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| author | Allen Byrne <50328838+byrnHDF@users.noreply.github.com> | 2021-03-12 13:47:47 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2021-03-12 13:47:47 (GMT) |
| commit | 748da20bbc42aa119305ee84f863361816e1517e (patch) | |
| tree | b794e206001650235f2977e31e44db0af81d9f68 /java | |
| parent | 6f760f200d6cb959c960b936af3fb2e68a55afde (diff) | |
| download | hdf5-748da20bbc42aa119305ee84f863361816e1517e.zip hdf5-748da20bbc42aa119305ee84f863361816e1517e.tar.gz hdf5-748da20bbc42aa119305ee84f863361816e1517e.tar.bz2 | |
develop JNI export references and java updates (#467)
* 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>
Diffstat (limited to 'java')
| -rw-r--r-- | java/src/hdf/hdf5lib/H5.java | 27 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/HDF5Constants.java | 10 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/HDF5GroupInfo.java | 24 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/HDFArray.java | 10 | ||||
| -rw-r--r-- | java/src/hdf/hdf5lib/structs/H5_ih_info_t.java | 6 | ||||
| -rw-r--r-- | java/src/jni/h5util.c | 543 | ||||
| -rw-r--r-- | java/src/jni/h5util.h | 14 | ||||
| -rw-r--r-- | java/test/CMakeLists.txt | 4 | ||||
| -rw-r--r-- | java/test/TestH5.java | 119 | ||||
| -rw-r--r-- | java/test/TestH5D.java | 2 | ||||
| -rw-r--r-- | java/test/TestH5Rref.java | 2 | ||||
| -rw-r--r-- | java/test/TestH5T.java | 4 | ||||
| -rw-r--r-- | java/test/junit.sh.in | 2 | ||||
| -rw-r--r-- | java/test/testfiles/JUnit-TestH5.txt | 4 |
14 files changed, 552 insertions, 219 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 960c872..aef0ba1 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -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 @@ -525,10 +525,31 @@ 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. * * @return true if hdf5 library implements threadsafe diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java index 334abee..4125907 100644 --- a/java/src/hdf/hdf5lib/HDF5Constants.java +++ b/java/src/hdf/hdf5lib/HDF5Constants.java @@ -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(); diff --git a/java/src/hdf/hdf5lib/HDF5GroupInfo.java b/java/src/hdf/hdf5lib/HDF5GroupInfo.java index e08f991..4c31af7 100644 --- a/java/src/hdf/hdf5lib/HDF5GroupInfo.java +++ b/java/src/hdf/hdf5lib/HDF5GroupInfo.java @@ -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; } diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java index 385d71b..bb9357e 100644 --- a/java/src/hdf/hdf5lib/HDFArray.java +++ b/java/src/hdf/hdf5lib/HDFArray.java @@ -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(); diff --git a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java index eec50c2..0c6111b 100644 --- a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java @@ -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) diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c index 2e02e4d..8ba6cf2 100644 --- a/java/src/jni/h5util.c +++ b/java/src/jni/h5util.c @@ -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) */ - H5_LIBRARY_ERROR(ENVONLY); - } - else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { - /* (H5R_OBJ_REF_BUF_SIZE == typeSize) */ + + if (H5Rdestroy(ref_vp) < 0) 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; - - /* 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); + hid_t region_id = H5I_INVALID_HID; + hid_t region_space = H5I_INVALID_HID; + H5S_sel_type region_type; - if (ret_value < 0) - break; - } - } - else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) { - ; - } - else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { - ; + /* 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; } 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); + if ((f_space = H5Dget_space(dset)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - break; - } + if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - case 2: { - if ((p_type = h5str_get_little_endian_type(f_type)) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0) + H5_LIBRARY_ERROR(ENVONLY); - break; - } + 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"); - case 3: { - if ((p_type = h5str_get_big_endian_type(f_type)) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + /* Read the data */ + if (H5Dread(dset, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, sm_buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); - break; + 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); } - - default: { - if ((p_type = H5Tcopy(f_type)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - break; + 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 ((f_space = H5Dget_space(dset)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + break; + } - if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + case 2: { + if ((p_type = h5str_get_little_endian_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - 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); + break; + } - /* Calculate the number of elements we're going to print */ - p_nelmts = 1; + case 3: { + if ((p_type = h5str_get_big_endian_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 */ + break; + } + + default: { + if ((p_type = H5Tcopy(f_type)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - 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; + break; + } + } - /* - * 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))) + 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 = (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]; + 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]; + } } - } - 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"); + 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"); - sm_nelmts = sm_nbytes / p_type_nbytes; + sm_nelmts = sm_nbytes / p_type_nbytes; - if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + /* The stripmine loop */ + HDmemset(hs_offset, 0, sizeof hs_offset); + HDmemset(zero, 0, sizeof zero); + + 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); - /* The stripmine loop */ - HDmemset(hs_offset, 0, sizeof hs_offset); - HDmemset(zero, 0, sizeof zero); - - 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(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_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (H5Sselect_all(sm_space) < 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); + hs_nelmts = 1; + } - if (H5Sselect_all(sm_space) < 0) + /* Read the data */ + if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 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); - - 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 (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); + } - /* Reclaim any VL memory, if necessary */ - if (vl_data) { - if (H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0) - H5_LIBRARY_ERROR(ENVONLY); - } + /* 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]; + /* 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; + 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 diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h index a5e9607..6c568e1 100644 --- a/java/src/jni/h5util.h +++ b/java/src/jni/h5util.h @@ -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__ */ diff --git a/java/test/CMakeLists.txt b/java/test/CMakeLists.txt index c791c79..10f9d52 100644 --- a/java/test/CMakeLists.txt +++ b/java/test/CMakeLists.txt @@ -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}) diff --git a/java/test/TestH5.java b/java/test/TestH5.java index c4f298e..1f298f3 100644 --- a/java/test/TestH5.java +++ b/java/test/TestH5.java @@ -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(); @@ -454,6 +461,86 @@ public class TestH5 { } @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, 111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171, @@ -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]); } } diff --git a/java/test/TestH5D.java b/java/test/TestH5D.java index 863ce79..dac3a9c 100644 --- a/java/test/TestH5D.java +++ b/java/test/TestH5D.java @@ -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(); diff --git a/java/test/TestH5Rref.java b/java/test/TestH5Rref.java index aeec64f..cbdabdd 100644 --- a/java/test/TestH5Rref.java +++ b/java/test/TestH5Rref.java @@ -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(); diff --git a/java/test/TestH5T.java b/java/test/TestH5T.java index c882f8e..ed4e2a9 100644 --- a/java/test/TestH5T.java +++ b/java/test/TestH5T.java @@ -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 { diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in index 81ce13b..3774cbd 100644 --- a/java/test/junit.sh.in +++ b/java/test/junit.sh.in @@ -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() diff --git a/java/test/testfiles/JUnit-TestH5.txt b/java/test/testfiles/JUnit-TestH5.txt index 59765d9..fb50a57 100644 --- a/java/test/testfiles/JUnit-TestH5.txt +++ b/java/test/testfiles/JUnit-TestH5.txt @@ -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) |