Merge pull request #800 from lesserwhirls/nilstr-5

[5.x]: Handle NULL string attributes in HDF5.

Author: haileyajohnson

cdm/core/src/main/java/ucar/nc2/internal/iosp/hdf5/H5headerNew.java

@@ -93,6 +93,9 @@ public class H5headerNew implements H5headerIF, HdfHeaderIF {
   private static boolean warnings = true, debugReference, debugRegionReference, debugCreationOrder, debugStructure;
   private static boolean debugDimensionScales;
 
+  // NULL string value, following netCDF-C, set to NIL
+  private static final String NULL_STRING_VALUE = "NIL";
+
   public static void setWarnings(boolean warn) {
     warnings = warn;
   }
@@ -2135,6 +2138,9 @@ Array getHeapDataArray(HeapIdentifier heapId, DataType dataType, int endian)
    */
   String readHeapString(long heapIdAddress) throws IOException {
     HeapIdentifier heapId = h5objects.readHeapIdentifier(heapIdAddress);
+    if (heapId.isEmpty()) {
+      return NULL_STRING_VALUE;
+    }
     GlobalHeap.HeapObject ho = heapId.getHeapObject();
     if (ho == null)
       throw new IllegalStateException("Cant find Heap Object,heapId=" + heapId);
@@ -2154,6 +2160,9 @@ String readHeapString(long heapIdAddress) throws IOException {
    */
   String readHeapString(ByteBuffer bb, int pos) throws IOException {
     HeapIdentifier heapId = h5objects.readHeapIdentifier(bb, pos);
+    if (heapId.isEmpty()) {
+      return NULL_STRING_VALUE;
+    }
     GlobalHeap.HeapObject ho = heapId.getHeapObject();
     if (ho == null)
       throw new IllegalStateException("Cant find Heap Object,heapId=" + heapId);

cdm/core/src/main/java/ucar/nc2/iosp/hdf5/H5header.java

@@ -60,6 +60,9 @@ public class H5header extends NCheader implements H5headerIF {
   private static boolean warnings = true, debugReference, debugRegionReference, debugCreationOrder, debugStructure;
   private static boolean debugDimensionScales;
 
+  // NULL string value, following netCDF-C, set to NIL
+  private static final String NULL_STRING_VALUE = "NIL";
+
   public static void setWarnings(boolean warn) {
     warnings = warn;
   }
@@ -4711,6 +4714,9 @@ Array getHeapDataArray(HeapIdentifier heapId, DataType dataType, int endian)
    */
   String readHeapString(long heapIdAddress) throws IOException {
     H5header.HeapIdentifier heapId = new HeapIdentifier(heapIdAddress);
+    if (heapId.isEmpty()) {
+      return NULL_STRING_VALUE;
+    }
     H5header.GlobalHeap.HeapObject ho = heapId.getHeapObject();
     if (ho == null)
       throw new IllegalStateException("Cant find Heap Object,heapId=" + heapId);
@@ -4730,6 +4736,9 @@ String readHeapString(long heapIdAddress) throws IOException {
    */
   String readHeapString(ByteBuffer bb, int pos) throws IOException {
     H5header.HeapIdentifier heapId = new HeapIdentifier(bb, pos);
+    if (heapId.isEmpty()) {
+      return NULL_STRING_VALUE;
+    }
     H5header.GlobalHeap.HeapObject ho = heapId.getHeapObject();
     if (ho == null)
       throw new IllegalStateException("Cant find Heap Object,heapId=" + heapId);

cdm/core/src/test/data/hdf5/string_attrs.nc4

@@ -0,0 +1,94 @@
+/*
+ * Copyright (c) 2021 University Corporation for Atmospheric Research/Unidata
+ * See LICENSE for license information.
+ */
+package ucar.nc2.iosp.hdf5;
+
+import org.junit.AfterClass;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import ucar.nc2.Attribute;
+import ucar.nc2.NetcdfFile;
+import ucar.nc2.NetcdfFiles;
+import ucar.nc2.Variable;
+import ucar.unidata.util.test.TestDir;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collection;
+
+import static com.google.common.truth.Truth.assertThat;
+
+/** Test String Attributes */
+@RunWith(Parameterized.class)
+public class TestNullStringAttr {
+
+  private static NetcdfFile ncfOld, ncfNew;
+  private static final String testFile = TestDir.cdmLocalTestDataDir + "hdf5/string_attrs.nc4";
+
+  private final NetcdfFile ncf;
+
+  public TestNullStringAttr(String apiType, NetcdfFile ncf) {
+    this.ncf = ncf;
+  }
+
+  @Parameterized.Parameters(name = "{0}")
+  public static Collection<?> netcdfFileObjects() throws IOException {
+    ncfOld = NetcdfFile.open(testFile);
+    ncfNew = NetcdfFiles.open(testFile);
+    return Arrays.asList(new Object[][] {{"Old API", ncfOld}, {"New API", ncfNew},});
+  }
+
+  @Test
+  public void testNullStringGlobalAttr() {
+    Attribute attr = ncf.findGlobalAttribute("NULL_STR_GATTR");
+    assertThat(attr).isNotNull();
+    String value = attr.getStringValue();
+    assertThat(value).isNotNull();
+    assertThat(value).isNotEmpty();
+    assertThat(value).isNotEqualTo("");
+    assertThat(value).isEqualTo("NIL");
+  }
+
+  @Test
+  public void testEmptyStringGlobalAttr() {
+    Attribute attr = ncf.findGlobalAttribute("EMPTY_STR_GATTR");
+    assertThat(attr).isNotNull();
+    String value = attr.getStringValue();
+    assertThat(value).isNotNull();
+    assertThat(value).isEmpty();
+    assertThat(value).isEqualTo("");
+  }
+
+  @Test
+  public void testNullStringAttr() {
+    Variable testVar = ncf.findVariable("/var");
+    assert null != testVar;
+    Attribute attr = testVar.findAttribute("NULL_STR_ATTR");
+    assertThat(attr).isNotNull();
+    String value = attr.getStringValue();
+    assertThat(value).isNotNull();
+    assertThat(value).isNotEmpty();
+    assertThat(value).isNotEqualTo("");
+    assertThat(value).isEqualTo("NIL");
+  }
+
+  @Test
+  public void testEmptyStringAttr() {
+    Variable testVar = ncf.findVariable("/var");
+    assert null != testVar;
+    Attribute attr = testVar.findAttribute("EMPTY_STR_ATTR");
+    assertThat(attr).isNotNull();
+    String value = attr.getStringValue();
+    assertThat(value).isNotNull();
+    assertThat(value).isEmpty();
+    assertThat(value).isEqualTo("");
+  }
+
+  @AfterClass
+  public static void closeFile() throws IOException {
+    ncfOld.close();
+    ncfNew.close();
+  }
+}