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

Example 16 with CommentStringTokenizer

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

the class SimulationJobDbDriver method getSimpleJobStatus.

/**
 * Insert the method's description here.
 * Creation date: (9/3/2003 8:59:46 AM)
 * @return java.util.List of SimpleJobStatus for managementGUI
 * @param conditions java.lang.String
 *
 * for the subqueries, here is a prototype query which returns the
 *
 * select
 *vc_simulation_1.id as simid,
 *(select max('{"bmid":"' || lpad(vc_biomodel.id,14,0) || '","scid":"' || lpad(vc_simcontext.id,14,0) || '","bmbranch":"' || lpad(vc_biomodel.versionbranchid,14,0) || '","scbranch":"' || lpad(vc_simcontext.versionbranchid,14,0) || '","bmname":"' || vc_biomodel.name || '","scname":"' || vc_simcontext.name || '"}')
 *from vc_biomodel, vc_biomodelsimcontext, VC_BIOMODELSIM, vc_simcontext
 *where vc_simulation_1.mathref = vc_simcontext.mathref
 *and VC_BIOMODELSIMCONTEXT.SIMCONTEXTREF = VC_SIMCONTEXT.id
 *and VC_BIOMODELSIMCONTEXT.BIOMODELREF = vc_biomodel.id
 *and VC_BIOMODELSIM.SIMREF = VC_SIMULATION_1.id
 *and VC_BIOMODELSIM.BIOMODELREF = vc_biomodel.id
 *) as bmLink,
 *(select max('{"mmid":"' || lpad(vc_mathmodel.id,14,0) || '","mmbranch":"' || lpad(vc_mathmodel.versionbranchid,14,0) || '","mmname":"' || vc_mathmodel.name || '"}')
 *from vc_mathmodel, VC_MATHMODELSIM
 *where vc_simulation_1.id = vc_mathmodelsim.SIMREF
 *and vc_mathmodelsim.MATHMODELREF = vc_mathmodel.id
 *) as mmLink
 *from vc_simulation vc_simulation_1
 *where rownum <= 10;
 *
 *which returns the biomodel link (bmlink) and the math model link (mmlink) as JSON strings to be interpreted as needed.
 *
 *simid		bmlink																																								mmlink
 *2,006,065	<null>																																								{"mmid":"00000002001619","mmbranch":"00000001008286","mmname":"Terasaki1"}
 *2,006,075	<null>																																								{"mmid":"00000002001626","mmbranch":"00000001008286","mmname":"Terasaki1"}
 *2,006,085	<null>																																								{"mmid":"00000002001636","mmbranch":"00000001008286","mmname":"Terasaki1"}
 *2,637,970	{"bmid":"00000002669821","scid":"00000002637934","bmbranch":"00000002622407","scbranch":"00000002637935","bmname":"aggregation","scname":"diagonal gradient"}		<null>
 *2,006,427	<null>																																								{"mmid":"00000002002108","mmbranch":"00000001002871","mmname":"DiffusionfromChannel"}
 *2,006,437	<null>																																								{"mmid":"00000002002110","mmbranch":"00000001002871","mmname":"DiffusionfromChannel"}
 *2,006,646	<null>																																								{"mmid":"00000002002254","mmbranch":"00000001118506","mmname":"AliciaProblem1"}
 *10,067,537	{"bmid":"00000010067543","scid":"00000010067469","bmbranch":"00000010033822","scbranch":"00000010067470","bmname":"BMTest_biphasicStatModule1","scname":"figure5"}	<null>
 *10,369,972	{"bmid":"00000010369990","scid":"00000010369900","bmbranch":"00000010009521","scbranch":"00000010369901","bmname":"MemBinding_1","scname":"comp"}					<null>
 *2,007,278	<null>																																								{"mmid":"00000002001884","mmbranch":"00000001036088","mmname":"Wave_no_nucl5"}
 */
public List<SimpleJobStatusPersistent> getSimpleJobStatus(Connection con, String conditions, int startRow, int maxNumRows) throws java.sql.SQLException, DataAccessException {
    BioModelSimulationLinkTable bioSimLinkTable = BioModelSimulationLinkTable.table;
    MathModelSimulationLinkTable mathSimLinkTable = MathModelSimulationLinkTable.table;
    final String BMLINK = "bmlink";
    final String MMLINK = "mmlink";
    String subquery = "SELECT " + "current_timestamp as " + DatabaseConstants.SYSDATE_COLUMN_NAME + "," + jobTable.getTableName() + ".*," + userTable.userid.getQualifiedColName() + "," + userTable.id.getQualifiedColName() + " as ownerkey" + "," + "vc_sim_1." + simTable.ownerRef.getUnqualifiedColName() + "," + "vc_sim_1." + simTable.name.getUnqualifiedColName() + "," + "vc_sim_1." + simTable.taskDescription.getUnqualifiedColName() + "," + "vc_sim_1." + simTable.meshSpecX.getUnqualifiedColName() + "," + "vc_sim_1." + simTable.meshSpecY.getUnqualifiedColName() + "," + "vc_sim_1." + simTable.meshSpecZ.getUnqualifiedColName() + "," + "vc_sim_1." + simTable.mathOverridesLarge.getUnqualifiedColName() + " as " + simTable.mathOverridesLarge.getUnqualifiedColName() + "," + "vc_sim_1." + simTable.mathOverridesSmall.getUnqualifiedColName() + " as " + simTable.mathOverridesSmall.getUnqualifiedColName() + "," + "(SELECT max('{\"" + BioModelLink.bmid + "\":\"' || lpad(vc_biomodel.id,14,0)" + " || '\",\"" + BioModelLink.scid + "\":\"' || lpad(vc_simcontext.id,14,0)" + " || '\",\"" + BioModelLink.bmbranch + "\":\"' || lpad(vc_biomodel.versionbranchid,14,0)" + " || '\",\"" + BioModelLink.scbranch + "\":\"' || lpad(vc_simcontext.versionbranchid,14,0)" + " || '\",\"" + BioModelLink.bmname + "\":\"' || vc_biomodel.name" + " || '\",\"" + BioModelLink.scname + "\":\"' || vc_simcontext.name || '\"}')" + " FROM vc_biomodel" + ", vc_biomodelsimcontext" + ", VC_BIOMODELSIM" + ", vc_simcontext" + " WHERE vc_sim_1.mathref = vc_simcontext.mathref" + " AND VC_BIOMODELSIMCONTEXT.SIMCONTEXTREF = VC_SIMCONTEXT.id" + " AND VC_BIOMODELSIMCONTEXT.BIOMODELREF = vc_biomodel.id" + " AND VC_BIOMODELSIM.SIMREF = vc_sim_1.id" + " AND VC_BIOMODELSIM.BIOMODELREF = vc_biomodel.id" + ") as " + BMLINK + "," + "(SELECT max('{\"" + MathModelLink.mmid + "\":\"' || lpad(vc_mathmodel.id,14,0)" + " || '\",\"" + MathModelLink.mmbranch + "\":\"' || lpad(vc_mathmodel.versionbranchid,14,0)" + " || '\",\"" + MathModelLink.mmname + "\":\"' || vc_mathmodel.name || '\"}')" + " FROM vc_mathmodel" + ", vc_mathmodelsim" + " WHERE vc_sim_1.id = vc_mathmodelsim.SIMREF" + " AND vc_mathmodelsim.MATHMODELREF = vc_mathmodel.id" + ") as " + MMLINK + " FROM " + jobTable.getTableName() + "," + simTable.getTableName() + " vc_sim_1" + "," + userTable.getTableName() + "," + bioSimLinkTable.getTableName() + "," + mathSimLinkTable.getTableName() + " WHERE " + "vc_sim_1." + simTable.id.getUnqualifiedColName() + "=" + jobTable.simRef.getQualifiedColName() + " AND " + "vc_sim_1." + simTable.ownerRef.getUnqualifiedColName() + "=" + userTable.id.getQualifiedColName() + " AND " + bioSimLinkTable.simRef.getQualifiedColName() + " (+) " + "=" + "vc_sim_1." + simTable.id.getUnqualifiedColName() + " AND " + mathSimLinkTable.simRef.getQualifiedColName() + " (+) " + "=" + "vc_sim_1." + simTable.id.getUnqualifiedColName();
    String additionalConditionsClause = "";
    if (conditions != null && conditions.length() > 0) {
        additionalConditionsClause = " AND (" + conditions + ")";
    }
    // most recent records first
    String orderByClause = " order by " + jobTable.submitDate.getQualifiedColName() + " DESC ";
    String sql = null;
    if (maxNumRows > 0) {
        if (startRow <= 1) {
            // simpler query, only limit rows, not starting row
            sql = "select * from " + "(" + subquery + " " + additionalConditionsClause + " " + orderByClause + ") " + "where rownum <= " + maxNumRows;
        } else {
            // full query, limit start and limit
            sql = "select * from " + "(select a.*, ROWNUM rnum from " + "(" + subquery + " " + additionalConditionsClause + " " + orderByClause + ") a " + " where rownum <= " + (startRow + maxNumRows - 1) + ") " + "where rnum >= " + startRow;
        }
    } else {
        sql = subquery + " " + additionalConditionsClause + " " + orderByClause;
    }
    if (lg.isTraceEnabled()) {
        lg.trace(sql);
    }
    List<SimpleJobStatusPersistent> resultList = new ArrayList<SimpleJobStatusPersistent>();
    Statement stmt = con.createStatement();
    SimulationJobStatusPersistent simJobStatus = null;
    cbit.vcell.solver.SolverTaskDescription std = null;
    String username = null;
    try {
        ResultSet rset = stmt.executeQuery(sql.toString());
        while (rset.next()) {
            simJobStatus = jobTable.getSimulationJobStatus(rset);
            username = rset.getString(userTable.userid.getUnqualifiedColName());
            BigDecimal ownerKeyDecimal = rset.getBigDecimal("ownerkey");
            User owner = new User(username, new KeyValue(ownerKeyDecimal));
            std = null;
            try {
                String taskDesc = rset.getString(SimulationTable.table.taskDescription.getUnqualifiedColName());
                if (taskDesc != null) {
                    std = new cbit.vcell.solver.SolverTaskDescription(new org.vcell.util.CommentStringTokenizer(org.vcell.util.TokenMangler.getSQLRestoredString(taskDesc)));
                }
            } catch (DataAccessException ex) {
                ex.printStackTrace();
                lg.error("failed to parse SolverTaskDescription", ex);
            }
            Integer meshSizeX = rset.getInt(SimulationTable.table.meshSpecX.getUnqualifiedColName());
            if (rset.wasNull()) {
                meshSizeX = null;
            }
            Integer meshSizeY = rset.getInt(SimulationTable.table.meshSpecY.getUnqualifiedColName());
            if (rset.wasNull()) {
                meshSizeY = null;
            }
            Integer meshSizeZ = rset.getInt(SimulationTable.table.meshSpecZ.getUnqualifiedColName());
            if (rset.wasNull()) {
                meshSizeZ = null;
            }
            String simname = rset.getString(SimulationTable.table.name.getUnqualifiedColName());
            SimulationDocumentLink simulationDocumentLink = null;
            String latestBioModelLinkJSON = rset.getString(BMLINK);
            if (latestBioModelLinkJSON != null) {
                try {
                    Gson gson = new Gson();
                    BioModelLink bioModelLink = gson.fromJson(latestBioModelLinkJSON, BioModelLink.class);
                    bioModelLink.clearZeroPadding();
                    simulationDocumentLink = bioModelLink;
                } catch (Exception e) {
                    e.printStackTrace();
                    lg.error("failed to parse BioModelLink", e);
                }
            }
            String latestMathModelLinkJSON = rset.getString(MMLINK);
            if (latestMathModelLinkJSON != null) {
                Gson gson = new Gson();
                try {
                    MathModelLink mathModelLink = gson.fromJson(latestMathModelLinkJSON, MathModelLink.class);
                    mathModelLink.clearZeroPadding();
                    simulationDocumentLink = mathModelLink;
                } catch (Exception e) {
                    e.printStackTrace();
                    lg.error("failed to parse MathModelLink", e);
                }
            }
            CommentStringTokenizer mathOverridesTokens = SimulationTable.getMathOverridesTokenizer(rset, dbSyntax);
            List<MathOverrides.Element> mathOverrideElements = MathOverrides.parseOverrideElementsFromVCML(mathOverridesTokens);
            int scanCount = 1;
            for (MathOverrides.Element element : mathOverrideElements) {
                if (element.getSpec() != null) {
                    scanCount *= element.getSpec().getNumValues();
                }
            }
            SimulationMetadata simulationMetadata = new SimulationMetadata(simJobStatus.getVCSimulationIdentifier(), simname, owner, std, meshSizeX, meshSizeY, meshSizeZ, new Integer(scanCount));
            resultList.add(new SimpleJobStatusPersistent(simulationMetadata, simulationDocumentLink, simJobStatus));
        }
    } finally {
        stmt.close();
    }
    return resultList;
}

Example 17 with CommentStringTokenizer

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

the class SimulationTable method getSimulation.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param rset java.sql.ResultSet
 */
public Simulation getSimulation(QueryHashtable dbc, ResultSet rset, Connection con, User user, MathDescriptionDbDriver mathDB, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException, PropertyVetoException {
    // 
    // get TaskDescription Data into parsable form
    // 
    // 
    // String taskDescriptionString = new String(solverTaskDescData);
    // 
    // System.out.println("taskDescriptionString '"+taskDescriptionString+"'");
    String taskDescriptionString = rset.getString(SimulationTable.table.taskDescription.getUnqualifiedColName());
    taskDescriptionString = TokenMangler.getSQLRestoredString(taskDescriptionString);
    CommentStringTokenizer solverTaskDescTokens = new CommentStringTokenizer(taskDescriptionString);
    // 
    // get MathOverride Data (language) (MUST BE READ FIRST)
    // 
    /*
	byte[] mathOverridesData = null;
	mathOverridesData = rset.getBytes(SimulationTable.table.mathOverrides.toString());
	if (rset.wasNull() || mathOverridesData==null || mathOverridesData.length==0){
		throw new DataAccessException("no data stored for MathOverrides");
	}
	String mathOverridesString = new String(mathOverridesData);
	*/
    // 
    CommentStringTokenizer mathOverrideTokens = getMathOverridesTokenizer(rset, dbSyntax);
    String dataProcessingInstructionString = rset.getString(dataProcInstr.getUnqualifiedColName());
    DataProcessingInstructions dpi = null;
    if (!rset.wasNull() && dataProcessingInstructionString != null && dataProcessingInstructionString.length() > 0) {
        dataProcessingInstructionString = TokenMangler.getSQLRestoredString(dataProcessingInstructionString);
        dpi = DataProcessingInstructions.fromDbXml(dataProcessingInstructionString);
    }
    // 
    // Get Version
    // 
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    SimulationVersion simulationVersion = (SimulationVersion) getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    java.math.BigDecimal bigD = rset.getBigDecimal(SimulationTable.table.mathRef.toString());
    KeyValue mathKey = null;
    if (!rset.wasNull()) {
        mathKey = new KeyValue(bigD);
    } else {
        throw new DataAccessException("Error:  MathDescription Reference Cannot be Null for Simulation");
    }
    MathDescription mathDesc = (MathDescription) mathDB.getVersionable(dbc, con, user, VersionableType.MathDescription, mathKey);
    Simulation simulation = new Simulation(simulationVersion, mathDesc, mathOverrideTokens, solverTaskDescTokens);
    simulation.setDataProcessingInstructions(dpi);
    // MeshSpec (Is This Correct?????)
    if (mathDesc != null && mathDesc.getGeometry() != null && mathDesc.getGeometry().getDimension() > 0) {
        int msX = rset.getInt(SimulationTable.table.meshSpecX.getUnqualifiedColName());
        int msY = rset.getInt(SimulationTable.table.meshSpecY.getUnqualifiedColName());
        int msZ = rset.getInt(SimulationTable.table.meshSpecZ.getUnqualifiedColName());
        MeshSpecification meshSpec = new MeshSpecification(simulation.getMathDescription().getGeometry());
        meshSpec.setSamplingSize(new ISize(msX, msY, msZ));
        simulation.getMeshSpecification().copyFrom(meshSpec);
    }
    return simulation;
}

Example 18 with CommentStringTokenizer

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

the class SimulationTable method getMathOverridesTokenizer.

public static CommentStringTokenizer getMathOverridesTokenizer(ResultSet rset, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    String mathOverridesString = DbDriver.varchar2_CLOB_get(rset, SimulationTable.table.mathOverridesSmall, SimulationTable.table.mathOverridesLarge, dbSyntax);
    if (mathOverridesString == null || mathOverridesString.length() == 0) {
        throw new DataAccessException("no data stored for MathOverrides");
    }
    // System.out.println("mathOverridesString '"+mathOverridesString+"'");
    if (mathOverridesString.endsWith(";}\n")) {
        StringBuffer buffer = new StringBuffer(mathOverridesString.substring(0, mathOverridesString.length() - 2));
        buffer.append("\n}\n");
        mathOverridesString = buffer.toString();
    }
    CommentStringTokenizer mathOverrideTokens = new CommentStringTokenizer(mathOverridesString);
    return mathOverrideTokens;
}

Example 19 with CommentStringTokenizer

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

the class MathDescTable method getMathDescription.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param rset java.sql.ResultSet
 */
public MathDescription getMathDescription(ResultSet rset, Connection con, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    // 
    // Get Version
    // 
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    // 
    // get MathDescription Data (language) (MUST BE READ FIRST)
    // 
    /*
	byte[] mathDescriptionData = null;
	try {
		mathDescriptionData = rset.getBytes(MathDescTable.table.language.toString());
	}catch (SQLException e){
	System.out.println("SQLException error_code = "+e.getErrorCode()+", localized Message = "+e.getLocalizedMessage());
		log.exception(e);
		try {
			rset.close();
		}catch (SQLException e2){
			log.exception(e2);
		}
		throw e;
	}
	if (rset.wasNull() || mathDescriptionData==null || mathDescriptionData.length==0){
		throw new DataAccessException("no data stored for MathDescription");
	}
	String mathDescriptionDataString = new String(mathDescriptionData);
	*/
    // 
    String mathDescriptionDataString = (String) DbDriver.getLOB(rset, MathDescTable.table.language, dbSyntax);
    if (mathDescriptionDataString == null || mathDescriptionDataString.length() == 0) {
        throw new DataAccessException("no data stored for MathDescription");
    }
    // 
    // System.out.println("mathDescriptionDataString '"+mathDescriptionDataString+"'");
    MathDescription mathDescription = new MathDescription(version);
    // 
    // setGeometry is done in calling parent
    // 
    // mathDescription.setGeometry(geom);
    CommentStringTokenizer tokens = new CommentStringTokenizer(mathDescriptionDataString);
    try {
        mathDescription.read_database(tokens);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new org.vcell.util.DataAccessException(e.getMessage(), e);
    }
    // 
    return mathDescription;
}