static rc_t report_ref_database( const VDBManager *vdb_mgr, VFSManager * vfs_mgr, const char * path, bool extended )
{
const VDatabase *db;
rc_t rc = VDBManagerOpenDBRead ( vdb_mgr, &db, NULL, "%s", path );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "VDBManagerOpenDBRead() failed" );
}
else
{
const ReferenceList * reflist;
uint32_t options = ( ereferencelist_usePrimaryIds | ereferencelist_useSecondaryIds | ereferencelist_useEvidenceIds );
rc = ReferenceList_MakeDatabase( &reflist, db, options, 0, NULL, 0 );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "ReferenceList_MakeDatabase() failed" );
}
else
{
uint32_t count;
rc = ReferenceList_Count( reflist, &count );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "ReferenceList_Count() failed" );
}
else
{
rc = KOutMsg( "this object uses %u references\n", count );
if ( rc == 0 )
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const ReferenceObj* ref_obj;
rc = ReferenceList_Get( reflist, &ref_obj, idx );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "ReferenceList_Get() failed" );
}
else
{
rc = report_ref_obj( vdb_mgr, vfs_mgr, path, idx, ref_obj, extended );
ReferenceObj_Release( ref_obj );
}
}
}
}
ReferenceList_Release( reflist );
}
VDatabaseRelease( db );
}
return rc;
}
static rc_t build_seq_id_tree( BSTree * tree, input_files * ifs )
{
rc_t rc = 0;
uint32_t i;
for ( i = 0; i < ifs->database_count && rc == 0; ++i )
{
input_database * id = VectorGet( &ifs->dbs, i );
if ( id != NULL )
{
uint32_t rcount;
rc = ReferenceList_Count( id->reflist, &rcount );
if ( rc == 0 && rcount > 0 )
{
uint32_t r_idx;
for ( r_idx = 0; r_idx < rcount && rc == 0; ++r_idx )
{
const ReferenceObj * ref_obj;
rc = ReferenceList_Get( id->reflist, &ref_obj, r_idx );
if ( rc == 0 && ref_obj != NULL )
{
const char * seqid;
rc = ReferenceObj_SeqId( ref_obj, &seqid );
if ( rc == 0 )
{
const char * name;
rc = ReferenceObj_Name( ref_obj, &name );
if ( rc == 0 )
{
INSDC_coord_len seq_len;
rc = ReferenceObj_SeqLength( ref_obj, &seq_len );
if ( rc == 0 )
{
seq_id_node * node = find_seq_id_node( tree, seqid );
if ( node != NULL )
{
if ( node->seq_len != seq_len )
rc = RC( rcApp, rcNoTarg, rcConstructing, rcData, rcInvalid );
}
else
rc = add_seq_id_node( tree, seqid, name, seq_len );
}
}
}
}
}
}
}
}
return rc;
}
static rc_t prepare_whole_file( prepare_ctx * ctx )
{
rc_t rc = 0;
if ( ctx->reflist != NULL )
{
uint32_t count;
rc = ReferenceList_Count( ctx->reflist, &count );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ReferenceList_Count() failed" );
}
else
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
rc = ReferenceList_Get( ctx->reflist, &ctx->refobj, idx );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ReferenceList_Get() failed" );
}
else
{
rc = ctx->on_section( ctx, 0, 0 );
if ( rc == 0 )
ReferenceObj_Release( ctx->refobj );
}
}
}
}
else
{
ctx->refobj = NULL;
rc = ctx->on_section( ctx, 0, 0 );
}
return rc;
}
static rc_t ref_walker_prepare_1_src( struct ref_walker * self, const char * name )
{
VPath * path = NULL;
const VPath * local_cache = NULL;
const KFile * remote_file = NULL;
rc_t rc = VFSManagerResolveSpec ( self->vfs_mgr, name, &path, &remote_file, &local_cache, true );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc, "cannot resolve '$(n)' via VFSManager", "n=%s", name ) );
}
else
{
char buffer[ 4096 ];
size_t num_read;
rc = VPathReadPath ( path, buffer, sizeof buffer, &num_read );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc, "cannot read path from vpath for '$(n)'", "n=%s", name ) );
}
else
{
if ( rc == 0 )
{
int path_type = ( VDBManagerPathType ( self->vmgr, "%s", buffer ) & ~ kptAlias );
if ( path_type == kptDatabase )
{
const ReferenceList * reflist;
uint32_t options = ( ereferencelist_usePrimaryIds |
ereferencelist_useSecondaryIds |
ereferencelist_useEvidenceIds );
rc = ReferenceList_MakePath( &reflist, self->vmgr, name, options, 0, NULL, 0 );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc, "cannot create ReferenceList for '$(n)'", "n=%s", name ) );
}
else
{
uint32_t count;
rc = ReferenceList_Count( reflist, &count );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc, "ReferenceList_Count() for '$(n)' failed", "n=%s", name ) );
}
else
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const ReferenceObj * refobj;
rc = ReferenceList_Get( reflist, &refobj, idx );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ReferenceList_Get() failed" );
}
else
{
const char * seqid;
rc = ReferenceObj_SeqId( refobj, &seqid );
if ( rc == 0 )
{
INSDC_coord_len seqlen;
rc = ReferenceObj_SeqLength( refobj, &seqlen );
if ( rc == 0 )
{
rc = add_region( &self->regions, seqid, 0, seqlen - 1 );
}
}
ReferenceObj_Release( refobj );
}
}
}
ReferenceList_Release( reflist );
}
}
}
}
KFileRelease( remote_file );
VPathRelease ( local_cache );
VPathRelease ( path );
}
return rc;
}
