Examples with ExpressionException cbit.vcell.parser.ExpressionException used on opensource projects

Example 91 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class ModelProcessEquation method parseReaction.

public static ReactionParticipant[] parseReaction(ReactionStep reactionStep, Model model, String equationString) throws ExpressionException, PropertyVetoException {
    int gotoIndex = equationString.indexOf(REACTION_GOESTO);
    if (gotoIndex < 1 && equationString.length() == 0) {
        throw new ExpressionException("Syntax error! " + REACTION_GOESTO + " not found. (e.g. a+b->c)");
    }
    if (reactionStep == null) {
        return null;
    }
    String leftHand = equationString.substring(0, gotoIndex);
    String rightHand = equationString.substring(gotoIndex + REACTION_GOESTO.length());
    StringTokenizer st = new StringTokenizer(leftHand, "+");
    ArrayList<ReactionParticipant> rplist = new ArrayList<ReactionParticipant>();
    HashMap<String, SpeciesContext> speciesContextMap = new HashMap<String, SpeciesContext>();
    Structure rxnStructure = reactionStep.getStructure();
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex).trim();
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, rxnStructure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        // if (reactionStep instanceof SimpleReaction) {
        rplist.add(new Reactant(null, (SimpleReaction) reactionStep, sc, stoichi));
    // } else if (reactionStep instanceof FluxReaction) {
    // rplist.add(new Flux(null, (FluxReaction) reactionStep, sc));
    // }
    }
    st = new StringTokenizer(rightHand, "+");
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex);
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, rxnStructure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        // if (reactionStep instanceof SimpleReaction) {
        rplist.add(new Product(null, (SimpleReaction) reactionStep, sc, stoichi));
    // } else if (reactionStep instanceof FluxReaction) {
    // rplist.add(new Flux(null, (FluxReaction) reactionStep, sc));
    // }
    }
    return rplist.toArray(new ReactionParticipant[0]);
}

Example 92 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class OutputFunctionsPanel method nextButtonClicked.

private void nextButtonClicked() throws ExpressionException, InconsistentDomainException {
    boolean bSpatial = simulationWorkspace.getSimulationOwner().getGeometry().getDimension() > 0;
    if (bSpatial) {
        DefaultComboBoxModel aModel = new DefaultComboBoxModel();
        ArrayList<Object> objectsList = null;
        String exprStr = getFunctionExpressionTextField().getText();
        if (exprStr == null) {
            throw new ExpressionException("No expression provided for output function.");
        }
        Expression expr = new Expression(exprStr);
        objectsList = getPossibleGeometryClassesAndVariableTypes(expr);
        for (Object ob : objectsList) {
            aModel.addElement(ob);
        }
        getSubdomainComboBox().setModel(aModel);
        getSubdomainComboBox().setSelectedIndex(0);
    }
    cardLayout.show(functionPanel, geometryClassPanel.getName());
}

Example 93 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class RestDatabaseService method query.

public SimulationStatusRepresentation[] query(SimulationStatusServerResource resource, User vcellUser) throws SQLException, DataAccessException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    String userID = vcellUser.getName();
    SimpleJobStatusQuerySpec simQuerySpec = new SimpleJobStatusQuerySpec();
    simQuerySpec.userid = userID;
    simQuerySpec.simId = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_SIM_ID);
    String hasData = resource.getQueryValue(SimulationStatusServerResource.PARAM_HAS_DATA);
    if (hasData != null && hasData.equals("yes")) {
        simQuerySpec.hasData = true;
    } else if (hasData != null && hasData.equals("no")) {
        simQuerySpec.hasData = false;
    } else {
        simQuerySpec.hasData = null;
    }
    simQuerySpec.waiting = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_ACTIVE, false);
    simQuerySpec.queued = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_ACTIVE, false);
    simQuerySpec.dispatched = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_ACTIVE, false);
    simQuerySpec.running = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_ACTIVE, false);
    simQuerySpec.completed = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_COMPLETED, false);
    simQuerySpec.failed = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_FAILED, false);
    simQuerySpec.stopped = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_STOPPED, false);
    simQuerySpec.submitLowMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_SUBMIT_LOW);
    simQuerySpec.submitHighMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_SUBMIT_HIGH);
    simQuerySpec.startLowMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_START_LOW);
    simQuerySpec.startHighMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_START_HIGH);
    simQuerySpec.endLowMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_END_LOW);
    simQuerySpec.endHighMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_END_HIGH);
    Long startRowParam = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_START_ROW);
    // default
    simQuerySpec.startRow = 1;
    if (startRowParam != null) {
        simQuerySpec.startRow = startRowParam.intValue();
    }
    Long maxRowsParam = resource.getLongQueryValue(SimulationTasksServerResource.PARAM_MAX_ROWS);
    // default
    simQuerySpec.maxRows = 10;
    if (maxRowsParam != null) {
        simQuerySpec.maxRows = maxRowsParam.intValue();
    }
    SimulationStatus[] simStatuses = null;
    HashMap<KeyValue, SimulationDocumentLink> simDocLinks = new HashMap<KeyValue, SimulationDocumentLink>();
    // 
    // ask server for simJobStatuses with above query spec.
    // find set of simulation IDs from the result set of simJobStatus
    // ask server for simulationStatuses from list of sim IDs.
    // 
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
        try {
            userLoginInfo.setUser(vcellUser);
        } catch (Exception e) {
            e.printStackTrace();
            throw new DataAccessException(e.getMessage());
        }
        RpcSimServerProxy rpcSimServerProxy = new RpcSimServerProxy(userLoginInfo, rpcSession);
        SimpleJobStatus[] simpleJobStatusArray = rpcSimServerProxy.getSimpleJobStatus(vcellUser, simQuerySpec);
        // gather unique simIDs and go back and ask server for SimulationStatuses
        for (SimpleJobStatus simpleJobStatus : simpleJobStatusArray) {
            KeyValue simulationKey = simpleJobStatus.jobStatus.getVCSimulationIdentifier().getSimulationKey();
            SimulationDocumentLink simulationDocumentLink = simpleJobStatus.simulationDocumentLink;
            simDocLinks.put(simulationKey, simulationDocumentLink);
        }
        KeyValue[] simKeys = simDocLinks.keySet().toArray(new KeyValue[0]);
        if (simKeys.length > 0) {
            simStatuses = rpcSimServerProxy.getSimulationStatus(vcellUser, simKeys);
        }
    } finally {
        rpcSession.close();
    }
    ArrayList<SimulationStatusRepresentation> simStatusReps = new ArrayList<SimulationStatusRepresentation>();
    for (int i = 0; simStatuses != null && i < simStatuses.length; i++) {
        KeyValue simulationKey = simStatuses[i].getVCSimulationIdentifier().getSimulationKey();
        SimulationRep simRep = getSimulationRep(simulationKey);
        try {
            SimulationRepresentation simRepresentation = new SimulationRepresentation(simRep, simDocLinks.get(simulationKey));
            simStatusReps.add(new SimulationStatusRepresentation(simRepresentation, simStatuses[i]));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
        }
    }
    return simStatusReps.toArray(new SimulationStatusRepresentation[0]);
}

Example 94 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class ElectricalStimulusPanel method getProtocolParameterExprPreview.

public static Expression getProtocolParameterExprPreview(Expression expr, SymbolTable symbolTable, ReservedSymbol timeSymbol) throws Exception {
    Expression protocolParameterExp = new Expression(expr);
    protocolParameterExp = MathUtilities.substituteModelParameters(protocolParameterExp, symbolTable);
    String[] symbols = protocolParameterExp.getSymbols();
    for (int i = 0; symbols != null && i < symbols.length; i++) {
        SymbolTableEntry ste = protocolParameterExp.getSymbolBinding(symbols[i]);
        if (!ste.equals(timeSymbol) && !(ste instanceof LocalProxyParameter && ((LocalProxyParameter) ste).getTarget().equals(timeSymbol))) {
            throw new ExpressionException("Expression symbol '" + ste.getName() + "' doesn't match timeSymbol " + timeSymbol.getName());
        }
    }
    return protocolParameterExp;
}

Example 95 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class ElectricalStimulusParameterTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    if (columnIndex < 0 || columnIndex >= getColumnCount()) {
        throw new RuntimeException("ParameterTableModel.setValueAt(), column = " + columnIndex + " out of range [" + 0 + "," + (getColumnCount() - 1) + "]");
    }
    Parameter parameter = getValueAt(rowIndex);
    // try {
    switch(columnIndex) {
        case COLUMN_VALUE:
            {
                try {
                    String newExpressionString = (String) aValue;
                    if (parameter instanceof LocalParameter) {
                        LocalParameter scsParm = (LocalParameter) parameter;
                        getElectricalStimulus().setParameterValue(scsParm, new Expression(newExpressionString));
                    // fireTableRowsUpdated(rowIndex,rowIndex);
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, e.getMessage(), e);
                }
                break;
            }
        case COLUMN_NAME:
            {
                try {
                    getElectricalStimulus().renameParameter(parameter.getName(), (String) aValue);
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, e.getMessage(), e);
                }
            }
    }
// }catch (java.beans.PropertyVetoException e){
// e.printStackTrace(System.out);
// }
}