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intermediate sirds reader
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7 files changed

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7 files changed

+373
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‎core/src/main/java/com/bc/fiduceo/reader/insitu/sirds_sst/SirdsInsituReader.java‎

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package com.bc.fiduceo.reader.insitu.sirds_sst;
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import com.bc.fiduceo.core.Dimension;
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import com.bc.fiduceo.core.Interval;
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import com.bc.fiduceo.core.NodeType;
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import com.bc.fiduceo.geometry.Polygon;
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import com.bc.fiduceo.location.PixelLocator;
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import com.bc.fiduceo.reader.AcquisitionInfo;
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import com.bc.fiduceo.reader.netcdf.NetCDFReader;
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import com.bc.fiduceo.reader.time.TimeLocator;
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import com.bc.fiduceo.util.TimeUtils;
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import ucar.ma2.Array;
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import ucar.ma2.ArrayInt;
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import ucar.ma2.InvalidRangeException;
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import ucar.nc2.Variable;
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import java.io.IOException;
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import java.util.Calendar;
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import java.util.List;
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public class SirdsInsituReader extends NetCDFReader {
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private static final String REGEX = "SSTCCI2_refdata_[a-z]+(_[a-z]+)?_\\d{6}.nc";
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private int[] timeMinMax;
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@Override
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public AcquisitionInfo read() throws IOException {
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final AcquisitionInfo info = new AcquisitionInfo();
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ensureSensingTimesAvailable();
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info.setSensingStart(TimeUtils.create(timeMinMax[0] * 1000L));
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info.setSensingStop(TimeUtils.create(timeMinMax[1] * 1000L));
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info.setNodeType(NodeType.UNDEFINED);
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return info;
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}
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private void ensureSensingTimesAvailable() throws IOException {
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if (timeMinMax == null) {
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final Calendar calendar = TimeUtils.getUTCCalendar();
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final Array year = arrayCache.get("YEAR");
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final Array month = arrayCache.get("MONTH");
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final Array day = arrayCache.get("DAY");
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final Array hour = arrayCache.get("HOUR");
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final Array minute = arrayCache.get("MINUTE");
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final Array second = arrayCache.get("SECOND");
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final int numMeasures = (int) year.getSize();
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final int[] timeStamps = new int[numMeasures];
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for (int i = 0; i < numMeasures; i++) {
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final short yearVal = year.getShort(i);
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final byte monthVal = (byte) (month.getByte(i) - 1);
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final byte dayVal = day.getByte(i);
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final byte hourVal = hour.getByte(i);
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final byte minuteVal = minute.getByte(i);
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final byte secondVal = second.getByte(i);
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//noinspection MagicConstant
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calendar.set(yearVal, monthVal, dayVal, hourVal, minuteVal, secondVal);
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timeStamps[i] = (int) (calendar.getTime().getTime() / 1000);
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}
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timeMinMax = extractMinMax(timeStamps);
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}
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}
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@Override
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public String getRegEx() {
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return REGEX;
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}
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@Override
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public PixelLocator getPixelLocator() throws IOException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public PixelLocator getSubScenePixelLocator(Polygon sceneGeometry) throws IOException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public TimeLocator getTimeLocator() throws IOException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public int[] extractYearMonthDayFromFilename(String fileName) {
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throw new RuntimeException("not implemented");
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}
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@Override
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public Array readRaw(int centerX, int centerY, Interval interval, String variableName) throws IOException, InvalidRangeException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public Array readScaled(int centerX, int centerY, Interval interval, String variableName) throws IOException, InvalidRangeException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public ArrayInt.D2 readAcquisitionTime(int x, int y, Interval interval) throws IOException, InvalidRangeException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public List<Variable> getVariables() throws InvalidRangeException, IOException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public Dimension getProductSize() throws IOException {
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throw new RuntimeException("not implemented");
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}
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@Override
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public String getLongitudeVariableName() {
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return "LONGITUDE";
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}
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@Override
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public String getLatitudeVariableName() {
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return "LATITUDE";
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}
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// package access for testing only tb 2021-07-21
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static int[] extractMinMax(int[] timeStamps) {
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int min = Integer.MAX_VALUE;
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int max = Integer.MIN_VALUE;
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for (int value : timeStamps) {
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if (value < min) {
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min = value;
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}
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if (value > max) {
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max = value;
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}
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}
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return new int[]{min, max};
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}
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@Override
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public void close() throws IOException {
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timeMinMax = null;
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super.close();
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}
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}

‎core/src/main/java/com/bc/fiduceo/reader/insitu/sirds_sst/SirdsInsituReaderPlugin.java‎

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package com.bc.fiduceo.reader.insitu.sirds_sst;
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import com.bc.fiduceo.reader.DataType;
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import com.bc.fiduceo.reader.Reader;
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import com.bc.fiduceo.reader.ReaderContext;
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import com.bc.fiduceo.reader.ReaderPlugin;
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public class SirdsInsituReaderPlugin implements ReaderPlugin {
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private final String[] SUPPORTED_KEYS = {"animal-sirds", "argo-sirds", "argo_surf-sirds", "bottle-sirds", "ctd-sirds", "drifter-sirds", "drifter_cmems-sirds", "gtmba-sirds", "mbt-sirds", "mooring-sirds", "ship-sirds", "xbt-sirds"};
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@Override
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public Reader createReader(ReaderContext readerContext) {
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return new SirdsInsituReader();
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}
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@Override
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public String[] getSupportedSensorKeys() {
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return SUPPORTED_KEYS;
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}
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@Override
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public DataType getDataType() {
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return DataType.INSITU;
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}
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}

‎core/src/test/java/com/bc/fiduceo/reader/insitu/sirds_sst/SirdsInsituReaderPluginTest.java‎

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package com.bc.fiduceo.reader.insitu.sirds_sst;
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import com.bc.fiduceo.reader.DataType;
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import com.bc.fiduceo.reader.Reader;
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import org.junit.Before;
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import org.junit.Test;
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import static org.junit.Assert.*;
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public class SirdsInsituReaderPluginTest {
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private SirdsInsituReaderPlugin plugin;
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@Before
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public void setUp() throws Exception {
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plugin = new SirdsInsituReaderPlugin();
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}
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@Test
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public void testGetSupportedSensorKeys() throws Exception {
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final String[] expected = {"animal-sirds", "argo-sirds", "argo_surf-sirds", "bottle-sirds", "ctd-sirds", "drifter-sirds", "drifter_cmems-sirds", "gtmba-sirds", "mbt-sirds", "mooring-sirds", "ship-sirds", "xbt-sirds"};
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final String[] sensorKeys = plugin.getSupportedSensorKeys();
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assertArrayEquals(expected, sensorKeys);
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}
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@Test
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public void testCreateReader() {
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final Reader reader = plugin.createReader(null);
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assertNotNull(reader);
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assertTrue(reader instanceof SirdsInsituReader);
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}
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@Test
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public void testGetDataType() {
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assertEquals(DataType.INSITU, plugin.getDataType());
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}
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}

‎core/src/test/java/com/bc/fiduceo/reader/insitu/sirds_sst/SirdsInsituReaderTest.java‎

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package com.bc.fiduceo.reader.insitu.sirds_sst;
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import org.junit.Before;
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import org.junit.Test;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import static org.junit.Assert.*;
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public class SirdsInsituReaderTest {
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private SirdsInsituReader insituReader;
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@Before
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public void setUp() {
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insituReader = new SirdsInsituReader();
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}
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@Test
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public void testGetRegEx() {
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final String expected = "SSTCCI2_refdata_[a-z]+(_[a-z]+)?_\\d{6}.nc";
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assertEquals(expected, insituReader.getRegEx());
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final Pattern pattern = java.util.regex.Pattern.compile(expected);
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Matcher matcher = pattern.matcher("SSTCCI2_refdata_argosurf_202005.nc");
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assertTrue(matcher.matches());
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matcher = pattern.matcher("SSTCCI2_refdata_bottle_198904.nc");
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assertTrue(matcher.matches());
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matcher = pattern.matcher("SSTCCI2_refdata_drifter_198802.nc");
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assertTrue(matcher.matches());
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matcher = pattern.matcher("SSTCCI2_refdata_drifter_cmems_201801.nc");
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assertTrue(matcher.matches());
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matcher = pattern.matcher("SSTCCI2_refdata_argosurf_201712.nc");
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assertTrue(matcher.matches());
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matcher = pattern.matcher("insitu_5_WMOID_5901880_20100514_20100627.nc");
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assertFalse(matcher.matches());
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matcher = pattern.matcher("insitu_9_WMOID_14456569_19980913_19981123.nc");
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assertFalse(matcher.matches());
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matcher = pattern.matcher("insitu_10_WMOID_9733500_19840123_19840404.nc");
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assertFalse(matcher.matches());
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matcher = pattern.matcher("AMSR_E_L2A_BrightnessTemperatures_V12_200502170536_D.hdf");
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assertFalse(matcher.matches());
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matcher = pattern.matcher("NSS.HIRX.TN.D79287.S1623.E1807.B0516566.GC.nc");
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assertFalse(matcher.matches());
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}
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@Test
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public void testGetLongitudeVariableName() {
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assertEquals("LONGITUDE", insituReader.getLongitudeVariableName());
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}
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@Test
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public void testGetLatitudeVariableName() {
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assertEquals("LATITUDE", insituReader.getLatitudeVariableName());
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}
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}

‎core/src/test/java/com/bc/fiduceo/reader/insitu/sirds_sst/SirdsInsituReader_IO_Test.java‎

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package com.bc.fiduceo.reader.insitu.sirds_sst;
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import com.bc.fiduceo.IOTestRunner;
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import com.bc.fiduceo.TestUtil;
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import com.bc.fiduceo.core.NodeType;
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import com.bc.fiduceo.reader.AcquisitionInfo;
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import org.junit.After;
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import org.junit.Before;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import java.io.File;
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import java.io.IOException;
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import static org.junit.Assert.*;
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@RunWith(IOTestRunner.class)
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public class SirdsInsituReader_IO_Test {
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private SirdsInsituReader insituReader;
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@Before
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public void setUp() throws Exception {
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insituReader = new SirdsInsituReader();
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}
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@After
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public void tearDown() throws Exception {
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insituReader.close();
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}
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@Test
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public void testReadAcquisitionInfo_drifter() throws Exception {
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openFile("SSTCCI2_refdata_drifter_201304.nc", "v1.0");
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final AcquisitionInfo info = insituReader.read();
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assertNotNull(info);
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TestUtil.assertCorrectUTCDate(2013, 4, 1, 0, 0, 0, 0, info.getSensingStart());
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TestUtil.assertCorrectUTCDate(2013, 4, 30, 23, 58, 47, 0, info.getSensingStop());
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assertEquals(NodeType.UNDEFINED, info.getNodeType());
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assertNull(info.getBoundingGeometry());
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}
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@Test
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public void testReadAcquisitionInfo_mooring() throws Exception {
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openFile("SSTCCI2_refdata_mooring_201602.nc", "v1.0");
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final AcquisitionInfo info = insituReader.read();
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assertNotNull(info);
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TestUtil.assertCorrectUTCDate(2016, 2, 1, 0, 0, 0, 0, info.getSensingStart());
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TestUtil.assertCorrectUTCDate(2016, 2, 29, 23, 58, 11, 0, info.getSensingStop());
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assertEquals(NodeType.UNDEFINED, info.getNodeType());
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assertNull(info.getBoundingGeometry());
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}
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@Test
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public void testReadAcquisitionInfo_xbt() throws Exception {
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openFile("SSTCCI2_refdata_xbt_200204.nc", "v1.0");
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final AcquisitionInfo info = insituReader.read();
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assertNotNull(info);
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TestUtil.assertCorrectUTCDate(2002, 4, 1, 0, 1, 12, 0, info.getSensingStart());
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TestUtil.assertCorrectUTCDate(2002, 4, 30, 23, 43, 48, 0, info.getSensingStop());
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assertEquals(NodeType.UNDEFINED, info.getNodeType());
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assertNull(info.getBoundingGeometry());
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}
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private void openFile(String fileName, String version) throws IOException {
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final String testFilePath = TestUtil.assembleFileSystemPath(new String[]{"insitu", "sirds", version, fileName}, false);
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final File insituDataFile = TestUtil.getTestDataFileAsserted(testFilePath);
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insituReader.open(insituDataFile);
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}
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}

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