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Added java wrappers and tests

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This commit is contained in:
Allen Byrne 2017-12-12 13:10:46 -06:00
parent 95e96246a6
commit 690cb84f10
12 changed files with 1171 additions and 494 deletions
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196
java/src/hdf/hdf5lib/H5.java
View File

@ -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 +6097,35 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException;
/**
* 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 +6345,37 @@ 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 +6478,76 @@ 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 +6698,7 @@ 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 +6733,7 @@ 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 +6890,14 @@ 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 +7050,7 @@ 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 +7081,7 @@ 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 +7109,7 @@ 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 +7256,28 @@ 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);

3
java/src/hdf/hdf5lib/HDF5Constants.java
View File

@ -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();

6
java/src/hdf/overview.html
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@ -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>

2
java/src/jni/h5Constants.c
View File

@ -140,6 +140,8 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5D_1VDS_1FIRST_1MISSING(JNIEnv *env, jclass cls) { return H5D_VDS_FIRST_MISSING; }
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5D_1VDS_1LAST_1AVAILABLE(JNIEnv *env, jclass cls) { return H5D_VDS_LAST_AVAILABLE; }
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5D_1CHUNK_1DONT_1FILTER_1PARTIAL_1CHUNKS(JNIEnv *env, jclass cls) { return H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS; }
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5E_1ALIGNMENT(JNIEnv *env, jclass cls) { return H5E_ALIGNMENT; }

246
java/src/jni/h5pImp.c
View File

@ -5733,6 +5733,252 @@ Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts
} /* end else */
} /* end Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_vds_file_cache_size
* Signature: (JI)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1vds_1file_1cache_1size
(JNIEnv *env, jclass clss, jlong plist, jint size)
{
unsigned sz = (unsigned)size;
if (H5Pset_vds_file_cache_size((hid_t)plist, (unsigned)sz) < 0)
h5libraryError(env);
} /* end Java_hdf_hdf5lib_H5_H5Pset_1vds_1file_1cache_1size */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_vds_file_cache_size
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1vds_1file_1cache_1size
(JNIEnv *env, jclass clss, jlong plist)
{
unsigned s;
if (H5Pget_vds_file_cache_size((hid_t)plist, &s) < 0)
h5libraryError(env);
return (jint)s;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1vds_1file_1cache_1size */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_virtual_prefix
* Signature: (JLjava/lang/String;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1virtual_1prefix
(JNIEnv *env, jclass clss, jlong dapl_id, jstring prefix)
{
herr_t retVal = -1;
const char *aName;
PIN_JAVA_STRING(prefix, aName);
if (aName != NULL) {
retVal = H5Pset_virtual_prefix((hid_t)dapl_id, aName);
UNPIN_JAVA_STRING(prefix, aName);
if(retVal < 0)
h5libraryError(env);
}
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1virtual_1prefix */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_prefix
* Signature: (J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1prefix
(JNIEnv *env, jclass clss, jlong dapl_id)
{
size_t size = 0;
char *pre;
jlong prefix_size = -1;
jstring str = NULL;
prefix_size = (jlong)H5Pget_virtual_prefix((hid_t)dapl_id, (char*)NULL, size);
if(prefix_size < 0) {
h5libraryError(env);
} /* end if */
else {
size = (size_t)prefix_size + 1;/* add extra space for the null terminator */
pre = (char*)HDmalloc(sizeof(char)*size);
if (pre == NULL) {
h5outOfMemory(env, "H5Pget_virtual_prefix: malloc failed ");
} /* end if */
else {
prefix_size = (jlong)H5Pget_virtual_prefix((hid_t)dapl_id, (char*)pre, size);
if (prefix_size >= 0) {
str = ENVPTR->NewStringUTF(ENVPAR pre);
HDfree(pre);
if (str == NULL)
h5JNIFatalError( env, "H5Pget_virtual_prefix: return string not allocated");
} /* end if */
else {
HDfree(pre);
h5libraryError(env);
} /* end else */
} /* end else */
} /* end else */
return (jstring)str;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1virtual_1prefix */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_efile_prefix
* Signature: (JLjava/lang/String;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1efile_1prefix
(JNIEnv *env, jclass clss, jlong dapl_id, jstring prefix)
{
herr_t retVal = -1;
const char *aName;
PIN_JAVA_STRING(prefix, aName);
if (aName != NULL) {
retVal = H5Pset_efile_prefix((hid_t)dapl_id, aName);
UNPIN_JAVA_STRING(prefix, aName);
if(retVal < 0)
h5libraryError(env);
}
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Pset_1efile_1prefix */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_efile_prefix
* Signature: (J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1efile_1prefix
(JNIEnv *env, jclass clss, jlong dapl_id)
{
size_t size = 0;
char *pre;
jlong prefix_size = -1;
jstring str = NULL;
prefix_size = (jlong)H5Pget_efile_prefix((hid_t)dapl_id, (char*)NULL, size);
if(prefix_size < 0) {
h5libraryError(env);
} /* end if */
else {
size = (size_t)prefix_size + 1;/* add extra space for the null terminator */
pre = (char*)HDmalloc(sizeof(char)*size);
if (pre == NULL) {
h5outOfMemory(env, "H5Pget_efile_prefix: malloc failed ");
} /* end if */
else {
prefix_size = (jlong)H5Pget_efile_prefix((hid_t)dapl_id, (char*)pre, size);
if (prefix_size >= 0) {
str = ENVPTR->NewStringUTF(ENVPAR pre);
HDfree(pre);
if (str == NULL)
h5JNIFatalError( env, "H5Pget_efile_prefix: return string not allocated");
} /* end if */
else {
HDfree(pre);
h5libraryError(env);
} /* end else */
} /* end else */
} /* end else */
return (jstring)str;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1efile_1prefix */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_evict_on_close
* Signature: (JZ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1evict_1on_1close
(JNIEnv *env, jclass clss, jlong fapl_id, jboolean evict_on_close)
{
herr_t retVal = -1;
hbool_t evict_on_close_val;
if (evict_on_close == JNI_TRUE)
evict_on_close_val = TRUE;
else
evict_on_close_val = FALSE;
retVal = H5Pset_evict_on_close((hid_t)fapl_id, (hbool_t)evict_on_close_val);
if (retVal < 0)
h5libraryError(env);
} /* end Java_hdf_hdf5lib_H5_H5Pset_1evict_1on_1close */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_evict_on_close
* Signature: (J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1evict_1on_1close
(JNIEnv *env, jclass clss, jlong fapl_id)
{
hbool_t evict_on_close_val = FALSE;
jboolean bval = JNI_FALSE;
if (H5Pget_evict_on_close((hid_t)fapl_id, (hbool_t *)&evict_on_close_val) < 0) {
h5libraryError(env);
} /* end if */
else {
if (evict_on_close_val == TRUE)
bval = JNI_TRUE;
} /* end else */
return bval;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1evict_1on_1close */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_chunk_opts
* Signature: (JI)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1chunk_1opts
(JNIEnv *env, jclass clss, jlong dcpl_id, jint opts)
{
herr_t retVal = -1;
retVal = H5Pset_chunk_opts((hid_t)dcpl_id, (unsigned)opts);
if (retVal < 0)
h5libraryError(env);
} /* end Java_hdf_hdf5lib_H5_H5Pset_1chunk_1opts */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_chunk_opts
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts
(JNIEnv *env, jclass clss, jlong dcpl_id)
{
unsigned opts = 0;
if (H5Pget_chunk_opts((hid_t)dcpl_id, opts) < 0)
h5libraryError(env);
return (jint)opts;
} /* end Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts */
#ifdef __cplusplus
} /* end extern "C" */
#endif /* __cplusplus */

91
java/src/jni/h5pImp.h
View File

@ -1533,7 +1533,6 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1metadata_1read_1attempts
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_metadata_read_attempts
@ -1543,6 +1542,96 @@ JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts
(JNIEnv *, jclass, jlong, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_vds_file_cache_size
* Signature: (JI)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1vds_1file_1cache_1size
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_vds_file_cache_size
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1vds_1file_1cache_1size
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_virtual_prefix
* Signature: (JLjava/lang/String;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1virtual_1prefix
(JNIEnv *, jclass, jlong, jstring);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_virtual_prefix
* Signature: (J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1virtual_1prefix
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_efile_prefix
* Signature: (JLjava/lang/String;)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1efile_1prefix
(JNIEnv *, jclass, jlong, jstring);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_efile_prefix
* Signature: (J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1efile_1prefix
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_evict_on_close
* Signature: (JZ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1evict_1on_1close
(JNIEnv *, jclass, jlong, jboolean);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_evict_on_close
* Signature: (J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1evict_1on_1close
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pset_chunk_opts
* Signature: (JI)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Pset_1chunk_1opts
(JNIEnv *, jclass, jlong, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Pget_chunk_opts
* Signature: (J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts
(JNIEnv *, jclass, jlong);
#ifdef __cplusplus
} /* end extern "C" */

10
java/test/JUnit-interface.txt
View File

@ -415,6 +415,7 @@ JUnit version 4.11
.testH5PH5Pset_shared_mesg_phase_change_HighMaxlistValue
.testH5P_layout
.testH5Pget_link_creation_order
.testH5Pget_efile_prefix
.testH5Pset_shared_mesg_nindexes_InvalidHIGHnindexes
.testH5P_file_space_page_size
.testH5Pget_shared_mesg_index_Invalid_indexnum
@ -444,6 +445,7 @@ JUnit version 4.11
.testH5Pset_est_link_info_InvalidValues
.testH5Pset_local_heap_size_hint
.testH5Pget_est_link_info
.testH5Pset_efile_prefix_null
.testH5Pset_scaleoffset
.testH5Pset_create_intermediate_group_invalidobject
.testH5PH5Pset_shared_mesg_phase_change_HighMinbtreeValue
@ -466,6 +468,7 @@ JUnit version 4.11
.testH5Pget_sym_k_null
.testH5Pset_nlinks
.testH5P_obj_track_times
.testH5Pset_efile_prefix
.testH5P_userblock
.testH5Pget_local_heap_size_hint
.testH5Pset_shared_mesg_index_Invalid_indexnum
@ -502,8 +505,10 @@ JUnit version 4.11
.testH5Fmdc_logging
.testH5Pget_elink_fapl
.testH5Pset_mdc_config
.testH5P_vds_file_cache_size
.testH5P_small_data_block_size
.testH5Pset_fapl_log
.testH5P_evict_on_close
.testH5Pset_libver_bounds
.testH5P_sieve_buf_size
.testH5P_elink_file_cache_size
@ -530,11 +535,14 @@ JUnit version 4.11
.testH5Pget_source_datasetname
.testH5Pvirtual_storage
.testH5Pget_selection_source_dataset
.testH5Pget_virtual_prefix
.testH5Pget_source_filename
.testH5Pset_get_virtual_printf_gap
.testH5Pget_virtual_count
.testH5Pset_virtual_prefix
.testH5Pset_get_virtual_view
.testH5Pget_mapping_parameters
.testH5Pset_virtual_prefix_null
.testH5P_genprop_basic_class
.testH5P_genprop_class_iter
.testH5P_genprop_basic_class_prop
@ -640,7 +648,7 @@ JUnit version 4.11
Time: XXXX
OK (638 tests)
OK (646 tests)
HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
#000: (file name) line (number) in H5Fopen(): can't set access and transfer property lists

53
java/test/TestH5P.java
View File

@ -28,6 +28,7 @@ import hdf.hdf5lib.exceptions.HDF5LibraryException;
import org.junit.After;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;
@ -852,7 +853,7 @@ public class TestH5P {
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pset_est_link_info: " + err);
fail("H5Pset_elink_prefix: " + err);
}
assertTrue("H5Pset_elink_prefix", ret_val >= 0);
}
@ -1232,4 +1233,54 @@ public class TestH5P {
fail("testH5P_file_space_page_size: " + err);
}
}
@Test
public void testH5Pset_efile_prefix() {
String prefix = "tmp";
try {
H5.H5Pset_efile_prefix(lapl_id, prefix);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pset_efile_prefix: " + err);
}
}
@Test(expected = NullPointerException.class)
public void testH5Pset_efile_prefix_null() throws Throwable{
H5.H5Pset_efile_prefix(lapl_id, null);
}
@Test
public void testH5Pget_efile_prefix() {
String prefix = "tmp";
String pre = "";
try {
H5.H5Pset_efile_prefix(lapl_id, prefix);
pre = H5.H5Pget_efile_prefix(lapl_id);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pget_efile_prefix: " + err);
}
assertTrue("The prefix: ", prefix.equals(pre));
}
@Ignore
public void testH5P_chunk_opts() {
int chunk_opts = -1;
try {
chunk_opts = H5.H5Pget_chunk_opts(ocpl_id);
assertTrue("chunk_opts: "+chunk_opts, chunk_opts == 0);
H5.H5Pset_chunk_opts(ocpl_id, HDF5Constants.H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS);
chunk_opts = H5.H5Pget_chunk_opts(ocpl_id);
assertTrue("chunk_opts: "+chunk_opts, chunk_opts == HDF5Constants.H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pget_lchunk_opts: " + err);
}
}
}

41
java/test/TestH5Pfapl.java
View File

@ -1376,4 +1376,45 @@ public class TestH5Pfapl {
deleteH5file();
_deleteLogFile();
}
@Test
public void testH5P_evict_on_close() {
boolean ret_val_id = false;
try {
H5.H5Pset_evict_on_close(fapl_id, true);
ret_val_id = H5.H5Pget_evict_on_close(fapl_id);
assertTrue("H5P_evict_on_close", ret_val_id);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5P_evict_on_close: " + err);
}
}
@Test
public void testH5P_vds_file_cache_size() {
int vds_size = 0;
try {
try {
vds_size = H5.H5Pget_vds_file_cache_size(fapl_id);
assertTrue("H5P_vds_file_cache_size default", vds_size == 0);
}
catch (UnsupportedOperationException err) {
System.out.println(err.getMessage());
}
try {
vds_size = 8;
H5.H5Pset_vds_file_cache_size(fapl_id, vds_size);
vds_size = H5.H5Pget_vds_file_cache_size(fapl_id);
assertTrue("H5P_vds_file_cache_size 8", vds_size == 8);
}
catch (UnsupportedOperationException err) {
System.out.println(err.getMessage());
}
}
catch (Throwable err) {
err.printStackTrace();
fail("H5P_vds_file_cache_size: " + err);
}
}
}

33
java/test/TestH5Pvirtual.java
View File

@ -429,4 +429,37 @@ public class TestH5Pvirtual {
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
}
@Test
public void testH5Pset_virtual_prefix() {
String prefix = "tmp";
try {
H5.H5Pset_virtual_prefix(H5dapl_id, prefix);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pset_virtual_prefix: " + err);
}
}
@Test(expected = NullPointerException.class)
public void testH5Pset_virtual_prefix_null() throws Throwable{
H5.H5Pset_virtual_prefix(H5dapl_id, null);
}
@Test
public void testH5Pget_virtual_prefix() {
String prefix = "tmp";
String pre = "";
try {
H5.H5Pset_virtual_prefix(H5dapl_id, prefix);
pre = H5.H5Pget_virtual_prefix(H5dapl_id);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pget_virtual_prefix: " + err);
}
assertTrue("The prefix: ", prefix.equals(pre));
}
}

32
release_docs/RELEASE.txt
View File

@ -58,7 +58,23 @@ New Features
Library:
--------
-
- Add prefix option to VDS files.
Currently, VDS source files must be in the active directory to be
found by the virtual file. Adding the option of a prefix to be set
on the virtual file, using a data access property list (DAPL),
allows the source files to located at an absolute or relative path
to the virtual file.
New public APIs:
herr_t H5Pset_virtual_prefix(hid_t dapl_id, const char* prefix);
ssize_t H5Pget_virtual_prefix(hid_t dapl_id, char* prefix /*out*/, size_t size);
herr_t H5Pset_vds_file_cache_size(hid_t plist_id, unsigned vds_size);
herr_t H5Pget_vds_file_cache_size(hid_t plist_id, unsigned *vds_size);
The prefix can also be set with an environment variable, HDF5_VDS_PREFIX.
(ADB - 2017/12/12, HDFFV-9724)
Parallel Library:
-----------------
@ -119,6 +135,20 @@ New Features
------------
-
Java Library:
----------------
- Wrappers added for the following APIs:
H5Pset_evict_on_close
H5Pget_evict_on_close
H5Pset_chunk_opts
H5Pget_chunk_opts
H5Pset_efile_prefix
H5Pget_efile_prefix
H5Pset_virtual_prefix
H5Pget_virtual_prefix
H5Pset_vds_file_cache_size
H5Pget_vds_file_cache_size
Tools:
------
- h5diff

952
src/H5Pfapl.c
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