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authorAllen Byrne <byrn@hdfgroup.org>2017-12-28 22:49:50 (GMT)
committerAllen Byrne <byrn@hdfgroup.org>2017-12-28 22:49:50 (GMT)
commitbd34c9e455988ab1d4e550ff16c0410b5624298a (patch)
treeb1514f2f775cf1329791dbb2a9e008256fb054d9 /java/src/hdf
parent732074d47e02c2e01fe794351c681d64b93a5f47 (diff)
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HDFFV-9724 Corrected files and verified tests
Diffstat (limited to 'java/src/hdf')
-rw-r--r--java/src/hdf/hdf5lib/H5.java197
-rw-r--r--java/src/hdf/hdf5lib/HDF5Constants.java3
-rw-r--r--java/src/hdf/overview.html6
3 files changed, 186 insertions, 20 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 7b5b5c9..78ebbe2 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -4451,7 +4451,7 @@ 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
@@ -4767,7 +4767,7 @@ 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.
@@ -5071,7 +5071,7 @@ 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.
@@ -5480,7 +5480,7 @@ 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.
@@ -5860,6 +5860,37 @@ 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 //
/**
@@ -6066,6 +6097,36 @@ 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.
*
@@ -6285,7 +6346,37 @@ 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
@@ -6388,12 +6479,76 @@ 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
@@ -6544,7 +6699,7 @@ 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
@@ -6579,7 +6734,7 @@ 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.
@@ -6736,14 +6891,14 @@ 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
@@ -6896,7 +7051,7 @@ 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.
@@ -6927,7 +7082,7 @@ 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.
@@ -6955,7 +7110,7 @@ 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;
@@ -7102,20 +7257,28 @@ 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..3e43ba2 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();
@@ -768,6 +769,8 @@ 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();
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>