Merge pull request #1998 in HDFFV/hdf5 from ~JHENDERSON/hdf5:bugfix/H5Dvlen_reclaim_ref_fix to develop

* commit '93f509a2f2d5143450a0e6753325557b2bb8b707':
  Fix various Java issues when deprecated symbols are disabled

11 files changed, 131 insertions, 27 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index adb50f1..09fb223 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -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;
 
     /**
@@ -10313,6 +10317,28 @@ 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.
      *
      * @param base_id
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index eaa356e..9f22665 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -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;
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index 5500847..b395189 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -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)
diff --git a/java/src/jni/h5fImp.c b/java/src/jni/h5fImp.c
index 4fd6807..2eb3ad5 100644
--- a/java/src/jni/h5fImp.c
+++ b/java/src/jni/h5fImp.c
@@ -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 */
diff --git a/java/src/jni/h5tImp.c b/java/src/jni/h5tImp.c
index 460f12e..3302b7d 100644
--- a/java/src/jni/h5tImp.c
+++ b/java/src/jni/h5tImp.c
@@ -980,6 +980,37 @@ done:
 
 /*
  * 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
  * Signature: (J)I
  */
diff --git a/java/src/jni/h5tImp.h b/java/src/jni/h5tImp.h
index 374d992..a63969b 100644
--- a/java/src/jni/h5tImp.h
+++ b/java/src/jni/h5tImp.h
@@ -401,6 +401,15 @@ Java_hdf_hdf5lib_H5_H5Tpack
 
 /*
  * 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
  * Signature: (J)I
  */
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index af83caa..700f75f 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -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);
                     }
 
diff --git a/java/test/TestH5Dparams.java b/java/test/TestH5Dparams.java
index a3618f2..621c000 100644
--- a/java/test/TestH5Dparams.java
+++ b/java/test/TestH5Dparams.java
@@ -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);
diff --git a/java/test/TestH5Tparams.java b/java/test/TestH5Tparams.java
index 53d3a37..8baccd1 100644
--- a/java/test/TestH5Tparams.java
+++ b/java/test/TestH5Tparams.java
@@ -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 {
diff --git a/java/test/testfiles/JUnit-TestH5Dparams.txt b/java/test/testfiles/JUnit-TestH5Dparams.txt
index 9751be4..9acedd7 100644
--- a/java/test/testfiles/JUnit-TestH5Dparams.txt
+++ b/java/test/testfiles/JUnit-TestH5Dparams.txt
@@ -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)
 
diff --git a/java/test/testfiles/JUnit-TestH5Tparams.txt b/java/test/testfiles/JUnit-TestH5Tparams.txt
index e61f1e4..9f725ac 100644
--- a/java/test/testfiles/JUnit-TestH5Tparams.txt
+++ b/java/test/testfiles/JUnit-TestH5Tparams.txt
@@ -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)