Examples with BNGInput cbit.vcell.server.bionetgen.BNGInput used on opensource projects

Example 1 with BNGInput

use of cbit.vcell.server.bionetgen.BNGInput in project vcell by virtualcell.

the class RulebasedTransformer method generateNetwork.

private void generateNetwork(SimulationContext simContext, Set<ReactionRule> fromReactions, MathMappingCallback mathMappingCallback) throws ClassNotFoundException, IOException {
    TaskCallbackMessage tcm;
    BNGOutputSpec outputSpec;
    speciesEquivalenceMap.clear();
    kineticsParameterMap.clear();
    NetworkGenerationRequirements networkGenerationRequirements = NetworkGenerationRequirements.ComputeFullNoTimeout;
    String input = convertToBngl(simContext, true, mathMappingCallback, networkGenerationRequirements);
    // System.out.println(input);		// TODO: uncomment to see the xml string
    for (Map.Entry<FakeSeedSpeciesInitialConditionsParameter, Pair<SpeciesContext, Expression>> entry : speciesEquivalenceMap.entrySet()) {
        FakeSeedSpeciesInitialConditionsParameter key = entry.getKey();
        Pair<SpeciesContext, Expression> value = entry.getValue();
        SpeciesContext sc = value.one;
        Expression initial = value.two;
        System.out.println("key: " + key.fakeParameterName + ",   species: " + sc.getName() + ", initial: " + initial.infix());
    }
    BNGInput bngInput = new BNGInput(input);
    BNGOutput bngOutput = null;
    try {
        // for the writeXML command we don't want to run iteration by iteration - it wouldn't even make sense since we don't flatten anything
        // so we run bionetgen the "old" way
        final BNGExecutorService bngService = BNGExecutorService.getInstanceOld(bngInput, networkGenerationRequirements.timeoutDurationMS);
        bngOutput = bngService.executeBNG();
    } catch (RuntimeException ex) {
        ex.printStackTrace(System.out);
        // rethrow without losing context
        throw ex;
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        throw new RuntimeException(ex.getMessage());
    }
    simContext.setInsufficientIterations(false);
    simContext.setInsufficientMaxMolecules(false);
    String bngConsoleString = bngOutput.getConsoleOutput();
    tcm = new TaskCallbackMessage(TaskCallbackStatus.DetailBatch, bngConsoleString);
    // simContext.appendToConsole(tcm);
    // String bngNetString = bngOutput.getNetFileContent();
    // outputSpec = BNGOutputFileParser.createBngOutputSpec(bngNetString);
    // //BNGOutputFileParser.printBNGNetOutput(outputSpec);			// prints all output to console
    // 
    // if (mathMappingCallback.isInterrupted()){
    // String msg = "Canceled by user.";
    // //			tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
    // //			simContext.appendToConsole(tcm);
    // //			simContext.setMd5hash(null);					// clean the cache if the user interrupts
    // throw new UserCancelException(msg);
    // }
    // if(outputSpec.getBNGSpecies().length > SimulationConsolePanel.speciesLimit) {
    // String message = SimulationConsolePanel.getSpeciesLimitExceededMessage(outputSpec);
    // //			tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
    // //			simContext.appendToConsole(tcm);
    // //			simContext.setMd5hash(null);
    // throw new RuntimeException(message);
    // }
    // if(outputSpec.getBNGReactions().length > SimulationConsolePanel.reactionsLimit) {
    // String message = SimulationConsolePanel.getReactionsLimitExceededMessage(outputSpec);
    // //			tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
    // //			simContext.appendToConsole(tcm);
    // //			simContext.setMd5hash(null);
    // throw new RuntimeException(message);
    // }
    // TODO: uncomment here to parse the xml file!!!
    parseBngOutput(simContext, fromReactions, bngOutput);
// 
// Saving the observables, as produced by bionetgen
// in debug configurations add to command line   -Ddebug.user=danv
// 
// String debugUser = PropertyLoader.getProperty("debug.user", "not_defined");
// if (debugUser.equals("danv") || debugUser.equals("mblinov")){
// System.out.println("Saving their observables");
// parseObservablesBngOutput(simContext, bngOutput);
// }
// compareOutputs(simContext);
}

Example 2 with BNGInput

use of cbit.vcell.server.bionetgen.BNGInput in project vcell by virtualcell.

the class BNGOutputPanel method runBNGButton_ActionPerformed.

/**
 * Comment
 */
private void runBNGButton_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    getConsoleTextArea().setText("");
    getOutputTextArea().setText("");
    getdefaultListModel().removeAllElements();
    refreshButton(true);
    // Do all the text checks here; and pop up warnings if needed, before going in to the BNGWindowManager to execute BNG.
    if (getBNGLInputPanel().getText() == null || getBNGLInputPanel().getText().equals("")) {
        PopupGenerator.showErrorDialog(this, "No input; Cannot run BioNetGen");
        return;
    }
    setbngInput(new BNGInput(getBNGLInputPanel().getText()));
    if (getbngInput() == null) {
        PopupGenerator.showErrorDialog(this, "No input; Cannot run BioNetGen");
        return;
    }
    // execute BNG thro' BNGWindowManager
    getBngWindowManager().runBioNetGen(getbngInput());
    // Clear the Output tab
    ((java.awt.CardLayout) getOutputsTextPanel().getLayout()).show(getOutputsTextPanel(), getOutputTextScrollPane().getName());
    getOutputTextArea().setText("");
    getOutputLabel().setText("");
}

Example 3 with BNGInput

use of cbit.vcell.server.bionetgen.BNGInput in project vcell by virtualcell.

the class NetworkConstraintsPanel method runBioNetGen.

private void runBioNetGen() {
    EditConstraintsPanel panel = new EditConstraintsPanel(this);
    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(this);
    ChildWindow childWindow = childWindowManager.addChildWindow(panel, panel, "Edit / Test Constraints");
    Dimension dim = new Dimension(320, 330);
    childWindow.pack();
    panel.setChildWindow(childWindow);
    childWindow.setPreferredSize(dim);
    childWindow.showModal();
    int maxIterations;
    int maxMolecules;
    int speciesLimit;
    int reactionsLimit;
    Map<MolecularType, Integer> testMaxStoichiometryMap = new LinkedHashMap<>();
    StoichiometryTableModel stoichiometryTableModel = panel.getStoichiometryTableModel();
    for (int row = 0; row < stoichiometryTableModel.getRowCount(); row++) {
        MaxStoichiometryEntity nce = stoichiometryTableModel.getValueAt(row);
        MolecularType key = nce.getMolecularType();
        Integer value = nce.getValue();
        testMaxStoichiometryMap.put(key, value);
    }
    if (panel.getButtonPushed() == ActionButtons.Run) {
        maxIterations = new Integer(panel.maxIterationTextField.getText());
        maxMolecules = new Integer(panel.maxMolTextField.getText());
        speciesLimit = new Integer(panel.speciesLimitTextField.getText());
        reactionsLimit = new Integer(panel.reactionsLimitTextField.getText());
        fieldSimulationContext.getNetworkConstraints().setTestConstraints(maxIterations, maxMolecules, speciesLimit, reactionsLimit, testMaxStoichiometryMap);
    } else if (panel.getButtonPushed() == ActionButtons.Apply) {
        activateConsole();
        maxIterations = new Integer(panel.maxIterationTextField.getText());
        maxMolecules = new Integer(panel.maxMolTextField.getText());
        speciesLimit = new Integer(panel.speciesLimitTextField.getText());
        reactionsLimit = new Integer(panel.reactionsLimitTextField.getText());
        fieldSimulationContext.getNetworkConstraints().setTestConstraints(maxIterations, maxMolecules, speciesLimit, reactionsLimit, testMaxStoichiometryMap);
        fieldSimulationContext.getNetworkConstraints().updateConstraintsFromTest();
        // apply will invalidate everything: generated species, reactions, console, cache, etc
        updateBioNetGenOutput(null);
        refreshInterface();
        TaskCallbackMessage tcm = new TaskCallbackMessage(TaskCallbackStatus.Clean, "");
        fieldSimulationContext.appendToConsole(tcm);
        String message = "Warning: The current Constraints are not tested / validated.";
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Warning, message);
        fieldSimulationContext.appendToConsole(tcm);
        message = "The Network generation may take a very long time or the generated network may be incomplete. " + "We recommend testing this set of constraints.";
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Notification, message);
        fieldSimulationContext.appendToConsole(tcm);
        return;
    } else {
        // when cancel we put back in sync the test values
        maxIterations = fieldSimulationContext.getNetworkConstraints().getMaxIteration();
        maxMolecules = fieldSimulationContext.getNetworkConstraints().getMaxMoleculesPerSpecies();
        speciesLimit = fieldSimulationContext.getNetworkConstraints().getSpeciesLimit();
        reactionsLimit = fieldSimulationContext.getNetworkConstraints().getReactionsLimit();
        fieldSimulationContext.getNetworkConstraints().setTestConstraints(maxIterations, maxMolecules, speciesLimit, reactionsLimit, testMaxStoichiometryMap);
        return;
    }
    // TODO: do not delete the commented code below
    // uncomment the next 6 lines to keep the data in the dialogs synchronized with the most recent reaction network
    // if(viewSpeciesDialog != null) {
    // viewSpeciesDialog.dispose();
    // }
    // if(viewReactionsDialog != null) {
    // viewReactionsDialog.dispose();
    // }
    activateConsole();
    // previousIterationSpecies = 0;
    synchronized (this) {
        fieldSimulationContext.setMd5hash(null);
        fieldSimulationContext.setMostRecentlyCreatedOutputSpec(null);
    }
    refreshInterface();
    if (!checkBnglRequirements()) {
        return;
    }
    NetworkTransformer transformer = new NetworkTransformer();
    MathMappingCallback dummyCallback = new MathMappingCallback() {

        public void setProgressFraction(float percentDone) {
        }

        public void setMessage(String message) {
        }

        public boolean isInterrupted() {
            return false;
        }
    };
    String input = transformer.convertToBngl(fieldSimulationContext, true, dummyCallback, NetworkGenerationRequirements.ComputeFullNoTimeout);
    // we alter the input string to use the test values for speciesLimit and reactionsLimit
    BufferedReader br = new BufferedReader(new StringReader(input));
    StringBuilder sb = new StringBuilder();
    int lineNumber = 0;
    while (true) {
        String line = null;
        try {
            line = br.readLine();
        } catch (IOException e) {
            e.printStackTrace();
        }
        if (line == null) {
            // end of document
            break;
        }
        if (line.isEmpty()) {
            sb.append("\n");
            lineNumber++;
            continue;
        }
        if (line.contains(NetworkConstraints.SPECIES_LIMIT_PARAMETER)) {
            sb.append(NetworkConstraints.SPECIES_LIMIT_PARAMETER + "\t\t" + speciesLimit + "\n");
        } else if (line.contains(NetworkConstraints.REACTIONS_LIMIT_PARAMETER)) {
            sb.append(NetworkConstraints.REACTIONS_LIMIT_PARAMETER + "\t\t" + reactionsLimit + "\n");
        } else {
            sb.append(line + "\n");
        }
    }
    input = sb.toString();
    // we alter the input string to use the test values for max iterations and max molecules per species
    // get rid of the default generate network command...
    input = input.substring(0, input.indexOf("generate_network({"));
    // ... and replace it with the "fake" one
    StringWriter bnglStringWriter = new StringWriter();
    PrintWriter pw = new PrintWriter(bnglStringWriter);
    // testMaxStoichiometryMap
    RbmNetworkGenerator.generateNetworkEx(maxIterations, maxMolecules, true, pw, fieldSimulationContext.getModel().getRbmModelContainer(), fieldSimulationContext, NetworkGenerationRequirements.ComputeFullNoTimeout);
    String genNetStr = bnglStringWriter.toString();
    pw.close();
    input += genNetStr;
    BNGInput bngInput = new BNGInput(input);
    final BNGExecutorService bngService = BNGExecutorService.getInstance(bngInput, NetworkGenerationRequirements.NoTimeoutMS);
    bngService.registerBngUpdaterCallback(this);
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    AsynchClientTask[] tasksArray = new AsynchClientTask[3];
    TaskCallbackMessage message = new TaskCallbackMessage(TaskCallbackStatus.Clean, "");
    fieldSimulationContext.appendToConsole(message);
    tasksArray[0] = new RunBioNetGen(bngService);
    tasksArray[1] = new CreateBNGOutputSpec(bngService);
    tasksArray[2] = new ReturnBNGOutput(bngService, fieldSimulationContext, this);
    ClientTaskDispatcher.dispatch(this, hash, tasksArray, false, true, new ProgressDialogListener() {

        @Override
        public void cancelButton_actionPerformed(EventObject newEvent) {
            try {
                bngService.stopBNG();
                String s = "...user cancelled.";
                TaskCallbackMessage tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskStopped, s);
                // message will be processed in TaskCallbackProcessor::case TaskStopped
                setNewCallbackMessage(tcm);
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    });
}

Example 4 with BNGInput

use of cbit.vcell.server.bionetgen.BNGInput in project vcell by virtualcell.

the class NetworkTransformer method generateNetwork.

private BNGOutputSpec generateNetwork(SimulationContext simContext, MathMappingCallback mathMappingCallback, NetworkGenerationRequirements networkGenerationRequirements) throws ClassNotFoundException, IOException {
    TaskCallbackMessage tcm;
    BNGOutputSpec outputSpec;
    speciesEquivalenceMap.clear();
    kineticsParameterMap.clear();
    String input = convertToBngl(simContext, true, mathMappingCallback, networkGenerationRequirements);
    for (Map.Entry<FakeSeedSpeciesInitialConditionsParameter, Pair<SpeciesContext, Expression>> entry : speciesEquivalenceMap.entrySet()) {
        FakeSeedSpeciesInitialConditionsParameter key = entry.getKey();
        Pair<SpeciesContext, Expression> value = entry.getValue();
        SpeciesContext sc = value.one;
        Expression initial = value.two;
        System.out.println("key: " + key.fakeParameterName + ",   species: " + sc.getName() + ", initial: " + initial.infix());
    }
    String md5hash = MD5.md5(input);
    if (isBngHashValid(input, md5hash, simContext)) {
        String s = "Previously saved outputSpec is up-to-date, no need to generate network.";
        System.out.println(s);
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Notification, s);
        simContext.appendToConsole(tcm);
        if (simContext.isInsufficientIterations()) {
            s = NetworkTransformer.getInsufficientIterationsMessage();
            System.out.println(s);
            tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, s);
            simContext.appendToConsole(tcm);
        }
        if (simContext.isInsufficientMaxMolecules()) {
            s = NetworkTransformer.getInsufficientMaxMoleculesMessage();
            System.out.println(s);
            tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, s);
            simContext.appendToConsole(tcm);
        }
        outputSpec = simContext.getMostRecentlyCreatedOutputSpec();
        return (BNGOutputSpec) BeanUtils.cloneSerializable(outputSpec);
    }
    BNGInput bngInput = new BNGInput(input);
    BNGOutput bngOutput = null;
    try {
        final BNGExecutorService bngService = BNGExecutorService.getInstance(bngInput, networkGenerationRequirements.timeoutDurationMS);
        bngService.registerBngUpdaterCallback(simContext);
        bngOutput = bngService.executeBNG();
    } catch (BNGException ex) {
        ex.printStackTrace(System.out);
        System.out.println("bionetgen exception");
        if (ex.getMessage().contains("was asked to write the network, but no reactions were found")) {
            RuntimeException rex = new RuntimeException("Specified species and reaction rules are not sufficient to define reaction network.");
            throw rex;
        } else {
            // rethrow without losing context
            throw ex;
        }
    } catch (RuntimeException ex) {
        ex.printStackTrace(System.out);
        System.out.println("runtime exception");
        throw ex;
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        System.out.println("other exception");
        throw new RuntimeException(ex.getMessage());
    }
    // simContext.setInsufficientIterations(false);
    // simContext.setInsufficientMaxMolecules(false);
    String bngConsoleString = bngOutput.getConsoleOutput();
    // TODO: this message we check if insufficient iterations / max molecules
    // DO IT OUTSIDE (in the bng service), we now can
    // tcm = new TaskCallbackMessage(TaskCallbackStatus.DetailBatch, bngConsoleString);
    // simContext.appendToConsole(tcm);
    tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskEndNotificationOnly, "");
    simContext.setNewCallbackMessage(tcm);
    tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskEndAdjustSimulationContextFlagsOnly, "");
    simContext.setNewCallbackMessage(tcm);
    String bngNetString = bngOutput.getNetFileContent();
    outputSpec = BNGOutputFileParser.createBngOutputSpec(bngNetString);
    // prints all output to console
    BNGOutputFileParser.printBNGNetOutput(outputSpec);
    if (mathMappingCallback.isInterrupted()) {
        String msg = "Canceled by user.";
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
        simContext.appendToConsole(tcm);
        // clean the cache if the user interrupts
        simContext.setMd5hash(null);
        throw new UserCancelException(msg);
    }
    if (outputSpec.getBNGSpecies().length > NetworkTransformer.getSpeciesLimit(simContext)) {
        String message = NetworkTransformer.getSpeciesLimitExceededMessage(outputSpec, simContext);
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
        simContext.appendToConsole(tcm);
        simContext.setMd5hash(null);
        message = "Unable to generate Math for Application " + simContext.getName() + ".\n" + message;
        throw new RuntimeException(message);
    }
    if (outputSpec.getBNGReactions().length > NetworkTransformer.getReactionsLimit(simContext)) {
        String message = NetworkTransformer.getReactionsLimitExceededMessage(outputSpec, simContext);
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
        simContext.appendToConsole(tcm);
        simContext.setMd5hash(null);
        message = "Unable to generate Math for Application " + simContext.getName() + ".\n" + message;
        throw new RuntimeException(message);
    }
    // System.out.println("old hash: " + simContext.getMd5hash());
    if (md5hash != null && md5hash.length() != 0 && outputSpec != null) {
        System.out.println("saving hash and output spec");
        synchronized (this) {
            simContext.setMd5hash(md5hash);
            simContext.setMostRecentlyCreatedOutputSpec(outputSpec);
        }
    } else {
        System.out.println("something is wrong with the hash and/or output spec");
    }
    return (BNGOutputSpec) BeanUtils.cloneSerializable(outputSpec);
}