[svn-r7243] Purpose:

    Bug fix

Description:
    Fix bug with combination of fill-values, chunked datasets and
    variable-length strings.

Platforms tested:
    FreeBSD 4.8 (sleipnir)
    h5committest

4 files changed, 182 insertions, 35 deletions

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 84048d4..396d5e9 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -34,17 +34,18 @@ CONTENTS
 New Features
 ============
 
-Configuration:
---------------
+    Configuration:
+    --------------
 
-Library:
---------
+    Library:
+    --------
 
-Parallel Library:
------------------
+    Parallel Library:
+    -----------------
+
+    Tools:
+    ------
 
-Tools:
-------
 
 Support for new platforms, languages and compilers.
 =======================================
@@ -53,31 +54,27 @@ Support for new platforms, languages and compilers.
 Bug Fixes since HDF5-1.6.0 release
 ==================================
 
-Library
--------
-    - Modified library and file format to support storing indexed storage
-        (chunked dataset) B-tree's with non-default internal 'K' values.
-        QAK - 2003/07/15
-    - Returned H5T_BKG_TEMP support to library after it was accidentally
-        removed.  QAK - 2003/07/14
-
-Configuration
--------------
-
-Performance
--------------
-
-Tools
------
-
-
-
-Documentation 
-------------- 
+    Library
+    -------
+        - Corrected error with variable-length datatypes and chunked datasets
+            which caused H5Dwrite to fail sometimes.  QAK - 2003/07/19
+        - Modified library and file format to support storing indexed storage
+            (chunked dataset) B-tree's with non-default internal 'K' values.
+            QAK - 2003/07/15
+        - Returned H5T_BKG_TEMP support to library after it was accidentally
+            removed.  QAK - 2003/07/14
 
+    Configuration
+    -------------
 
+    Performance
+    -------------
 
+    Tools
+    -----
 
+    Documentation 
+    ------------- 
 
 
 Platforms Tested
diff --git a/src/H5D.c b/src/H5D.c
index 6126350..d741b32 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -39,7 +39,7 @@ static int interface_initialize_g = 0;
 /* Local functions */
 static herr_t H5D_init_interface(void);
 static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite, hid_t dxpl_id);
-static H5D_t * H5D_new(hid_t dcpl_id, hbool_t creating);
+static H5D_t * H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type);
 static H5D_t * H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, 
            const H5S_t *space, hid_t dcpl_id, hid_t dxpl_id);
 static H5D_t * H5D_open_oid(const H5G_entry_t *ent, hid_t dxpl_id);
@@ -1242,7 +1242,7 @@ done:
  *-------------------------------------------------------------------------
  */
 static H5D_t *
-H5D_new(hid_t dcpl_id, hbool_t creating)
+H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type)
 {
     H5P_genplist_t	*plist;    /* Property list created */
     H5D_t	*new_dset = NULL;  /* New dataset object */
@@ -1256,7 +1256,7 @@ H5D_new(hid_t dcpl_id, hbool_t creating)
     /* If we are using the default dataset creation property list, during creation
      * don't bother to copy it, just increment the reference count
      */
-    if(creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) {
+    if(!vl_type && creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) {
         /* Copy the default dataset information */
         HDmemcpy(new_dset,&H5D_def_dset,sizeof(H5D_t));
 
@@ -1388,9 +1388,15 @@ H5D_update_entry_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, H5P_genplist_t *p
     /* Special case handling for variable-length types */
     if(H5T_detect_class(type, H5T_VLEN)) {
         /* If the default fill value is chosen for variable-length types, always write it */
-        if(fill_time==H5D_FILL_TIME_IFSET && fill_status==H5D_FILL_VALUE_DEFAULT)
+        if(fill_time==H5D_FILL_TIME_IFSET && fill_status==H5D_FILL_VALUE_DEFAULT) {
             dset->fill_time=fill_time=H5D_FILL_TIME_ALLOC;
 
+            /* Update dataset creation property */
+            assert(dset->dcpl_id!=H5P_DATASET_CREATE_DEFAULT);
+            if (H5P_set(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
+                HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill time")
+        } /* end if */
+
         /* Don't allow never writing fill values with variable-length types */
         if(fill_time==H5D_FILL_TIME_NEVER)
             HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Dataset doesn't support VL datatype when fill value is not defined")
@@ -1437,6 +1443,7 @@ H5D_update_entry_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, H5P_genplist_t *p
             HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update fill value header message")
 
         /* Update dataset creation property */
+        assert(dset->dcpl_id!=H5P_DATASET_CREATE_DEFAULT);
         if (H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0)
             HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value")
     } /* end if */
@@ -1593,6 +1600,7 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space
     unsigned            chunk_ndims = 0;        /* Dimensionality of chunk */
     hsize_t             chunk_size[H5O_LAYOUT_NDIMS]={0};
     H5P_genplist_t 	*dc_plist=NULL;         /* New Property list */
+    hbool_t             has_vl_type=FALSE;      /* Flag to indicate a VL-type for dataset */
     H5D_t		*ret_value;             /* Return value */
 
     FUNC_ENTER_NOAPI(H5D_create, NULL)
@@ -1617,8 +1625,12 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space
     if(H5T_is_sensible(type)!=TRUE)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "datatype is not sensible")
 
+    /* Check if the datatype is/contains a VL-type */
+    if(H5T_detect_class(type, H5T_VLEN))
+        has_vl_type=TRUE;
+
     /* Initialize the dataset object */
-    if(NULL == (new_dset = H5D_new(dcpl_id,TRUE)))
+    if(NULL == (new_dset = H5D_new(dcpl_id,TRUE,has_vl_type)))
         HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
 
     /* Make the "set local" filter callbacks for this dataset */
@@ -2017,7 +2029,8 @@ H5D_open_oid(const H5G_entry_t *ent, hid_t dxpl_id)
     assert (ent);
     
     /* Allocate the dataset structure */
-    if(NULL==(dataset = H5D_new(H5P_DATASET_CREATE_DEFAULT,FALSE)))
+    /* (Set the 'vl_type' parameter to FALSE since it doesn't matter from here) */
+    if(NULL==(dataset = H5D_new(H5P_DATASET_CREATE_DEFAULT,FALSE,FALSE)))
         HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
 
     /* Shallow copy (take ownership) of the group entry object */
diff --git a/test/Makefile.in b/test/Makefile.in
index 3c7b79e..fc03b62 100644
--- a/test/Makefile.in
+++ b/test/Makefile.in
@@ -58,6 +58,7 @@ MOSTLYCLEAN=cmpd_dset.h5 compact_dataset.h5 dataset.h5 extend.h5 istore.h5   \
             tvlstr.h5 flush.h5 enum1.h5 titerate.h5 ttsafe.h5 tarray1.h5     \
             tgenprop.h5 tmisc.h5 tmisc2a.h5 tmisc2b.h5 tmisc3.h5 tmisc4a.h5  \
             tmisc4b.h5 tmisc5.h5 tmisc6.h5 tmisc7.h5 tmisc8.h5 tmisc9.h5     \
+            tmisc10.h5 tmisc11.h5 tmisc12.h5                                 \
             set_extent_read.h5 set_extent_create.h5 getname.h5 getname1.h5   \
             getname2.h5 getname3.h5 sec2_file.h5 family_file000[0-3][0-9].h5 \
             multi_file-[rs].h5 core_file new_move_[ab].h5 ntypes.h5 dangle.h5 \
diff --git a/test/tmisc.c b/test/tmisc.c
index 8667cac..a0e8486 100644
--- a/test/tmisc.c
+++ b/test/tmisc.c
@@ -156,6 +156,14 @@ typedef struct
 #define MISC11_SYM_IK           32
 #define MISC11_ISTORE_IK        64
 
+/* Definitions for misc. test #12 */
+#define MISC12_FILE             "tmisc12.h5"
+#define MISC12_DSET_NAME        "Dataset"
+#define MISC12_SPACE1_RANK	1
+#define MISC12_SPACE1_DIM1	4
+#define MISC12_CHUNK_SIZE       2
+#define MISC12_APPEND_SIZE      5
+
 /****************************************************************
 **
 **  test_misc1(): test unlinking a dataset from a group and immediately
@@ -1818,6 +1826,132 @@ test_misc11(void)
 
 /****************************************************************
 **
+**  test_misc12(): Test that VL-types operate correctly in chunked
+**      datasets that are extended.
+**
+****************************************************************/
+static void
+test_misc12(void)
+{
+    const char *wdata [MISC12_SPACE1_DIM1]= {
+        "Four score and seven years ago our forefathers brought forth on this continent a new nation,",
+        "conceived in liberty and dedicated to the proposition that all men are created equal.",
+        "Now we are engaged in a great civil war,",
+        "testing whether that nation or any nation so conceived and so dedicated can long endure."
+        };   
+    const char *wdata1 [MISC12_APPEND_SIZE]= {
+       "O Gloria inmarcesible! O Jubilo inmortal! En surcos de dolores, el",
+       "bien germina ya! Ceso la horrible noche, La libertad sublime",
+       "derrama las auroras de su invencible luz.",
+       "La humanidad entera, que entre cadenas gime, comprende", 
+       "las palabras del que murio en la cruz."
+        };
+    char        *rdata [MISC12_SPACE1_DIM1+MISC12_APPEND_SIZE]; /* Information read in */
+    hid_t		fid1;		      
+    hid_t		dataset;	    
+    hid_t		sid1, space, memspace;
+    hid_t		tid1, cparms;  
+    hsize_t		dims1[] = {MISC12_SPACE1_DIM1};
+    hsize_t		dimsn[] = {MISC12_APPEND_SIZE};
+    hsize_t		maxdims1[1] = {H5S_UNLIMITED};
+    hsize_t		chkdims1[1] = {MISC12_CHUNK_SIZE};
+    hsize_t     	newsize[1] = {MISC12_SPACE1_DIM1+MISC12_APPEND_SIZE};
+    hssize_t    	offset[1] = {MISC12_SPACE1_DIM1};
+    hsize_t     	count[1] = {MISC12_APPEND_SIZE};
+    int                 i;          /* counting variable */
+    herr_t		ret;		/* Generic return value  */
+
+    /* Output message about test being performed */
+    MESSAGE(5, ("Testing VL-type in chunked dataset\n"));
+
+    /* This test requirese a relatively "fresh" library environment */
+    ret=H5garbage_collect();
+    CHECK(ret, FAIL, "H5garbage_collect");
+
+    /* Create file */
+    fid1 = H5Fcreate (MISC12_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+    CHECK(fid1, FAIL, "H5Fcreate");
+
+    /* Create dataspace for datasets */
+    sid1 = H5Screate_simple (MISC12_SPACE1_RANK, dims1, maxdims1);
+    CHECK(sid1, FAIL, "H5Screate_simple");
+
+    /* Create a datatype to refer to */
+    tid1 = H5Tcopy (H5T_C_S1);
+    CHECK(tid1, FAIL, "H5Tcopy");
+
+    ret = H5Tset_size (tid1,H5T_VARIABLE);
+    CHECK(ret, FAIL, "H5Tset_size");
+
+    cparms = H5Pcreate (H5P_DATASET_CREATE);
+    CHECK(cparms, FAIL, "H5Pcreate");
+
+    ret = H5Pset_chunk ( cparms, 1, chkdims1);
+    CHECK(ret, FAIL, "H5Pset_chunk");
+
+    /* Create a dataset */
+    dataset = H5Dcreate (fid1, MISC12_DSET_NAME, tid1, sid1, cparms);
+    CHECK(dataset, FAIL, "H5Dcreate");
+
+    /* Write dataset to disk */
+    ret = H5Dwrite (dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
+    CHECK(ret, FAIL, "H5Dwrite");
+    
+    /* Extend dataset */
+    ret = H5Dextend (dataset, newsize);
+    CHECK(ret, FAIL, "H5Dextend");
+
+    memspace = H5Screate_simple (MISC12_SPACE1_RANK, dimsn, NULL);
+    CHECK(memspace, FAIL, "H5Screate_simple");
+
+    space = H5Dget_space (dataset);
+    CHECK(space, FAIL, "H5Dget_space");
+
+    ret = H5Sselect_hyperslab (space, H5S_SELECT_SET, offset, NULL, count, NULL);
+    CHECK(ret, FAIL, "H5Sselect_hyperslab");
+
+    /* Write data to new portion of dataset */
+    ret = H5Dwrite (dataset, tid1, memspace, space, H5P_DEFAULT, wdata1);
+    CHECK(ret, FAIL, "H5Dwrite");
+
+    /* Read all data back */
+    ret= H5Dread (dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
+    CHECK(ret, FAIL, "H5Dread");
+
+    for(i=0; i<MISC12_SPACE1_DIM1; i++)
+        if(HDstrcmp(wdata[i],rdata[i])) {
+            num_errs++;
+            printf("Error on line %d: wdata[%d]=%s, rdata[%d]=%s\n",__LINE__,i,wdata[i],i,rdata[i]);
+        } /* end if */
+    for(; i<(MISC12_SPACE1_DIM1+MISC12_APPEND_SIZE); i++)
+        if(HDstrcmp(wdata1[i-MISC12_SPACE1_DIM1],rdata[i])) {
+            num_errs++;
+            printf("Error on line %d: wdata1[%d]=%s, rdata[%d]=%s\n",__LINE__,i-MISC12_SPACE1_DIM1,wdata1[i-MISC12_SPACE1_DIM1],i,rdata[i]);
+        } /* end if */
+
+    /* Reclaim VL data memory */
+    ret = H5Dvlen_reclaim (tid1, sid1, H5P_DEFAULT, rdata);
+    CHECK(ret, FAIL, "H5Dvlen_reclaim");
+
+    /* Close Everything */
+    ret = H5Dclose (dataset);
+    CHECK(ret, FAIL, "H5Dclose");
+    ret = H5Tclose (tid1);
+    CHECK(ret, FAIL, "H5Tclose");
+    ret = H5Sclose (space);
+    CHECK(ret, FAIL, "H5Sclose");
+    ret = H5Sclose (memspace);
+    CHECK(ret, FAIL, "H5Sclose");
+    ret = H5Sclose (sid1);
+    CHECK(ret, FAIL, "H5Sclose");
+    ret = H5Pclose (cparms);
+    CHECK(ret, FAIL, "H5Pclose");
+    ret = H5Fclose (fid1);
+    CHECK(ret, FAIL, "H5Fclose");
+} /* end test_misc12() */
+
+/****************************************************************
+**
 **  test_misc(): Main misc. test routine.
 ** 
 ****************************************************************/
@@ -1838,6 +1972,7 @@ test_misc(void)
     test_misc9();       /* Test for opening (not creating) core files */
     test_misc10();      /* Test for using dataset creation property lists from old files */
     test_misc11();      /* Test for all properties of a file creation property list being stored */
+    test_misc12();      /* Test VL-strings in chunked datasets operating correctly */
 
 } /* test_misc() */
 
@@ -1872,4 +2007,5 @@ cleanup_misc(void)
     HDremove(MISC9_FILE);
     HDremove(MISC10_FILE_NEW);
     HDremove(MISC11_FILE);
+    HDremove(MISC12_FILE);
 }