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-rw-r--r--MANIFEST1
-rw-r--r--release_docs/RELEASE.txt2
-rwxr-xr-xtools/h5repack/h5repack.sh.in9
-rw-r--r--tools/h5repack/h5repack_copy.c237
-rw-r--r--tools/h5repack/h5repacktst.c159
-rw-r--r--tools/h5repack/testfiles/h5repack_named_dtypes.h5bin0 -> 4304 bytes
6 files changed, 387 insertions, 21 deletions
diff --git a/MANIFEST b/MANIFEST
index f475808..2c56bc4 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1520,6 +1520,7 @@
./tools/h5repack/testfiles/h5repack_ext.bin
./tools/h5repack/testfiles/h5repack_ext.h5
./tools/h5repack/testfiles/ublock.bin
+./tools/h5repack/testfiles/h5repack_named_dtypes.h5
# jam utility and tests
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index b702907..33fed05 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -293,6 +293,8 @@ Bug Fixes since HDF5-1.8.0 release
Tools
-----
+ - Fixed many problems that could occur when using h5repack with named
+ datatypes. (NAF - 2009/4/20 - 1516/1466)
- h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets
that have a datatype datum size greater than H5TOOLS_BUFSIZE, a
constant defined as 1024Kb, such as array types with large
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 4a48c8a..a09e8b9 100755
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -53,6 +53,7 @@ FILE12=h5repack_nbit.h5
FILE13=h5repack_soffset.h5
FILE14=h5repack_layouto.h5 # A file with an older version of the layout message
# (copy of test/tlayouto.h5)
+FILE15=h5repack_named_dtypes.h5
nerrors=0
@@ -455,7 +456,10 @@ TOOLTEST $FILE4 -l dset_chunk:CONTI
TOOLTEST $FILE4 -l dset_chunk:CHUNK=18x13
# Native option
-TOOLTEST $FILE1 -n
+# Do not use FILE1, as the named dtype will be converted to native, and h5diff will
+# report a difference.
+TOOLTEST $FILE0 -n
+TOOLTEST $FILE2 -n
# latest file format with long switches. use FILE4=h5repack_layout.h5 (no filters)
@@ -507,6 +511,9 @@ TOOLTEST $FILE14
# test for datum size > H5TOOLS_MALLOCSIZE
TOOLTEST $FILE1 -f GZIP=1
+# Check repacking file with committed datatypes in odd configurations
+TOOLTEST $FILE15
+
if test $nerrors -eq 0 ; then
echo "All $H5REPACK tests passed."
fi
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 8ab5a35..73f57e3 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -21,8 +21,21 @@
#include "h5tools.h"
#include "h5tools_utils.h"
-extern char *progname;
+/*-------------------------------------------------------------------------
+* typedefs
+*-------------------------------------------------------------------------
+*/
+typedef struct named_dt_t {
+ haddr_t addr_in; /* Address of the named dtype in the in file */
+ hid_t id_out; /* Open identifier for the dtype in the out file */
+ struct named_dt_t *next; /* Next dtype */
+} named_dt_t;
+/*-------------------------------------------------------------------------
+* globals
+*-------------------------------------------------------------------------
+*/
+extern char *progname;
/*-------------------------------------------------------------------------
* macros
@@ -36,7 +49,11 @@ extern char *progname;
*/
static void print_dataset_info(hid_t dcpl_id,char *objname,double per, int pr);
static int do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options);
-static int copy_attr(hid_t loc_in,hid_t loc_out,pack_opt_t *options);
+static int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
+ trav_table_t *travt, pack_opt_t *options);
+static hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p,
+ trav_table_t *travt, pack_opt_t *options);
+static int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err);
static int copy_user_block(const char *infile, const char *outfile, hsize_t size);
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static void print_user_block(const char *filename, hid_t fid);
@@ -506,6 +523,7 @@ int do_copy_objects(hid_t fidin,
hid_t f_space_id=-1; /* file space ID */
hid_t ftype_id=-1; /* file type ID */
hid_t wtype_id=-1; /* read/write type ID */
+ named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes copied */
size_t msize; /* size of type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
@@ -522,6 +540,7 @@ int do_copy_objects(hid_t fidin,
unsigned i;
unsigned u;
int is_ref=0;
+ htri_t is_named;
/*-------------------------------------------------------------------------
* copy the suppplied object list
@@ -605,7 +624,7 @@ int do_copy_objects(hid_t fidin,
* copy attrs
*-------------------------------------------------------------------------
*/
- if(copy_attr(grp_in,grp_out,options) < 0)
+ if(copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
goto error;
@@ -657,6 +676,14 @@ int do_copy_objects(hid_t fidin,
goto error;
if(H5T_REFERENCE == H5Tget_class(ftype_id))
is_ref = 1;
+
+ /* Check if the datatype is committed */
+ if((is_named = H5Tcommitted(ftype_id)) < 0)
+ goto error;
+ if(is_named)
+ if((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0)
+ goto error;
+
if(H5Tclose(ftype_id) < 0)
goto error;
if(H5Dclose(dset_in) < 0)
@@ -672,7 +699,8 @@ int do_copy_objects(hid_t fidin,
if ( options->op_tbl->nelems ||
options->all_filter == 1 ||
options->all_layout == 1 ||
- is_ref)
+ is_ref ||
+ is_named)
{
int j;
@@ -698,10 +726,13 @@ int do_copy_objects(hid_t fidin,
nelmts *= dims[j];
}
- if(options->use_native == 1)
- wtype_id = h5tools_get_native_type(ftype_id);
- else
- wtype_id = H5Tcopy(ftype_id);
+ /* wtype_id will have already been set if using a named dtype */
+ if(!is_named) {
+ if(options->use_native == 1)
+ wtype_id = h5tools_get_native_type(ftype_id);
+ else
+ wtype_id = H5Tcopy(ftype_id);
+ } /* end if */
if((msize = H5Tget_size(wtype_id)) == 0)
goto error;
@@ -933,7 +964,7 @@ int do_copy_objects(hid_t fidin,
* copy attrs
*-------------------------------------------------------------------------
*/
- if (copy_attr(dset_in,dset_out,options) < 0)
+ if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
goto error;
/*close */
@@ -1004,7 +1035,7 @@ int do_copy_objects(hid_t fidin,
goto error;
if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
- if(copy_attr(dset_in, dset_out, options) < 0)
+ if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
goto error;
if(H5Dclose(dset_in) < 0)
goto error;
@@ -1033,17 +1064,21 @@ int do_copy_objects(hid_t fidin,
if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
- if((type_out = H5Tcopy(type_in)) < 0)
+ /* Copy the datatype anonymously */
+ if((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
+ travt, options)) < 0)
goto error;
- if((H5Tcommit2(fidout, travt->objs[i].name, type_out, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ /* Link in to group structure */
+ if(H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
+ H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
- if(copy_attr(type_in, type_out, options) < 0)
+ if(copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
goto error;
if(H5Tclose(type_in) < 0)
@@ -1094,6 +1129,9 @@ int do_copy_objects(hid_t fidin,
} /* i */
+ /* Finalize (link) the stack of named datatypes (if any) */
+ named_datatype_free(&named_dt_head, 0);
+
return 0;
error:
@@ -1110,6 +1148,7 @@ error:
H5Tclose(wtype_id);
H5Tclose(type_in);
H5Tclose(type_out);
+ named_datatype_free(&named_dt_head, 1);
} H5E_END_TRY;
/* free */
if (buf!=NULL)
@@ -1139,6 +1178,8 @@ error:
int copy_attr(hid_t loc_in,
hid_t loc_out,
+ named_dt_t **named_dt_head_p,
+ trav_table_t *travt,
pack_opt_t *options
)
{
@@ -1151,6 +1192,7 @@ int copy_attr(hid_t loc_in,
void *buf=NULL; /* data buffer */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
+ htri_t is_named; /* Whether the datatype is named */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* object info */
@@ -1182,6 +1224,27 @@ int copy_attr(hid_t loc_in,
if ((ftype_id = H5Aget_type( attr_id )) < 0 )
goto error;
+ /* Check if the datatype is committed */
+ if((is_named = H5Tcommitted(ftype_id)) < 0)
+ goto error;
+ if(is_named) {
+ hid_t fidout;
+
+ /* Create out file id */
+ if((fidout = H5Iget_file_id(loc_out)) < 0)
+ goto error;
+
+ /* Copy named dt */
+ if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
+ travt, options)) < 0) {
+ H5Fclose(fidout);
+ goto error;
+ } /* end if */
+
+ if(H5Fclose(fidout) < 0)
+ goto error;
+ } /* end if */
+
/* get the dataspace handle */
if ((space_id = H5Aget_space( attr_id )) < 0 )
goto error;
@@ -1194,10 +1257,13 @@ int copy_attr(hid_t loc_in,
for (j=0; j<rank; j++)
nelmts*=dims[j];
- if (options->use_native==1)
- wtype_id = h5tools_get_native_type(ftype_id);
- else
- wtype_id = H5Tcopy(ftype_id);
+ /* wtype_id will have already been set if using a named dtype */
+ if(!is_named) {
+ if (options->use_native==1)
+ wtype_id = h5tools_get_native_type(ftype_id);
+ else
+ wtype_id = H5Tcopy(ftype_id);
+ } /* end if */
if ((msize=H5Tget_size(wtype_id))==0)
goto error;
@@ -1234,7 +1300,7 @@ int copy_attr(hid_t loc_in,
*-------------------------------------------------------------------------
*/
- if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(H5Awrite(attr_out, wtype_id, buf) < 0)
goto error;
@@ -1282,8 +1348,6 @@ error:
}
-
-
/*-------------------------------------------------------------------------
* Function: print_dataset_info
*
@@ -1388,6 +1452,139 @@ static void print_dataset_info(hid_t dcpl_id,
}
}
+
+/*-------------------------------------------------------------------------
+* Function: copy_named_datatype
+*
+* Purpose: Copies the specified datatype anonymously, and returns an open
+* id for that datatype in the output file. The first time this
+* is called it scans every named datatype in travt into a
+* private stack, afterwards it simply scans that stack. The id
+* returned must be closed after it is no longer needed.
+* named_datatype_free must be called before the program exits
+* to free the stack.
+*
+* Programmer: Neil Fortner
+*
+* Date: April 14, 2009
+*
+*-------------------------------------------------------------------------
+*/
+static hid_t
+copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
+{
+ named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
+ named_dt_t *dt_ret = NULL; /* Datatype to return */
+ H5O_info_t oinfo; /* Object info of input dtype */
+ hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
+
+ if(H5Oget_info(type_in, &oinfo) < 0)
+ goto error;
+
+ if(*named_dt_head_p) {
+ /* Stack already exists, search for the datatype */
+ while(dt && dt->addr_in != oinfo.addr)
+ dt = dt->next;
+
+ dt_ret = dt;
+ } else {
+ /* Create the stack */
+ size_t i;
+
+ for(i=0; i<travt->nobjs; i++)
+ if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
+ /* Push onto the stack */
+ if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
+ goto error;
+ dt->next = *named_dt_head_p;
+ *named_dt_head_p = dt;
+
+ /* Update the address and id */
+ dt->addr_in = travt->objs[i].objno;
+ dt->id_out = -1;
+
+ /* Check if this type is the one requested */
+ if(oinfo.addr == dt->addr_in) {
+ HDassert(!dt_ret);
+ dt_ret = dt;
+ } /* end if */
+ } /* end if */
+ } /* end else */
+
+ /* Handle the case that the requested datatype was not found. This is
+ * possible if the datatype was committed anonymously in the input file. */
+ if(!dt_ret) {
+ /* Push the new datatype onto the stack */
+ if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
+ goto error;
+ dt_ret->next = *named_dt_head_p;
+ *named_dt_head_p = dt_ret;
+
+ /* Update the address and id */
+ dt_ret->addr_in = oinfo.addr;
+ dt_ret->id_out = -1;
+ } /* end if */
+
+ /* If the requested datatype does not yet exist in the output file, copy it
+ * anonymously */
+ if(dt_ret->id_out < 0) {
+ if (options->use_native==1)
+ dt_ret->id_out = h5tools_get_native_type(type_in);
+ else
+ dt_ret->id_out = H5Tcopy(type_in);
+ if(dt_ret->id_out < 0)
+ goto error;
+ if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto error;
+ } /* end if */
+
+ /* Set return value */
+ ret_value = dt_ret->id_out;
+
+ /* Increment the ref count on id_out, because the calling function will try
+ * to close it */
+ if(H5Iinc_ref(ret_value) < 0)
+ goto error;
+
+ return(ret_value);
+
+error:
+ return(-1);
+} /* end copy_named_datatype */
+
+
+/*-------------------------------------------------------------------------
+* Function: named_datatype_free
+*
+* Purpose: Frees the stack of named datatypes.
+*
+* Programmer: Neil Fortner
+*
+* Date: April 14, 2009
+*
+*-------------------------------------------------------------------------
+*/
+static int
+named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
+{
+ named_dt_t *dt = *named_dt_head_p;
+
+ while(dt) {
+ /* Pop the datatype off the stack and free it */
+ if(H5Tclose(dt->id_out) < 0 && !ignore_err)
+ goto error;
+ dt = dt->next;
+ HDfree(*named_dt_head_p);
+ *named_dt_head_p = dt;
+ } /* end while */
+
+ return 0;
+
+error:
+ return -1;
+} /* end named_datatype_free */
+
+
/*-------------------------------------------------------------------------
* Function: copy_user_block
*
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 9a753ef..af4d671 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -72,6 +72,9 @@
/* File w/userblock */
#define FNAME16 "h5repack_ub.h5"
#define FNAME16OUT "h5repack_ub_out.h5"
+/* Named datatypes */
+#define FNAME17 "h5repack_named_dtypes.h5"
+#define FNAME17OUT "h5repack_named_dtypes_out.h5"
#define FNAME_UB "ublock.bin"
@@ -129,6 +132,7 @@ static int make_external(hid_t loc_id);
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);
/*-------------------------------------------------------------------------
@@ -1487,6 +1491,26 @@ int main (void)
#endif
+ /*-------------------------------------------------------------------------
+ * test file with userblock
+ *-------------------------------------------------------------------------
+ */
+ TESTING(" file with committed datatypes");
+
+ if(h5repack_init(&pack_options, 0) < 0)
+ GOERROR;
+
+ if(h5repack(FNAME17, FNAME17OUT, &pack_options) < 0)
+ GOERROR;
+ if(h5diff(FNAME17, FNAME17OUT, NULL, NULL, &diff_options) > 0)
+ GOERROR;
+ if(h5repack_verify(FNAME17OUT, &pack_options) <= 0)
+ GOERROR;
+ if(h5repack_end(&pack_options) < 0)
+ GOERROR;
+
+
+ PASSED();
@@ -1706,6 +1730,17 @@ int make_testfiles(void)
if(make_userblock_file() < 0)
goto out;
+ /*-------------------------------------------------------------------------
+ * create a file with named datatypes
+ *-------------------------------------------------------------------------
+ */
+ if((fid = H5Fcreate(FNAME17,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT)) < 0)
+ return -1;
+ if (make_named_dtype(fid) < 0)
+ goto out;
+ if(H5Fclose(fid) < 0)
+ return -1;
+
return 0;
out:
@@ -5374,4 +5409,128 @@ out:
}
+/*-------------------------------------------------------------------------
+* Function: make_named_dtype
+*
+* Purpose: create a file with named datatypes in various configurations
+*
+*-------------------------------------------------------------------------
+*/
+static
+int make_named_dtype(hid_t loc_id)
+{
+ hsize_t dims[1] ={3};
+ hid_t did=-1;
+ hid_t aid=-1;
+ hid_t sid=-1;
+ hid_t tid=-1;
+ hid_t gid=-1;
+
+ if ((sid = H5Screate_simple(1, dims, NULL)) < 0)
+ goto out;
+
+ /* Create a dataset with an anonymous committed datatype as the first thing
+ * h5repack sees */
+ if((tid = H5Tcopy(H5T_STD_I16LE)) < 0)
+ goto out;
+ if(H5Tcommit_anon(loc_id, tid, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto out;
+ if ((did = H5Dcreate2(loc_id, "A", tid, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Tclose(tid) < 0)
+ goto out;
+
+ /* Create an attribute on that dataset that uses a committed datatype in
+ * a remote group */
+ if((gid = H5Gcreate2(loc_id, "M", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Gclose(gid) < 0)
+ goto out;
+ if((gid = H5Gcreate2(loc_id, "M/M", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Gclose(gid) < 0)
+ goto out;
+ if((tid = H5Tcopy(H5T_STD_I16BE)) < 0)
+ goto out;
+ if(H5Tcommit2(loc_id, "/M/M/A", tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto out;
+ if((aid = H5Acreate2(did, "A", tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Aclose(aid) < 0)
+ goto out;
+ if(H5Tclose(tid) < 0)
+ goto out;
+ if(H5Dclose(did) < 0)
+ goto out;
+
+ /* Create a dataset in the remote group that uses a committed datatype in
+ * the root group */
+ if((tid = H5Tcopy(H5T_STD_I32LE)) < 0)
+ goto out;
+ if(H5Tcommit2(loc_id, "N", tid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto out;
+ if((did = H5Dcreate2(loc_id, "M/M/B", tid, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Tclose(tid) < 0)
+ goto out;
+
+ /* Create an attribute on the remote dataset that uses an anonymous
+ * committed datatype */
+ if((tid = H5Tcopy(H5T_STD_I32BE)) < 0)
+ goto out;
+ if(H5Tcommit_anon(loc_id, tid, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto out;
+ if((aid = H5Acreate2(did, "A", tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Aclose(aid) < 0)
+ goto out;
+
+ /* Create another attribute that uses the same anonymous datatype */
+ if((aid = H5Acreate2(did, "B", tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Aclose(aid) < 0)
+ goto out;
+ if(H5Tclose(tid) < 0)
+ goto out;
+ if(H5Dclose(did) < 0)
+ goto out;
+
+ /* Create a dataset in the root group that uses the committed datatype in
+ * the root group */
+ if((tid = H5Topen2(loc_id, "N", H5P_DEFAULT)) < 0)
+ goto out;
+ if((did = H5Dcreate2(loc_id, "O", tid, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Dclose(did) < 0)
+ goto out;
+
+ /* Create 2 attributes on the committed datatype that use that datatype */
+ if((aid = H5Acreate2(tid, "A", tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Aclose(aid) < 0)
+ goto out;
+ if((aid = H5Acreate2(tid, "B", tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto out;
+ if(H5Aclose(aid) < 0)
+ goto out;
+ if(H5Tclose(tid) < 0)
+ goto out;
+
+ /* Close */
+ if (H5Sclose(sid) < 0)
+ goto out;
+
+ return 0;
+
+out:
+ H5E_BEGIN_TRY
+ {
+ H5Tclose(tid);
+ H5Aclose(aid);
+ H5Sclose(sid);
+ H5Dclose(did);
+ H5Gclose(gid);
+ } H5E_END_TRY;
+ return -1;
+} /* end make_named_dtype() */
diff --git a/tools/h5repack/testfiles/h5repack_named_dtypes.h5 b/tools/h5repack/testfiles/h5repack_named_dtypes.h5
new file mode 100644
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