Java tutorial
/******************************************************************************* * In the Hi-WAY project we propose a novel approach of executing scientific * workflows processing Big Data, as found in NGS applications, on distributed * computational infrastructures. The Hi-WAY software stack comprises the func- * tional workflow language Cuneiform as well as the Hi-WAY ApplicationMaster * for Apache Hadoop 2.x (YARN). * * List of Contributors: * * Jrgen Brandt (HU Berlin) * Marc Bux (HU Berlin) * Ulf Leser (HU Berlin) * * Jrgen Brandt is funded by the European Commission through the BiobankCloud * project. Marc Bux is funded by the Deutsche Forschungsgemeinschaft through * research training group SOAMED (GRK 1651). * * Copyright 2014 Humboldt-Universitt zu Berlin * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. ******************************************************************************/ package de.huberlin.wbi.cuneiform.core.cre; import java.io.BufferedReader; import java.io.BufferedWriter; import java.io.IOException; import java.nio.charset.Charset; import java.nio.file.DirectoryStream; import java.nio.file.Files; import java.nio.file.LinkOption; import java.nio.file.Path; import java.nio.file.Paths; import java.nio.file.StandardOpenOption; import java.nio.file.attribute.PosixFilePermissions; import java.util.HashSet; import java.util.Set; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.json.JSONObject; import de.huberlin.wbi.cuneiform.core.actormodel.Message; import de.huberlin.wbi.cuneiform.core.invoc.Invocation; import de.huberlin.wbi.cuneiform.core.semanticmodel.JsonReportEntry; import de.huberlin.wbi.cuneiform.core.semanticmodel.Ticket; import de.huberlin.wbi.cuneiform.core.ticketsrc.TicketFailedMsg; import de.huberlin.wbi.cuneiform.core.ticketsrc.TicketFinishedMsg; import de.huberlin.wbi.cuneiform.core.ticketsrc.TicketSrcActor; public class LocalThread implements Runnable { private static final int WAIT_INTERVAL = 100; private static final int MAX_TRIALS = 4; private final Invocation invoc; private final Log log; private final Path buildDir; private final TicketSrcActor ticketSrc; private final BaseCreActor cre; private final Path centralRepo; public LocalThread(TicketSrcActor ticketSrc, BaseCreActor cre, Ticket ticket, Path buildDir, Path centralRepo) { if (buildDir == null) throw new NullPointerException("Build directory must not be null."); if (!Files.exists(buildDir)) throw new RuntimeException("Build directory does not exist."); if (!Files.isDirectory(buildDir)) throw new RuntimeException("Build path expected to be a directory."); if (cre == null) throw new NullPointerException("CRE actor must not be null."); if (ticketSrc == null) throw new NullPointerException("Ticket source must not be null."); if (centralRepo == null) throw new NullPointerException("Central repository must not be null."); if (!Files.exists(centralRepo)) throw new RuntimeException("Central repository does not exist."); if (!Files.isDirectory(centralRepo)) throw new RuntimeException("Central repository path expected to be a directory."); this.ticketSrc = ticketSrc; this.cre = cre; this.buildDir = buildDir; this.centralRepo = centralRepo; invoc = Invocation.createInvocation(ticket); log = LogFactory.getLog(LocalThread.class); } @Override public void run() { Path scriptFile, location, successMarker, reportFile, callLocation, stdErrFile, stdOutFile; // Path lockMarker; Process process; int exitValue; Set<JsonReportEntry> report; JsonReportEntry entry; String line; StringBuffer buf; Path srcPath, destPath; ProcessBuilder processBuilder; Ticket ticket; String script, stdOut, stdErr; long tic, toc; JSONObject obj; Message msg; Charset cs; int trial; boolean suc; Exception ex; if (log.isDebugEnabled()) log.debug("Starting up local thread for ticket " + invoc.getTicketId() + "."); if (invoc == null) throw new NullPointerException("Invocation must not be null."); ticket = invoc.getTicket(); process = null; stdOut = null; stdErr = null; // lockMarker = null; script = null; successMarker = null; cs = Charset.forName("UTF-8"); try { callLocation = Paths.get(System.getProperty("user.dir")); location = buildDir.resolve(String.valueOf(invoc.getTicketId())); // lockMarker = location.resolve( Invocation.LOCK_FILENAME ); successMarker = location.resolve(Invocation.SUCCESS_FILENAME); reportFile = location.resolve(Invocation.REPORT_FILENAME); script = invoc.toScript(); // if( Files.exists( lockMarker ) ) // throw new IOException( "Lock held on ticket "+invoc.getTicketId() ); if (!Files.exists(successMarker)) { deleteIfExists(location); Files.createDirectories(location); // Files.createFile( lockMarker ); scriptFile = invoc.getExecutablePath(location); Files.createFile(scriptFile, PosixFilePermissions.asFileAttribute(PosixFilePermissions.fromString("rwxr-x---"))); // write executable script try (BufferedWriter writer = Files.newBufferedWriter(scriptFile, cs, StandardOpenOption.CREATE)) { writer.write(script); } // write executable log entry try (BufferedWriter writer = Files.newBufferedWriter(reportFile, cs, StandardOpenOption.CREATE)) { writer.write(ticket.getExecutableLogEntry().toString()); writer.write('\n'); } for (String filename : invoc.getStageInList()) { if (filename.charAt(0) == '/') throw new UnsupportedOperationException("Absolute path encountered '" + filename + "'."); srcPath = centralRepo.resolve(filename); destPath = location.resolve(filename); if (!Files.exists(srcPath)) { srcPath = callLocation.resolve(filename); if (log.isTraceEnabled()) log.trace("Resolving relative path '" + srcPath + "'."); } else if (log.isTraceEnabled()) log.trace("Resolving path to central repository '" + srcPath + "'."); if (log.isTraceEnabled()) log.trace("Trying to create symbolic link from '" + srcPath + "' to '" + destPath + "'."); if (!Files.exists(destPath.getParent())) Files.createDirectories(destPath.getParent()); Files.createSymbolicLink(destPath, srcPath); } // run script processBuilder = new ProcessBuilder(invoc.getCmd()); processBuilder.directory(location.toFile()); stdOutFile = location.resolve(Invocation.STDOUT_FILENAME); stdErrFile = location.resolve(Invocation.STDERR_FILENAME); processBuilder.redirectOutput(stdOutFile.toFile()); processBuilder.redirectError(stdErrFile.toFile()); trial = 1; suc = false; ex = null; tic = System.currentTimeMillis(); do { try { process = processBuilder.start(); suc = true; } catch (IOException e) { ex = e; if (log.isWarnEnabled()) log.warn("Unable to start process on trial " + (trial++) + " Waiting " + WAIT_INTERVAL + "ms: " + e.getMessage()); Thread.sleep(WAIT_INTERVAL); } } while (suc == false && trial <= MAX_TRIALS); if (process == null) { ticketSrc.sendMsg(new TicketFailedMsg(cre, ticket, ex, script, null, null)); // Files.delete( lockMarker ); return; } exitValue = process.waitFor(); toc = System.currentTimeMillis(); try (BufferedWriter writer = Files.newBufferedWriter(reportFile, cs, StandardOpenOption.APPEND)) { obj = new JSONObject(); obj.put(JsonReportEntry.LABEL_REALTIME, toc - tic); entry = invoc.createJsonReportEntry(tic, JsonReportEntry.KEY_INVOC_TIME, obj); writer.write(entry.toString()); writer.write('\n'); try (BufferedReader reader = Files.newBufferedReader(stdOutFile, cs)) { buf = new StringBuffer(); while ((line = reader.readLine()) != null) buf.append(line).append('\n'); stdOut = buf.toString(); if (!stdOut.isEmpty()) { entry = invoc.createJsonReportEntry(JsonReportEntry.KEY_INVOC_STDOUT, stdOut); writer.write(entry.toString()); writer.write('\n'); } } try (BufferedReader reader = Files.newBufferedReader(stdErrFile, cs)) { buf = new StringBuffer(); while ((line = reader.readLine()) != null) buf.append(line).append('\n'); stdErr = buf.toString(); if (!stdErr.isEmpty()) { entry = invoc.createJsonReportEntry(JsonReportEntry.KEY_INVOC_STDERR, stdErr); writer.write(entry.toString()); writer.write('\n'); } } if (exitValue == 0) Files.createFile(successMarker); else { ticketSrc.sendMsg(new TicketFailedMsg(cre, ticket, null, script, stdOut, stdErr)); // Files.delete( lockMarker ); return; } } } // gather report report = new HashSet<>(); try (BufferedReader reader = Files.newBufferedReader(reportFile, cs)) { while ((line = reader.readLine()) != null) { line = line.trim(); if (line.isEmpty()) continue; entry = new JsonReportEntry(line); // If the report comes from the hard cache then the run id // is different from the run id of this invocation. This is // corrected here. entry.setRunId(invoc.getRunId()); report.add(entry); } } invoc.evalReport(report); // create link in central data repository for (String f : invoc.getStageOutList()) { srcPath = location.resolve(f); destPath = centralRepo.resolve(f); if (Files.exists(destPath)) continue; if (log.isTraceEnabled()) log.trace("Creating link from " + srcPath + " to " + destPath + "."); Files.createSymbolicLink(destPath, srcPath); } ticketSrc.sendMsg(new TicketFinishedMsg(cre, invoc.getTicket(), report)); if (log.isTraceEnabled()) log.trace("Local thread ran through without exception."); // Files.deleteIfExists( lockMarker ); } catch (InterruptedException e) { if (log.isTraceEnabled()) log.trace("Local thread has been interrupted."); } catch (Exception e) { if (log.isTraceEnabled()) log.trace("Something went wrong. Deleting success marker if present."); if (successMarker != null) try { Files.deleteIfExists(successMarker); } catch (IOException e1) { e1.printStackTrace(); } msg = new TicketFailedMsg(cre, ticket, e, script, stdOut, stdErr); ticketSrc.sendMsg(msg); } finally { if (process != null) { if (log.isDebugEnabled()) log.debug("Stopping local thread for ticket " + invoc.getTicketId() + "."); process.destroy(); } } } public static void deleteIfExists(Path f) throws IOException { if (!Files.exists(f, LinkOption.NOFOLLOW_LINKS)) return; if (Files.isDirectory(f)) try (DirectoryStream<Path> stream = Files.newDirectoryStream(f)) { for (Path p : stream) deleteIfExists(p); } Files.delete(f); } }