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));
  }
Esempio n. 3
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 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);
   }
 }
Esempio n. 4
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 /** @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;
 }
Esempio n. 5
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 /** @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;
 }
Esempio n. 7
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 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;
 }
Esempio n. 8
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 @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;
 }
Esempio n. 10
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 // 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$Final();
   getSuperClassAccessOpt_value = getSuperClassAccessOpt_compute();
   setSuperClassAccessOpt(getSuperClassAccessOpt_value);
   if (isFinal && num == boundariesCrossed) getSuperClassAccessOpt_computed = true;
   return (Opt) ASTNode.getChild(this, getSuperClassAccessOptChildPosition());
 }
Esempio n. 11
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 // Declared in AnonymousClasses.jrag at line 38
 @SuppressWarnings({"unchecked", "cast"})
 public List getImplementsList() {
   if (getImplementsList_computed)
     return (List) ASTNode.getChild(this, getImplementsListChildPosition());
   int num = boundariesCrossed;
   boolean isFinal = this.is$Final();
   getImplementsList_value = getImplementsList_compute();
   setImplementsList(getImplementsList_value);
   if (isFinal && num == boundariesCrossed) getImplementsList_computed = true;
   return (List) ASTNode.getChild(this, getImplementsListChildPosition());
 }
Esempio n. 12
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 /**
  * 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);
 }
Esempio n. 17
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 private void print(String what, ASTNode where) {
   String addr = StringUtil.addrToString(segment.getCurrentAddress());
   modulePrinter.println(
       segment.getName()
           + " @ "
           + addr
           + ": "
           + what
           + " on line "
           + where.getLeftMostToken().beginLine);
 }
Esempio n. 18
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  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);
  }
Esempio n. 19
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 public void flushCollectionCache() {
   super.flushCollectionCache();
 }
Esempio n. 20
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  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());
  }
Esempio n. 21
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 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));
 }
Esempio n. 23
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  /** @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);
  }
Esempio n. 24
0
        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
        }
Esempio n. 25
0
 public void flushCache() {
   super.flushCache();
 }
Esempio n. 26
0
  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;
  }