private void log(String s) { fireEventOccurred(new GeneralOutputEvent(s, "")); }
@Override public void start() throws Exception { GeneralOutputEvent goe = new GeneralOutputEvent("Start parsing Phytozome organism...", "[Parser - start()]"); goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe); //parse FASTA, GFF3 and SYNONYM files GenomicParser genomic = new GenomicParser(genomeReg); genomic.start(graph, args, this); goe = new GeneralOutputEvent("Successfully parsed Phytozome.", "[Parser - start()]"); fireEventOccurred(goe); }
private void log(String s) { fireEventOccurred(new GeneralOutputEvent(s, "")); }
@Override public void start() throws PluginConfigurationException { setOptionalArguements(); getInputAndStart(); GeneralOutputEvent so1 = new GeneralOutputEvent( "OXL parsing finished.", "[Parser - start]"); so1.setLog4jLevel(Level.INFO); fireEventOccurred(so1); }
@Override public void start() throws Exception { errorReport = new StringBuffer(); File file = new File( (String) args.getUniqueValue(FileArgumentDefinition.INPUT_FILE)); fireEventOccurred(new GeneralOutputEvent("Parsing " + file.getAbsolutePath(), "[Parser - start]")); parseFile(file); // output optional log file if (args.getOptions().containsKey(ERRORLOG_ARG)) { file = new File((String) args.getUniqueValue(ERRORLOG_ARG)); fireEventOccurred(new GeneralOutputEvent("Saving log to " + file.getAbsolutePath(), "[Parser - start]")); BufferedWriter writer = new BufferedWriter(new FileWriter(file)); writer.write(errorReport.toString()); writer.flush(); writer.close(); } }
/** * Takes a given AbstractONDEXGraph and builds the index around it. * * @param aog * AbstractONDEXGraph * @throws AccessDeniedException */ public void setONDEXGraph(ONDEXGraph aog) throws AccessDeniedException { GeneralOutputEvent so = new GeneralOutputEvent( "Using Lucene with index dir: " + this.indexdir, "[LuceneEnv - setONDEXGraph]"); so.setLog4jLevel(Level.INFO); // todo: fix this - should be configured // externally fireEventOccurred(so); // start indexing indexONDEXGraph(aog, create); // make the ONDEXGraph immutable og = new LuceneONDEXGraph(aog); }
@Override public void start() throws Exception { // get file content InputStream in = new BufferedInputStream(new FileInputStream(args .getUniqueValue(FileArgumentDefinition.INPUT_FILE).toString())); // parse XML content DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder dBuilder = dbFactory.newDocumentBuilder(); Document doc = dBuilder.parse(in); doc.getDocumentElement().normalize(); // get all target elements NodeList nList = doc.getElementsByTagName("target"); // utility class providing XML parsing ChEMBLWrapper wrapper = new ChEMBLWrapper(graph); // iterate over all targets Set<ONDEXConcept> created = new HashSet<ONDEXConcept>(); for (int temp = 0; temp < nList.getLength(); temp++) { Node nNode = nList.item(temp); if (nNode.getNodeType() == Node.ELEMENT_NODE) { Element eElement = (Element) nNode; // parse concept from XML ONDEXConcept c = wrapper.parseTarget(eElement, null); created.add(c); } } fireEventOccurred(new GeneralOutputEvent("Total targets parsed:" + created.size(), getCurrentMethodName())); }
@Override public void start() throws Exception { GeneralOutputEvent goe = new GeneralOutputEvent("Start parsing Poplar genome...", "[Parser - start()]"); goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe); goe = new GeneralOutputEvent("Successfully parsed Poplar genome.", "[Parser - start()]"); fireEventOccurred(goe);
String fileName = ((String) args .getUniqueValue(FileArgumentDefinition.EXPORT_FILE)).trim(); fireEventOccurred(new GeneralOutputEvent( "fileName set to: " + fileName, "[Export - start]")); fireEventOccurred(new GeneralOutputEvent("packed set to: " + packed, "[Export - start]"));
infilesdir = infilesdir + File.separator; GeneralOutputEvent goe = new GeneralOutputEvent( "Reading EC import files...", ONDEXParser.getCurrentMethodName()); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe);
GeneralOutputEvent so = new GeneralOutputEvent( "FillUps between " + targetTaxid + " and " + queryTaxid + " found: " + fillUps,
GeneralOutputEvent goe = new GeneralOutputEvent( "Extract enzyme classes...", ONDEXParser.getCurrentMethodName()); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe); goe = new GeneralOutputEvent("Open file " + filename_ec_classes, ONDEXParser.getCurrentMethodName()); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe); goe = new GeneralOutputEvent("Successfully read file.", ONDEXParser.getCurrentMethodName()); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe); goe = new GeneralOutputEvent("Successfully extracted " + entries.size() + " enzyme classes.", ONDEXParser.getCurrentMethodName()); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe);
.fireEventOccurred(new GeneralOutputEvent( element + " parsed "
public void start() throws InvalidPluginArgumentException { GeneralOutputEvent so = new GeneralOutputEvent("Started TAIR Database Parser...", getCurrentMethodName()); so.setLog4jLevel(Level.INFO); fireEventOccurred(so); File dir = new File((String) args.getUniqueValue(FileArgumentDefinition.INPUT_DIR)); //Get Dir for the tair files: String inFilesDir = dir.getAbsolutePath() + File.separator; //Parse The Genome ParseGenome genome = new ParseGenome(); genome.parseGenome(inFilesDir, graph); boolean parseAnnotation = (Boolean) args.getUniqueValue(ArgumentNames.ANNOTATION); if (parseAnnotation) { //parse protein domain information ParseProtein protDomain = new ParseProtein(); protDomain.parse(inFilesDir, graph, genome.getProteinsMap()); //parse publications ParseAnnotation genePubs = new ParseAnnotation(); genePubs.parse(inFilesDir, graph, genome.getProteinsMap()); } //Parse ... (other things) so = new GeneralOutputEvent("Finished TAIR Database Parser...", getCurrentMethodName()); so.setLog4jLevel(Level.INFO); fireEventOccurred(so); }
/** * Opens XML file to write to. * * @param xmlw * WstxOutputFactory * @return XMLStreamWriter2 * @throws InvalidPluginArgumentException * @throws XMLStreamException * @throws IOException */ protected XMLStreamWriter2 getXMLStreamWriter2(WstxOutputFactory xmlw) throws InvalidPluginArgumentException, XMLStreamException, IOException { // get filename from arguments String fileName = ((String) args .getUniqueValue(FileArgumentDefinition.EXPORT_FILE)).trim(); fireEventOccurred(new GeneralOutputEvent( "fileName set to: " + fileName, "[Export - start]")); if (!fileName.toLowerCase().endsWith(".xml")) { fileName += ".xml"; } File file = new File(fileName); // output file writer outStream = new FileOutputStream(file); // wrap into XML stream XMLStreamWriter2 xmlWriteStream = (XMLStreamWriter2) xmlw .createXMLStreamWriter(outStream, CharsetNames.CS_UTF8); return xmlWriteStream; }
GeneralOutputEvent so = new GeneralOutputEvent( "Using transpath input directory " + dir.getAbsolutePath(), "setONDEXGraph(AbstractONDEXGraph graph)"); so.setLog4jLevel(Level.INFO); fireEventOccurred(so); so = new GeneralOutputEvent("Transpath parsing finished!", "setONDEXGraph(AbstractONDEXGraph graph)"); so.setLog4jLevel(Level.INFO); fireEventOccurred(so);
@Override public void start() throws Exception { // get parser arguments for expanded boolean expanded = (Boolean) args.getUniqueValue(EXPANDED_ARG); // which directory to parse XML files File dir = new File((String) args.getUniqueValue(FileArgumentDefinition.INPUT_DIR)); fireEventOccurred(new GeneralOutputEvent("Parsing files from " + dir.getAbsolutePath(), "[Parser - start]")); // get all xml files from directory File[] files = dir.listFiles(new FileFilter() { @Override public boolean accept(File pathname) { return pathname.getName().endsWith("xml"); } }); // parse every xml file int nbFiles = files.length; for (int i = 0; i < files.length; i++) { parse(files[i], expanded); if (i % 1000 == 0) { fireEventOccurred(new GeneralOutputEvent("Processing finished " + i + " out of " + nbFiles, "[Parser - start]")); } } }
GeneralOutputEvent so = new GeneralOutputEvent( "Using transfac input directory " + dir.getAbsolutePath(), ""); so.setLog4jLevel(Level.INFO); fireEventOccurred(so); so = new GeneralOutputEvent("Transfac parsing finished!", "[Parser - start]"); so.setLog4jLevel(Level.INFO); fireEventOccurred(so);
/** * @see net.sourceforge.ondex.ONDEXPlugin#start() */ public void start() throws PluginException { fetchArguments(); PathNode result = search(); conceptDefaultBitSet = new HashSet<Integer>(); relationDefaultBitSet = new HashSet<Integer>(); if (result != null) { conceptDefaultBitSet.add(result.getCid()); traceBack(result); fireEventOccurred(new GeneralOutputEvent("Finished: Found " + conceptDefaultBitSet.size() + " Concepts and " + relationDefaultBitSet.size() + " Relations", getCurrentMethodName())); } else { ready = true; throw new PluginException("No path exists!"); } ready = true; }
fireEventOccurred(new GeneralOutputEvent( Config.properties .getProperty("persistent.BerkeleyEnv.PreparingDirectory"), "[BerkeleyEnv - constructor]")); if (dir.mkdirs()) fireEventOccurred(new GeneralOutputEvent( Config.properties.getProperty("persistent.BerkeleyEnv.CreatedDirectory") + path, "[BerkeleyEnv - constructor]")); GeneralOutputEvent so = new GeneralOutputEvent( Config.properties.getProperty("persistent.BerkeleyEnv.UsingBerkeley") + path, "[BerkeleyEnv - constructor]"); so.setLog4jLevel(Level.INFO); fireEventOccurred(so);