package org.ensembl.mart.lib;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStreamReader;
import java.sql.Connection;
import java.util.List;
/*
Copyright (C) 2003 EBI, GRL
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
/**
* UnprocessedFilterHandler implementing object designed to process File type
* IDListFilter objects into STRING type IDListFilter objects. Expects that
* files contain one or more ids, one per line.
*
* @author <a href="mailto:dlondon@ebi.ac.uk">Darin London</a>
* @author <a href="mailto:craig@ebi.ac.uk">Craig Melsopp</a>
*/
public class FileIDListFilterHandler extends IDListFilterHandlerBase {
/* (non-Javadoc)
* @see org.ensembl.mart.lib.UnprocessedFilterHandler#ModifyQuery(org.ensembl.mart.lib.Engine, org.ensembl.mart.lib.IDListFilter, org.ensembl.mart.lib.Query)
*/
public Query ModifyQuery(Engine engine, List filters, Query query) throws InvalidQueryException {
Query newQuery = new Query(query);
for (int i = 0, n = filters.size(); i < n; i++) {
IDListFilter idfilter = (IDListFilter) filters.get(i);
newQuery.removeFilter(idfilter);
File idFile = idfilter.getFile();
String[] unversionedIds = null;
Connection conn = null;
try {
conn = query.getDataSource().getConnection();
unversionedIds =
HarvestStream( new InputStreamReader(new FileInputStream(idFile)));
} catch (Exception e) {
throw new InvalidQueryException("Could not parse File IDListFilter: " + e.getMessage(), e);
} finally {
DetailedDataSource.close( conn );
}
if (unversionedIds.length > 0)
newQuery.addFilter(new IDListFilter(idfilter.getField(), idfilter.getTableConstraint(), idfilter.getKey(), unversionedIds));
}
return newQuery;
}
}