Examples with KeyValue org.vcell.util.document.KeyValue used on opensource projects

Example 46 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class VCellPubUtils method readNewRecords.

private static void readNewRecords(File xmlFile) throws IOException {
    System.out.println("starting to read");
    /**
     * 	public final Field id					= new Field("title",			"VARCHAR2(4000)",	"")
     * 	public final Field title				= new Field("title",			"VARCHAR2(4000)",	"")
     *  public final Field authors				= new Field("authors",			"VARCHAR2(4000)",	"");
     *  public final Field year					= new Field("year",				"Integer",			"");
     *  public final Field citation				= new Field("citation",			"VARCHAR2(4000)",	"");
     *  public final Field pubmedid				= new Field("pubmedid",			"VARCHAR2(32)",		"");
     *  public final Field doi					= new Field("doi",				"VARCHAR2(50)",		"");
     *  public final Field endnodeid			= new Field("endnoteid",		"VARCHAR2(50)",		"");
     *  public final Field url					= new Field("url",				"VARCHAR2(128)",	"");
     *  public final Field wittid				= new Field("wittid",			"Integer",			"");
     */
    Document doc = XmlUtil.readXML(xmlFile);
    List<Element> recordList = doc.getRootElement().getChild("records").getChildren("record");
    int foundCount = 0;
    for (Element record : recordList) {
        String titleString = record.getChild("titles").getChild("title").getChild("style").getText();
        ArrayList<String> authorsArray = new ArrayList<String>();
        List<Element> authorElements = (List<Element>) record.getChild("contributors").getChild("authors").getChildren("author");
        for (Element authorElement : authorElements) {
            authorsArray.add(authorElement.getChild("style").getText());
        }
        String title = "'" + TokenMangler.getSQLEscapedString(titleString) + "'";
        String authors = "'" + TokenMangler.getSQLEscapedString(String.join(";", authorsArray)) + "'";
        String citation = "NULL";
        String pubmedid = "NULL";
        String year = "NULL";
        try {
            year = "" + Integer.parseInt(record.getChild("dates").getChild("year").getChild("style").getText());
        } catch (Exception e) {
            System.err.println("failed to parse year : " + e.getMessage());
        }
        try {
            pubmedid = "'" + record.getChild("accession-num").getChild("style").getText() + "'";
        } catch (Exception e) {
        }
        String doi = "NULL";
        try {
            doi = "'" + record.getChild("electronic-resource-num").getChild("style").getText() + "'";
        } catch (Exception e) {
        }
        String endnoteid = record.getChild("rec-number").getText();
        String url = "NULL";
        try {
            url = "'" + record.getChild("urls").getChild("related-urls").getChild("url").getChild("style").getText() + "'";
        } catch (Exception e) {
        }
        int wittid = -1;
        String sql = "insert into vc_publication (id, title, authors, year, citation, pubmedid, doi, endnoteid, url, wittid) " + "values (NewSeq.NEXTVAL," + title + "," + authors + "," + year + "," + citation + "," + pubmedid + "," + doi + "," + endnoteid + "," + url + "," + wittid + ")";
        System.out.println(sql + ";");
        Element biomodelRefsElement = record.getChild("custom3");
        if (biomodelRefsElement != null) {
            String biomodelsString = biomodelRefsElement.getChildText("style");
            if (biomodelsString != null) {
                String[] bmRefs = biomodelsString.replace(" ", "").split(",");
                for (String bmRef : bmRefs) {
                    KeyValue pmKey = new KeyValue(bmRef);
                    String sql_link = "insert into vc_publicationmodellink (id, pubRef, bioModelRef, mathModelRef) " + "values (NewSeq.NEXTVAL,(select id from vc_publication where title = " + title + " and year is not null)," + pmKey + ",NULL);";
                    System.out.println(sql_link);
                }
            }
        }
        System.out.println("");
    }
}

Example 47 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class NagiosVCellMonitor method checkVCell.

private CheckResults checkVCell(VCELL_CHECK_LEVEL checkLevel, String rmiHostName, int rmiPort, String rmiBootstrapStubName, String vcellNagiosPassword, int criticalTimeout, int monitorPort) throws Exception {
    SimulationStatusPersistent lastSimStatus = null;
    String vcellVersion = null;
    TreeMap<VCELL_CHECK_LEVEL, Long> levelTimesMillisec = new TreeMap<NagiosVCellMonitor.VCELL_CHECK_LEVEL, Long>();
    long startTime = System.currentTimeMillis();
    VCellConnection vcellConnection = null;
    try {
        if (rmiHostName == null || rmiPort == -1) {
            throw new UnexpectedTestStateException("Host name/ip and rmiPort required for testing, rmihostname=" + rmiHostName + " rmiport=" + rmiPort);
        }
        String rmiUrl = "//" + rmiHostName + ":" + rmiPort + "/" + rmiBootstrapStubName;
        VCellBootstrap vcellBootstrap = null;
        try {
            vcellBootstrap = (VCellBootstrap) Naming.lookup(rmiUrl);
        } catch (Exception e) {
            throw new UnexpectedTestStateException("Error during bootstrap lookup, " + e.getClass().getSimpleName() + " " + e.getMessage());
        }
        vcellVersion = vcellBootstrap.getVCellSoftwareVersion();
        levelTimesMillisec.put(VCELL_CHECK_LEVEL.RMI_ONLY_0, System.currentTimeMillis() - startTime);
        if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.CONNECT_1.ordinal()) {
            if (vcellNagiosPassword == null) {
                throw new UnexpectedTestStateException("vcellNagios Password required for " + VCELL_CHECK_LEVEL.CONNECT_1.toString() + " and above");
            }
            UserLoginInfo userLoginInfo = new UserLoginInfo(VCELL_NAGIOS_USER, new DigestedPassword(vcellNagiosPassword));
            vcellConnection = vcellBootstrap.getVCellConnection(userLoginInfo);
            levelTimesMillisec.put(VCELL_CHECK_LEVEL.CONNECT_1, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.RMI_ONLY_0));
            if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.INFOS_2.ordinal()) {
                VCInfoContainer vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
                levelTimesMillisec.put(VCELL_CHECK_LEVEL.INFOS_2, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.CONNECT_1));
                if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.LOAD_3.ordinal()) {
                    KeyValue bioModelKey = null;
                    final String testModelName = "Solver Suite 5.1 (BETA only ode)";
                    for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                        if (userLoginInfo.getUserName().equals(bioModelInfo.getVersion().getOwner().getName()) && bioModelInfo.getVersion().getName().equals(testModelName)) {
                            bioModelKey = bioModelInfo.getVersion().getVersionKey();
                            break;
                        }
                    }
                    BigString bioModelXML = vcellConnection.getUserMetaDbServer().getBioModelXML(bioModelKey);
                    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                    bioModel.refreshDependencies();
                    levelTimesMillisec.put(VCELL_CHECK_LEVEL.LOAD_3, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.INFOS_2));
                    if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.DATA_4.ordinal()) {
                        final String testSimContextName = "non-spatial ODE";
                        SimulationContext simulationContext = bioModel.getSimulationContext(testSimContextName);
                        final String testSimName = "Copy of combined ida/cvode";
                        Simulation simulation = simulationContext.getSimulation(testSimName);
                        if (simulation == null) {
                            throw new UnexpectedTestStateException("Couldn't find sim '" + testSimName + "' for " + checkLevel.toString());
                        }
                        VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                        ArrayList<AnnotatedFunction> outputFunctionsList = simulationContext.getOutputFunctionContext().getOutputFunctionsList();
                        OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
                        double[] times = vcellConnection.getDataSetController().getDataSetTimes(vcSimulationDataIdentifier);
                        ODESimData odeSimData = vcellConnection.getDataSetController().getODEData(vcSimulationDataIdentifier);
                        levelTimesMillisec.put(VCELL_CHECK_LEVEL.DATA_4, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.LOAD_3));
                        if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.RUN_5.ordinal()) {
                            KeyValue copy1Key = null;
                            KeyValue copy2Key = null;
                            VCSimulationIdentifier testRunSimID = null;
                            try {
                                if (simulationContext.getSimulations().length != 1) {
                                    throw new UnexpectedTestStateException("Expecting only 1 sim to be copied for " + checkLevel.toString());
                                }
                                SimulationStatusPersistent simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(simulation.getVersion().getVersionKey());
                                if (!simulationStatus.isCompleted()) {
                                    throw new UnexpectedTestStateException("Expecting completed sim to copy for " + checkLevel.toString());
                                }
                                String copyModelName = testModelName + "_" + rmiHostName + "_rmi" + rmiPort + "_siteprt" + monitorPort;
                                boolean bForceCleanup = true;
                                while (true) {
                                    boolean bMessy = false;
                                    for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                                        if (userLoginInfo.getUserName().equals(bioModelInfo.getVersion().getOwner().getName()) && bioModelInfo.getVersion().getName().equals(copyModelName)) {
                                            bMessy = true;
                                            if (bForceCleanup) {
                                                try {
                                                    vcellConnection.getUserMetaDbServer().deleteBioModel(bioModelInfo.getVersion().getVersionKey());
                                                } catch (Exception e) {
                                                    e.printStackTrace();
                                                }
                                            } else {
                                                throw new MessyTestEnvironmentException("Messy test environment, not expecting " + copyModelName + " and couldn't cleanup");
                                            }
                                        }
                                    }
                                    if (!bMessy) {
                                        break;
                                    }
                                    // get new vcInfoContainer without cleaned-up model
                                    vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
                                    bForceCleanup = false;
                                }
                                BigString copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModelAs(bioModelXML, copyModelName, null);
                                BioModel copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                                copy1Key = copyBioModel.getVersion().getVersionKey();
                                copyBioModel.refreshDependencies();
                                Simulation copySim = copyBioModel.getSimulationContext(testSimContextName).copySimulation(copyBioModel.getSimulationContext(testSimContextName).getSimulation(testSimName));
                                final String copyTestSimName = "test";
                                copySim.setName(copyTestSimName);
                                copyBioModel.refreshDependencies();
                                copyBioModelXMLStr = new BigString(XmlHelper.bioModelToXML(copyBioModel));
                                copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModel(copyBioModelXMLStr, null);
                                copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                                copy2Key = copyBioModel.getVersion().getVersionKey();
                                copyBioModel.refreshDependencies();
                                Simulation newSimulation = copyBioModel.getSimulationContext(testSimContextName).getSimulation(copyTestSimName);
                                simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                                if (simulationStatus != null && !simulationStatus.isNeverRan()) {
                                    throw new UnexpectedTestStateException("Expecting new sim to have 'never ran' status for " + checkLevel.toString());
                                }
                                testRunSimID = new VCSimulationIdentifier(newSimulation.getVersion().getVersionKey(), copyBioModel.getVersion().getOwner());
                                vcellConnection.getSimulationController().startSimulation(testRunSimID, 1);
                                lastSimStatus = simulationStatus;
                                MessageEvent[] messageEvents = null;
                                while (simulationStatus == null || (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed())) {
                                    Thread.sleep(200);
                                    if (((System.currentTimeMillis() - startTime) / 1000) > criticalTimeout) {
                                        vcellConnection.getSimulationController().stopSimulation(testRunSimID);
                                        vcellConnection.getMessageEvents();
                                        break;
                                    }
                                    simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                                    if (simulationStatus != null && !simulationStatus.toString().equals((lastSimStatus == null ? null : lastSimStatus.toString()))) {
                                        lastSimStatus = simulationStatus;
                                    }
                                    if (simulationStatus != null && simulationStatus.isFailed()) {
                                        throw new Exception("time " + ((System.currentTimeMillis() - startTime) / 1000) + ", Sim execution failed key:" + testRunSimID.getSimulationKey() + " sim " + newSimulation.getName() + " model " + copyBioModel.getVersion().getName() + " messg " + simulationStatus.getFailedMessage());
                                    }
                                    messageEvents = vcellConnection.getMessageEvents();
                                }
                            } finally {
                                try {
                                    if (copy1Key != null) {
                                        vcellConnection.getUserMetaDbServer().deleteBioModel(copy1Key);
                                    }
                                } catch (Exception e) {
                                    e.printStackTrace();
                                }
                                try {
                                    if (copy2Key != null) {
                                        vcellConnection.getUserMetaDbServer().deleteBioModel(copy2Key);
                                    }
                                } catch (Exception e) {
                                    e.printStackTrace();
                                }
                                if (testRunSimID != null) {
                                    deleteSimData(testRunSimID);
                                }
                            }
                            levelTimesMillisec.put(VCELL_CHECK_LEVEL.RUN_5, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.DATA_4));
                        }
                    }
                }
            }
        }
        return new CheckResults(vcellVersion, levelTimesMillisec, lastSimStatus, System.currentTimeMillis() - startTime, null);
    } catch (Exception e) {
        return new CheckResults(vcellVersion, levelTimesMillisec, lastSimStatus, System.currentTimeMillis() - startTime, e);
    } finally {
        vcellConnection = null;
    }
}

Example 48 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class TestBlobRpcMessages method main.

public static void main(String[] args) throws Exception {
    try {
        PropertyLoader.loadProperties();
        // System.getProperties().setProperty(PropertyLoader.jmsURL,"tcp://nrcamdev5.cam.uchc.edu:61616");
        VCMessagingService messagingService = new VCMessagingServiceActiveMQ();
        messagingService.setDelegate(new SimpleMessagingDelegate());
        // reading message and computing sum
        // create N comsumers
        MyRpcServer myRpcServer = new MyRpcServer();
        for (int i = 0; i < NUM_COMSUMERS; i++) {
            VCRpcMessageHandler rpcMessageHandler = new VCRpcMessageHandler(myRpcServer, VCellTestQueue.JimQueue);
            VCQueueConsumer rpcConsumer = new VCQueueConsumer(VCellTestQueue.JimQueue, rpcMessageHandler, null, "Queue[" + VCellTestQueue.JimQueue.getName() + "] ==== RPC Consumer Thread " + i, 1);
            messagingService.addMessageConsumer(rpcConsumer);
        }
        // creating one messageProducer session
        ArrayList<VCMessageSession> sessions = new ArrayList<VCMessageSession>();
        for (int i = 0; i < NUM_PRODUCERS; i++) {
            sessions.add(messagingService.createProducerSession());
        }
        for (int i = 0; i < NUM_MESSAGES; i++) {
            for (int s = 0; s < NUM_PRODUCERS; s++) {
                VCMessageSession session = sessions.get(s);
                try {
                    // 
                    // create simple RPC request for service "Testing_Service"
                    // 
                    User user = new User("schaff", new KeyValue("17"));
                    byte[] array1 = new byte[20000000];
                    byte[] array2 = new byte[20000000];
                    VCRpcRequest rpcRequest = new VCRpcRequest(user, RpcServiceType.TESTING_SERVICE, "concat", new Object[] { array1, array2 });
                    // 
                    // send request and block for response (or timeout).
                    // RPC invocations don't need commits.
                    // 
                    Object returnValue = session.sendRpcMessage(VCellTestQueue.JimQueue, rpcRequest, true, 20000, null, null, null);
                    // 
                    if (returnValue instanceof byte[]) {
                        System.out.println("concat(byte[" + array1.length + "], byte[" + array2.length + "]) ===> byte[" + (((byte[]) returnValue).length) + "]");
                    } else {
                        System.out.println("unexpected return value of " + returnValue);
                    }
                } catch (VCMessagingInvocationTargetException e) {
                    e.printStackTrace(System.out);
                    System.out.println("the rpc service threw an exception");
                    e.getTargetException().printStackTrace(System.out);
                }
            }
        }
        System.out.println("main program calling closeAll()");
        messagingService.close();
        System.out.println("main program exiting");
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 49 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class BioModelMultiVisitor method visitBioModel.

public void visitBioModel(BioModel bioModel, PrintStream logFilePrintStream) {
    KeyValue currentKey = bioModel.getVersion().getVersionKey();
    BioModelInfo bmInfo = bioModelInfoHash.get(currentKey);
    logFilePrintStream.append(" == SUCEEDED IN READING BIOMODEL " + bmInfo.getVersion().getName() + "; key : " + currentKey.toString() + "\n");
    unparsedBioModels.remove(currentKey);
    for (Iterator<KeyValue> iterator = unparsedBioModels.iterator(); iterator.hasNext(); ) {
        KeyValue key = iterator.next();
        bmInfo = bioModelInfoHash.get(key);
        logFilePrintStream.append(" == FAILED TO READ BIOMODEL : " + bmInfo.getVersion().getName() + "; key : " + key.toString() + "\n");
        iterator.remove();
    }
    return;
}

Example 50 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class NFSimMathGenerationHashVisitor method filterBioModel.

public boolean filterBioModel(BioModelInfo bioModelInfo) {
    // 
    // check for applicability of the model
    // 
    // does this model have either
    // 1) a nonspatial stochastic application which can be copied as a rule-based model
    // 2) a rulebased application
    // 
    boolean bHasNonspatialStochastic = false;
    boolean bHasRulebased = false;
    for (ApplicationInfo appInfo : bioModelInfo.getBioModelChildSummary().getApplicationInfo()) {
        if (appInfo.type == MathType.Stochastic && appInfo.dimensions == 0) {
            bHasNonspatialStochastic = true;
        }
        if (appInfo.type == MathType.RuleBased) {
            bHasRulebased = true;
        }
    }
    // skip
    if (bioModelInfo.getVersion().getVersionKey().equals(new KeyValue("93037435"))) {
        return false;
    }
    // candidate models
    if (bHasNonspatialStochastic || bHasRulebased) {
        // }
        return true;
    }
    return false;
}