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Fix NcmlReader.mergeNcml with groups
Ensure reference group is passed into readGroup when using NcmlReader.mergeNcml, and make sure the reference group information is taken into account by the readGroup code. Fixes #1403
1 parent 5e5b339 commit dd197b8

4 files changed

Lines changed: 73 additions & 8 deletions

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‎cdm/core/src/main/java/ucar/nc2/internal/ncml/NcmlReader.java‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -288,7 +288,7 @@ public static NetcdfDataset.Builder mergeNcml(NetcdfFile ref, @Nullable Element
288288

289289
if (ncmlElem != null) {
290290
NcmlReader reader = new NcmlReader();
291-
reader.readGroup(targetDS, null, null, ncmlElem);
291+
reader.readGroup(targetDS, null, ref.getRootGroup(), ncmlElem);
292292
}
293293

294294
setEnhanceMode(targetDS, ncmlElem, null);
@@ -574,9 +574,12 @@ private Group.Builder readGroup(NetcdfDataset.Builder builder, @Nullable Group.B
574574
Group refGroup = null;
575575

576576
if (parent == null) {
577-
refGroup = this.refFile == null ? null : this.refFile.getRootGroup();
577+
if (this.refFile != null) {
578+
refGroup = this.refFile.getRootGroup();
579+
} else if (refParent != null) {
580+
refGroup = refParent;
581+
}
578582
groupBuilder = builder.rootGroup;
579-
580583
} else {
581584
String name = groupElem.getAttributeValue("name");
582585
if (name == null) {

‎cdm/core/src/test/data/ncml/modifyNestedGroups.xml‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2"
3+
location="nc/example.nc">
4+
<group name="outer_group">
5+
<attribute name="new_outer_attr" value="new_outer_attr_value" />
6+
<variable name="lat">
7+
<attribute name="new_lat_attr" value="new_lat_attr_value" />
8+
</variable>
9+
<group name="inner_group">
10+
<attribute name="new_inner_attr" value="new_inner_attr_value" />
11+
<variable name="lon">
12+
<attribute name="new_lon_attr" value="new_lon_attr_value" />
13+
</variable>
14+
</group>
15+
</group>
16+
</netcdf>

‎cdm/core/src/test/data/testModifyNestedGroups.nc4‎

8.41 KB
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‎cdm/core/src/test/java/ucar/nc2/internal/ncml/TestNcmlReader.java‎

Lines changed: 51 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,8 @@
1010
import org.jdom2.input.SAXBuilder;
1111
import org.junit.Test;
1212
import ucar.ma2.Array;
13+
import ucar.nc2.Attribute;
14+
import ucar.nc2.Group;
1315
import ucar.nc2.NetcdfFile;
1416
import ucar.nc2.Variable;
1517
import ucar.nc2.dataset.NetcdfDataset;
@@ -25,8 +27,9 @@ public class TestNcmlReader {
2527
public void shouldMergeNcml() throws IOException, JDOMException {
2628
final String filename = TestDir.cdmLocalTestDataDir + "example1.nc";
2729

28-
try (NetcdfFile netcdfFile = NetcdfDatasets.openFile(filename, null)) {
29-
final NetcdfDataset netcdfDataset = NcmlReader.mergeNcml(netcdfFile, getNcmlElement("modifyVars.xml")).build();
30+
try (NetcdfFile netcdfFile = NetcdfDatasets.openFile(filename, null);
31+
final NetcdfDataset netcdfDataset =
32+
NcmlReader.mergeNcml(netcdfFile, getNcmlElement("modifyVars.xml")).build();) {
3033

3134
final Variable ncmlVariable = netcdfDataset.findVariable("deltaLat");
3235
assertThat((Object) ncmlVariable).isInstanceOf(VariableDS.class);
@@ -40,9 +43,9 @@ public void shouldMergeNcml() throws IOException, JDOMException {
4043
public void shouldMergeNcmlWithEnhancements() throws IOException, JDOMException {
4144
final String filename = TestDir.cdmLocalTestDataDir + "example1.nc";
4245

43-
try (NetcdfFile netcdfFile = NetcdfDatasets.openFile(filename, null)) {
44-
final NetcdfDataset netcdfDataset =
45-
NcmlReader.mergeNcml(netcdfFile, getNcmlElement("enhance/testStandardizer.ncml")).build();
46+
try (NetcdfFile netcdfFile = NetcdfDatasets.openFile(filename, null);
47+
final NetcdfDataset netcdfDataset =
48+
NcmlReader.mergeNcml(netcdfFile, getNcmlElement("enhance/testStandardizer.ncml")).build();) {
4649

4750
final Variable ncmlVariable = netcdfDataset.findVariable("doublevar");
4851
assertThat((Object) ncmlVariable).isNotNull();
@@ -51,6 +54,49 @@ public void shouldMergeNcmlWithEnhancements() throws IOException, JDOMException
5154
}
5255
}
5356

57+
@Test
58+
public void mergeWithExistingGroups() throws IOException, JDOMException {
59+
final String filename = TestDir.cdmLocalTestDataDir + "testModifyNestedGroups.nc4";
60+
61+
try (NetcdfFile netcdfFile = NetcdfDatasets.openFile(filename, null);
62+
final NetcdfDataset netcdfDataset =
63+
NcmlReader.mergeNcml(netcdfFile, getNcmlElement("modifyNestedGroups.xml")).build()) {
64+
65+
final Group ncmlOuterGroup = netcdfDataset.findGroup("/outer_group");
66+
assertThat(ncmlOuterGroup).isNotNull();
67+
68+
final Attribute ncmlOuterAttribute = ncmlOuterGroup.findAttribute("new_outer_attr");
69+
assertThat(ncmlOuterAttribute).isNotNull();
70+
assertThat(ncmlOuterAttribute.getStringValue()).isNotNull();
71+
assertThat(ncmlOuterAttribute.getStringValue()).isEqualTo("new_outer_attr_value");
72+
73+
final Variable ncmlOuterVar = ncmlOuterGroup.findVariableLocal("lat");
74+
assertThat(ncmlOuterVar != null).isTrue();
75+
assertThat(ncmlOuterVar.attributes().hasAttribute("new_lat_attr")).isTrue();
76+
assertThat(ncmlOuterVar.attributes().findAttribute("new_lat_attr")).isNotNull();
77+
assertThat(ncmlOuterVar.attributes().findAttribute("new_lat_attr").getStringValue()).isNotNull();
78+
assertThat(ncmlOuterVar.attributes().findAttribute("new_lat_attr").getStringValue())
79+
.isEqualTo("new_lat_attr_value");
80+
// <attribute name="new_lat_attr" value="new_lat_attr_value" />
81+
82+
final Group ncmlInnerGroup = netcdfDataset.findGroup("/outer_group/inner_group");
83+
assertThat(ncmlInnerGroup).isNotNull();
84+
85+
final Attribute ncmlInnerAttribute = ncmlInnerGroup.findAttribute("new_inner_attr");
86+
assertThat(ncmlInnerAttribute).isNotNull();
87+
assertThat(ncmlInnerAttribute.getStringValue()).isNotNull();
88+
assertThat(ncmlInnerAttribute.getStringValue()).isEqualTo("new_inner_attr_value");
89+
90+
final Variable ncmlInnerVar = ncmlInnerGroup.findVariableLocal("lon");
91+
assertThat(ncmlInnerVar != null).isTrue();
92+
assertThat(ncmlInnerVar.attributes().hasAttribute("new_lon_attr")).isTrue();
93+
assertThat(ncmlInnerVar.attributes().findAttribute("new_lon_attr")).isNotNull();
94+
assertThat(ncmlInnerVar.attributes().findAttribute("new_lon_attr").getStringValue()).isNotNull();
95+
assertThat(ncmlInnerVar.attributes().findAttribute("new_lon_attr").getStringValue())
96+
.isEqualTo("new_lon_attr_value");
97+
}
98+
}
99+
54100
private static Element getNcmlElement(String filename) throws IOException, JDOMException {
55101
final String ncml = TestNcmlRead.topDir + filename;
56102

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