[svn-r19712] Purpose:

    Fixed h5diff to handle variable-length strings in a compound dataset 
    correctly. Also variable-length string array in a compound dataset.
    Bug #1989.
    

Description:
    Garbage values were displayed when h5diff compared variable-length 
    strings (or string array) in a compound type dataset. 


Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (Mac32)

8 files changed, 411 insertions, 30 deletions

diff --git a/MANIFEST b/MANIFEST
index 708d708..c8aa72d 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1634,6 +1634,7 @@
 ./tools/h5diff/testfiles/h5diff_516.txt
 ./tools/h5diff/testfiles/h5diff_517.txt
 ./tools/h5diff/testfiles/h5diff_518.txt
+./tools/h5diff/testfiles/h5diff_530.txt
 
 ./tools/h5diff/testfiles/h5diff_attr1.h5
 ./tools/h5diff/testfiles/h5diff_attr2.h5
@@ -1665,6 +1666,7 @@
 ./tools/h5diff/testfiles/h5diff_exclude1-2.h5
 ./tools/h5diff/testfiles/h5diff_exclude2-1.h5
 ./tools/h5diff/testfiles/h5diff_exclude2-2.h5
+./tools/h5diff/testfiles/h5diff_comp_vl_strs.h5
 
 
 #test files for h5repack
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index c43de9c..4f513c0 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -474,6 +474,11 @@ Bug Fixes since HDF5-1.8.0 release
 
     Tools
     -----
+        - Fixed h5diff to handle variable-length strings in a compound dataset 
+          correctly. (also variable-length string array in a compound dataset)
+          Garbage values were displayed when h5diff compared multiple 
+          variable-length strings in a compound type dataset. 
+          Bug#1989 (JKM 2010/10/28)
         - Fixed h5copy to fail gracefully when copying object to non-exist
           group without -p option. Bug#2040 (JKM 2010/10/18)
         - Fixed to compare member objects and groups recursively when two 
diff --git a/tools/h5diff/CMakeLists.txt b/tools/h5diff/CMakeLists.txt
index a784ae7..b86a804 100644
--- a/tools/h5diff/CMakeLists.txt
+++ b/tools/h5diff/CMakeLists.txt
@@ -147,6 +147,7 @@ IF (BUILD_TESTING)
       h5diff_516.txt
       h5diff_517.txt
       h5diff_518.txt
+      h5diff_530.txt
       h5diff_600.txt
       h5diff_601.txt
       h5diff_603.txt
@@ -209,6 +210,7 @@ IF (BUILD_TESTING)
       h5diff_exclude1-2.h5
       h5diff_exclude2-1.h5
       h5diff_exclude2-2.h5
+      h5diff_comp_vl_strs.h5
   )
 
   FOREACH (txt_file ${HDF5_REFERENCE_FILES})
@@ -326,6 +328,8 @@ IF (BUILD_TESTING)
   # different structure and obj names
   SET (EXCLUDE_FILE2_1 h5diff_exclude2-1.h5)
   SET (EXCLUDE_FILE2_2 h5diff_exclude2-2.h5)
+  # compound type with multiple vlen string types
+  SET (COMP_VL_STRS_FILE h5diff_comp_vl_strs.h5)
 
   # Remove any output file left over from previous test run
   ADD_TEST (
@@ -540,6 +544,8 @@ IF (BUILD_TESTING)
           h5diff_517.out.err
           h5diff_518.out
           h5diff_518.out.err
+          h5diff_530.out
+          h5diff_530.out.err
           h5diff_600.out
           h5diff_600.out.err
           h5diff_601.out
@@ -1057,6 +1063,11 @@ ADD_H5_TEST (h5diff_483 1 -v --exclude-path "/group1" ${EXCLUDE_FILE2_1} ${EXCLU
 # Exclude from group compare
 ADD_H5_TEST (h5diff_484 0 -v --exclude-path "/dset3" ${EXCLUDE_FILE1_1} ${EXCLUDE_FILE1_2} /group1)
 
+# ##############################################################################
+# # diff various multiple vlen and fixed strings in a compound type dataset
+# ##############################################################################
+ADD_H5_TEST (h5diff_530 0 -v  ${COMP_VL_STRS_FILE} ${COMP_VL_STRS_FILE})
+
   
 ENDIF (BUILD_TESTING)
 
diff --git a/tools/h5diff/h5diffgentest.c b/tools/h5diff/h5diffgentest.c
index d66f821..fd4f2a9 100644
--- a/tools/h5diff/h5diffgentest.c
+++ b/tools/h5diff/h5diffgentest.c
@@ -68,6 +68,8 @@
 /* different structure and obj names */
 #define EXCLUDE_FILE2_1     "h5diff_exclude2-1.h5"
 #define EXCLUDE_FILE2_2     "h5diff_exclude2-2.h5"
+/* compound type with multiple vlen string types */
+#define COMP_VL_STRS_FILE   "h5diff_comp_vl_strs.h5"
 
 #define UIMAX    4294967295u /*Maximum value for a variable of type unsigned int */
 #define STR_SIZE 3
@@ -116,6 +118,7 @@ static int test_group_recurse(const char *fname1, const char *fname2);
 static int test_group_recurse2();
 static int test_exclude_obj1(const char *fname1, const char *fname2);
 static int test_exclude_obj2(const char *fname1, const char *fname2);
+static int test_comp_vlen_strings(const char *fname1);
 
 /* called by test_attributes() and test_datasets() */
 static void write_attr_in(hid_t loc_id,const char* dset_name,hid_t fid,int make_diffs);
@@ -171,6 +174,9 @@ int main(void)
     test_exclude_obj1(EXCLUDE_FILE1_1, EXCLUDE_FILE1_2);
     test_exclude_obj2(EXCLUDE_FILE2_1, EXCLUDE_FILE2_2);
 
+    /* diff various multiple vlen and fixlen string types in a compound dataset */
+    test_comp_vlen_strings(COMP_VL_STRS_FILE );
+
     return 0;
 }
 
@@ -2919,6 +2925,298 @@ out:
 }
 
 /*-------------------------------------------------------------------------
+*
+* Purpose: Create test files for multiple variable length string/string array
+*          along with fixed length string/string array types in 
+*          a compound type dataset.
+*
+* Programmer: Jonathan Kim (Oct, 26, 2010)
+*
+*-------------------------------------------------------------------------*/
+#define STR_RANK 1
+#define VLSTR1_DIM 1
+#define FLSTR2_SIZE 21
+#define FLSTR2_DIM 1
+#define VLSTRARRY3_DIM 3
+#define FLSTRARRY4_DIM 3
+#define FLSTRARRY4_SIZE 30
+#define COMP_RANK 1
+#define COMP_DIM 1
+static int test_comp_vlen_strings(const char *fname1)
+{
+    int i;
+
+    hid_t    fid1;      /* file id */
+
+    /* compound datatype */
+    typedef struct comp_t
+    {
+        char   *str1;  /* vlen string */
+        char   *str1_again;  /* vlen string */
+        char   str2[FLSTR2_SIZE];  /* fixed len string */
+        char   str2_again[FLSTR2_SIZE];  /* fixed len string */
+        char   *str3[VLSTRARRY3_DIM];  /* vlen string array */
+        char   *str3_again[VLSTRARRY3_DIM];  /* vlen string array */
+        char   str4[FLSTRARRY4_DIM][FLSTRARRY4_SIZE];  /* fixed len string array */
+        char   str4_again[FLSTRARRY4_DIM][FLSTRARRY4_SIZE];  /* fixed len string array */
+    } comp_t;
+
+    /* vlen string1 */
+    hid_t    sid_str1=0;      /* dataspace ID */
+    hid_t    tid_str1=0;      /* datatype ID */
+    hid_t    did_str1=0;      /* dataset ID */
+    const char vlstr1_buf[]= {
+        "Variable length string"
+        };
+    hsize_t dims_str1[]  = {VLSTR1_DIM};
+
+    /* fixlen string2 */
+    hid_t    sid_str2=0;      /* dataspace ID */
+    hid_t    tid_str2=0;      /* datatype ID */
+    hid_t    did_str2=0;      /* dataset ID */
+    const char flstr2_buf[FLSTR2_SIZE]= {
+        "Fixed length string"
+        };
+    hsize_t dims_str2[]  = {FLSTR2_DIM};
+
+    /* vlen string3 array */
+    hid_t    sid_str3=0;      /* dataspace ID */
+    hid_t    tid_str3=0;      /* datatype ID */
+    hid_t    tid_str3_array=0; /* datatype ID */
+    hid_t    did_str3=0;      /* dataset ID */
+    const char *vlstr3_buf[VLSTRARRY3_DIM]= {
+        "1 - Variable length string Array",
+        "2 - Testing variable length string array in compound type",
+        "3 - Four score and seven\n years ago our forefathers brought forth on this continent a new nation,"
+        };
+    hsize_t dims_str3[]  = {VLSTRARRY3_DIM};
+
+    /* fixlen string array 4 */
+    hid_t    sid_str4=0;      /* dataspace ID */
+    hid_t    tid_str4=0;      /* datatype ID */
+    hid_t    tid_str4_array=0; /* datatype ID */
+    hid_t    did_str4=0;      /* dataset ID */
+    const char *flstr4_buf[FLSTRARRY4_DIM]= {
+        "1 - Fixed length string Array",
+        "2 - Fixed length string Array",
+        "3 - Fixed length string Array"
+        };
+    hsize_t dims_str4[]  = {FLSTRARRY4_DIM};
+
+    /*------------------------------------------ 
+     * compound dataset 
+     *------------------------------------------*/
+    hid_t    sid_comp=0;      /* dataspace ID */
+    hid_t    tid_comp=0;      /* datatype ID */
+    hid_t    did_comp=0;      /* dataset ID */
+    hsize_t dims_comp[]  = {COMP_DIM};
+    herr_t  status = SUCCEED;
+
+    /* make compound strings data */
+    comp_t comp_buf;
+
+    /* copy string1 type to compound buffer */
+    comp_buf.str1 = comp_buf.str1_again = vlstr1_buf;
+    /* copy string2 type to compound buffer */
+    HDstrcpy(comp_buf.str2, flstr2_buf);
+    HDstrcpy(comp_buf.str2_again, flstr2_buf);
+    /* copy string3 type to compound buffer */
+    for (i=0; i < VLSTRARRY3_DIM; i++)
+        comp_buf.str3[i] = comp_buf.str3_again[i] = vlstr3_buf[i];
+    /* copy string4 type to compound buffer */
+    for (i=0; i < FLSTRARRY4_DIM; i++)
+    {
+        HDstrcpy(comp_buf.str4[i], flstr4_buf[i]);
+        HDstrcpy(comp_buf.str4_again[i], flstr4_buf[i]);
+    }
+
+    /*-----------------------------------------------------------------------
+    * Create file(s)
+    *------------------------------------------------------------------------*/
+    fid1 = H5Fcreate (fname1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+    if (fid1 < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Fcreate failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+    /*-----------------------------------------------------------------------
+    * Variable length String1 - Create space and type
+    *------------------------------------------------------------------------*/
+    sid_str1 = H5Screate_simple(STR_RANK, dims_str1, NULL);
+    if (sid_str1 < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+    tid_str1 = H5Tcopy(H5T_C_S1);
+    status = H5Tset_size(tid_str1, H5T_VARIABLE);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Tset_size failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+    /*-----------------------------------------------------------------------
+    * Fixed length String2 - Create space and type
+    *------------------------------------------------------------------------*/
+    sid_str2 = H5Screate_simple(STR_RANK, dims_str2, NULL);
+    if (sid_str2 < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+    tid_str2 = H5Tcopy(H5T_C_S1);
+    status = H5Tset_size(tid_str2, FLSTR2_SIZE);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Tset_size failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+    /*-----------------------------------------------------------------------
+    * Fixed length String3 array - Create space and type
+    *------------------------------------------------------------------------*/
+    sid_str3 = H5Screate_simple(STR_RANK, dims_str3, NULL);
+    if (sid_str3 < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+    tid_str3 = H5Tcopy(H5T_C_S1);
+    status = H5Tset_size(tid_str3, H5T_VARIABLE);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Tset_size failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+     /* Create the array data type for the string array                */
+    tid_str3_array = H5Tarray_create2(tid_str3, COMP_RANK, dims_str3);
+    if (tid_str3_array < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Tarray_create2 failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+    /*-----------------------------------------------------------------------
+    * Variable length String4 array - Create space and type
+    *------------------------------------------------------------------------*/
+    sid_str4 = H5Screate_simple(STR_RANK, dims_str4, NULL);
+    if (sid_str4 < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+    tid_str4 = H5Tcopy(H5T_C_S1);
+    status = H5Tset_size(tid_str4, FLSTRARRY4_SIZE);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Tset_size failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+     /* Create the array data type for the string array                */
+    tid_str4_array = H5Tarray_create2(tid_str4, COMP_RANK, dims_str4);
+    if (tid_str4_array < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Tarray_create2 failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+
+   /*-------------------------------------------------------------------------
+    * Compound dataset
+    *------------------------------------------------------------------------*/
+    sid_comp = H5Screate_simple(COMP_RANK, dims_comp, NULL);
+    if (sid_comp < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+    tid_comp = H5Tcreate (H5T_COMPOUND, sizeof(comp_t));
+    H5Tinsert(tid_comp, "VLEN_STR1", HOFFSET(comp_t, str1), tid_str1 );
+    H5Tinsert(tid_comp, "VLEN_STR2", HOFFSET(comp_t, str1_again), tid_str1 );
+    H5Tinsert(tid_comp, "FIXLEN_STR1", HOFFSET(comp_t, str2), tid_str2 );
+    H5Tinsert(tid_comp, "FIXLEN_STR2", HOFFSET(comp_t, str2_again), tid_str2 );
+    H5Tinsert(tid_comp, "VLEN_STR_ARRAY1", HOFFSET(comp_t, str3), tid_str3_array);
+    H5Tinsert(tid_comp, "VLEN_STR_ARRAY2", HOFFSET(comp_t, str3_again), tid_str3_array);
+    H5Tinsert(tid_comp, "FIXLEN_STR_ARRAY1", HOFFSET(comp_t, str4), tid_str4_array);
+    H5Tinsert(tid_comp, "FIXLEN_STR_ARRAY2", HOFFSET(comp_t, str4_again), tid_str4_array);
+
+    /* Write data to compound dataset buffer */
+    did_comp = H5Dcreate2(fid1, "Compound_dset", tid_comp, sid_comp, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    status = H5Dwrite(did_comp, tid_comp, H5S_ALL, H5S_ALL, H5P_DEFAULT, &comp_buf);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
+        status = FAIL;
+        goto out;
+    }
+out:
+   /*-----------------------------------------------------------------------
+    * Close
+    *-----------------------------------------------------------------------*/
+    if(fid1)
+        H5Fclose(fid1);
+    /* string1 */
+    if(tid_str1)
+        H5Tclose(tid_str1);
+    if(did_str1)
+        H5Dclose(did_str1);
+    if(sid_str1)
+        H5Sclose(sid_str1);
+    /* string2 */
+    if(tid_str2)
+        H5Tclose(tid_str2);
+    if(did_str2)
+        H5Dclose(did_str2);
+    if(sid_str2)
+        H5Sclose(sid_str2);
+    /* string3 */
+    if(tid_str3)
+        H5Tclose(tid_str3);
+    if(tid_str3_array)
+        H5Tclose(tid_str3_array);
+    if(did_str3)
+        H5Dclose(did_str3);
+    if(sid_str3)
+        H5Sclose(sid_str3);
+    /* string4 */
+    if(tid_str4)
+        H5Tclose(tid_str4);
+    if(tid_str4_array)
+        H5Tclose(tid_str4_array);
+    if(did_str4)
+        H5Dclose(did_str4);
+    if(sid_str4)
+        H5Sclose(sid_str4);
+    /* compound */
+    if(tid_comp)
+        H5Tclose(tid_comp);
+    if(did_comp)
+        H5Dclose(did_comp);
+    if(sid_comp)
+        H5Sclose(sid_comp);
+
+    return status;
+}
+
+/*-------------------------------------------------------------------------
 * Function: write_attr_in
 *
 * Purpose: write attributes in LOC_ID (dataset, group, named datatype)
diff --git a/tools/h5diff/testfiles/h5diff_530.txt b/tools/h5diff/testfiles/h5diff_530.txt
new file mode 100644
index 0000000..6f7e08f
--- /dev/null
+++ b/tools/h5diff/testfiles/h5diff_530.txt
@@ -0,0 +1,11 @@
+
+file1     file2
+---------------------------------------
+    x      x    /              
+    x      x    /Compound_dset 
+
+group  : </> and </>
+0 differences found
+dataset: </Compound_dset> and </Compound_dset>
+0 differences found
+EXIT CODE: 0
diff --git a/tools/h5diff/testfiles/h5diff_comp_vl_strs.h5 b/tools/h5diff/testfiles/h5diff_comp_vl_strs.h5
new file mode 100644
index 0000000..348cfee
--- /dev/null
+++ b/tools/h5diff/testfiles/h5diff_comp_vl_strs.h5
diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index dc3c9fb..6005ed8 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -447,21 +447,43 @@ hsize_t diff_datum(void       *_mem1,
         {
             offset    = H5Tget_member_offset(m_type, (unsigned)j);
             memb_type = H5Tget_member_type(m_type, (unsigned)j);
-            nfound+=diff_datum(
-                mem1+offset,
-                mem2+offset,
-                memb_type,
-                i,
-                rank,
-                dims,
-                acc,
-                pos,
-                options,
-                obj1,
-                obj2,
-                container1_id,
-                container2_id,
-                ph);
+            /* if member type is vlen string */
+            if(H5Tis_variable_str(memb_type))
+            {
+                nfound+=diff_datum(
+                    ((unsigned char**)mem1)[j],
+                    ((unsigned char**)mem2)[j],
+                    memb_type,
+                    i,
+                    rank,
+                    dims,
+                    acc,
+                    pos,
+                    options,
+                    obj1,
+                    obj2,
+                    container1_id,
+                    container2_id,
+                    ph);
+            }
+            else
+            {
+                nfound+=diff_datum(
+                    mem1+offset,
+                    mem2+offset,
+                    memb_type,
+                    i,
+                    rank,
+                    dims,
+                    acc,
+                    pos,
+                    options,
+                    obj1,
+                    obj2,
+                    container1_id,
+                    container2_id,
+                    ph);
+            }
             H5Tclose(memb_type);
         }
         break;
@@ -631,21 +653,45 @@ hsize_t diff_datum(void       *_mem1,
             for (u = 0, nelmts = 1; u <ndims; u++)
                 nelmts *= adims[u];
             for (u = 0; u < nelmts; u++)
-                nfound+=diff_datum(
-                mem1 + u * size,
-                mem2 + u * size, /* offset */
-                memb_type,
-                i,               /* index position */
-                rank,
-                dims,
-                acc,
-                pos,
-                options,
-                obj1,
-                obj2,
-                container1_id,
-                container2_id,
-                ph);
+            {
+                /* if member type is vlen string */
+                if(H5Tis_variable_str(memb_type))
+                {
+                    nfound+=diff_datum(
+                    ((unsigned char**)mem1)[u],
+                    ((unsigned char**)mem2)[u],
+                    memb_type,
+                    i,               /* index position */
+                    rank,
+                    dims,
+                    acc,
+                    pos,
+                    options,
+                    obj1,
+                    obj2,
+                    container1_id,
+                    container2_id,
+                    ph);
+                }
+                else
+                {
+                    nfound+=diff_datum(
+                    mem1 + u * size,
+                    mem2 + u * size, /* offset */
+                    memb_type,
+                    i,               /* index position */
+                    rank,
+                    dims,
+                    acc,
+                    pos,
+                    options,
+                    obj1,
+                    obj2,
+                    container1_id,
+                    container2_id,
+                    ph);
+                }
+           }
             H5Tclose(memb_type);
         }
         break;
diff --git a/windows/tools/h5diff/testh5diff.bat b/windows/tools/h5diff/testh5diff.bat
index 29be753..f745c42 100644
--- a/windows/tools/h5diff/testh5diff.bat
+++ b/windows/tools/h5diff/testh5diff.bat
@@ -58,6 +58,7 @@ set srcexclude1_1=h5diff_exclude1-1.h5
 set srcexclude1_2=h5diff_exclude1-2.h5

 set srcexclude2_1=h5diff_exclude2-1.h5

 set srcexclude2_2=h5diff_exclude2-2.h5

+set src_comp_vl_strs=h5diff_comp_vl_strs.h5

 

 set file1=%indir%\h5diff_basic1.h5

 set file2=%indir%\h5diff_basic2.h5

@@ -89,6 +90,7 @@ set exclude1_1=%indir%\h5diff_exclude1-1.h5
 set exclude1_2=%indir%\h5diff_exclude1-2.h5

 set exclude2_1=%indir%\h5diff_exclude2-1.h5

 set exclude2_2=%indir%\h5diff_exclude2-2.h5

+set comp_vl_strs=%indir%\h5diff_comp_vl_strs.h5

 

 

 rem The tool name

@@ -853,6 +855,12 @@ rem ############################################################################
     call :testing %h5diff% -v --exclude-path "/dset3" %srcexclude1_1% %srcexclude1_2% /group1

     call :tooltest h5diff_484.txt -v --exclude-path "/dset3"  %exclude1_1% %exclude1_2% /group1

 

+    rem ##############################################################################

+    rem # diff various multiple vlen and fixed strings in a compound type dataset

+    rem ##############################################################################

+    call :testing %h5diff% -v %src_comp_vl_strs% %src_comp_vl_strs%

+    call :tooltest h5diff_530.txt -v  %comp_vl_strs% %comp_vl_strs%

+

 	

     rem #######################################################################

     rem # END