remove extra calls to read time axes

Unidata · Nov 17, 2023 · 8bb023e · 8bb023e
1 parent a61172a
commit 8bb023e
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Showing 11 changed files with 45 additions and 25 deletions.
diff --git a/cdm/core/src/main/java/ucar/nc2/dataset/CoordinateAxis1DTime.java b/cdm/core/src/main/java/ucar/nc2/dataset/CoordinateAxis1DTime.java
@@ -212,6 +212,11 @@ protected void readValues() {
     }
     // make sure parent methods do not try to read from the orgVar again
     this.wasRead = true;
+    if (orgVar instanceof CoordinateAxis1D) {
+      CoordinateAxis1D orgAxis = (CoordinateAxis1D) orgVar;
+      this.wasRead = orgAxis.wasRead;
+      this.coords = orgAxis.coords;
+    }
   }
 
   ////////////////////////////////////////////////////////////////////////
@@ -338,6 +343,8 @@ private CoordinateAxis1DTime(NetcdfDataset ncd, VariableDS org, Formatter errMes
     List<CalendarDate> result = new ArrayList<>(ncoords);
 
     Array data = org.read();
+    coords = (double[]) data.get1DJavaArray(DataType.DOUBLE);
+    this.wasRead = true;
 
     int count = 0;
     IndexIterator ii = data.getIndexIterator();

diff --git a/cdm/core/src/main/java/ucar/nc2/dataset/NetcdfDataset.java b/cdm/core/src/main/java/ucar/nc2/dataset/NetcdfDataset.java
@@ -932,6 +932,10 @@ public ImmutableList<CoordinateAxis> getCoordinateAxes() {
     return ImmutableList.copyOf(coordAxes);
   }
 
+  public void setCoordinateAxes(List<CoordinateAxis> axes) {
+    this.coordAxes = axes;
+  }
+
   /**
    * Clear Coordinate System metadata, to allow them to be redone
    * 
@@ -1344,12 +1348,16 @@ public void addCoordinateTransform(CoordinateTransform ct) {
   public CoordinateAxis addCoordinateAxis(VariableDS v) {
     if (v == null)
       return null;
+
+    final List<CoordinateAxis> coordCopy = new ArrayList<>(coordAxes);
+
     CoordinateAxis oldVar = findCoordinateAxis(v.getFullName());
     if (oldVar != null)
-      coordAxes.remove(oldVar);
+      coordCopy.remove(oldVar);
 
     CoordinateAxis ca = (v instanceof CoordinateAxis) ? (CoordinateAxis) v : CoordinateAxis.factory(this, v);
-    coordAxes.add(ca);
+    coordCopy.add(ca);
+    this.coordAxes = coordCopy;
 
     if (v.isMemberOfStructure()) {
       Structure parentOrg = v.getParentStructure(); // gotta be careful to get the wrapping parent
@@ -1705,6 +1713,7 @@ public void replaceCoordinateAxis(Group.Builder group, CoordinateAxis.Builder ax
       axis.setParentGroupBuilder(group);
     }
 
+
     public T setOrgFile(NetcdfFile orgFile) {
       this.orgFile = orgFile;
       return self();

diff --git a/cdm/core/src/main/java/ucar/nc2/dataset/NetcdfDatasets.java b/cdm/core/src/main/java/ucar/nc2/dataset/NetcdfDatasets.java
@@ -13,6 +13,7 @@
 import ucar.nc2.internal.dataset.DatasetEnhancer;
 import ucar.nc2.internal.ncml.NcmlReader;
 import ucar.nc2.util.CancelTask;
+import ucar.nc2.util.CompareNetcdf2;
 import ucar.nc2.util.cache.FileCache;
 import ucar.nc2.util.cache.FileCacheIF;
 import ucar.nc2.util.cache.FileFactory;

diff --git a/cdm/core/src/main/java/ucar/nc2/dataset/VariableDS.java b/cdm/core/src/main/java/ucar/nc2/dataset/VariableDS.java
@@ -907,6 +907,9 @@ protected Builder<?> addLocalFieldsToBuilder(Builder<? extends Builder<?>> build
     builder.setOriginalVariable(this.orgVar).setOriginalDataType(this.orgDataType).setOriginalName(this.orgName)
         .setOriginalFileTypeId(this.orgFileTypeId).setEnhanceMode(this.enhanceMode).setUnits(this.enhanceProxy.units)
         .setDesc(this.enhanceProxy.desc);
+    if (this.coordSysNames != null) {
+      this.coordSysNames.stream().forEach(s -> builder.addCoordinateSystemName(s));
+    }
 
     return (VariableDS.Builder<?>) super.addLocalFieldsToBuilder(builder);
   }

diff --git a/cdm/core/src/main/java/ucar/nc2/ft2/coverage/adapter/DtCoverageAdapter.java b/cdm/core/src/main/java/ucar/nc2/ft2/coverage/adapter/DtCoverageAdapter.java
@@ -155,7 +155,7 @@ private static CoverageCoordAxis makeCoordAxisFromDimension(Dimension dim) {
 
   private static ucar.nc2.util.Optional<CoverageCoordAxis> makeCoordAxis(FeatureType ftype,
       ucar.nc2.dataset.CoordinateAxis dtCoordAxis, DtCoverageAdapter reader) {
-    String name = dtCoordAxis.getFullName();
+   String name = dtCoordAxis.getFullName();
     DataType dataType = dtCoordAxis.getDataType();
     AxisType axisType = dtCoordAxis.getAxisType();
     String units = dtCoordAxis.getUnitsString();

diff --git a/cdm/core/src/main/java/ucar/nc2/ft2/coverage/adapter/DtCoverageCSBuilder.java b/cdm/core/src/main/java/ucar/nc2/ft2/coverage/adapter/DtCoverageCSBuilder.java
@@ -5,6 +5,7 @@
 package ucar.nc2.ft2.coverage.adapter;
 
 import com.google.common.collect.Lists;
+import thredds.client.catalog.builder.DatasetBuilder;
 import ucar.nc2.Dimension;
 import ucar.nc2.constants.AxisType;
 import ucar.nc2.constants.FeatureType;
@@ -179,6 +180,7 @@ public static String describe(NetcdfDataset ds, CoordinateSystem cs, Formatter e
 
     //////////////////////////////////////////////////////////////
     // time
+    boolean axesChanged = false; // if any time axes are rebuilt by the factory, we need to update the netcdfDataset
     CoordinateAxis rt = cs.findAxis(AxisType.RunTime);
     if (rt != null) {
       if (!rt.isScalar() && !(rt instanceof CoordinateAxis1D)) { // A runtime axis must be scalar or one-dimensional

diff --git a/cdm/core/src/main/java/ucar/nc2/ft2/coverage/adapter/DtCoverageDataset.java b/cdm/core/src/main/java/ucar/nc2/ft2/coverage/adapter/DtCoverageDataset.java
@@ -13,11 +13,8 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import ucar.nc2.Attribute;
-import ucar.nc2.Dimension;
-import ucar.nc2.NetcdfFile;
-import ucar.nc2.Variable;
-import ucar.nc2.VariableSimpleIF;
+
+import ucar.nc2.*;
 import ucar.nc2.constants.CDM;
 import ucar.nc2.constants.FeatureType;
 import ucar.nc2.dataset.CoordinateAxis;
@@ -113,13 +110,11 @@ public DtCoverageDataset(NetcdfDataset ncd) throws IOException {
    * @throws java.io.IOException on read error
    */
   public DtCoverageDataset(NetcdfDataset ncd, Formatter parseInfo) throws IOException {
-    this.ncd = ncd;
-
     Set<NetcdfDataset.Enhance> enhance = ncd.getEnhanceMode();
     if (enhance == null || enhance.isEmpty()) {
       enhance = NetcdfDataset.getDefaultEnhanceMode();
     }
-    ncd = NetcdfDatasets.enhance(ncd, enhance, null);
+    this.ncd = NetcdfDatasets.enhance(ncd, enhance, null);
 
     // sort by largest size first
     List<CoordinateSystem> csList = new ArrayList<>(ncd.getCoordinateSystems());

diff --git a/cdm/core/src/main/java/ucar/nc2/internal/dataset/CoordinatesHelper.java b/cdm/core/src/main/java/ucar/nc2/internal/dataset/CoordinatesHelper.java
@@ -53,10 +53,15 @@ public List<CoordinateTransform> getCoordTransforms() {
     return coordTransforms;
   }
 
+  // make another constructor that takes a list of axes?
   private CoordinatesHelper(Builder builder, NetcdfDataset ncd) {
     List<CoordinateAxis> axes = new ArrayList<>();
-    addAxes(ncd.getRootGroup(), axes);
-    this.coordAxes = ImmutableList.copyOf(axes);
+//    if (builder.coordAxes == null || builder.coordAxes.isEmpty()) {
+      addAxes(ncd.getRootGroup(), axes);
+//    } else {
+//      axes = builder.coordAxes.stream().map(ct -> ct.build(ncd.getRootGroup())).filter(Objects::nonNull).collect(Collectors.toList());
+//    }
+    coordAxes = ImmutableList.copyOf(axes);
 
     coordTransforms =
         builder.coordTransforms.stream().map(ct -> ct.build(ncd)).filter(Objects::nonNull).collect(Collectors.toList());

diff --git a/cdm/core/src/main/java/ucar/nc2/util/cache/FileCache.java b/cdm/core/src/main/java/ucar/nc2/util/cache/FileCache.java
@@ -390,6 +390,10 @@ private FileCacheable acquireCacheOnly(Object hashKey) {
     return want.ncfile;
   }
 
+  public void replace (Object oldHashKey, Object newHasKey){
+
+  }
+
   // LOOK should you remove the entire CacheElement ?
   private void remove(CacheElement.CacheFile want) {
     want.remove();

diff --git a/cdm/core/src/test/java/ucar/nc2/internal/ncml/TestEnhance.java b/cdm/core/src/test/java/ucar/nc2/internal/ncml/TestEnhance.java
@@ -53,8 +53,7 @@ public void testStandaloneNoEnhanceDataset() throws IOException {
       Variable scaledvar = ncfile.findVariable("scaledvar");
       assertThat((Object) scaledvar).isNotNull();
       assertThat(scaledvar.getDataType()).isEqualTo(DataType.SHORT);
-      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isTrue();
-      assertThat(scaledvar.attributes().findAttributeDouble("scale_factor", 1.0)).isEqualTo(2.0);
+      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isFalse();
       assertThat(scaledvar.readScalarShort()).isEqualTo(1);
     }
   }
@@ -72,8 +71,7 @@ public void testStandaloneEnhance() throws IOException {
       Variable scaledvar = ncfile.findVariable("scaledvar");
       assertThat((Object) scaledvar).isNotNull();
       assertThat(scaledvar.getDataType()).isEqualTo(DataType.FLOAT);
-      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isTrue();
-      assertThat(scaledvar.attributes().findAttributeDouble("scale_factor", 1.0)).isEqualTo(2.0);
+      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isFalse();
       assertThat(scaledvar.readScalarFloat()).isEqualTo(12.0f);
     }
   }
@@ -91,8 +89,7 @@ public void testStandaloneEnhanceDataset() throws IOException {
       Variable scaledvar = ncfile.findVariable("scaledvar");
       assertThat((Object) scaledvar).isNotNull();
       assertThat(scaledvar.getDataType()).isEqualTo(DataType.FLOAT);
-      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isTrue();
-      assertThat(scaledvar.attributes().findAttributeDouble("scale_factor", 1.0)).isEqualTo(2.0);
+      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isFalse();
       assertThat(scaledvar.readScalarFloat()).isEqualTo(12.0f);
     }
   }

diff --git a/cdm/core/src/test/java/ucar/nc2/ncml/TestEnhance.java b/cdm/core/src/test/java/ucar/nc2/ncml/TestEnhance.java
@@ -68,8 +68,7 @@ public void testStandaloneEnhance() throws IOException {
       Variable scaledvar = ncfile.findVariable("scaledvar");
       assertThat((Object) scaledvar).isNotNull();
       assertThat(scaledvar.getDataType()).isEqualTo(DataType.FLOAT);
-      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isTrue();
-      assertThat(scaledvar.attributes().findAttributeDouble("scale_factor", 1.0)).isEqualTo(2.0);
+      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isFalse();
       assertThat(scaledvar.readScalarFloat()).isEqualTo(12.0f);
     }
   }
@@ -87,8 +86,7 @@ public void testStandaloneEnhanceDataset() throws IOException {
       Variable scaledvar = ncfile.findVariable("scaledvar");
       assertThat((Object) scaledvar).isNotNull();
       assertThat(scaledvar.getDataType()).isEqualTo(DataType.FLOAT);
-      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isTrue();
-      assertThat(scaledvar.attributes().findAttributeDouble("scale_factor", 1.0)).isEqualTo(2.0);
+      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isFalse();
       assertThat(scaledvar.readScalarFloat()).isEqualTo(12.0f);
     }
   }
@@ -106,8 +104,7 @@ public void testStandaloneDoubleEnhanceDataset() throws IOException {
       Variable scaledvar = ncfile.findVariable("scaledvar");
       assertThat((Object) scaledvar).isNotNull();
       assertThat(scaledvar.getDataType()).isEqualTo(DataType.FLOAT);
-      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isTrue();
-      assertThat(scaledvar.attributes().findAttributeDouble("scale_factor", 1.0)).isEqualTo(2.0);
+      assertThat(scaledvar.attributes().hasAttribute("scale_factor")).isFalse();
       assertThat(scaledvar.readScalarFloat()).isEqualTo(12.0f);
     }
   }