Merge/update CMake, presets,java and tools (#3393)

1 files changed, 142 insertions, 419 deletions

diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index c8dc0c3..de7fb21 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -181,47 +181,71 @@ Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong me
                             jlong file_space_id, jlong xfer_plist_id, jbyteArray buf,
                             jboolean isCriticalPinning)
 {
-    jboolean readBufIsCopy;
-    jbyte   *readBuf = NULL;
-    htri_t   vl_data_class;
-    herr_t   status = FAIL;
+    jboolean    readBufIsCopy;
+    jbyte      *readBuf = NULL;
+    size_t      typeSize;
+    H5T_class_t type_class;
+    jsize       vl_array_len; // Only used by vl_data_class types
+    htri_t      vl_data_class;
+    herr_t      status = FAIL;
 
     UNUSED(clss);
 
     if (NULL == buf)
         H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dread: read buffer is NULL");
 
-    /* Get size of data array */
-    if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
-        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
-        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
-    }
-
     if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
-    if (isCriticalPinning) {
-        PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
-                                "H5Dread: read buffer not critically pinned");
+    if (vl_data_class) {
+        /* Get size of data array */
+        if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
+        }
+
+        if (!(typeSize = H5Tget_size(mem_type_id)))
+            H5_LIBRARY_ERROR(ENVONLY);
+
+        if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dread: failed to allocate raw VL read buffer");
     }
     else {
-        PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread: read buffer not pinned");
+        if (isCriticalPinning) {
+            PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, readBuf, &readBufIsCopy,
+                                    "H5Dread: read buffer not critically pinned");
+        }
+        else {
+            PIN_BYTE_ARRAY(ENVONLY, buf, readBuf, &readBufIsCopy, "H5Dread: read buffer not pinned");
+        }
     }
 
     if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
-                          (hid_t)xfer_plist_id, readBuf)) < 0)
+                          (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
+    if (vl_data_class) {
+        if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+            H5_LIBRARY_ERROR(ENVONLY);
+
+        translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf);
+    }
+
 done:
     if (readBuf) {
         if ((status >= 0) && vl_data_class)
             H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
 
-        if (isCriticalPinning) {
-            UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
+        if (vl_data_class) {
+            HDfree(readBuf);
         }
         else {
-            UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
+            if (isCriticalPinning) {
+                UNPIN_ARRAY_CRITICAL(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
+            }
+            else {
+                UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
+            }
         }
     }
 
@@ -238,31 +262,50 @@ Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong m
                              jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jbyteArray buf,
                              jboolean isCriticalPinning)
 {
-    jboolean writeBufIsCopy;
-    jbyte   *writeBuf = NULL;
-    htri_t   vl_data_class;
-    herr_t   status = FAIL;
+    jboolean    writeBufIsCopy;
+    jbyte      *writeBuf = NULL;
+    size_t      typeSize;
+    H5T_class_t type_class;
+    jsize       vl_array_len; // Only used by vl_data_class types
+    htri_t      vl_data_class;
+    herr_t      status = FAIL;
 
     UNUSED(clss);
 
     if (NULL == buf)
         H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer is NULL");
 
-    /* Get size of data array */
-    if (ENVPTR->GetArrayLength(ENVONLY, buf) < 0) {
-        CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
-        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dread: readBuf length < 0");
-    }
-
     if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
-    if (isCriticalPinning) {
-        PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
-                                "H5Dwrite: write buffer not critically pinned");
+    if (vl_data_class) {
+        /* Get size of data array */
+        if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+            CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Dwrite: write buffer length < 0");
+        }
+
+        if (!(typeSize = H5Tget_size(mem_type_id)))
+            H5_LIBRARY_ERROR(ENVONLY);
+
+        if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Dwrite: failed to allocate raw VL write buffer");
     }
     else {
-        PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite: write buffer not pinned");
+        if (isCriticalPinning) {
+            PIN_BYTE_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, &writeBufIsCopy,
+                                    "H5Dwrite: write buffer not critically pinned");
+        }
+        else {
+            PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5Dwrite: write buffer not pinned");
+        }
+    }
+
+    if (vl_data_class) {
+        if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+            H5_LIBRARY_ERROR(ENVONLY);
+
+        translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
     }
 
     if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
@@ -274,11 +317,16 @@ done:
         if ((status >= 0) && vl_data_class)
             H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
 
-        if (isCriticalPinning) {
-            UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
+        if (vl_data_class) {
+            HDfree(writeBuf);
         }
         else {
-            UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
+            if (isCriticalPinning) {
+                UNPIN_ARRAY_CRITICAL(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
+            }
+            else {
+                UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
+            }
         }
     }
 
@@ -1086,234 +1134,52 @@ JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5DreadVL(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)
 {
+    jbyte      *readBuf = NULL;
+    size_t      typeSize;
     H5T_class_t type_class;
-    jsize       n;
+    jsize       vl_array_len;
     htri_t      vl_data_class;
-    herr_t      status  = FAIL;
-    jbyteArray *readBuf = NULL;
+    herr_t      status      = FAIL;
+    htri_t      is_variable = 0;
 
     UNUSED(clss);
 
     if (NULL == buf)
         H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: read buffer is NULL");
 
+    if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
     /* Get size of data array */
-    if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+    if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
         CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
         H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: readBuf length < 0");
     }
-
-    if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+    if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
-    if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+    if (!(typeSize = H5Tget_size(mem_type_id)))
         H5_LIBRARY_ERROR(ENVONLY);
-    if (type_class == H5T_VLEN) {
-        size_t       typeSize;
-        hid_t        memb = H5I_INVALID_HID;
-        H5T_class_t  vlClass;
-        size_t       vlSize;
-        void        *rawBuf = NULL;
-        jobjectArray jList  = NULL;
-
-        size_t i, j, x;
-
-        if (!(typeSize = H5Tget_size(mem_type_id)))
-            H5_LIBRARY_ERROR(ENVONLY);
-
-        if (!(memb = H5Tget_super(mem_type_id)))
-            H5_LIBRARY_ERROR(ENVONLY);
-        if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
-            H5_LIBRARY_ERROR(ENVONLY);
-        if (!(vlSize = H5Tget_size(memb)))
-            H5_LIBRARY_ERROR(ENVONLY);
 
-        if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
-            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer");
-
-        if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
-                              (hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)rawBuf)) < 0)
-            H5_LIBRARY_ERROR(ENVONLY);
+    if (NULL == (readBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer");
 
-        /* Cache class types */
-        /* jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
-        jclass cByte   = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
-        jclass cShort  = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
-        jclass cInt    = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
-        jclass cLong   = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
-        jclass cFloat  = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
-        jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
-        /*
-        jmethodID boolValueMid =
-            ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
-        */
-        jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
-        jmethodID shortValueMid =
-            ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
-        jmethodID intValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cInt, "valueOf", "(I)Ljava/lang/Integer;");
-        jmethodID longValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cLong, "valueOf", "(J)Ljava/lang/Long;");
-        jmethodID floatValueMid =
-            ENVPTR->GetStaticMethodID(ENVONLY, cFloat, "valueOf", "(F)Ljava/lang/Float;");
-        jmethodID doubleValueMid =
-            ENVPTR->GetStaticMethodID(ENVONLY, cDouble, "valueOf", "(D)Ljava/lang/Double;");
-
-        // retrieve the java.util.List interface class
-        jclass    cList     = ENVPTR->FindClass(ENVONLY, "java/util/List");
-        jmethodID addMethod = ENVPTR->GetMethodID(ENVONLY, cList, "add", "(Ljava/lang/Object;)Z");
-
-        /* Convert each element to a list */
-        for (i = 0; i < (size_t)n; i++) {
-            hvl_t vl_elem;
-
-            // The list we're going to return:
-            if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
-                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
-            /* Get the number of sequence elements */
-            HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
-
-            jsize nelmts = (jsize)vl_elem.len;
-            if (vl_elem.len != (size_t)nelmts)
-                H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of number of VL elements");
-            if (nelmts < 0)
-                H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: number of VL elements < 0");
-
-            jobject jobj = NULL;
-            for (j = 0; j < (size_t)nelmts; j++) {
-                switch (vlClass) {
-                    /*case H5T_BOOL: {
-                        jboolean boolValue;
-                        for (x = 0; x < vlSize; x++) {
-                            ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
-                        }
-
-                        jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
-                        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                        break;
-                    } */
-                    case H5T_INTEGER: {
-                        switch (vlSize) {
-                            case sizeof(jbyte): {
-                                jbyte byteValue;
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
-                                }
-
-                                jobj =
-                                    ENVPTR->CallStaticObjectMethod(ENVONLY, cByte, byteValueMid, byteValue);
-                                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                                break;
-                            }
-                            case sizeof(jshort): {
-                                jshort shortValue;
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
-                                }
-
-                                jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
-                                                                      shortValue);
-                                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                                break;
-                            }
-                            case sizeof(jint): {
-                                jint intValue;
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
-                                }
-
-                                jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
-                                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                                break;
-                            }
-                            case sizeof(jlong): {
-                                jlong longValue;
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
-                                }
-
-                                jobj =
-                                    ENVPTR->CallStaticObjectMethod(ENVONLY, cLong, longValueMid, longValue);
-                                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                                break;
-                            }
-                        }
-                        break;
-                    }
-                    case H5T_FLOAT: {
-                        switch (vlSize) {
-                            case sizeof(jfloat): {
-                                jfloat floatValue;
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
-                                }
-
-                                jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
-                                                                      (double)floatValue);
-                                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                                break;
-                            }
-                            case sizeof(jdouble): {
-                                jdouble doubleValue;
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
-                                }
-
-                                jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
-                                                                      doubleValue);
-                                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                                break;
-                            }
-                        }
-                        break;
-                    }
-                    case H5T_REFERENCE: {
-                        jboolean bb;
-                        jbyte   *barray = NULL;
-
-                        jsize byteArraySize = (jsize)vlSize;
-                        if (vlSize != (size_t)byteArraySize)
-                            H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of byteArraySize");
-
-                        if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
-                            CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
-                        PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
-                                       "readVL reference: byte array not pinned");
-
-                        for (x = 0; x < vlSize; x++) {
-                            barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x];
-                        }
-                        if (barray)
-                            UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
-                        break;
-                    }
-                    default:
-                        H5_UNIMPLEMENTED(ENVONLY, "H5DreadVL: invalid class type");
-                        break;
-                }
-
-                // Add it to the list
-                ENVPTR->CallBooleanMethod(ENVONLY, jList, addMethod, jobj);
-                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-            }
-        } /* end for */
+    if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
+                          (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+    if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
 
-        if (rawBuf)
-            HDfree(rawBuf);
-    }
-    else {
-        if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
-                              (hid_t)file_space_id, (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
-            H5_LIBRARY_ERROR(ENVONLY);
-    }
+    translate_rbuf(env, buf, mem_type_id, type_class, vl_array_len, readBuf);
 
 done:
     if (readBuf) {
         if ((status >= 0) && vl_data_class)
             H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, readBuf);
-
-        UNPIN_BYTE_ARRAY(ENVONLY, buf, readBuf, (status < 0) ? JNI_ABORT : 0);
+        if (is_variable) {
+            for (size_t i = 0; i < (size_t)vl_array_len; i++)
+                HDfree(((char **)readBuf)[i]);
+        }
+        HDfree(readBuf);
     }
 
     return (jint)status;
@@ -1328,201 +1194,55 @@ JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5DwriteVL(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)
 {
+    jbyte      *writeBuf = NULL;
+    size_t      typeSize;
     H5T_class_t type_class;
-    jsize       n;
+    jsize       vl_array_len; // Only used by vl_data_class types
     htri_t      vl_data_class;
-    herr_t      status = FAIL;
-    jboolean    writeBufIsCopy;
-    jbyteArray  writeBuf = NULL;
+    herr_t      status      = FAIL;
+    htri_t      is_variable = 0;
 
     UNUSED(clss);
 
     if (NULL == buf)
         H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer is NULL");
 
+    if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
     /* Get size of data array */
-    if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
+    if ((vl_array_len = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
         CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
-        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: readBuf length < 0");
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: write buffer length < 0");
     }
-
-    if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
+    if ((is_variable = H5Tis_variable_str(mem_type_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
-    if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+    if (!(typeSize = H5Tget_size(mem_type_id)))
         H5_LIBRARY_ERROR(ENVONLY);
-    if (type_class == H5T_VLEN) {
-        size_t       typeSize;
-        hid_t        memb = H5I_INVALID_HID;
-        H5T_class_t  vlClass;
-        size_t       vlSize;
-        void        *rawBuf = NULL;
-        jobjectArray jList  = NULL;
-
-        size_t i, j, x;
-
-        if (!(typeSize = H5Tget_size(mem_type_id)))
-            H5_LIBRARY_ERROR(ENVONLY);
-
-        if (!(memb = H5Tget_super(mem_type_id)))
-            H5_LIBRARY_ERROR(ENVONLY);
-        if ((vlClass = H5Tget_class((hid_t)memb)) < 0)
-            H5_LIBRARY_ERROR(ENVONLY);
-        if (!(vlSize = H5Tget_size(memb)))
-            H5_LIBRARY_ERROR(ENVONLY);
-
-        if (NULL == (rawBuf = HDcalloc((size_t)n, typeSize)))
-            H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer");
-
-        /* Cache class types */
-        /* jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
-        jclass cByte   = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
-        jclass cShort  = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
-        jclass cInt    = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
-        jclass cLong   = ENVPTR->FindClass(ENVONLY, "java/lang/Long");
-        jclass cFloat  = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
-        jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
-
-        /* jmethodID boolValueMid   = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */
-        jmethodID byteValueMid   = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
-        jmethodID shortValueMid  = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
-        jmethodID intValueMid    = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
-        jmethodID longValueMid   = ENVPTR->GetMethodID(ENVONLY, cLong, "longValue", "()J");
-        jmethodID floatValueMid  = ENVPTR->GetMethodID(ENVONLY, cFloat, "floatValue", "()F");
-        jmethodID doubleValueMid = ENVPTR->GetMethodID(ENVONLY, cDouble, "doubleValue", "()D");
-
-        /* Convert each list to a vlen element */
-        for (i = 0; i < (size_t)n; i++) {
-            hvl_t vl_elem;
-
-            if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
-                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
-            // retrieve the java.util.List interface class
-            jclass cList = ENVPTR->FindClass(ENVONLY, "java/util/List");
-
-            // retrieve the toArray method and invoke it
-            jmethodID mToArray = ENVPTR->GetMethodID(ENVONLY, cList, "toArray", "()[Ljava/lang/Object;");
-            if (mToArray == NULL)
-                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-            jobjectArray array   = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
-            jsize        jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
-
-            if (jnelmts < 0)
-                H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: number of VL elements < 0");
-
-            HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
-            vl_elem.len = (size_t)jnelmts;
-
-            if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
-                H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate vlen ptr buffer");
-
-            jobject jobj = NULL;
-            for (j = 0; j < (size_t)jnelmts; j++) {
-                if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
-                    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-
-                switch (vlClass) {
-                    /* case H5T_BOOL: {
-                            jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
-                            for (x = 0; x < vlSize; x++) {
-                                ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
-                            }
-                            break;
-                    } */
-                    case H5T_INTEGER: {
-                        switch (vlSize) {
-                            case sizeof(jbyte): {
-                                jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x];
-                                }
-                                break;
-                            }
-                            case sizeof(jshort): {
-                                jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x];
-                                }
-                                break;
-                            }
-                            case sizeof(jint): {
-                                jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x];
-                                }
-                                break;
-                            }
-                            case sizeof(jlong): {
-                                jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
-                                }
-                                break;
-                            }
-                        }
-                        break;
-                    }
-                    case H5T_FLOAT: {
-                        switch (vlSize) {
-                            case sizeof(jfloat): {
-                                jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x];
-                                }
-                                break;
-                            }
-                            case sizeof(jdouble): {
-                                jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
-                                for (x = 0; x < vlSize; x++) {
-                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
-                                }
-                                break;
-                            }
-                        }
-                        break;
-                    }
-                    case H5T_REFERENCE: {
-                        jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
-                        for (x = 0; x < vlSize; x++) {
-                            ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
-                        }
-                        ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
-                        break;
-                    }
-                    default:
-                        H5_UNIMPLEMENTED(ENVONLY, "H5DwriteVL: invalid class type");
-                        break;
-                }
-                ENVPTR->DeleteLocalRef(ENVONLY, jobj);
-            }
 
-            HDmemcpy((char *)rawBuf + i * typeSize, &vl_elem, sizeof(hvl_t));
+    if (NULL == (writeBuf = HDcalloc((size_t)vl_array_len, typeSize)))
+        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer");
 
-            ENVPTR->DeleteLocalRef(ENVONLY, jList);
-        } /* end for (i = 0; i < n; i++) */
+    if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
 
-        if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
-                               (hid_t)file_space_id, (hid_t)xfer_plist_id, rawBuf)) < 0)
-            CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+    translate_wbuf(ENVONLY, buf, mem_type_id, type_class, vl_array_len, writeBuf);
 
-        if (rawBuf)
-            HDfree(rawBuf);
-    }
-    else {
-        PIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, &writeBufIsCopy, "H5DwriteVL: write buffer not pinned");
-        if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id,
-                               (hid_t)file_space_id, (hid_t)xfer_plist_id, writeBuf)) < 0)
-            H5_LIBRARY_ERROR(ENVONLY);
-    }
+    if ((status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
+                           (hid_t)xfer_plist_id, writeBuf)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
 
 done:
     if (writeBuf) {
         if ((status >= 0) && vl_data_class)
             H5Treclaim(dataset_id, mem_space_id, H5P_DEFAULT, writeBuf);
+        if (is_variable) {
+            for (size_t i = 0; i < (size_t)vl_array_len; i++)
+                HDfree(((char **)writeBuf)[i]);
+        }
 
-        if (type_class != H5T_VLEN)
-            UNPIN_BYTE_ARRAY(ENVONLY, buf, writeBuf, (status < 0) ? JNI_ABORT : 0);
+        HDfree(writeBuf);
     }
 
     return (jint)status;
@@ -1958,21 +1678,24 @@ H5DwriteVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_si
             continue;
         }
 
-        /*
-         * length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
-         * CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-         */
-
         PIN_JAVA_STRING(ENVONLY, jstr, utf8, NULL, "H5DwriteVL_asstr: failed to pin string buffer");
 
         /*
-         * TODO: If the string isn't a copy, we should probably make
-         * one before destroying it with h5str_convert.
+         * Make a copy of the string since h5str_convert uses strtok.
          */
+        char *utf8_copy = NULL;
+
+        jsize length = ENVPTR->GetStringUTFLength(ENVONLY, jstr);
+        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+
+        if (NULL == (utf8_copy = HDstrndup(utf8, (size_t)length)))
+            H5_LIBRARY_ERROR(ENVONLY);
 
-        if (!h5str_convert(ENVONLY, (char **)&utf8, did, tid, &(((char *)writeBuf)[i * typeSize]), 0))
+        if (!h5str_convert(ENVONLY, &utf8_copy, did, tid, &(((char *)writeBuf)[i * typeSize]), 0))
             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
+        HDfree(utf8_copy);
+
         UNPIN_JAVA_STRING(ENVONLY, jstr, utf8);
         utf8 = NULL;