
urlPath.append("\"/" + pathElement + "\"");
} else if (position == 0) {
urlPath.append("\"/\"+" + pathElement.substring(1, pathElement.length() - 1));
} else {
urlPath.append("\"/" + pathElement.replace("{format}", "json") + "\"");
}
}
}
}
method.setResourcePath(endPoint.getPath());
method.setName(nameGenerator.getMethodName(endPoint.getPath(), this.getNickname()));
// create method argument
/**
* 1. API token need not be included as that is always added to the calls as HTTP headers 2.
* We need to handle auth token specially, hence need to differentiate that 3. Query
* parameters needs to be added as query string hence need to separate them out 4. Post
* parameters are usually WordnikObjects, hence we need to handle them separately
*/
List<String> argNames = new ArrayList<String>();
if (this.getParameters() != null) {
List<MethodArgument> arguments = new ArrayList<MethodArgument>();
List<MethodArgument> queryParams = new ArrayList<MethodArgument>();
List<MethodArgument> pathParams = new ArrayList<MethodArgument>();
List<MethodArgument> headerParams = new ArrayList<MethodArgument>();
method.setArguments(arguments);
method.setQueryParameters(queryParams);
method.setPathParameters(pathParams);
method.setHeaderParameters(headerParams);
for (ModelField modelField : this.getParameters()) {
if (!argNames.contains(modelField.getName())) {
argNames.add(modelField.getName());
MethodArgument anArgument = new MethodArgument();
anArgument.setAllowedValues(modelField.getAllowedValuesString());
// check if arguments has auth token
if (modelField.getParamType().equalsIgnoreCase(PARAM_TYPE_HEADER)
&& modelField.getName().equals(AUTH_TOKEN_PARAM_NAME)) {
method.setAuthToken(true);
anArgument.setName(AUTH_TOKEN_ARGUMENT_NAME);
anArgument.setDataType(
dataTypeMapper.getClassType(MethodArgument.ARGUMENT_STRING, true));
anArgument.setDescription(modelField.getDescription());
anArgument.setRequired(modelField.isRequired());
anArgument.setDefaultValue(modelField.getDefaultValue());
arguments.add(anArgument);
headerParams.add(anArgument);
} else if (modelField.getParamType().equalsIgnoreCase(PARAM_TYPE_HEADER)
&& modelField.getName().equals(API_KEY_PARAM_NAME)) {
anArgument.setName(API_KEY_PARAM_NAME);
anArgument.setDataType(
dataTypeMapper.getClassType(MethodArgument.ARGUMENT_STRING, true));
anArgument.setRequired(true);
arguments.add(anArgument);
headerParams.add(anArgument);
} else if (modelField.getParamType().equalsIgnoreCase(PARAM_TYPE_PATH)
&& !modelField.getName().equalsIgnoreCase(FORMAT_PARAM_NAME)) {
anArgument.setName(modelField.getName());
anArgument.setDataType(
dataTypeMapper.getClassType(MethodArgument.ARGUMENT_STRING, true));
anArgument.setDescription(modelField.getDescription());
anArgument.setRequired(true); // always true
anArgument.setDefaultValue(modelField.getDefaultValue());
arguments.add(anArgument);
pathParams.add(anArgument);
} else if (modelField.getParamType().equalsIgnoreCase(PARAM_TYPE_QUERY)) {
anArgument.setName(modelField.getName());
anArgument.setDataType(
dataTypeMapper.getClassType(MethodArgument.ARGUMENT_STRING, true));
anArgument.setDescription(modelField.getDescription());
anArgument.setRequired(modelField.isRequired());
anArgument.setDefaultValue(modelField.getDefaultValue());
queryParams.add(anArgument);
arguments.add(anArgument);
} else if (modelField.getParamType().equalsIgnoreCase(PARAM_TYPE_BODY)) {
if (modelField.getName() == null) {
modelField.setName(POST_PARAM_NAME);
}
anArgument.setName(modelField.getName());
anArgument.setDataType(dataTypeMapper.getClassType(modelField.getDataType(), false));
anArgument.setDescription(modelField.getDescription());
anArgument.setRequired(modelField.isRequired());
anArgument.setDefaultValue(modelField.getDefaultValue());
arguments.add(anArgument);
method.setPostObject(true);
}
if (modelField.isAllowMultiple()
&& dataTypeMapper.isPrimitiveType(modelField.getDataType())) {
anArgument.setDataType(
dataTypeMapper.getListReturnTypeSignature(
dataTypeMapper.getClassType(modelField.getDataType(), false)));
}
anArgument.setInputModelClassArgument(inputobjectName, nameGenerator);
}
}
}
// check if input model with the given name is already generated for some other path
boolean inputModelAlreadyGenerated = false;
if (alreadyGeneratedModels.containsKey(inputobjectName)) {
if (!alreadyGeneratedModels.get(inputobjectName).equals(endPoint.getPath())) {
inputModelAlreadyGenerated = true;
}
}
// check for number of arguments, if we have more than 4 then send the arguments as input
// object
if (method.getArguments() != null
&& method.getArguments().size() > ARG_COUNT_FOR_INPUT_MODEL
&& !inputModelAlreadyGenerated) {
List<MethodArgument> arguments = new ArrayList<MethodArgument>();
Model modelforMethodInput = new Model();
modelforMethodInput.setName(inputobjectName);
List<ModelField> fields = new ArrayList<ModelField>();
for (MethodArgument argument : method.getArguments()) {
if (!argument.getName().equals(POST_PARAM_NAME)) {
ModelField aModelField = new ModelField();
aModelField.setAllowedValues(argument.getAllowedValues());
aModelField.setDescription(argument.getDescription());
aModelField.setName(argument.getName());
aModelField.setParamType(argument.getDataType());
fields.add(aModelField);
} else {
arguments.add(argument);
}
}
modelforMethodInput.setFields(fields);
MethodArgument anArgument = new MethodArgument();
anArgument.setDataType(inputobjectName);
anArgument.setName(nameGenerator.applyMethodNamingPolicy(inputobjectName));
arguments.add(anArgument);
method.setArguments(arguments);
method.setInputModel(modelforMethodInput);
alreadyGeneratedModels.put(inputobjectName, endPoint.getPath());
}
List<String> argumentDefinitions = new ArrayList<String>();
List<String> argumentNames = new ArrayList<String>();
if (method.getArguments() != null && method.getArguments().size() > 0) {
for (MethodArgument arg : method.getArguments()) {
if (!arg.getName().equalsIgnoreCase(FORMAT_PARAM_NAME)) {
argumentDefinitions.add(
dataTypeMapper.getArgumentDefinition(arg.getDataType(), arg.getName()));
argumentNames.add(arg.getName());
}
}
method.setArgumentDefinitions(argumentDefinitions);
method.setArgumentNames(argumentNames);
}
// get method type
method.setMethodType(this.getHttpMethod());
// get return value
String returnType = dataTypeMapper.getClassType(responseClass, false);
if ("".equals(returnType)) {
method.setHasResponseValue(false);
} else {
method.setHasResponseValue(true);
}
// set the original response name, this is used in identifying if the respone is single valued
// or multi valued
method.setReturnValueFromOperationJson(responseClass);
method.setReturnValue(dataTypeMapper.getClassType(responseClass, false));
method.setReturnClassName(dataTypeMapper.getGenericType(responseClass));
// if this is a list return type
if (method
.getReturnClassName()
.equals(dataTypeMapper.getListReturnTypeSignature(responseClass))) {
String returnValueTypeName = method.getReturnValue();
Model listWrapperModel = new Model();
listWrapperModel.setName(nameGenerator.getListWrapperName(returnValueTypeName));
List<ModelField> fields = new ArrayList<ModelField>();
ModelField aModelField = new ModelField();
aModelField.setName(nameGenerator.applyMethodNamingPolicy(returnValueTypeName));
aModelField.setParamType(responseClass);
fields.add(aModelField);
listWrapperModel.setFields(fields);
method.setListWrapperModel(listWrapperModel);
}
// get description string for exception
method.setExceptionDescription(calculateExceptionMessage());
}
return method;
}