Update reference files and fix int as string

7 files changed, 50 insertions, 44 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 01c18dc..3420862 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -8122,7 +8122,7 @@ public class H5 implements java.io.Serializable {
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native byte[] H5Rcreate_object(long loc_id, String name)
+    public synchronized static native byte[] H5Rcreate_object(long loc_id, String name, long access_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
@@ -8145,7 +8145,7 @@ public class H5 implements java.io.Serializable {
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native byte[] H5Rcreate_region(long loc_id, String name, long space_id)
+    public synchronized static native byte[] H5Rcreate_region(long loc_id, String name, long space_id, long access_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
@@ -8168,7 +8168,7 @@ public class H5 implements java.io.Serializable {
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native byte[] H5Rcreate_attr(long loc_id, String name, String attr_name)
+    public synchronized static native byte[] H5Rcreate_attr(long loc_id, String name, String attr_name, long access_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
diff --git a/java/src/jni/h5rImp.c b/java/src/jni/h5rImp.c
index f7dcb30..3f1fd96 100644
--- a/java/src/jni/h5rImp.c
+++ b/java/src/jni/h5rImp.c
@@ -36,7 +36,7 @@ extern "C" {
  */
 JNIEXPORT jbyteArray JNICALL
 Java_hdf_hdf5lib_H5_H5Rcreate_1object
-  (JNIEnv *env, jclass clss, jlong loc_id, jstring name)
+  (JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong aid)
 {
     const char *refName = NULL;
     jboolean    isCopy;
@@ -54,7 +54,7 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1object
     if (NULL == (refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
         H5_JNI_FATAL_ERROR(ENVONLY, "H5Rcreate_object: failed to allocate reference buffer");
 
-    if ((status = H5Rcreate_object((hid_t)loc_id, refName, (const H5R_ref_t *)refBuf)) < 0)
+    if ((status = H5Rcreate_object((hid_t)loc_id, refName, (hid_t)aid, (const H5R_ref_t *)refBuf)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (NULL == (ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
@@ -80,7 +80,7 @@ done:
  */
 JNIEXPORT jbyteArray JNICALL
 Java_hdf_hdf5lib_H5_H5Rcreate_1region
-  (JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong space_id)
+  (JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong space_id, jlong aid)
 {
     const char *refName = NULL;
     jboolean    isCopy;
@@ -98,7 +98,7 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1region
     if (NULL == (refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
         H5_JNI_FATAL_ERROR(ENVONLY, "H5Rcreate_region: failed to allocate reference buffer");
 
-    if ((status = H5Rcreate_region((hid_t)loc_id, refName, space_id, (const H5R_ref_t *)refBuf)) < 0)
+    if ((status = H5Rcreate_region((hid_t)loc_id, refName, space_id, (hid_t)aid, (const H5R_ref_t *)refBuf)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (NULL == (ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
@@ -123,7 +123,7 @@ done:
  */
 JNIEXPORT jbyteArray JNICALL
 Java_hdf_hdf5lib_H5_H5Rcreate_1attr
-  (JNIEnv *env, jclass clss, jlong loc_id, jstring name, jstring attr_name)
+  (JNIEnv *env, jclass clss, jlong loc_id, jstring name, jstring attr_name, jlong aid)
 {
     const char *refName = NULL;
     const char *attrName = NULL;
@@ -146,7 +146,7 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1attr
     if (NULL == (refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
         H5_JNI_FATAL_ERROR(ENVONLY, "H5Rcreate_attr: failed to allocate reference buffer");
 
-    if ((status = H5Rcreate_attr((hid_t)loc_id, refName, attrName, (const H5R_ref_t *)refBuf)) < 0)
+    if ((status = H5Rcreate_attr((hid_t)loc_id, refName, attrName, (hid_t)aid, (const H5R_ref_t *)refBuf)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (NULL == (ref = ENVPTR->NewByteArray(ENVONLY, (jsize)H5R_REF_BUF_SIZE)))
diff --git a/java/src/jni/h5rImp.h b/java/src/jni/h5rImp.h
index 7749f91..3bdb266 100644
--- a/java/src/jni/h5rImp.h
+++ b/java/src/jni/h5rImp.h
@@ -30,7 +30,7 @@ extern "C" {
  */
 JNIEXPORT jbyteArray JNICALL
 Java_hdf_hdf5lib_H5_H5Rcreate_1object
-  (JNIEnv *, jclass, jlong, jstring);
+  (JNIEnv *, jclass, jlong, jstring, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5
@@ -39,7 +39,7 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1object
  */
 JNIEXPORT jbyteArray JNICALL
 Java_hdf_hdf5lib_H5_H5Rcreate_1region
-  (JNIEnv *, jclass, jlong, jstring, jlong);
+  (JNIEnv *, jclass, jlong, jstring, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5
@@ -48,7 +48,7 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1region
  */
 JNIEXPORT jbyteArray JNICALL
 Java_hdf_hdf5lib_H5_H5Rcreate_1attr
-  (JNIEnv *, jclass, jlong, jstring, jstring);
+  (JNIEnv *, jclass, jlong, jstring, jstring, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index 0c56426..9504b55 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -803,6 +803,7 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info,
     HDmemset(&str, 0, sizeof(h5tools_str_t));
 
     /* Terminate previous line, if any */
+    H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "before CR elmtno=%ld, ctx->cur_column=%d, info->idx_fmt=%s, info->line_suf=%s", elmtno, ctx->cur_column, info->idx_fmt, info->line_suf);
     if (ctx->cur_column) {
         PUTSTREAM(OPT(info->line_suf, ""), stream);
         HDputc('\n', stream);
@@ -1023,6 +1024,7 @@ h5tools_render_element(FILE *stream, const h5tool_format_t *info,
              */
             ctx->need_prefix = TRUE;
         }
+        H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ctx->need_prefix=%d", ctx->need_prefix);
     }
 
     /*
@@ -1038,8 +1040,9 @@ h5tools_render_element(FILE *stream, const h5tool_format_t *info,
             ctx->need_prefix = TRUE;
             dimension_break = FALSE;
         }
+        H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ctx->need_prefix=%d", ctx->need_prefix);
     }
-    H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "elmt_counter=%ld - ctx->size_last_dim=%ld", elmt_counter, ctx->size_last_dim);
+    H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "elmt_counter=%ld - ctx->size_last_dim=%ld info->line_suf=%s", elmt_counter, ctx->size_last_dim, info->line_suf);
 
     /*
      * If the previous element occupied multiple lines and this element
@@ -1053,6 +1056,7 @@ h5tools_render_element(FILE *stream, const h5tool_format_t *info,
             HDstrlen(OPT(info->elmt_suf2, " ")) +
             HDstrlen(OPT(info->line_suf, ""))) > ncols)
         ctx->need_prefix = TRUE;
+    H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ctx->need_prefix=%d", ctx->need_prefix);
 
     /*
      * If too many elements have already been printed then we need to
@@ -1060,6 +1064,7 @@ h5tools_render_element(FILE *stream, const h5tool_format_t *info,
      */
     if (info->line_per_line > 0 && ctx->cur_elmt >= info->line_per_line)
         ctx->need_prefix = TRUE;
+    H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ctx->need_prefix=%d", ctx->need_prefix);
 
     /*
      * Each OPTIONAL_LINE_BREAK embedded in the rendered string can cause
@@ -1088,6 +1093,7 @@ h5tools_render_element(FILE *stream, const h5tool_format_t *info,
          * Print the prefix or separate the beginning of this element
          * from the previous element.
          */
+        H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ctx->need_prefix=%d", ctx->need_prefix);
         if (ctx->need_prefix) {
             if (secnum)
                 multiline++;
diff --git a/tools/test/h5dump/errfiles/tarray1_big.err b/tools/test/h5dump/errfiles/tarray1_big.err
index 536b5a4..a20b0b7 100644
--- a/tools/test/h5dump/errfiles/tarray1_big.err
+++ b/tools/test/h5dump/errfiles/tarray1_big.err
@@ -1,31 +1,31 @@
-HDF5-DIAG: Error detected in HDF5 (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/src/H5R.c line 730 in H5Rget_obj_type3(): unable to get object token
+HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
+  #000: (file name) line (number) in H5Rget_obj_type3(): unable to get object token
     major: References
     minor: Can't get value
-  #001: /home/byrn/HDF_Projects/hdf5/dev/src/H5Rint.c line 731 in H5R__get_obj_token(): NULL token size
+  #001: (file name) line (number) in H5R__get_obj_token(): NULL token size
     major: References
     minor: Unable to copy object
-HDF5-DIAG: Error detected in HDF5 (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/src/H5R.c line 730 in H5Rget_obj_type3(): unable to get object token
+HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
+  #000: (file name) line (number) in H5Rget_obj_type3(): unable to get object token
     major: References
     minor: Can't get value
-  #001: /home/byrn/HDF_Projects/hdf5/dev/src/H5Rint.c line 731 in H5R__get_obj_token(): NULL token size
+  #001: (file name) line (number) in H5R__get_obj_token(): NULL token size
     major: References
     minor: Unable to copy object
-HDF5-DIAG: Error detected in HDF5 (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/src/H5R.c line 730 in H5Rget_obj_type3(): unable to get object token
+HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
+  #000: (file name) line (number) in H5Rget_obj_type3(): unable to get object token
     major: References
     minor: Can't get value
-  #001: /home/byrn/HDF_Projects/hdf5/dev/src/H5Rint.c line 731 in H5R__get_obj_token(): NULL token size
+  #001: (file name) line (number) in H5R__get_obj_token(): NULL token size
     major: References
     minor: Unable to copy object
-H5tools-DIAG: Error detected in HDF5:tools (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/tools/lib/h5tools_dump.c line 4044 in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
+H5tools-DIAG: Error detected in HDF5:tools (version (number)) thread (IDs):
+  #000: (file name) line (number) in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
     major: Failure in tools library
     minor: error in function
-  #001: /home/byrn/HDF_Projects/hdf5/dev/tools/lib/h5tools_dump.c line 4044 in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
+  #001: (file name) line (number) in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
     major: Failure in tools library
     minor: error in function
-  #002: /home/byrn/HDF_Projects/hdf5/dev/tools/lib/h5tools_dump.c line 4044 in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
+  #002: (file name) line (number) in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
     major: Failure in tools library
     minor: error in function
diff --git a/tools/test/h5dump/errfiles/tattrregR.err b/tools/test/h5dump/errfiles/tattrregR.err
index f81f99f..fa2014a 100644
--- a/tools/test/h5dump/errfiles/tattrregR.err
+++ b/tools/test/h5dump/errfiles/tattrregR.err
@@ -1,21 +1,21 @@
-HDF5-DIAG: Error detected in HDF5 (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/src/H5R.c line 730 in H5Rget_obj_type3(): unable to get object token
+HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
+  #000: (file name) line (number) in H5Rget_obj_type3(): unable to get object token
     major: References
     minor: Can't get value
-  #001: /home/byrn/HDF_Projects/hdf5/dev/src/H5Rint.c line 731 in H5R__get_obj_token(): NULL token size
+  #001: (file name) line (number) in H5R__get_obj_token(): NULL token size
     major: References
     minor: Unable to copy object
-HDF5-DIAG: Error detected in HDF5 (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/src/H5R.c line 730 in H5Rget_obj_type3(): unable to get object token
+HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
+  #000: (file name) line (number) in H5Rget_obj_type3(): unable to get object token
     major: References
     minor: Can't get value
-  #001: /home/byrn/HDF_Projects/hdf5/dev/src/H5Rint.c line 731 in H5R__get_obj_token(): NULL token size
+  #001: (file name) line (number) in H5R__get_obj_token(): NULL token size
     major: References
     minor: Unable to copy object
-H5tools-DIAG: Error detected in HDF5:tools (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/tools/lib/h5tools_dump.c line 4044 in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
+H5tools-DIAG: Error detected in HDF5:tools (version (number)) thread (IDs):
+  #000: (file name) line (number) in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
     major: Failure in tools library
     minor: error in function
-  #001: /home/byrn/HDF_Projects/hdf5/dev/tools/lib/h5tools_dump.c line 4044 in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
+  #001: (file name) line (number) in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
     major: Failure in tools library
     minor: error in function
diff --git a/tools/test/h5dump/errfiles/tdataregR.err b/tools/test/h5dump/errfiles/tdataregR.err
index f81f99f..fa2014a 100644
--- a/tools/test/h5dump/errfiles/tdataregR.err
+++ b/tools/test/h5dump/errfiles/tdataregR.err
@@ -1,21 +1,21 @@
-HDF5-DIAG: Error detected in HDF5 (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/src/H5R.c line 730 in H5Rget_obj_type3(): unable to get object token
+HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
+  #000: (file name) line (number) in H5Rget_obj_type3(): unable to get object token
     major: References
     minor: Can't get value
-  #001: /home/byrn/HDF_Projects/hdf5/dev/src/H5Rint.c line 731 in H5R__get_obj_token(): NULL token size
+  #001: (file name) line (number) in H5R__get_obj_token(): NULL token size
     major: References
     minor: Unable to copy object
-HDF5-DIAG: Error detected in HDF5 (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/src/H5R.c line 730 in H5Rget_obj_type3(): unable to get object token
+HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
+  #000: (file name) line (number) in H5Rget_obj_type3(): unable to get object token
     major: References
     minor: Can't get value
-  #001: /home/byrn/HDF_Projects/hdf5/dev/src/H5Rint.c line 731 in H5R__get_obj_token(): NULL token size
+  #001: (file name) line (number) in H5R__get_obj_token(): NULL token size
     major: References
     minor: Unable to copy object
-H5tools-DIAG: Error detected in HDF5:tools (1.13.0) thread 0:
-  #000: /home/byrn/HDF_Projects/hdf5/dev/tools/lib/h5tools_dump.c line 4044 in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
+H5tools-DIAG: Error detected in HDF5:tools (version (number)) thread (IDs):
+  #000: (file name) line (number) in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
     major: Failure in tools library
     minor: error in function
-  #001: /home/byrn/HDF_Projects/hdf5/dev/tools/lib/h5tools_dump.c line 4044 in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
+  #001: (file name) line (number) in h5tools_dump_data(): H5Rget_obj_type3 H5R_OBJECT1 failed
     major: Failure in tools library
     minor: error in function