Issue #2905 moved bufr splitter to separate utility
BUFR parser now only processes one file at a time added method to scan for field in structure (cherry picked from commit429056b078[formerlyc330bbb7e4] [formerlyec6f8bb961[formerly c701947f1bf6135bf53a650425f0cc4b5bd88e3c]]) Former-commit-id:13fb37e993[formerly a062930ed70a686f0adcd49a85d9c2fa3131e012] Former-commit-id:91c211cc4b
This commit is contained in:
Brian Clements
Steve Harris
parent
7dbd9922b5
commit
3f2d7e4b0f
4 changed files with 350 additions and 172 deletions
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@ -0,0 +1,87 @@
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/**
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* This software was developed and / or modified by Raytheon Company,
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* pursuant to Contract DG133W-05-CQ-1067 with the US Government.
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*
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* U.S. EXPORT CONTROLLED TECHNICAL DATA
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* This software product contains export-restricted data whose
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* export/transfer/disclosure is restricted by U.S. law. Dissemination
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* to non-U.S. persons whether in the United States or abroad requires
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* an export license or other authorization.
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*
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* Contractor Name: Raytheon Company
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* Contractor Address: 6825 Pine Street, Suite 340
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* Mail Stop B8
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* Omaha, NE 68106
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* 402.291.0100
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*
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* See the AWIPS II Master Rights File ("Master Rights File.pdf") for
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* further licensing information.
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**/
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package com.raytheon.uf.common.nc.bufr;
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import ucar.ma2.DataType;
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import ucar.nc2.Variable;
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/**
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* Parsed BUFR data field value bundled with metadata
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*
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* <pre>
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*
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* SOFTWARE HISTORY
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*
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* Date Ticket# Engineer Description
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* ------------ ---------- ----------- --------------------------
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* Mar 31, 2014 2905 bclement Initial creation
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*
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* </pre>
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*
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* @author bclement
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* @version 1.0
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*/
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public class BufrDataItem {
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private final String name;
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private final Object value;
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private final DataType type;
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private final Variable variable;
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public BufrDataItem(String name, Object value, DataType type,
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Variable variable) {
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this.name = name;
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this.value = value;
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this.type = type;
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this.variable = variable;
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}
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/**
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* @return the name
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*/
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public String getName() {
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return name;
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}
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/**
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* @return the value
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*/
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public Object getValue() {
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return value;
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}
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/**
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* @return the type
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*/
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public DataType getType() {
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return type;
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}
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/**
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* @return the variable
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*/
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public Variable getVariable() {
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return variable;
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}
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}
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@ -0,0 +1,132 @@
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/**
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* This software was developed and / or modified by Raytheon Company,
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* pursuant to Contract DG133W-05-CQ-1067 with the US Government.
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*
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* U.S. EXPORT CONTROLLED TECHNICAL DATA
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* This software product contains export-restricted data whose
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* export/transfer/disclosure is restricted by U.S. law. Dissemination
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* to non-U.S. persons whether in the United States or abroad requires
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* an export license or other authorization.
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*
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* Contractor Name: Raytheon Company
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* Contractor Address: 6825 Pine Street, Suite 340
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* Mail Stop B8
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* Omaha, NE 68106
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* 402.291.0100
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*
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* See the AWIPS II Master Rights File ("Master Rights File.pdf") for
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* further licensing information.
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**/
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package com.raytheon.uf.common.nc.bufr;
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import java.io.File;
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import java.io.FilenameFilter;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import ucar.nc2.iosp.bufr.writer.BufrSplitter;
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import ucar.nc2.iosp.bufr.writer.BufrSplitter.Options;
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import com.raytheon.uf.common.status.IUFStatusHandler;
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import com.raytheon.uf.common.status.UFStatus;
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/**
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* Utility to split mixed-type BUFR files into separate messages. Creates a new
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* BUFR file on the file system for each separate message.
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*
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* <pre>
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*
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* SOFTWARE HISTORY
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*
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* Date Ticket# Engineer Description
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* ------------ ---------- ----------- --------------------------
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* Apr 1, 2014 2905 bclement Initial creation
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*
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* </pre>
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*
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* @author bclement
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* @version 1.0
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*/
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public class BufrFileSeparator {
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private static final IUFStatusHandler log = UFStatus
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.getHandler(BufrFileSeparator.class);
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public static final File DEFAULT_TMP_DIR;
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static {
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final String edexHomeProp = "edex.home";
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String baseDir = System.getProperty(edexHomeProp);
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if (baseDir == null || baseDir.trim().isEmpty()) {
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log.warn("Property '" + edexHomeProp
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+ "' not set, defaulting to system tmp directory");
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DEFAULT_TMP_DIR = new File(System.getProperty("java.io.tmpdir"));
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} else {
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DEFAULT_TMP_DIR = new File(baseDir + File.separator + "data",
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"processing");
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}
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}
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private static final FilenameFilter BUFR_FILTER = new FilenameFilter() {
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@Override
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public boolean accept(File dir, String name) {
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return name.endsWith(".bufr");
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}
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};
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/**
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* Splits the mixed BUFR file into homogeneous BUFR files that are written
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* to the file system.
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*
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* @param mixedBufrFile
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* @return list of absolute paths to new BUFR files
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* @throws IOException
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*/
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public static List<String> separate(File mixedBufrFile) throws IOException {
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final File outputBaseDir = DEFAULT_TMP_DIR;
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final String inputFile = mixedBufrFile.getAbsolutePath();
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final File outputDir = getOutputDir(mixedBufrFile.getName(),
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outputBaseDir);
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Options options = new Options() {
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@Override
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public String getFileSpec() {
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return inputFile;
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}
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@Override
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public String getDirOut() {
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return outputDir.getAbsolutePath();
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}
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};
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BufrSplitter splitter = new BufrSplitter(options);
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splitter.execute();
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File[] files = outputDir.listFiles(BUFR_FILTER);
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List<String> rval = new ArrayList<String>(files.length);
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for (File f : files) {
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rval.add(f.getAbsolutePath());
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}
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return rval;
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}
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/**
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* Create a temporary output directory based on the input file name
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*
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* @param inputName
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* @param outputBaseDir
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* @return
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*/
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private static File getOutputDir(final String inputName,
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final File outputBaseDir) {
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String name = inputName + "-" + System.currentTimeMillis() + "-split";
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File rval = new File(outputBaseDir, name);
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if (rval.exists()) {
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log.warn("BUFR splitter output directory already exists, is file "
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+ inputName + " being processed twice?");
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}
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return rval;
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}
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}
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@ -20,11 +20,11 @@
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package com.raytheon.uf.common.nc.bufr;
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import java.io.File;
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import java.io.FilenameFilter;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Stack;
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import ucar.ma2.Array;
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@ -37,8 +37,6 @@ import ucar.nc2.Attribute;
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import ucar.nc2.NetcdfFile;
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import ucar.nc2.Structure;
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import ucar.nc2.Variable;
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import ucar.nc2.iosp.bufr.writer.BufrSplitter;
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import ucar.nc2.iosp.bufr.writer.BufrSplitter.Options;
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import com.raytheon.uf.common.numeric.UnsignedNumbers;
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import com.raytheon.uf.common.status.IUFStatusHandler;
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@ -58,6 +56,8 @@ import com.raytheon.uf.common.status.UFStatus;
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* ------------ ---------- ----------- --------------------------
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* Mar 18, 2014 2905 bclement Initial creation
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* Mar 26, 2014 2905 bclement fixed types, added scale/offset
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* Apr 01, 2014 2905 bclement moved splitter functionality to separate utility
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* added scanForStructField()
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*
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* </pre>
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*
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@ -79,30 +79,11 @@ public class BufrParser {
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private static final IUFStatusHandler log = UFStatus
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.getHandler(BufrParser.class);
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private final static File DEFAULT_TMP_DIR;
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private final File bufrFile;
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static {
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final String edexHomeProp = "edex.home";
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String baseDir = System.getProperty(edexHomeProp);
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if (baseDir == null || baseDir.trim().isEmpty()) {
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log.warn("Property '" + edexHomeProp
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+ "' not set, defaulting to system tmp directory");
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DEFAULT_TMP_DIR = new File(System.getProperty("java.io.tmpdir"));
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} else {
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DEFAULT_TMP_DIR = new File(baseDir + File.separator + "data",
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"processing");
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}
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}
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private final NetcdfFile ncfile;
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private final Options options;
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private final File[] splitFiles;
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private int fileIndex = 0;
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private NetcdfFile currentNcfile;
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private Iterator<Variable> varIter;
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private final Iterator<Variable> varIter;
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private Variable currentVar;
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@ -118,59 +99,9 @@ public class BufrParser {
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* @throws IOException
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*/
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public BufrParser(final File bufrFile) throws IOException {
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this(bufrFile, DEFAULT_TMP_DIR);
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}
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/**
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* @param bufrFile
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* BUFR file, may contain mixed message types
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* @param outputBaseDir
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* base directory for temporary storage of split files
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* @throws IOException
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*/
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public BufrParser(final File bufrFile, final File outputBaseDir)
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throws IOException {
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final String inputFile = bufrFile.getAbsolutePath();
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final File outputDir = getOutputDir(bufrFile.getName(), outputBaseDir);
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options = new Options() {
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@Override
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public String getFileSpec() {
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return inputFile;
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}
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@Override
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public String getDirOut() {
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return outputDir.getAbsolutePath();
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}
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};
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BufrSplitter splitter = new BufrSplitter(options);
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splitter.execute();
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splitFiles = outputDir.listFiles(new FilenameFilter() {
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@Override
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public boolean accept(File dir, String name) {
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return name.endsWith(".bufr");
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}
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});
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}
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/**
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* Create a temporary output directory based on the input file name
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*
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* @param inputName
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* @param outputBaseDir
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* @return
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*/
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private static File getOutputDir(final String inputName,
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final File outputBaseDir) {
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String name = inputName + "-" + System.currentTimeMillis() + "-split";
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File rval = new File(outputBaseDir, name);
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if (rval.exists()) {
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log.warn("BUFR splitter output directory already exists, is a file being processed twice?");
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}
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return rval;
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this.bufrFile = bufrFile;
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this.ncfile = NetcdfFile.open(bufrFile.getAbsolutePath());
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this.varIter = ncfile.getVariables().iterator();
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}
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/**
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@ -178,6 +109,10 @@ public class BufrParser {
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* @throws IOException
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*/
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public boolean hasNext() throws IOException {
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if (lastEvent == null) {
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/* we haven't started the file yet */
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return true;
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}
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if (!structStack.isEmpty()) {
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StructureLevel level = structStack.peek();
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if (level.hasNext()) {
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@ -190,11 +125,8 @@ public class BufrParser {
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if (varIter != null && varIter.hasNext()) {
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return true;
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}
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if (fileIndex < splitFiles.length) {
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return true;
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}
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if (lastEvent != null && !lastEvent.equals(Event.END_FILE)) {
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/* only one more event left, the end of the last file */
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/* only one more event left, the end of the file */
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return true;
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}
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return false;
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@ -209,7 +141,9 @@ public class BufrParser {
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*/
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public Event next() throws IOException {
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Event rval;
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if (!structStack.isEmpty()) {
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if (lastEvent == null) {
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rval = Event.START_FILE;
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} else if (!structStack.isEmpty()) {
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rval = nextMember();
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} else if (structIter != null && structIter.hasNext()) {
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/* in a variable with a sequence of structures, get the next one */
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@ -229,14 +163,8 @@ public class BufrParser {
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/* no more variables, we are at the end of the bufr file */
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structIter = null;
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currentVar = null;
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varIter = null;
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rval = endFile();
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rval = Event.END_FILE;
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}
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} else if (fileIndex < splitFiles.length) {
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/* start the next bufr file */
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rval = startFile();
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} else if (lastEvent != null && !lastEvent.equals(Event.END_FILE)) {
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rval = endFile();
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} else {
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/* don't set rval to null so we preserve the correct lastEvent */
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return null;
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@ -323,10 +251,9 @@ public class BufrParser {
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log.error("Structure variable members out of sync");
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throw new IllegalStateException("Structure variable members out of sync");
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}
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Iterator<Variable> memberVarIter = ((Structure) parentVar)
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.getVariables().iterator();
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List<Variable> memberVars = ((Structure) parentVar).getVariables();
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return startStructure(new StructureLevel(childData, childMembers,
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memberVarIter));
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memberVars));
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}
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/**
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@ -340,8 +267,7 @@ public class BufrParser {
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*/
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private Event startStructure(Structure s, StructureData structData)
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throws IOException {
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StructureLevel level = new StructureLevel(structData, s.getVariables()
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.iterator());
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StructureLevel level = new StructureLevel(structData, s.getVariables());
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return startStructure(level);
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}
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@ -400,49 +326,17 @@ public class BufrParser {
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}
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/**
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* Start processing the next NetCDF file
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*
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* @return
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* @throws IOException
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* @return the NetCDF File
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*/
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private Event startFile() throws IOException {
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File f = splitFiles[fileIndex];
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fileIndex += 1;
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currentNcfile = NetcdfFile.open(f.getAbsolutePath());
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varIter = currentNcfile.getVariables().iterator();
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return Event.START_FILE;
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public NetcdfFile getNcfile() {
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return ncfile;
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}
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/**
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* Finalize processing of NetCDF file
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*
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* @return
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* @throws IOException
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* @return BUFR file being processed
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*/
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private Event endFile() throws IOException {
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if (currentNcfile != null) {
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currentNcfile.close();
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currentNcfile = null;
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}
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return Event.END_FILE;
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}
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/**
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* @return null if no file is currently being processed
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*/
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public NetcdfFile getCurrentNcfile() {
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return currentNcfile;
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}
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/**
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* @return null if no file has started being processed
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*/
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public File getCurrentFile() {
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if (fileIndex < splitFiles.length) {
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return splitFiles[fileIndex];
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} else {
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return null;
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}
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public File getFile() {
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return bufrFile;
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}
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/**
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@ -534,7 +428,7 @@ public class BufrParser {
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* @param var
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* @return
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*/
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private DataType getUnscaledDataType(Variable var) {
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private static DataType getUnscaledDataType(Variable var) {
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DataType rval;
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/*
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* We will promote unsigned values to the next largest signed type
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|
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@ -566,7 +460,7 @@ public class BufrParser {
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* @param var
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* @return true if the field has a scale factor or addition offset
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*/
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private boolean isScaledOrOffset(Variable var) {
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private static boolean isScaledOrOffset(Variable var) {
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return var.findAttribute(OFFSET_ATTRIB) != null
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|| var.findAttribute(SCALE_FACTOR_ATTRIB) != null;
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}
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@ -583,6 +477,22 @@ public class BufrParser {
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if (typedArray == null) {
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return null;
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}
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Variable var = getFieldVariable();
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return getFieldScalarValue(typedArray, var, charArrayAsString);
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}
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/**
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* @param typedArray
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* storage for field value
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* @param var
|
||||
* NetCDF variable
|
||||
* @param charArrayAsString
|
||||
* true if character arrays should be treated as strings
|
||||
* @return null if value is a missing value
|
||||
* @throws IOException
|
||||
*/
|
||||
private static Object getFieldScalarValue(TypedArray typedArray,
|
||||
Variable var, boolean charArrayAsString) {
|
||||
Array array = typedArray.array;
|
||||
DataType type = typedArray.type;
|
||||
Object value;
|
||||
|
|
@ -598,23 +508,23 @@ public class BufrParser {
|
|||
value = array.getObject(0);
|
||||
}
|
||||
|
||||
return processValue(value);
|
||||
return processValue(value, var);
|
||||
}
|
||||
|
||||
/**
|
||||
* Perform any promotion, scaling or missing value operations
|
||||
*
|
||||
* @param value
|
||||
* @param var
|
||||
* @return
|
||||
*/
|
||||
private Object processValue(Object value) {
|
||||
Variable var = getFieldVariable();
|
||||
Object rval = promoteValueType(var, value);
|
||||
if (isMissingValue(var, rval)) {
|
||||
private static Object processValue(Object value, Variable var) {
|
||||
Object rval = promoteValueType(value, var);
|
||||
if (isMissingValue(rval, var)) {
|
||||
rval = null;
|
||||
} else if (isScaledOrOffset(var)) {
|
||||
if (value instanceof Number) {
|
||||
rval = scaleAndOffset((Number) rval);
|
||||
rval = scaleAndOffset((Number) rval, var);
|
||||
} else {
|
||||
log.warn("Scale or offset attribute on non-numerical field: "
|
||||
+ var.getFullName());
|
||||
|
|
@ -626,11 +536,11 @@ public class BufrParser {
|
|||
/**
|
||||
* Promote unsigned numbers to next largest data type if needed
|
||||
*
|
||||
* @param var
|
||||
* @param value
|
||||
* @param var
|
||||
* @return
|
||||
*/
|
||||
private Object promoteValueType(Variable var, Object value) {
|
||||
private static Object promoteValueType(Object value, Variable var) {
|
||||
if (value == null) {
|
||||
return null;
|
||||
}
|
||||
|
|
@ -660,14 +570,15 @@ public class BufrParser {
|
|||
* Apply scale factor or addition offset if present
|
||||
*
|
||||
* @param value
|
||||
* @param var
|
||||
* @return
|
||||
*/
|
||||
public Number scaleAndOffset(Number value) {
|
||||
Number scaleFactor = getScaleFactor();
|
||||
public static Number scaleAndOffset(Number value, Variable var) {
|
||||
Number scaleFactor = getFieldAttributeAsNum(SCALE_FACTOR_ATTRIB, var);
|
||||
if (scaleFactor != null) {
|
||||
value = value.doubleValue() * scaleFactor.doubleValue();
|
||||
}
|
||||
Number offset = getOffset();
|
||||
Number offset = getFieldAttributeAsNum(OFFSET_ATTRIB, var);
|
||||
if (offset != null) {
|
||||
value = value.doubleValue() + offset.doubleValue();
|
||||
}
|
||||
|
|
@ -687,11 +598,12 @@ public class BufrParser {
|
|||
if (typedArray == null) {
|
||||
return null;
|
||||
}
|
||||
Variable var = getFieldVariable();
|
||||
Array array = typedArray.array;
|
||||
int len = (int) array.getSize();
|
||||
Collection<Object> rval = new ArrayList<Object>(len);
|
||||
for (int i = 0; i < len; ++i) {
|
||||
rval.add(processValue(array.getObject(i)));
|
||||
rval.add(processValue(array.getObject(i), var));
|
||||
}
|
||||
return rval;
|
||||
}
|
||||
|
|
@ -777,6 +689,22 @@ public class BufrParser {
|
|||
return rval;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get attribute value for field from variable
|
||||
*
|
||||
* @param name
|
||||
* @param var
|
||||
* @return
|
||||
*/
|
||||
private static Number getFieldAttributeAsNum(String name, Variable var) {
|
||||
Number rval = null;
|
||||
Attribute attr = var.findAttributeIgnoreCase(name);
|
||||
if (attr != null) {
|
||||
rval = attr.getNumericValue();
|
||||
}
|
||||
return rval;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get variable object for current field
|
||||
*
|
||||
|
|
@ -794,17 +722,18 @@ public class BufrParser {
|
|||
}
|
||||
|
||||
/**
|
||||
* @param var
|
||||
* @param unscaledValue
|
||||
* field value before any scaling or offset is applied
|
||||
* @param var
|
||||
* @return true if value matches the missing value for field
|
||||
*/
|
||||
private boolean isMissingValue(Variable var, Object unscaledValue) {
|
||||
private static boolean isMissingValue(Object unscaledValue, Variable var) {
|
||||
if (unscaledValue == null) {
|
||||
return true;
|
||||
}
|
||||
boolean rval;
|
||||
Attribute missingAttrib = getFieldAttribute(MISSING_VAL_ATTRIB);
|
||||
Attribute missingAttrib = var
|
||||
.findAttributeIgnoreCase(MISSING_VAL_ATTRIB);
|
||||
if (missingAttrib == null) {
|
||||
/* if there is no special missing value, all values are valid */
|
||||
rval = false;
|
||||
|
|
@ -851,19 +780,41 @@ public class BufrParser {
|
|||
}
|
||||
|
||||
/**
|
||||
* clean up temporary files
|
||||
* Get field from current structure level. Does not affect the current state
|
||||
* of the parser. Only searches current level (does not go into
|
||||
* substructures).
|
||||
*
|
||||
* @param fieldName
|
||||
* @param charArrayAsString
|
||||
* @return null if no field found or parser is not currently parsing a
|
||||
* structure
|
||||
*/
|
||||
public void clean() {
|
||||
for (File f : splitFiles) {
|
||||
if (!f.delete()) {
|
||||
log.error("Unable to delete temporary file: "
|
||||
+ f.getAbsolutePath());
|
||||
public BufrDataItem scanForStructField(String fieldName, boolean charArrayAsString) {
|
||||
BufrDataItem rval = null;
|
||||
if ( structStack.isEmpty()){
|
||||
return rval;
|
||||
}
|
||||
StructureLevel level = structStack.peek();
|
||||
Iterator<Member> memberIter = level.getMemberList().iterator();
|
||||
Iterator<Variable> varIter = level.getMemberVarList().iterator();
|
||||
while (memberIter.hasNext() && varIter.hasNext()) {
|
||||
Member member = memberIter.next();
|
||||
Variable variable = varIter.next();
|
||||
DataType type = member.getDataType();
|
||||
if (!type.equals(DataType.STRUCTURE) && !type.equals(DataType.SEQUENCE)) {
|
||||
/* current member is a field */
|
||||
if (member.getName().equals(fieldName)){
|
||||
StructureData sd = level.getStructData();
|
||||
Array array = sd.getArray(member);
|
||||
Object value = getFieldScalarValue(new TypedArray(array,
|
||||
type), variable, charArrayAsString);
|
||||
rval = new BufrDataItem(member.getName(), value, type,
|
||||
variable);
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
File outdir = new File(options.getDirOut());
|
||||
if (!outdir.delete()) {
|
||||
log.error("Unable to delete temporary directory: "
|
||||
+ outdir.getAbsolutePath());
|
||||
}
|
||||
return rval;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -20,6 +20,7 @@
|
|||
package com.raytheon.uf.common.nc.bufr;
|
||||
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
|
||||
import ucar.ma2.ArraySequence;
|
||||
import ucar.ma2.StructureData;
|
||||
|
|
@ -40,6 +41,7 @@ import com.raytheon.uf.common.status.UFStatus;
|
|||
* Date Ticket# Engineer Description
|
||||
* ------------ ---------- ----------- --------------------------
|
||||
* Mar 25, 2014 2905 bclement Initial creation
|
||||
* Apr 01, 2014 2905 bclement added references to member and variable lists
|
||||
*
|
||||
* </pre>
|
||||
*
|
||||
|
|
@ -53,8 +55,12 @@ public class StructureLevel {
|
|||
|
||||
private final StructureData structData;
|
||||
|
||||
private final List<Member> memberList;
|
||||
|
||||
private final Iterator<Member> memberIter;
|
||||
|
||||
private final List<Variable> memberVarList;
|
||||
|
||||
private final Iterator<Variable> memberVarIter;
|
||||
|
||||
private Member currentMember;
|
||||
|
|
@ -66,8 +72,8 @@ public class StructureLevel {
|
|||
* @param memberVarIter
|
||||
*/
|
||||
public StructureLevel(StructureData structData,
|
||||
Iterator<Variable> memberVarIter) {
|
||||
this(structData, structData.getStructureMembers(), memberVarIter);
|
||||
List<Variable> memberVariables) {
|
||||
this(structData, structData.getStructureMembers(), memberVariables);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -76,10 +82,12 @@ public class StructureLevel {
|
|||
* @param memberVarIter
|
||||
*/
|
||||
public StructureLevel(StructureData structData, StructureMembers members,
|
||||
Iterator<Variable> memberVarIter) {
|
||||
List<Variable> memberVariables) {
|
||||
this.structData = structData;
|
||||
this.memberIter = members.getMembers().iterator();
|
||||
this.memberVarIter = memberVarIter;
|
||||
this.memberList = members.getMembers();
|
||||
this.memberIter = memberList.iterator();
|
||||
this.memberVarList = memberVariables;
|
||||
this.memberVarIter = memberVarList.iterator();
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -126,17 +134,17 @@ public class StructureLevel {
|
|||
}
|
||||
|
||||
/**
|
||||
* @return the memberIter
|
||||
* @return the memberList
|
||||
*/
|
||||
public Iterator<Member> getMemberIter() {
|
||||
return memberIter;
|
||||
public List<Member> getMemberList() {
|
||||
return memberList;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the memberVarIter
|
||||
* @return the memberVarList
|
||||
*/
|
||||
public Iterator<Variable> getMemberVarIter() {
|
||||
return memberVarIter;
|
||||
public List<Variable> getMemberVarList() {
|
||||
return memberVarList;
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue