From ad2a7f47896cf636b42fbc73b96781b2d5200f56 Mon Sep 17 00:00:00 2001
From: Jacob Smith <jake.smith@hdfgroup.org>
Date: Fri, 31 May 2019 17:24:26 -0500
Subject: First pass at repack consolidating external storage if layout given.
 Checks out manually, tests still complain.

---
 tools/src/h5repack/h5repack_copy.c    | 15 ++++++++++++---
 tools/test/h5repack/Makefile.am       |  3 ++-
 tools/test/h5repack/h5repack.sh.in    |  3 ++-
 tools/test/h5repack/h5repackgentest.c |  8 ++++----
 4 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 544793a..c638f3d 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -807,8 +807,17 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
                     if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
-                    if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
+                    /* If the input dataset has external storage, it must be contiguous.
+                     * Accordingly, there would be no filter or chunk properties to preserve.
+                     */
+                    if (H5Pget_external_count(dcpl_in)) {
+                        if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
+                    }
+                    else {
+                        if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
+                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
+                    }
                     if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
                     HDmemset(dims, 0, sizeof dims);
@@ -1175,7 +1184,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
                 }
                 /*-------------------------------------------------------------------------
-                 * we do not have request for filter/chunking use H5Ocopy instead
+                 * we do not have request for filter/chunking; use H5Ocopy instead
                  *-------------------------------------------------------------------------
                  */
                 else {
diff --git a/tools/test/h5repack/Makefile.am b/tools/test/h5repack/Makefile.am
index ff950e4..38f7b2f 100644
--- a/tools/test/h5repack/Makefile.am
+++ b/tools/test/h5repack/Makefile.am
@@ -59,7 +59,8 @@ endif
 
 # Temporary files.  *.h5 are generated by h5repack.  They should
 # copied to the testfiles/ directory if update is required.
-CHECK_CLEANFILES+=*.h5 *.bin testfiles/h5diff_attr1.h5 testfiles/tfamily*.h5
+# *.dat files may be created by h5repackgentest.
+CHECK_CLEANFILES+=*.h5 *.dat *.bin testfiles/h5diff_attr1.h5 testfiles/tfamily*.h5
 DISTCLEANFILES=h5repack.sh h5repack_plugin.sh
 
 include $(top_srcdir)/config/conclude.am
diff --git a/tools/test/h5repack/h5repack.sh.in b/tools/test/h5repack/h5repack.sh.in
index 9851e89..56df3c8 100644
--- a/tools/test/h5repack/h5repack.sh.in
+++ b/tools/test/h5repack/h5repack.sh.in
@@ -675,7 +675,8 @@ VERIFY_EXTERNAL_CONSOLIDATION()
         )
 
         # flag if any of the above checks failed
-        if [ $prev_nerrors != $nerrors ]; then
+        if [ $prev_nerrors != $nerrors ]
+        then
              echo ". . . *FAILED*"
              nerrors="`expr $prev_nerrors + 1`"
         else
diff --git a/tools/test/h5repack/h5repackgentest.c b/tools/test/h5repack/h5repackgentest.c
index 8076b42..0eec88c 100644
--- a/tools/test/h5repack/h5repackgentest.c
+++ b/tools/test/h5repack/h5repackgentest.c
@@ -8,7 +8,7 @@
 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  */
 static void
-generate_external_int32le(hbool_t external)
+generate_int32le(hbool_t external)
 {
     char    filename[MAX_NAME_SIZE];
     hid_t   file;
@@ -67,7 +67,7 @@ generate_external_int32le(hbool_t external)
     HDassert(H5Dclose(dset) >= 0);
     HDassert(H5Sclose(dspace) >= 0);
     HDassert(H5Fclose(file) >= 0);
-} /* end generate_external_int32le() */
+} /* end generate_int32le() */
 
 
 /* ----------------------------------------------------------------------------
@@ -75,8 +75,8 @@ generate_external_int32le(hbool_t external)
 int
 main(void)
 {
-    generate_external_int32le(FALSE);
-    generate_external_int32le(TRUE);
+    generate_int32le(FALSE);
+    generate_int32le(TRUE);
     return 0;
 } /* end main() */
 
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