VFD SWMR: Normalization with develop (#1078)

Brings many changes from develop, particularly VOL changes for async

8 files changed, 61 insertions, 86 deletions

diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java
index bb9357e..21e2b02 100644
--- a/java/src/hdf/hdf5lib/HDFArray.java
+++ b/java/src/hdf/hdf5lib/HDFArray.java
@@ -46,10 +46,10 @@ public class HDFArray {
      *
      * @param anArray
      *                The array object.
-     * @exception hdf.hdf5lib.exceptions.HDF5Exception
-     *                                                 object is not an array.
+     * @exception hdf.hdf5lib.exceptions.HDF5JavaException
+     *                object is not an array.
      */
-    public HDFArray(Object anArray) throws HDF5Exception
+    public HDFArray(Object anArray) throws HDF5JavaException
     {
         if (anArray == null) {
             HDF5JavaException ex = new HDF5JavaException("HDFArray: array is null?: ");
@@ -76,16 +76,14 @@ public class HDFArray {
      * @return A one-D array of bytes, filled with zeroes. The bytes are sufficient to hold the data of the Array passed
      *         to the constructor.
      * @exception hdf.hdf5lib.exceptions.HDF5JavaException
-     *                                                     Allocation failed.
+     *                Allocation failed.
      */
 
-    public byte[] emptyBytes()
-            throws HDF5JavaException
+    public byte[] emptyBytes() throws HDF5JavaException
     {
         byte[] b = null;
 
-        if ((ArrayDescriptor.dims == 1)
-                && (ArrayDescriptor.NT == 'B')) {
+        if ((ArrayDescriptor.dims == 1) && (ArrayDescriptor.NT == 'B')) {
             b = (byte[]) _theArray;
         }
         else {
@@ -103,10 +101,9 @@ public class HDFArray {
      *
      * @return A one-D array of bytes, constructed from the Array passed to the constructor.
      * @exception hdf.hdf5lib.exceptions.HDF5JavaException
-     *                                                     the object not an array or other internal error.
+     *                the object not an array or other internal error.
      */
-    public byte[] byteify()
-            throws HDF5JavaException
+    public byte[] byteify() throws HDF5JavaException
     {
         if (_barray != null) {
             return _barray;
@@ -224,8 +221,6 @@ public class HDFArray {
                 if (ArrayDescriptor.NT == 'J') {
                     arow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                             (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
-                    arow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims],
-                            (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                 }
                 else if (ArrayDescriptor.NT == 'I') {
                     arow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims],
@@ -552,8 +547,7 @@ public class HDFArray {
                                 + "?"));
             }
         }
-        if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims
-                - 1]) {
+        if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) {
             throw new java.lang.InternalError(
                     new String("HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = "
                             + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i]) + "?"));
@@ -580,7 +574,7 @@ public class HDFArray {
         Integer[] out = new Integer[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Integer(in[i]);
+            out[i] = Integer.valueOf(in[i]);
         }
         return out;
     }
@@ -592,7 +586,7 @@ public class HDFArray {
         Integer[] out = new Integer[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Integer(in[i]);
+            out[i] = Integer.valueOf(in[i]);
         }
         return out;
     }
@@ -615,7 +609,7 @@ public class HDFArray {
         Short[] out = new Short[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Short(in[i]);
+            out[i] = Short.valueOf(in[i]);
         }
         return out;
     }
@@ -627,7 +621,7 @@ public class HDFArray {
         Short[] out = new Short[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Short(in[i]);
+            out[i] = Short.valueOf(in[i]);
         }
         return out;
     }
@@ -649,7 +643,7 @@ public class HDFArray {
         Byte[] out = new Byte[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Byte(bin[i]);
+            out[i] = Byte.valueOf(bin[i]);
         }
         return out;
     }
@@ -659,7 +653,7 @@ public class HDFArray {
         Byte[] out = new Byte[len];
 
         for (int i = 0; i < len; i++) {
-            out[i] = new Byte(bin[i]);
+            out[i] = Byte.valueOf(bin[i]);
         }
         return out;
     }
@@ -682,7 +676,7 @@ public class HDFArray {
         Float[] out = new Float[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Float(in[i]);
+            out[i] = Float.valueOf(in[i]);
         }
         return out;
     }
@@ -694,7 +688,7 @@ public class HDFArray {
         Float[] out = new Float[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Float(in[i]);
+            out[i] = Float.valueOf(in[i]);
         }
         return out;
     }
@@ -717,7 +711,7 @@ public class HDFArray {
         Double[] out = new Double[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Double(in[i]);
+            out[i] = Double.valueOf(in[i]);
         }
         return out;
     }
@@ -729,7 +723,7 @@ public class HDFArray {
         Double[] out = new Double[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Double(in[i]);
+            out[i] = Double.valueOf(in[i]);
         }
         return out;
     }
@@ -752,7 +746,7 @@ public class HDFArray {
         Long[] out = new Long[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Long(in[i]);
+            out[i] = Long.valueOf(in[i]);
         }
         return out;
     }
@@ -764,7 +758,7 @@ public class HDFArray {
         Long[] out = new Long[nelems];
 
         for (int i = 0; i < nelems; i++) {
-            out[i] = new Long(in[i]);
+            out[i] = Long.valueOf(in[i]);
         }
         return out;
     }
@@ -790,12 +784,12 @@ class ArrayDescriptor {
     static int dims = 0;
     static String className;
 
-    public ArrayDescriptor(Object anArray) throws HDF5Exception
+    public ArrayDescriptor(Object anArray) throws HDF5JavaException
     {
         Class tc = anArray.getClass();
         if (tc.isArray() == false) {
             /* exception: not an array */
-            HDF5Exception ex = new HDF5JavaException("ArrayDescriptor: not an array?: ");
+            HDF5JavaException ex = new HDF5JavaException("ArrayDescriptor: not an array?: ");
             throw (ex);
         }
 
diff --git a/java/src/hdf/hdf5lib/HDFNativeData.java b/java/src/hdf/hdf5lib/HDFNativeData.java
index 5b29050..85378db 100644
--- a/java/src/hdf/hdf5lib/HDFNativeData.java
+++ b/java/src/hdf/hdf5lib/HDFNativeData.java
@@ -153,8 +153,7 @@ public class HDFNativeData {
      *            The input array of bytes
      * @return an array of 'len' float
      */
-    public synchronized static native float[] byteToFloat(int start, int len,
-            byte[] data);
+    public synchronized static native float[] byteToFloat(int start, int len, byte[] data);
 
     /**
      * Convert 4 bytes from an array of bytes into a single float
@@ -437,41 +436,38 @@ public class HDFNativeData {
      *                - Error unsupported type.
      */
     public synchronized static Object byteToNumber(byte[] barray, Object obj)
-            throws HDF5Exception {
+            throws HDF5Exception
+    {
         Class theClass = obj.getClass();
         String type = theClass.getName();
         Object retobj = null;
 
         if (type.equals("java.lang.Integer")) {
             int[] i = hdf.hdf5lib.HDFNativeData.byteToInt(0, 1, barray);
-            retobj = new Integer(i[0]);
+            retobj = Integer.valueOf(i[0]);
         }
         else if (type.equals("java.lang.Byte")) {
-            retobj = new Byte(barray[0]);
+            retobj = Byte.valueOf(barray[0]);
         }
         else if (type.equals("java.lang.Short")) {
-            short[] f = hdf.hdf5lib.HDFNativeData
-                    .byteToShort(0, 1, barray);
-            retobj = new Short(f[0]);
+            short[] f = hdf.hdf5lib.HDFNativeData.byteToShort(0, 1, barray);
+            retobj = Short.valueOf(f[0]);
         }
         else if (type.equals("java.lang.Float")) {
-            float[] f = hdf.hdf5lib.HDFNativeData
-                    .byteToFloat(0, 1, barray);
-            retobj = new Float(f[0]);
+            float[] f = hdf.hdf5lib.HDFNativeData.byteToFloat(0, 1, barray);
+            retobj = Float.valueOf(f[0]);
         }
         else if (type.equals("java.lang.Long")) {
             long[] f = hdf.hdf5lib.HDFNativeData.byteToLong(0, 1, barray);
-            retobj = new Long(f[0]);
+            retobj = Long.valueOf(f[0]);
         }
         else if (type.equals("java.lang.Double")) {
-            double[] f = hdf.hdf5lib.HDFNativeData.byteToDouble(0, 1,
-                    barray);
-            retobj = new Double(f[0]);
+            double[] f = hdf.hdf5lib.HDFNativeData.byteToDouble(0, 1, barray);
+            retobj = Double.valueOf(f[0]);
         }
         else {
             /* exception: unsupported type */
-            HDF5Exception ex = new HDF5JavaException(
-                    "byteToNumber: setfield bad type: " + obj + " " + type);
+            HDF5Exception ex = new HDF5JavaException("byteToNumber: setfield bad type: " + obj + " " + type);
             throw (ex);
         }
         return (retobj);
diff --git a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
index 5da4abd..95a9254 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
@@ -1,15 +1,14 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Read-Only HDFS Virtual File Driver (VFD)                                  *
- * Copyright (c) 2018, The HDF Group.                                        *
+ * Copyright by The HDF Group.                                               *
  *                                                                           *
  * All rights reserved.                                                      *
  *                                                                           *
- * NOTICE:                                                                   *
- * All information contained herein is, and remains, the property of The HDF *
- * Group. The intellectual and technical concepts contained herein are       *
- * proprietary to The HDF Group. Dissemination of this information or        *
- * reproduction of this material is strictly forbidden unless prior written  *
- * permission is obtained from The HDF Group.                                *
+ * 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://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 package hdf.hdf5lib.structs;
diff --git a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
index 39f5424..ad02979 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
@@ -1,15 +1,14 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Read-Only S3 Virtual File Driver (VFD)                                    *
- * Copyright (c) 2017-2018, The HDF Group.                                   *
+ * Copyright by The HDF Group.                                               *
  *                                                                           *
  * All rights reserved.                                                      *
  *                                                                           *
- * NOTICE:                                                                   *
- * All information contained herein is, and remains, the property of The HDF *
- * Group. The intellectual and technical concepts contained herein are       *
- * proprietary to The HDF Group. Dissemination of this information or        *
- * reproduction of this material is strictly forbidden unless prior written  *
- * permission is obtained from The HDF Group.                                *
+ * 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://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 package hdf.hdf5lib.structs;
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index 7354e95..bdffdbd 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -26,8 +26,8 @@ extern "C" {
 #include <stdlib.h>
 #include "h5jni.h"
 
-H5_GCC_DIAG_OFF("missing-prototypes")
-H5_GCC_DIAG_OFF("unused-parameter")
+H5_GCC_CLANG_DIAG_OFF("missing-prototypes")
+H5_GCC_CLANG_DIAG_OFF("unused-parameter")
 
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5_1QUARTER_1HADDR_1MAX(JNIEnv *env, jclass cls)
@@ -1212,7 +1212,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5ES_1STATUS_1FAIL(JNIEnv *env, jclass cls)
 }
 
 /* Java does not have unsigned native types */
-H5_GCC_DIAG_OFF("sign-conversion")
+H5_GCC_CLANG_DIAG_OFF("sign-conversion")
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1CREAT(JNIEnv *env, jclass cls)
 {
@@ -1253,7 +1253,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1SWMR_1WRITE(JNIEnv *env, jclass cls)
 {
     return H5F_ACC_SWMR_WRITE;
 }
-H5_GCC_DIAG_ON("sign-conversion")
+H5_GCC_CLANG_DIAG_ON("sign-conversion")
 
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5F_1CLOSE_1DEFAULT(JNIEnv *env, jclass cls)
@@ -3724,8 +3724,8 @@ Java_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1ALL(JNIEnv *env, jclass cls)
     return H5Z_FILTER_ALL;
 }
 
-H5_GCC_DIAG_ON("missing-prototypes")
-H5_GCC_DIAG_ON("unused-parameter")
+H5_GCC_CLANG_DIAG_ON("missing-prototypes")
+H5_GCC_CLANG_DIAG_ON("unused-parameter")
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 8021438..4272205 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -870,11 +870,8 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
             }
             else {
                 if (typeSize > 0) {
-                    if (NULL == (this_str = (char *)HDmalloc(typeSize + 1)))
+                    if (NULL == (this_str = HDstrdup(tmp_str)))
                         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
-
-                    HDstrncpy(this_str, tmp_str, typeSize);
-                    this_str[typeSize] = '\0';
                 }
             }
 
@@ -3664,19 +3661,14 @@ obj_info_all(hid_t loc_id, const char *name, const H5L_info2_t *info, void *op_d
     info_all_t *datainfo = (info_all_t *)op_data;
     H5O_info2_t object_info;
     htri_t      object_exists;
-    size_t      str_len;
 
     datainfo->otype[datainfo->count]     = -1;
     datainfo->ltype[datainfo->count]     = -1;
     datainfo->obj_token[datainfo->count] = H5O_TOKEN_UNDEF;
 
-    str_len = HDstrlen(name);
-    if (NULL == (datainfo->objname[datainfo->count] = (char *)HDmalloc(str_len + 1)))
+    if (NULL == (datainfo->objname[datainfo->count] = HDstrdup(name)))
         goto done;
 
-    HDstrncpy(datainfo->objname[datainfo->count], name, str_len);
-    (datainfo->objname[datainfo->count])[str_len] = '\0';
-
     if ((object_exists = H5Oexists_by_name(loc_id, name, H5P_DEFAULT)) < 0)
         goto done;
 
@@ -3702,7 +3694,6 @@ obj_info_max(hid_t loc_id, const char *name, const H5L_info2_t *info, void *op_d
 {
     info_all_t *datainfo = (info_all_t *)op_data;
     H5O_info2_t object_info;
-    size_t      str_len;
 
     datainfo->otype[datainfo->count]     = -1;
     datainfo->ltype[datainfo->count]     = -1;
@@ -3710,13 +3701,9 @@ obj_info_max(hid_t loc_id, const char *name, const H5L_info2_t *info, void *op_d
     datainfo->obj_token[datainfo->count] = H5O_TOKEN_UNDEF;
 
     /* This will be freed by h5str_array_free(oName, n) */
-    str_len = HDstrlen(name);
-    if (NULL == (datainfo->objname[datainfo->count] = (char *)HDmalloc(str_len + 1)))
+    if (NULL == (datainfo->objname[datainfo->count] = HDstrdup(name)))
         goto done;
 
-    HDstrncpy(datainfo->objname[datainfo->count], name, str_len);
-    (datainfo->objname[datainfo->count])[str_len] = '\0';
-
     if (H5Oget_info3(loc_id, &object_info, H5O_INFO_ALL) < 0)
         goto done;
 
diff --git a/java/test/TestH5Arw.java b/java/test/TestH5Arw.java
index 282b736..8ce2fee 100644
--- a/java/test/TestH5Arw.java
+++ b/java/test/TestH5Arw.java
@@ -100,7 +100,7 @@ public class TestH5Arw {
         if (H5aid >= 0)
             try {H5.H5Aclose(H5aid);} catch (Exception ex) {}
         if (H5did >= 0)
-            try {H5.H5Aclose(H5did);} catch (Exception ex) {}
+            try {H5.H5Dclose(H5did);} catch (Exception ex) {}
         if (H5fid > 0)
             try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
         H5fid = HDF5Constants.H5I_INVALID_HID;
diff --git a/java/test/TestH5Pfapl.java b/java/test/TestH5Pfapl.java
index cc674e2..a65b52e 100644
--- a/java/test/TestH5Pfapl.java
+++ b/java/test/TestH5Pfapl.java
@@ -102,7 +102,7 @@ public class TestH5Pfapl {
         for(int indx = 0; ;indx++) {
             java.text.DecimalFormat myFormat = new java.text.DecimalFormat("00000");
             try {
-                file = new File("test"+myFormat.format(new Integer(indx))+".h5");
+                file = new File("test"+myFormat.format(Integer.valueOf(indx))+".h5");
             }
             catch (Throwable err) {}