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Fix various Java issues when deprecated symbols are disabled

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This commit is contained in:
Jordan Henderson 2019-10-10 13:37:18 -05:00
parent 3506207344
commit 93f509a2f2
11 changed files with 131 additions and 27 deletions
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26
java/src/hdf/hdf5lib/H5.java
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@ -2155,7 +2155,10 @@ public class H5 implements java.io.Serializable {
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
*
* @deprecated As of HDF5 1.12.0 in favor of H5Treclaim
**/
@Deprecated
public synchronized static native int H5Dvlen_reclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf)
throws HDF5LibraryException, NullPointerException;
@ -3093,6 +3096,7 @@ public class H5 implements java.io.Serializable {
*
* @deprecated As of HDF5 1.10.5 in favor of H5Fis_accessible.
**/
@Deprecated
public synchronized static native boolean H5Fis_hdf5(String name) throws HDF5LibraryException, NullPointerException;
/**
@ -10312,6 +10316,28 @@ public class H5 implements java.io.Serializable {
**/
public synchronized static native int H5Tpack(long type_id) throws HDF5LibraryException;
/**
* H5Treclaim reclaims buffer used for VL data.
*
* @param type_id
* Identifier of the datatype.
* @param space_id
* Identifier of the dataspace.
* @param xfer_plist_id
* Identifier of a transfer property list for this I/O operation.
* @param buf
* Buffer with data to be reclaimed.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
**/
public synchronized static native int H5Treclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tvlen_create creates a new variable-length (VL) dataype.
*

29
java/src/jni/h5aImp.c
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@ -94,11 +94,18 @@ JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Aopen_1name
(JNIEnv *env, jclass clss, jlong loc_id, jstring name)
{
#ifndef H5_NO_DEPRECATED_SYMBOLS
const char *attrName = NULL;
#endif
hid_t attr_id = H5I_INVALID_HID;
UNUSED(clss);
#ifdef H5_NO_DEPRECATED_SYMBOLS
UNUSED(loc_id);
UNUSED(name);
H5_UNIMPLEMENTED(ENVONLY, "H5Aopen_name: not implemented");
#else
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Aopen_name: attribute name is null");
@ -106,10 +113,13 @@ Java_hdf_hdf5lib_H5__1H5Aopen_1name
if((attr_id = H5Aopen_name((hid_t)loc_id, attrName)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
#endif
done:
#ifndef H5_NO_DEPRECATED_SYMBOLS
if (attrName)
UNPIN_JAVA_STRING(ENVONLY, name, attrName);
#endif
return (jlong)attr_id;
} /* end Java_hdf_hdf5lib_H5__1H5Aopen_1name */
@ -127,8 +137,14 @@ Java_hdf_hdf5lib_H5__1H5Aopen_1idx
UNUSED(clss);
#ifdef H5_NO_DEPRECATED_SYMBOLS
UNUSED(loc_id);
UNUSED(idx);
H5_UNIMPLEMENTED(ENVONLY, "H5Aopen_idx: not implemented");
#else
if ((attr_id = H5Aopen_idx((hid_t) loc_id, (unsigned int) idx)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
#endif
done:
return (jlong)attr_id;
@ -1028,7 +1044,7 @@ H5AreadVL_str
/*
* When 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
* H5Treclaim() may crash on Windows because the Java GC will not be able to collect
* free space in time. Instead, we use "H5free_memory(strs[i])" to free individual strings
* once done.
*/
@ -1125,7 +1141,7 @@ done:
if (h5str.s)
h5str_free(&h5str);
if (readBuf) {
H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, readBuf);
H5Treclaim(tid, sid, H5P_DEFAULT, readBuf);
HDfree(readBuf);
}
if (sid >= 0)
@ -1313,7 +1329,7 @@ H5AwriteVL_asstr
/*
* When repeatedly writing 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
* H5Treclaim() may crash on Windows because the Java GC will not be able to collect
* free space in time. Instead, we use "H5free_memory(strs[i])" to free individual strings
* once done.
*/
@ -1356,7 +1372,7 @@ done:
if (utf8)
UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
if (writeBuf) {
H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, writeBuf);
H5Treclaim(tid, sid, H5P_DEFAULT, writeBuf);
HDfree(writeBuf);
}
if (sid >= 0)
@ -1512,8 +1528,13 @@ Java_hdf_hdf5lib_H5_H5Aget_1num_1attrs
UNUSED(clss);
#ifdef H5_NO_DEPRECATED_SYMBOLS
UNUSED(loc_id);
H5_UNIMPLEMENTED(ENVONLY, "H5Aget_num_attrs: not implemented");
#else
if ((retVal = H5Aget_num_attrs((hid_t)loc_id)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
#endif
done:
return (jint)retVal;

22
java/src/jni/h5dImp.c
View File

@ -340,12 +340,21 @@ Java_hdf_hdf5lib_H5_H5Dvlen_1reclaim
(JNIEnv *env, jclass clss, jlong type_id, jlong space_id,
jlong xfer_plist_id, jbyteArray buf)
{
#ifndef H5_NO_DEPRECATED_SYMBOLS
jboolean vlenBufIsCopy;
jbyte *vlenBuf = NULL;
#endif
herr_t status = FAIL;
UNUSED(clss);
#ifdef H5_NO_DEPRECATED_SYMBOLS
UNUSED(type_id);
UNUSED(space_id);
UNUSED(xfer_plist_id);
UNUSED(buf);
H5_UNIMPLEMENTED(ENVONLY, "H5Dvlen_reclaim: not implemented");
#else
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dvlen_reclaim: buffer is NULL");
@ -353,10 +362,13 @@ Java_hdf_hdf5lib_H5_H5Dvlen_1reclaim
if ((status = H5Dvlen_reclaim((hid_t)type_id, (hid_t)space_id, (hid_t)xfer_plist_id, vlenBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
#endif
done:
#ifndef H5_NO_DEPRECATED_SYMBOLS
if (vlenBuf)
UNPIN_BYTE_ARRAY(ENVONLY, buf, vlenBuf, (status < 0) ? JNI_ABORT : 0);
#endif
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dvlen_1reclaim */
@ -1172,7 +1184,7 @@ H5DreadVL_str
/*
* When 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
* H5Treclaim() may crash on Windows because the Java GC will not be able to collect
* free space in time. Instead, we use "H5free_memory(strs[i])" to free individual strings
* once done.
*/
@ -1230,7 +1242,7 @@ H5DreadVL_asstr
if (mem_space == H5S_ALL) {
/*
* Retrieve a valid dataspace for H5Dvlen_reclaim().
* Retrieve a valid dataspace for H5Treclaim().
*/
if ((mem_space = H5Dget_space(did)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@ -1285,7 +1297,7 @@ done:
if (h5str.s)
h5str_free(&h5str);
if (readBuf) {
H5Dvlen_reclaim(tid, mem_space, xfer_plist_id, readBuf);
H5Treclaim(tid, mem_space, xfer_plist_id, readBuf);
HDfree(readBuf);
}
if (close_mem_space)
@ -1504,7 +1516,7 @@ H5DwriteVL_asstr
if (mem_space == H5S_ALL) {
/*
* Retrieve a valid dataspace for H5Dvlen_reclaim().
* Retrieve a valid dataspace for H5Treclaim().
*/
if ((mem_space = H5Dget_space(did)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
@ -1565,7 +1577,7 @@ done:
if (utf8)
UNPIN_JAVA_STRING(ENVONLY, obj, utf8);
if (writeBuf) {
H5Dvlen_reclaim(tid, mem_space, xfer_plist_id, writeBuf);
H5Treclaim(tid, mem_space, xfer_plist_id, writeBuf);
HDfree(writeBuf);
}
if (close_mem_space)

9
java/src/jni/h5fImp.c
View File

@ -156,15 +156,17 @@ JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Fis_1hdf5
(JNIEnv *env, jclass clss, jstring name)
{
#ifndef H5_NO_DEPRECATED_SYMBOLS
const char *fileName = NULL;
#endif
htri_t bval = JNI_FALSE;
UNUSED(clss);
#ifdef H5_NO_DEPRECATED_SYMBOLS
UNUSED(name);
H5_UNIMPLEMENTED(ENVONLY, "H5Fis_hdf5: not implemented");
#endif
#else
if (NULL == name)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fis_hdf5: file name is NULL");
@ -174,10 +176,13 @@ Java_hdf_hdf5lib_H5_H5Fis_1hdf5
H5_LIBRARY_ERROR(ENVONLY);
bval = (bval > 0) ? JNI_TRUE : JNI_FALSE;
#endif
done:
#ifndef H5_NO_DEPRECATED_SYMBOLS
if (fileName)
UNPIN_JAVA_STRING(ENVONLY, name, fileName);
#endif
return (jboolean)bval;
} /* end Java_hdf_hdf5lib_H5_H5Fis_1hdf5 */

31
java/src/jni/h5tImp.c
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@ -978,6 +978,37 @@ done:
return (jint)retVal;
} /* end Java_hdf_hdf5lib_H5_H5Tpack */
/*
* Class: hdf_hdf5lib_H5
* Method: H5Treclaim
* Signature: (JJJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Treclaim
(JNIEnv *env, jclass clss, jlong type_id, jlong space_id,
jlong xfer_plist_id, jbyteArray buf)
{
jboolean bufIsCopy;
jbyte *pinBuf = NULL;
herr_t status = FAIL;
UNUSED(clss);
if (NULL == buf)
H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Treclaim: buffer is NULL");
PIN_BYTE_ARRAY(ENVONLY, buf, pinBuf, &bufIsCopy, "H5Treclaim: buffer not pinned");
if ((status = H5Treclaim((hid_t)type_id, (hid_t)space_id, (hid_t)xfer_plist_id, pinBuf)) < 0)
H5_LIBRARY_ERROR(ENVONLY);
done:
if (pinBuf)
UNPIN_BYTE_ARRAY(ENVONLY, buf, pinBuf, (status < 0) ? JNI_ABORT : 0);
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Treclaim */
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Tclose

9
java/src/jni/h5tImp.h
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@ -399,6 +399,15 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Tpack
(JNIEnv *, jclass, jlong);
/*
* Class: hdf_hdf5lib_H5
* Method: H5Treclaim
* Signature: (JJJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Treclaim
(JNIEnv*, jclass, jlong, jlong, jlong, jbyteArray);
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Tclose

2
java/src/jni/h5util.c
View File

@ -2781,7 +2781,7 @@ h5str_dump_simple_dset
/* Reclaim any VL memory, if necessary */
if (vl_data) {
if (H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0)
if (H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0)
H5_LIBRARY_ERROR(ENVONLY);
}

11
java/test/TestH5Dparams.java
View File

@ -113,17 +113,6 @@ public class TestH5Dparams {
H5.H5Dvlen_get_buf_size(-1, -1, -1);
}
@Test(expected = HDF5LibraryException.class)
public void testH5Dvlen_reclaim_invalid() throws Throwable {
byte[] buf = new byte[2];
H5.H5Dvlen_reclaim(-1, -1, -1, buf);
}
@Test(expected = NullPointerException.class)
public void testH5Dvlen_reclaim_null() throws Throwable {
H5.H5Dvlen_reclaim(-1, -1, -1, null);
}
@Test(expected = IllegalArgumentException.class)
public void testH5Dget_storage_size_invalid() throws Throwable {
H5.H5Dget_storage_size(-1);

11
java/test/TestH5Tparams.java
View File

@ -274,6 +274,17 @@ public class TestH5Tparams {
public void testH5Tpack_invalid() throws Throwable {
H5.H5Tpack(-1);
}
@Test(expected = HDF5LibraryException.class)
public void testH5Treclaim_invalid() throws Throwable {
byte[] buf = new byte[2];
H5.H5Treclaim(-1, -1, -1, buf);
}
@Test(expected = NullPointerException.class)
public void testH5Treclaim_null() throws Throwable {
H5.H5Treclaim(-1, -1, -1, null);
}
@Test(expected = HDF5LibraryException.class)
public void testH5Tvlen_create_invalid() throws Throwable {

4
java/test/testfiles/JUnit-TestH5Dparams.txt
View File

@ -7,11 +7,9 @@ JUnit version 4.11
.testH5Dvlen_get_buf_size_invalid
.testH5Dcreate_null
.testH5Dset_extent_status_null
.testH5Dvlen_reclaim_null
.testH5Dcreate_invalid
.testH5Dcreate_anon_invalid
.testH5Dset_extent_status_invalid
.testH5Dvlen_reclaim_invalid
.testH5Dopen_invalid
.testH5Dclose_invalid
.testH5Dflush_invalid
@ -22,5 +20,5 @@ JUnit version 4.11
Time: XXXX
OK (20 tests)
OK (18 tests)

4
java/test/testfiles/JUnit-TestH5Tparams.txt
View File

@ -1,5 +1,6 @@
JUnit version 4.11
.testH5Tget_member_type_invalid
.testH5Treclaim_invalid
.testH5Tenum_insert_null
.testH5Tget_offset_invalid
.testH5Tset_precision_invalid
@ -68,9 +69,10 @@ JUnit version 4.11
.testH5Tget_member_index_null
.testH5Trefresh_invalid
.testH5Tset_sign_invalid
.testH5Treclaim_null
.testH5Tenum_insert_name_null
Time: XXXX
OK (70 tests)
OK (72 tests)