Merge pull request #1254 from tdrwenski/rename-variable-used-in-agg

Fix renamed variable reading in aggregations
Unidata · Oct 30, 2023 · 027414a · 027414a
2 parents 9449937 + cd16856
commit 027414a
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Showing 4 changed files with 74 additions and 5 deletions.
diff --git a/cdm/core/src/main/java/ucar/nc2/internal/ncml/AggDataset.java b/cdm/core/src/main/java/ucar/nc2/internal/ncml/AggDataset.java
@@ -145,6 +145,10 @@ protected Array read(Variable mainv, CancelTask cancelTask) throws IOException {
         return null;
 
       Variable v = findVariable(ncd, mainv);
+      if (v == null) {
+        Aggregation.logger.error("AggDataset can't find " + mainv.getFullName() + " in " + ncd.getLocation());
+        throw new IllegalArgumentException("Variable '" + mainv.getFullName() + "' does not exist in aggregation.");
+      }
       if (debugRead)
         System.out.printf("Agg.read %s from %s in %s%n", mainv.getNameAndDimensions(), v.getNameAndDimensions(),
             getLocation());

diff --git a/cdm/core/src/main/java/ucar/nc2/internal/ncml/AggDatasetOuter.java b/cdm/core/src/main/java/ucar/nc2/internal/ncml/AggDatasetOuter.java
@@ -285,10 +285,8 @@ protected Array read(Variable mainv, CancelTask cancelTask, List<Range> section)
 
       Variable v = findVariable(ncd, mainv);
       if (v == null) {
-        Aggregation.logger.error("AggOuterDimension cant find " + mainv.getFullName() + " in " + ncd.getLocation()
-            + "; return all zeroes!!!");
-        return Array.factory(mainv.getDataType(), new Section(section).getShape()); // all zeros LOOK need missing
-                                                                                    // value
+        Aggregation.logger.error("AggOuterDimension can't find " + mainv.getFullName() + " in " + ncd.getLocation());
+        throw new IllegalArgumentException("Variable '" + mainv.getFullName() + "' does not exist in aggregation.");
       }
 
       if (Aggregation.debugRead) {

diff --git a/cdm/core/src/main/java/ucar/nc2/internal/ncml/NcmlReader.java b/cdm/core/src/main/java/ucar/nc2/internal/ncml/NcmlReader.java
@@ -989,7 +989,7 @@ private Optional<Builder> readVariableExisting(Group.Builder groupBuilder,
             .orElseThrow(() -> new IllegalStateException("Cant find variable " + nameInFile));
       }
     }
-    vb.setName(name).setDataType(dtype);
+    vb.setOriginalName(nameInFile).setName(name).setDataType(dtype);
     if (typedefS != null) {
       vb.setEnumTypeName(typedefS);
     }

diff --git a/cdm/core/src/test/java/ucar/nc2/internal/ncml/TestRenameVariableInAggregation.java b/cdm/core/src/test/java/ucar/nc2/internal/ncml/TestRenameVariableInAggregation.java
@@ -0,0 +1,67 @@
+package ucar.nc2.internal.ncml;
+
+import static com.google.common.truth.Truth.assertThat;
+
+import java.io.IOException;
+import java.io.StringReader;
+import org.junit.Test;
+import ucar.ma2.Array;
+import ucar.ma2.InvalidRangeException;
+import ucar.ma2.Section;
+import ucar.nc2.NetcdfFile;
+import ucar.nc2.Variable;
+
+public class TestRenameVariableInAggregation {
+  private static final double TOLERANCE = 1.0e-6;
+
+  @Test
+  public void shouldRenameVariableUsedInAggregation() throws IOException, InvalidRangeException {
+    final String ncml = "<?xml version='1.0' encoding='UTF-8'?>\n" // leavit
+        + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2'>\n" // leavit
+        + "  <variable name='temperature' orgName='T' />\n" // leavit
+        + "  <aggregation  dimName='time' type='joinNew'>\n" // leavit
+        + "    <variableAgg name='T'/>\n" // leavit
+        + "    <netcdf location='src/test/data/ncml/nc/scalarTime0.nc'/>\n" // leavit
+        + "    <netcdf location='src/test/data/ncml/nc/scalarTime1.nc'/>\n" // leavit
+        + "    <netcdf location='src/test/data/ncml/nc/scalarTime2.nc'/>\n" // leavit
+        + "  </aggregation>\n" // leavit
+        + "</netcdf>"; // leavit
+
+    checkNcmlDataset(ncml);
+  }
+
+  @Test
+  public void shouldRenameVariableUsedInAggregationWithScan() throws IOException, InvalidRangeException {
+    final String ncml = "<?xml version='1.0' encoding='UTF-8'?>\n" // leavit
+        + "<netcdf xmlns='http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2'>\n" // leavit
+        + "  <variable name='temperature' orgName='T' />\n" // leavit
+        + "  <aggregation  dimName='time' type='joinNew'>\n" // leavit
+        + "    <variableAgg name='T'/>\n" // leavit
+        + "    <scan location='src/test/data/ncml/nc/' subdirs='false' regExp='scalarTime.*nc'/>\n" // leavit
+        + "  </aggregation>\n" // leavit
+        + "</netcdf>"; // leavit
+
+    checkNcmlDataset(ncml);
+  }
+
+  private static void checkNcmlDataset(String ncml) throws InvalidRangeException, IOException {
+    try (NetcdfFile ncfile = NcmlReader.readNcml(new StringReader(ncml), null, null).build()) {
+      final Variable oldVariable = ncfile.findVariable("T");
+      assertThat((Object) oldVariable).isNull();
+      final Variable newVariable = ncfile.findVariable("temperature");
+      assertThat((Object) newVariable).isNotNull();
+
+      final Array partialArray = newVariable.read(new Section("0:2, 0:0, 0:0"));
+      assertThat(partialArray.getSize()).isEqualTo(3);
+      assertThat(partialArray.getDouble(0)).isWithin(TOLERANCE).of(0.0);
+      assertThat(partialArray.getDouble(1)).isWithin(TOLERANCE).of(100.0);
+      assertThat(partialArray.getDouble(2)).isWithin(TOLERANCE).of(200.0);
+
+      final Array array = newVariable.read();
+      assertThat(array.getSize()).isEqualTo(36);
+      assertThat(array.getDouble(0)).isWithin(TOLERANCE).of(0.0);
+      assertThat(array.getDouble(12)).isWithin(TOLERANCE).of(100.0);
+      assertThat(array.getDouble(24)).isWithin(TOLERANCE).of(200.0);
+    }
+  }
+}