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authorBinh-Minh Ribler <bmribler@hdfgroup.org>2018-12-23 06:18:42 (GMT)
committerBinh-Minh Ribler <bmribler@hdfgroup.org>2018-12-23 06:18:42 (GMT)
commitc3f51c52d098d6cd2e6c2955a50140bdb45571c6 (patch)
tree3fbc8a16ba3140b0f7ed1febfbff9afb511073bd /java
parent251ba120b5e3277a0e53e9ea2417f6b370cf7d05 (diff)
parent7d28a4295ebac24dd0a84da9f4b880488d8bd32f (diff)
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Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop
Diffstat (limited to 'java')
-rw-r--r--java/src/hdf/hdf5lib/H5.java554
-rw-r--r--java/src/hdf/hdf5lib/HDF5Constants.java57
-rw-r--r--java/src/jni/CMakeLists.txt6
-rw-r--r--java/src/jni/Makefile.am2
-rw-r--r--java/src/jni/h5Constants.c43
-rw-r--r--java/src/jni/h5aImp.c1104
-rw-r--r--java/src/jni/h5aImp.h151
-rw-r--r--java/src/jni/h5dImp.c78
-rw-r--r--java/src/jni/h5dImp.h11
-rw-r--r--java/src/jni/h5fImp.c29
-rw-r--r--java/src/jni/h5fImp.h9
-rw-r--r--java/src/jni/h5vlImp.c206
-rw-r--r--java/src/jni/h5vlImp.h91
-rw-r--r--java/test/CMakeLists.txt1
-rw-r--r--java/test/Makefile.am1
-rw-r--r--java/test/TestH5Fbasic.java13
-rw-r--r--java/test/TestH5Fparams.java5
-rw-r--r--java/test/TestH5VL.java117
-rw-r--r--java/test/junit.sh.in22
-rw-r--r--java/test/testfiles/JUnit-TestH5Edefault.txt26
-rw-r--r--java/test/testfiles/JUnit-TestH5Fbasic.txt3
-rw-r--r--java/test/testfiles/JUnit-TestH5Fparams.txt3
-rw-r--r--java/test/testfiles/JUnit-TestH5VL.txt11
23 files changed, 2190 insertions, 353 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index f9f9b65..e354207 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -499,9 +499,9 @@ public class H5 implements java.io.Serializable {
private synchronized static native boolean H5is_library_threadsafe();
// /////// unimplemented ////////
- // H5_DLL herr_t H5free_memory(void *mem);
- // H5_DLL void *H5allocate_memory(size_t size, hbool_t clear);
- // H5_DLL void *H5resize_memory(void *mem, size_t size);
+ // herr_t H5free_memory(void *mem);
+ // void *H5allocate_memory(size_t size, hbool_t clear);
+ // void *H5resize_memory(void *mem, size_t size);
// ////////////////////////////////////////////////////////////
// //
@@ -852,7 +852,8 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
- public static long H5Aget_space(long attr_id) throws HDF5LibraryException {
+ public static long H5Aget_space(long attr_id) throws HDF5LibraryException
+ {
long id = _H5Aget_space(attr_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aget_space add {}", id);
@@ -888,7 +889,8 @@ public class H5 implements java.io.Serializable {
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
- public static long H5Aget_type(long attr_id) throws HDF5LibraryException {
+ public static long H5Aget_type(long attr_id) throws HDF5LibraryException
+ {
long id = _H5Aget_type(attr_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aget_type add {}", id);
@@ -918,8 +920,9 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - Name is null.
**/
- public static long H5Aopen(long obj_id, String attr_name, long aapl_id) throws HDF5LibraryException,
- NullPointerException {
+ public static long H5Aopen(long obj_id, String attr_name, long aapl_id)
+ throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Aopen(obj_id, attr_name, aapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen add {}", id);
@@ -959,7 +962,8 @@ public class H5 implements java.io.Serializable {
* - Name is null.
**/
public static long H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, long aapl_id,
- long lapl_id) throws HDF5LibraryException, NullPointerException {
+ long lapl_id) throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen_by_idx add {}", id);
@@ -994,7 +998,8 @@ public class H5 implements java.io.Serializable {
* - obj_name is null.
**/
public static long H5Aopen_by_name(long loc_id, String obj_name, String attr_name, long aapl_id, long lapl_id)
- throws HDF5LibraryException, NullPointerException {
+ throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Aopen_by_name(loc_id, obj_name, attr_name, aapl_id, lapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen_by_name add {}", id);
@@ -1015,8 +1020,10 @@ public class H5 implements java.io.Serializable {
* IN: Identifier of an attribute to read.
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
- * @param buf
- * IN: Buffer for data to be read.
+ * @param obj
+ * Buffer to store data read from the file.
+ * @param isCriticalPinning
+ * request lock on data reference.
*
* @return a non-negative value if successful
*
@@ -1025,9 +1032,19 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - data buffer is null.
**/
- public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] buf)
+ public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] obj, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
+ public synchronized static int H5Aread(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
+ return H5Aread(attr_id, mem_type_id, obj, true);
+ }
+
/**
* H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with
* mem_type_id. The entire attribute is read into data object from the file.
@@ -1038,31 +1055,143 @@ public class H5 implements java.io.Serializable {
* IN: Identifier of the attribute datatype (in memory).
* @param obj
* IN: Object for data to be read.
+ * @param isCriticalPinning
+ * request lock on data reference.
*
* @return a non-negative value if successful
*
+ * @exception HDF5Exception
+ * - Failure in the data conversion.
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data buffer is null. See public synchronized static native int H5Aread( )
**/
- public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception,
- NullPointerException {
- HDFArray theArray = new HDFArray(obj);
- byte[] buf = theArray.emptyBytes();
+ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning)
+ throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
+ int status = -1;
+ boolean is1D = false;
- // This will raise an exception if there is an error
- int status = H5Aread(attr_id, mem_type_id, buf);
+ Class dataClass = obj.getClass();
+ if (!dataClass.isArray()) {
+ throw (new HDF5JavaException("H5Aread: data is not an array"));
+ }
- // No exception: status really ought to be OK
- if (status >= 0) {
- obj = theArray.arrayify(buf);
+ String cname = dataClass.getName();
+ is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
+ char dname = cname.charAt(cname.lastIndexOf("[") + 1);
+ log.trace("H5Aread: cname={} is1D={} dname={}", cname, is1D, dname);
+
+ if (is1D && (dname == 'B')) {
+ log.trace("H5Aread_dname_B");
+ status = H5Aread(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'S')) {
+ log.trace("H5Aread_dname_S");
+ status = H5Aread_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'I')) {
+ log.trace("H5Aread_dname_I");
+ status = H5Aread_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'J')) {
+ log.trace("H5Aread_dname_J");
+ status = H5Aread_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'F')) {
+ log.trace("H5Aread_dname_F");
+ status = H5Aread_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'D')) {
+ log.trace("H5Aread_dname_D");
+ status = H5Aread_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
+ }
+ else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) && (is1D && (dataClass.getComponentType() == String.class))) || H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
+ log.trace("H5Aread_reg_ref");
+ status = H5Aread_reg_ref(attr_id, mem_type_id, (String[]) obj);
+ }
+ else if (is1D && (dataClass.getComponentType() == String.class)) {
+ log.trace("H5Aread_string type");
+ status = H5Aread_string(attr_id, mem_type_id, (String[]) obj);
+ }
+ else {
+ // Create a data buffer to hold the data into a Java Array
+ HDFArray theArray = new HDFArray(obj);
+ byte[] buf = theArray.emptyBytes();
+ log.trace("H5Aread_else");
+
+ // This will raise an exception if there is an error
+ status = H5Aread(attr_id, mem_type_id, buf, isCriticalPinning);
+
+ // No exception: status really ought to be OK
+ if (status >= 0) {
+ obj = theArray.arrayify(buf);
+ }
+
+ // clean up these: assign 'null' as hint to gc()
+ buf = null;
+ theArray = null;
}
return status;
}
- public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, String[] buf)
+ public synchronized static native int H5Aread_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_double(long attr_id, long mem_type_id, double[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_double(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_float(long attr_id, long mem_type_id, float[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_float(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_int(long attr_id, long mem_type_id, int[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_int(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_long(long attr_id, long mem_type_id, long[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_long(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Aread_short(long attr_id, long mem_type_id, short[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Aread_short(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, Object[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_string(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf)
@@ -1123,7 +1252,9 @@ public class H5 implements java.io.Serializable {
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
* @param buf
- * IN: Data to be written.
+ * IN: Buffer with data to be written to the file.
+ * @param isCriticalPinning
+ * IN: request lock on data reference.
*
* @return a non-negative value if successful
*
@@ -1132,9 +1263,21 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - data is null.
**/
- public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf)
+ public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
+ public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj)
+ throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite(attr_id, mem_type_id, obj, true);
+ }
+
/**
* H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with
* mem_type_id. The entire attribute is written from data object to the file.
@@ -1145,28 +1288,140 @@ public class H5 implements java.io.Serializable {
* IN: Identifier of the attribute datatype (in memory).
* @param obj
* IN: Data object to be written.
+ * @param isCriticalPinning
+ * request lock on data reference.
*
* @return a non-negative value if successful
*
+ * @exception HDF5Exception
+ * - Failure in the data conversion.
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
- * - data object is null. See public synchronized static native int H5Awrite(int attr_id, int
- * mem_type_id, byte[] buf);
+ * - data object is null
**/
- public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj)
- throws HDF5Exception, NullPointerException
+ public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj, boolean isCriticalPinning)
+ throws HDF5Exception, HDF5LibraryException, NullPointerException
{
- HDFArray theArray = new HDFArray(obj);
- byte[] buf = theArray.byteify();
+ int status = -1;
+ boolean is1D = false;
- int retVal = H5Awrite(attr_id, mem_type_id, buf);
- buf = null;
- theArray = null;
- return retVal;
+ Class dataClass = obj.getClass();
+ if (!dataClass.isArray()) {
+ throw (new HDF5JavaException("H5Dwrite: data is not an array"));
+ }
+
+ String cname = dataClass.getName();
+ is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
+ char dname = cname.charAt(cname.lastIndexOf("[") + 1);
+
+ if (is1D && (dname == 'B')) {
+ status = H5Awrite(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'S')) {
+ status = H5Awrite_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'I')) {
+ status = H5Awrite_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'J')) {
+ status = H5Awrite_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'F')) {
+ status = H5Awrite_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dname == 'D')) {
+ status = H5Awrite_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
+ }
+ else if (is1D && (dataClass.getComponentType() == String.class)) {
+ log.trace("H5Dwrite_string type");
+ status = H5Awrite_string(attr_id, mem_type_id, (String[]) obj);
+ }
+ else {
+ HDFArray theArray = new HDFArray(obj);
+ byte[] buf = theArray.byteify();
+
+ status = H5Awrite(attr_id, mem_type_id, buf);
+ buf = null;
+ theArray = null;
+ }
+
+ return status;
}
- public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, String[] buf)
+ public synchronized static native int H5Awrite_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_double(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_float(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_int(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_long(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf)
+ throws HDF5LibraryException, NullPointerException
+ {
+ return H5Awrite_short(attr_id, mem_type_id, buf, true);
+ }
+
+ public synchronized static native int H5Awrite_string(long attr_id, long mem_type_id, String[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf)
+ throws HDF5LibraryException, NullPointerException;
+
+ /**
+ * H5Awrite_VLStrings writes a variable length String dataset, specified by its identifier attr_id, from
+ * the application memory buffer buf into the file.
+ *
+ * ---- contributed by Rosetta Biosoftware
+ *
+ * @param attr_id
+ * Identifier of the attribute read from.
+ * @param mem_type_id
+ * Identifier of the memory datatype.
+ * @param buf
+ * Buffer with data to be written to the file.
+ *
+ * @return a non-negative value if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+
+ public synchronized static native int H5Awrite_VLStrings(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException;
/**
@@ -1614,8 +1869,8 @@ public class H5 implements java.io.Serializable {
* @exception NullPointerException
* - name is null.
**/
- public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException,
- NullPointerException {
+ public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException
+ {
long id = _H5Dopen2(loc_id, name, dapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Dopen add {}", id);
@@ -1664,12 +1919,14 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true);
}
@@ -1703,7 +1960,8 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException,
- NullPointerException {
+ NullPointerException
+ {
int status = -1;
boolean is1D = false;
@@ -1734,7 +1992,8 @@ public class H5 implements java.io.Serializable {
}
else if (is1D && (dname == 'J')) {
log.trace("H5Dread_dname_J");
- status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj);
+ status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj,
+ isCriticalPinning);
}
else if (is1D && (dname == 'F')) {
log.trace("H5Dread_dname_F");
@@ -1783,7 +2042,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1792,7 +2052,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1801,7 +2062,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1810,22 +2072,21 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dread_reg_ref(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;
- public synchronized static native int H5Dread_reg_ref_data(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;
-
public synchronized static native int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -1929,12 +2190,14 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
- long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException {
+ long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
+ {
return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true);
}
@@ -1968,7 +2231,8 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException,
- NullPointerException {
+ NullPointerException
+ {
int status = -1;
boolean is1D = false;
@@ -2031,7 +2295,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -2040,7 +2305,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -2049,7 +2315,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -2058,7 +2325,8 @@ public class H5 implements java.io.Serializable {
NullPointerException;
public synchronized static int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -2067,7 +2335,8 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id,
- long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException {
+ long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException
+ {
return H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
}
@@ -2133,10 +2402,10 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Drefresh(long dset_id) throws HDF5LibraryException;
// /////// unimplemented ////////
- // H5_DLL herr_t H5Ddebug(hid_t dset_id);
- // H5_DLL herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
- // H5_DLL herr_t H5Dformat_convert(hid_t dset_id);
- // H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
+ // herr_t H5Ddebug(hid_t dset_id);
+ // herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
+ // herr_t H5Dformat_convert(hid_t dset_id);
+ // herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
// herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id,
// size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data);
@@ -2808,10 +3077,29 @@ public class H5 implements java.io.Serializable {
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
+ *
+ * @deprecated As of HDF5 1.10.5 in favor of H5Fis_accessible.
**/
public synchronized static native boolean H5Fis_hdf5(String name) throws HDF5LibraryException, NullPointerException;
/**
+ * H5Fis_accessible determines if the file can be opened with the given fapl.
+ *
+ * @param name
+ * IN: File name to check.
+ * @param file_id
+ * IN: File identifier for a currently-open HDF5 file
+ *
+ * @return true if file is accessible, false if not.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - name is null.
+ **/
+ public synchronized static native boolean H5Fis_accessible(String name, long file_id) throws HDF5LibraryException, NullPointerException;
+
+ /**
* H5Fmount mounts the file specified by child_id onto the group specified by loc_id and name using the mount
* properties plist_id.
*
@@ -2942,20 +3230,20 @@ public class H5 implements java.io.Serializable {
throws HDF5LibraryException, NullPointerException;
// /////// unimplemented ////////
- // H5_DLL herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa);
- // H5_DLL herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment);
+ // herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa);
+ // herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment);
// ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len);
// herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info);
// ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t *sect_info/*out*/);
- // H5_DLL herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver_t high);
- // H5_DLL herr_t H5Fformat_convert(hid_t fid);
- // H5_DLL herr_t H5Freset_page_buffering_stats(hid_t file_id);
- // H5_DLL herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2],
+ // herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver_t high);
+ // herr_t H5Fformat_convert(hid_t fid);
+ // herr_t H5Freset_page_buffering_stats(hid_t file_id);
+ // herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2],
// unsigned hits[2], unsigned misses[2], unsigned evictions[2], unsigned bypasses[2]);
- // H5_DLL herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size);
+ // herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size);
// #ifdef H5_HAVE_PARALLEL
- // H5_DLL herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag);
- // H5_DLL herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag);
+ // herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag);
+ // herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag);
// #endif /* H5_HAVE_PARALLEL */
// /**
@@ -3015,25 +3303,25 @@ public class H5 implements java.io.Serializable {
// ////////////////////////////////////////////////////////////
// /////// unimplemented ////////
- // H5_DLL hid_t H5FDregister(const H5FD_class_t *cls);
- // H5_DLL herr_t H5FDunregister(hid_t driver_id);
- // H5_DLL H5FD_t *H5FDopen(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr);
- // H5_DLL herr_t H5FDclose(H5FD_t *file);
- // H5_DLL int H5FDcmp(const H5FD_t *f1, const H5FD_t *f2);
- // H5_DLL int H5FDquery(const H5FD_t *f, unsigned long *flags);
- // H5_DLL haddr_t H5FDalloc(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size);
- // H5_DLL herr_t H5FDfree(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size);
- // H5_DLL haddr_t H5FDget_eoa(H5FD_t *file, H5FD_mem_t type);
- // H5_DLL herr_t H5FDset_eoa(H5FD_t *file, H5FD_mem_t type, haddr_t eoa);
- // H5_DLL haddr_t H5FDget_eof(H5FD_t *file, H5FD_mem_t type);
- // H5_DLL herr_t H5FDget_vfd_handle(H5FD_t *file, hid_t fapl, void**file_handle);
- // H5_DLL herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, void *buf/*out*/);
- // H5_DLL herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, const void *buf);
- // H5_DLL herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
- // H5_DLL herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
- // H5_DLL herr_t H5FDlock(H5FD_t *file, hbool_t rw);
- // H5_DLL herr_t H5FDunlock(H5FD_t *file);
- // H5_DLL herr_t H5FDdriver_query(hid_t driver_id, unsigned long *flags/*out*/);
+ // hid_t H5FDregister(const H5FD_class_t *cls);
+ // herr_t H5FDunregister(hid_t driver_id);
+ // H5FD_t *H5FDopen(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr);
+ // herr_t H5FDclose(H5FD_t *file);
+ // int H5FDcmp(const H5FD_t *f1, const H5FD_t *f2);
+ // int H5FDquery(const H5FD_t *f, unsigned long *flags);
+ // haddr_t H5FDalloc(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size);
+ // herr_t H5FDfree(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size);
+ // haddr_t H5FDget_eoa(H5FD_t *file, H5FD_mem_t type);
+ // herr_t H5FDset_eoa(H5FD_t *file, H5FD_mem_t type, haddr_t eoa);
+ // haddr_t H5FDget_eof(H5FD_t *file, H5FD_mem_t type);
+ // herr_t H5FDget_vfd_handle(H5FD_t *file, hid_t fapl, void**file_handle);
+ // herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, void *buf/*out*/);
+ // herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, const void *buf);
+ // herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
+ // herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
+ // herr_t H5FDlock(H5FD_t *file, hbool_t rw);
+ // herr_t H5FDunlock(H5FD_t *file);
+ // herr_t H5FDdriver_query(hid_t driver_id, unsigned long *flags/*out*/);
// ////////////////////////////////////////////////////////////
// //
@@ -3506,7 +3794,7 @@ public class H5 implements java.io.Serializable {
// ////////////////////////////////////////////////////////////
// //
- // H5I: HDF5 1.8 Identifier Interface API Functions //
+ // H5I: HDF5 Identifier Interface API Functions //
// //
// ////////////////////////////////////////////////////////////
@@ -3662,12 +3950,20 @@ public class H5 implements java.io.Serializable {
// hid_t H5Iregister(H5I_type_t type, const void *object);
+ // typedef herr_t (*H5I_free_t)(void *);
// H5I_type_t H5Iregister_type(size_t hash_size, unsigned reserved, H5I_free_t free_func);
// void *H5Iremove_verify(hid_t id, H5I_type_t id_type);
+ // Type of the function to compare objects & keys
+ // typedef int (*H5I_search_func_t)(void *obj, hid_t id, void *key);
// void *H5Isearch(H5I_type_t type, H5I_search_func_t func, void *key);
+ // Type of the H5Iiterate callback function
+ // typedef herr_t (*H5I_iterate_func_t)(hid_t id, void *udata);
+ // herr_t H5Iiterate(H5I_type_t type, H5I_iterate_func_t op, void *op_data);
+
+
// //////////////////////////////////////////////////////////////////
// H5L: Link Interface Functions //
// //////////////////////////////////////////////////////////////////
@@ -4695,9 +4991,9 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Orefresh(long object_id) throws HDF5LibraryException;
// /////// unimplemented ////////
- // H5_DLL herr_t H5Odisable_mdc_flushes(hid_t object_id);
- // H5_DLL herr_t H5Oenable_mdc_flushes(hid_t object_id);
- // H5_DLL herr_t H5Oare_mdc_flushes_disabled(hid_t object_id, hbool_t *are_disabled);
+ // herr_t H5Odisable_mdc_flushes(hid_t object_id);
+ // herr_t H5Oenable_mdc_flushes(hid_t object_id);
+ // herr_t H5Oare_mdc_flushes_disabled(hid_t object_id, hbool_t *are_disabled);
// ////////////////////////////////////////////////////////////
// //
@@ -4982,6 +5278,27 @@ public class H5 implements java.io.Serializable {
private synchronized static native long _H5Pcopy(long plist) throws HDF5LibraryException;
+ // Define property list class callback function pointer types
+ // typedef herr_t (*H5P_cls_create_func_t)(hid_t prop_id, void *create_data);
+ // typedef herr_t (*H5P_cls_copy_func_t)(hid_t new_prop_id, hid_t old_prop_id, void *copy_data);
+ // typedef herr_t (*H5P_cls_close_func_t)(hid_t prop_id, void *close_data);
+
+ // Define property list callback function pointer types
+ // typedef herr_t (*H5P_prp_cb1_t)(const char *name, size_t size, void *value);
+ // typedef herr_t (*H5P_prp_cb2_t)(hid_t prop_id, const char *name, size_t size, void *value);
+ // typedef H5P_prp_cb1_t H5P_prp_create_func_t;
+ // typedef H5P_prp_cb2_t H5P_prp_set_func_t;
+ // typedef H5P_prp_cb2_t H5P_prp_get_func_t;
+ // typedef herr_t (*H5P_prp_encode_func_t)(const void *value, void **buf, size_t *size);
+ // typedef herr_t (*H5P_prp_decode_func_t)(const void **buf, void *value);
+ // typedef H5P_prp_cb2_t H5P_prp_delete_func_t;
+ // typedef H5P_prp_cb1_t H5P_prp_copy_func_t;
+ // typedef int (*H5P_prp_compare_func_t)(const void *value1, const void *value2, size_t size);
+ // typedef H5P_prp_cb1_t H5P_prp_close_func_t;
+
+ // Define property list iteration function type
+ // typedef herr_t (*H5P_iterate_t)(hid_t id, const char *name, void *iter_data);
+
public static long H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException {
long id = _H5Pcreate_class_nocb(parent_class, name);
if (id > 0) {
@@ -6145,6 +6462,11 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close)
throws HDF5LibraryException;
+ // ///// unimplemented /////
+ // herr_t H5Pset_vol(hid_t plist_id, hid_t new_vol_id, const void *new_vol_info);
+ // herr_t H5Pget_vol_id(hid_t plist_id, hid_t *vol_id);
+ // herr_t H5Pget_vol_info(hid_t plist_id, void **vol_info);
+
// Dataset creation property list (DCPL) routines //
/**
@@ -7523,13 +7845,13 @@ public class H5 implements java.io.Serializable {
// herr_t H5Pget_core_write_tracking(hid_t fapl_id, hbool_t *is_enabled, size_t *page_size);
// #ifdef H5_HAVE_PARALLEL
// herr_t H5Pset_all_coll_metadata_ops(hid_t accpl_id, hbool_t is_collective);
- // H5_DLL herr_t H5Pget_all_coll_metadata_ops(hid_t plist_id, hbool_t *is_collective);
+ // herr_t H5Pget_all_coll_metadata_ops(hid_t plist_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);
// #endif /* H5_HAVE_PARALLEL */
- // H5_DLL herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr);
- // H5_DLL herr_t H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr /*out*/);
- // H5_DLL herr_t H5Pset_page_buffer_size(hid_t plist_id, size_t buf_size, unsigned min_meta_per, unsigned min_raw_per);
+ // herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr);
+ // herr_t H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr /*out*/);
+ // herr_t H5Pset_page_buffer_size(hid_t plist_id, size_t buf_size, unsigned min_meta_per, unsigned min_raw_per);
// 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);
@@ -7552,9 +7874,9 @@ public class H5 implements java.io.Serializable {
// herr_t H5Pget_type_conv_cb(hid_t plist, H5T_conv_except_func_t *func, void **op_data)
// herr_t H5Pset_type_conv_cb( hid_t plist, H5T_conv_except_func_t func, void *op_data)
// #ifdef H5_HAVE_PARALLEL
- // H5_DLL herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t *actual_chunk_opt_mode);
- // H5_DLL herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t *actual_io_mode);
- // H5_DLL herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_cause, uint32_t *global_no_collective_cause);
+ // herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t *actual_chunk_opt_mode);
+ // herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t *actual_io_mode);
+ // herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_cause, uint32_t *global_no_collective_cause);
// #endif /* H5_HAVE_PARALLEL */
// Link creation property list (LCPL) routines //
@@ -8497,16 +8819,17 @@ public class H5 implements java.io.Serializable {
// /////// unimplemented ////////
// #ifdef NEW_HYPERSLAB_API
- // H5_DLL hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op,
+ // hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op,
// const hsize_t start[],
// const hsize_t _stride[],
// const hsize_t count[],
// const hsize_t _block[]);
- // H5_DLL herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op,
+ // herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op,
// hid_t space2_id);
- // H5_DLL hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op,
+ // hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op,
// hid_t space2_id);
// #endif /* NEW_HYPERSLAB_API */
+ // herr_t H5Sselect_copy(hid_t dst_id, hid_t src_id);
@@ -9985,6 +10308,25 @@ public class H5 implements java.io.Serializable {
// ////////////////////////////////////////////////////////////
// //
+ // H5VL: VOL Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ /// VOL Connector Functionality
+ public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id);
+ public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id);
+ public synchronized static native boolean H5VLis_connector_registered(String name);
+ public synchronized static native long H5VLget_connector_id(String name);
+ public synchronized static native String H5VLget_connector_name(long object_id);
+ public synchronized static native void H5VLclose(long connector_id);
+ public synchronized static native void H5VLunregister_connector(long connector_id);
+
+ // /////// unimplemented ////////
+ // hid_t H5VLregister_connector(const H5VL_class_t *cls, hid_t vipl_id);
+
+
+ // ////////////////////////////////////////////////////////////
+ // //
// H5Z: Filter Interface Functions //
// //
// ////////////////////////////////////////////////////////////
@@ -9995,9 +10337,9 @@ public class H5 implements java.io.Serializable {
public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException;
-}
+ // /////// unimplemented ////////
-// /////// unimplemented ////////
+ // herr_t H5Zregister(const void *cls);
-// herr_t H5Zregister(const void *cls);
+}
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index b530f4b..a0c2ed6 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -195,6 +195,11 @@ public class HDF5Constants {
public static final long H5E_WALK_UPWARD = H5E_WALK_UPWARD();
public static final long H5E_WRITEERROR = H5E_WRITEERROR();
+ private static final int H5ES_STATUS_IN_PROGRESS = H5ES_STATUS_IN_PROGRESS();
+ private static final int H5ES_STATUS_SUCCEED = H5ES_STATUS_SUCCEED();
+ private static final int H5ES_STATUS_FAIL = H5ES_STATUS_FAIL();
+ private static final int H5ES_STATUS_CANCELED = H5ES_STATUS_CANCELED();
+
public static final int H5F_ACC_CREAT = H5F_ACC_CREAT();
public static final int H5F_ACC_EXCL = H5F_ACC_EXCL();
public static final int H5F_ACC_RDONLY = H5F_ACC_RDONLY();
@@ -315,7 +320,6 @@ public class HDF5Constants {
public static final int H5I_GROUP = H5I_GROUP();
public static final int H5I_INVALID_HID = H5I_INVALID_HID();
public static final int H5I_NTYPES = H5I_NTYPES();
- public static final int H5I_REFERENCE = H5I_REFERENCE();
public static final int H5I_UNINIT = H5I_UNINIT();
public static final int H5I_VFL = H5I_VFL();
public static final int H5I_VOL = H5I_VOL();
@@ -390,7 +394,10 @@ public class HDF5Constants {
public static final int H5PL_TYPE_ERROR = H5PL_TYPE_ERROR();
public static final int H5PL_TYPE_FILTER = H5PL_TYPE_FILTER();
+ public static final int H5PL_TYPE_VOL = H5PL_TYPE_VOL();
+ public static final int H5PL_TYPE_NONE = H5PL_TYPE_NONE();
public static final int H5PL_FILTER_PLUGIN = H5PL_FILTER_PLUGIN();
+ public static final int H5PL_VOL_PLUGIN = H5PL_VOL_PLUGIN();
public static final int H5PL_ALL_PLUGIN = H5PL_ALL_PLUGIN();
public static final int H5R_BADTYPE = H5R_BADTYPE();
@@ -626,6 +633,18 @@ public class HDF5Constants {
public static final long H5T_VARIABLE = H5T_VARIABLE();
public static final int H5T_VLEN = H5T_VLEN();
public static final int H5T_VL_T = H5T_VL_T();
+
+ public static final int H5VL_CAP_FLAG_NONE = H5VL_CAP_FLAG_NONE();
+ public static final int H5VL_CAP_FLAG_THREADSAFE = H5VL_CAP_FLAG_THREADSAFE();
+ public static final long H5VL_NATIVE = H5VL_NATIVE();
+ public static final String H5VL_NATIVE_NAME = H5VL_NATIVE_NAME();
+ public static final int H5VL_NATIVE_VALUE = H5VL_NATIVE_VALUE();
+ public static final int H5VL_NATIVE_VERSION = H5VL_NATIVE_VERSION();
+ public static final int H5_VOL_INVALID = H5_VOL_INVALID();
+ public static final int H5_VOL_NATIVE = H5_VOL_NATIVE();
+ public static final int H5_VOL_RESERVED = H5_VOL_RESERVED();
+ public static final int H5_VOL_MAX = H5_VOL_MAX();
+
public static final int H5Z_CB_CONT = H5Z_CB_CONT();
public static final int H5Z_CB_ERROR = H5Z_CB_ERROR();
public static final int H5Z_CB_FAIL = H5Z_CB_FAIL();
@@ -990,6 +1009,14 @@ public class HDF5Constants {
private static native final long H5E_WRITEERROR();
+ private static native final int H5ES_STATUS_IN_PROGRESS();
+
+ private static native final int H5ES_STATUS_SUCCEED();
+
+ private static native final int H5ES_STATUS_FAIL();
+
+ private static native final int H5ES_STATUS_CANCELED();
+
private static native final int H5F_ACC_CREAT();
private static native final int H5F_ACC_EXCL();
@@ -1222,8 +1249,6 @@ public class HDF5Constants {
private static native final int H5I_NTYPES();
- private static native final int H5I_REFERENCE();
-
private static native final int H5I_UNINIT();
private static native final int H5I_VFL();
@@ -1364,10 +1389,16 @@ public class HDF5Constants {
private static native final int H5PL_TYPE_FILTER();
+ private static native final int H5PL_TYPE_VOL();
+
+ private static native final int H5PL_TYPE_NONE();
+
private static native final int H5PL_FILTER_PLUGIN();
private static native final int H5PL_ALL_PLUGIN();
+ private static native final int H5PL_VOL_PLUGIN();
+
private static native final int H5R_BADTYPE();
private static native final int H5R_DATASET_REGION();
@@ -1834,6 +1865,26 @@ public class HDF5Constants {
private static native final int H5T_VL_T();
+ private static native final int H5VL_CAP_FLAG_NONE();
+
+ private static native final int H5VL_CAP_FLAG_THREADSAFE();
+
+ private static native final long H5VL_NATIVE();
+
+ private static native final String H5VL_NATIVE_NAME();
+
+ private static native final int H5VL_NATIVE_VALUE();
+
+ private static native final int H5VL_NATIVE_VERSION();
+
+ private static native final int H5_VOL_INVALID();
+
+ private static native final int H5_VOL_NATIVE();
+
+ private static native final int H5_VOL_RESERVED();
+
+ private static native final int H5_VOL_MAX();
+
private static native final int H5Z_CB_CONT();
private static native final int H5Z_CB_ERROR();
diff --git a/java/src/jni/CMakeLists.txt b/java/src/jni/CMakeLists.txt
index 7b95e0b..00c2b34 100644
--- a/java/src/jni/CMakeLists.txt
+++ b/java/src/jni/CMakeLists.txt
@@ -19,6 +19,7 @@ set (HDF5_JAVA_JNI_CSRCS
${HDF5_JAVA_JNI_SOURCE_DIR}/h5sImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5tImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5util.c
+ ${HDF5_JAVA_JNI_SOURCE_DIR}/h5vlImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/h5zImp.c
${HDF5_JAVA_JNI_SOURCE_DIR}/nativeData.c
)
@@ -40,6 +41,7 @@ set (HDF5_JAVA_JNI_CHDRS
${HDF5_JAVA_JNI_SOURCE_DIR}/h5sImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5tImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5util.h
+ ${HDF5_JAVA_JNI_SOURCE_DIR}/h5vlImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/h5zImp.h
${HDF5_JAVA_JNI_SOURCE_DIR}/nativeData.h
)
@@ -48,7 +50,9 @@ set (CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON)
########### JNI libraries always must be built shared ###############
add_library (${HDF5_JAVA_JNI_LIB_TARGET} SHARED ${HDF5_JAVA_JNI_CSRCS} ${HDF5_JAVA_JNI_CHDRS})
-target_include_directories(${HDF5_JAVA_JNI_LIB_TARGET} PRIVATE ${HDF5_BINARY_DIR} ${HDF5_JAVA_JNI_SOURCE_DIR})
+target_include_directories(${HDF5_JAVA_JNI_LIB_TARGET}
+ PRIVATE "${HDF5_BINARY_DIR};${HDF5_JAVA_JNI_SOURCE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
+)
TARGET_C_PROPERTIES (${HDF5_JAVA_JNI_LIB_TARGET} SHARED)
target_link_libraries (${HDF5_JAVA_JNI_LIB_TARGET} PUBLIC ${HDF5_LIBSH_TARGET})
set_target_properties (${HDF5_JAVA_JNI_LIB_TARGET} PROPERTIES FOLDER libraries/jni)
diff --git a/java/src/jni/Makefile.am b/java/src/jni/Makefile.am
index 6ded371..370b08b 100644
--- a/java/src/jni/Makefile.am
+++ b/java/src/jni/Makefile.am
@@ -34,7 +34,7 @@ libhdf5_java_la_LDFLAGS = -avoid-version -shared -export-dynamic -version-info $
# Source files for the library
libhdf5_java_la_SOURCES=exceptionImp.c h5Constants.c nativeData.c h5util.c h5Imp.c \
h5aImp.c h5dImp.c h5eImp.c h5fImp.c h5gImp.c h5iImp.c h5lImp.c h5oImp.c \
- h5pImp.c h5plImp.c h5rImp.c h5sImp.c h5tImp.c h5zImp.c
+ h5pImp.c h5plImp.c h5rImp.c h5sImp.c h5tImp.c h5vlImp.c h5zImp.c
# HDF5 Java (JNI) library depends on HDF5 Library.
libhdf5_java_la_LIBADD=$(LIBHDF5)
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index fdec61a..e88fa55 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -21,8 +21,10 @@
extern "C" {
#endif /* __cplusplus */
-#include <jni.h>
#include "hdf5.h"
+#include <jni.h>
+#include <stdlib.h>
+#include "h5jni.h"
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wmissing-prototypes"
@@ -352,6 +354,15 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1WALK_1UPWARD(JNIEnv *env, jclass cls) { retu
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5E_1WRITEERROR(JNIEnv *env, jclass cls) { return H5E_WRITEERROR; }
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5ES_1STATUS_1IN_1PROGRESS(JNIEnv *env, jclass cls) { return H5ES_STATUS_IN_PROGRESS; }
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5ES_1STATUS_1SUCCEED(JNIEnv *env, jclass cls) { return H5ES_STATUS_SUCCEED; }
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5ES_1STATUS_1FAIL(JNIEnv *env, jclass cls) { return H5ES_STATUS_FAIL; }
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5ES_1STATUS_1CANCELED(JNIEnv *env, jclass cls) { return H5ES_STATUS_CANCELED; }
+
/* Java does not have unsigned native types */
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wsign-conversion"
@@ -603,8 +614,6 @@ Java_hdf_hdf5lib_HDF5Constants_H5I_1DATASET(JNIEnv *env, jclass cls) { return H5
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5I_1ATTR(JNIEnv *env, jclass cls) { return H5I_ATTR; }
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5I_1REFERENCE(JNIEnv *env, jclass cls) { return H5I_REFERENCE; }
-JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5I_1VFL(JNIEnv *env, jclass cls) { return H5I_VFL; }
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5I_1VOL(JNIEnv *env, jclass cls) { return H5I_VOL; }
@@ -763,8 +772,14 @@ Java_hdf_hdf5lib_HDF5Constants_H5PL_1TYPE_1ERROR(JNIEnv *env, jclass cls) { retu
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5PL_1TYPE_1FILTER(JNIEnv *env, jclass cls) { return H5PL_TYPE_FILTER; }
JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5PL_1TYPE_1VOL(JNIEnv *env, jclass cls) { return H5PL_TYPE_VOL; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5PL_1TYPE_1NONE(JNIEnv *env, jclass cls) { return H5PL_TYPE_NONE; }
+JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5PL_1FILTER_1PLUGIN(JNIEnv *env, jclass cls) { return H5PL_FILTER_PLUGIN; }
JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5PL_1VOL_1PLUGIN(JNIEnv *env, jclass cls) { return H5PL_VOL_PLUGIN; }
+JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5PL_1ALL_1PLUGIN(JNIEnv *env, jclass cls) { return H5PL_ALL_PLUGIN; }
JNIEXPORT jint JNICALL
@@ -1239,6 +1254,28 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5T_1VL_1T(JNIEnv *env, jclass cls) { return sizeof(hvl_t); }
JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5VL_1CAP_1FLAG_1NONE(JNIEnv *env, jclass cls) { return H5VL_CAP_FLAG_NONE; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5VL_1CAP_1FLAG_1THREADSAFE(JNIEnv *env, jclass cls) { return H5VL_CAP_FLAG_THREADSAFE; }
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5VL_1NATIVE(JNIEnv *env, jclass cls) { return H5VL_NATIVE; }
+JNIEXPORT jobject JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5VL_1NATIVE_1NAME(JNIEnv *env, jclass cls) { return (jstring)ENVPTR->NewStringUTF(ENVPAR H5VL_NATIVE_NAME); }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5VL_1NATIVE_1VALUE(JNIEnv *env, jclass cls) { return H5VL_NATIVE_VALUE; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5VL_1NATIVE_1VERSION(JNIEnv *env, jclass cls) { return H5VL_NATIVE_VERSION; }
+
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5_1VOL_1INVALID(JNIEnv *env, jclass cls) { return H5_VOL_INVALID; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5_1VOL_1NATIVE(JNIEnv *env, jclass cls) { return H5_VOL_NATIVE; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5_1VOL_1RESERVED(JNIEnv *env, jclass cls) { return H5_VOL_RESERVED; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5_1VOL_1MAX(JNIEnv *env, jclass cls) { return H5_VOL_MAX; }
+
+JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5Z_1CB_1CONT(JNIEnv *env, jclass cls) { return H5Z_CB_CONT; }
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_HDF5Constants_H5Z_1CB_1ERROR(JNIEnv *env, jclass cls) { return H5Z_CB_ERROR; }
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index aba2240..e0ec4ca 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -60,6 +60,94 @@ static herr_t H5AreadVL_str (JNIEnv *env, hid_t attr_id, hid_t mem_id, jobjectAr
static herr_t H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *info, void *cb_data);
+/********************/
+/* Local Macros */
+/********************/
+
+#define PIN_BYTE_ARRAY() { \
+ if (isCriticalPinning) \
+ buffP = (jbyte*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+ else \
+ buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_BYTE_ARRAY(mode) { \
+ if (isCriticalPinning) \
+ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+ else \
+ ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_SHORT_ARRAY() { \
+ if (isCriticalPinning) \
+ buffP = (jshort*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+ else \
+ buffP = ENVPTR->GetShortArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_SHORT_ARRAY(mode) { \
+ if (isCriticalPinning) \
+ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+ else \
+ ENVPTR->ReleaseShortArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_INT_ARRAY() { \
+ if (isCriticalPinning) \
+ buffP = (jint*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+ else \
+ buffP = ENVPTR->GetIntArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_INT_ARRAY(mode) { \
+ if (isCriticalPinning) \
+ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+ else \
+ ENVPTR->ReleaseIntArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_LONG_ARRAY() { \
+ if (isCriticalPinning) \
+ buffP = (jlong*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+ else \
+ buffP = ENVPTR->GetLongArrayElements(ENVPAR buf,&isCopy); \
+}
+
+#define UNPIN_LONG_ARRAY(mode) { \
+ if (isCriticalPinning) \
+ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+ else \
+ ENVPTR->ReleaseLongArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_FLOAT_ARRAY() { \
+ if (isCriticalPinning) \
+ buffP = (jfloat*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+ else \
+ buffP = ENVPTR->GetFloatArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_FLOAT_ARRAY(mode) { \
+ if (isCriticalPinning) \
+ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+ else \
+ ENVPTR->ReleaseFloatArrayElements(ENVPAR buf, buffP, mode); \
+}
+
+#define PIN_DOUBLE_ARRAY() { \
+ if (isCriticalPinning) \
+ buffP = (jdouble*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \
+ else \
+ buffP = ENVPTR->GetDoubleArrayElements(ENVPAR buf, &isCopy); \
+}
+
+#define UNPIN_DOUBLE_ARRAY(mode) { \
+ if (isCriticalPinning) \
+ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \
+ else \
+ ENVPTR->ReleaseDoubleArrayElements(ENVPAR buf, buffP, mode); \
+}
+
/*
* Class: hdf_hdf5lib_H5
@@ -129,36 +217,129 @@ Java_hdf_hdf5lib_H5__1H5Aopen_1idx
return (jlong)attr_id;
} /* end Java_hdf_hdf5lib_H5__1H5Aopen_1idx */
+static htri_t
+H5Tdetect_variable_str
+ (hid_t tid) {
+ htri_t ret_val = 0;
+
+ if (H5Tget_class(tid) == H5T_COMPOUND) {
+ unsigned i;
+ unsigned nm = (unsigned)H5Tget_nmembers(tid);
+ for(i = 0; i < nm; i++) {
+ htri_t status = 0;
+ hid_t mtid = 0;
+ if((mtid = H5Tget_member_type(tid, i)) < 0)
+ return -1; /* exit immediately on error */
+ if((status = H5Tdetect_variable_str(mtid)) < 0)
+ return status; /* exit immediately on error */
+ ret_val |= status;
+ H5Tclose (mtid);
+ } /* end for */
+ } /* end if */
+ else
+ ret_val = H5Tis_variable_str(tid);
+
+ return ret_val;
+} /* end H5Tdetect_variable_str */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread
+ * Signature: (JJ[BZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jbyte *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument( env,"H5Aread: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread: buf does not support variable length type");
+ } /* end else if */
+ else {
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_BYTE_ARRAY();
+
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, buffP);
+ if (status < 0) {
+ UNPIN_BYTE_ARRAY(JNI_ABORT);
+ h5libraryError(env);
+ } /* end if */
+ else {
+ UNPIN_BYTE_ARRAY(0); /* update java buffer for return */
+ } /* end else */
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Aread */
+
/*
* Class: hdf_hdf5lib_H5
* Method: H5Awrite
- * Signature: (JJ[B)I
+ * Signature: (JJ[BZ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Awrite
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf)
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf, jboolean isCriticalPinning)
{
herr_t status = -1;
- jbyte *byteP;
+ jbyte *buffP;
jboolean isCopy;
+ htri_t data_class;
if (buf == NULL) {
h5nullArgument( env,"H5Awrite: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite: buf does not support variable length type");
+ } /* end else if */
else {
- byteP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy);
- if (byteP == NULL) {
- h5JNIFatalError(env,"H5Awrite: buf is not pinned");
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Awrite: H5Tdetect_variable_str() failed");
} /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite: buf does not support variable length type");
+ } /* end else if */
else {
- status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, byteP);
+ PIN_BYTE_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- /* free the buffer without copying back */
- ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT);
+ UNPIN_BYTE_ARRAY(JNI_ABORT); /* no need to update buffer */
- if (status < 0)
- h5libraryError(env);
- }
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
} /* end else */
return (jint)status;
@@ -166,190 +347,653 @@ Java_hdf_hdf5lib_H5_H5Awrite
/*
* Class: hdf_hdf5lib_H5
- * Method: H5Aread
- * Signature: (JJ[B)I
+ * Method: H5Aread_short
+ * Signature: (JJ[SZ)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5Aread
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf)
+Java_hdf_hdf5lib_H5_H5Aread_1short
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jshortArray buf, jboolean isCriticalPinning)
{
herr_t status = -1;
- jbyte *byteP;
+ jshort *buffP;
jboolean isCopy;
+ htri_t data_class;
if (buf == NULL) {
- h5nullArgument( env,"H5Aread: buf is NULL");
+ h5nullArgument(env, "H5Aread_short: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_short: buf does not support variable length type");
+ } /* end else if */
else {
- byteP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy);
- if (byteP == NULL) {
- h5JNIFatalError( env,"H5Aread: buf is not pinned");
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread_short: H5Tdetect_variable_str() failed");
} /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_short: buf does not support variable length type");
+ } /* end else if */
else {
- status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP);
- if (status < 0) {
- ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT);
- h5libraryError(env);
+ PIN_SHORT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_short: buf not pinned");
} /* end if */
- else {
- ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, 0);
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, buffP);
+
+ if (status < 0) {
+ UNPIN_SHORT_ARRAY(JNI_ABORT);
+ h5libraryError(env);
+ } /* end if */
+ else {
+ UNPIN_SHORT_ARRAY(0);
+ } /* end else */
} /* end else */
} /* end else */
} /* end else */
return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5Aread */
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1short */
/*
* Class: hdf_hdf5lib_H5
- * Method: H5AwriteVL
- * Signature: (JJ[Ljava/lang/String;)I
+ * Method: H5Awrite_short
+ * Signature: (JJ[SZ)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AwriteVL
- (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
+Java_hdf_hdf5lib_H5_H5Awrite_1short
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jshortArray buf, jboolean isCriticalPinning)
{
- herr_t status = -1;
- htri_t isStr = 0;
- htri_t isVlenStr = 0;
- htri_t isComplex = 0;
+ herr_t status = -1;
+ jshort *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL ) {
+ h5nullArgument(env, "H5Awrite_short: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_short: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_short: buf does not support variable length type");
+ } /* end else if */
+ else {
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_short: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_short: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_SHORT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_short: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
+
+ UNPIN_SHORT_ARRAY(JNI_ABORT);
+
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1short */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_int
+ * Signature: (JJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1int
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jintArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jint *buffP;
+ jboolean isCopy;
+ htri_t data_class;
if (buf == NULL) {
- h5nullArgument(env, "H5AwriteVL: buf is NULL");
+ h5nullArgument(env, "H5Aread_int: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread_int: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_int: buf does not support variable length type");
+ } /* end else if */
else {
- isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
- if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) {
- unsigned i;
- int nm = H5Tget_nmembers(mem_type_id);
- for(i = 0; i <nm; i++) {
- hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i);
- isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) ||
- H5Tdetect_class((hid_t)nested_tid, H5T_VLEN);
- H5Tclose(nested_tid);
- }
- }
- else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) {
- isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */
- }
- if (isStr == 0 || isComplex>0 || isVlenStr) {
- status = H5AwriteVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
- }
- else if (isStr > 0) {
- status = H5AwriteVL_str(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
- }
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread_int: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_int: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_INT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_int: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, buffP);
+
+ if (status < 0) {
+ UNPIN_INT_ARRAY(JNI_ABORT);
+ h5libraryError(env);
+ } /* end if */
+ else {
+ UNPIN_INT_ARRAY(0);
+ } /* end else */
+ } /* end else */
+ } /* end else */
} /* end else */
return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VL */
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1int */
-herr_t
-H5AwriteVL_str
- (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_int
+ * Signature: (JJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1int
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jintArray buf, jboolean isCriticalPinning)
{
- herr_t status = -1;
- char **wdata;
- jsize size;
- jint i;
+ herr_t status = -1;
+ jint *buffP;
+ jboolean isCopy;
+ htri_t data_class;
- size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf);
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Awrite_int: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_int: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_int: buf does not support variable length type");
+ } /* end else if */
+ else {
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_int: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_int: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_INT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_int: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*));
- if (!wdata) {
- h5JNIFatalError(env, "H5AwriteVL_str: cannot allocate buffer");
+ UNPIN_INT_ARRAY(JNI_ABORT);
+
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1int */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_long
+ * Signature: (JJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1long
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jlongArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jlong *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Aread_long: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread_long: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_long: buf does not support variable length type");
+ } /* end else if */
else {
- HDmemset(wdata, 0, (size_t)size * sizeof(char*));
- for (i = 0; i < size; ++i) {
- jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray) buf, i);
- if (obj != 0) {
- jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj);
- const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread_long: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_long: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_LONG_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_long: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- if (utf8) {
- wdata[i] = (char*)HDmalloc((size_t)length + 1);
- if (wdata[i]) {
- HDmemset(wdata[i], 0, ((size_t)length + 1));
- HDstrncpy(wdata[i], utf8, (size_t)length);
- } /* end if */
+ if (status < 0) {
+ UNPIN_LONG_ARRAY(JNI_ABORT);
+ h5libraryError(env);
} /* end if */
+ else {
+ UNPIN_LONG_ARRAY(0);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+ } /* end else */
- ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
- ENVPTR->DeleteLocalRef(ENVPAR obj);
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1long */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_long
+ * Signature: (JJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1long
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jlongArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jlong *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Awrite_long: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Dwrite_long: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_long: buf does not support variable length type");
+ } /* end else if */
+ else {
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_long: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_long: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_LONG_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_long: buf not pinned");
} /* end if */
- } /* end for (i = 0; i < size; ++i) */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- status = H5Awrite((hid_t)aid, (hid_t)tid, wdata);
+ UNPIN_LONG_ARRAY(JNI_ABORT);
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
+ } /* end else */
- for (i = 0; i < size; i++) {
- if(wdata[i]) {
- HDfree(wdata[i]);
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1long */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_float
+ * Signature: (JJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1float
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jfloatArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jfloat *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Aread_float: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Dread_float: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_float: buf does not support variable length type");
+ } /* end else if */
+ else {
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread_float: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_float: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_FLOAT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_float: buf not pinned");
} /* end if */
- } /* end for */
- HDfree(wdata);
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- if (status < 0)
- h5libraryError(env);
+ if (status < 0) {
+ UNPIN_FLOAT_ARRAY(JNI_ABORT);
+ h5libraryError(env);
+ } /* end if */
+ else {
+ UNPIN_FLOAT_ARRAY(0);
+ } /* end else */
+ } /* end else */
+ } /* end else */
} /* end else */
return (jint)status;
-}
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1float */
-herr_t
-H5AwriteVL_asstr
- (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_float
+ * Signature: (JJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1float
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jfloatArray buf, jboolean isCriticalPinning)
{
- char **strs;
- jstring jstr;
- jint i;
- jint n;
- hid_t sid;
- hsize_t dims[H5S_MAX_RANK];
- herr_t status = -1;
+ herr_t status = -1;
+ jfloat *buffP;
+ jboolean isCopy;
+ htri_t data_class;
- n = ENVPTR->GetArrayLength(ENVPAR buf);
- strs =(hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Awrite_float: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_float: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_float: buf does not support variable length type");
+ } /* end else if */
+ else {
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_float: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_float: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_FLOAT_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_float: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- if (strs == NULL) {
- h5JNIFatalError(env, "H5AwriteVL_asstr: failed to allocate buff for read variable length strings");
+ UNPIN_FLOAT_ARRAY(JNI_ABORT);
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1float */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_double
+ * Signature: (JJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1double
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jdoubleArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jdouble *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Aread_double: buf is NULL");
} /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Aread_double: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_double: buf does not support variable length type");
+ } /* end else if */
else {
- status = H5Awrite(aid, tid, strs);
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Aread_double: H5Tdetect_variable_str() failed");
+ } /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Aread_double: buf does not support variable length type");
+ } /* end else if */
+ else {
+ PIN_DOUBLE_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Aread_double: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, buffP);
- if (status < 0) {
- dims[0] = (hsize_t)n;
- sid = H5Screate_simple(1, dims, NULL);
- H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
- H5Sclose(sid);
- HDfree(strs);
- h5JNIFatalError(env, "H5AwriteVL_str: failed to read variable length strings");
+ if (status < 0) {
+ UNPIN_DOUBLE_ARRAY(JNI_ABORT);
+ h5libraryError(env);
+ } /* end if */
+ else {
+ UNPIN_DOUBLE_ARRAY(0);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1double */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_double
+ * Signature: (JJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1double
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jdoubleArray buf, jboolean isCriticalPinning)
+{
+ herr_t status = -1;
+ jdouble *buffP;
+ jboolean isCopy;
+ htri_t data_class;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5Awrite_double: buf is NULL");
+ } /* end if */
+ else if((data_class = H5Tdetect_class(mem_type_id, H5T_VLEN)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_double: H5Tdetect_class() failed");
+ } /* end else if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_double: buf does not support variable length type");
+ } /* end else if */
+ else {
+ /* recursive detect any vlen string in type (compound, array ...) */
+ if((data_class = H5Tdetect_variable_str(mem_type_id)) < 0) {
+ h5JNIFatalError(env, "H5Awrite_double: H5Tdetect_variable_str() failed");
} /* end if */
+ else if(data_class == 1) {
+ h5badArgument(env, "H5Awrite_double: buf does not support variable length type");
+ } /* end else if */
else {
- for (i=0; i < n; i++) {
- jstr = ENVPTR->NewStringUTF(ENVPAR strs[i]);
- ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
- H5free_memory (strs[i]);
+ PIN_DOUBLE_ARRAY();
+ if (buffP == NULL) {
+ h5JNIFatalError(env, "H5Awrite_double: buf not pinned");
+ } /* end if */
+ else {
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, buffP);
+
+ UNPIN_DOUBLE_ARRAY(JNI_ABORT);
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+ } /* end else */
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1double */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_string
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1string
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray j_buf)
+{
+ herr_t status = -1;
+ char *c_buf;
+ char *cstr;
+ size_t str_len;
+ jsize i;
+ jsize n;
+ size_t pos;
+ jstring jstr;
+
+ c_buf = cstr = NULL;
+ if (j_buf == NULL) {
+ h5nullArgument(env, "H5Aread_string: buf is NULL");
+ } /* end if */
+ else if ((n = ENVPTR->GetArrayLength(ENVPAR j_buf)) <= 0) {
+ h5nullArgument(env, "H5Aread_string: buf length <= 0");
+ } /* end else if */
+ else if ((str_len = H5Tget_size((hid_t)mem_type_id)) <=0) {
+ h5libraryError(env);
+ } /* end else if */
+ else {
+ if ((cstr = (char*)HDmalloc(str_len + 1)) == NULL) {
+ h5JNIFatalError(env, "H5Aread_string: memory allocation failed.");
+ } /* end if */
+ else {
+ if ((c_buf = (char*)HDmalloc((size_t)n * str_len)) == NULL) {
+ if (cstr)
+ HDfree(cstr);
+ cstr = NULL;
+ h5JNIFatalError(env, "H5Aread_string: memory allocation failed.");
+ } /* end if */
+ else {
+ status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, c_buf);
+
+ if (status < 0) {
+ if (cstr)
+ HDfree(cstr);
+ cstr = NULL;
+ if (c_buf)
+ HDfree(c_buf);
+ c_buf = NULL;
+ h5libraryError(env);
+ } /* end if */
+ else {
+ pos = 0;
+ for (i = 0; i < n; i++) {
+ HDmemcpy(cstr, c_buf+pos, str_len);
+ cstr[str_len] = '\0';
+ jstr = ENVPTR->NewStringUTF(ENVPAR cstr);
+ ENVPTR->SetObjectArrayElement(ENVPAR j_buf, i, jstr);
+ pos += str_len;
+ } /* end for */
+ } /* end else */
+
+ if (c_buf)
+ HDfree(c_buf);
+ } /* end else cbuf allocation*/
+
+ if (cstr)
+ HDfree(cstr);
+ } /* end else cstr allocation*/
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1string */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_string
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1string
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray j_buf)
+{
+ herr_t status = -1;
+ char *c_buf;
+ jsize str_len;
+ jsize i;
+ jsize n;
+
+ if (j_buf == NULL) {
+ h5nullArgument(env, "H5Awrite_string: buf is NULL");
+ } /* end if */
+ else if ((n = ENVPTR->GetArrayLength(ENVPAR j_buf)) <= 0) {
+ h5nullArgument(env, "H5Awrite_string: buf length <= 0");
+ } /* end else if */
+ else if ((str_len = (jsize)H5Tget_size((hid_t)mem_type_id)) <=0) {
+ h5libraryError(env);
+ } /* end else if */
+ else {
+ if ((c_buf = (char*)HDmalloc((size_t)n * (size_t)str_len)) == NULL) {
+ h5JNIFatalError(env, "H5Awrite_string: memory allocation failed.");
+ } /* end if */
+ else {
+ for (i = 0; i < n; i++) {
+ jstring obj = (jstring)ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray)j_buf, i);
+ if (obj != 0) {
+ jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj);
+ const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
+
+ if (utf8) {
+ HDstrncpy(&c_buf[i * str_len], utf8, str_len);
+ } /* end if */
+
+ ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
+ ENVPTR->DeleteLocalRef(ENVPAR obj);
+ } /* end if */
} /* end for */
- /*
- for repeatedly reading a dataset with a large number of strs (e.g., 1,000,000 strings,
- H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect
- free space in time. Instead, use "H5free_memory(strs[i])" above to free individual strings
- after it is done.
- H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs);
- */
+ status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, c_buf);
- HDfree(strs);
+ if (c_buf)
+ HDfree(c_buf);
+ c_buf = NULL;
+
+ if (status < 0) {
+ h5libraryError(env);
+ } /* end if */
} /* end else */
} /* end else */
- return status;
-} /* end H5AwriteVL_str */
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1string */
/*
* Class: hdf_hdf5lib_H5
* Method: H5AreadVL
- * Signature: (JJJJJ[Ljava/lang/String;)I
+ * Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5AreadVL
@@ -519,6 +1163,206 @@ H5AreadVL_str
/*
* Class: hdf_hdf5lib_H5
+ * Method: H5AwriteVL
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5AwriteVL
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
+{
+ herr_t status = -1;
+ htri_t isStr = 0;
+ htri_t isVlenStr = 0;
+ htri_t isComplex = 0;
+
+ if (buf == NULL) {
+ h5nullArgument(env, "H5AwriteVL: buf is NULL");
+ } /* end if */
+ else {
+ isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
+ if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) {
+ unsigned i;
+ int nm = H5Tget_nmembers(mem_type_id);
+ for(i = 0; i <nm; i++) {
+ hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, i);
+ isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) ||
+ H5Tdetect_class((hid_t)nested_tid, H5T_VLEN);
+ H5Tclose(nested_tid);
+ }
+ }
+ else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) {
+ isVlenStr = 1; /* strings created by H5Tvlen_create(H5T_C_S1) */
+ }
+ if (isStr == 0 || isComplex>0 || isVlenStr) {
+ status = H5AwriteVL_asstr(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
+ }
+ else if (isStr > 0) {
+ status = H5AwriteVL_str(env, (hid_t)attr_id, (hid_t)mem_type_id, buf);
+ }
+ } /* end else */
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Awrite_1VL */
+
+herr_t
+H5AwriteVL_str
+ (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+{
+ herr_t status = -1;
+ char **wdata;
+ jsize size;
+ jint i;
+
+ size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf);
+
+ wdata = (char**)HDcalloc((size_t)size + 1, sizeof(char*));
+ if (!wdata) {
+ h5JNIFatalError(env, "H5AwriteVL_str: cannot allocate buffer");
+ } /* end if */
+ else {
+ HDmemset(wdata, 0, (size_t)size * sizeof(char*));
+ for (i = 0; i < size; ++i) {
+ jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray) buf, i);
+ if (obj != 0) {
+ jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj);
+ const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
+
+ if (utf8) {
+ wdata[i] = (char*)HDmalloc((size_t)length + 1);
+ if (wdata[i]) {
+ HDmemset(wdata[i], 0, ((size_t)length + 1));
+ HDstrncpy(wdata[i], utf8, (size_t)length);
+ } /* end if */
+ } /* end if */
+
+ ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
+ ENVPTR->DeleteLocalRef(ENVPAR obj);
+ } /* end if */
+ } /* end for (i = 0; i < size; ++i) */
+
+ status = H5Awrite((hid_t)aid, (hid_t)tid, wdata);
+
+ for (i = 0; i < size; i++) {
+ if(wdata[i]) {
+ HDfree(wdata[i]);
+ } /* end if */
+ } /* end for */
+ HDfree(wdata);
+
+ if (status < 0)
+ h5libraryError(env);
+ } /* end else */
+
+ return (jint)status;
+}
+
+herr_t
+H5AwriteVL_asstr
+ (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
+{
+ char **strs;
+ jstring jstr;
+ jint i;
+ jint n;
+ hid_t sid;
+ hsize_t dims[H5S_MAX_RANK];
+ herr_t status = -1;
+
+ n = ENVPTR->GetArrayLength(ENVPAR buf);
+ strs =(hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
+
+ if (strs == NULL) {
+ h5JNIFatalError(env, "H5AwriteVL_asstr: failed to allocate buff for read variable length strings");
+ } /* end if */
+ else {
+ status = H5Awrite(aid, tid, strs);
+
+ if (status < 0) {
+ dims[0] = (hsize_t)n;
+ sid = H5Screate_simple(1, dims, NULL);
+ H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
+ H5Sclose(sid);
+ HDfree(strs);
+ h5JNIFatalError(env, "H5AwriteVL_str: failed to read variable length strings");
+ } /* end if */
+ else {
+ for (i=0; i < n; i++) {
+ jstr = ENVPTR->NewStringUTF(ENVPAR strs[i]);
+ ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
+ H5free_memory (strs[i]);
+ } /* end for */
+
+ /*
+ for repeatedly reading a dataset with a large number of strs (e.g., 1,000,000 strings,
+ H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect
+ free space in time. Instead, use "H5free_memory(strs[i])" above to free individual strings
+ after it is done.
+ H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs);
+ */
+
+ HDfree(strs);
+ } /* end else */
+ } /* end else */
+
+ return status;
+} /* end H5AwriteVL_str */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_reg_ref
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref
+ (JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
+{
+ herr_t status = -1;
+ h5str_t h5str;
+ size_t size;
+ hdset_reg_ref_t *ref_data;
+ jint i;
+ jint n;
+ jstring jstr;
+
+ hid_t region = -1;
+ hid_t aid = (hid_t) attr_id;
+ hid_t tid = (hid_t) mem_type_id;
+
+ n = ENVPTR->GetArrayLength(ENVPAR buf);
+ size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/
+ ref_data = (hdset_reg_ref_t*)HDmalloc(size * (size_t)n);
+
+ if (ref_data == NULL) {
+ h5JNIFatalError(env, "H5Aread_reg_ref: failed to allocate buff for read");
+ return -1;
+ } /* end if */
+
+ status = H5Aread(aid, tid, ref_data);
+
+ if (status < 0) {
+ HDfree(ref_data);
+ h5JNIFatalError(env, "H5Aread_reg_ref: failed to read data");
+ return -1;
+ } /* end if */
+
+ HDmemset(&h5str, 0, sizeof(h5str_t));
+ h5str_new(&h5str, 1024);
+ for (i=0; i<n; i++) {
+ h5str.s[0] = '\0';
+ h5str_sprintf(&h5str, aid, tid, ref_data[i], 0, 0);
+ jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
+
+ ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
+ } /* end for */
+
+ h5str_free(&h5str);
+ HDfree(ref_data);
+
+ return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref */
+
+/*
+ * Class: hdf_hdf5lib_H5
* Method: H5Aget_space
* Signature: (J)J
*/
diff --git a/java/src/jni/h5aImp.h b/java/src/jni/h5aImp.h
index f3758eb..15cc83e 100644
--- a/java/src/jni/h5aImp.h
+++ b/java/src/jni/h5aImp.h
@@ -51,21 +51,120 @@ Java_hdf_hdf5lib_H5__1H5Aopen_1idx
/*
* Class: hdf_hdf5lib_H5
+ * Method: H5Aread
+ * Signature: (JJ[B)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread
+ (JNIEnv *, jclass, jlong, jlong, jbyteArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
* Method: H5Awrite
* Signature: (JJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Awrite
- (JNIEnv *, jclass, jlong, jlong, jbyteArray);
+ (JNIEnv *, jclass, jlong, jlong, jbyteArray, jboolean);
/*
* Class: hdf_hdf5lib_H5
- * Method: H5Aread
- * Signature: (JJ[B)I
+ * Method: H5Aread_short
+ * Signature: (JJ[SZ)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5Aread
- (JNIEnv *, jclass, jlong, jlong, jbyteArray);
+Java_hdf_hdf5lib_H5_H5Aread_1short
+ (JNIEnv*, jclass, jlong, jlong, jshortArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_short
+ * Signature: (JJ[SZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1short
+ (JNIEnv*, jclass, jlong, jlong, jshortArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_int
+ * Signature: (JJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1int
+ (JNIEnv*, jclass, jlong, jlong, jintArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_int
+ * Signature: (JJ[IZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1int
+ (JNIEnv*, jclass, jlong, jlong, jintArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_long
+ * Signature: (JJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1long
+ (JNIEnv*, jclass, jlong, jlong, jlongArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_long
+ * Signature: (JJ[JZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1long
+ (JNIEnv*, jclass, jlong, jlong, jlongArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_float
+ * Signature: (JJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1float
+ (JNIEnv*, jclass, jlong, jlong, jfloatArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_float
+ * Signature: (JJ[FZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1float
+ (JNIEnv*, jclass, jlong, jlong, jfloatArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_double
+ * Signature: (JJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1double
+ (JNIEnv*, jclass, jlong, jlong, jdoubleArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_double
+ * Signature: (JJ[DZ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1double
+ (JNIEnv*, jclass, jlong, jlong, jdoubleArray, jboolean);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5AreadVL
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5AreadVL
+ (JNIEnv *, jclass, jlong, jlong, jobjectArray);
/*
* Class: hdf_hdf5lib_H5
@@ -78,12 +177,48 @@ Java_hdf_hdf5lib_H5_H5AwriteVL
/*
* Class: hdf_hdf5lib_H5
- * Method: H5AreadVL
+ * Method: H5Aread_string
* Signature: (JJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5AreadVL
- (JNIEnv *, jclass, jlong, jlong, jobjectArray);
+Java_hdf_hdf5lib_H5_H5Aread_1string
+ (JNIEnv*, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_string
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1string
+(JNIEnv*, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_VLStrings
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1VLStrings
+(JNIEnv*, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Awrite_VLStrings
+ * Signature: (JJ[B)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Awrite_1VLStrings
+ (JNIEnv*, jclass, jlong, jlong, jobjectArray);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5Aread_reg_ref
+ * Signature: (JJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref
+(JNIEnv*, jclass, jlong, jlong, jobjectArray);
/*
* Class: hdf_hdf5lib_H5
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index 652c873..79a5d0a 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -1574,84 +1574,6 @@ Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref
/*
* Class: hdf_hdf5lib_H5
- * Method: H5Dread_reg_ref_data
- * Signature: (JJJJJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data
- (JNIEnv *env, jclass clss,
- jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
- jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
-{
- herr_t status = -1;
- h5str_t h5str;
- size_t size;
- hdset_reg_ref_t *ref_data;
- jint i;
- jint n;
- jstring jstr;
-
- hid_t region_obj;
- H5S_sel_type region_type;
-
- hid_t region = -1;
- hid_t did = (hid_t) dataset_id;
- hid_t tid = (hid_t) mem_type_id;
- hid_t mem_sid = (hid_t) mem_space_id;
- hid_t file_sid = (hid_t) file_space_id;
-
- n = ENVPTR->GetArrayLength(ENVPAR buf);
- size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/
- ref_data = (hdset_reg_ref_t*)HDmalloc(size * (size_t)n);
-
- if (ref_data == NULL) {
- h5JNIFatalError(env, "H5Dread_reg_ref_data: failed to allocate buff for read");
- return -1;
- } /* end if */
-
- status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, ref_data);
-
- if (status < 0) {
- HDfree(ref_data);
- h5JNIFatalError(env, "H5Dread_reg_ref_data: failed to read data");
- return -1;
- } /* end if */
-
- HDmemset(&h5str, 0, sizeof(h5str_t));
- h5str_new(&h5str, 1024);
- for (i=0; i<n; i++) {
- h5str.s[0] = '\0';
-
- /* get name of the dataset the region reference points to using H5Rget_name */
- region_obj = H5Rdereference2(did, H5P_DEFAULT, H5R_DATASET_REGION, ref_data[i]);
- if (region_obj >= 0) {
- region = H5Rget_region(did, H5R_DATASET_REGION, ref_data[i]);
- if (region >= 0) {
- region_type = H5Sget_select_type(region);
- if(region_type==H5S_SEL_POINTS) {
- h5str_dump_region_points_data(&h5str, region, region_obj);
- } /* end if */
- else {
- h5str_dump_region_blocks_data(&h5str, region, region_obj);
- } /* end else */
-
- H5Sclose(region);
- } /* end if */
- H5Dclose(region_obj);
- } /* end if */
- jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
-
- ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
- } /* end for */
-
- h5str_free(&h5str);
- HDfree(ref_data);
-
- return (jint)status;
-} /* end Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data */
-
-/*
- * Class: hdf_hdf5lib_H5
* Method: _H5Dcreate2
* Signature: (JLjava/lang/String;JJJJJ)J
*/
diff --git a/java/src/jni/h5dImp.h b/java/src/jni/h5dImp.h
index 1fe71a8..f824452 100644
--- a/java/src/jni/h5dImp.h
+++ b/java/src/jni/h5dImp.h
@@ -250,7 +250,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1VLStrings
/*
* Class: hdf_hdf5lib_H5
* Method: H5Dwrite_VLStrings
- * Signature: (JJJJJ[BZ)I
+ * Signature: (JJJJJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1VLStrings
@@ -267,15 +267,6 @@ Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref
/*
* Class: hdf_hdf5lib_H5
- * Method: H5Dread_reg_ref_data
- * Signature: (JJJJJ[Ljava/lang/String;)I
- */
-JNIEXPORT jint JNICALL
-Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data
- (JNIEnv*, jclass, jlong, jlong, jlong, jlong, jlong, jobjectArray);
-
-/*
- * Class: hdf_hdf5lib_H5
* Method: _H5Dcreate2
* Signature: (JLjava/lang/String;JJJJJ)J
*/
diff --git a/java/src/jni/h5fImp.c b/java/src/jni/h5fImp.c
index 9d68290..248e654 100644
--- a/java/src/jni/h5fImp.c
+++ b/java/src/jni/h5fImp.c
@@ -168,6 +168,33 @@ Java_hdf_hdf5lib_H5_H5Fis_1hdf5
/*
* Class: hdf_hdf5lib_H5
+ * Method: H5Fis_accessible
+ * Signature: (Ljava/lang/String;J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Fis_1accessible
+ (JNIEnv *env, jclass clss, jstring name, jlong file_id)
+{
+ htri_t bval = JNI_FALSE;
+ const char *fileName;
+
+ PIN_JAVA_STRING(name, fileName);
+ if (fileName != NULL) {
+ bval = H5Fis_accessible(fileName, (hid_t)file_id);
+
+ UNPIN_JAVA_STRING(name, fileName);
+
+ if (bval > 0)
+ bval = JNI_TRUE;
+ else if (bval < 0)
+ h5libraryError(env);
+ }
+
+ return (jboolean)bval;
+} /* end Java_hdf_hdf5lib_H5_H5Fis_1accessible */
+
+/*
+ * Class: hdf_hdf5lib_H5
* Method: H5Fget_create_plist
* Signature: (J)J
*/
@@ -177,7 +204,7 @@ Java_hdf_hdf5lib_H5__1H5Fget_1create_1plist
{
hid_t retVal = -1;
- retVal = H5Fget_create_plist((hid_t)file_id );
+ retVal = H5Fget_create_plist((hid_t)file_id);
if (retVal < 0)
h5libraryError(env);
diff --git a/java/src/jni/h5fImp.h b/java/src/jni/h5fImp.h
index fcfdedf..af0fa1d 100644
--- a/java/src/jni/h5fImp.h
+++ b/java/src/jni/h5fImp.h
@@ -68,6 +68,15 @@ Java_hdf_hdf5lib_H5_H5Fis_1hdf5
/*
* Class: hdf_hdf5lib_H5
+ * Method: H5Fis_accessible
+ * Signature: (Ljava/lang/String;J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Fis_1ccessible
+ (JNIEnv*, jclass, jstring, jlong);
+
+/*
+ * Class: hdf_hdf5lib_H5
* Method: H5Fget_create_plist
* Signature: (J)J
*/
diff --git a/java/src/jni/h5vlImp.c b/java/src/jni/h5vlImp.c
new file mode 100644
index 0000000..89ea703
--- /dev/null
+++ b/java/src/jni/h5vlImp.c
@@ -0,0 +1,206 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * For details of the HDF libraries, see the HDF Documentation at:
+ * http://hdfgroup.org/HDF5/doc/
+ *
+ */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#include "hdf5.h"
+#include <jni.h>
+#include <stdlib.h>
+#include "h5jni.h"
+#include "h5vlImp.h"
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLregister_connector_by_name
+ * Signature: (Ljava/lang/String;J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5VLregister_1connector_1by_1name
+ (JNIEnv *env, jclass clss, jobject connector_name, jlong vipl_id)
+{
+ hid_t status = -1;
+ const char *vlName;
+
+ PIN_JAVA_STRING(connector_name, vlName);
+ if (vlName != NULL) {
+ status = H5VLregister_connector_by_name(vlName, (hid_t)vipl_id);
+
+ UNPIN_JAVA_STRING(connector_name, vlName);
+
+ if (status < 0)
+ h5libraryError(env);
+ }
+
+ return (jlong)status;
+} /* end Java_hdf_hdf5lib_H5_H5VLregister_1connector_1by_1name */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLregister_connector_by_value
+ * Signature: (IJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5VLregister_1connector_1by_1value
+ (JNIEnv *env, jclass clss, jint connector_value, jlong vipl_id)
+{
+ hid_t status = H5VLregister_connector_by_value((H5VL_class_value_t)connector_value, (hid_t)vipl_id);
+
+ if (status < 0)
+ h5libraryError(env);
+
+ return (jlong)status;
+} /* end Java_hdf_hdf5lib_H5_H5VLregister_1connector_1by_1value */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLis_connector_registered
+ * Signature: (Ljava/lang/String;)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5VLis_1connector_1registered
+ (JNIEnv *env, jclass clss, jobject connector_name)
+{
+ htri_t bval = JNI_FALSE;
+ const char *vlName;
+
+ PIN_JAVA_STRING(connector_name, vlName);
+ if (vlName != NULL) {
+ bval = H5VLis_connector_registered(vlName);
+
+ UNPIN_JAVA_STRING(connector_name, vlName);
+
+ if (bval > 0)
+ bval = JNI_TRUE;
+ else if (bval < 0)
+ h5libraryError(env);
+ }
+
+ return (jboolean)bval;
+} /* end Java_hdf_hdf5lib_H5_H5VLis_1connector_1registered */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLget_connector_id
+ * Signature: (Ljava/lang/String;)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5VLget_1connector_1id
+ (JNIEnv *env, jclass clss, jobject connector_name)
+{
+ hid_t status = -1;
+ const char *vlName;
+
+ PIN_JAVA_STRING(connector_name, vlName);
+ if (vlName != NULL) {
+ status = H5VLget_connector_id(vlName);
+
+ UNPIN_JAVA_STRING(connector_name, vlName);
+
+ if (status < 0)
+ h5libraryError(env);
+ }
+
+ return (jlong)status;
+} /* end Java_hdf_hdf5lib_H5_H5VLget_1connector_1id */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLget_connector_name
+ * Signature: (J)Ljava/lang/String;
+ */
+
+JNIEXPORT jobject JNICALL
+Java_hdf_hdf5lib_H5_H5VLget_1connector_1name
+ (JNIEnv *env, jclass clss, jlong object_id)
+{
+ char *vlName;
+ ssize_t buf_size;
+ ssize_t status;
+ jstring str = NULL;
+
+ /* get the length of the comment */
+ buf_size = H5VLget_connector_name((hid_t)object_id, NULL, 0);
+ if (buf_size < 0) {
+ H5Eprint2(H5E_DEFAULT, NULL);
+
+ h5badArgument(env, "H5VLget_connector_name: buf_size < 0");
+ } /* end if */
+ else if (buf_size > 0) {
+ buf_size++; /* add extra space for the null terminator */
+ vlName = (char *)HDmalloc(sizeof(char) * (size_t)buf_size);
+ if (vlName == NULL) {
+ /* exception -- out of memory */
+ h5outOfMemory(env, "H5VLget_connector_name: malloc failed");
+ } /* end if */
+ else {
+ status = H5VLget_connector_name((hid_t)object_id, vlName, (size_t)buf_size);
+
+ if (status < 0) {
+ h5libraryError(env);
+ } /* end if */
+ else {
+ /* may throw OutOfMemoryError */
+ str = ENVPTR->NewStringUTF(ENVPAR vlName);
+ if (str == NULL) {
+ h5JNIFatalError(env, "H5VLget_connector_name: return string not allocated");
+ } /* end if */
+ } /* end else */
+ HDfree(vlName);
+ }
+ } /* end else if */
+
+ return (jstring)str;
+} /* end Java_hdf_hdf5lib_H5_H5VLget_1connector_1name */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLclose
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5VLclose
+ (JNIEnv *env, jclass clss, jlong connector_id)
+{
+ herr_t retValue = H5VLclose((hid_t)connector_id);
+
+ if (retValue < 0)
+ h5libraryError(env);
+} /* end Java_hdf_hdf5lib_H5_H5VLclose */
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLunregister_connector
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5VLunregister_1connector
+ (JNIEnv *env, jclass clss, jlong connector_id)
+{
+ herr_t retValue = H5VLunregister_connector((hid_t)connector_id);
+
+ if (retValue < 0)
+ h5libraryError(env);
+} /* end Java_hdf_hdf5lib_H5_H5VLunregister_1connector */
+
+
+#ifdef __cplusplus
+} /* end extern "C" */
+#endif /* __cplusplus */
diff --git a/java/src/jni/h5vlImp.h b/java/src/jni/h5vlImp.h
new file mode 100644
index 0000000..af824a9
--- /dev/null
+++ b/java/src/jni/h5vlImp.h
@@ -0,0 +1,91 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#include <jni.h>
+/* Header for class hdf_hdf5lib_H5_H5VL */
+
+#ifndef _Included_hdf_hdf5lib_H5_H5VL
+#define _Included_hdf_hdf5lib_H5_H5VL
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLregister_connector_by_name
+ * Signature: (Ljava/lang/String;J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5VLregister_1connector_1by_1name
+ (JNIEnv *, jclass, jobject, jlong);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLregister_connector_by_value
+ * Signature: (IJ)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5VLregister_1connector_1by_1value
+ (JNIEnv *, jclass, jint, jlong);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLis_connector_registered
+ * Signature: (Ljava/lang/String;)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5VLis_connector_registered
+ (JNIEnv *, jclass, jobject);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLget_connector_id
+ * Signature: (Ljava/lang/String;)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5VLget_1connector_1id
+ (JNIEnv *, jclass, jobject);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLget_connector_name
+ * Signature: (J)Ljava/lang/String;
+ */
+
+JNIEXPORT jobject JNICALL
+Java_hdf_hdf5lib_H5_H5VLget_1connector_1name
+ (JNIEnv *, jclass, jlong);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLclose
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5VLclose
+ (JNIEnv *, jclass, jlong);
+
+/*
+ * Class: hdf_hdf5lib_H5
+ * Method: H5VLunregister_connector
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5VLunregister_1connector
+ (JNIEnv *, jclass, jlong);
+
+#ifdef __cplusplus
+} /* end extern "C" */
+#endif /* __cplusplus */
+
+#endif /* _Included_hdf_hdf5lib_H5_H5VL */
diff --git a/java/test/CMakeLists.txt b/java/test/CMakeLists.txt
index b76f572..937b129 100644
--- a/java/test/CMakeLists.txt
+++ b/java/test/CMakeLists.txt
@@ -38,6 +38,7 @@ set (HDF5_JAVA_TEST_SOURCES
TestH5Ocreate
TestH5Ocopy
TestH5PL
+ TestH5VL
TestH5Z
)
diff --git a/java/test/Makefile.am b/java/test/Makefile.am
index 6635ef7..af99d92 100644
--- a/java/test/Makefile.am
+++ b/java/test/Makefile.am
@@ -69,6 +69,7 @@ noinst_JAVA = \
TestH5Ocreate.java \
TestH5Ocopy.java \
TestH5PL.java \
+ TestH5VL.java \
TestH5Z.java \
TestH5E.java \
TestH5Edefault.java \
diff --git a/java/test/TestH5Fbasic.java b/java/test/TestH5Fbasic.java
index 11d6644..a5afb6e 100644
--- a/java/test/TestH5Fbasic.java
+++ b/java/test/TestH5Fbasic.java
@@ -81,6 +81,19 @@ public class TestH5Fbasic {
assertTrue(isH5 == true);
}
+ @Test
+ public void testH5Fis_accessible() {
+ boolean isH5 = false;
+
+ try {
+ isH5 = H5.H5Fis_accessible(H5_FILE, HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Throwable err) {
+ fail("H5.H5Fis_accessible failed on " + H5_FILE + ": " + err);
+ }
+ assertTrue(isH5 == true);
+ }
+
@Test(expected = HDF5LibraryException.class)
public void testH5Fcreate_EXCL() throws Throwable {
H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_EXCL,
diff --git a/java/test/TestH5Fparams.java b/java/test/TestH5Fparams.java
index fffded1..3d64aa9 100644
--- a/java/test/TestH5Fparams.java
+++ b/java/test/TestH5Fparams.java
@@ -60,6 +60,11 @@ public class TestH5Fparams {
}
@Test(expected = NullPointerException.class)
+ public void testH5Fis_accessible_null() throws Throwable {
+ H5.H5Fis_accessible(null, -1);
+ }
+
+ @Test(expected = NullPointerException.class)
public void testH5Fmount_null() throws Throwable {
H5.H5Fmount(-1, null, -1, HDF5Constants.H5P_DEFAULT);
}
diff --git a/java/test/TestH5VL.java b/java/test/TestH5VL.java
new file mode 100644
index 0000000..0397be1
--- /dev/null
+++ b/java/test/TestH5VL.java
@@ -0,0 +1,117 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+package test;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import hdf.hdf5lib.H5;
+import hdf.hdf5lib.HDF5Constants;
+import hdf.hdf5lib.exceptions.HDF5LibraryException;
+
+import java.io.File;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TestName;
+
+public class TestH5VL {
+ @Rule public TestName testname = new TestName();
+
+ private final void _deleteFile(String filename) {
+ File file = new File(filename);
+
+ if (file.exists()) {
+ try {file.delete();} catch (SecurityException e) {}
+ }
+ }
+
+ @Before
+ public void checkOpenIDs() {
+ assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
+ System.out.print(testname.getMethodName());
+ }
+ @After
+ public void nextTestName() {
+ System.out.println();
+ }
+
+ @Test
+ public void testH5VLnative_init() {
+ try {
+ boolean is_registered;
+
+ is_registered = H5.H5VLis_connector_registered(HDF5Constants.H5VL_NATIVE_NAME);
+ assertTrue("H5.H5VLis_connector_registered H5VL_NATIVE_NAME", is_registered);
+
+ is_registered = H5.H5VLis_connector_registered("FAKE_VOL_NAME");
+ assertFalse("H5.H5VLis_connector_registered FAKE_VOL_NAME", is_registered);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.H5VLis_connector_registered " + err);
+ }
+ }
+
+ @Test
+ public void testH5VLget_connector_id() {
+ try {
+ long native_id = H5.H5VLget_connector_id(HDF5Constants.H5VL_NATIVE_NAME);
+ assertTrue("H5.H5VLget_connector_id H5VL_NATIVE_NAME", native_id >= 0);
+ assertEquals(HDF5Constants.H5VL_NATIVE, native_id);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.H5VLget_connector_id " + err);
+ }
+ }
+
+ @Test
+ public void testH5VLget_connector_name() {
+ String H5_FILE = "testFvl.h5";
+
+ long H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+
+ try {
+ String native_name = H5.H5VLget_connector_name(H5fid);
+ assertTrue("H5.H5VLget_connector_name H5VL_NATIVE", native_name.compareToIgnoreCase(HDF5Constants.H5VL_NATIVE_NAME)==0);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ fail("H5.H5VLget_connector_name " + err);
+ }
+ finally {
+ if (H5fid > 0) {
+ try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
+ }
+ _deleteFile(H5_FILE);
+ }
+ }
+
+ @Test(expected = HDF5LibraryException.class)
+ public void testH5VLclose_NegativeID() throws Throwable {
+ H5.H5VLclose(-1);
+ }
+
+ @Test(expected = HDF5LibraryException.class)
+ public void testH5VLunregister_connector_NegativeID() throws Throwable {
+ H5.H5VLunregister_connector(-1);
+ }
+}
+
diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
index 350fb7b..add1af4 100644
--- a/java/test/junit.sh.in
+++ b/java/test/junit.sh.in
@@ -101,6 +101,7 @@ $HDFTEST_HOME/testfiles/JUnit-TestH5Obasic.txt
$HDFTEST_HOME/testfiles/JUnit-TestH5Ocreate.txt
$HDFTEST_HOME/testfiles/JUnit-TestH5Ocopy.txt
$HDFTEST_HOME/testfiles/JUnit-TestH5PL.txt
+$HDFTEST_HOME/testfiles/JUnit-TestH5VL.txt
$HDFTEST_HOME/testfiles/JUnit-TestH5Z.txt
$HDFTEST_HOME/testfiles/JUnit-TestH5E.txt
$HDFTEST_HOME/testfiles/JUnit-TestH5Edefault.txt
@@ -989,6 +990,27 @@ else
test yes = "$verbose" && $DIFF JUnit-TestH5PL.txt JUnit-TestH5PL.out |sed 's/^/ /'
fi
+echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH -ea org.junit.runner.JUnitCore test.TestH5VL"
+TESTING JUnit-TestH5VL
+($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH -ea org.junit.runner.JUnitCore test.TestH5VL > JUnit-TestH5VL.ext)
+
+# Extract file name, line number, version and thread IDs because they may be different
+sed -e 's/thread [0-9]*/thread (IDs)/' -e 's/: .*\.c /: (file name) /' \
+ -e 's/line [0-9]*/line (number)/' \
+ -e 's/Time: [0-9]*\.[0-9]*/Time: XXXX/' \
+ -e 's/v[1-9]*\.[0-9]*\./version (number)\./' \
+ -e 's/[1-9]*\.[0-9]*\.[0-9]*[^)]*/version (number)/' \
+ JUnit-TestH5VL.ext > JUnit-TestH5VL.out
+
+if diff JUnit-TestH5VL.out JUnit-TestH5VL.txt > /dev/null; then
+ echo " PASSED JUnit-TestH5VL"
+else
+ echo "**FAILED** JUnit-TestH5VL"
+ echo " Expected result differs from actual result"
+ nerrors="`expr $nerrors + 1`"
+ test yes = "$verbose" && $DIFF JUnit-TestH5VL.txt JUnit-TestH5VL.out |sed 's/^/ /'
+fi
+
echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH -ea org.junit.runner.JUnitCore test.TestH5Z"
TESTING JUnit-TestH5Z
($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH -ea org.junit.runner.JUnitCore test.TestH5Z > JUnit-TestH5Z.ext)
diff --git a/java/test/testfiles/JUnit-TestH5Edefault.txt b/java/test/testfiles/JUnit-TestH5Edefault.txt
index 71d1431..48c6254 100644
--- a/java/test/testfiles/JUnit-TestH5Edefault.txt
+++ b/java/test/testfiles/JUnit-TestH5Edefault.txt
@@ -38,17 +38,20 @@ HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
minor: Unable to open file
#001: (file name) line (number) in H5VL_file_open(): open failed
major: Virtual Object Layer
- minor: Unable to initialize object
- #002: (file name) line (number) in H5VL_native_file_open(): unable to open file
+ minor: Can't open object
+ #002: (file name) line (number) in H5VL__file_open(): open failed
+ major: Virtual Object Layer
+ minor: Can't open object
+ #003: (file name) line (number) in H5VL__native_file_open(): unable to open file
major: File accessibility
minor: Unable to open file
- #003: (file name) line (number) in H5F_open(): unable to open file: name = 'test', tent_flags = 1
+ #004: (file name) line (number) in H5F_open(): unable to open file: name = 'test', tent_flags = 1
major: File accessibility
minor: Unable to open file
- #004: (file name) line (number) in H5FD_open(): open failed
+ #005: (file name) line (number) in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
- #005: (file name) line (number) in H5FD_sec2_open(): unable to open file: name = 'test', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2
+ #006: (file name) line (number) in H5FD_sec2_open(): unable to open file: name = 'test', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2
major: File accessibility
minor: Unable to open file
HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
@@ -57,16 +60,19 @@ HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
minor: Unable to open file
#001: (file name) line (number) in H5VL_file_open(): open failed
major: Virtual Object Layer
- minor: Unable to initialize object
- #002: (file name) line (number) in H5VL_native_file_open(): unable to open file
+ minor: Can't open object
+ #002: (file name) line (number) in H5VL__file_open(): open failed
+ major: Virtual Object Layer
+ minor: Can't open object
+ #003: (file name) line (number) in H5VL__native_file_open(): unable to open file
major: File accessibility
minor: Unable to open file
- #003: (file name) line (number) in H5F_open(): unable to open file: name = 'test', tent_flags = 1
+ #004: (file name) line (number) in H5F_open(): unable to open file: name = 'test', tent_flags = 1
major: File accessibility
minor: Unable to open file
- #004: (file name) line (number) in H5FD_open(): open failed
+ #005: (file name) line (number) in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
- #005: (file name) line (number) in H5FD_sec2_open(): unable to open file: name = 'test', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2
+ #006: (file name) line (number) in H5FD_sec2_open(): unable to open file: name = 'test', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2
major: File accessibility
minor: Unable to open file
diff --git a/java/test/testfiles/JUnit-TestH5Fbasic.txt b/java/test/testfiles/JUnit-TestH5Fbasic.txt
index 467e2fb..2654624 100644
--- a/java/test/testfiles/JUnit-TestH5Fbasic.txt
+++ b/java/test/testfiles/JUnit-TestH5Fbasic.txt
@@ -9,6 +9,7 @@ JUnit version 4.11
.testH5Freopen_closed
.testH5Freset_mdc_hit_rate_stats
.testH5Fget_name
+.testH5Fis_accessible
.testH5Fcreate
.testH5Fclear_elink_file_cache
.testH5Fclose_twice
@@ -17,5 +18,5 @@ JUnit version 4.11
Time: XXXX
-OK (15 tests)
+OK (16 tests)
diff --git a/java/test/testfiles/JUnit-TestH5Fparams.txt b/java/test/testfiles/JUnit-TestH5Fparams.txt
index 9d35220..e91cbdc 100644
--- a/java/test/testfiles/JUnit-TestH5Fparams.txt
+++ b/java/test/testfiles/JUnit-TestH5Fparams.txt
@@ -1,4 +1,5 @@
JUnit version 4.11
+.testH5Fis_accessible_null
.testH5Fcreate_null
.testH5Fflush_local
.testH5Fget_info
@@ -13,5 +14,5 @@ JUnit version 4.11
Time: XXXX
-OK (11 tests)
+OK (12 tests)
diff --git a/java/test/testfiles/JUnit-TestH5VL.txt b/java/test/testfiles/JUnit-TestH5VL.txt
new file mode 100644
index 0000000..caadf26
--- /dev/null
+++ b/java/test/testfiles/JUnit-TestH5VL.txt
@@ -0,0 +1,11 @@
+JUnit version 4.11
+.testH5VLget_connector_id
+.testH5VLnative_init
+.testH5VLget_connector_name
+.testH5VLclose_NegativeID
+.testH5VLunregister_connector_NegativeID
+
+Time: XXXX
+
+OK (5 tests)
+