static void get_meta_bam_hdr( vdb_info_bam_hdr * bam_hdr, const KMetadata * meta )
{
const KMDataNode * node;
rc_t rc = KMetadataOpenNodeRead ( meta, &node, "BAM_HEADER" );
bam_hdr -> present = ( rc == 0 );
if ( bam_hdr -> present )
{
bam_hdr->hdr_bytes = get_node_size( node );
if ( bam_hdr->hdr_bytes > 0 )
{
char * buffer = malloc( bam_hdr->hdr_bytes );
if ( buffer != NULL )
{
size_t num_read, remaining;
rc = KMDataNodeRead( node, 0, buffer, bam_hdr->hdr_bytes, &num_read, &remaining );
if ( rc == 0 )
{
parse_buffer( bam_hdr, buffer, bam_hdr->hdr_bytes );
}
free( buffer );
}
}
KMDataNodeRelease ( node );
}
}
static size_t get_node_size( const KMDataNode * node )
{
char buffer[ 10 ];
size_t num_read, remaining, res = 0;
rc_t rc = KMDataNodeRead( node, 0, buffer, sizeof( buffer ), &num_read, &remaining );
if ( rc == 0 ) res = num_read + remaining;
return res;
}
static rc_t copy_metadata_data ( const KMDataNode *snode, KMDataNode *dnode )
{
char buffer [ 1024 ];
size_t total, bytes, remaining;
/* copy node data unless already set */
rc_t rc = KMDataNodeRead ( dnode, 0, buffer, 0, & bytes, & total );
DISP_RC( rc, "copy_metadata_child:KMDataNodeRead(dst) failed" );
if ( rc == 0 && total == 0 )
do
{
rc = KMDataNodeRead ( snode, total, buffer, sizeof buffer, & bytes, & remaining );
DISP_RC( rc, "copy_metadata_child:KMDataNodeRead(src) failed" );
if ( rc == 0 )
{
rc = KMDataNodeAppend ( dnode, buffer, bytes );
DISP_RC( rc, "copy_metadata_child:KMDataNodeAppend(dst) failed" );
if ( rc != 0 ) break;
}
total += bytes;
} while ( remaining != 0 );
return rc;
}
static
bool KMetadataEmpty ( const KMetadata *meta, const char *path )
{
size_t num_read, remaining;
const KMDataNode *node;
rc_t rc = KMetadataOpenNodeRead ( meta, & node, "%s", path );
if ( rc != 0 )
return true;
rc = KMDataNodeRead ( node, 0, & num_read, 0, & num_read, & remaining );
KMDataNodeRelease ( node );
if ( rc == 0 && remaining != 0 )
return false;
return true;
}
static rc_t print_headers_from_metadata( const VDatabase * db, bool * recalc, const char * path )
{
const KMetadata * meta;
rc_t rc = VDatabaseOpenMetadataRead( db, &meta );
if ( rc != 0 )
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot open metadata from '$(t)'", "t=%s", path ) );
else
{
const KMDataNode * node;
rc = KMetadataOpenNodeRead( meta, &node, "BAM_HEADER" );
if ( rc != 0 )
{
if ( GetRCState( rc ) == rcNotFound )
{
*recalc = true;
rc = 0;
}
else
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot open meta-node 'BAM_HEADER' from '$(t)'", "t=%s", path ) );
}
else
{
size_t offset = 0, num_read, remaining = ~0;
char buffer[ 40960 ];
while ( rc == 0 && remaining > 0 )
{
rc = KMDataNodeRead( node, offset, buffer, sizeof( buffer ),
&num_read, &remaining );
if ( rc == 0 )
{
rc = KOutMsg( "%.*s", ( uint32_t )num_read, buffer );
offset += num_read;
}
}
if ( rc == 0 && buffer[ num_read - 1 ] != '\n' )
{
rc = KOutMsg( "\n" );
}
KMDataNodeRelease( node );
}
KMetadataRelease( meta );
}
return rc;
}
static rc_t CC read_from_metadata_node( const void * src, uint64_t pos, void * buffer, size_t bsize, size_t * num_read )
{
const KMDataNode * node = src;
size_t remaining;
return KMDataNodeRead( node, pos, buffer, bsize, num_read, &remaining );
}
/* Read
* read a node value
*
* "offset" [ IN ] - initial offset into metadata
*
* "buffer" [ OUT ] and "bsize" [ IN ] - return buffer for read
*
* "num_read" [ OUT ] - number of bytes actually read
*
* "remaining" [ OUT, NULL OKAY ] - optional return parameter for
* the number of bytes remaining to be read.
* specifically, "offset" + "num_read" + "remaining" == sizeof node data
*/
inline rc_t Read ( size_t offset, void *buffer, size_t bsize,
size_t *num_read, size_t *remaining ) const throw()
{ return KMDataNodeRead ( this, offset, buffer, bsize, num_read, remaining ); }