Java tutorial
/* * Copyright (c) 2017 Memorial Sloan-Kettering Cancer Center. * * 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. The software and documentation provided hereunder * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no * obligations to provide maintenance, support, updates, enhancements or * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be * liable to any party for direct, indirect, special, incidental or * consequential damages, including lost profits, arising out of the use of this * software and its documentation, even if Memorial Sloan-Kettering Cancer * Center has been advised of the possibility of such damage. */ /* * This file is part of cBioPortal CMO-Pipelines. * * cBioPortal is free software: you can redistribute it and/or modify * it under the terms of the GNU Affero General Public License as * published by the Free Software Foundation, either version 3 of the * License. * * This program 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 Affero General Public License for more details. * * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package org.cbioportal.database.annotator; import com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException; import static com.querydsl.core.alias.Alias.$; import static com.querydsl.core.alias.Alias.alias; import com.querydsl.core.types.Projections; import com.querydsl.sql.SQLQueryFactory; import java.sql.*; import java.util.List; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.cbioportal.database.annotator.model.*; import org.springframework.batch.item.*; import org.springframework.beans.factory.annotation.Autowired; /** * * @author heinsz */ public class AnnotateRecordsWriter implements ItemStreamWriter<MutationEvent> { @Autowired SQLQueryFactory databaseAnnotatorQueryFactory; private Connection con; private final Log log = LogFactory.getLog(AnnotateRecordsWriter.class); @Override public void open(ExecutionContext ec) throws ItemStreamException { con = databaseAnnotatorQueryFactory.getConnection(); } @Override public void update(ExecutionContext ec) throws ItemStreamException { } @Override public void close() throws ItemStreamException { try { con.close(); } catch (SQLException e) { log.error("Failed to close connection!!"); } } @Override public void write(List<? extends MutationEvent> list) throws Exception { for (MutationEvent event : list) { updateMutationEventInDb(event); } } private void updateMutationEventInDb(MutationEvent annotatedEvent) throws Exception { if (!annotatedEvent.getPROTEIN_CHANGE().equals("MUTATED")) { PreparedStatement pstmt = con.prepareStatement( "UPDATE mutation_event set chr = ?, start_position = ?, end_position = ?, reference_allele = ?, tumor_seq_allele = ?, protein_change = ?, mutation_type = ?, oncotator_codon_change = ?, oncotator_protein_pos_start = ?, oncotator_protein_pos_end = ? where mutation_event_id = ?"); pstmt.setString(1, annotatedEvent.getCHR()); pstmt.setInt(2, annotatedEvent.getSTART_POSITION()); pstmt.setInt(3, annotatedEvent.getEND_POSITION()); pstmt.setString(4, annotatedEvent.getREFERENCE_ALLELE()); pstmt.setString(5, annotatedEvent.getTUMOR_SEQ_ALLELE()); pstmt.setString(6, annotatedEvent.getPROTEIN_CHANGE()); pstmt.setString(7, annotatedEvent.getMUTATION_TYPE()); pstmt.setString(8, annotatedEvent.getONCOTATOR_CODON_CHANGE()); pstmt.setInt(9, annotatedEvent.getONCOTATOR_PROTEIN_POS_START()); pstmt.setInt(10, annotatedEvent.getONCOTATOR_PROTEIN_POS_END()); pstmt.setInt(11, annotatedEvent.getMUTATION_EVENT_ID()); try { Integer rs = pstmt.executeUpdate(); log.info("Updated mutation event. Mutation event id: " + annotatedEvent.getMUTATION_EVENT_ID()); } catch (MySQLIntegrityConstraintViolationException e) { List<MutationEvent> mutationEvents = getDuplicatedMutationEvents(annotatedEvent); for (MutationEvent event : mutationEvents) { if (event.getPROTEIN_CHANGE().equals(annotatedEvent.getPROTEIN_CHANGE())) { updateMutationsInDb(annotatedEvent, event); deleteMutationEvent(annotatedEvent); } } } } else { log.error("Event " + annotatedEvent.getMUTATION_EVENT_ID() + " unable to be fixed."); } } private List<MutationEvent> getDuplicatedMutationEvents(MutationEvent annotatedEvent) { MutationEvent qMutationEvent = alias(MutationEvent.class, BatchConfiguration.MUTATION_EVENT_TABLE); List<MutationEvent> mutationEvents = databaseAnnotatorQueryFactory .select(Projections.constructor(MutationEvent.class, $(qMutationEvent.getMUTATION_EVENT_ID()), $(qMutationEvent.getCHR()), $(qMutationEvent.getSTART_POSITION()), $(qMutationEvent.getEND_POSITION()), $(qMutationEvent.getREFERENCE_ALLELE()), $(qMutationEvent.getTUMOR_SEQ_ALLELE()), $(qMutationEvent.getPROTEIN_CHANGE()), $(qMutationEvent.getMUTATION_TYPE()), $(qMutationEvent.getONCOTATOR_CODON_CHANGE()), $(qMutationEvent.getONCOTATOR_PROTEIN_POS_START()), $(qMutationEvent.getONCOTATOR_PROTEIN_POS_END()))) .from($(qMutationEvent)) .where($(qMutationEvent.getCHR()).eq(annotatedEvent.getCHR()) .and($(qMutationEvent.getSTART_POSITION()).eq(annotatedEvent.getSTART_POSITION())) .and($(qMutationEvent.getEND_POSITION()).eq(annotatedEvent.getEND_POSITION())) .and($(qMutationEvent.getTUMOR_SEQ_ALLELE()).eq(annotatedEvent.getTUMOR_SEQ_ALLELE())) .and($(qMutationEvent.getMUTATION_TYPE()).eq(annotatedEvent.getMUTATION_TYPE()))) .fetch(); return mutationEvents; } private void updateMutationsInDb(MutationEvent eventToBeDeleted, MutationEvent properlyAnnotatedEvent) throws Exception { PreparedStatement pstmt = con .prepareStatement("UPDATE mutation set mutation_event_id = ? where mutation_event_id = ?"); pstmt.setInt(1, properlyAnnotatedEvent.getMUTATION_EVENT_ID()); pstmt.setInt(2, eventToBeDeleted.getMUTATION_EVENT_ID()); pstmt.executeUpdate(); log.info( "Updating mutations - mutations linked to mutation event " + eventToBeDeleted.getMUTATION_EVENT_ID() + " now linked to " + properlyAnnotatedEvent.getMUTATION_EVENT_ID()); } private void deleteMutationEvent(MutationEvent event) throws Exception { PreparedStatement pstmt = con.prepareStatement("delete from mutation_event where mutation_event_id = ?"); pstmt.setInt(1, event.getMUTATION_EVENT_ID()); log.info("Deleting mutation event. Properly annotated event already exists in database: " + event.getMUTATION_EVENT_ID()); } }