Examples with ObjectNotFoundException org.vcell.util.ObjectNotFoundException used on opensource projects

Example 11 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class GeomDbDriver method getImageRefKeyFromGeometry.

/**
 * getModel method comment.
 */
private KeyValue getImageRefKeyFromGeometry(Connection con, KeyValue geomKey) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (geomKey == null) {
        throw new IllegalArgumentException("Improper parameters for getImageRefKeyFromGeometry");
    }
    // log.print("GeomDbDriver.getImageRefKeyFromGeometry(id="+geomKey+")");
    String sql;
    sql = " SELECT " + geomTable.imageRef + " FROM " + geomTable.getTableName() + " WHERE " + geomTable.id + " = " + geomKey;
    // System.out.println(sql);
    // Connection con = conFact.getConnection();
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            java.math.BigDecimal iR = rset.getBigDecimal(geomTable.imageRef.toString());
            if (rset.wasNull()) {
                return null;
            }
            return new KeyValue(iR);
        } else {
            throw new ObjectNotFoundException("getSizeKeyFromGeometry for Image id=" + geomKey + " not found");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
}

Example 12 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class GeomDbDriver method getExtentRefKeyFromImage.

/**
 * getModel method comment.
 */
private KeyValue getExtentRefKeyFromImage(Connection con, KeyValue imageKey) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (imageKey == null) {
        throw new IllegalArgumentException("Improper parameters for getSizeKeyFromImage");
    }
    // log.print("GeomDbDriver.getSizeRefKeyFromImage(id="+imageKey+")");
    String sql;
    sql = " SELECT " + imageTable.extentRef + " FROM " + imageTable.getTableName() + " WHERE " + imageTable.id + " = " + imageKey;
    // System.out.println(sql);
    // Connection con = conFact.getConnection();
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            return new KeyValue(rset.getBigDecimal(imageTable.extentRef.toString()));
        } else {
            throw new ObjectNotFoundException("getSizeKeyFromImage for Image id=" + imageKey + " not found");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
}

Example 13 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class MathDescriptionDbDriver method getMathDescriptionSQL.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param mathDescKey cbit.sql.KeyValue
 */
private MathDescription getMathDescriptionSQL(QueryHashtable dbc, Connection con, User user, KeyValue mathDescKey) throws SQLException, DataAccessException, ObjectNotFoundException {
    String sql;
    Field[] f = { userTable.userid, new cbit.sql.StarField(mathDescTable) };
    Table[] t = { mathDescTable, userTable };
    String condition = mathDescTable.id.getQualifiedColName() + " = " + mathDescKey + " AND " + userTable.id.getQualifiedColName() + " = " + mathDescTable.ownerRef.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // System.out.println(sql);
    MathDescription mathDescription = null;
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            // 
            // note: must call mathDescTable.getMathDescription() first (rset.getBytes(language) must be called first)
            // 
            mathDescription = mathDescTable.getMathDescription(rset, con, dbSyntax);
            // 
            // get Geometry reference and assign to mathDescription
            // 
            java.math.BigDecimal bigD = rset.getBigDecimal(MathDescTable.table.geometryRef.toString());
            KeyValue geomRef = null;
            if (!rset.wasNull()) {
                geomRef = new KeyValue(bigD);
            } else {
                throw new DataAccessException("Error:  Geometry Reference Cannot be Null for MathDescription");
            }
            Geometry geom = (Geometry) geomDB.getVersionable(dbc, con, user, VersionableType.Geometry, geomRef, false);
            try {
                mathDescription.setGeometry(geom);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new DataAccessException("DataAccess Exception: " + e.getMessage());
            }
        } else {
            throw new ObjectNotFoundException("MathDescription id=" + mathDescKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return mathDescription;
}

Example 14 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class MathVerifier method testMathGeneration.

public MathGenerationResults testMathGeneration(KeyValue simContextKey) throws SQLException, ObjectNotFoundException, DataAccessException, XmlParseException, MappingException, MathException, MatrixException, ExpressionException, ModelException, PropertyVetoException {
    User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new org.vcell.util.document.KeyValue(PropertyLoader.ADMINISTRATOR_ID));
    if (lg.isTraceEnabled())
        lg.trace("Testing SimContext with key '" + simContextKey + "'");
    // get biomodel refs
    java.sql.Connection con = null;
    java.sql.Statement stmt = null;
    con = conFactory.getConnection(new Object());
    cbit.vcell.modeldb.BioModelSimContextLinkTable bmscTable = cbit.vcell.modeldb.BioModelSimContextLinkTable.table;
    cbit.vcell.modeldb.BioModelTable bmTable = cbit.vcell.modeldb.BioModelTable.table;
    cbit.vcell.modeldb.UserTable userTable = cbit.vcell.modeldb.UserTable.table;
    String sql = "SELECT " + bmscTable.bioModelRef.getQualifiedColName() + "," + bmTable.ownerRef.getQualifiedColName() + "," + userTable.userid.getQualifiedColName() + " FROM " + bmscTable.getTableName() + "," + bmTable.getTableName() + "," + userTable.getTableName() + " WHERE " + bmscTable.simContextRef.getQualifiedColName() + " = " + simContextKey + " AND " + bmTable.id.getQualifiedColName() + " = " + bmscTable.bioModelRef.getQualifiedColName() + " AND " + bmTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
    ArrayList<KeyValue> bioModelKeys = new ArrayList<KeyValue>();
    stmt = con.createStatement();
    User owner = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            KeyValue key = new KeyValue(rset.getBigDecimal(bmscTable.bioModelRef.getUnqualifiedColName()));
            bioModelKeys.add(key);
            KeyValue ownerRef = new KeyValue(rset.getBigDecimal(bmTable.ownerRef.getUnqualifiedColName()));
            String userid = rset.getString(userTable.userid.getUnqualifiedColName());
            owner = new User(userid, ownerRef);
        }
    } finally {
        if (stmt != null) {
            stmt.close();
        }
        con.close();
    }
    // use the first biomodel...
    if (bioModelKeys.size() == 0) {
        throw new RuntimeException("zombie simContext ... no biomodels");
    }
    BioModelInfo bioModelInfo = dbServerImpl.getBioModelInfo(owner, bioModelKeys.get(0));
    // 
    // read in the BioModel from the database
    // 
    BigString bioModelXML = dbServerImpl.getBioModelXML(owner, bioModelInfo.getVersion().getVersionKey());
    BioModel bioModelFromDB = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    BioModel bioModelNewMath = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    bioModelFromDB.refreshDependencies();
    bioModelNewMath.refreshDependencies();
    // 
    // get all Simulations for this model
    // 
    Simulation[] modelSimsFromDB = bioModelFromDB.getSimulations();
    // 
    // ---> only for the SimContext we started with...
    // recompute mathDescription, and verify it is equivalent
    // then check each associated simulation to ensure math overrides are applied in an equivalent manner also.
    // 
    SimulationContext[] simContextsFromDB = bioModelFromDB.getSimulationContexts();
    SimulationContext[] simContextsNewMath = bioModelNewMath.getSimulationContexts();
    SimulationContext simContextFromDB = null;
    SimulationContext simContextNewMath = null;
    for (int k = 0; k < simContextsFromDB.length; k++) {
        // find it...
        if (simContextsFromDB[k].getKey().equals(simContextKey)) {
            simContextFromDB = simContextsFromDB[k];
            simContextNewMath = simContextsNewMath[k];
            break;
        }
    }
    if (simContextFromDB == null) {
        throw new RuntimeException("BioModel referred to by this SimContext does not contain this SimContext");
    } else {
        MathDescription origMathDesc = simContextFromDB.getMathDescription();
        // 
        try {
            if (simContextNewMath.getGeometry().getDimension() > 0 && simContextNewMath.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() == null) {
                simContextNewMath.getGeometry().getGeometrySurfaceDescription().updateAll();
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
        // 
        // updated mathDescription loaded into copy of bioModel, then test for equivalence.
        // 
        cbit.vcell.mapping.MathMapping mathMapping = simContextNewMath.createNewMathMapping();
        MathDescription mathDesc_latest = mathMapping.getMathDescription();
        MathMapping_4_8 mathMapping_4_8 = new MathMapping_4_8(simContextNewMath);
        MathDescription mathDesc_4_8 = mathMapping_4_8.getMathDescription();
        String issueString = null;
        org.vcell.util.Issue[] issues = mathMapping.getIssues();
        if (issues != null && issues.length > 0) {
            StringBuffer buffer = new StringBuffer("Issues(" + issues.length + "):\n");
            for (int l = 0; l < issues.length; l++) {
                buffer.append(" <<" + issues[l].toString() + ">>\n");
            }
            issueString = buffer.toString();
        }
        simContextNewMath.setMathDescription(mathDesc_latest);
        MathCompareResults mathCompareResults_latest = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_latest);
        MathCompareResults mathCompareResults_4_8 = null;
        try {
            mathCompareResults_4_8 = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_4_8);
        } catch (Exception e) {
            e.printStackTrace(System.out);
            mathCompareResults_4_8 = new MathCompareResults(Decision.MathDifferent_FAILURE_UNKNOWN, e.getMessage());
        }
        return new MathGenerationResults(bioModelFromDB, simContextFromDB, origMathDesc, mathDesc_latest, mathCompareResults_latest, mathDesc_4_8, mathCompareResults_4_8);
    }
}

Example 15 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class ModelDbDriver method getModel.

/**
 * getModel method comment.
 */
private cbit.vcell.model.Model getModel(QueryHashtable dbc, Connection con, User user, KeyValue modelKey) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (user == null || modelKey == null) {
        throw new IllegalArgumentException("Improper parameters for getModel");
    }
    // log.print("ModelDbDriver.getModel(user=" + user + ", id=" + modelKey + ")");
    String sql;
    Field[] f = { new cbit.sql.StarField(modelTable), userTable.userid };
    Table[] t = { modelTable, userTable };
    String condition = modelTable.id.getQualifiedColName() + " = " + modelKey + " AND " + userTable.id.getQualifiedColName() + " = " + modelTable.ownerRef.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    Statement stmt = con.createStatement();
    Model model = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            model = getModel(dbc, rset, con, user);
        } else {
            throw new org.vcell.util.ObjectNotFoundException("Model id=" + modelKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    // GlobalModelParameterTable.table.setModelParameters(con, model);
    return model;
}