Java tutorial
/* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you 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 org.apache.airavata.datacat.parsers.gridchem; import org.apache.airavata.datacat.models.OutputMetadataDTO; import org.apache.airavata.datacat.models.OutputMonitorMessage; import org.apache.airavata.datacat.parsers.IParser; import org.apache.airavata.datacat.parsers.gridchem.inchi.InChI; import org.apache.airavata.datacat.parsers.gridchem.inchi.InChIGenerator; import org.apache.airavata.datacat.parsers.gridchem.util.Constants; import org.apache.airavata.datacat.parsers.gridchem.util.GridChemProperties; import org.apache.commons.io.FileUtils; import org.apache.log4j.LogManager; import org.apache.log4j.Logger; import java.io.File; import java.io.FileReader; import java.io.FilenameFilter; import java.io.IOException; import java.lang.reflect.Constructor; import java.lang.reflect.InvocationTargetException; import java.text.DateFormat; import java.text.SimpleDateFormat; import java.util.Date; import java.util.HashMap; import java.util.Map; import java.util.UUID; public class GridChemParser implements IParser { private final Logger logger = LogManager.getLogger(GridChemParser.class); private String[] gridChemQueueParserses; public GridChemParser() { } public OutputMetadataDTO parse(OutputMonitorMessage outputMonitorMessage) { gridChemQueueParserses = GridChemProperties.getInstance().getParserSequence(); logger.info("Loaded the GridChem Parser Sequence ..."); logger.info("Started passing new file monitor message..."); OutputMetadataDTO outputMetadataDTO = new OutputMetadataDTO(); //For Solr requirement date is in the format of yyyy-MM-ddTHH:mm:ssZ DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); Date now = new Date(); String date = dateFormat.format(now).split(" ")[0] + "T" + dateFormat.format(now).split(" ")[1] + "Z"; //setting the basic file meta-data outputMetadataDTO.setCreatedDate(date); outputMetadataDTO.setHost(computingResourceName()); outputMetadataDTO.setExperimentName(outputMonitorMessage.getExperimentName()); outputMetadataDTO.setExperimentId(outputMonitorMessage.getExperimentID()); outputMetadataDTO.setOutputPath(outputMonitorMessage.getOutputPath()); outputMetadataDTO.setApplicationName(applicationName()); outputMetadataDTO.setOwnerId(getOwnerId()); String[] outPutFiles = (new File(outputMonitorMessage.getOutputPath())).list(new FilenameFilter() { public boolean accept(File dir, String filename) { return filename.endsWith(".out"); } }); Map<String, String> results = new HashMap<String, String>(); if (outPutFiles != null && outPutFiles.length > 0) { // have a copy of the file in a temp location //FIXME: is this really necessary? String outFilePath = outputMonitorMessage.getOutputPath() + File.separator + outPutFiles[0]; String uniqueID = UUID.randomUUID().toString(); File source = new File(outFilePath); File dest = new File( GridChemProperties.getInstance().getProperty(Constants.TMP_DIR, "") + "/" + uniqueID + ".out"); try { FileUtils.copyFile(source, dest); try { InChIGenerator inChIGenerator = new InChIGenerator(uniqueID); InChI inChI = inChIGenerator.getInChI(); results.put("InChi", inChI.getInchi()); results.put("InChiKey", inChI.getInchiKey()); //running the parser queue serially Map<String, String> parserResult; for (int j = 0; j < gridChemQueueParserses.length; j++) { try { long time = System.currentTimeMillis(); //copying the file to the memory //FIXME make this file shared rather than re-reading it. FileReader fileReader = new FileReader(dest); parserResult = loadAndParse(gridChemQueueParserses[j], fileReader); results.putAll(parserResult); } catch (Exception ex) { logger.error("Parser Failure in " + outputMetadataDTO.getOutputPath() + "/" + outputMetadataDTO.getOutputPath() + " in " + gridChemQueueParserses[j]); } } } catch (Exception ex) { logger.error("Parser Failure in " + outputMetadataDTO.getOutputPath() + "/" + outputMetadataDTO.getExperimentName() + " in InChi Generators"); } } catch (IOException ex) { logger.error("Cannot copy temp file to the tmp directory"); } //adding the custom parsed data to the fileMetaDataObject outputMetadataDTO.setCustomMetaData(results); return outputMetadataDTO; } logger.info("No output file corresponding to the file monitor message location"); return null; } private HashMap<String, String> loadAndParse(String classname, final FileReader reader) throws Exception { ClassLoader classLoader = ClassLoader.getSystemClassLoader(); Class parser = null; try { //todo: handle unparsed documents and log and ignore parser = classLoader.loadClass(classname); Constructor parserConstructor = parser.getConstructor(FileReader.class); GridChemQueueParser queueParser = (GridChemQueueParser) parserConstructor.newInstance(reader); HashMap<String, String> parsedData = queueParser.getParsedData(); return parsedData; } catch (ClassNotFoundException e) { logger.error("Could not load the class ..." + e.getMessage()); } catch (NoSuchMethodException e) { logger.error("Could not load the constructor ... " + e.getMessage()); } catch (InvocationTargetException e) { logger.error("Could not load the Class ... " + e.getMessage()); } catch (InstantiationException e) { logger.error("Could not load the Class ... " + e.getMessage()); } catch (IllegalAccessException e) { logger.error("Could not load the Class ... " + e.getMessage()); } return null; } public String computingResourceName() { return GridChemProperties.getInstance().getProperty(Constants.ARCHIVING_NODE, ""); } public String applicationName() { return GridChemProperties.getInstance().getProperty(Constants.APPLICATION_NAME, ""); } public String getOwnerId() { return GridChemProperties.getInstance().getProperty(Constants.USERNAME, ""); } }