예제 #1
0
 public void testParameterEdit() throws Exception {
   ConfigurationContext configCtx = ConfigurationContextFactory.createEmptyConfigurationContext();
   AxisConfiguration axisConfig = configCtx.getAxisConfiguration();
   Parameter parameter = new Parameter();
   parameter.setValue("true");
   parameter.setName("enableMTOM");
   axisConfig.addParameter(parameter);
   parameter.setValue("true");
   AxisServiceGroup serviceGroup = new AxisServiceGroupImpl();
   serviceGroup.setName("testServiceGroup");
   AxisService service = new AxisService();
   service.setName("service");
   serviceGroup.addService(service);
   axisConfig.addServiceGroup(serviceGroup);
   parameter = serviceGroup.getParameter("enableMTOM");
   parameter.setValue("true");
   Parameter para2 = serviceGroup.getParameter("enableMTOM");
   assertEquals(para2.getValue(), "true");
   Parameter test = new Parameter();
   test.setName("test");
   test.setValue("test");
   serviceGroup.addParameter(test);
   Parameter para = serviceGroup.getParameter("test");
   assertNotNull(para);
   assertEquals(para.getValue(), "test");
   para.setValue("newValue");
   para = serviceGroup.getParameter("test");
   assertNotNull(para);
   assertEquals(para.getValue(), "newValue");
 }
예제 #2
0
 public ParameterTable add(String pname, String pvalue, String desc) {
   Parameter p = get(pname, false);
   if (p != null) // update value
   {
     p.setValue(pvalue).setDesc(desc);
   } else {
     p = Parameter.by(pname);
     p.setValue(pvalue).setDesc(desc);
     synchronized (table) {
       table.add(p);
     }
   }
   return this;
 }
예제 #3
0
파일: NodeTest.java 프로젝트: fdb/nodebox
 public void testNodeAttributeEvent() {
   TestAttributeListener l = new TestAttributeListener();
   Node test = Node.ROOT_NODE.newInstance(testLibrary, "test");
   test.addNodeAttributeListener(l);
   // Setting the name to itself does not trigger an event.
   test.setName("test");
   assertEquals(0, l.nameCounter);
   test.setName("newname");
   assertEquals(1, l.nameCounter);
   Parameter p1 = test.addParameter("p1", Parameter.Type.FLOAT);
   assertEquals(1, l.parameterCounter);
   p1.setName("parameter1");
   assertEquals(2, l.parameterCounter);
   // TODO: These trigger ParameterAttributeChanged
   // p1.setBoundingMethod(Parameter.BoundingMethod.HARD);
   // assertEquals(3, l.parameterCounter);
   // p1.setMinimumValue(0F);
   // assertEquals(4, l.parameterCounter);
   // Changing the value does not trigger the event.
   // The event only happens for metadata, not data.
   // If you want to catch that, use DirtyListener.
   p1.setValue(20F);
   assertEquals(2, l.parameterCounter);
   test.removeParameter("parameter1");
   assertEquals(3, l.parameterCounter);
 }
  @Override
  public Parameter getParameter(ParameterKey key) {
    Connection connection = connectionDaoService.getRiceConnection();
    try (PreparedStatement stmt =
            setString(
                4,
                key.getApplicationId(),
                setString(
                    3,
                    key.getName(),
                    setString(
                        2,
                        key.getComponentCode(),
                        setString(
                            1,
                            key.getNamespaceCode(),
                            connection.prepareStatement(
                                "SELECT VAL, PARM_DESC_TXT, PARM_TYP_CD, EVAL_OPRTR_CD "
                                    + " FROM KRCR_PARM_T WHERE NMSPC_CD = ? AND CMPNT_CD = ? AND PARM_NM = ? AND APPL_ID = ?")))));
        ResultSet result = stmt.executeQuery()) {
      if (result.next()) {
        Parameter p = new Parameter();
        p.setParameterKey(key);
        p.setValue(result.getString(1));
        p.setDescription(result.getString(2));
        p.setParameterTypeCode(result.getString(3));
        p.setEvaluationOperatorCode(result.getString(4));

        return p;
      }
      return null;
    } catch (SQLException e) {
      throw new RuntimeException(e);
    }
  }
예제 #5
0
 /* (non-Javadoc)
  * @see java.lang.Object#clone()
  */
 @Override
 public Parameter clone() throws CloneNotSupportedException {
   Parameter param = new Parameter(name);
   param.setValue(value);
   param.setHelp(help);
   param.setReadOnly(readOnly);
   return param;
 }
예제 #6
0
파일: TestParameter.java 프로젝트: CRBS/cws
  @Test
  public void testGettersAndSetters() {
    Parameter p = new Parameter();
    assertTrue(p.getName() == null);
    assertTrue(p.getValue() == null);

    p.setName("bob");
    p.setValue("val");
    assertTrue(p.getName().equals("bob"));
    assertTrue(p.getValue().equals("val"));
  }
예제 #7
0
  private static List<Parameter> getParameters(ArrayList<CustomField> infos, Entry entry) {
    List<Parameter> parameters = new ArrayList<>();

    if (infos == null) return parameters;

    for (CustomField info : infos) {
      Parameter param = new Parameter();
      param.setEntry(entry);
      param.setKey(info.getName());
      param.setValue(info.getValue());
      parameters.add(param);
    }
    return parameters;
  }
예제 #8
0
파일: TestParameter.java 프로젝트: CRBS/cws
  @Test
  public void testAsString() {
    Parameter p = new Parameter();
    assertTrue(p.asString().equals("name=null,value=null"));

    p.setName("bob");
    assertTrue(p.asString().equals("name=bob,value=null"));

    p.setValue("val");
    assertTrue(p.asString().equals("name=bob,value=val"));

    p.setName(null);
    assertTrue(p.asString().equals("name=null,value=val"));
  }
예제 #9
0
 public Parameter clone() {
   Parameter clone = null;
   try {
     clone = this.getClass().newInstance();
     clone.setParameterList(parameterList);
     clone.setName(getName());
     clone.setValue(value);
   } catch (InstantiationException exception) {
     exception.printStackTrace();
   } catch (IllegalAccessException exception) {
     exception.printStackTrace();
   }
   return clone;
   // Parameter clone = new DefaultParameter(this.processor, this.name);
 }
예제 #10
0
  /** @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);
  }
예제 #11
0
  private static void parseConfiguration(String stringUrl, Product product) {
    try {
      URL url = new URL(stringUrl);
      URLConnection connection = url.openConnection();
      int fileLength = connection.getContentLength();

      if (fileLength == -1) {
        System.out.println("Invalide URL or file.");
        return;
      }

      CommandClass currentCC = null;
      Parameter currentParameter = null;
      Association currentAssociation = null;

      XMLInputFactory inputFactory = XMLInputFactory.newInstance();
      InputStream input = connection.getInputStream();
      final XMLEventReader eventReader = inputFactory.createXMLEventReader(input);

      while (eventReader.hasNext()) {
        XMLEvent event = eventReader.nextEvent();
        if (event.isStartElement()) {
          StartElement startElt = event.asStartElement();
          if (startElt.getName().getLocalPart().equals("CommandClass")) {
            CommandClass cc = product.view().createCommandClass();

            Iterator<Attribute> attributes = startElt.getAttributes();
            while (attributes.hasNext()) {
              Attribute next = attributes.next();
              String attrName = next.getName().toString();

              if (attrName.equals("id")) {
                cc.setId(Integer.parseInt(next.getValue(), 16));
              }
            }
            product.addCommandClasses(cc);
            currentCC = cc;

          } else if (startElt.getName().getLocalPart().equals("Value")) {

            Parameter param = product.view().createParameter();

            Iterator<Attribute> attributes = startElt.getAttributes();
            while (attributes.hasNext()) {
              Attribute next = attributes.next();
              String attrName = next.getName().toString();
              if (!next.getValue().equals("")) {
                if (attrName.equals("type")) {
                  param.setType(ParameterType.valueOf(next.getValue().toUpperCase()));
                } else if (attrName.equals("genre")) {
                  param.setGenre(next.getValue());
                } else if (attrName.equals("instance")) {
                  param.setInstance(Integer.valueOf(next.getValue()));
                } else if (attrName.equals("index")) {
                  param.setIndex(Integer.valueOf(next.getValue()));
                } else if (attrName.equals("label")) {
                  param.setLabel(next.getValue());
                } else if (attrName.equals("value")) {
                  param.setValue(next.getValue());
                } else if (attrName.equals("min")) {

                  param.setMin(Integer.valueOf(next.getValue()));
                } else if (attrName.equals("max")) {

                  param.setMax(Integer.valueOf(next.getValue()));
                } else if (attrName.equals("size")) {
                  param.setSize(Integer.valueOf(next.getValue()));
                }
              }
            }
            currentCC.addParameters(param);
            currentParameter = param;

          } else if (startElt.getName().getLocalPart().equals("Help")) {
            // help

          } else if (startElt.getName().getLocalPart().equals("Item")) {
            ParameterItem item = product.view().createParameterItem();

            Iterator<Attribute> attributes = startElt.getAttributes();
            while (attributes.hasNext()) {
              Attribute next = attributes.next();
              String attrName = next.getName().toString();
              if (attrName.equals("label")) {
                item.setLabel(next.getValue());
              } else if (attrName.equals("value")) {
                item.setValue(Integer.valueOf(next.getValue()));
              }
            }
            currentParameter.addItems(item);
          } else if (startElt.getName().getLocalPart().equals("Associations")) {
            Association assoc = product.view().createAssociation();

            Iterator<Attribute> attributes = startElt.getAttributes();
            while (attributes.hasNext()) {
              Attribute next = attributes.next();
              String attrName = next.getName().toString();
              if (attrName.equals("num_groups")) {
                assoc.setNumGroups(Integer.valueOf(next.getValue()));
              }
            }
            currentCC.addAssociations(assoc);
            currentAssociation = assoc;
          } else if (startElt.getName().getLocalPart().equals("Group")) {
            AssociationGroup group = product.view().createAssociationGroup();

            Iterator<Attribute> attributes = startElt.getAttributes();
            while (attributes.hasNext()) {
              Attribute next = attributes.next();
              String attrName = next.getName().toString();
              if (attrName.equals("label")) {
                group.setLabel(next.getValue());
              } else if (attrName.equals("index")) {
                group.setIndex(Integer.valueOf(next.getValue()));
              } else if (attrName.equals("max_associations")) {
                group.setMaxAssociations(Integer.valueOf(next.getValue()));
              } else if (attrName.equals("auto")) {
                group.setAuto(Boolean.valueOf(next.getValue()));
              }
              currentAssociation.addGroups(group);
            }
          }
        }
      }

    } catch (MalformedURLException e) {
      e.printStackTrace();
    } catch (XMLStreamException e) {
      e.printStackTrace();
    } catch (IOException e) {
      e.printStackTrace();
    }
  }
예제 #12
0
 public void setValue(T value) {
   baseParam.setValue(value);
 }
예제 #13
0
  public PresentationObject getChooser(IWContext iwc, IWBundle bundle) {
    if (useOldLogic) { //	Old chooser
      Table table = new Table(2, 1);
      table.setCellpadding(0);
      table.setCellspacing(0);

      Parameter value = new Parameter(getChooserParameter(), "");
      if (this._stringValue != null) {
        value.setValue(this._stringValue);
      }
      table.add(value);

      PresentationObject object = getPresentationObject(iwc);

      table.add(new Parameter(VALUE_PARAMETER_NAME, value.getName()));
      // GenericButton button = new
      // GenericButton("chooserbutton",bundle.getResourceBundle(iwc).getLocalizedString(chooserText,"Choose"));
      if (this._addForm) {
        SubmitButton button = new SubmitButton(this._iwrb.getLocalizedString("choose", "Choose"));
        table.add(button, 2, 1);
        this._form.addParameter(CHOOSER_SELECTION_PARAMETER, getChooserParameter());
        this._form.addParameter(
            FORM_ID_PARAMETER,
            "window.opener.document.getElementById(\"" + this._form.getID() + "\").");
        this._form.addParameter(SCRIPT_SUFFIX_PARAMETER, "value");
        if (this.filter != null) {
          if (this.filter.length() > 0) {
            this._form.addParameter(FILTER_PARAMETER, this.filter);
          }
        }
        addParametersToForm(this._form);
      } else {
        getLink(this._iwrb);

        if (getUsePublicWindowOpener()) {
          this.link.setPublicWindowToOpen(getChooserWindowClass());
        } else {
          this.link.setWindowToOpen(getChooserWindowClass());
        }
        this.link.addParameter(CHOOSER_SELECTION_PARAMETER, getChooserParameter());

        this.link.addParameter(FORM_ID_PARAMETER, getParentFormID());

        // TODO Make the javascript work for other objects than form elements,
        // e.g. a Link
        /*
         * if(object instanceof Layer){
         * link.addParameter(SCRIPT_SUFFIX_PARAMETER,"title"); }
         */
        this.link.addParameter(SCRIPT_SUFFIX_PARAMETER, "value");
        // }

        // this was object.getID() but the id could change if this object was kept in session but
        // the form changed
        // by using getName() the reference is not lost, however we might need to add extra steps
        // for handling more than one
        // chooser of the same type in the same form.
        this.link.addParameter(DISPLAYSTRING_PARAMETER_NAME, object.getName());
        this.link.addParameter(VALUE_PARAMETER_NAME, value.getName());
        if (this._attributeName != null && this._attributeValue != null) {
          this.link.addParameter(this._attributeName, this._attributeValue);
        }
        if (this.filter != null) {
          if (this.filter.length() > 0) {
            this.link.addParameter(FILTER_PARAMETER, this.filter);
          }
        }

        addParametersToLink(this.link);

        table.add(this.link, 2, 1);
      }

      table.add(object, 1, 1);
      table.add(new Parameter(DISPLAYSTRING_PARAMETER_NAME, "151324213"));
      return (table);
    } else { //	New chooser
      Layer container = new Layer();

      String chooserObject = getChooserHelperVarName();
      if (chooserObject == null) {
        chooserObject = AbstractChooserBlock.GLOBAL_HELPER_NAME;
      } else {
        add(
            PresentationUtil.getJavaScriptAction(
                PresentationUtil.getJavaScriptLinesLoadedLazily(
                    CoreUtil.getResourcesForChooser(iwc),
                    new StringBuilder("if (!")
                        .append(chooserObject)
                        .append(") var ")
                        .append(chooserObject)
                        .append(" = new ChooserHelper();")
                        .toString())));
      }

      PresentationObject object = getPresentationObject(iwc);
      container.add(object);

      Image chooser = getChooser(bundle);
      chooser.setStyleClass("chooserStyle");

      chooser.setMarkupAttribute("choosername", chooserObject);

      //	OnClick action
      StringBuffer action =
          new StringBuffer("addChooserObject('").append(chooser.getId()).append("', '");
      action.append(getChooserWindowClass().getName());
      if (getHiddenInputAttribute() == null) {
        action.append("', null, '");
      } else {
        action.append("', '").append(getHiddenInputAttribute()).append("', '");
      }
      action.append(ICBuilderConstants.CHOOSER_VALUE_VIEWER_ID_ATTRIBUTE).append("', '");
      action
          .append(getResourceBundle().getLocalizedString("loading", "Loading..."))
          .append("', ")
          .append(
              _stringValue == null
                  ? "null"
                  : new StringBuilder("'").append(_stringValue).append("'").toString())
          .append(", ")
          .append(
              _stringDisplay == null
                  ? "null"
                  : new StringBuilder("'").append(_stringDisplay).append("'").toString())
          .append(");");
      chooser.setOnClick(action.toString());

      container.add(chooser);

      return container;
    }
  }