[svn-r18425] Purpose:

    Fix for bug1814 - NPOESS: h5repack doesn't handle references to the groups 
    as an element of a dataset 

Description:
    handles object reference to named-datatype as well.
    Add test cases.

Tested:
    jam, amani, linew

6 files changed, 342 insertions, 6 deletions

diff --git a/MANIFEST b/MANIFEST
index d13e1ea..9ab9509 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1609,7 +1609,7 @@
 ./tools/h5repack/testfiles/h5repack_ext.h5
 ./tools/h5repack/testfiles/ublock.bin
 ./tools/h5repack/testfiles/h5repack_named_dtypes.h5
-
+./tools/h5repack/testfiles/h5repack_refs.h5
 
 # jam utility and tests
 ./tools/h5jam/h5jam.c
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 32622a0..35fc5fd 100755
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -59,6 +59,7 @@ FILE14=h5repack_layouto.h5      # A file with an older version of the layout mes
                                 # (copy of test/tlayouto.h5)
 FILE15=h5repack_named_dtypes.h5
 FILE16=tfamily%05d.h5           # located in common testfiles folder
+FILE_REF=h5repack_refs.h5
 
 
 nerrors=0
@@ -531,6 +532,9 @@ TOOLTEST $FILE15
 # tests family driver (file is located in common testfiles folder, uses TOOLTEST1
 TOOLTEST1 $FILE16
 
+# test various references (bug 1814)
+TOOLTEST $FILE_REF
+
 if test $nerrors -eq 0 ; then
     echo "All $TESTNAME tests passed."
     exit $EXIT_SUCCESS
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index fddcf0e..9945f49 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -690,23 +690,31 @@ static const char* MapIdToName(hid_t refobj_id,
                                trav_table_t *travt)
 {
     unsigned int i;
+    const char* ret = NULL;
+    H5O_info_t   ref_oinfo;     /* Stat for the refobj id */
 
     /* linear search */
     for(i = 0; i < travt->nobjs; i++)
     {
-        if(travt->objs[i].type == H5O_TYPE_DATASET)
+        if(travt->objs[i].type == H5O_TYPE_DATASET || 
+           travt->objs[i].type == H5O_TYPE_GROUP ||
+           travt->objs[i].type == H5O_TYPE_NAMED_DATATYPE)
         {
             H5O_info_t   ref_oinfo;     /* Stat for the refobj id */
 
             /* obtain information to identify the referenced object uniquely */
             if(H5Oget_info(refobj_id, &ref_oinfo) < 0)
-                return NULL;
+                goto out;
 
             if(ref_oinfo.addr == travt->objs[i].objno)
-                return(travt->objs[i].name);
+            {
+                ret = travt->objs[i].name;
+                goto out;
+            }
         }  /* end if */
     } /* i */
 
-    return NULL;
+out:
+    return ret;
 }
 
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 17ece99..d4cd347 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -78,6 +78,8 @@
 
 #define FNAME_UB   "ublock.bin"
 
+/* obj and region references */
+#define FNAME_REF   "h5repack_refs.h5"
 
 const char *H5REPACK_FILENAMES[] = {
     "h5repack_big_out",
@@ -100,6 +102,13 @@ int d_status = EXIT_SUCCESS;
 /* Size of userblock (for userblock test) */
 #define USERBLOCK_SIZE  2048
 
+/* obj and region references */
+#define NAME_OBJ_DS "Dset1"
+#define NAME_OBJ_GRP "Group"
+#define NAME_OBJ_NDTYPE "NamedDatatype"
+#define REG_REF_DS1 "Dset_REGREF"
+#define REG_REF_DS2 "Dset2"
+
 /*-------------------------------------------------------------------------
 * prototypes
 *-------------------------------------------------------------------------
@@ -132,6 +141,7 @@ static int make_userblock(void);
 static int verify_userblock( const char* filename);
 static int make_userblock_file(void);
 static int make_named_dtype(hid_t loc_id);
+static int make_references(hid_t loc_id);
 
 
 /*-------------------------------------------------------------------------
@@ -1763,6 +1773,16 @@ int make_testfiles(void)
     if(H5Fclose(fid) < 0)
         return -1;
 
+    /*-------------------------------------------------------------------------
+    * create a file with obj and region references 
+    *-------------------------------------------------------------------------*/
+    if((fid = H5Fcreate(FNAME_REF,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT)) < 0)
+        return -1;
+    if (make_references(fid) < 0)
+        goto out;
+    if(H5Fclose(fid) < 0)
+        return -1;
+
     return 0;
 
 out:
@@ -5583,3 +5603,306 @@ out:
     return -1;
 } /* end make_named_dtype() */
 
+/*-------------------------------------------------------------------------
+ * Function: gen_obj_ref
+ *
+ * Purpose: 
+ *  Generate object references to objects (dataset,group and named datatype)
+ *
+ * Note:
+ *  copied from h5copygentest.c and upate to create named datatype  
+ *
+ * Programmer: Jonathan Kim (March 18, 2010)
+ *------------------------------------------------------------------------*/
+static herr_t gen_obj_ref(hid_t loc_id)
+{
+    hid_t sid=0, oid=0, tid=0;
+    hsize_t dims1[1]={3};
+    hsize_t dims2[1]={3};
+    int data[3] = {10,20,30};
+    int status;
+    herr_t ret = SUCCEED;
+
+    /*--------------
+     * add dataset */
+    sid = H5Screate_simple(1, dims1, NULL);
+    if (sid < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    oid = H5Dcreate2 (loc_id, NAME_OBJ_DS, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    if (oid < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    status = H5Dwrite(oid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    H5Dclose(oid);
+    H5Sclose(sid);
+
+    /*--------------
+     * add group  */
+     oid = H5Gcreate2 (loc_id, NAME_OBJ_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    if (oid < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Gcreate2 failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+     H5Gclose(oid);
+
+    /*----------------------
+     * add named datatype
+     */
+     tid = H5Tcopy(H5T_NATIVE_INT);
+     status = H5Tcommit2(loc_id, NAME_OBJ_NDTYPE, tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+     if (status < 0)
+     {
+        fprintf(stderr, "Error: %s %d> H5Tcommit2 failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+     }
+
+    /*---------------------------------------------------------
+     * create obj references to the previously created objects.
+     * Passing -1 as reference is an object.*/
+     hobj_ref_t objref_buf[3];  /* write buffer for  */
+
+    /* obj ref to dataset */
+    status = H5Rcreate (&objref_buf[0], loc_id, NAME_OBJ_DS, H5R_OBJECT, -1);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* obj ref to group */
+    status = H5Rcreate (&objref_buf[1], loc_id, NAME_OBJ_GRP, H5R_OBJECT, -1);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* obj ref to named-datatype */
+    status = H5Rcreate (&objref_buf[2], loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT, -1);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /*---------------------------------------------------------
+     * create dataset contain references 
+     */
+    sid = H5Screate_simple (1, dims2, NULL);
+    if (sid < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    oid = H5Dcreate2 (loc_id, "Dset_OBJREF", H5T_STD_REF_OBJ, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
+    if (oid < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    status = H5Dwrite(oid, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, objref_buf);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+out:
+    if(oid > 0)
+        H5Dclose(oid);
+    if(tid > 0)
+        H5Tclose(tid);
+    if(sid > 0)
+        H5Sclose(sid);
+
+    return ret;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: gen_region_ref
+ *
+ * Purpose: Generate dataset region references
+ *
+ * Note:
+ *  copied from h5copygentest.c 
+ *
+ * Programmer: Jonathan Kim (March 18, 2010)
+ *------------------------------------------------------------------------*/
+static herr_t gen_region_ref(hid_t loc_id)
+{
+    hid_t sid=0, oid1=0, oid2=0;
+    int status;
+    herr_t ret = SUCCEED;
+    char  data[3][16] = {"The quick brown", "fox jumps over ", "the 5 lazy dogs"};
+    hsize_t dims2[2] = {3,16};
+    hsize_t coords[4][2] = { {0,1}, {2,11}, {1,0}, {2,4} };
+
+    hdset_reg_ref_t  rr_data[2];
+    hsize_t start[2] = {0,0};
+    hsize_t stride[2] = {2,11};
+    hsize_t count[2] = {2,2};
+    hsize_t block[2] = {1,3};
+    hsize_t dims1[1] = {2};
+
+    sid = H5Screate_simple (2, dims2, NULL);
+    if (sid < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* create normal dataset which is refered */
+    oid2 = H5Dcreate2 (loc_id, REG_REF_DS2, H5T_STD_I8LE, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
+    if (oid2 < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* write values to dataset */
+    status = H5Dwrite (oid2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* select elements space for reference */
+    status = H5Sselect_elements (sid, H5S_SELECT_SET, 4, coords[0]);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Sselect_elements failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* create region reference from elements space */
+    status = H5Rcreate (&rr_data[0], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* select hyperslab space for reference */
+    status = H5Sselect_hyperslab (sid, H5S_SELECT_SET, start, stride, count, block);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Sselect_hyperslab failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* create region reference from hyperslab space */
+    status = H5Rcreate (&rr_data[1], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    H5Sclose (sid);
+
+    /* Create dataspace. */
+    sid = H5Screate_simple (1, dims1, NULL);
+    if (sid < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* create region reference dataset */
+    oid1 = H5Dcreate2 (loc_id, REG_REF_DS1, H5T_STD_REF_DSETREG, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
+    if (oid1 < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* write data as region references */
+    status = H5Dwrite (oid1, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, rr_data);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+out:
+    if (oid1 > 0)
+        H5Dclose (oid1);
+    if (oid2 > 0)
+        H5Dclose (oid2);
+    if (sid > 0)
+        H5Sclose (sid);
+
+    return ret;
+}
+
+/*-------------------------------------------------------------------------
+* Function: make_references
+*
+* Purpose: create a file with obj and region references 
+*
+* Programmer: Jonathan Kim (March 18, 2010)
+*-------------------------------------------------------------------------
+*/
+static herr_t make_references(hid_t loc_id)
+{
+    herr_t ret = SUCCEED;
+    herr_t status;
+
+    /* add object reference */
+    status = gen_obj_ref(loc_id);
+    if (status == FAIL)
+    {
+        fprintf(stderr, "Failed to generate object reference.\n");
+        ret = FAIL;
+    }
+
+    /* add region reference */
+    status = gen_region_ref(loc_id);
+    if (status == FAIL)
+    {
+        fprintf(stderr, "Failed to generate region reference.\n");
+        ret = FAIL;
+    }
+
+    return ret;
+}
+
diff --git a/tools/h5repack/testfiles/h5repack_refs.h5 b/tools/h5repack/testfiles/h5repack_refs.h5
new file mode 100644
index 0000000..23d53e6
--- /dev/null
+++ b/tools/h5repack/testfiles/h5repack_refs.h5
diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index 6572594..48e08a5 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -747,7 +747,8 @@ hsize_t diff_datum(void       *_mem1,
                     NULL,
                     options);
                 else {
-                    parallel_print("Warning: Comparison not possible of object types referenced: <%s> and <%s>",
+                    if(options->m_verbose)
+                        parallel_print("Warning: Comparison not possible of object types referenced: <%s> and <%s>\n",
                         obj1, obj2);
                     options->not_cmp = 1;
                 }