public void addCompileWarning(String msg, ASTNode node) {
Token token =
new Token(Types.UNKNOWN, node.getText(), node.getLineNumber(), node.getColumnNumber());
sourceUnit
.getErrorCollector()
.addWarning(WarningMessage.POSSIBLE_ERRORS, msg, token, sourceUnit);
}
public void staticBlockInlining(SootClass sootClass) {
this.sootClass = sootClass;
// retrieve the clinit method if any for sootClass
if (!sootClass.declaresMethod("void <clinit>()")) {
System.out.println("no clinit");
return;
}
SootMethod clinit = sootClass.getMethod("void <clinit>()");
// System.out.println(clinit);
// retireve the active body
if (!clinit.hasActiveBody())
throw new RuntimeException("method " + clinit.getName() + " has no active body!");
Body clinitBody = clinit.getActiveBody();
Chain units = ((DavaBody) clinitBody).getUnits();
if (units.size() != 1) {
throw new RuntimeException("DavaBody AST doesn't have single root.");
}
ASTNode AST = (ASTNode) units.getFirst();
if (!(AST instanceof ASTMethodNode))
throw new RuntimeException("Starting node of DavaBody AST is not an ASTMethodNode");
AST.apply(new MethodCallFinder(this));
}
private void printAST(ASTNode<?> ast, int level) {
if (ast != null) {
printTab(level);
System.out.println(level + ":" + ast.getClass().getName() + "@" + ast.getId());
int n = ast.getNumChild();
for (int i = 0; i < n; i++) printAST(ast.getChild(i), level + 1);
}
}
/** @apilevel low-level */
@SuppressWarnings({"unchecked", "cast"})
public RawMethodDecl fullCopy() {
RawMethodDecl res = (RawMethodDecl) copy();
for (int i = 0; i < getNumChildNoTransform(); i++) {
ASTNode node = getChildNoTransform(i);
if (node != null) node = node.fullCopy();
res.setChild(node, i);
}
return res;
}
/** @apilevel low-level */
@SuppressWarnings({"unchecked", "cast"})
public AssignPlusExpr fullCopy() {
AssignPlusExpr res = (AssignPlusExpr) copy();
for (int i = 0; i < getNumChildNoTransform(); i++) {
ASTNode node = getChildNoTransform(i);
if (node != null) node = node.fullCopy();
res.setChild(node, i);
}
return res;
}
@SuppressWarnings({"unchecked", "cast"})
public ArrayTypeWithSizeAccess fullCopy() {
ArrayTypeWithSizeAccess res = (ArrayTypeWithSizeAccess) copy();
for (int i = 0; i < getNumChildNoTransform(); i++) {
ASTNode node = getChildNoTransform(i);
if (node != null) node = node.fullCopy();
res.setChild(node, i);
}
return res;
}
public String getInsertClause() {
String insertString = "";
ASTNode destTree = qb.getParseInfo().getDestForClause(clauseName);
if (destTree != null
&& ((ASTNode) (destTree.getChild(0))).getToken().getType() != TOK_TMP_FILE) {
insertString =
"INSERT OVERWRITE" + HQLParser.getString(qb.getParseInfo().getDestForClause(clauseName));
}
return insertString;
}
@SuppressWarnings({"unchecked", "cast"})
public IfStmt fullCopy() {
IfStmt res = (IfStmt) copy();
for (int i = 0; i < getNumChildNoTransform(); i++) {
ASTNode node = getChildNoTransform(i);
if (node != null) node = node.fullCopy();
res.setChild(node, i);
}
return res;
}
@SuppressWarnings({"unchecked", "cast"})
public ParSuperConstructorAccess fullCopy() {
ParSuperConstructorAccess res = (ParSuperConstructorAccess) copy();
for (int i = 0; i < getNumChildNoTransform(); i++) {
ASTNode node = getChildNoTransform(i);
if (node != null) node = node.fullCopy();
res.setChild(node, i);
}
return res;
}
// Declared in AnonymousClasses.jrag at line 32
@SuppressWarnings({"unchecked", "cast"})
public Opt getSuperClassAccessOpt() {
if (getSuperClassAccessOpt_computed)
return (Opt) ASTNode.getChild(this, getSuperClassAccessOptChildPosition());
int num = boundariesCrossed;
boolean isFinal = this.is$Final();
getSuperClassAccessOpt_value = getSuperClassAccessOpt_compute();
setSuperClassAccessOpt(getSuperClassAccessOpt_value);
if (isFinal && num == boundariesCrossed) getSuperClassAccessOpt_computed = true;
return (Opt) ASTNode.getChild(this, getSuperClassAccessOptChildPosition());
}
// Declared in AnonymousClasses.jrag at line 38
@SuppressWarnings({"unchecked", "cast"})
public List getImplementsList() {
if (getImplementsList_computed)
return (List) ASTNode.getChild(this, getImplementsListChildPosition());
int num = boundariesCrossed;
boolean isFinal = this.is$Final();
getImplementsList_value = getImplementsList_compute();
setImplementsList(getImplementsList_value);
if (isFinal && num == boundariesCrossed) getImplementsList_computed = true;
return (List) ASTNode.getChild(this, getImplementsListChildPosition());
}
/**
* Create a deep copy of the AST subtree at this node. The copy is dangling, i.e. has no parent.
*
* @return dangling copy of the subtree at this node
* @apilevel low-level
*/
@SuppressWarnings({"unchecked", "cast"})
public Wildcard fullCopy() {
Wildcard tree = (Wildcard) copy();
if (children != null) {
for (int i = 0; i < children.length; ++i) {
ASTNode child = (ASTNode) children[i];
if (child != null) {
child = child.fullCopy();
tree.setChild(child, i);
}
}
}
return tree;
}
/**
* @declaredat /home/uoji/JastAddJ/Java1.4Frontend/TypeAnalysis.jrag:577
* @apilevel internal
*/
public TypeDecl Define_TypeDecl_hostType(ASTNode caller, ASTNode child) {
if (caller == getSuperInterfaceIdListNoTransform()) {
int childIndex = caller.getIndexOfChild(child);
return hostType();
}
return super.Define_TypeDecl_hostType(caller, child);
}
// Declared in GenericMethods.jrag at line 108
public SimpleSet Define_SimpleSet_lookupType(ASTNode caller, ASTNode child, String name) {
if (caller == getTypeArgumentListNoTransform()) {
int childIndex = caller.getIndexOfChild(child);
return unqualifiedScope().lookupType(name);
}
return super.Define_SimpleSet_lookupType(caller, child, name);
}
// Declared in GenericMethods.jrag at line 107
public NameType Define_NameType_nameType(ASTNode caller, ASTNode child) {
if (caller == getTypeArgumentListNoTransform()) {
int childIndex = caller.getIndexOfChild(child);
return NameType.TYPE_NAME;
}
return super.Define_NameType_nameType(caller, child);
}
// Declared in TypeAnalysis.jrag at line 257
public TypeDecl Define_TypeDecl_declType(ASTNode caller, ASTNode child) {
if (caller == getVariableDeclListNoTransform()) {
int childIndex = caller.getIndexOfChild(child);
return null;
}
return getParent().Define_TypeDecl_declType(this, caller);
}
private void print(String what, ASTNode where) {
String addr = StringUtil.addrToString(segment.getCurrentAddress());
modulePrinter.println(
segment.getName()
+ " @ "
+ addr
+ ": "
+ what
+ " on line "
+ where.getLeftMostToken().beginLine);
}
boolean isCubeMeasure(ASTNode node) {
String tabname = null;
String colname;
int nodeType = node.getToken().getType();
if (!(nodeType == HiveParser.TOK_TABLE_OR_COL || nodeType == HiveParser.DOT)) {
return false;
}
if (nodeType == HiveParser.TOK_TABLE_OR_COL) {
colname = ((ASTNode) node.getChild(0)).getText();
} else {
// node in 'alias.column' format
ASTNode tabident = HQLParser.findNodeByPath(node, TOK_TABLE_OR_COL, Identifier);
ASTNode colIdent = (ASTNode) node.getChild(1);
colname = colIdent.getText();
tabname = tabident.getText();
}
String msrname = StringUtils.isBlank(tabname) ? colname : tabname + "." + colname;
return isCubeMeasure(msrname);
}
public void flushCollectionCache() {
super.flushCollectionCache();
}
public void print() {
if (!log.isDebugEnabled()) {
return;
}
StringBuilder builder = new StringBuilder();
builder.append("ASTNode:" + ast.dump() + "\n");
builder.append("QB:");
builder.append("\n numJoins:" + qb.getNumJoins());
builder.append("\n numGbys:" + qb.getNumGbys());
builder.append("\n numSels:" + qb.getNumSels());
builder.append("\n numSelDis:" + qb.getNumSelDi());
builder.append("\n aliasToTabs:");
Set<String> tabAliases = qb.getTabAliases();
for (String alias : tabAliases) {
builder.append("\n\t" + alias + ":" + qb.getTabNameForAlias(alias));
}
builder.append("\n aliases:");
for (String alias : qb.getAliases()) {
builder.append(alias);
builder.append(", ");
}
builder.append("id:" + qb.getId());
builder.append("isQuery:" + qb.getIsQuery());
builder.append("\n QBParseInfo");
QBParseInfo parseInfo = qb.getParseInfo();
builder.append("\n isSubQ: " + parseInfo.getIsSubQ());
builder.append("\n alias: " + parseInfo.getAlias());
if (parseInfo.getJoinExpr() != null) {
builder.append("\n joinExpr: " + parseInfo.getJoinExpr().dump());
}
builder.append("\n hints: " + parseInfo.getHints());
builder.append("\n aliasToSrc: ");
for (String alias : tabAliases) {
builder.append("\n\t" + alias + ": " + parseInfo.getSrcForAlias(alias).dump());
}
TreeSet<String> clauses = new TreeSet<String>(parseInfo.getClauseNames());
for (String clause : clauses) {
builder.append("\n\t" + clause + ": " + parseInfo.getClauseNamesForDest());
}
String clause = clauses.first();
if (parseInfo.getWhrForClause(clause) != null) {
builder.append("\n whereexpr: " + parseInfo.getWhrForClause(clause).dump());
}
if (parseInfo.getGroupByForClause(clause) != null) {
builder.append("\n groupby expr: " + parseInfo.getGroupByForClause(clause).dump());
}
if (parseInfo.getSelForClause(clause) != null) {
builder.append("\n sel expr: " + parseInfo.getSelForClause(clause).dump());
}
if (parseInfo.getHavingForClause(clause) != null) {
builder.append("\n having expr: " + parseInfo.getHavingForClause(clause).dump());
}
if (parseInfo.getDestLimit(clause) != null) {
builder.append("\n limit: " + parseInfo.getDestLimit(clause));
}
if (parseInfo.getAllExprToColumnAlias() != null
&& !parseInfo.getAllExprToColumnAlias().isEmpty()) {
builder.append("\n exprToColumnAlias:");
for (Map.Entry<ASTNode, String> entry : parseInfo.getAllExprToColumnAlias().entrySet()) {
builder.append("\n\t expr: " + entry.getKey().dump() + " ColumnAlias: " + entry.getValue());
}
}
if (parseInfo.getAggregationExprsForClause(clause) != null) {
builder.append("\n aggregateexprs:");
for (Map.Entry<String, ASTNode> entry :
parseInfo.getAggregationExprsForClause(clause).entrySet()) {
builder.append("\n\t key: " + entry.getKey() + " expr: " + entry.getValue().dump());
}
}
if (parseInfo.getDistinctFuncExprsForClause(clause) != null) {
builder.append("\n distinctFuncExprs:");
for (ASTNode entry : parseInfo.getDistinctFuncExprsForClause(clause)) {
builder.append("\n\t expr: " + entry.dump());
}
}
if (qb.getQbJoinTree() != null) {
builder.append("\n\n JoinTree");
QBJoinTree joinTree = qb.getQbJoinTree();
printJoinTree(joinTree, builder);
}
if (qb.getParseInfo().getDestForClause(clause) != null) {
builder.append("\n Destination:");
builder.append("\n\t dest expr:" + qb.getParseInfo().getDestForClause(clause).dump());
}
log.debug(builder.toString());
}
public void addExprToAlias(ASTNode expr, ASTNode alias) {
exprToAlias.put(HQLParser.getString(expr).trim(), alias.getText().toLowerCase());
}
private void addCompileError(String msg, ASTNode node) {
SyntaxException se = new SyntaxException(msg, node.getLineNumber(), node.getColumnNumber());
sourceUnit.getErrorCollector().addFatalError(new SyntaxErrorMessage(se, sourceUnit));
}
/** @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);
}
public void call(SourceUnit source, GeneratorContext context, ClassNode classNode)
throws CompilationFailedException {
optimizer.visitClass(
classNode, source); // GROOVY-4272: repositioned it here from staticImport
if (!classNode.isSynthetic()) {
GenericsVisitor genericsVisitor = new GenericsVisitor(source);
genericsVisitor.visitClass(classNode);
}
//
// Run the Verifier on the outer class
//
try {
verifier.visitClass(classNode);
} catch (GroovyRuntimeException rpe) {
ASTNode node = rpe.getNode();
getErrorCollector()
.addError(
new SyntaxException(
rpe.getMessage(),
node.getLineNumber(),
node.getColumnNumber(),
node.getLastLineNumber(),
node.getLastColumnNumber()),
source);
}
LabelVerifier lv = new LabelVerifier(source);
lv.visitClass(classNode);
ClassCompletionVerifier completionVerifier = new ClassCompletionVerifier(source);
completionVerifier.visitClass(classNode);
ExtendedVerifier xverifier = new ExtendedVerifier(source);
xverifier.visitClass(classNode);
// because the class may be generated even if a error was found
// and that class may have an invalid format we fail here if needed
getErrorCollector().failIfErrors();
//
// Prep the generator machinery
//
ClassVisitor visitor = createClassVisitor();
String sourceName =
(source == null ? classNode.getModule().getDescription() : source.getName());
// only show the file name and its extension like javac does in its stacktraces rather
// than the full path
// also takes care of both \ and / depending on the host compiling environment
if (sourceName != null)
sourceName =
sourceName.substring(
Math.max(sourceName.lastIndexOf('\\'), sourceName.lastIndexOf('/')) + 1);
AsmClassGenerator generator = new AsmClassGenerator(source, context, visitor, sourceName);
//
// Run the generation and create the class (if required)
//
// GRECLIPSE: if there are errors, don't generate code.
// code gen can fail unexpectedly if there was an earlier error.
if (!source.getErrorCollector().hasErrors()) {
// end
generator.visitClass(classNode);
byte[] bytes = ((ClassWriter) visitor).toByteArray();
/// GRECLIPSE: start: added classNode, sourceUnit
/*old{
generatedClasses.add(new GroovyClass(classNode.getName(), bytes));
}*/
// newcode
generatedClasses.add(new GroovyClass(classNode.getName(), bytes, classNode, source));
// end
//
// Handle any callback that's been set
//
if (CompilationUnit.this.classgenCallback != null) {
classgenCallback.call(visitor, classNode);
}
//
// Recurse for inner classes
//
LinkedList innerClasses = generator.getInnerClasses();
while (!innerClasses.isEmpty()) {
classgen.call(source, context, (ClassNode) innerClasses.removeFirst());
}
// GRECLIPSE: if there are errors, don't generate code
}
// end
}
public void flushCache() {
super.flushCache();
}
public JavaRefactoringDescriptor buildEclipseDescriptor() throws Exception {
System.err.println("[eclipse-rename] Building descriptor...");
IJavaElement element = location.getIJavaElement();
String kind = getRenameKind(element);
// [1] BUGFIX was needed: The scripting interface didn't allow VariableDeclarationFragments as
// IJavaElements
// and thus had to be extended
// [2] WORKAROUND for scripting interface bug (see below)
if (kind.equals(IJavaRefactorings.RENAME_METHOD)) {
IMethod m = (IMethod) element;
if (m.isConstructor()) {
// Rename the type instead (as the UI would do-- the scripting interface will only rename
// the constructor, which is broken)
kind = IJavaRefactorings.RENAME_TYPE;
element = m.getDeclaringType();
}
}
System.err.println("[eclipse-rename] Kind = " + kind + ", element = " + element);
// [3] Don't test for package fragments now
if (kind.equals(IJavaRefactorings.RENAME_PACKAGE)) return null; // don't bother with this now
if (element == null) {
System.err.println("!!! ABORT: No IJavaElement to represent location");
throw new RuntimeException("!!! ABORT: No IJavaElement for location");
}
if (element instanceof ILocalVariable) {
System.err.println("element is of type " + element.getClass());
final ILocalVariable fLocalVariable = (ILocalVariable) element;
final ISourceRange sourceRange = fLocalVariable.getNameRange();
final CompilationUnit fCompilationUnitNode = location.getCompilationUnit();
ASTNode name = NodeFinder.perform(fCompilationUnitNode, sourceRange);
System.err.println("node is of type " + name.getClass());
if (name == null) System.err.println("!!! ILV doesn't have associated name!");
if (name.getParent() instanceof VariableDeclaration)
System.err.println("ILV has parent : " + (VariableDeclaration) name.getParent());
else
System.err.println(
"!!! ILV doesn't have var declaration parent, instead " + name.getParent().getClass());
}
System.err.println("Trying to rename a " + kind + ": " + element);
if (element instanceof SimpleName)
System.err.println(" Name = '" + ((SimpleName) element).getIdentifier() + "'");
if (kind.equals(IJavaRefactorings.RENAME_TYPE)) {
System.err.println("(Possibly need a new launch configuration)");
tproject.renameClass((IType) element, new_name);
}
final RenameJavaElementDescriptor descriptor =
(RenameJavaElementDescriptor) getDescriptor(kind);
descriptor.setJavaElement(element);
descriptor.setNewName(this.new_name);
if (element.getElementType() == IJavaElement.TYPE
|| element.getElementType() == IJavaElement.PACKAGE_FRAGMENT)
descriptor.setUpdateQualifiedNames(true);
else descriptor.setUpdateQualifiedNames(false);
descriptor.setUpdateReferences(true);
descriptor.setDeprecateDelegate(false);
descriptor.setRenameGetters(false);
descriptor.setRenameSetters(false);
descriptor.setKeepOriginal(false);
descriptor.setUpdateHierarchy(false);
descriptor.setUpdateSimilarDeclarations(false);
// [3] Fix: Eclipse will complain if the transformation is a no-op, but we don't want that:
if (element.getElementName().equals(this.new_name)) throw new NOPException();
System.err.println("[eclipse-rename] Computed descriptor.");
return descriptor;
}