Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into merge_func_enter_vol

Plus initial steps toward merging API context push into FUNC_ENTER_API* macros

5 files changed, 210 insertions, 26 deletions

diff --git a/java/src/hdf/CMakeLists.txt b/java/src/hdf/CMakeLists.txt
index 84bda53..ecff984 100644
--- a/java/src/hdf/CMakeLists.txt
+++ b/java/src/hdf/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.2.2)
+cmake_minimum_required (VERSION 3.10)
 PROJECT (HDF5_JAVA_HDF)
 
-add_subdirectory (${HDF5_JAVA_HDF_SOURCE_DIR}/hdf5lib     hdf5lib)
+add_subdirectory (hdf5lib)
diff --git a/java/src/hdf/hdf5lib/CMakeLists.txt b/java/src/hdf/hdf5lib/CMakeLists.txt
index c856c04..9506fc1 100644
--- a/java/src/hdf/hdf5lib/CMakeLists.txt
+++ b/java/src/hdf/hdf5lib/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.2.2)
+cmake_minimum_required (VERSION 3.10)
 PROJECT (HDF5_JAVA_HDF_HDF5 Java)
 
 set (CMAKE_VERBOSE_MAKEFILE 1)
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 3d87c28..58a5703 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -214,7 +214,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * exception handlers to print out the HDF-5 error stack.
  * <hr>
  *
- * @version HDF5 1.11.0 <BR>
+ * @version HDF5 1.11.2 <BR>
  *          <b>See also: <a href ="./hdf.hdf5lib.HDFArray.html"> hdf.hdf5lib.HDFArray</a> </b><BR>
  *          <a href ="./hdf.hdf5lib.HDF5Constants.html"> hdf.hdf5lib.HDF5Constants</a><BR>
  *          <a href ="./hdf.hdf5lib.HDF5CDataTypes.html"> hdf.hdf5lib.HDF5CDataTypes</a><BR>
@@ -237,7 +237,7 @@ public class H5 implements java.io.Serializable {
      *
      * Make sure to update the versions number when a different library is used.
      */
-    public final static int LIB_VERSION[] = { 1, 11, 0 };
+    public final static int LIB_VERSION[] = { 1, 11, 2 };
 
     public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib";
 
@@ -424,7 +424,7 @@ public class H5 implements java.io.Serializable {
     private synchronized static native int H5dont_atexit() throws HDF5LibraryException;
 
     /**
-     * Turn off error handling By default, the C library prints the error stack of the HDF-5 C library on stdout. This
+     * Turn off error handling. By default, the C library prints the error stack of the HDF-5 C library on stdout. This
      * behavior may be disabled by calling H5error_off().
      *
      * @return a non-negative value if successful
@@ -432,6 +432,12 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5error_off();
 
     /**
+     * Turn on error handling. By default, the C library prints the error stack of the HDF-5 C library on stdout. This
+     * behavior may be reenabled by calling H5error_on().
+     */
+    public synchronized static native void H5error_on();
+
+    /**
      * H5garbage_collect collects on all free-lists of all types.
      *
      * @return a non-negative value if successful
@@ -4435,7 +4441,7 @@ public class H5 implements java.io.Serializable {
     // //
     // ////////////////////////////////////////////////////////////
 
-    // Generic property list routines
+    // /////// Generic property list routines ///////
 
     /**
      * H5Pget_class_name retrieves the name of a generic property list class
@@ -4751,7 +4757,7 @@ public class H5 implements java.io.Serializable {
 
     public synchronized static native int H5Piterate(long plist, int[] idx, H5P_iterate_cb op, H5P_iterate_t op_data) throws HDF5LibraryException;
 
-    // Object creation property list (OCPL) routines
+    // /////// Object creation property list (OCPL) routines ///////
 
     /**
      * H5Pget_attr_phase_change retrieves attribute storage phase change thresholds.
@@ -5055,7 +5061,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_fletcher32(long plist) throws HDF5LibraryException,
     NullPointerException;
 
-    // File creation property list (FCPL) routines
+    // /////// File creation property list (FCPL) routines ///////
 
     /**
      * H5Pget_userblock retrieves the size of a user block in a file creation property list.
@@ -5464,7 +5470,7 @@ public class H5 implements java.io.Serializable {
            throws HDF5LibraryException, IllegalArgumentException;
 
 
-    // File access property list (FAPL) routines
+    // /////// File access property list (FAPL) routines ///////
 
     /**
      * H5Pget_alignment retrieves the current settings for alignment properties from a file access property list.
@@ -5844,6 +5850,37 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_metadata_read_attempts(long plist_id, long attempts)
             throws HDF5LibraryException;
 
+    /**
+     * H5Pget_evict_on_close retrieves the file access property list setting that determines whether an HDF5 object
+     * will be evicted from the library's metadata cache when it is closed.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return indication if the object will be evicted on close.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native boolean H5Pget_evict_on_close(long fapl_id)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pset_evict_on_close controls the library's behavior of evicting metadata associated with a closed object.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param evict_on_close
+     *            IN: Whether the HDF5 object should be evicted on close.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close)
+            throws HDF5LibraryException;
+
     // Dataset creation property list (DCPL) routines //
 
     /**
@@ -6050,6 +6087,36 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException;
 
+//    /////  unimplemented /////
+//    /**
+//     * H5Pget_vds_file_cache_size retrieves the size of the vds link open file cache.
+//     *
+//     * @param fapl_id
+//     *            IN: File access property list identifier
+//     *
+//     * @return VDS link open file cache size in number of files.
+//     *
+//     * @exception HDF5LibraryException
+//     *                - Error from the HDF-5 Library.
+//     *
+//     **/
+//    public synchronized static native int H5Pget_vds_file_cache_size(long fapl_id) throws HDF5LibraryException;
+//
+//    /**
+//     * H5Pset_vds_file_cache_size sets the number of files that can be held open in an vds link open file cache.
+//     *
+//     * @param fapl_id
+//     *            IN: File access property list identifier
+//     * @param efc_size
+//     *            IN: VDS link open file cache size in number of files.
+//     *
+//     * @exception HDF5LibraryException
+//     *                - Error from the HDF-5 Library.
+//     *
+//     **/
+//    public synchronized static native void H5Pset_vds_file_cache_size(long fapl_id, int efc_size)
+//            throws HDF5LibraryException;
+
     /**
      * H5Pget_external returns information about an external file.
      *
@@ -6269,7 +6336,37 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException,
     NullPointerException;
 
-    // Dataset access property list (DAPL) routines //
+    // /////// Dataset creation property list (DCPL) routines ///////
+
+    /**
+     * H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list.
+     *
+     * @param dcpl_id
+     *            IN: Dataset creation property list identifier
+     * @param opts
+     *            IN: Edge chunk option flag. Valid values are:
+     *                H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS - filters are not applied to partial edge chunks.
+     *                0 - Disables option; partial edge chunks will be compressed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library
+     **/
+    public synchronized static native void H5Pset_chunk_opts(long dcpl_id, int opts) throws HDF5LibraryException;
+
+    /**
+     * H5Pget_chunk_opts retrieves the edge chunk option setting stored in the dataset creation property list .
+     *
+     * @param dcpl_id
+     *            IN: Dataset creation property list
+
+     * @return The edge chunk option setting.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library
+     **/
+    public synchronized static native int H5Pget_chunk_opts(long dcpl_id) throws HDF5LibraryException;
+
+    // /////// Dataset access property list (DAPL) routines ///////
 
     /**
      * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible number of bytes
@@ -6372,12 +6469,76 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native long H5Pget_virtual_printf_gap(long dapl_id) throws HDF5LibraryException;
 
+    /**
+     * H5Pget_virtual_prefix Retrieves prefix applied to virtual file paths.
+     *
+     * @param dapl_id
+     *            IN: Link access property list identifier
+     *
+     * @return the prefix to be applied to virtual file paths.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native String H5Pget_virtual_prefix(long dapl_id)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pset_virtual_prefix Sets prefix to be applied to virtual file paths.
+     *
+     * @param dapl_id
+     *            IN: Dataset access property list identifier
+     * @param prefix
+     *            IN: Prefix to be applied to virtual file paths
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - prefix is null.
+     *
+     **/
+    public synchronized static native void H5Pset_virtual_prefix(long dapl_id, String prefix)
+            throws HDF5LibraryException, NullPointerException;
+
+    /**
+     * H5Pget_efile_prefix Retrieves prefix applied to external file paths.
+     *
+     * @param dapl_id
+     *            IN: Link access property list identifier
+     *
+     * @return the prefix to be applied to external file paths.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native String H5Pget_efile_prefix(long dapl_id)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pset_efile_prefix Sets prefix to be applied to external file paths.
+     *
+     * @param dapl_id
+     *            IN: Dataset access property list identifier
+     * @param prefix
+     *            IN: Prefix to be applied to external file paths
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - prefix is null.
+     *
+     **/
+    public synchronized static native void H5Pset_efile_prefix(long dapl_id, String prefix)
+            throws HDF5LibraryException, NullPointerException;
+
     // public synchronized static native void H5Pset_append_flush(long plist_id, int ndims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException;
 
     // public synchronized static native void H5Pget_append_flush(long plist_id, int dims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException;
 
 
-    // Dataset xfer property list (DXPL) routines //
+    // /////// Dataset xfer property list (DXPL) routines ///////
 
     /**
      * H5Pget_data_transform retrieves the data transform expression previously set in the dataset transfer property
@@ -6528,7 +6689,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_hyper_vector_size(long dxpl_id, long vector_size)
             throws HDF5LibraryException, NullPointerException;
 
-    // Link creation property list (LCPL) routines //
+    // /////// Link creation property list (LCPL) routines ///////
 
     /**
      * H5Pget_create_intermediate_group determines whether property is set to enable creating missing intermediate
@@ -6563,7 +6724,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_create_intermediate_group(long lcpl_id, boolean crt_intermed_group)
             throws HDF5LibraryException;
 
-    // Group creation property list (GCPL) routines //
+    // /////// Group creation property list (GCPL) routines ///////
 
     /**
      * H5Pget_local_heap_size_hint Retrieves the anticipated size of the local heap for original-style groups.
@@ -6720,14 +6881,14 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_link_creation_order(long gcpl_id, int crt_order_flags)
             throws HDF5LibraryException;
 
-    // String creation property list (STRCPL) routines //
+    // /////// String creation property list (STRCPL) routines ///////
 
     public synchronized static native int H5Pget_char_encoding(long plist_id) throws HDF5LibraryException;
 
     public synchronized static native void H5Pset_char_encoding(long plist_id, int encoding)
             throws HDF5LibraryException;
 
-    // Link access property list (LAPL) routines //
+    // /////// Link access property list (LAPL) routines ///////
 
     /**
      * H5Pget_nlinks retrieves the maximum number of soft or user-defined link traversals allowed, nlinks, before the
@@ -6880,7 +7041,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pset_elink_acc_flags(long lapl_id, int flags) throws HDF5LibraryException,
     IllegalArgumentException;
 
-    // Object copy property list (OCPYPL) routines //
+    // /////// Object copy property list (OCPYPL) routines ///////
 
     /**
      * H5Pget_copy_object retrieves the properties to be used when an object is copied.
@@ -6911,7 +7072,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_copy_object(long ocp_plist_id, int copy_options)
             throws HDF5LibraryException;
 
-    // Other/Older property list routines //
+    // /////// Other/Older property list routines ///////
 
     /**
      * H5Pget_version retrieves the version information of various objects for a file creation property list.
@@ -6939,7 +7100,7 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Pget_version(long plist, int[] version_info) throws HDF5LibraryException,
     NullPointerException, IllegalArgumentException;
 
-    // file drivers property list routines //
+    // /////// file drivers property list routines ///////
 
     public synchronized static native void H5Pget_fapl_core(long fapl_id, long[] increment, boolean[] backing_store)
             throws HDF5LibraryException, NullPointerException;
@@ -7086,20 +7247,28 @@ public class H5 implements java.io.Serializable {
     // File creation property list (FCPL) routines //
 
     // File access property list (FAPL) routines //
-    // herr_t H5Pset_driver( hid_t plist_id, hid_t new_driver_id, const void *new_driver_info )
-    // const void *H5Pget_driver_info( hid_t plist_id )
-    // herr_t H5Pget_multi_type ( hid_t fapl_id, H5FD_mem_t *type )
-    // herr_t H5Pset_multi_type ( hid_t fapl_id, H5FD_mem_t type )
+    // herr_t H5Pset_driver(hid_t plist_id, hid_t new_driver_id, const void *new_driver_info)
+    // const void *H5Pget_driver_info(hid_t plist_id)
+    // herr_t H5Pget_multi_type(hid_t fapl_id, H5FD_mem_t *type)
+    // herr_t H5Pset_multi_type(hid_t fapl_id, H5FD_mem_t type)
     // herr_t H5Pget_file_image(hid_t fapl_id, void **buf_ptr_ptr, size_t *buf_len_ptr);
     // herr_t H5Pset_file_image(hid_t fapl_id, void *buf_ptr, size_t buf_len);
     // herr_t H5Pget_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callbacks_ptr);
     // herr_t H5Pset_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callbacks_ptr);
     // herr_t H5Pset_core_write_tracking(hid_t fapl_id, hbool_t is_enabled, size_t page_size);
     // herr_t H5Pget_core_write_tracking(hid_t fapl_id, hbool_t *is_enabled, size_t *page_size);
+    // herr_t H5Pset_all_coll_metadata_ops(hid_t accpl_id, hbool_t is_collective);
+    // herr_t H5Pset_coll_metadata_write(hid_t fapl_id, hbool_t is_collective);
+    // herr_t H5Pget_coll_metadata_write(hid_t fapl_id, hbool_t *is_collective);
+    // herr_t H5Pget_page_buffer_size(hid_t fapl_id, size_t *buf_size, unsigned *min_meta_perc, unsigned *min_raw_perc);
+    // herr_t H5Pset_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t func, void *user_data);
+    // herr_t H5Pget_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t *func, void **user_data);
 
     // Dataset creation property list (DCPL) routines //
 
     // Dataset access property list (DAPL) routines //
+    // herr_t H5Pset_append_flush (hid_t dapl_id, int ndims, const hsize_t boundary[], H5D_append_cb_t func, void *user_data);
+    // herr_t H5Pget_append_flush(hid_t dapl_id, int ndims, hsize_t boundary[], H5D_append_cb_t *func, void **user_data)
 
     // Dataset xfer property list (DXPL) routines //
     // herr_t H5Pset_buffer(hid_t plist_id, size_t size, void *tconv, void *bkg);
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 8a3d6c8..eb4055d 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -88,6 +88,7 @@ public class HDF5Constants {
     public static final int H5D_VDS_ERROR = H5D_VDS_ERROR();
     public static final int H5D_VDS_FIRST_MISSING = H5D_VDS_FIRST_MISSING();
     public static final int H5D_VDS_LAST_AVAILABLE = H5D_VDS_LAST_AVAILABLE();
+    public static final int H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS = H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS();
 
     public static final int H5E_MAJOR = H5E_MAJOR();
     public static final int H5E_MINOR = H5E_MINOR();
@@ -205,7 +206,11 @@ public class HDF5Constants {
     public static final int H5F_CLOSE_SEMI = H5F_CLOSE_SEMI();
     public static final int H5F_CLOSE_STRONG = H5F_CLOSE_STRONG();
     public static final int H5F_CLOSE_WEAK = H5F_CLOSE_WEAK();
+    public static final int H5F_LIBVER_ERROR = H5F_LIBVER_ERROR();
     public static final int H5F_LIBVER_EARLIEST = H5F_LIBVER_EARLIEST();
+    public static final int H5F_LIBVER_V18 = H5F_LIBVER_V18();
+    public static final int H5F_LIBVER_V110 = H5F_LIBVER_V110();
+    public static final int H5F_LIBVER_NBOUNDS = H5F_LIBVER_NBOUNDS();
     public static final int H5F_LIBVER_LATEST = H5F_LIBVER_LATEST();
     public static final int H5F_OBJ_ALL = H5F_OBJ_ALL();
     public static final int H5F_OBJ_ATTR = H5F_OBJ_ATTR();
@@ -768,6 +773,8 @@ public class HDF5Constants {
 
     private static native final int H5D_VDS_LAST_AVAILABLE();
 
+    private static native final int H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS();
+
     private static native final long H5E_ALIGNMENT();
 
     private static native final long H5E_ALREADYEXISTS();
@@ -996,8 +1003,16 @@ public class HDF5Constants {
 
     private static native final int H5F_CLOSE_WEAK();
 
+    private static native final int H5F_LIBVER_ERROR();
+
     private static native final int H5F_LIBVER_EARLIEST();
 
+    private static native final int H5F_LIBVER_V18();
+
+    private static native final int H5F_LIBVER_V110();
+
+    private static native final int H5F_LIBVER_NBOUNDS();
+
     private static native final int H5F_LIBVER_LATEST();
 
     private static native final int H5F_OBJ_ALL();
diff --git a/java/src/hdf/overview.html b/java/src/hdf/overview.html
index 39d75b7..9c19442 100644
--- a/java/src/hdf/overview.html
+++ b/java/src/hdf/overview.html
@@ -47,20 +47,20 @@ which has a method:
 The native method is implemented in C using the
 <a href="http://java.sun.com/javase/6/docs/technotes/guides/jni/index.html">Java
 Native Method Interface </a>(JNI). This is written something like the following:
-<pre><b>JNIEXPORT jint
+<pre><b>JNIEXPORT jlong
 JNICALL Java_hdf_hdf5lib_H5_H5Fopen
 (
 &nbsp;JNIEnv *env,
 &nbsp;jclass class,
 &nbsp;jstring hdfFile,
 &nbsp;jint flags,
-&nbsp;jint access)
+&nbsp;jlong access)
 &nbsp;{
 
 &nbsp;/* ...convert Java String to (char *) */
 
 &nbsp;/* call the HDF library */
-&nbsp;retVal = H5Fopen((char *)file, (unsigned)flags, (hid_t)access );
+&nbsp;retVal = H5Fopen((char *)file, (unsigned)flags, (hid_t)access);
 
 &nbsp;/* ... */
 }</b></pre>