Examples with SimulationRep cbit.vcell.modeldb.SimulationRep used on opensource projects

Example 1 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class RestDatabaseService method query.

public BioModelRep[] query(BiomodelsServerResource resource, User vcellUser) throws SQLException, DataAccessException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    String bioModelName = resource.getQueryValue(BiomodelsServerResource.PARAM_BM_NAME);
    Long bioModelID = resource.getLongQueryValue(BiomodelsServerResource.PARAM_BM_ID);
    Long savedLow = resource.getLongQueryValue(BiomodelsServerResource.PARAM_SAVED_LOW);
    Long savedHigh = resource.getLongQueryValue(BiomodelsServerResource.PARAM_SAVED_HIGH);
    Long startRowParam = resource.getLongQueryValue(BiomodelsServerResource.PARAM_START_ROW);
    Long maxRowsParam = resource.getLongQueryValue(BiomodelsServerResource.PARAM_MAX_ROWS);
    // it is ok if the category is null;
    String categoryParam = resource.getQueryValue(BiomodelsServerResource.PARAM_CATEGORY);
    // it is ok if the ownerName is null;
    String ownerParam = resource.getQueryValue(BiomodelsServerResource.PARAM_BM_OWNER);
    // it is ok if the orderBy is null;
    String orderByParam = resource.getQueryValue(BiomodelsServerResource.PARAM_ORDERBY);
    // default
    int startRow = 1;
    if (startRowParam != null) {
        startRow = startRowParam.intValue();
    }
    // default
    int maxRows = 10;
    if (maxRowsParam != null) {
        maxRows = maxRowsParam.intValue();
    }
    ArrayList<String> conditions = new ArrayList<String>();
    java.text.SimpleDateFormat df = new java.text.SimpleDateFormat("MM/dd/yyyy HH:mm:ss", java.util.Locale.US);
    if (savedLow != null) {
        conditions.add("(" + BioModelTable.table.versionDate.getQualifiedColName() + " >= to_date('" + df.format(new Date(savedLow)) + "', 'mm/dd/yyyy HH24:MI:SS'))");
    }
    if (savedHigh != null) {
        conditions.add("(" + BioModelTable.table.versionDate.getQualifiedColName() + " <= to_date('" + df.format(new Date(savedHigh)) + "', 'mm/dd/yyyy HH24:MI:SS'))");
    }
    if (bioModelName != null && bioModelName.trim().length() > 0) {
        String pattern = bioModelName.trim();
        pattern = pattern.replace("  ", " ");
        pattern = pattern.replace("(", " ");
        pattern = pattern.replace(")", " ");
        pattern = pattern.replace("'", " ");
        pattern = pattern.replace("\"", " ");
        pattern = pattern.replace("*", "%");
        pattern = "%" + pattern + "%";
        pattern = pattern.replace("%%", "%");
        conditions.add("(" + "lower(" + BioModelTable.table.name.getQualifiedColName() + ")" + " like " + "lower('" + pattern + "')" + ")");
    }
    if (bioModelID != null) {
        conditions.add("(" + BioModelTable.table.id.getQualifiedColName() + " = " + bioModelID + ")");
    }
    // 
    if (categoryParam == null && ownerParam != null) {
        if (ownerParam.equals(VCellApiApplication.PSEUDOOWNER_PUBLIC)) {
            categoryParam = VCellApiApplication.CATEGORY_PUBLIC;
            ownerParam = null;
        } else if (ownerParam.equals(VCellApiApplication.PSEUDOOWNER_EDUCATION)) {
            categoryParam = VCellApiApplication.CATEGORY_EDUCATION;
            ownerParam = null;
        } else if (ownerParam.equals(VCellApiApplication.PSEUDOOWNER_SHARED)) {
            categoryParam = VCellApiApplication.CATEGORY_SHARED;
            ownerParam = null;
        } else if (ownerParam.equals(VCellApiApplication.PSEUDOOWNER_TUTORIAL)) {
            categoryParam = VCellApiApplication.CATEGORY_TUTORIAL;
            ownerParam = null;
        } else {
            categoryParam = VCellApiApplication.CATEGORY_ALL;
        }
    } else if (categoryParam == null && ownerParam == null) {
        categoryParam = VCellApiApplication.CATEGORY_ALL;
    }
    if (categoryParam.equals(VCellApiApplication.CATEGORY_MINE)) {
        // 
        // return all models owned by me (none if not authenticated).
        // 
        conditions.add("(" + UserTable.table.userid.getQualifiedColName() + " = '" + vcellUser.getName() + "')");
    } else if (categoryParam.equals(VCellApiApplication.CATEGORY_PUBLIC)) {
        // 
        // public models that aren't "Tutorial" or "Education"
        // 
        // we will display all public models (even if owned by this user)
        // 
        conditions.add("(" + BioModelTable.table.privacy.getQualifiedColName() + " = " + GroupAccess.GROUPACCESS_ALL + ")");
        if (ownerParam != null && ownerParam.trim().length() > 0) {
            conditions.add("(" + UserTable.table.userid.getQualifiedColName() + " = '" + ownerParam + "')");
        }
        conditions.add("(" + UserTable.table.userid.getQualifiedColName() + " != '" + VCellApiApplication.USERNAME_TUTORIAL + "')");
        conditions.add("(" + UserTable.table.userid.getQualifiedColName() + " != '" + VCellApiApplication.USERNAME_EDUCATION + "')");
    } else if (categoryParam.equals(VCellApiApplication.CATEGORY_EDUCATION)) {
        // 
        // public models from "Education"
        // 
        conditions.add("(" + UserTable.table.userid.getQualifiedColName() + " = '" + VCellApiApplication.USERNAME_EDUCATION + "')");
        conditions.add("(" + BioModelTable.table.privacy.getQualifiedColName() + " = " + GroupAccess.GROUPACCESS_ALL + ")");
    } else if (categoryParam.equals(VCellApiApplication.CATEGORY_TUTORIAL)) {
        // 
        // public models from "tutorial"
        // 
        conditions.add("(" + UserTable.table.userid.getQualifiedColName() + " = '" + VCellApiApplication.USERNAME_TUTORIAL + "')");
        conditions.add("(" + BioModelTable.table.privacy.getQualifiedColName() + " = " + GroupAccess.GROUPACCESS_ALL + ")");
    } else if (categoryParam.equals(VCellApiApplication.CATEGORY_SHARED)) {
        // 
        if (!vcellUser.compareEqual(VCellApiApplication.DUMMY_USER)) {
            conditions.add("(" + UserTable.table.userid.getQualifiedColName() + " != '" + vcellUser.getName() + "')");
        }
        if (ownerParam != null && ownerParam.trim().length() > 0) {
            conditions.add("(" + UserTable.table.userid.getQualifiedColName() + " = '" + ownerParam + "')");
        }
        conditions.add("(" + BioModelTable.table.privacy.getQualifiedColName() + " != " + GroupAccess.GROUPACCESS_ALL + ")");
        conditions.add("(" + BioModelTable.table.privacy.getQualifiedColName() + " != " + GroupAccess.GROUPACCESS_NONE + ")");
    } else if (categoryParam.equals(VCellApiApplication.CATEGORY_ALL)) {
        // 
        if (ownerParam != null && ownerParam.length() > 0) {
            conditions.add("(" + UserTable.table.userid.getQualifiedColName() + " = '" + ownerParam + "')");
        }
    }
    StringBuffer conditionsBuffer = new StringBuffer();
    for (String condition : conditions) {
        if (conditionsBuffer.length() > 0) {
            conditionsBuffer.append(" AND ");
        }
        conditionsBuffer.append(condition);
    }
    // default
    OrderBy orderBy = OrderBy.date_desc;
    if (orderByParam != null) {
        if (orderByParam.equals(BiomodelsServerResource.PARAM_ORDERBY_DATE_ASC)) {
            orderBy = OrderBy.date_asc;
        } else if (orderByParam.equals(BiomodelsServerResource.PARAM_ORDERBY_DATE_DESC)) {
            orderBy = OrderBy.date_desc;
        } else if (orderByParam.equals(BiomodelsServerResource.PARAM_ORDERBY_NAME_ASC)) {
            orderBy = OrderBy.name_asc;
        } else if (orderByParam.equals(BiomodelsServerResource.PARAM_ORDERBY_NAME_DESC)) {
            orderBy = OrderBy.name_desc;
        }
    }
    BioModelRep[] bioModelReps = databaseServerImpl.getBioModelReps(vcellUser, conditionsBuffer.toString(), orderBy, startRow, maxRows);
    for (BioModelRep bioModelRep : bioModelReps) {
        KeyValue[] simContextKeys = bioModelRep.getSimContextKeyList();
        for (KeyValue scKey : simContextKeys) {
            SimContextRep scRep = getSimContextRep(scKey);
            if (scRep != null) {
                bioModelRep.addSimContextRep(scRep);
            }
        }
        KeyValue[] simulationKeys = bioModelRep.getSimKeyList();
        for (KeyValue simKey : simulationKeys) {
            SimulationRep simulationRep = getSimulationRep(simKey);
            if (simulationRep != null) {
                bioModelRep.addSimulationRep(simulationRep);
            }
        }
    }
    return bioModelReps;
}

Example 2 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class RestDatabaseService method saveSimulation.

public SimulationSaveResponse saveSimulation(BiomodelSimulationSaveServerResource resource, User vcellUser, List<OverrideRepresentation> overrideRepresentations) throws PermissionException, ObjectNotFoundException, DataAccessException, SQLException, XmlParseException, PropertyVetoException, MappingException, ExpressionException {
    String simId = resource.getAttribute(VCellApiApplication.SIMULATIONID);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    boolean myModel = simRep.getOwner().compareEqual(vcellUser);
    // get the bioModel
    String biomodelId = resource.getAttribute(VCellApiApplication.BIOMODELID);
    KeyValue biomodelKey = new KeyValue(biomodelId);
    BigString bioModelXML = this.databaseServerImpl.getBioModelXML(vcellUser, biomodelKey);
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    // copy the simulation as new
    Simulation origSimulation = null;
    for (Simulation sim : bioModel.getSimulations()) {
        if (sim.getKey().equals(simKey)) {
            origSimulation = sim;
        }
    }
    if (origSimulation == null) {
        throw new RuntimeException("cannot find original Simulation");
    }
    SimulationContext simContext = bioModel.getSimulationContext(origSimulation);
    Simulation newUnsavedSimulation = simContext.copySimulation(origSimulation);
    // make appropriate changes
    // MATH OVERRIDES
    MathOverrides mathOverrides = new MathOverrides(newUnsavedSimulation);
    for (OverrideRepresentation overrideRep : overrideRepresentations) {
        overrideRep.applyMathOverrides(mathOverrides);
    }
    newUnsavedSimulation.setMathOverrides(mathOverrides);
    // save bioModel
    String editedBioModelXML = XmlHelper.bioModelToXML(bioModel);
    ServerDocumentManager serverDocumentManager = new ServerDocumentManager(this.databaseServerImpl);
    String modelName = bioModel.getName();
    if (!myModel) {
        modelName = modelName + "_" + Math.abs(new Random().nextInt());
    }
    String newBioModelXML = serverDocumentManager.saveBioModel(new QueryHashtable(), vcellUser, editedBioModelXML, modelName, null);
    BioModel savedBioModel = XmlHelper.XMLToBioModel(new XMLSource(newBioModelXML));
    Simulation savedSimulation = null;
    for (Simulation sim : savedBioModel.getSimulations()) {
        if (sim.getName().equals(newUnsavedSimulation.getName())) {
            savedSimulation = sim;
        }
    }
    if (savedSimulation == null) {
        throw new RuntimeException("cannot find new Simulation");
    }
    return new SimulationSaveResponse(savedBioModel, savedSimulation);
}

Example 3 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class RestDatabaseService method getDataSetMetadata.

public DataSetMetadata getDataSetMetadata(SimDataServerResource resource, User vcellUser) throws ObjectNotFoundException, DataAccessException, SQLException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String simId = resource.getAttribute(VCellApiApplication.SIMDATAID);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    User owner = simRep.getOwner();
    int jobIndex = 0;
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        RpcDataServerProxy rpcDataServerProxy = new RpcDataServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        VCDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
        DataSetMetadata dataSetMetadata = rpcDataServerProxy.getDataSetMetadata(vcdID);
        return dataSetMetadata;
    } finally {
        rpcSession.close();
    }
}

Example 4 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class RestDatabaseService method query.

public SimulationRepresentation query(BiomodelSimulationServerResource resource, User vcellUser) throws SQLException, DataAccessException, ExpressionException, XmlParseException, MappingException, MathException, MatrixException, ModelException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    ArrayList<String> conditions = new ArrayList<String>();
    String bioModelID = (String) resource.getRequestAttributes().get(VCellApiApplication.BIOMODELID);
    if (bioModelID != null) {
        conditions.add("(" + BioModelTable.table.id.getQualifiedColName() + " = " + bioModelID + ")");
    } else {
        throw new RuntimeException(VCellApiApplication.BIOMODELID + " not specified");
    }
    StringBuffer conditionsBuffer = new StringBuffer();
    for (String condition : conditions) {
        if (conditionsBuffer.length() > 0) {
            conditionsBuffer.append(" AND ");
        }
        conditionsBuffer.append(condition);
    }
    int startRow = 1;
    int maxRows = 1;
    BioModelRep[] bioModelReps = databaseServerImpl.getBioModelReps(vcellUser, conditionsBuffer.toString(), null, startRow, maxRows);
    for (BioModelRep bioModelRep : bioModelReps) {
        KeyValue[] simContextKeys = bioModelRep.getSimContextKeyList();
        for (KeyValue scKey : simContextKeys) {
            SimContextRep scRep = getSimContextRep(scKey);
            if (scRep != null) {
                bioModelRep.addSimContextRep(scRep);
            }
        }
        KeyValue[] simulationKeys = bioModelRep.getSimKeyList();
        for (KeyValue simKey : simulationKeys) {
            SimulationRep simulationRep = getSimulationRep(simKey);
            if (simulationRep != null) {
                bioModelRep.addSimulationRep(simulationRep);
            }
        }
    }
    if (bioModelReps == null || bioModelReps.length != 1) {
        // 
        // try to determine if the current credentials are insufficient, try to fetch BioModel again with administrator privilege.
        // 
        User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new KeyValue(PropertyLoader.ADMINISTRATOR_ID));
        BioModelRep[] allBioModelReps = databaseServerImpl.getBioModelReps(adminUser, conditionsBuffer.toString(), null, startRow, 1);
        if (allBioModelReps != null && allBioModelReps.length >= 0) {
            throw new PermissionException("insufficient privilege to retrive BioModel " + bioModelID);
        } else {
            throw new RuntimeException("failed to get biomodel");
        }
    }
    String simulationId = (String) resource.getRequestAttributes().get(VCellApiApplication.SIMULATIONID);
    if (simulationId == null) {
        throw new RuntimeException(VCellApiApplication.SIMULATIONID + " not specified");
    }
    SimulationRep simRep = getSimulationRep(new KeyValue(simulationId));
    BigString bioModelXML = databaseServerImpl.getBioModelXML(vcellUser, bioModelReps[0].getBmKey());
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    return new SimulationRepresentation(simRep, bioModel);
}

Example 5 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep 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]);
}