[svn-r11899] Purpose:

    Bug fix & new feature

Description:
    Support variable-length datatypes in compact data storage and chunked
data storage, along with attributes.

    Bug fix on the H5T_vlen_set_loc to allow for changing the file on a
variable-length datatype on disk.

Platforms tested:
    FreeBSD 4.11 (sleipnir)
    Linux 2.4
    Can't h5committest right now, due to missing cache files.

1 files changed, 155 insertions, 0 deletions

diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c
index 83f9b8c..0ad8e05 100644
--- a/src/H5Dcompact.c
+++ b/src/H5Dcompact.c
@@ -36,6 +36,7 @@
 #include "H5Fprivate.h"		/* Files				*/
 #include "H5FDprivate.h"	/* File drivers				*/
 #include "H5FLprivate.h"	/* Free Lists                           */
+#include "H5Iprivate.h"		/* IDs			  		*/
 #include "H5Oprivate.h"		/* Object headers		  	*/
 #include "H5Vprivate.h"		/* Vector and array functions		*/
 
@@ -59,6 +60,9 @@
 /* Local Variables */
 /*******************/
 
+/* Declare extern the free list to manage blocks of type conversion data */
+H5FL_BLK_EXTERN(type_conv);
+
 
 /*-------------------------------------------------------------------------
  * Function:    H5D_compact_readvv
@@ -141,3 +145,154 @@ H5D_compact_writevv(const H5D_io_info_t *io_info,
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 }   /* end H5D_compact_writevv() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5D_compact_copy
+ *
+ * Purpose:     Copy compact storage raw data from SRC file to DST file.
+ *
+ * Return:      Non-negative on success, negative on failure.
+ *
+ * Programmer:  Peter Cao
+ *              December 11, 2005       
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src,
+    H5F_t *f_dst,  H5O_layout_t *layout_dst, H5T_t *dt_src, hid_t dxpl_id)
+{
+    hid_t       tid_src = -1;           /* Datatype ID for source datatype */
+    hid_t       tid_dst = -1;           /* Datatype ID for destination datatype */
+    hid_t       tid_mem = -1;           /* Datatype ID for memory datatype */
+    void       *buf = NULL;             /* Buffer for copying data */
+    void       *reclaim_buf = NULL;     /* Buffer for reclaiming data */
+    hid_t       buf_sid = -1;           /* ID for buffer dataspace */
+    herr_t      ret_value = SUCCEED;    /* Return value */
+
+    FUNC_ENTER_NOAPI(H5D_compact_copy, FAIL)
+
+    /* Check args */
+    HDassert(f_src);
+    HDassert(f_dst);
+    HDassert(layout_src && H5D_COMPACT == layout_src->type);
+    HDassert(layout_dst && H5D_COMPACT == layout_dst->type);
+
+    /* If there's a source datatype, set up type conversion information */
+    if (!dt_src)  
+        /* Type conversion not necessary */
+        HDmemcpy(layout_dst->u.compact.buf, layout_src->u.compact.buf, layout_src->u.compact.size);
+    else {         
+        H5T_path_t  *tpath_src_mem, *tpath_mem_dst;   /* Datatype conversion paths */
+        H5T_t *dt_dst;              /* Destination datatype */
+        H5T_t *dt_mem;              /* Memory datatype */
+        H5S_t *buf_space;           /* Dataspace describing buffer */
+        size_t buf_size;            /* Size of copy buffer */
+        size_t nelmts;              /* Number of elements in buffer */
+        size_t src_dt_size;         /* Source datatype size */
+        size_t tmp_dt_size;         /* Temporary datatype size */
+        size_t max_dt_size;         /* Max atatype size */
+        hsize_t buf_dim;            /* Dimension for buffer */
+
+        /* Create datatype ID for src datatype */
+        if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0)
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
+
+        /* create a memory copy of the variable-length datatype */
+        if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
+        if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem)) < 0)
+            HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
+
+        /* create variable-length datatype at the destinaton file */
+        if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
+        if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0)
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk")
+        if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst)) < 0)
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype")
+
+        /* Set up the conversion functions */
+        if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE)))
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes")
+        if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE)))
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes")
+
+        /* Determine largest datatype size */
+        if(0 == (src_dt_size = H5T_get_size(dt_src)))
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
+        if(0 == (tmp_dt_size = H5T_get_size(dt_mem)))
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
+        max_dt_size = MAX(src_dt_size, tmp_dt_size);
+        if(0 == (tmp_dt_size = H5T_get_size(dt_dst)))
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
+        max_dt_size = MAX(max_dt_size, tmp_dt_size);
+
+        /* Set number of whole elements that fit in buffer */
+        if(0 == (nelmts = layout_src->u.compact.size / src_dt_size))
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "element size too large")
+
+        /* Set up number of bytes to copy, and initial buffer size */
+        buf_size = nelmts * max_dt_size;
+
+        /* Create dataspace for number of elements in buffer */
+        buf_dim = nelmts;
+
+        /* Create the space and set the initial extent */
+        if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL)))
+            HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
+
+        /* Atomize */
+        if((buf_sid = H5I_register(H5I_DATASPACE, buf_space)) < 0) {
+            H5S_close(buf_space);
+            HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID")
+        } /* end if */
+
+        /* Allocate memory for recclaim buf */
+        if(NULL == (reclaim_buf = H5FL_BLK_MALLOC(type_conv, buf_size)))
+            HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
+
+        /* Allocate memory for copying the chunk */
+        if(NULL == (buf = H5FL_BLK_MALLOC(type_conv, buf_size)))
+            HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
+
+        HDmemcpy(buf, layout_src->u.compact.buf, layout_src->u.compact.size);
+
+        /* Convert from source file to memory */
+        if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0)
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed")
+
+        HDmemcpy(reclaim_buf, buf, buf_size);
+
+        /* Convert from memory to destination file */
+        if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0)
+            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed")
+
+        HDmemcpy(layout_dst->u.compact.buf, buf, layout_dst->u.compact.size);
+
+        if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to reclaim variable-length data")
+    } /* end if */
+
+done:
+    if(buf_sid > 0)
+        if(H5I_dec_ref(buf_sid) < 0)
+            HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary dataspace ID")
+    if(tid_src > 0)
+        if(H5I_dec_ref(tid_src) < 0)
+            HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
+    if(tid_dst > 0)
+        if(H5I_dec_ref(tid_dst) < 0)
+            HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
+    if(tid_mem > 0)
+        if(H5I_dec_ref(tid_mem) < 0)
+            HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
+    if(buf)
+        H5FL_BLK_FREE(type_conv, buf);
+    if(reclaim_buf)
+        H5FL_BLK_FREE(type_conv, reclaim_buf);
+
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_compact_copy() */
+