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develop JNI export references and java updates (#467)

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* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* correct window os name

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
This commit is contained in:
Allen Byrne 2021-03-12 07:47:47 -06:00 committed by GitHub
parent 6f760f200d
commit 748da20bbc
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GPG Key ID: 4AEE18F83AFDEB23
16 changed files with 562 additions and 229 deletions
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27
java/src/hdf/hdf5lib/H5.java
View File

@ -512,8 +512,8 @@ public class H5 implements java.io.Serializable {
*
* @param file_export_name
* The file name to export data into.
* @param file_name
* The name of the HDF5 file containing the dataset.
* @param file_id
* The identifier of the HDF5 file containing the dataset.
* @param object_path
* The full path of the dataset to be exported.
* @param binary_order
@ -525,9 +525,30 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5export_dataset(String file_export_name, String file_name,
public synchronized static native void H5export_dataset(String file_export_name, long file_id,
String object_path, int binary_order) throws HDF5LibraryException;
/**
* H5export_attribute is a utility function to save data in a file.
*
* @param file_export_name
* The file name to export data into.
* @param dataset_id
* The identifier of the dataset containing the attribute.
* @param attribute_name
* The attribute to be exported.
* @param binary_order
* 99 - export data as text.
* 1 - export data as binary Native Order.
* 2 - export data as binary Little Endian.
* 3 - export data as binary Big Endian.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5export_attribute(String file_export_name, long dataset_id,
String attribute_name, int binary_order) throws HDF5LibraryException;
/**
* H5is_library_threadsafe Checks to see if the library was built with thread-safety enabled.
*

10
java/src/hdf/hdf5lib/HDF5Constants.java
View File

@ -55,15 +55,15 @@ public class HDF5Constants {
public static final int H5_INDEX_CRT_ORDER = H5_INDEX_CRT_ORDER();
/** indices on links, number of indices defined */
public static final int H5_INDEX_N = H5_INDEX_N();
/** */
/** Common iteration orders, Unknown order */
public static final int H5_ITER_UNKNOWN = H5_ITER_UNKNOWN();
/** */
/** Common iteration orders, Increasing order */
public static final int H5_ITER_INC = H5_ITER_INC();
/** */
/** Common iteration orders, Decreasing order */
public static final int H5_ITER_DEC = H5_ITER_DEC();
/** */
/** Common iteration orders, No particular order, whatever is fastest */
public static final int H5_ITER_NATIVE = H5_ITER_NATIVE();
/** */
/** Common iteration orders, Number of iteration orders */
public static final int H5_ITER_N = H5_ITER_N();
/** */
public static final int H5AC_CURR_CACHE_CONFIG_VERSION = H5AC_CURR_CACHE_CONFIG_VERSION();

24
java/src/hdf/hdf5lib/HDF5GroupInfo.java
View File

@ -90,32 +90,44 @@ public class HDF5GroupInfo {
linklen = 0;
}
/** fileno accessors */
/** fileno accessors
* @return the file number if successful
*/
public long[] getFileno() {
return fileno;
}
/** accessors */
/** accessors
* @return the object number if successful
*/
public long[] getObjno() {
return objno;
}
/** accessors */
/** accessors
* @return type of group if successful
*/
public int getType() {
return type;
}
/** accessors */
/** accessors
* @return the number of links in the group if successful
*/
public int getNlink() {
return nlink;
}
/** accessors */
/** accessors
* @return the modified time value if successful
*/
public long getMtime() {
return mtime;
}
/** accessors */
/** accessors
* @return a length of link name if successful
*/
public int getLinklen() {
return linklen;
}

10
java/src/hdf/hdf5lib/HDFArray.java
View File

@ -827,12 +827,10 @@ class ArrayDescriptor {
else if (NT == 'S') {
NTsize = 2;
}
else if ((NT == 'I')
|| (NT == 'F')) {
else if ((NT == 'I') || (NT == 'F')) {
NTsize = 4;
}
else if ((NT == 'J')
|| (NT == 'D')) {
else if ((NT == 'J') || (NT == 'D')) {
NTsize = 8;
}
else if (css.startsWith("Ljava.lang.Byte")) {
@ -925,8 +923,8 @@ class ArrayDescriptor {
System.out.println("Type: " + theType);
System.out.println("Class: " + theClass);
System.out.println("NT: " + NT + " NTsize: " + NTsize);
System.out
.println("Array has " + dims + " dimensions (" + totalSize + " bytes, " + totalElements + " elements)");
System.out.println("Array has " + dims + " dimensions (" + totalSize
+ " bytes, " + totalElements + " elements)");
int i;
for (i = 0; i <= dims; i++) {
Class tc = objs[i].getClass();

6
java/src/hdf/hdf5lib/structs/H5_ih_info_t.java
View File

@ -20,9 +20,9 @@ import java.io.Serializable;
*/
public class H5_ih_info_t implements Serializable {
private static final long serialVersionUID = -142238015615462707L;
/** */
public long index_size; /* btree and/or list */
/** */
/** btree and/or list size of index */
public long index_size;
/** btree and/or list size of hp */
public long heap_size;
H5_ih_info_t (long index_size, long heap_size)

549
java/src/jni/h5util.c
View File

@ -52,6 +52,8 @@ void * edata;
/* Local Prototypes */
/********************/
int h5str_region_dataset(JNIEnv *env, h5str_t *out_str, H5R_ref_t *ref_vp, int expand_data);
static int h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj,
int expand_data);
static int h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj,
@ -1098,14 +1100,15 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
}
case H5T_REFERENCE: {
if (H5Tequal(tid, H5T_STD_REF)) {
hid_t new_obj_id = H5I_INVALID_HID;
H5O_type_t obj_type = -1; /* Object type */
H5R_type_t ref_type; /* Reference type */
/* H5T_STD_REF */
hid_t new_obj_id = H5I_INVALID_HID;
H5O_type_t obj_type = -1; /* Object type */
H5R_type_t ref_type; /* Reference type */
H5R_ref_t *ref_vp = (H5R_ref_t *)cptr;
H5R_ref_t *ref_vp = (H5R_ref_t *)cptr;
ref_type = H5Rget_type(ref_vp);
ref_type = H5Rget_type(ref_vp);
if (!h5str_is_zero(ref_vp, H5Tget_size(H5T_STD_REF))) {
switch (ref_type) {
case H5R_OBJECT1:
if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) {
@ -1209,18 +1212,10 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
default:
break;
} /* end switch */
}
if (H5Rdestroy(ref_vp) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
/* (H5R_DSET_REG_REF_BUF_SIZE == typeSize) */
if (H5Rdestroy(ref_vp) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
else if (H5Tequal(tid, H5T_STD_REF_OBJ)) {
/* (H5R_OBJ_REF_BUF_SIZE == typeSize) */
H5_LIBRARY_ERROR(ENVONLY);
}
break;
}
@ -2240,39 +2235,31 @@ h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hs
}
case H5T_REFERENCE: {
if (H5Tequal(tid, H5T_STD_REF)) {
hid_t region_id = H5I_INVALID_HID;
hid_t region_space = H5I_INVALID_HID;
H5S_sel_type region_type;
hid_t region_id = H5I_INVALID_HID;
hid_t region_space = H5I_INVALID_HID;
H5S_sel_type region_type;
/* Region data */
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char *)_mem) + block_index * size;
if ((region_id = H5Ropen_object((H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) < 0)
continue;
if ((region_space = H5Ropen_region((H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
if (!h5str_is_zero(mem, H5Tget_size(H5T_STD_REF))) {
region_type = H5Sget_select_type(region_space);
if (region_type == H5S_SEL_POINTS)
ret_value = render_bin_output_region_points(stream, region_space, region_id,
container);
else if (region_type == H5S_SEL_HYPERSLABS)
ret_value = render_bin_output_region_blocks(stream, region_space, region_id,
container);
}
H5Sclose(region_space);
} /* end if (region_space >= 0) */
H5Dclose(region_id);
/* Region data */
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char *)_mem) + block_index * size;
if ((region_id = H5Ropen_object((H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) < 0)
continue;
if ((region_space = H5Ropen_region((H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
if (!h5str_is_zero(mem, H5Tget_size(H5T_STD_REF))) {
region_type = H5Sget_select_type(region_space);
if (region_type == H5S_SEL_POINTS)
ret_value =
render_bin_output_region_points(stream, region_space, region_id, container);
else if (region_type == H5S_SEL_HYPERSLABS)
ret_value =
render_bin_output_region_blocks(stream, region_space, region_id, container);
}
H5Sclose(region_space);
} /* end if (region_space >= 0) */
H5Dclose(region_id);
if (ret_value < 0)
break;
}
}
else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
;
}
else if (H5Tequal(tid, H5T_STD_REF_OBJ)) {
;
if (ret_value < 0)
break;
}
break;
@ -2762,11 +2749,11 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
size_t p_type_nbytes; /* size of memory type */
/* Stripmine info */
unsigned char *sm_buf = NULL; /* buffer for raw data */
hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */
hsize_t sm_nbytes; /* bytes per stripmine */
hsize_t sm_nelmts; /* elements per stripmine */
hid_t sm_space = H5I_INVALID_HID; /* stripmine data space */
void * sm_buf = NULL; /* buffer for raw data */
hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */
hsize_t sm_nbytes; /* bytes per stripmine */
hsize_t sm_nelmts; /* elements per stripmine */
hid_t sm_space = H5I_INVALID_HID; /* stripmine data space */
/* Hyperslab info */
hsize_t hs_offset[H5S_MAX_RANK]; /* starting offset */
@ -2786,142 +2773,168 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
if ((f_type = H5Dget_type(dset)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
switch (binary_order) {
case 1: {
if ((p_type = h5str_get_native_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case 2: {
if ((p_type = h5str_get_little_endian_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case 3: {
if ((p_type = h5str_get_big_endian_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
default: {
if ((p_type = H5Tcopy(f_type)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
break;
}
}
if ((f_space = H5Dget_space(dset)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) {
if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) {
p_nelmts = H5Sget_simple_extent_npoints(f_space);
if (NULL ==
(sm_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
/* Read the data */
if (H5Dread(dset, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, sm_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Calculate the number of elements we're going to print */
p_nelmts = 1;
if (binary_order == 99) {
if (h5str_dump_simple_data(ENVONLY, stream, dset, H5T_STD_REF, sm_buf, p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
if (h5str_render_bin_output(stream, dset, H5T_STD_REF, sm_buf, p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
}
else {
switch (binary_order) {
case 1: {
if ((p_type = h5str_get_native_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
if (ndims > 0) {
for (i = 0; i < (size_t)ndims; i++)
p_nelmts *= total_size[i];
} /* end if */
if (p_nelmts > 0) {
/* Check if we have VL data in the dataset's datatype */
if (h5str_detect_vlen(p_type) != 0)
vl_data = 1;
/*
* Determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
if (!(sm_nbytes = p_type_nbytes = H5Tget_size(p_type)))
H5_LIBRARY_ERROR(ENVONLY);
if (ndims > 0) {
for (i = (size_t)ndims; i > 0; --i) {
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if (size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = (((total_size[i - 1]) < (size)) ? (total_size[i - 1]) : (size));
sm_nbytes *= sm_size[i - 1];
}
break;
}
if (sm_nbytes > 0) {
if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)sm_nbytes)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_dset: failed to allocate sm_buf");
case 2: {
if ((p_type = h5str_get_little_endian_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
sm_nelmts = sm_nbytes / p_type_nbytes;
break;
}
if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0)
case 3: {
if ((p_type = h5str_get_big_endian_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
default: {
if ((p_type = H5Tcopy(f_type)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* The stripmine loop */
HDmemset(hs_offset, 0, sizeof hs_offset);
HDmemset(zero, 0, sizeof zero);
break;
}
}
for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) {
/* Calculate the hyperslab size */
if (ndims > 0) {
for (i = 0, hs_nelmts = 1; i < (size_t)ndims; i++) {
hs_size[i] = (((total_size[i] - hs_offset[i]) < (sm_size[i]))
? (total_size[i] - hs_offset[i])
: (sm_size[i]));
hs_nelmts *= hs_size[i];
}
if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) {
if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Calculate the number of elements we're going to print */
p_nelmts = 1;
if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (ndims > 0) {
for (i = 0; i < (size_t)ndims; i++)
p_nelmts *= total_size[i];
} /* end if */
if (p_nelmts > 0) {
/* Check if we have VL data in the dataset's datatype */
if (h5str_detect_vlen(p_type) != 0)
vl_data = 1;
/*
* Determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
if (!(sm_nbytes = p_type_nbytes = H5Tget_size(p_type)))
H5_LIBRARY_ERROR(ENVONLY);
if (ndims > 0) {
for (i = (size_t)ndims; i > 0; --i) {
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if (size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = (((total_size[i - 1]) < (size)) ? (total_size[i - 1]) : (size));
sm_nbytes *= sm_size[i - 1];
}
else {
if (H5Sselect_all(f_space) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
if (H5Sselect_all(sm_space) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (sm_nbytes > 0) {
if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)sm_nbytes)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_dset: failed to allocate sm_buf");
hs_nelmts = 1;
}
sm_nelmts = sm_nbytes / p_type_nbytes;
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0)
if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (binary_order == 99) {
if (h5str_dump_simple_data(ENVONLY, stream, dset, p_type, sm_buf, hs_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
if (h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
/* The stripmine loop */
HDmemset(hs_offset, 0, sizeof hs_offset);
HDmemset(zero, 0, sizeof zero);
/* Reclaim any VL memory, if necessary */
if (vl_data) {
if (H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0)
for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) {
/* Calculate the hyperslab size */
if (ndims > 0) {
for (i = 0, hs_nelmts = 1; i < (size_t)ndims; i++) {
hs_size[i] = (((total_size[i] - hs_offset[i]) < (sm_size[i]))
? (total_size[i] - hs_offset[i])
: (sm_size[i]));
hs_nelmts *= hs_size[i];
}
if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) <
0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) <
0)
H5_LIBRARY_ERROR(ENVONLY);
}
else {
if (H5Sselect_all(f_space) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Sselect_all(sm_space) < 0)
H5_LIBRARY_ERROR(ENVONLY);
hs_nelmts = 1;
}
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
/* Calculate the next hyperslab offset */
for (i = (size_t)ndims, carry = 1; i > 0 && carry; --i) {
hs_offset[i - 1] += hs_size[i - 1];
if (binary_order == 99) {
if (h5str_dump_simple_data(ENVONLY, stream, dset, p_type, sm_buf, hs_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
if (h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
if (hs_offset[i - 1] == total_size[i - 1])
hs_offset[i - 1] = 0;
else
carry = 0;
/* Reclaim any VL memory, if necessary */
if (vl_data) {
if (H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
/* Calculate the next hyperslab offset */
for (i = (size_t)ndims, carry = 1; i > 0 && carry; --i) {
hs_offset[i - 1] += hs_size[i - 1];
if (hs_offset[i - 1] == total_size[i - 1])
hs_offset[i - 1] = 0;
else
carry = 0;
}
}
}
}
@ -2945,6 +2958,148 @@ done:
return ret_value;
} /* end h5str_dump_simple_dset */
int
h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order)
{
hid_t f_space = H5I_INVALID_HID; /* file data space */
hsize_t alloc_size;
int ndims; /* rank of dataspace */
unsigned i; /* counters */
hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/
hsize_t p_nelmts; /* total selected elmts */
void * sm_buf = NULL; /* buffer for raw data */
hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */
int ret_value = 0;
/* VL data special information */
unsigned int vl_data = 0; /* contains VL datatypes */
hid_t p_type = H5I_INVALID_HID;
hid_t f_type = H5I_INVALID_HID;
if (attr_id < 0)
H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_dump_simple_mem: attr ID < 0");
if ((f_type = H5Aget_type(attr_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5I_INVALID_HID == (f_space = H5Aget_space(attr_id)))
H5_LIBRARY_ERROR(ENVONLY);
if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) {
p_nelmts = H5Sget_simple_extent_npoints(f_space);
if (NULL ==
(sm_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
/* Read the data */
if (H5Aread(attr_id, H5T_STD_REF, sm_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (binary_order == 99) {
if (h5str_dump_simple_data(ENVONLY, stream, attr_id, H5T_STD_REF, sm_buf, p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
if (h5str_render_bin_output(stream, attr_id, H5T_STD_REF, sm_buf, p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
}
else {
switch (binary_order) {
case 1: {
if ((p_type = h5str_get_native_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case 2: {
if ((p_type = h5str_get_little_endian_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
case 3: {
if ((p_type = h5str_get_big_endian_type(f_type)) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
break;
}
default: {
if ((p_type = H5Tcopy(f_type)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
break;
}
}
if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) {
if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
H5_LIBRARY_ERROR(ENVONLY);
/* Calculate the number of elements we're going to print */
p_nelmts = 1;
if (ndims > 0) {
for (i = 0; i < (size_t)ndims; i++)
p_nelmts *= total_size[i];
} /* end if */
if (p_nelmts > 0) {
/* Check if we have VL data in the dataset's datatype */
if (h5str_detect_vlen(p_type) != 0)
vl_data = 1;
alloc_size = p_nelmts * H5Tget_size(p_type);
if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)alloc_size)))
H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
/* Read the data */
if (H5Aread(attr_id, p_type, sm_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
if (binary_order == 99) {
if (h5str_dump_simple_data(ENVONLY, stream, attr_id, p_type, sm_buf, p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
else {
if (h5str_render_bin_output(stream, attr_id, p_type, sm_buf, p_nelmts) < 0)
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
}
/* Reclaim any VL memory, if necessary */
if (vl_data) {
if (H5Treclaim(p_type, f_space, H5P_DEFAULT, sm_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}
}
}
}
ret_value = SUCCEED;
done:
if (sm_buf)
HDfree(sm_buf);
if (f_space >= 0)
H5Sclose(f_space);
if (p_type >= 0)
H5Tclose(p_type);
if (f_type >= 0)
H5Tclose(f_type);
return ret_value;
}
htri_t
H5Tdetect_variable_str(hid_t tid)
{
@ -3007,7 +3162,6 @@ h5str_dump_simple_data(JNIEnv *env, FILE *stream, hid_t container, hid_t type, v
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_data: HDfprintf failure");
}
}
if (HDfprintf(stream, "%s", buffer.s) < 0)
H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_data: HDfprintf failure");
@ -3577,18 +3731,16 @@ done:
/*
* Class: hdf_hdf5lib_H5
* Method: H5export_dataset
* Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V
* Signature: (Ljava/lang/String;JLjava/lang/String;I)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_export_name, jstring file_name,
Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_export_name, jlong file_id,
jstring object_path, jint binary_order)
{
const char *file_export = NULL;
const char *object_name = NULL;
const char *fileName = NULL;
jboolean isCopy;
herr_t ret_val = FAIL;
hid_t file_id = H5I_INVALID_HID;
hid_t dataset_id = H5I_INVALID_HID;
FILE * stream = NULL;
@ -3597,17 +3749,9 @@ Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_exp
if (NULL == file_export_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_export_name is NULL");
if (NULL == file_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_name is NULL");
if (NULL == object_path)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: object_path is NULL");
PIN_JAVA_STRING(ENVONLY, file_name, fileName, NULL, "H5export_dataset: file name not pinned");
if ((file_id = H5Fopen(fileName, (unsigned)H5F_ACC_RDWR, (hid_t)H5P_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
PIN_JAVA_STRING(ENVONLY, object_path, object_name, &isCopy, "H5export_dataset: object_path not pinned");
if ((dataset_id = H5Dopen2(file_id, object_name, H5P_DEFAULT)) < 0)
@ -3634,14 +3778,65 @@ done:
UNPIN_JAVA_STRING(ENVONLY, file_export_name, file_export);
if (object_name)
UNPIN_JAVA_STRING(ENVONLY, object_path, object_name);
if (fileName)
UNPIN_JAVA_STRING(ENVONLY, file_name, fileName);
if (dataset_id >= 0)
H5Dclose(dataset_id);
if (file_id >= 0)
H5Fclose(file_id);
} /* end Java_hdf_hdf5lib_H5_H5export_1dataset */
/*
* Class: hdf_hdf5lib_H5
* Method: H5export_attribute
* Signature: (Ljava/lang/String;JLjava/lang/String;I)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5export_1attribute(JNIEnv *env, jclass clss, jstring file_export_name, jlong dset_id,
jstring attribute_name, jint binary_order)
{
const char *file_export = NULL;
const char *object_name = NULL;
jboolean isCopy;
herr_t ret_val = FAIL;
hid_t attr_id = H5I_INVALID_HID;
FILE * stream = NULL;
UNUSED(clss);
if (NULL == file_export_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_export_name is NULL");
if (NULL == attribute_name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: object_path is NULL");
PIN_JAVA_STRING(ENVONLY, attribute_name, object_name, &isCopy,
"H5export_dataset: object_path not pinned");
if ((attr_id = H5Aopen(dset_id, object_name, H5P_DEFAULT)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
PIN_JAVA_STRING(ENVONLY, file_export_name, file_export, NULL,
"H5export_dataset: file_export name not pinned");
if (NULL == (stream = HDfopen(file_export, "w+")))
H5_JNI_FATAL_ERROR(ENVONLY, "HDfopen failed");
if ((ret_val = h5str_dump_simple_mem(ENVONLY, stream, attr_id, binary_order)) < 0)
H5_ASSERTION_ERROR(ENVONLY, "h5str_dump_simple_dset failed");
if (stream) {
HDfclose(stream);
stream = NULL;
}
done:
if (stream)
HDfclose(stream);
if (file_export)
UNPIN_JAVA_STRING(ENVONLY, file_export_name, file_export);
if (object_name)
UNPIN_JAVA_STRING(ENVONLY, attribute_name, object_name);
if (attr_id >= 0)
H5Aclose(attr_id);
} /* end Java_hdf_hdf5lib_H5_H5export_1attribute */
#ifdef __cplusplus
}
#endif

14
java/src/jni/h5util.h
View File

@ -46,6 +46,7 @@ extern size_t h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_
int expand_data);
extern void h5str_array_free(char **strs, size_t len);
extern int h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order);
extern int h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr, int binary_order);
extern htri_t H5Tdetect_variable_str(hid_t tid);
@ -105,9 +106,16 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1max(JNIEnv *, jcla
/*
* Class: hdf_hdf5lib_H5
* Method: H5export_dataset
* Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V
* Signature: (Ljava/lang/String;JLjava/lang/String;I)V
*/
JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *, jclass, jstring, jstring, jstring,
jint);
JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *, jclass, jstring, jlong, jstring, jint);
/*
* Class: hdf_hdf5lib_H5
* Method: H5export_attribute
* Signature: (Ljava/lang/String;JLjava/lang/String;I)V
*/
JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1attribute(JNIEnv *, jclass, jstring, jlong, jstring,
jint);
#endif /* H5UTIL_H__ */

4
java/test/CMakeLists.txt
View File

@ -96,6 +96,8 @@ HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/h5ex_g_iterate.orig" "${PROJECT_BINARY_
HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/h5ex_g_iterate.orig" "${PROJECT_BINARY_DIR}/h5ex_g_iterateO2.hdf" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/trefer_reg.h5" "${PROJECT_BINARY_DIR}/trefer_reg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/trefer_attr.h5" "${PROJECT_BINARY_DIR}/trefer_attr.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tdatareg.h5" "${PROJECT_BINARY_DIR}/tdatareg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tattrreg.h5" "${PROJECT_BINARY_DIR}/tattrreg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_files")
add_custom_target(${HDF5_JAVA_TEST_LIB_TARGET}_files ALL COMMENT "Copying files needed by ${HDF5_JAVA_TEST_LIB_TARGET} tests" DEPENDS ${${HDF5_JAVA_TEST_LIB_TARGET}_files_list})
@ -213,6 +215,8 @@ if (HDF5_TEST_JAVA AND HDF5_TEST_SERIAL)
HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/h5ex_g_iterate.orig" "${PROJECT_BINARY_DIR}/${voltest}/h5ex_g_iterateO2.hdf" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/trefer_reg.h5" "${PROJECT_BINARY_DIR}/${voltest}/trefer_reg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/trefer_attr.h5" "${PROJECT_BINARY_DIR}/${voltest}/trefer_attr.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tdatareg.h5" "${PROJECT_BINARY_DIR}/${voltest}/tdatareg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
HDFTEST_COPY_FILE("${HDF5_TOOLS_DIR}/testfiles/tattrreg.h5" "${PROJECT_BINARY_DIR}/${voltest}/tattrreg.h5" "${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files")
add_custom_target(${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files ALL COMMENT "Copying files needed by ${HDF5_JAVA_TEST_LIB_TARGET} tests" DEPENDS ${${HDF5_JAVA_TEST_LIB_TARGET}_${voltest}_files_list})

119
java/test/TestH5.java
View File

@ -49,9 +49,13 @@ public class TestH5 {
@Rule public TestName testname = new TestName();
private static final String H5_FILE = "testData.h5";
private static final String EXPORT_FILE = "testExport.txt";
private static final String H5_DREG_FILE = "trefer_reg.h5";
private static final String EXPORT_DREG_FILE = "testExportReg.txt";
private static final String H5_AREG_FILE = "trefer_attr.h5";
private static final String H5_REGION_FILE = "trefer_reg.h5";
private static final String EXPORT_REGION_FILE = "testExportReg.txt";
private static final String H5_ATTR_FILE = "trefer_attr.h5";
private static final String EXPORT_ATTR_FILE = "testExportAttr.txt";
private static final String H5_DREG_FILE = "tdatareg.h5";
private static final String EXPORT_DREG_FILE = "testExportDReg.txt";
private static final String H5_AREG_FILE = "tattrreg.h5";
private static final String EXPORT_AREG_FILE = "testExportAReg.txt";
private static final int DIM_X = 4;
private static final int DIM_Y = 6;
@ -129,7 +133,7 @@ public class TestH5 {
public void _openH5File(String filename, String dsetname) {
try {
H5fid = H5.H5Fopen(filename,
HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
@ -162,6 +166,7 @@ public class TestH5 {
@After
public void closeH5File() throws HDF5LibraryException {
_closeH5File();
assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0);
System.out.println();
}
@ -415,8 +420,10 @@ public class TestH5 {
_closeH5File();
_openH5File(H5_FILE, "/dset");
try {
H5.H5export_dataset(EXPORT_FILE, H5_FILE, "/dset", 99);
H5.H5export_dataset(EXPORT_FILE, H5fid, "/dset", 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
@ -453,6 +460,86 @@ public class TestH5 {
_deleteH5file();
}
@Test
public void testH5export_region() {
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
String objName = "/Dataset1";
_openH5File(H5_REGION_FILE, objName);
try {
H5.H5export_dataset(EXPORT_REGION_FILE, H5fid, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_REGION_FILE);
try {
Reader reader = new FileReader(EXPORT_REGION_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("testH5export_region: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
@Test
public void testH5export_attribute() {
int[] dset_data_expect = {0, 3, 6, 9, 1, 4, 7, 10, 2, 5, 8, 11};
int[] dset_indata = new int[DIM_ATTR];
String objName = "/Dataset3";
_openH5File(H5_ATTR_FILE, objName);
try {
H5.H5export_dataset(EXPORT_ATTR_FILE, H5did, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_ATTR_FILE);
try {
Reader reader = new FileReader(EXPORT_ATTR_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
int jndx = 0;
while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("testH5export_attribute: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
@Test
public void testH5export_regdataset() {
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
@ -465,7 +552,7 @@ public class TestH5 {
_openH5File(H5_DREG_FILE, objName);
try {
H5.H5export_dataset(EXPORT_DREG_FILE, H5_DREG_FILE, objName, 99);
H5.H5export_dataset(EXPORT_DREG_FILE, H5fid, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
@ -491,23 +578,27 @@ public class TestH5 {
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("H5export_dataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
assertTrue("testH5export_regdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
@Test
public void testH5export_attrdataset() {
int[] dset_data_expect = {0, 3, 6, 9, 1, 4, 7, 10, 2, 5, 8, 11};
int[] dset_indata = new int[DIM_ATTR];
String objName = "/Dataset3";
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
String dsetName = "/Dataset1";
String objName = "Attribute1";
_openH5File(H5_AREG_FILE, objName);
_openH5File(H5_AREG_FILE, dsetName);
try {
H5.H5export_dataset(EXPORT_AREG_FILE, H5_AREG_FILE, objName, 99);
H5.H5export_attribute(EXPORT_AREG_FILE, H5did, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
fail("H5export_attribute failed: " + err);
}
File file = new File(EXPORT_AREG_FILE);
@ -530,6 +621,6 @@ public class TestH5 {
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("H5export_dataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
assertTrue("testH5export_attrdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
}

2
java/test/TestH5D.java
View File

@ -197,7 +197,7 @@ public class TestH5D {
private final void _openH5file(String filename, String dsetname, long dapl) {
try {
H5fid = H5.H5Fopen(filename,
HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();

2
java/test/TestH5Rref.java
View File

@ -53,7 +53,7 @@ public class TestH5Rref {
public void openH5file(String filename, String dsetname) {
try {
H5fid = H5.H5Fopen(filename,
HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();

4
java/test/TestH5T.java
View File

@ -206,7 +206,7 @@ public class TestH5T {
@Test
public void testH5Tenum_functions() {
long filetype_id =HDF5Constants.H5I_INVALID_HID;
long filetype_id = HDF5Constants.H5I_INVALID_HID;
String enum_type ="Enum_type";
byte[] enum_val = new byte[1];
String enum_name = null;
@ -398,7 +398,7 @@ public class TestH5T {
@Test
public void testH5Tcompound_functions() {
long filetype_id =HDF5Constants.H5I_INVALID_HID;
long filetype_id = HDF5Constants.H5I_INVALID_HID;
// Create a compound datatype
try {

2
java/test/junit.sh.in
View File

@ -252,6 +252,8 @@ COPY_DATAFILES_TO_BLDDIR()
$CP -f $HDFTEST_HOME/h5ex_g_iterate.orig $BLDDIR/h5ex_g_iterateO2.hdf
$CP -f $TOOLS_TESTFILES/trefer_reg.h5 $BLDDIR/trefer_reg.h5
$CP -f $TOOLS_TESTFILES/trefer_attr.h5 $BLDDIR/trefer_attr.h5
$CP -f $TOOLS_TESTFILES/tdatareg.h5 $BLDDIR/tdatareg.h5
$CP -f $TOOLS_TESTFILES/tattrreg.h5 $BLDDIR/tattrreg.h5
}
CLEAN_DATAFILES_AND_BLDDIR()

4
java/test/testfiles/JUnit-TestH5.txt
View File

@ -1,4 +1,5 @@
JUnit version 4.11
.testH5export_region
.testH5get_libversion_null_param
.testJ2C
.testH5export_dataset
@ -7,6 +8,7 @@ JUnit version 4.11
.testH5garbage_collect
.testH5error_off
.testH5export_regdataset
.testH5export_attribute
.serializeToDisk
.testH5open
.testH5check_version
@ -15,5 +17,5 @@ JUnit version 4.11
Time: XXXX
OK (13 tests)
OK (15 tests)

10
src/H5Spkg.h
View File

@ -12,12 +12,12 @@
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Quincey Koziol
* Thursday, September 28, 2000
* Programmer: Quincey Koziol
* Thursday, September 28, 2000
*
* Purpose: This file contains declarations which are visible only within
* the H5S package. Source files outside the H5S package should
* include H5Sprivate.h instead.
* Purpose: This file contains declarations which are visible only within
* the H5S package. Source files outside the H5S package should
* include H5Sprivate.h instead.
*/
#if !(defined H5S_FRIEND || defined H5S_MODULE)
#error "Do not include this file outside the H5S package!"

4
tools/lib/h5diff_array.c
View File

@ -3388,7 +3388,7 @@ print_pos(diff_opt_t *opts, hsize_t idx, size_t u)
H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - c:%ld b:%ld s:%ld", j,
curr_pos, curr_idx, cnt_idx, blk_idx, str_idx);
dim_size = opts->dims[j]; /* Current dimension size */
// elmnt_cnt *= dim_size; /* Total number of elements in dimension */
/* elmnt_cnt *= dim_size; /* Total number of elements in dimension */
H5TOOLS_DEBUG("... sset loop:%d with elmnt_cnt:%ld - (prev_dim_size:%ld - dim_size:%ld) "
"- str_cnt:%ld",
j, elmnt_cnt, prev_dim_size, dim_size, str_cnt);
@ -3411,7 +3411,7 @@ print_pos(diff_opt_t *opts, hsize_t idx, size_t u)
"(curr_idx:%ld - data_idx:%ld)",
i, dim_size, str_cnt, curr_idx, data_idx);
}
next_idx += dim_size * str_cnt; // + prev_dim_size;
next_idx += dim_size * str_cnt;
H5TOOLS_DEBUG("... sset loop:%d with curr_idx:%ld (next_idx:%ld)", j, curr_idx, next_idx);
str_cnt = 0;
prev_str = str_idx;