static rc_t report_deletes_spec( const VDBManager *vdb_mgr,
VFSManager * vfs_mgr,
const char * spec,
uint32_t min_len )
{
rc_t rc = KOutMsg( "\nreporting deletes of '%s'\n", spec );
if ( rc == 0 )
{
VPath * path = NULL;
const VPath * local_cache = NULL;
const KFile * remote_file = NULL;
rc = VFSManagerResolveSpec ( vfs_mgr, spec, &path, &remote_file, &local_cache, true );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot resolve spec via VFSManager" );
}
else
{
char buffer[ 4096 ];
size_t num_read;
rc = VPathReadPath ( path, buffer, sizeof buffer, &num_read );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot read path from vpath" );
}
else
{
int path_type = ( VDBManagerPathType ( vdb_mgr, "%s", buffer ) & ~ kptAlias );
switch( path_type )
{
case kptDatabase : rc = report_deletes_db( vdb_mgr, buffer, min_len ); break;
case kptTable : KOutMsg( "cannot report deletes on a table-object\n" );
rc = RC ( rcApp, rcNoTarg, rcAccessing, rcParam, rcInvalid );
(void)LOGERR( klogErr, rc, "cannot report references on a table-object" );
break;
default : KOutMsg( "the given object is not a vdb-database\n" );
rc = RC ( rcApp, rcNoTarg, rcAccessing, rcParam, rcInvalid );
(void)LOGERR( klogErr, rc, "the given object is not a vdb-database" );
break;
}
}
KFileRelease( remote_file );
VPathRelease ( local_cache );
VPathRelease ( path );
}
}
return rc;
}
static rc_t report_references( const VDBManager *vdb_mgr, VFSManager * vfs_mgr, const char * spec,
bool extended )
{
rc_t rc = KOutMsg( "\nreporting references of '%s'\n", spec );
if ( rc == 0 )
{
VPath * path = NULL;
const VPath * local_cache = NULL;
const KFile * remote_file = NULL;
rc = VFSManagerResolveSpec ( vfs_mgr, spec, &path, &remote_file, &local_cache, true );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot resolve spec via VFSManager" );
}
else
{
char buffer[ 4096 ];
size_t num_read;
rc = VPathReadPath ( path, buffer, sizeof buffer, &num_read );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot read path from vpath" );
}
else
{
rc = KOutMsg( "resolved into '%s'\n", buffer );
if ( rc == 0 )
{
int path_type = ( VDBManagerPathType ( vdb_mgr, "%s", buffer ) & ~ kptAlias );
switch( path_type )
{
case kptDatabase : rc = report_ref_database( vdb_mgr, vfs_mgr, buffer, extended );
break;
case kptTable : rc = KOutMsg( "cannot report references on a table-object\n" );
break;
default : rc = KOutMsg( "the given object is not a vdb-database\n" );
break;
}
}
}
KFileRelease( remote_file );
VPathRelease ( local_cache );
VPathRelease ( path );
}
}
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;
}
