Example usage for java.math BigInteger intValue

List of usage examples for java.math BigInteger intValue

  1. HOME
  2. Java
  3. java
  4. java.math.*
  5. BigInteger
  6. intValue

Introduction

In this page you can find the example usage for java.math BigInteger intValue.

Prototype

public int intValue()

Source Link

Document

Converts this BigInteger to an int .

Usage

From source file:org.alfresco.opencmis.AlfrescoCmisServiceImpl.java

@Override
public List<ObjectInFolderContainer> getFolderTree(String repositoryId, String folderId, BigInteger depth,
        String filter, Boolean includeAllowableActions, IncludeRelationships includeRelationships,
        String renditionFilter, Boolean includePathSegment, ExtensionsData extension) {
    long start = System.currentTimeMillis();

    checkRepositoryId(repositoryId);//from  w  w w.  jav  a  2 s  .c  o m

    List<ObjectInFolderContainer> result = new ArrayList<ObjectInFolderContainer>();

    getDescendantsTree(repositoryId, getOrCreateFolderInfo(folderId, "Folder").getNodeRef(), depth.intValue(),
            filter, includeAllowableActions, includeRelationships, renditionFilter, includePathSegment, true,
            result);

    logGetObjectsCall("getFolderTree", start, folderId, countDescendantsTree(result), filter,
            includeAllowableActions, includeRelationships, renditionFilter, includePathSegment, extension, null,
            null, null, depth);

    return result;
}

From source file:edu.pitt.apollo.db.ApolloDbUtils.java

public Map<String, ByteArrayOutputStream> getDataContentForSoftware(BigInteger runKey, int sourceSoftwareIdKey,
        int destinationSoftwareIdKey) throws ApolloDatabaseException {
    Map<String, ByteArrayOutputStream> result = new HashMap<>();

    String query = "SELECT " + "rddv.label, " + "rdc.text_content " + "FROM " + "run_data_content rdc, "
            + "run_data rd, " + "run_data_description_view rddv " + "WHERE " + "rd.content_id = rdc.id AND "
            + "rd.run_id = ? AND " + "rddv.run_data_description_id = rd.description_id AND "
            + "rddv.source_software = ? AND " + "rddv.destination_software = ?";

    PreparedStatement pstmt = null;
    try {//from   ww  w . j  a v  a2 s  . com
        try (Connection conn = datasource.getConnection()) {

            pstmt = conn.prepareStatement(query);
            pstmt.setInt(1, runKey.intValue());
            pstmt.setInt(2, sourceSoftwareIdKey);
            pstmt.setInt(3, destinationSoftwareIdKey);
            ResultSet rs = pstmt.executeQuery();
            while (rs.next()) {
                String label = rs.getString(1);
                String dataContent = rs.getString(2);
                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                baos.write(dataContent.getBytes());
                result.put(label, baos);
            }
        } finally {
            pstmt.close();
        }

    } catch (IOException ex) {
        throw new ApolloDatabaseException("IOException attempting to get data content for software for run ID "
                + runKey + ": " + ex.getMessage());
    } catch (SQLException ex) {
        throw new ApolloDatabaseException("SQLException attempting to get data content for software for run ID "
                + runKey + ": " + ex.getMessage());
    }

    return result;

}

From source file:jp.aegif.nemaki.cmis.aspect.query.solr.SolrQueryProcessor.java

@Override
public ObjectList query(CallContext callContext, String repositoryId, String statement,
        Boolean searchAllVersions, Boolean includeAllowableActions, IncludeRelationships includeRelationships,
        String renditionFilter, BigInteger maxItems, BigInteger skipCount) {

    SolrServer solrServer = solrUtil.getSolrServer();

    // TODO walker is required?
    QueryUtilStrict util = new QueryUtilStrict(statement, new CmisTypeManager(repositoryId, typeManager), null);
    QueryObject queryObject = util.getQueryObject();

    // Get where caluse as Tree
    Tree whereTree = null;/* ww w.  j a  v a 2s .c  o m*/
    try {
        util.processStatement();
        Tree tree = util.parseStatement();
        whereTree = extractWhereTree(tree);
    } catch (Exception e) {
        e.printStackTrace();
    }

    // Build solr statement of WHERE
    String whereQueryString = "";
    if (whereTree == null || whereTree.isNil()) {
        whereQueryString = "*:*";
    } else {
        try {
            SolrPredicateWalker solrPredicateWalker = new SolrPredicateWalker(repositoryId, queryObject,
                    solrUtil, contentService);
            Query whereQuery = solrPredicateWalker.walkPredicate(whereTree);
            whereQueryString = whereQuery.toString();
        } catch (Exception e) {
            e.printStackTrace();
            // TODO Output more detailed exception
            exceptionService.invalidArgument("Invalid CMIS SQL statement!");
        }
    }

    // Build solr query of FROM
    String fromQueryString = "";

    String repositoryQuery = "repository_id:" + repositoryId;

    fromQueryString += repositoryQuery + " AND ";

    TypeDefinition td = queryObject.getMainFromName();
    // includedInSupertypeQuery
    List<TypeDefinitionContainer> typeDescendants = typeManager.getTypesDescendants(repositoryId, td.getId(),
            BigInteger.valueOf(-1), false);
    Iterator<TypeDefinitionContainer> iterator = typeDescendants.iterator();
    List<String> tables = new ArrayList<String>();
    while (iterator.hasNext()) {
        TypeDefinition descendant = iterator.next().getTypeDefinition();
        if (td.getId() != descendant.getId()) {
            boolean isq = (descendant.isIncludedInSupertypeQuery() == null) ? false
                    : descendant.isIncludedInSupertypeQuery();
            if (!isq)
                continue;
        }
        String table = descendant.getQueryName();
        tables.add(table.replaceAll(":", "\\\\:"));
    }

    Term t = new Term(solrUtil.getPropertyNameInSolr(PropertyIds.OBJECT_TYPE_ID),
            StringUtils.join(tables, " "));
    fromQueryString += new TermQuery(t).toString();

    // Execute query
    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery(whereQueryString);
    solrQuery.setFilterQueries(fromQueryString);

    //TEST
    solrQuery.set(CommonParams.START, 0);
    solrQuery.set(CommonParams.ROWS, maxItems.intValue());

    QueryResponse resp = null;
    try {
        resp = solrServer.query(solrQuery);
    } catch (SolrServerException e) {
        e.printStackTrace();
    }

    // Output search results to ObjectList
    if (resp != null && resp.getResults() != null && resp.getResults().getNumFound() != 0) {
        SolrDocumentList docs = resp.getResults();

        List<Content> contents = new ArrayList<Content>();
        for (SolrDocument doc : docs) {
            String docId = (String) doc.getFieldValue("object_id");
            Content c = contentService.getContent(repositoryId, docId);

            // When for some reason the content is missed, pass through
            if (c == null) {
                logger.warn("[objectId=" + docId + "]It is missed in DB but still rests in Solr.");
            } else {
                contents.add(c);
            }

        }

        List<Lock> locks = threadLockService.readLocks(repositoryId, contents);
        try {
            threadLockService.bulkLock(locks);

            // Filter out by permissions
            List<Content> permitted = permissionService.getFiltered(callContext, repositoryId, contents);

            // Filter return value with SELECT clause
            Map<String, String> requestedWithAliasKey = queryObject.getRequestedPropertiesByAlias();
            String filter = null;
            if (!requestedWithAliasKey.keySet().contains("*")) {
                // Create filter(queryNames) from query aliases
                filter = StringUtils.join(requestedWithAliasKey.values(), ",");
            }

            // Build ObjectList
            String orderBy = orderBy(queryObject);
            ObjectList result = compileService.compileObjectDataList(callContext, repositoryId, permitted,
                    filter, includeAllowableActions, includeRelationships, renditionFilter, false, maxItems,
                    skipCount, false, orderBy);

            return result;

        } finally {
            threadLockService.bulkUnlock(locks);
        }
    } else {
        ObjectListImpl nullList = new ObjectListImpl();
        nullList.setHasMoreItems(false);
        nullList.setNumItems(BigInteger.ZERO);
        return nullList;
    }
}

From source file:edu.pitt.apollo.db.ApolloDbUtils.java

public Map<BigInteger, FileAndURLDescription> getListOfFilesForRunId(BigInteger runId)
        throws ApolloDatabaseException {
    HashMap<BigInteger, FileAndURLDescription> contentIdToFileDescriptionMap = new HashMap<>();

    try (Connection conn = datasource.getConnection()) {

        PreparedStatement pstmt = conn.prepareStatement(
                "SELECT runData.content_id, rddv.source_software, rddv.destination_software, rddv.format, rddv.type, rddv.label FROM run_data runData "
                        + "JOIN run_data_description_view rddv ON rddv.run_data_description_id=runData.description_id WHERE runData.run_id=? AND rddv.format='TEXT'");
        //            PreparedStatement pstmt = conn.prepareStatement(
        //                    "SELECT runData.content_id, rddv.label FROM run_data runData " +
        //                            "JOIN run_data_description_view rddv ON rddv.run_data_description_id=runData.description_id WHERE runData.run_id=? AND rddv.format='TEXT';");
        pstmt.setInt(1, runId.intValue());
        ResultSet resultSet = pstmt.executeQuery();

        while (resultSet.next()) {
            FileAndURLDescription fileDescription = new FileAndURLDescription();
            fileDescription.setContentFormat(ContentDataFormatEnum.valueOf(resultSet.getString("format")));
            fileDescription.setContentType(ContentDataTypeEnum.fromValue(resultSet.getString("type")));
            if (resultSet.getInt("source_software") != 0) {
                SoftwareIdentification source = getSoftwareIdentification(resultSet.getInt("source_software"));
                fileDescription.setSourceSoftwareIdentification(source);
            } else {
                fileDescription.setSourceSoftwareIdentification(null);
            }/* w  w w .j a  va2s.  c o m*/
            if (resultSet.getInt("destination_software") != 0) {
                SoftwareIdentification destination = getSoftwareIdentification(
                        resultSet.getInt("destination_software"));
                fileDescription.setDestinationSoftwareIdentification(destination);
            } else {
                fileDescription.setDestinationSoftwareIdentification(null);
            }
            fileDescription.setName(resultSet.getString("label"));
            int content_id = resultSet.getInt("content_id");
            contentIdToFileDescriptionMap.put(BigInteger.valueOf(content_id), fileDescription);

        }

    } catch (SQLException e) {
        throw new ApolloDatabaseException(
                "SQLException retrieving content ID and labels for run " + runId + ": " + e.getMessage());
    }
    //        catch (ClassNotFoundException e) {
    //            throw new ApolloDatabaseException("ClassNotFoundException retrieving content ID and labels for run ID " + runId + ": " + e.getMessage());
    //        }
    return contentIdToFileDescriptionMap;
}

From source file:edu.pitt.apollo.db.ApolloDbUtils.java

public HashMap<BigInteger, FileAndURLDescription> getListOfURLsForRunId(BigInteger runId)
        throws ApolloDatabaseException {
    HashMap<BigInteger, FileAndURLDescription> contentIdToURLDescriptionMap = new HashMap<BigInteger, FileAndURLDescription>();

    try (Connection conn = datasource.getConnection()) {

        PreparedStatement pstmt = conn.prepareStatement(
                "SELECT runData.content_id, rddv.source_software, rddv.destination_software, rddv.format, rddv.type, rddv.label FROM run_data runData "
                        + "JOIN run_data_description_view rddv ON rddv.run_data_description_id=runData.description_id WHERE runData.run_id=? AND (rddv.format='URL' OR rddv.format='ZIP')");
        //            PreparedStatement pstmt = conn.prepareStatement(
        //                    "SELECT runData.content_id, rddv.label FROM run_data runData " +
        //                            "JOIN run_data_description_view rddv ON rddv.run_data_description_id=runData.description_id WHERE runData.run_id=? AND (rddv.format='URL' OR rddv.format='ZIP');");

        pstmt.setInt(1, runId.intValue());
        ResultSet resultSet = pstmt.executeQuery();
        while (resultSet.next()) {
            FileAndURLDescription urlDescription = new FileAndURLDescription();
            urlDescription.setContentFormat(ContentDataFormatEnum.valueOf(resultSet.getString("format")));
            urlDescription.setContentType(ContentDataTypeEnum.fromValue(resultSet.getString("type")));
            if (resultSet.getInt("source_software") != 0) {
                SoftwareIdentification source = getSoftwareIdentification(resultSet.getInt("source_software"));
                urlDescription.setSourceSoftwareIdentification(source);
            } else {
                urlDescription.setSourceSoftwareIdentification(null);
            }/*from www  . ja  va 2s  . co m*/
            if (resultSet.getInt("destination_software") != 0) {
                SoftwareIdentification destination = getSoftwareIdentification(
                        resultSet.getInt("destination_software"));
                urlDescription.setDestinationSoftwareIdentification(destination);
            } else {
                urlDescription.setDestinationSoftwareIdentification(null);
            }

            urlDescription.setName(resultSet.getString("label"));
            int content_id = resultSet.getInt("content_id");
            contentIdToURLDescriptionMap.put(BigInteger.valueOf(content_id), urlDescription);

        }

    } catch (SQLException e) {
        throw new ApolloDatabaseException(
                "SQLException retrieving content ID and labels for run " + runId + ": " + e.getMessage());
    }
    //        catch (ClassNotFoundException e) {
    //            throw new ApolloDatabaseException("ClassNotFoundException retrieving content ID and labels for run ID " + runId + ": " + e.getMessage());
    //        }
    return contentIdToURLDescriptionMap;
}

From source file:edu.pitt.apollo.db.ApolloDbUtils.java

public ResultSet getRunIdAndRunSimulationMessagesForBatch(BigInteger batchRunId, int endUserSoftwareId,
        int translatorSoftwareId, Connection conn) throws ApolloDatabaseException {

    String query = "SELECT" + "   sgd.run_id," + "   rdc.text_content AS run_message," + "   rsd.status,"
            + "   rs.message " + " FROM" + "   run r," + "   run_data_content rdc," + "   run_data rd,"
            + "   simulation_group_definition sgd," + "   run_data_description_view rddv," + "   run_status rs,"
            + "   run_status_description rsd " + " WHERE" + "   rd.content_id = rdc.id AND"
            + "   rddv.run_data_description_id = rd.description_id AND" + "   rddv.source_software = ? AND"
            + "   rddv.destination_software = ? AND" + "   rddv.label = \"run_message.json\" AND"
            + "   rd.run_id = sgd.run_id AND" + "   r.id = ? AND"
            + "   sgd.simulation_group_id = r.simulation_group_id AND" + "   rs.run_id = r.id AND"
            + "   rsd.id = rs.status_id";

    try {/*from  w w  w  .  j a  v  a2 s  . c  o m*/
        PreparedStatement pstmt = conn.prepareStatement(query);
        pstmt.setInt(1, endUserSoftwareId);
        pstmt.setInt(2, translatorSoftwareId);
        pstmt.setInt(3, batchRunId.intValue());

        ResultSet rs = pstmt.executeQuery();
        return rs;
    } catch (SQLException ex) {
        throw new ApolloDatabaseException(
                "SQLException getting run IDs and runSimulationMessages for batch: " + ex.getMessage());
    }

}

From source file:edu.pitt.apollo.db.ApolloDbUtils.java

public PreparedStatement getDataContentForBatchSimulations(BigInteger batchRunId, List<String> fileNamesToMatch,
        Connection conn) throws ApolloDatabaseException {

    String query = "SELECT" + " rddav.value AS name," + "   rdc.text_content," + " r2.id" + " FROM"
            + " run_data_description_axis_value rddav," + " run_data_description_axis rdda,"
            + "   run_data_content rdc," + "   run_data rd," + " simulation_group_definition sgd," + " run r1,"
            + " run r2" + " WHERE" + "   rd.content_id = rdc.id AND" + " r2.id = sgd.run_id AND"
            + " rd.run_id = r2.id AND";

    if (!fileNamesToMatch.isEmpty()) {

        query += " (rddav.value = '" + fileNamesToMatch.get(0) + "'";
        for (int i = 1; i < fileNamesToMatch.size(); i++) {
            query += " OR rddav.value = '" + fileNamesToMatch.get(i) + "'";
        }/*w  ww .j  a v  a  2 s  . c o  m*/
        query += ") AND";

    }

    query += " rddav.run_data_description_axis_id = rdda.id AND"
            + " rddav.run_data_description_id = rd.description_id AND"
            + " sgd.simulation_group_id = r1.simulation_group_id AND" + " r1.id = ? AND"
            + " rdda.label = 'label'";

    System.out.println(query);

    PreparedStatement pstmt = null;
    try {
        pstmt = conn.prepareStatement(query, ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
        pstmt.setFetchSize(Integer.MIN_VALUE);
        pstmt.setInt(1, batchRunId.intValue());
        return pstmt;

    } catch (SQLException ex) {
        throw new ApolloDatabaseException("SQLException attempting to get data content for batch run ID "
                + batchRunId + ": " + ex.getMessage());
    }
}

From source file:org.alfresco.opencmis.CMISConnector.java

@SuppressWarnings("unchecked")
public ObjectList query(String statement, Boolean includeAllowableActions,
        IncludeRelationships includeRelationships, String renditionFilter, BigInteger maxItems,
        BigInteger skipCount/*, CmisVersion cmisVersion*/) {
    // prepare results
    ObjectListImpl result = new ObjectListImpl();
    result.setObjects(new ArrayList<ObjectData>());

    // prepare query
    CMISQueryOptions options = new CMISQueryOptions(statement, getRootStoreRef());
    CmisVersion cmisVersion = getRequestCmisVersion();
    options.setCmisVersion(cmisVersion);
    options.setQueryMode(CMISQueryMode.CMS_WITH_ALFRESCO_EXTENSIONS);

    int skip = 0;
    if ((skipCount != null) && (skipCount.intValue() >= 0)) {
        skip = skipCount.intValue();//from w w  w.  ja va 2s.  com
        options.setSkipCount(skip);
    }

    if ((maxItems != null) && (maxItems.intValue() >= 0)) {
        options.setMaxItems(maxItems.intValue());
    }

    boolean fetchObject = includeAllowableActions || (includeRelationships != IncludeRelationships.NONE)
            || (!RENDITION_NONE.equals(renditionFilter));

    // query
    CMISResultSet rs = getOpenCMISQueryService().query(options);
    try {
        CMISResultSetColumn[] columns = rs.getMetaData().getColumns();

        for (CMISResultSetRow row : rs) {
            NodeRef nodeRef = row.getNodeRef();

            if (!nodeService.exists(nodeRef) || filter(nodeRef)) {
                continue;
            }

            TypeDefinitionWrapper type = getType(nodeRef);
            if (type == null) {
                continue;
            }

            ObjectDataImpl hit = new ObjectDataImpl();
            PropertiesImpl properties = new PropertiesImpl();
            hit.setProperties(properties);

            Map<String, Serializable> values = row.getValues();

            for (CMISResultSetColumn column : columns) {
                AbstractPropertyData<?> property = getProperty(column.getCMISDataType(),
                        column.getCMISPropertyDefinition(), values.get(column.getName()));
                property.setQueryName(column.getName());
                properties.addProperty(property);
            }

            if (fetchObject) {
                // set allowable actions
                if (includeAllowableActions) {
                    CMISNodeInfoImpl nodeInfo = createNodeInfo(nodeRef);
                    if (!nodeInfo.getObjectVariant().equals(CMISObjectVariant.NOT_EXISTING)) {
                        hit.setAllowableActions(getAllowableActions(nodeInfo));
                    }
                }

                // set relationships
                if (includeRelationships != IncludeRelationships.NONE) {
                    hit.setRelationships(getRelationships(nodeRef, includeRelationships/*, cmisVersion*/));
                }

                // set renditions
                if (!RENDITION_NONE.equals(renditionFilter)) {
                    List<RenditionData> renditions = getRenditions(nodeRef, renditionFilter, null, null);
                    if ((renditions != null) && (!renditions.isEmpty())) {
                        hit.setRenditions(renditions);
                    } else {
                        hit.setRenditions(Collections.EMPTY_LIST);
                    }
                }
            }

            result.getObjects().add(hit);
        }

        long numberFound = rs.getNumberFound();
        if (numberFound != -1) {
            result.setNumItems(BigInteger.valueOf(numberFound));
        }
        result.setHasMoreItems(rs.hasMore());

    } finally {
        rs.close();
    }

    return result;
}

From source file:edu.hawaii.soest.kilonalu.ctd.CTDParser.java

public void setData(String dataString) throws ParseException {
    logger.debug("CTDParser.setData() called.");

    // make the observations available to the class
    this.observationsString = dataString;

    // build the list of data variable names and offsets

    // handle profile mode
    if (this.samplingMode.equals("profile")) {

        // handle the raw frquencies and voltages in Hex OUTPUTFORMAT (0)
        if (this.outputFormat.equals("raw HEX")) {
            this.dataVariableNames = new ArrayList<String>();
            this.dataVariableNames.add(this.RAW_TEMPERATURE_FIELD_NAME);
            this.dataVariableNames.add(this.RAW_CONDUCTIVITY_FIELD_NAME);

            this.dataVariableUnits = new ArrayList<String>();
            this.dataVariableUnits.add("counts");
            this.dataVariableUnits.add("Hz");

            this.currentOffset = 6;
            this.dataVariableOffsets = new ArrayList<Integer>();
            this.dataVariableOffsets.add(currentOffset);
            this.currentOffset = currentOffset + 6;
            this.dataVariableOffsets.add(currentOffset);

            // Is pressure present?
            if (this.hasPressure) {
                this.dataVariableNames.add(this.RAW_PRESSURE_FIELD_NAME);
                this.dataVariableUnits.add("counts");
                this.currentOffset = this.currentOffset + 6;
                this.dataVariableOffsets.add(this.currentOffset);

                // And is it a strain gauge sensor?
                if (this.hasStrainGaugePressure) {
                    dataVariableNames.add(this.RAW_PRESSURE_TEMP_COMP_FIELD_NAME);
                    dataVariableUnits.add("counts");
                    currentOffset = currentOffset + 4;
                    dataVariableOffsets.add(currentOffset);

                }//from w w w  .  j  a  va2 s.  co m

            } else {
                logger.info("There is no pressure sensor.");
            }

            // Is there a channel zero voltage present?
            if (this.hasVoltageChannelZero) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_ZERO_FIELD_NAME);
                this.dataVariableUnits.add("V");
                this.currentOffset = this.currentOffset + 4;
                this.dataVariableOffsets.add(this.currentOffset);

            }

            // Is there a channel one voltage present?
            if (this.hasVoltageChannelOne) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_ONE_FIELD_NAME);
                this.dataVariableUnits.add("V");
                this.currentOffset = this.currentOffset + 4;
                this.dataVariableOffsets.add(this.currentOffset);

            }

            // Is there a channel two voltage present?
            if (this.hasVoltageChannelTwo) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_TWO_FIELD_NAME);
                this.dataVariableUnits.add("V");
                this.currentOffset = this.currentOffset + 4;
                this.dataVariableOffsets.add(this.currentOffset);

            }

            // Is there a channel three voltage present?
            if (this.hasVoltageChannelThree) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_THREE_FIELD_NAME);
                this.dataVariableUnits.add("V");
                this.currentOffset = this.currentOffset + 4;
                this.dataVariableOffsets.add(this.currentOffset);

            }

            /*
             * @todo - handle SBE38, SBE50, and/or gasTensionDevice data
             */

            // We now know the data variable names, units, and corresponding
            // character offsets for each Hex data string found in the 
            // dataValuesMap.  Build a raw matrix from the dataValuesMap by only
            // applying output factors.  Conversion to useful variable units
            // will happen in the calling source driver since voltage channel
            // semantics are unknown to the parser
            int beginIndex = 0;
            int endIndex = 0;
            int offsetIndex = 0;
            String hexSubstring = "";
            String hexDataString = "";
            Hex decoder = new Hex();
            double value = 0d;
            this.convertedDataValuesMatrix = new Array2DRowRealMatrix(this.dataValuesMap.size() - 1,
                    this.dataVariableOffsets.size());

            for (int rowIndex = 1; rowIndex < this.dataValuesMap.size(); rowIndex++) {
                hexDataString = this.dataValuesMap.get(rowIndex);
                logger.debug(rowIndex + ") hexDataString is: " + hexDataString);

                for (offsetIndex = 0; offsetIndex < this.dataVariableOffsets.size(); offsetIndex++) {
                    endIndex = this.dataVariableOffsets.get(offsetIndex);
                    hexSubstring = hexDataString.substring(beginIndex, endIndex);

                    try {
                        // convert the hex characters to bytes
                        byte[] hexAsBytes = decoder.decodeHex(hexSubstring.toCharArray());

                        BigInteger bigInteger = new BigInteger(hexAsBytes);
                        int intValue = bigInteger.intValue();

                        // the hex values are either 2 or 3 bytes long (AABBCC or AABB)
                        // BigInteger fills in missing bits with 0xFF. Remove them.  This
                        // is only a problem with large bytes that cause the value to 
                        // become negative.
                        if (hexAsBytes.length < 3) {
                            intValue = (intValue & 0x0000FFFF);

                        } else {
                            intValue = (intValue & 0x00FFFFFF);

                        }
                        value = new Integer(intValue).doubleValue();

                        // convert the value based on the CTD User manual conversion using
                        // the corresponding data variable name to determine which conversion
                        double convertedValue = convert(value, this.dataVariableNames.get(offsetIndex));

                        convertedDataValuesMatrix.setEntry(rowIndex - 1, offsetIndex, convertedValue);
                        logger.debug("\t" + this.dataVariableNames.get(offsetIndex) + " is:\t" + value
                                + "\tConverted: " + convertedValue);
                        // set the beginIndex to start at the endIndex
                        beginIndex = endIndex;

                    } catch (DecoderException de) {
                        logger.debug("Could not decode the Hex string: " + hexSubstring);
                    }

                } // for

                // reset the offsetIndex for the next hexDataString
                offsetIndex = 0;
                beginIndex = 0;
            } // for

            // handle the engineering units in Hex OUTPUTFORMAT (1)
        } else if (this.outputFormat.equals("converted Hex")) {

            /*
             * @todo - handle OUTPUTFORMAT (1)
             */

            // handle the raw frquencies and voltages in decimal OUTPUTFORMAT (2)
        } else if (this.outputFormat.equals("raw decimal")) {

            /*
             * @todo - handle OUTPUTFORMAT (2)
             */

            // handle the engineering units in decimal OUTPUTFORMAT (3)
        } else if (this.outputFormat.equals("converted decimal")) {

            /*
             * @todo - handle OUTPUTFORMAT (3)
             */
        }

        // handle moored mode
    } else if (this.samplingMode.equals("moored")) {

        // handle the raw frequencies and voltages in Hex OUTPUTFORMAT (0)
        if (this.outputFormat.equals("raw HEX")) {

            // handle the engineering units in Hex OUTPUTFORMAT (1)
        } else if (this.outputFormat.equals("converted Hex")) {

            /*
             * @todo - handle OUTPUTFORMAT (1)
             */

            // handle the raw frequencies and voltages in decimal OUTPUTFORMAT (2)
        } else if (this.outputFormat.equals("raw decimal")) {

            /*
             * @todo - handle OUTPUTFORMAT (2)
             */

            // handle the engineering units in decimal OUTPUTFORMAT (3)
        } else if (this.outputFormat.equals("converted decimal")) {

            this.dataVariableNames = new ArrayList<String>();
            this.dataVariableNames.add(this.TEMPERATURE_FIELD_NAME);
            this.dataVariableNames.add(this.CONDUCTIVITY_FIELD_NAME);

            this.dataVariableUnits = new ArrayList<String>();
            this.dataVariableUnits.add("degrees C");
            this.dataVariableUnits.add("S/m");

            // Is pressure present?
            if (this.hasPressure) {
                this.dataVariableNames.add(this.PRESSURE_FIELD_NAME);
                this.dataVariableUnits.add("decibars");

            } else {
                logger.info("There is no pressure sensor.");
            }

            // Is there a channel zero voltage present?
            if (this.hasVoltageChannelZero) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_ZERO_FIELD_NAME);
                this.dataVariableUnits.add("V");

            }

            // Is there a channel one voltage present?
            if (this.hasVoltageChannelOne) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_ONE_FIELD_NAME);
                this.dataVariableUnits.add("V");

            }

            // Is there a channel two voltage present?
            if (this.hasVoltageChannelTwo) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_TWO_FIELD_NAME);
                this.dataVariableUnits.add("V");

            }

            // Is there a channel three voltage present?
            if (this.hasVoltageChannelThree) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_THREE_FIELD_NAME);
                this.dataVariableUnits.add("V");

            }

            // Is there a channel four voltage present?
            if (this.hasVoltageChannelFour) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_FOUR_FIELD_NAME);
                this.dataVariableUnits.add("V");

            }

            // Is there a channel five voltage present?
            if (this.hasVoltageChannelFive) {
                this.dataVariableNames.add(this.RAW_VOLTAGE_CHANNEL_FIVE_FIELD_NAME);
                this.dataVariableUnits.add("V");

            }

            /*
             * @todo - handle SBE38, SBE50, and/or gasTensionDevice data
             */

            // Will salinity be output?
            if (this.willOutputSalinity) {
                this.dataVariableNames.add(this.SALINITY_FIELD_NAME);
                this.dataVariableUnits.add("psu");

            }

            // Will sound velocity be output?
            if (this.willOutputSalinity) {
                this.dataVariableNames.add(this.SOUND_VELOCITY_FIELD_NAME);
                this.dataVariableUnits.add("m/s");

            }

            // Add the date and time fields
            this.dataVariableNames.add(this.DATE_FIELD_NAME);
            this.dataVariableUnits.add("dd MMM yyyy");
            this.dataVariableNames.add(this.TIME_FIELD_NAME);
            this.dataVariableUnits.add("hh:mm:ss");

        }

        this.convertedDataValuesMatrix = new Array2DRowRealMatrix(this.dataValuesMap.size() - 1,
                this.dataVariableOffsets.size()); // CSJ fix this

    } else {
        throw new ParseException(
                "There was an error parsing the data string. " + "The sampling mode is not recognized.", 0);

    }

}

From source file:org.eclipse.smila.connectivity.framework.crawler.jdbc.JdbcCrawler.java

/**
 * Populates the {@link #_groupingRanges}-{@link ArrayList} according to the configuration specified in the
 * {@link Grouping}-attribute of the {@link DataSourceConnectionConfig}. The SQL-statements needed for this are
 * executed via a local {@link Statement}-object, just as the data is retrieved via a local {@link ResultSet}-object.
 * /*ww  w .ja  va 2s  .c o m*/
 * @throws CrawlerCriticalException
 *           If any of the following conditions occur:
 *           <ul>
 *           <li>Any of the columns used for grouping has a data type which is not supported: !(Number||String)</li>
 *           <li>A SQLException is raised while retrieving the grouping data from the database</li>
 *           </ul>
 */
private void prepareGrouping() throws CrawlerCriticalException {
    final Grouping grouping = _process.getSelections().getGrouping();
    BigInteger stepping = BigInteger.ONE;
    ResultSet groupingResultSet = null;
    ResultSetMetaData groupingMetaData = null;
    if (grouping != null) {
        _groupingRanges = new ArrayList<GroupingRange>();
        final String groupingSQL = grouping.getSQL();
        stepping = grouping.getStepping();
        Statement groupingStatement = null;
        try {
            groupingStatement = _connection.createStatement(ResultSet.TYPE_SCROLL_INSENSITIVE,
                    ResultSet.CONCUR_READ_ONLY);

            _log.debug("Executing SQL for grouping preparation: [" + groupingSQL + "]");
            groupingResultSet = groupingStatement.executeQuery(groupingSQL);
            groupingMetaData = groupingResultSet.getMetaData();
            _log.debug("Retrieved groupingResultSet with [" + groupingMetaData.getColumnCount() + "] columns");
            for (int i = 1; i <= groupingMetaData.getColumnCount(); i++) {
                Class<?> columnClass = null;
                try {
                    columnClass = Class.forName(groupingMetaData.getColumnClassName(i));

                } catch (final ClassNotFoundException e) {
                    _log.error("This should never happen: the class[" + groupingMetaData.getColumnClassName(i)
                            + "] for the column " + i + " in the grouping result set could not be resolved");
                }
                if (Number.class.isAssignableFrom(columnClass)) {
                    _log.debug("RowNr " + i + " of the grouping result set is of type [" + columnClass.getName()
                            + "], which is derived from [Number]: fine for use in a grouping");
                    continue;
                } else if (String.class.equals(columnClass)) {
                    _log.debug("RowNr " + i
                            + " of the grouping result set is of type [String]: fine for use in a grouping");
                } else {
                    throw new CrawlerCriticalException("RowNr " + i + " of the grouping result set is of type ["
                            + columnClass.getName() + "]: NOT supported as a grouping field");
                }
            }
            int groupingRecords = 0;
            PreparedStatementTypedParameter[] startValues = null;
            PreparedStatementTypedParameter[] endValues = null;
            final PreparedStatementTypedParameter[] finalValues = new PreparedStatementTypedParameter[groupingMetaData
                    .getColumnCount()];

            while (groupingResultSet.next()) {

                if (groupingRecords == 0) {

                    startValues = new PreparedStatementTypedParameter[groupingMetaData.getColumnCount()];
                    for (int i = 1; i <= groupingMetaData.getColumnCount(); i++) {

                        startValues[i - 1] = new PreparedStatementTypedParameter(groupingResultSet.getObject(i),
                                (i * 2) - 1, groupingMetaData.getColumnType(i));
                    }

                }
                groupingRecords++;

                if (groupingRecords == stepping.intValue()) {
                    endValues = new PreparedStatementTypedParameter[groupingMetaData.getColumnCount()];
                    for (int i = 1; i <= groupingMetaData.getColumnCount(); i++) {
                        endValues[i - 1] = new PreparedStatementTypedParameter(groupingResultSet.getObject(i),
                                i * 2, groupingMetaData.getColumnType(i));
                    }
                    final GroupingRange groupingRange = new GroupingRange(startValues, endValues);
                    _groupingRanges.add(groupingRange);
                    if (_log.isTraceEnabled()) {
                        _log.trace(
                                "Added GroupingRange: [" + groupingRange.toString() + "] to _groupingRanges");
                    }
                    groupingRecords = 0;
                    continue;
                }

                for (int i = 1; i <= groupingMetaData.getColumnCount(); i++) {
                    finalValues[i - 1] = new PreparedStatementTypedParameter(groupingResultSet.getObject(i),
                            i * 2, groupingMetaData.getColumnType(i));

                }

            }
            if (groupingRecords != 0 && stepping.intValue() != 1) {
                final GroupingRange finalgroupingRange = new GroupingRange(startValues, finalValues);
                _groupingRanges.add(finalgroupingRange);
                _log.debug(
                        "Added final GroupingRange [" + finalgroupingRange.toString() + "] to _groupingRanges");
            }
        } catch (final SQLException e1) {
            throw new CrawlerCriticalException("Encountered SQLException while preparing Groupings");
        } finally {
            try {
                if (groupingStatement != null) {
                    groupingStatement.close();
                }
            } catch (final SQLException e) {
                _log.error("Could not closeGrouping statement");
            }
            try {
                groupingResultSet.close();
                _log.debug("Closed Grouping Resultset");
            } catch (final SQLException e) {
                _log.error("Could not close Resultset for Grouping statement");
            }
        }

    }
    // set current grouping to first grouping in list (if list is not empty)
    _groupingRangesIterator = _groupingRanges.iterator();
    if (_groupingRangesIterator.hasNext()) {
        _currentGroupingRange = _groupingRangesIterator.next();
    }

    _log.debug(String.format("Prepared %d grouping ranges based on specified stepping of %d",
            _groupingRanges.size(), stepping.intValue()));
}