static rc_t bam_header(const VDatabase* db) {
rc_t rc = 0;
const char path[] = "BAM_HEADER";
const KMetadata* meta = NULL;
const KMDataNode* node = NULL;
char* buffer = NULL;
assert(db);
if (rc == 0) {
rc = VDatabaseOpenMetadataRead(db, &meta);
DISP_RC(rc, "while calling VDatabaseOpenMetadataRead");
}
if (rc == 0) {
rc = KMetadataOpenNodeRead(meta, &node, "%s", path);
if (GetRCState(rc) == rcNotFound)
{ rc = 0; }
else {
DISP_RC2(rc, path, "while calling KMetadataOpenNodeRead");
if (rc == 0) {
int i = 0;
size_t bsize = 0;
size_t size = 1024;
for (i = 0; i < 2; ++i) {
free(buffer);
bsize = size + 1;
buffer = malloc(bsize);
if (buffer == NULL) {
rc = RC(rcExe, rcStorage, rcAllocating,
rcMemory, rcExhausted);
}
else {
rc = KMDataNodeReadCString(node, buffer, bsize, &size);
if (rc == 0) {
break;
}
else if (i == 0
&& GetRCObject(rc) == (enum RCObject)rcBuffer
&& GetRCState (rc) == rcInsufficient)
{
rc = 0;
}
}
DISP_RC2(rc, path, "while calling KMDataNodeReadCString");
}
}
}
}
if (rc == 0 && buffer)
{ OUTMSG(("BAM_HEADER: {\n%s}\n\n", buffer)); }
DESTRUCT(KMDataNode, node);
DESTRUCT(KMetadata, meta);
free(buffer);
return rc;
}
rc_t AlignRefTableCursor(const VTable* table, const VCursor *native_curs, const VCursor** ref_cursor,const VTable **reftbl)
{
rc_t rc = 0;
char ref_tbl_name[512] = "REFERENCE";
const KMetadata* meta;
const VCursor *curs;
if( (rc = VTableOpenMetadataRead(table, &meta)) == 0 ) {
const KMDataNode* node;
if( (rc = KMetadataOpenNodeRead(meta, &node, "CONFIG/REF_TABLE")) == 0 ) {
size_t sz;
rc = KMDataNodeReadCString(node, ref_tbl_name, sizeof(ref_tbl_name), &sz);
ref_tbl_name[sz] = '\0';
KMDataNodeRelease(node);
}
KMetadataRelease(meta);
}
rc = VCursorLinkedCursorGet(native_curs,ref_tbl_name,&curs);
if(rc != 0){
const VDatabase *db;
const VTable *tbl;
/* get at the parent database */
rc = VTableOpenParentRead ( table, & db );
if(rc != 0) return rc;
/* open the table */
rc = VDatabaseOpenTableRead ( db, &tbl, ref_tbl_name);
VDatabaseRelease ( db );
if(rc != 0) return rc;
/* create a cursor */
rc = VTableCreateCachedCursorRead(tbl, &curs,256*1024*1024);
if(reftbl){
*reftbl = tbl;
} else {
VTableRelease(tbl);
}
if(rc != 0) return rc;
rc = VCursorPermitPostOpenAdd( curs );
if(rc != 0) return rc;
rc = VCursorOpen( curs );
if(rc != 0) return rc;
if(native_curs){
rc = VCursorLinkedCursorSet(native_curs,ref_tbl_name,curs);
}
if(rc != 0) return rc;
} else {
VCursorAddRef(curs);
}
*ref_cursor = curs;
return 0;
}
static
bool KMetadataStrEqual ( const KMetadata *meta, const char *path, const char *str )
{
const KMDataNode *node;
rc_t rc = KMetadataOpenNodeRead ( meta, & node, "%s", path );
if ( rc == 0 )
{
size_t num_read;
char buff [ 4096 ];
rc = KMDataNodeReadCString ( node, buff, sizeof buff, & num_read );
KMDataNodeRelease ( node );
if ( rc == 0 )
{
if ( strcmp ( buff, str ) == 0 )
return true;
}
}
return false;
}
/* Read ( formatted )
* reads as C-string
*
* "buffer" [ OUT ] and "bsize" [ IN ] - output buffer for
* NUL terminated string.
*
* "size" [ OUT ] - return parameter giving size of string
* not including NUL byte. the size is set both upon success
* and insufficient buffer space error.
*/
inline rc_t Read ( char *buffer, size_t bsize, size_t *size ) const throw()
{ return KMDataNodeReadCString ( this, buffer, bsize, size ); }
