Merge branch 'main' into tdsdap4fixes1.dmh

.github/workflows/deps.yml

@@ -5,7 +5,7 @@ jobs:
     name: Check fresh compile and assemble of TDS project
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up JDK 11
         uses: actions/setup-java@v2
         with:

.github/workflows/docs.yml

@@ -9,7 +9,7 @@ jobs:
     name: TDS Documentation Build Check
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup Java 11
         uses: actions/setup-java@v2
         with:

.github/workflows/style.yml

@@ -5,7 +5,7 @@ jobs:
     name: Code Style Check
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up JDK 11
         uses: actions/setup-java@v2
         with:

.github/workflows/tds.yml

@@ -19,7 +19,7 @@ jobs:
             java-vendor: 'zulu'
             servletcontainer: 'tomcat9'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Build and test with Gradle (${{ matrix.java-vendor }} ${{ matrix.java-version }})
         uses: Unidata/thredds-test-action@v2
         with:
@@ -32,6 +32,6 @@ jobs:
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
-          name: tds_JUnit_Results_${{ github.sha }}_AdoptOpenJDK-HS-${{ matrix.java }}-matrix.servletcontainer }}
+          name: tds_JUnit_Results_${{ github.sha }}_AdoptOpenJDK-HS-${{ matrix.java }}-${{ matrix.servletcontainer }}
           path: build/reports/allTests
 

.github/workflows/update-docker.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout default branch
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Verify variables
       run: |

opendap/server/src/main/java/opendap/servers/SubClause.java

@@ -45,7 +45,7 @@
  * Represents a sub-clause of the selection portion of a constraint
  * expression. A sub-clause is any part of a constraint that
  * can be evaluated to a BaseType value. For instance, the constraint
- * "var1>=function(var2,var3)" would have sub clauses "var1" and
+ * "{@code var1>=function(var2,var3)}" would have sub clauses "var1" and
  * "function(var2,var3)". The latter would in turn have the sub-clauses
  * "var2" and "var3".
  * <p>

opendap/server/src/main/java/opendap/servers/TopLevelClause.java

@@ -45,7 +45,7 @@
  * <p>
  * <p/>
  * A top-level clause is a boolean expression
- * preceded by "&" in the CE, such as "lat>10.0", or "function(var1,var2)".
+ * preceded by "{@code &}" in the CE, such as "{@code lat>10.0}", or "{@code function(var1,var2)}".
  * The top-level clause may contain sub-clauses which can be evaluated
  * individually.
  * <p/>

opendap/server/src/main/java/opendap/servers/parsers/CeParser.java

@@ -1398,7 +1398,7 @@ private static final byte yytranslate_(int t) {
   /**
    * Instantiates the Bison-generated parser.
    * 
-   * @param yylexer The scanner that will supply tokens to the parser.
+   * @param factory The scanner that will supply tokens to the parser.
    */
 
   public CeParser(BaseTypeFactory factory) {

opendap/server/src/main/java/opendap/servlet/DummySink.java

@@ -62,7 +62,7 @@ public class DummySink extends DeflaterOutputStream {
    *
    * @param out the output stream
    * @param def the compressor ("deflater")
-   * @throws IllegalArgumentException if size is <= 0
+   * @throws IllegalArgumentException if size is {@code <= 0}
    */
   public DummySink(OutputStream out, Deflater def, int size) {
     super(out);

tdcommon/src/main/java/thredds/server/catalog/DataRoot.java

@@ -15,7 +15,7 @@
 
 /**
  * A DataRoot matches URLs to the objects that can serve them.
- * A DataRootPathMatcher manages a hash tree of path -> DataRoot
+ * A DataRootPathMatcher manages a hash tree of path {@literal ->} DataRoot
  * <p/>
  * Possible design:
  * catKey : which catalog defined this? not present at the moment

tdcommon/src/main/java/thredds/util/ThreddsConfigReader.java

@@ -21,7 +21,7 @@
 
 /**
  * read threddsConfig.xml, make elements available
- * used by Tds & Tdm
+ * used by Tds and Tdm
  *
  * @author caron
  * @since 5/15/13

tds-platform/build.gradle

@@ -33,6 +33,7 @@ dependencies {
     api 'edu.ucar:cdm-misc'
     api 'edu.ucar:cdm-image'
     api 'edu.ucar:cdm-s3'
+    api 'edu.ucar:cdm-zarr'
     api 'edu.ucar:netcdf4'
     api 'edu.ucar:cdm-mcidas'
     api 'edu.ucar:waterml'
@@ -88,6 +89,7 @@ dependencies {
     api "org.hibernate.validator:hibernate-validator:${depVersion.hibernateValidator}"
     api "org.hibernate.validator:hibernate-validator-annotation-processor:${depVersion.hibernateValidator}"
     api 'jakarta.el:jakarta.el-api'
+    api'org.apache.commons:commons-lang3:3.4'
     runtime 'org.glassfish:javax.el:3.0.0'
     runtime "jaxen:jaxen:${depVersion.jaxen}"
 

tds-test-utils/src/main/java/thredds/test/util/TdsUnitTestCommon.java

@@ -384,7 +384,7 @@ public static String canonicalpath(String path) {
   /**
    * return true if this path appears to start with a windows drive letter
    *
-   * @param path
+   * @param path to check
    * @return true, if path has drive letter
    */
 

tds-testing-platform/build.gradle

@@ -35,7 +35,6 @@ dependencies {
     api 'org.hamcrest:hamcrest-core:2.2'
 
     // only needed for it subproject
-    api 'org.apache.commons:commons-lang3:3.4' // replace?
     api 'org.xmlunit:xmlunit-core:2.7.0'  // For comparing catalog XML.
 
   }

tds-ugrid/src/main/java/ucar/nc2/dt/UGridDatatype.java

@@ -255,12 +255,12 @@ public interface UGridDatatype extends ucar.nc2.dt.GridDatatype {
    * This reads an arbitrary data slice, returning the data in
    * canonical order (rt-e-t-z-y-x). If any dimension does not exist, ignore it.
    *
-   * @param rt_index if < 0, get all of runtime dim; if valid index, fix slice to that value.
-   * @param e_index if < 0, get all of ensemble dim; if valid index, fix slice to that value.
-   * @param t_index if < 0, get all of time dim; if valid index, fix slice to that value.
-   * @param z_index if < 0, get all of z dim; if valid index, fix slice to that value.
-   * @param y_index if < 0, get all of y dim; if valid index, fix slice to that value.
-   * @param x_index if < 0, get all of x dim; if valid index, fix slice to that value.
+   * @param rt_index if {@code < 0}, get all of runtime dim; if valid index, fix slice to that value.
+   * @param e_index if {@code < 0}, get all of ensemble dim; if valid index, fix slice to that value.
+   * @param t_index if {@code < 0}, get all of time dim; if valid index, fix slice to that value.
+   * @param z_index if {@code < 0}, get all of z dim; if valid index, fix slice to that value.
+   * @param y_index if {@code < 0}, get all of y dim; if valid index, fix slice to that value.
+   * @param x_index if {@code < 0}, get all of x dim; if valid index, fix slice to that value.
    * @return data[rt,e,t,z,y,x], eliminating missing or fixed dimension.
    * @throws java.io.IOException on io error
    */
@@ -272,10 +272,10 @@ public Array readDataSlice(int rt_index, int e_index, int t_index, int z_index,
    * canonical order (t-z-y-x). If any dimension does not exist, ignore it.
    * For backwards compatibility for grids with no runtime or ensemble dimensions.
    *
-   * @param t_index if < 0, get all of time dim; if valid index, fix slice to that value.
-   * @param z_index if < 0, get all of z dim; if valid index, fix slice to that value.
-   * @param y_index if < 0, get all of y dim; if valid index, fix slice to that value.
-   * @param x_index if < 0, get all of x dim; if valid index, fix slice to that value.
+   * @param t_index if {@code < 0}, get all of time dim; if valid index, fix slice to that value.
+   * @param z_index if {@code < 0}, get all of z dim; if valid index, fix slice to that value.
+   * @param y_index if {@code < 0}, get all of y dim; if valid index, fix slice to that value.
+   * @param x_index if {@code < 0}, get all of x dim; if valid index, fix slice to that value.
    * @return data[rt,e,t,z,y,x], eliminating missing or fixed dimension.
    * @throws java.io.IOException on io error
    */

tds-ugrid/src/main/java/ucar/nc2/dt/ugrid/geom/LatLonPoint2D.java

@@ -420,7 +420,7 @@ public Double(double lat, double lon) {
      *        latitude
      * @param lon
      *        longitude.
-     * @param isRadians
+     * @param isRadian true if in radians, false if in degrees
      *        true of values are radians.
      */
     public Double(double lat, double lon, boolean isRadian) {

tds-ugrid/src/main/java/ucar/nc2/dt/ugrid/geom/LatLonRectangle2D.java

@@ -344,7 +344,6 @@ public void extend(LatLonPoint2D point) {
    * arrangement of LLy, LLx,
    * URy, URx.
    * 
-   * @param rect
    * @param bounds
    */
   public void extend(double[] bounds) {

tds-ugrid/src/main/java/ucar/nc2/dt/ugrid/geom/Point3D.java

@@ -258,8 +258,9 @@ public String toString() {
    * instantiation and provide a number of formats for storing the information necessary to satisfy the various accessor
    * methods below.
    * 
-   * @see java.awt.geom.Point3D.Float
-   * @see java.awt.geom.Point3D.Double
+   * see java.awt.geom.Point3D.Float
+   * see java.awt.geom.Point3D.Double
+   * 
    * @see java.awt.Point
    */
   protected Point3D() {}

tds-ugrid/src/main/java/ucar/nc2/dt/ugrid/geom/Polygon2D.java

@@ -1145,9 +1145,8 @@ public Float(float x, float y) {
     }
 
     /**
-     * Create a new polygon with the provided x & y locations. If the two arrays are of unequal length, an empty polygon
-     * is created. NaN
-     * values are ignored
+     * Create a new polygon with the provided x and y locations. If the two arrays are of unequal length, an empty
+     * polygon is created. NaN values are ignored
      * 
      * @param xlocs
      *        the array of x locations.
@@ -1504,9 +1503,8 @@ public Double(double x, double y) {
     }
 
     /**
-     * Create a new polygon with the provided x & y locations. If the two arrays are of unequal length, an empty polygon
-     * is created. NaN
-     * values are ignored
+     * Create a new polygon with the provided x and y locations. If the two arrays are of unequal length, an empty
+     * polygon is created. NaN values are ignored
      * 
      * @param xlocs
      *        the array of x locations.

tds-ugrid/src/main/java/ucar/nc2/dt/ugrid/geom/Vector3D.java

@@ -34,7 +34,7 @@ public Vector3D() {
   }
 
   /**
-   * Creates a new instance of Vector3D with an origin of (0, 0, 0) and the specified u, v & w magnitudes.
+   * Creates a new instance of Vector3D with an origin of (0, 0, 0) and the specified u, v, and w magnitudes.
    * 
    * @param u
    *        The <CODE>double</CODE> u-component of the vector.
@@ -50,7 +50,7 @@ public Vector3D(double u, double v, double w) {
   }
 
   /**
-   * Creates a new instance of Vector3D with the specified origin and u, v & w magnitudes.
+   * Creates a new instance of Vector3D with the specified origin and u, v, and w magnitudes.
    * 
    * @param origin
    *        the <code>Point3D</code> origin of the vector.
@@ -209,28 +209,28 @@ public static Vector3D sub(Vector3D v1, Vector3D v2) {
   }
 
   /**
-   * Multiplies the numerical value of each component of the first vector with the values in the second vector.
+   * Multiplies the numerical value of each component of the vector by a given scalar.
    * 
-   * @param v1
-   *        the first <code>Vector3D</code>
-   * @param v2
-   *        the second <code>Vector3D</code>
+   * @param v
+   *        the <code>Vector3D</code>
+   * @param d
+   *        the value to multiply the vector by
    * 
-   * @return a <code>Vector3D</code> representing the product of the two vectors
+   * @return a <code>Vector3D</code> representing the rescaled vector
    */
   public static Vector3D mult(Vector3D v, double d) {
     return (new Vector3D(v.getU() * d, v.getV() * d, v.getW() * d));
   }
 
   /**
-   * Divides the numerical value of each component of the first vector by the values in the second vector.
+   * Divides the numerical value of each component of the vector by a given scalar.
    * 
-   * @param v1
-   *        the first <code>Vector3D</code>
-   * @param v2
-   *        the second <code>Vector3D</code>
+   * @param v
+   *        the <code>Vector3D</code>
+   * @param d
+   *        the value to divide the vector by
    * 
-   * @return a <code>Vector3D</code> representing the quotient of the two vectors
+   * @return a <code>Vector3D</code> representing the rescaled vector
    */
   public static Vector3D div(Vector3D v, double d) {
     return (new Vector3D(v.getU() / d, v.getV() / d, v.getW() / d));

tds-ugrid/src/main/java/ucar/nc2/dt/ugrid/rtree/IntProcedureEntriesList.java

@@ -21,7 +21,7 @@
  * <br />
  * Simply pass an instance of this class to an rtree search and access the retrieved nodes' indices with
  * {@link #get(int)} and
- * {@link #getValues())}. These indices are returned as <code>Integer</code> objects.
+ * {@link #getValues()}. These indices are returned as <code>Integer</code> objects.
  * 
  * 
  * @author TPL <[email protected]>
@@ -76,7 +76,7 @@ public void clear() {
    * @return the <code>int</code> value of the entry at the given index
    * 
    * @throws IndexOutOfBoundsException
-   *         if index is out of range (index < 0 || index >= size())
+   *         if index is out of range ({@code index < 0 || index >= size()})
    */
   public int get(int index) throws IndexOutOfBoundsException {
     return entryList.get(index);

tds-ugrid/src/main/java/ucar/nc2/dt/ugrid/rtree/IntProcedureEntriesStack.java

@@ -135,13 +135,13 @@ public Integer peek() {
   /**
    * Retrieves the value of the top-most item on this stack
    * 
-   * @param indices
-   *        an integer indices
+   * @param index
+   *        an integer index
    * 
    * @return an <code>Integer</code> value
    * 
    * @throws IndexOutOfBoundsException
-   *         if the indices is out of range (indices < 0 || indices >= size())
+   *         if the indices is out of range ({@code indices < 0 || indices >= size()})
    */
   public Integer peek(int index) throws IndexOutOfBoundsException {
     return this.indices.get(index);

tds-ugrid/src/main/java/ucar/nc2/dt/ugrid/rtree/Node.java

@@ -183,7 +183,7 @@ void recalculateMBR(LatLonPolygon2D deletedRectangle) {
 
 
   /**
-   * Adds the the given <code>poly</code> to <code>mbr</code> as if mbr were a rectangle. Neither objects are modified.
+   * Adds the given <code>poly</code> to <code>mbr</code> as if mbr were a rectangle. Neither objects are modified.
    *
    * @param mbr
    *        the minimum bounding rectangle
@@ -201,12 +201,12 @@ public static LatLonRectangle2D expandMBR(final LatLonRectangle2D mbr, final Lat
 
 
   /**
-   * Adds the the given <code>rect</code> to <code>mbr</code> as if mbr were a rectangle. Neither objects are modified.
+   * Adds the given <code>rect</code> to <code>mbr</code> as if mbr were a rectangle. Neither objects are modified.
    *
    * @param mbr
    *        the minimum bounding rectangle
-   * @param poly
-   *        a polygon to be fit inside the mbr
+   * @param rect
+   *        a rectangle to be fit inside the mbr
    *
    * @return the bounding rectangle of the union between mbr and poly as polgon2d object
    */
@@ -218,12 +218,12 @@ public static LatLonRectangle2D expandMBR(final LatLonRectangle2D mbr, final Lat
 
 
   /**
-   * Adds the the given <code>rect</code> to <code>mbr</code> as if mbr were a rectangle. Neither objects are modified.
+   * Adds the given <code>rect</code> to <code>mbr</code> as if mbr were a rectangle. Neither objects are modified.
    *
    * @param mbr
    *        the minimum bounding rectangle
-   * @param poly
-   *        a polygon to be fit inside the mbr
+   * @param latLons
+   *        lat/lon array with a length of 4 which contains lat/lon coords in the arrangement of LLy, LLx, URy, URx.
    *
    * @return the bounding rectangle of the union between mbr and poly as polgon2d object
    */