Examples with BioModelMetaData cbit.vcell.biomodel.BioModelMetaData used on opensource projects

Example 1 with BioModelMetaData

use of cbit.vcell.biomodel.BioModelMetaData in project vcell by virtualcell.

the class LocalUserMetaDbServerMessaging method getBioModelMetaDatas.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public BioModelMetaData[] getBioModelMetaDatas(boolean bAll) throws DataAccessException {
    try {
        log.print("LocalUserMetaDbServerMessaging.getBioModelMetaDatas(bAll=" + bAll + ")");
        BioModelMetaData[] bioModelMetaDataArray = dbServerProxy.getBioModelMetaDatas(bAll);
        return bioModelMetaDataArray;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 2 with BioModelMetaData

use of cbit.vcell.biomodel.BioModelMetaData in project vcell by virtualcell.

the class BioModelDbDriver method getBioModelMetaDatas.

/**
 * getModel method comment.
 */
BioModelMetaData[] getBioModelMetaDatas(Connection con, User user, boolean bAll, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (user == null) {
        throw new IllegalArgumentException("Improper parameters for getBioModelMetaDatas");
    }
    if (lg.isTraceEnabled())
        lg.trace("BioModelDbDriver.getBioModelMetaDatas(user=" + user + ", bAll=" + bAll + ")");
    // 
    // to construct a BioModelMetaData as an immutable object, lets collect all keys first
    // (even before authentication).  If the user doesn't authenticate, then throw away the
    // child keys (from link tables).
    // 
    // 
    // get BioModelMetaData object for bioModelKey
    // 
    String sql;
    Field[] f = { new cbit.sql.StarField(bioModelTable), userTable.userid };
    Table[] t = { bioModelTable, userTable };
    String condition = userTable.id.getQualifiedColName() + " = " + bioModelTable.ownerRef.getQualifiedColName();
    if (!bAll) {
        condition += " AND " + userTable.id.getQualifiedColName() + " = " + user.getID();
    }
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // 
    StringBuffer newSQL = new StringBuffer(sql);
    newSQL.insert(7, Table.SQL_GLOBAL_HINT);
    sql = newSQL.toString();
    // 
    Statement stmt = con.createStatement();
    Vector<BioModelMetaData> bioModelMetaDataList = new Vector<BioModelMetaData>();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            BioModelMetaData bioModelMetaData = bioModelTable.getBioModelMetaData(rset, this, con, dbSyntax);
            bioModelMetaDataList.addElement(bioModelMetaData);
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    BioModelMetaData[] bioModelMetaDataArray = new BioModelMetaData[bioModelMetaDataList.size()];
    bioModelMetaDataList.copyInto(bioModelMetaDataArray);
    return bioModelMetaDataArray;
}

Example 3 with BioModelMetaData

use of cbit.vcell.biomodel.BioModelMetaData in project vcell by virtualcell.

the class BioModelDbDriver method getBioModelMetaData.

/**
 * getModel method comment.
 */
private BioModelMetaData getBioModelMetaData(Connection con, User user, KeyValue bioModelKey, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (user == null || bioModelKey == null) {
        throw new IllegalArgumentException("Improper parameters for getBioModelMetaData");
    }
    // if (lg.isTraceEnabled()) lg.trace("BioModelDbDriver.getBioModelMetaData(user=" + user + ", id=" + bioModelKey + ")");
    // 
    // to construct a BioModelMetaData as an immutable object, lets collect all keys first
    // (even before authentication).  If the user doesn't authenticate, then throw away the
    // child keys (from link tables).
    // 
    // 
    // get Simulation Keys for bioModelKey
    // 
    KeyValue[] simKeys = getSimulationEntriesFromBioModel(con, bioModelKey);
    // 
    // get SimulationContext Keys for bioModelKey
    // 
    KeyValue[] simContextKeys = getSimContextEntriesFromBioModel(con, bioModelKey);
    // 
    // get BioModelMetaData object for bioModelKey
    // 
    String sql;
    VCMetaDataTable vcMetadataTable = VCMetaDataTable.table;
    Field[] f = { new StarField(bioModelTable), userTable.userid, new StarField(vcMetadataTable) };
    Table[] t = { bioModelTable, userTable, vcMetadataTable };
    switch(dbSyntax) {
        case ORACLE:
            {
                String condition = bioModelTable.id.getQualifiedColName() + " = " + bioModelKey + " AND " + userTable.id.getQualifiedColName() + " = " + bioModelTable.ownerRef.getQualifiedColName() + " AND " + vcMetadataTable.bioModelRef.getQualifiedColName() + "(+) = " + bioModelTable.id.getQualifiedColName();
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, null, condition, null, dbSyntax, true);
                break;
            }
        case POSTGRES:
            {
                String condition = bioModelTable.id.getQualifiedColName() + " = " + bioModelKey + " AND " + userTable.id.getQualifiedColName() + " = " + bioModelTable.ownerRef.getQualifiedColName() + " ";
                // " AND "+ VCMetaDataTable.table.bioModelRef.getQualifiedColName() + "(+) = " + bioModelTable.id.getQualifiedColName();
                OuterJoin outerJoin = new OuterJoin(vcMetadataTable, bioModelTable, JoinOp.RIGHT_OUTER_JOIN, vcMetadataTable.bioModelRef, bioModelTable.id);
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, outerJoin, condition, null, dbSyntax, true);
                break;
            }
        default:
            {
                throw new RuntimeException("unexpected DatabaseSyntax " + dbSyntax);
            }
    }
    Statement stmt = con.createStatement();
    BioModelMetaData bioModelMetaData = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            bioModelMetaData = bioModelTable.getBioModelMetaData(rset, con, simContextKeys, simKeys, dbSyntax);
        } else {
            throw new ObjectNotFoundException("BioModel id=" + bioModelKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return bioModelMetaData;
}

Example 4 with BioModelMetaData

use of cbit.vcell.biomodel.BioModelMetaData in project vcell by virtualcell.

the class BioModelTable method getBioModelMetaData.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param rset java.sql.ResultSet
 */
public BioModelMetaData getBioModelMetaData(ResultSet rset, BioModelDbDriver bioModelDbDriver, Connection con, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    // 
    // Get Version
    // 
    BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    KeyValue bioModelKey = version.getVersionKey();
    KeyValue modelRef = new KeyValue(rset.getBigDecimal(table.modelRef.toString()));
    // 
    // get Simulation Keys for bioModelKey
    // 
    KeyValue[] simKeys = bioModelDbDriver.getSimulationEntriesFromBioModel(con, bioModelKey);
    // 
    // get SimulationContext Keys for bioModelKey
    // 
    KeyValue[] simContextKeys = bioModelDbDriver.getSimContextEntriesFromBioModel(con, bioModelKey);
    // 
    // Get VCMetaData XML
    // 
    String vcMetaDataXML = VCMetaDataTable.getVCMetaDataXML(rset, dbSyntax);
    BioModelMetaData bioModelMetaData = new BioModelMetaData(version, modelRef, simContextKeys, simKeys, vcMetaDataXML);
    return bioModelMetaData;
}

Example 5 with BioModelMetaData

use of cbit.vcell.biomodel.BioModelMetaData in project vcell by virtualcell.

the class ServerDocumentManager method getBioModelUnresolved.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 4:02:44 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
// 
// this returns a BioModel that contains multiple instances of objects.
// 
public String getBioModelUnresolved(QueryHashtable dbc, User user, KeyValue bioModelKey) throws DataAccessException, XmlParseException, java.sql.SQLException {
    // 
    // get meta data associated with BioModel
    // 
    BioModelMetaData bioModelMetaData = dbServer.getDBTopLevel().getBioModelMetaData(dbc, user, bioModelKey);
    // 
    // get list of appropriate child components
    // 
    KeyValue modelKey = bioModelMetaData.getModelKey();
    KeyValue[] simKeys = getKeyArrayFromEnumeration(bioModelMetaData.getSimulationKeys());
    KeyValue[] scKeys = getKeyArrayFromEnumeration(bioModelMetaData.getSimulationContextKeys());
    Model model = dbServer.getDBTopLevel().getModel(dbc, user, modelKey);
    Simulation[] simArray = new Simulation[simKeys.length];
    for (int i = 0; i < simKeys.length; i++) {
        Simulation sim = dbServer.getDBTopLevel().getSimulation(dbc, user, simKeys[i]);
        // 
        try {
            simArray[i] = (Simulation) BeanUtils.cloneSerializable(sim);
        } catch (Throwable e) {
            lg.error(e.getLocalizedMessage(), e);
            throw new RuntimeException("exception cloning Simulation: " + e.getMessage());
        }
    }
    SimulationContext[] scArray = new SimulationContext[scKeys.length];
    for (int i = 0; i < scKeys.length; i++) {
        SimulationContext sc = dbServer.getDBTopLevel().getSimulationContext(dbc, user, scKeys[i]);
        // 
        try {
            scArray[i] = (SimulationContext) BeanUtils.cloneSerializable(sc);
            scArray[i].getModel().refreshDependencies();
            scArray[i].refreshDependencies();
            scArray[i].setModel(model);
        } catch (Throwable e) {
            lg.error(e.getLocalizedMessage(), e);
            throw new RuntimeException("exception cloning Application: " + e.getMessage());
        }
        if (!scArray[i].getModel().getKey().compareEqual(modelKey)) {
            // throw new DataAccessException("simulationContext("+scKeys[i]+").model = "+scArray[i].getModel().getKey()+", BioModel.model = "+modelKey);
            if (lg.isWarnEnabled())
                lg.warn("simulationContext(" + scKeys[i] + ").model = " + scArray[i].getModel().getKey() + ", BioModel.model = " + modelKey);
        }
    }
    // 
    // create new BioModel according to loaded BioModelMetaData
    // 
    BioModel newBioModel = new BioModel(bioModelMetaData.getVersion());
    try {
        // newBioModel.setMIRIAMAnnotation(bioModelMetaData.getMIRIAMAnnotation());
        if (lg.isWarnEnabled())
            lg.warn("< < < < NEED TO GET VCMETADATA FROM METADATA TABLE ... METADATA IS EMPTY. > > > >");
        newBioModel.setModel(model);
        newBioModel.setSimulationContexts(scArray);
        // 
        for (int i = 0; i < simArray.length; i++) {
            boolean bMathFound = false;
            for (int j = 0; j < scArray.length; j++) {
                if (simArray[i].getMathDescription().getVersion().getVersionKey().compareEqual(scArray[j].getMathDescription().getVersion().getVersionKey())) {
                    simArray[i].setMathDescription(scArray[j].getMathDescription());
                    bMathFound = true;
                    break;
                }
            }
            if (!bMathFound) {
                if (lg.isWarnEnabled())
                    lg.warn("<<<<WARNING>>>>> ClientDocumentManager.getBioModel(), Simulation " + simArray[i].getName() + " is orphaned, Math(" + simArray[i].getMathDescription().getName() + ") not found in Applications");
                simArray = (Simulation[]) BeanUtils.removeElement(simArray, simArray[i]);
                i--;
            }
        }
        newBioModel.setSimulations(simArray);
    } catch (java.beans.PropertyVetoException e) {
        lg.error(e.getLocalizedMessage(), e);
        throw new DataAccessException("PropertyVetoException caught " + e.getMessage());
    }
    // 
    // The BioModel is no longer cloned because the reference to this BioModel is no longer returned to the calling method.
    // the only possible side effect is the "BioModel:refreshDependencies()" method call.
    // this will reconnect internal listeners and other transient fields, and is not going to harm the cache integrity.
    // 
    // //
    // // clone BioModel (so that children can't be corrupted in the cache)
    // //
    // try {
    // newBioModel = (BioModel)BeanUtils.cloneSerializable(newBioModel);
    // }catch (Exception e){
    // lg.error(e.getLocalizedMessage(),e);
    // throw new DataAccessException("BioModel clone failed: "+e.getMessage());
    // }
    newBioModel.refreshDependencies();
    // 
    return cbit.vcell.xml.XmlHelper.bioModelToXML(newBioModel);
}