Merge branch 'maint-5.x' into fix_gradle_dependency_keywords_in_docs

Author: haileyajohnson

docs/src/site/_data/sidebars/netcdfJavaTutorial_sidebar.yml

@@ -267,6 +267,10 @@ entries:
       url: /read_over_http.html
       output: web, pdf
 
+    - title: Reading Zarr
+      url: /reading_zarr.html
+      output: web, pdf
+
     - title: Standard Horizontal Coordinate Transforms
       url: /std_horizonal_coord_transforms.html
       output: web, pdf

docs/src/site/pages/netcdfJava/ReadingZarr.md

@@ -0,0 +1,100 @@
+---
+title: Reading the Zarr data model
+last_updated: 2021-12-22
+sidebar: netcdfJavaTutorial_sidebar
+toc: false
+permalink: reading_zarr.html
+---
+## Zarr
+
+As of version 5.5.1, the netCDF-Java library provides read-only support for the [Zarr v2 data model](https://zarr.readthedocs.io/en/stable/spec/v2.html#){:target="_blank"}. 
+Any dataset that adheres to the v2 spec can be read into a `NetcdfFile` object, as long as the following is true:
+
+* all filters and compressors used by the dataset must be known to the netCDF-Java library (see [Filters](reading_zarr.html#filters))
+* the underlying storage of the dataset must be a directory store, zip store, or object store
+
+### Enabling Zarr support
+
+To use Zarr in the netCDF-Java library, you must include the `cdm-zarr` module in your netCDF-Java build. 
+See [here](using_netcdf_java_artifacts.html) for more information on including optional modules.
+
+### How to read a Zarr dataset
+
+Reading a Zarr dataset is syntactically the same as reading a netCDF file:
+
+{% capture rmd %}
+{% includecodeblock netcdf-java&docs/src/test/java/examples/ZarrExamples.java&readZarrStores %}
+{% endcapture %}
+{{ rmd | markdownify }}
+
+If the file is a legal Zarr dataset, the library will map it to a `NetcdfFile` object for reading.
+See [reading CDM files](reading_cdm.html) for more examples on accessing data once the `NetcdfFile` object is returned.
+
+## Filters
+
+As of netCDF-Java version 5.5.1, a `ucar.nc2.filter` package is included, that provides a suite of implemented filters and compressors,
+as well as a mechanism for user-supplied filters. This package is used by both the Zarr and HDF5 IOSPs, and is available for public use.
+
+The current list of filters included natively in the netCDF-Java library is:
+
+* Deflate (zlib)
+* Shuffle
+* 32-bit Checksum (CRC, Fletcher, and Adler)
+* ScaleOffset
+
+This list is still expanding, but if the filter you are looking for is not provided at this time, you are able to provide it yourself 
+(See [Implementing a Filter](#implementing-a-filter)) for details.)
+
+### Implementing a Filter
+
+To add a user-supplied `Filter` to the netDF-Java library, you will have to provide two classes:
+
+* A class that extends the `ucar.nc2.filter.Filter` abstract class
+* A class that implements the `ucar.nc2.filter.FilterProvider` interface
+
+Once implemented, you will need to include these classes as JAR files in your classpath. See [here](runtime_loading.html) for more information.
+
+#### `Filter` implementation
+
+To implement a user-supplied filter, you will need to extend the abstract `ucar.nc2.filter.Filter` class, and provide implementations for the following methods:
+* `encode` takes a `byte[]` of unfiltered data and returns a `byte[]` of filtered data
+* `decode` takes a `byte[]` of filtered data and returns a `byte[]` of unfiltered data
+
+Your `Filter` class should look something like this:
+
+{% capture rmd %}
+{% includecodeblock netcdf-java&docs/src/test/java/examples/ZarrExamples.java&implementFilter %}
+{% endcapture %}
+{{ rmd | markdownify }}
+
+#### `FilterProvider` implementation
+
+For the netCDF-Java library to find your `Filter` implementation, you will need to provide a `FilterProvider` as well. 
+
+{% capture rmd %}
+{% includecodeblock netcdf-java&docs/src/test/java/examples/ZarrExamples.java&implementFilterProvider %}
+{% endcapture %}
+{{ rmd | markdownify }}
+
+{%include note.html content="
+`getName` and `getId`   
+When reading data, [IOSPs](writing_iosp.html) can look up filters by either a `String` or `int` (name or id). Currently, the `ucar.nc2.filter` 
+package is shared by the Zarr and HDF5 IOSPs. The Zarr IOSP looks up filters by name; if you plan to use your third party filter with Zarr data,
+the string returned by `getName` should match that specified by the [NumCodecs](https://numcodecs.readthedocs.io/en/stable/) library. 
+The HDF5 IOSP looks up filters by id; if you plan to use your third party filter with HDF5 data, the int returned by `getId` should adhere to the 
+[guidelines](https://portal.hdfgroup.org/display/support/Registered+Filter+Plugins) set by the HDF group. 
+If your filter is registered with the HDF group, your `getId` method should return the HDF id. If your filter is not registered with the HDF group,
+" %}
+
+There are two more methods in the `FilterProvider` interface: the `canProvide` methods. By default, these methods work as follows:
+* `boolean canProvide(String name)` returns true if the string returned by `getName()` matches the string passed to the method
+* `boolean canProvide(int id)` returns true if the int returned by `getId()` matches the int passed to the method
+
+It is unlikely that you would want to override these methods, as the netCDF-Java [IOSPs](writing_iosp.html) look for the correct filter implementations 
+for a dataset by either name or numeric id. However, it is possible to write your own implementation of `canProvide`; for example, the 
+following `FilterProvider` returns an instance of a `DefaultFilter` regardless of the name or id provided.
+
+{% capture rmd %}
+{% includecodeblock netcdf-java&docs/src/test/java/examples/ZarrExamples.java&implementFilterProvider2 %}
+{% endcapture %}
+{{ rmd | markdownify }}

docs/src/site/pages/netcdfJava/Upgrade.md

@@ -37,6 +37,7 @@ Point release notes:
 
 5.5.x is the first release that includes read support for [Zarr](https://zarr.readthedocs.io/en/stable/index.html){:target="_blank"}. 
 There is also a new package for filters, `ucar.ma2.filters`, which allows user-provided compressors and filters to be supplied through a [Service Provider Interface](https://www.baeldung.com/java-spi){:target="_blank"}.
+Read about Zarr support and the `filter` package [here](reading_zarr.html)
 
 ## netCDF-Java API Changes (5.4.x)
 

docs/src/site/pages/netcdfJava/developer/FileTypes.md

@@ -50,4 +50,5 @@ To register your format/IOServiceProvider, or to send corrections and additions
 | UAMIV | CAMx UAM-IV formatted files | `cdm-radial` | <http://www.camx.com/> |
 | UniversalRadarFormat | Universal Radar Format | `cdm-radial` | <ftp://ftp.sigmet.com/outgoing/manuals/program/cuf.pdf> |
 | USPLN | US Precision Lightning Network | `cdm-misc` | <http://www.uspln.com/> |
-| VIS5D | Vis5D grid file | `cdm-vs5d` | <http://www.ssec.wisc.edu/~billh/vis5d.html>
+| VIS5D | Vis5D grid file | `cdm-vs5d` | <http://www.ssec.wisc.edu/~billh/vis5d.html>|
+| Zarr | Zarr dataset | `cdm-zarr` | <https://zarr.readthedocs.io/en/stable/> |

docs/src/site/pages/netcdfJava_tutorial/runtime/runtimeloading.md

@@ -88,6 +88,19 @@ See [GribTables](grib_tables.html)  for more information about lookup tables.
 
 The file must be a [BUFR table lookup file](bufr_tables.html).
 
+### Register a `Filter` implementation:
+Users-supplied filters must be provided using the [Service Provider](https://docs.oracle.com/javase/tutorial/ext/basics/spi.html){:target="_blank"}
+mechanism and included in a JAR on the classpath, where it is dynamically loaded at runtime. 
+In your JAR, include a file named `META-INF/services/ucar.nc2.filter.FilterProvider` containing the name(s) of your implementations, eg:
+
+~~~
+ucar.nc2.filter.BloscFilter
+ucar.nc2.filter.GZipFilter
+~~~
+
+Your `FilterProvider` classes must implement the `ucar.nc2.filter.FilterProvider` interface. 
+See [here](reading_zarr.html#implementing-a-filter) for details on implementing user-supplied filters.
+
 ## Runtime Configuration
 
 Instead of calling the above routines in your code, you can pass the CDM library an XML configuration file. 

docs/src/test/java/examples/ZarrExamples.java

@@ -0,0 +1,144 @@
+package examples;
+
+import ucar.ma2.Array;
+import ucar.ma2.InvalidRangeException;
+import ucar.ma2.Section;
+import ucar.nc2.Group;
+import ucar.nc2.NetcdfFile;
+import ucar.nc2.NetcdfFiles;
+import ucar.nc2.Variable;
+import ucar.nc2.filter.Filter;
+import ucar.nc2.filter.FilterProvider;
+import ucar.nc2.filter.Filters;
+import ucar.nc2.filter.Shuffle;
+import ucar.nc2.iosp.AbstractIOServiceProvider;
+import ucar.nc2.util.CancelTask;
+import ucar.unidata.io.RandomAccessFile;
+import ucar.unidata.util.test.TestDir;
+
+import java.io.IOException;
+import java.util.Map;
+
+public class ZarrExamples {
+
+  private static String pathToDirectoryStore = "";
+  private static String pathToZipStore = "";
+  private static String pathToObjectStore = "";
+
+  public static void readZarrStores() throws IOException {
+    // a local file path
+    NetcdfFile directoryStoreZarr = NetcdfFiles.open(pathToDirectoryStore);
+    // a local file path + '.zip'
+    NetcdfFile zipdirectoryStoreZarr = NetcdfFiles.open(pathToZipStore);
+    // an object store path, sarting with 'cdms3:' and ending with 'delimiter=' + the store delimiter
+    NetcdfFile objectStoreZarr = NetcdfFiles.open(pathToObjectStore);
+  }
+
+  public static void implementFilter() {
+    byte[] dataOut = null;
+    /* DOCS-IGNORE */
+    /* INSERT public */class MyFilter extends Filter {
+
+      @Override
+      public byte[] encode(byte[] dataIn) throws IOException {
+        // your encoding implementation here
+        return dataOut;
+      }
+
+      @Override
+      public byte[] decode(byte[] dataIn) throws IOException {
+        // your decoding implementation here
+        return dataOut;
+      }
+    }
+  }
+
+  public static void implementFilterProvider() {
+    /* INSERT public */class MyFilterProvider implements FilterProvider {
+
+      @Override
+      public String getName() {
+        // returns a string identifier for your filter
+        return "myFilter"; // see notes on filter names and ids
+      }
+
+      @Override
+      public int getId() {
+        // returns a numeric identifier for your filter
+        return 32768; // see notes on filter names and ids
+      }
+
+      @Override
+      public Filter create(Map<String, Object> properties) {
+        return new MyFilter(properties); // return an instance of your filter
+      }
+    }
+  }
+
+  public static void implementFilterProvider2() {
+    /* INSERT public */class DefaultFilterProvider implements FilterProvider {
+
+      @Override
+      public String getName() {
+        return "defaultFilter";
+      }
+
+      @Override
+      public int getId() {
+        return -1;
+      }
+
+      @Override
+      public boolean canProvide(String name) {
+        return true;
+      }
+
+      @Override
+      public boolean canProvide(int id) {
+        return true;
+      }
+
+      @Override
+      public Filter create(Map<String, Object> properties) {
+        return new DefaultFilter(properties); // return an instance of your filter
+      }
+    }
+  }
+
+  /**
+   * Shell classes for code snippets
+   */
+  static class MyFilter extends Filter {
+
+    public MyFilter(Map<String, Object> properties) {
+      super();
+    }
+
+    @Override
+    public byte[] encode(byte[] dataIn) throws IOException {
+      return new byte[0];
+    }
+
+    @Override
+    public byte[] decode(byte[] dataIn) throws IOException {
+      return new byte[0];
+    }
+  }
+
+  static class DefaultFilter extends Filter {
+
+    public DefaultFilter(Map<String, Object> properties) {
+      super();
+    }
+
+    @Override
+    public byte[] encode(byte[] dataIn) throws IOException {
+      return new byte[0];
+    }
+
+    @Override
+    public byte[] decode(byte[] dataIn) throws IOException {
+      return new byte[0];
+    }
+  }
+}

docs/src/test/java/examples/writingiosp/LightningExampleTutorial.java

@@ -59,7 +59,7 @@ public String getFileTypeDescription() {
         return "Data from lightning data test file";
       }
     }
-    return new UspLightning();
+    return new UspLightning(); /* DOCS-IGNORE */
   }
 
   /**

docs/src/test/java/tests/TestZarrExamples.java

@@ -0,0 +1,25 @@
+package tests;
+
+import examples.ZarrExamples;
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.io.FileNotFoundException;
+
+public class TestZarrExamples {
+
+  @Test
+  public void testReadZarrExample() {
+    Assert.assertThrows(FileNotFoundException.class, () -> {
+      ZarrExamples.readZarrStores();
+    });
+  }
+
+  @Test
+  public void testImplementFilterAndProvider() {
+    // just verify the example code compiles with no deprecations
+    ZarrExamples.implementFilter();
+    ZarrExamples.implementFilterProvider();
+    ZarrExamples.implementFilterProvider2();
+  }
+}