Rewrite groovy tests as junit

netcdf4/src/main/java/ucar/nc2/jni/netcdf/Nc4Iosp.java

@@ -1131,7 +1131,7 @@ private String nc_inq_var_name(int grpid, int varno) throws IOException {
   }
   //////////////////////////////////////////////////////////////////////////
 
-  private static class Vinfo {
+  static class Vinfo {
     final Group4 g4;
     int varid, typeid;
     UserType utype; // may be null
@@ -1143,7 +1143,7 @@ private static class Vinfo {
     }
   }
 
-  private static class Group4 {
+  static class Group4 {
     final int grpid;
     final Group g;
     final Group4 parent;

netcdf4/src/test/java/ucar/nc2/jni/netcdf/TestNc4IospMisc.java

@@ -0,0 +1,144 @@
+package ucar.nc2.jni.netcdf;
+
+import static com.google.common.truth.Truth.assertThat;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import ucar.ma2.Array;
+import ucar.ma2.ArrayChar;
+import ucar.ma2.DataType;
+import ucar.ma2.MAMath;
+import ucar.nc2.Attribute;
+import ucar.nc2.Dimension;
+import ucar.nc2.NetcdfFile;
+import ucar.nc2.NetcdfFileWriter;
+import ucar.nc2.Variable;
+
+public class TestNc4IospMisc {
+
+  @Rule
+  public final TemporaryFolder tempFolder = new TemporaryFolder();
+
+  /*
+   * Demonstrates bug from https://www.unidata.ucar.edu/mailing_lists/archives/netcdf-java/2017/msg00012.html
+   * Prior to fix, this test would fail for 'u_short', 'u_int', and 'u_long' variables with
+   * "Unknown userType == 8", "Unknown userType == 9", and "Unknown userType == 11" errors respectively.
+   */
+  @Test
+  public void shouldReadDataSectionOfVariables() throws Exception {
+    String[] varNames = new String[] {"u_byte", "u_short", "u_int", "u_long"};
+    List<Array> expectedData = new ArrayList<>();
+    // Will overflow to [-128, -127, -126]
+    expectedData
+        .add(Array.makeFromJavaArray(new byte[] {(byte) (1 << 7), (byte) ((1 << 7) + 1), (byte) ((1 << 7) + 2)}));
+    expectedData.add(
+        Array.makeFromJavaArray(new short[] {(short) (1 << 15), (short) ((1 << 15) + 1), (short) ((1 << 15) + 2)}));
+    expectedData.add(Array.makeFromJavaArray(new int[] {(1 << 31), (1 << 31) + 1, (1 << 31) + 2}));
+    expectedData.add(Array.makeFromJavaArray(new long[] {(1L << 63), (1L << 63) + 1, (1L << 63) + 2}));
+
+    File file = new File(getClass().getResource("unsigned.nc4").toURI());
+    assertThat(file.exists()).isTrue();
+
+    try (
+        NetcdfFile ncFile = NetcdfFile.open(file.getAbsolutePath(), Nc4Iosp.class.getCanonicalName(), -1, null, null)) {
+      Nc4Iosp nc4Iosp = (Nc4Iosp) ncFile.getIosp();
+
+      for (int i = 0; i < varNames.length; i++) {
+        Variable var = ncFile.findVariable(varNames[i]);
+        Nc4Iosp.Vinfo vinfo = (Nc4Iosp.Vinfo) var.getSPobject();
+        Array array = nc4Iosp.readDataSection(vinfo.g4.grpid, vinfo.varid, vinfo.typeid, var.getShapeAsSection());
+        MAMath.nearlyEquals(array, expectedData.get(i));
+      }
+    }
+  }
+
+  /*
+   * Demonstrates bug from
+   * https://andy.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=viewticket&ticketid=28098
+   * Prior to fix, primary2Dim and primary3Dim were not being identified as unlimited.
+   */
+  @Test
+  public void shouldContainMultipleGroupsWithUnlimitedDimensions() throws Exception {
+    File file = new File(this.getClass().getResource("DBP-690959.nc4").toURI());
+    assertThat(file.exists()).isTrue();
+
+    try (
+        NetcdfFile ncFile = NetcdfFile.open(file.getAbsolutePath(), Nc4Iosp.class.getCanonicalName(), -1, null, null)) {
+      Dimension primary1Dim = ncFile.findDimension("/group1/primary");
+      Dimension primary2Dim = ncFile.findDimension("/group2/primary");
+      Dimension primary3Dim = ncFile.findDimension("/group3/primary");
+
+      assertThat(primary1Dim.isUnlimited()).isTrue();
+      assertThat(primary2Dim.isUnlimited()).isTrue();
+      assertThat(primary3Dim.isUnlimited()).isTrue();
+    }
+  }
+
+  @Test
+  public void shouldWriteUnlimitedDimension() throws Exception {
+    File tempFile = new File(tempFolder.getRoot(), "Nc4IospMiscSpec.nc4");
+
+    try (NetcdfFileWriter ncWriter =
+        NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf4, tempFile.getAbsolutePath())) {
+      Dimension dimBefore = ncWriter.addDimension(null, "dim", 3, true, false);
+      ncWriter.create();
+      ncWriter.close();
+
+      try (NetcdfFile ncFile = NetcdfFile.open(tempFile.getAbsolutePath())) {
+        Dimension dimAfter = ncFile.findDimension(dimBefore.getFullName());
+        // Failed prior to fix, because dimAfter was not unlimited.
+        assertThat(dimBefore).isEqualTo(dimAfter);
+      }
+    }
+  }
+
+  @Test
+  public void shouldCreateFileWithNullValuedAttributes() throws Exception {
+    File tempFile = new File(tempFolder.getRoot(), "Nc4IospMiscSpec.nc4");
+
+    try (NetcdfFileWriter ncWriter =
+        NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf4, tempFile.getAbsolutePath())) {
+      Attribute attrNum = new Attribute("nullvalnum", DataType.INT);
+      Attribute attrNumBefore = ncWriter.addGlobalAttribute(attrNum);
+
+      Attribute attrStr = new Attribute("nullvalstr", DataType.STRING);
+      Attribute attrStrBefore = ncWriter.addGlobalAttribute(attrStr);
+
+      Attribute attrChar = new Attribute("nullvalchar", DataType.CHAR);
+      Attribute attrCharBefore = ncWriter.addGlobalAttribute(attrChar);
+
+      // add a character valued attribute with a specific null char value"
+      Attribute attrNullChar = new Attribute("nullcharvalchar", DataType.CHAR);
+      Array attrNullCharValue = ArrayChar.makeFromString("\0", 1);
+      attrNullChar.setValues(attrNullCharValue);
+      Attribute attrNullCharBefore = ncWriter.addGlobalAttribute(attrNullChar);
+
+      ncWriter.create();
+      ncWriter.close();
+
+      try (NetcdfFile ncFile = NetcdfFile.open(tempFile.getAbsolutePath())) {
+        Attribute attrNumAfter = ncFile.findGlobalAttribute(attrNumBefore.getFullName());
+        assertThat(attrNumBefore.getValues()).isEqualTo(attrNumAfter.getValues());
+        assertThat(attrNumBefore.getValues()).isNull();
+
+        Attribute attrStrAfter = ncFile.findGlobalAttribute(attrStrBefore.getFullName());
+        assertThat(attrStrAfter.getValues()).isEqualTo(attrStrBefore.getValues());
+        assertThat(attrStrAfter.getValues()).isNull();
+
+        Attribute attrCharAfter = ncFile.findGlobalAttribute(attrCharBefore.getFullName());
+        assertThat(attrCharAfter.getValues()).isEqualTo(attrCharBefore.getValues());
+        assertThat(attrCharAfter.getValues()).isNull();
+
+        Attribute attrNullCharAfter = ncFile.findGlobalAttribute(attrNullCharBefore.getFullName());
+        assertThat(attrNullCharAfter.getValues().getSize()).isEqualTo(attrNullCharBefore.getValues().getSize());
+        assertThat(attrNullCharAfter.getValues().getSize()).isEqualTo(1);
+        assertThat(attrNullCharAfter.getValue(0)).isEqualTo(attrNullCharBefore.getValue(0));
+        assertThat(attrNullCharAfter).isEqualTo(attrNullCharBefore);
+      }
+    }
+  }
+}