Merge pull request #2059 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:topic_nullref to develop

* commit '6b68cc352ffabb5fe997db1eb52216b3ee80e669':
  H5R: fix H5Tconv to check for null references

5 files changed, 304 insertions, 46 deletions

diff --git a/src/H5Rint.c b/src/H5Rint.c
index adf6e4e..558c095 100644
--- a/src/H5Rint.c
+++ b/src/H5Rint.c
@@ -413,6 +413,7 @@ H5R__destroy(H5R_ref_priv_t *ref)
             break;
         case H5R_OBJECT1:
         case H5R_DATASET_REGION1:
+            break;
         case H5R_BADTYPE:
         case H5R_MAXTYPE:
             HDassert("invalid reference type" && 0);
@@ -423,7 +424,7 @@ H5R__destroy(H5R_ref_priv_t *ref)
     } /* end switch */
 
     /* Decrement refcount of attached loc_id */
-    if((ref->loc_id != H5I_INVALID_HID) && (H5I_dec_ref(ref->loc_id) < 0))
+    if(ref->type && (ref->loc_id != H5I_INVALID_HID) && (H5I_dec_ref(ref->loc_id) < 0))
         HGOTO_ERROR(H5E_REFERENCE, H5E_CANTDEC, FAIL, "decrementing location ID failed")
 
 done:
diff --git a/src/H5Tconv.c b/src/H5Tconv.c
index 6aea00e..4cc5f3c 100644
--- a/src/H5Tconv.c
+++ b/src/H5Tconv.c
@@ -3609,39 +3609,52 @@ H5T__conv_ref(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
                 for(elmtno = 0; elmtno < safe; elmtno++) {
                     size_t buf_size;
                     hbool_t dst_copy = FALSE;
+                    hbool_t is_nil; /* Whether sequence is "nil" */
 
-                    /* Get size of references */
-                    if(0 == (buf_size = src->shared->u.atomic.u.r.cls->getsize(
-                        src->shared->u.atomic.u.r.file, s, src->shared->size,
-                        dst->shared->u.atomic.u.r.file, &dst_copy)))
-                        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "incorrect size")
-
-                    /* Check if conversion buffer is large enough, resize if necessary. */
-                    if(conv_buf_size < buf_size) {
-                        conv_buf_size = buf_size;
-                        if(NULL == (conv_buf = H5FL_BLK_REALLOC(ref_seq, conv_buf, conv_buf_size)))
-                            HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
-                        HDmemset(conv_buf, 0, conv_buf_size);
-                    } /* end if */
+                    /* Check for "nil" source sequence */
+                    if((*(src->shared->u.atomic.u.r.cls->isnull))(src->shared->u.atomic.u.r.file, s, &is_nil) < 0)
+                        HGOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "can't check if reference data is 'nil'")
 
-                    if(dst_copy && (src->shared->u.atomic.u.r.loc == H5T_LOC_DISK)) {
-                        H5MM_memcpy(conv_buf, s, buf_size);
-                    } else {
-                        /* Read reference */
-                        if(src->shared->u.atomic.u.r.cls->read(
+                    if(is_nil) {
+
+                        /* Write "nil" sequence to destination location */
+                        if((*(dst->shared->u.atomic.u.r.cls->setnull))(dst->shared->u.atomic.u.r.file, d, b) < 0)
+                            HGOTO_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "can't set reference data to 'nil'")
+                    } /* end else-if */
+                    else {
+                        /* Get size of references */
+                        if(0 == (buf_size = src->shared->u.atomic.u.r.cls->getsize(
                             src->shared->u.atomic.u.r.file, s, src->shared->size,
-                            dst->shared->u.atomic.u.r.file, conv_buf, buf_size) < 0)
-                            HGOTO_ERROR(H5E_DATATYPE, H5E_READERROR, FAIL, "can't read reference data")
-                    }
+                            dst->shared->u.atomic.u.r.file, &dst_copy)))
+                            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "incorrect size")
+
+                        /* Check if conversion buffer is large enough, resize if necessary. */
+                        if(conv_buf_size < buf_size) {
+                            conv_buf_size = buf_size;
+                            if(NULL == (conv_buf = H5FL_BLK_REALLOC(ref_seq, conv_buf, conv_buf_size)))
+                                HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
+                            HDmemset(conv_buf, 0, conv_buf_size);
+                        } /* end if */
 
-                    if(dst_copy && (dst->shared->u.atomic.u.r.loc == H5T_LOC_DISK)) {
-                        H5MM_memcpy(d, conv_buf, buf_size);
-                    } else {
-                        /* Write reference to destination location */
-                        if(dst->shared->u.atomic.u.r.cls->write(
-                            src->shared->u.atomic.u.r.file, conv_buf, buf_size, src->shared->u.atomic.u.r.rtype,
-                            dst->shared->u.atomic.u.r.file, d, dst->shared->size, b) < 0)
-                            HGOTO_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "can't write reference data")
+                        if(dst_copy && (src->shared->u.atomic.u.r.loc == H5T_LOC_DISK)) {
+                            H5MM_memcpy(conv_buf, s, buf_size);
+                        } else {
+                            /* Read reference */
+                            if(src->shared->u.atomic.u.r.cls->read(
+                                src->shared->u.atomic.u.r.file, s, src->shared->size,
+                                dst->shared->u.atomic.u.r.file, conv_buf, buf_size) < 0)
+                                HGOTO_ERROR(H5E_DATATYPE, H5E_READERROR, FAIL, "can't read reference data")
+                        }
+
+                        if(dst_copy && (dst->shared->u.atomic.u.r.loc == H5T_LOC_DISK)) {
+                            H5MM_memcpy(d, conv_buf, buf_size);
+                        } else {
+                            /* Write reference to destination location */
+                            if(dst->shared->u.atomic.u.r.cls->write(
+                                src->shared->u.atomic.u.r.file, conv_buf, buf_size, src->shared->u.atomic.u.r.rtype,
+                                dst->shared->u.atomic.u.r.file, d, dst->shared->size, b) < 0)
+                                HGOTO_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "can't write reference data")
+                        }
                     }
 
                     /* Advance pointers */
diff --git a/src/H5Tpkg.h b/src/H5Tpkg.h
index 1dbc229..39bff15 100644
--- a/src/H5Tpkg.h
+++ b/src/H5Tpkg.h
@@ -182,11 +182,15 @@ struct H5T_path_t {
 };
 
 /* Reference function pointers */
+typedef herr_t (*H5T_ref_isnullfunc_t)(const H5VL_object_t *file, const void *src_buf, hbool_t *isnull);
+typedef herr_t (*H5T_ref_setnullfunc_t)(H5VL_object_t *file, void *dst_buf, void *bg_buf);
 typedef size_t (*H5T_ref_getsizefunc_t)(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, hbool_t *dst_copy);
 typedef herr_t (*H5T_ref_readfunc_t)(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, void *dst_buf, size_t dst_size);
 typedef herr_t (*H5T_ref_writefunc_t)(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5R_type_t src_type, H5VL_object_t *dst_file, void *dst_buf, size_t dst_size, void *bg_buf);
 
 typedef struct H5T_ref_class_t {
+    H5T_ref_isnullfunc_t    isnull;     /* check if reference value is NIL */
+    H5T_ref_setnullfunc_t   setnull;    /* set a reference value to NIL */
     H5T_ref_getsizefunc_t   getsize;    /* get reference size (bytes)   */
     H5T_ref_readfunc_t      read;       /* read reference into buffer   */
     H5T_ref_writefunc_t     write;      /* write reference from buffer  */
diff --git a/src/H5Tref.c b/src/H5Tref.c
index 20c6e41..823def9 100644
--- a/src/H5Tref.c
+++ b/src/H5Tref.c
@@ -54,18 +54,24 @@ struct H5Tref_dsetreg {
 /* Local Prototypes */
 /********************/
 
+static herr_t H5T__ref_mem_isnull(const H5VL_object_t *src_file, const void *src_buf, hbool_t *isnull);
+static herr_t H5T__ref_mem_setnull(H5VL_object_t *dst_file, void *dst_buf, void *bg_buf);
 static size_t H5T__ref_mem_getsize(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, hbool_t *dst_copy);
 static herr_t H5T__ref_mem_read(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, void *dst_buf, size_t dst_size);
 static herr_t H5T__ref_mem_write(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5R_type_t src_type, H5VL_object_t *dst_file, void *dst_buf, size_t dst_size, void *bg_buf);
 
+static herr_t H5T__ref_disk_isnull(const H5VL_object_t *src_file, const void *src_buf, hbool_t *isnull);
+static herr_t H5T__ref_disk_setnull(H5VL_object_t *dst_file, void *dst_buf, void *bg_buf);
 static size_t H5T__ref_disk_getsize(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, hbool_t *dst_copy);
 static herr_t H5T__ref_disk_read(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, void *dst_buf, size_t dst_size);
 static herr_t H5T__ref_disk_write(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5R_type_t src_type, H5VL_object_t *dst_file, void *dst_buf, size_t dst_size, void *bg_buf);
 
 /* For compatibility */
+static herr_t H5T__ref_obj_disk_isnull(const H5VL_object_t *src_file, const void *src_buf, hbool_t *isnull);
 static size_t H5T__ref_obj_disk_getsize(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, hbool_t *dst_copy);
 static herr_t H5T__ref_obj_disk_read(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, void *dst_buf, size_t dst_size);
 
+static herr_t H5T__ref_dsetreg_disk_isnull(const H5VL_object_t *src_file, const void *src_buf, hbool_t *isnull);
 static size_t H5T__ref_dsetreg_disk_getsize(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, hbool_t *dst_copy);
 static herr_t H5T__ref_dsetreg_disk_read(H5VL_object_t *src_file, const void *src_buf, size_t src_size, H5VL_object_t *dst_file, void *dst_buf, size_t dst_size);
 
@@ -75,24 +81,32 @@ static herr_t H5T__ref_dsetreg_disk_read(H5VL_object_t *src_file, const void *sr
 
 /* Class for reference in memory */
 static const H5T_ref_class_t H5T_ref_mem_g = {
+    H5T__ref_mem_isnull,            /* 'isnull' */
+    H5T__ref_mem_setnull,           /* 'setnull' */
     H5T__ref_mem_getsize,           /* 'getsize' */
     H5T__ref_mem_read,              /* 'read' */
     H5T__ref_mem_write              /* 'write' */
 };
 
 static const H5T_ref_class_t H5T_ref_disk_g = {
+    H5T__ref_disk_isnull,           /* 'isnull' */
+    H5T__ref_disk_setnull,          /* 'setnull' */
     H5T__ref_disk_getsize,          /* 'getsize' */
     H5T__ref_disk_read,             /* 'read' */
     H5T__ref_disk_write             /* 'write' */
 };
 
 static const H5T_ref_class_t H5T_ref_obj_disk_g = {
+    H5T__ref_obj_disk_isnull,       /* 'isnull' */
+    NULL,                           /* 'setnull' */
     H5T__ref_obj_disk_getsize,      /* 'getsize' */
     H5T__ref_obj_disk_read,         /* 'read' */
     NULL                            /* 'write' */
 };
 
 static const H5T_ref_class_t H5T_ref_dsetreg_disk_g = {
+    H5T__ref_dsetreg_disk_isnull,   /* 'isnull' */
+    NULL,                           /* 'setnull' */
     H5T__ref_dsetreg_disk_getsize,  /* 'getsize' */
     H5T__ref_dsetreg_disk_read,     /* 'read' */
     NULL                            /* 'write' */
@@ -268,6 +282,57 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:    H5T__ref_mem_isnull
+ *
+ * Purpose: Check if it's a NULL / uninitialized reference.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5T__ref_mem_isnull(const H5VL_object_t H5_ATTR_UNUSED *src_file,
+    const void *src_buf, hbool_t *isnull)
+{
+    const unsigned char zeros[H5T_REF_MEM_SIZE] = { 0 };
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_STATIC_NOERR
+
+    /* Check parameters */
+    HDassert(src_buf);
+    HDassert(isnull);
+
+    *isnull = (0 == HDmemcmp(src_buf, zeros, H5T_REF_MEM_SIZE)) ? TRUE : FALSE;
+
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5T__ref_mem_isnull() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5T__ref_mem_setnull
+ *
+ * Purpose: Set a reference as NULL / uninitialized.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5T__ref_mem_setnull(H5VL_object_t H5_ATTR_UNUSED *dst_file, void *dst_buf,
+    H5_ATTR_UNUSED void *bg_buf)
+{
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_STATIC_NOERR
+
+    HDmemset(dst_buf, 0, H5T_REF_MEM_SIZE);
+
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5T__ref_mem_setnull() */
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5T__ref_mem_getsize
  *
  * Purpose:	Retrieves the size of a memory based reference.
@@ -484,6 +549,96 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:    H5T__ref_disk_isnull
+ *
+ * Purpose: Check if it's a NULL / uninitialized reference.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5T__ref_disk_isnull(const H5VL_object_t *src_file, const void *src_buf,
+    hbool_t *isnull)
+{
+    const uint8_t *p = (const uint8_t *)src_buf;
+    H5R_type_t ref_type;
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_STATIC
+
+    /* Check parameters */
+    HDassert(src_file);
+    HDassert(src_buf);
+    HDassert(isnull);
+
+    /* Try to check encoded reference type */
+    ref_type = (H5R_type_t)*p++;
+    if(ref_type) {
+        /* This is a valid reference */
+        *isnull = FALSE;
+    } else {
+        /* Skip the size / header */
+        p = (const uint8_t *)src_buf + H5R_ENCODE_HEADER_SIZE + H5_SIZEOF_UINT32_T;
+
+        /* Check if blob ID is "nil" */
+        if(H5VL_blob_specific(src_file, (void *)p, H5VL_BLOB_ISNULL, isnull) < 0)
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "unable to check if a blob ID is 'nil'")
+    }
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5T__ref_disk_isnull() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5T__ref_disk_setnull
+ *
+ * Purpose: Set a reference as NULL / uninitialized.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5T__ref_disk_setnull(H5VL_object_t *dst_file, void *dst_buf, void *bg_buf)
+{
+    uint8_t *q = (uint8_t *)dst_buf;
+    uint8_t *p_bg = (uint8_t *)bg_buf;
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_STATIC
+
+    HDassert(dst_file);
+    HDassert(dst_buf);
+
+    /* TODO Should get rid of bg stuff */
+    if(p_bg) {
+        /* Skip the size / header */
+        p_bg += (H5_SIZEOF_UINT32_T + H5R_ENCODE_HEADER_SIZE);
+
+        /* Remove blob for old data */
+        if(H5VL_blob_specific(dst_file, (void *)p_bg, H5VL_BLOB_DELETE) < 0)
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREMOVE, FAIL, "unable to delete blob")
+    } /* end if */
+
+    /* Copy header manually so that it does not get encoded into the blob */
+    HDmemset(q, 0, H5R_ENCODE_HEADER_SIZE);
+    q += H5R_ENCODE_HEADER_SIZE;
+
+    /* Set the size */
+    UINT32ENCODE(q, 0);
+
+    /* Set blob ID to "nil" */
+    if(H5VL_blob_specific(dst_file, q, H5VL_BLOB_SETNULL) < 0)
+        HGOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "unable to set a blob ID to 'nil'")
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5T__ref_disk_setnull() */
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5T__ref_disk_getsize
  *
  * Purpose:	Retrieves the length of a disk based reference.
@@ -562,7 +717,7 @@ H5T__ref_disk_read(H5VL_object_t *src_file, const void *src_buf, size_t src_size
     q += H5R_ENCODE_HEADER_SIZE;
     blob_size -= H5R_ENCODE_HEADER_SIZE;
 
-    /* Skip the length of the sequence */
+    /* Skip the size */
     p += H5_SIZEOF_UINT32_T;
     HDassert(src_size > (H5R_ENCODE_HEADER_SIZE + H5_SIZEOF_UINT32_T));
 
@@ -606,10 +761,10 @@ H5T__ref_disk_write(H5VL_object_t H5_ATTR_UNUSED *src_file, const void *src_buf,
     if(p_bg) {
         size_t p_buf_size_left = dst_size;
 
-        /* Skip the length of the reference */
-        p_bg += H5_SIZEOF_UINT32_T;
-        HDassert(p_buf_size_left > H5_SIZEOF_UINT32_T);
-        p_buf_size_left -= H5_SIZEOF_UINT32_T;
+        /* Skip the size / header */
+        p_bg += (H5_SIZEOF_UINT32_T + H5R_ENCODE_HEADER_SIZE);
+        HDassert(p_buf_size_left > (H5_SIZEOF_UINT32_T + H5R_ENCODE_HEADER_SIZE));
+        p_buf_size_left -= (H5_SIZEOF_UINT32_T + H5R_ENCODE_HEADER_SIZE);
 
         /* Remove blob for old data */
         if(H5VL_blob_specific(dst_file, (void *)p_bg, H5VL_BLOB_DELETE) < 0)
@@ -638,6 +793,48 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:    H5T__ref_obj_disk_isnull
+ *
+ * Purpose: Check if it's a NULL / uninitialized reference.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t H5T__ref_obj_disk_isnull(const H5VL_object_t *src_file,
+    const void *src_buf, hbool_t *isnull)
+{
+    H5F_t *src_f;
+    const uint8_t *p = (const uint8_t *)src_buf;
+    haddr_t addr;
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_STATIC
+
+    /* Check parameters */
+    HDassert(src_file);
+    HDassert(src_buf);
+    HDassert(isnull);
+
+    /* We should assert here that the terminal connector is H5VL_NATIVE once
+     * there is a facility to do so -NAF 2019/10/30 */
+
+    /* Retrieve file from VOL object */
+    if(NULL == (src_f = (H5F_t *)H5VL_object_data(src_file)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid VOL object")
+
+    /* Get the object address */
+    H5F_addr_decode(src_f, &p, &addr);
+
+    /* Check if heap address is 'nil' */
+    *isnull = (addr == 0) ? TRUE : FALSE;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5T__ref_obj_disk_isnull() */
+
+
+/*-------------------------------------------------------------------------
  * Function:    H5T__ref_obj_disk_getsize
  *
  * Purpose: Retrieves the length of a disk based reference.
@@ -709,7 +906,7 @@ H5T__ref_obj_disk_read(H5VL_object_t *src_file, const void *src_buf, size_t src_
 
     /* Get object address */
     if(H5R__decode_token_obj_compat((const unsigned char *)src_buf, &src_size,
-        (unsigned char *)dst_buf, H5F_SIZEOF_ADDR(src_f)) < 0)
+        (H5VL_token_t *)dst_buf, H5F_SIZEOF_ADDR(src_f)) < 0)
         HGOTO_ERROR(H5E_REFERENCE, H5E_CANTDECODE, FAIL, "unable to get object address")
 
 done:
@@ -718,6 +915,49 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:    H5T__ref_dsetreg_disk_isnull
+ *
+ * Purpose: Check if it's a NULL / uninitialized reference.
+ *
+ * Return:  Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5T__ref_dsetreg_disk_isnull(const H5VL_object_t *src_file, const void *src_buf,
+    hbool_t *isnull)
+{
+    H5F_t *src_f;
+    const uint8_t *p = (const uint8_t *)src_buf;
+    haddr_t addr;
+    herr_t ret_value = SUCCEED;
+
+    FUNC_ENTER_STATIC
+
+    /* Check parameters */
+    HDassert(src_file);
+    HDassert(src_buf);
+    HDassert(isnull);
+
+    /* We should assert here that the terminal connector is H5VL_NATIVE once
+     * there is a facility to do so -NAF 2019/10/30 */
+
+    /* Retrieve file from VOL object */
+    if(NULL == (src_f = (H5F_t *)H5VL_object_data(src_file)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid VOL object")
+
+    /* Get the heap address */
+    H5F_addr_decode(src_f, &p, &addr);
+
+    /* Check if heap address is 'nil' */
+    *isnull = (addr == 0) ? TRUE : FALSE;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5T__ref_dsetreg_disk_isnull() */
+
+
+/*-------------------------------------------------------------------------
  * Function:    H5T__ref_dsetreg_disk_getsize
  *
  * Purpose: Retrieves the length of a disk based reference.
@@ -727,28 +967,28 @@ done:
  *-------------------------------------------------------------------------
  */
 static size_t
-H5T__ref_dsetreg_disk_getsize(H5VL_object_t H5_ATTR_UNUSED *file,
-    const void H5_ATTR_UNUSED *buf, size_t H5_ATTR_UNUSED buf_size,
+H5T__ref_dsetreg_disk_getsize(H5VL_object_t H5_ATTR_UNUSED *src_file,
+    const void H5_ATTR_UNUSED *src_buf, size_t H5_ATTR_UNUSED src_size,
     H5VL_object_t H5_ATTR_UNUSED *dst_file, hbool_t H5_ATTR_UNUSED *dst_copy)
 {
     size_t ret_value = sizeof(struct H5Tref_dsetreg);
 
     FUNC_ENTER_STATIC
 
-    HDassert(buf);
+    HDassert(src_buf);
 
 #ifndef NDEBUG
     {
-        H5F_t *f;
+        H5F_t *src_f;
 
         /* We should assert here that the terminal connector is H5VL_NATIVE once
          * there is a facility to do so -NAF 2019/10/30 */
 
         /* Retrieve file from VOL object */
-        if(NULL == (f = (H5F_t *)H5VL_object_data(file)))
+        if(NULL == (src_f = (H5F_t *)H5VL_object_data(src_file)))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "invalid VOL object")
 
-        HDassert(buf_size == H5T_REF_DSETREG_DISK_SIZE(f));
+        HDassert(src_size == H5T_REF_DSETREG_DISK_SIZE(src_f));
     } /* end block */
 #endif /* NDEBUG */
 
diff --git a/test/trefer.c b/test/trefer.c
index 7d87ea9..0f9e4f9 100644
--- a/test/trefer.c
+++ b/test/trefer.c
@@ -793,7 +793,7 @@ test_reference_region(H5F_libver_t libver_low, H5F_libver_t libver_high)
     } H5E_END_TRY;
 
     if(libver_high < H5F_LIBVER_V110)
-        VERIFY(ret, FAIL, "H5Dread");
+        CHECK(ret, FAIL, "H5Dread");
     else {
         CHECK(ret, FAIL, "H5Dread");
 
@@ -2102,7 +2102,7 @@ test_reference_compat_conv(void)
     hid_t   tid1, tid2;         /* Datatype ID              */
     hsize_t dims1[] = {SPACE1_DIM1},
             dims2[] = {SPACE2_DIM1, SPACE2_DIM2},
-            dims3[] = {2};
+            dims3[] = {SPACE1_DIM1}; /* Purposedly set dimension larger to test NULL references */
     hsize_t start[SPACE2_RANK]; /* Starting location of hyperslab */
     hsize_t stride[SPACE2_RANK];/* Stride of hyperslab      */
     hsize_t count[SPACE2_RANK]; /* Element count of hyperslab */
@@ -2122,8 +2122,8 @@ test_reference_compat_conv(void)
     /* Allocate write & read buffers */
     wbuf_obj = (hobj_ref_t *)HDcalloc(sizeof(hobj_ref_t), SPACE1_DIM1);
     rbuf_obj = (H5R_ref_t *)HDcalloc(sizeof(H5R_ref_t), SPACE1_DIM1);
-    wbuf_reg = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), 2);
-    rbuf_reg = (H5R_ref_t *)HDcalloc(sizeof(H5R_ref_t), 2);
+    wbuf_reg = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1);
+    rbuf_reg = (H5R_ref_t *)HDcalloc(sizeof(H5R_ref_t), SPACE1_DIM1);
 
     /* Create file */
     fid1 = H5Fcreate(FILE_REF_COMPAT, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);