Example usage for java.io File getAbsolutePath

List of usage examples for java.io File getAbsolutePath

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Introduction

In this page you can find the example usage for java.io File getAbsolutePath.

Prototype

public String getAbsolutePath()

Source Link

Document

Returns the absolute pathname string of this abstract pathname.

Usage

From source file:act.installer.reachablesexplorer.WordCloudGenerator.java

public static void main(String[] args) {

    CLIUtil cliUtil = new CLIUtil(Loader.class, HELP_MESSAGE, OPTION_BUILDERS);
    CommandLine cl = cliUtil.parseCommandLine(args);

    // TODO add possibility to run wordcloud generation as a post processing step, from a loaded reachables database
    File inchisFile = new File(cl.getOptionValue(OPTION_INPUT_INCHIS));
    L2InchiCorpus inchiCorpus = new L2InchiCorpus();
    try {//from   ww w .j  a  v  a2 s.c o  m
        inchiCorpus.loadCorpus(inchisFile);
    } catch (IOException e) {
        cliUtil.failWithMessage("Could not load inchi corpus from input file %s", inchisFile.getAbsolutePath());
    }
    WordCloudGenerator wordCloudGenerator = new WordCloudGenerator(
            cl.getOptionValue(OPTION_DB_HOST, DEFAULT_HOST),
            Integer.parseInt(cl.getOptionValue(OPTION_DB_PORT, DEFAULT_PORT)),
            cl.getOptionValue(OPTION_INSTALLER_SOURCE_DB, DEFAULT_CHEMICALS_DATABASE),
            cl.getOptionValue(OPTION_RENDERING_CACHE, DEFAULT_ASSETS_LOCATION),
            cl.getOptionValue(OPTION_RSCRIPT_EXE_PATH, RSCRIPT_EXE_PATH));
    inchiCorpus.getInchiList().forEach(wordCloudGenerator::generateWordCloud);
}

From source file:iac.cnr.it.TestSearcher.java

public static void main(String[] args) throws IOException, ParseException {
    /** Command line parser and options */
    CommandLineParser parser = new PosixParser();

    Options options = new Options();
    options.addOption(OPT_INDEX, true, "Index path");
    options.addOption(OPT_QUERY, true, "The query");

    CommandLine cmd = null;/*  w  w w .  ja v  a  2s. c  o m*/
    try {
        cmd = parser.parse(options, args);
    } catch (org.apache.commons.cli.ParseException e) {
        logger.fatal("Error while parsing command line arguments");
        System.exit(1);
    }

    /** Check for mandatory options */
    if (!cmd.hasOption(OPT_INDEX) || !cmd.hasOption(OPT_QUERY)) {
        usage();
        System.exit(0);
    }

    /** Read options */
    File casePath = new File(cmd.getOptionValue(OPT_INDEX));
    String query = cmd.getOptionValue(OPT_QUERY);

    /** Check correctness of the path containing an ISODAC case */
    if (!casePath.exists() || !casePath.isDirectory()) {
        logger.fatal("The case directory \"" + casePath.getAbsolutePath() + "\" is not valid");
        System.exit(1);
    }

    /** Check existance of the info.dat file */
    File infoFile = new File(casePath, INFO_FILENAME);
    if (!infoFile.exists()) {
        logger.fatal("Can't find " + INFO_FILENAME + " within the case directory (" + casePath + ")");
        System.exit(1);
    }

    /** Load the mapping image_uuid --> image_filename */
    imagesMap = new HashMap<Integer, String>();
    BufferedReader reader = new BufferedReader(new FileReader(infoFile));
    while (reader.ready()) {
        String line = reader.readLine();

        logger.info("Read the line: " + line);
        String currentID = line.split("\t")[0];
        String currentImgFile = line.split("\t")[1];
        imagesMap.put(Integer.parseInt(currentID), currentImgFile);
        logger.info("ID: " + currentID + " - IMG: " + currentImgFile + " added to the map");

    }
    reader.close();

    /** Load all the directories containing an index */
    ArrayList<String> indexesDirs = new ArrayList<String>();
    for (File f : casePath.listFiles()) {
        logger.info("Analyzing: " + f);
        if (f.isDirectory())
            indexesDirs.add(f.getAbsolutePath());
    }
    logger.info(indexesDirs.size() + " directories found!");

    /** Set-up the searcher */
    Searcher searcher = null;
    try {
        String[] array = indexesDirs.toArray(new String[indexesDirs.size()]);
        searcher = new Searcher(array);
        TopDocs results = searcher.search(query, Integer.MAX_VALUE);

        ScoreDoc[] hits = results.scoreDocs;
        int numTotalHits = results.totalHits;

        System.out.println(numTotalHits + " total matching documents");

        for (int i = 0; i < numTotalHits; i++) {
            Document doc = searcher.doc(hits[i].doc);

            String path = doc.get(FIELD_PATH);
            String filename = doc.get(FIELD_FILENAME);
            String image_uuid = doc.get(FIELD_IMAGE_ID);

            if (path != null) {
                //System.out.println((i + 1) + ". " + path + File.separator + filename + " - score: " + hits[i].score);
                //               System.out.println((i + 1) + ". " + path + File.separator + filename + " - image_file: " + image_uuid);
                System.out.println((i + 1) + ". " + path + File.separator + filename + " - image_file: "
                        + imagesMap.get(Integer.parseInt(image_uuid)));
            } else {
                System.out.println((i + 1) + ". " + "No path for this document");
            }
        }

    } catch (Exception e) {
        System.err.println("An error occurred: " + e.getMessage());
        e.printStackTrace();
    } finally {
        if (searcher != null)
            searcher.close();
    }
}

From source file:it.geosolutions.imageio.plugins.nitronitf.ImageIOUtils.java

public static void main(String[] args) {
    List<File> files = getFiles(new String[] { "c:/", "c:/dev/" }, new String[] { "jpg" });
    for (File file : files) {
        log.info(file.getAbsolutePath());
    }// ww w .j  a v  a  2  s.c  om
}

From source file:com.act.analysis.surfactant.SurfactantLabeler.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());//  w w w . j  a  v  a  2  s  .co  m
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        return;
    }

    File inputFile = new File(cl.getOptionValue(OPTION_INPUT_FILE));
    if (!inputFile.isFile()) {
        System.err.format("No input file at: %s\n", inputFile.getAbsolutePath());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_FILE));
    if (outputFile.exists()) {
        System.err.format("WARNING: output file at %s already exists\n", outputFile.getAbsolutePath());
    }

    /* Sometimes the InChIs might not appear in the input file (like in regression results).  Instead a corpus of
     * names and InChIs can be specified in a separate file and looked up as molecules are read/visualized.  The join
     * field is the key on which the InChI for a given row in the input file is found. */
    File inchiSourceFile = null;
    if (cl.hasOption(OPTION_INCHI_SOURCE)) {
        inchiSourceFile = new File(cl.getOptionValue(OPTION_INCHI_SOURCE));
        boolean err = false;
        if (!inchiSourceFile.isFile()) {
            System.err.format("No inchi source file at: %s\n", inchiSourceFile.getAbsolutePath());
            err = true;
        }
        if (!cl.hasOption(OPTION_INCHI_SOURCE_JOIN_FIELD)) {
            System.err.format("Must specify a join field when using an inchi source file.\n");
            err = true;
        }
        if (err) {
            HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts,
                    null, true);
            System.exit(1);
        }
    }

    SurfactantLabeler surfactantLabeler = new SurfactantLabeler();
    surfactantLabeler.runAnalysis(cl.getOptionValue(OPTION_LICENSE_FILE), inputFile, outputFile,
            inchiSourceFile, cl.getOptionValue(OPTION_INCHI_SOURCE_JOIN_FIELD));
}

From source file:Inmemantlr.java

public static void main(String[] args) {
    LOGGER.info("Inmemantlr tool");

    HelpFormatter hformatter = new HelpFormatter();

    Options options = new Options();

    // Binary arguments
    options.addOption("h", "print this message");

    Option grmr = Option.builder().longOpt("grmrfiles").hasArgs().desc("comma-separated list of ANTLR files")
            .required(true).argName("grmrfiles").type(String.class).valueSeparator(',').build();

    Option infiles = Option.builder().longOpt("infiles").hasArgs()
            .desc("comma-separated list of files to parse").required(true).argName("infiles").type(String.class)
            .valueSeparator(',').build();

    Option utilfiles = Option.builder().longOpt("utilfiles").hasArgs()
            .desc("comma-separated list of utility files to be added for " + "compilation").required(false)
            .argName("utilfiles").type(String.class).valueSeparator(',').build();

    Option odir = Option.builder().longOpt("outdir")
            .desc("output directory in which the dot files will be " + "created").required(false).hasArg(true)
            .argName("outdir").type(String.class).build();

    options.addOption(infiles);/*from w w  w  .  j a v  a2s.c  o  m*/
    options.addOption(grmr);
    options.addOption(utilfiles);
    options.addOption(odir);

    CommandLineParser parser = new DefaultParser();

    CommandLine cmd = null;

    try {
        cmd = parser.parse(options, args);
        if (cmd.hasOption('h')) {
            hformatter.printHelp("java -jar inmemantlr.jar", options);
            System.exit(0);
        }
    } catch (ParseException e) {
        hformatter.printHelp("java -jar inmemantlr.jar", options);
        LOGGER.error(e.getMessage());
        System.exit(-1);
    }

    // input files
    Set<File> ins = getFilesForOption(cmd, "infiles");
    // grammar files
    Set<File> gs = getFilesForOption(cmd, "grmrfiles");
    // utility files
    Set<File> uf = getFilesForOption(cmd, "utilfiles");
    // output dir
    Set<File> od = getFilesForOption(cmd, "outdir");

    if (od.size() > 1) {
        LOGGER.error("output directories must be less than or equal to 1");
        System.exit(-1);
    }

    if (ins.size() <= 0) {
        LOGGER.error("no input files were specified");
        System.exit(-1);
    }

    if (gs.size() <= 0) {
        LOGGER.error("no grammar files were specified");
        System.exit(-1);
    }

    LOGGER.info("create generic parser");
    GenericParser gp = null;
    try {
        gp = new GenericParser(gs.toArray(new File[gs.size()]));
    } catch (FileNotFoundException e) {
        LOGGER.error(e.getMessage());
        System.exit(-1);
    }

    if (!uf.isEmpty()) {
        try {
            gp.addUtilityJavaFiles(uf.toArray(new String[uf.size()]));
        } catch (FileNotFoundException e) {
            LOGGER.error(e.getMessage());
            System.exit(-1);
        }
    }

    LOGGER.info("create and add parse tree listener");
    DefaultTreeListener dt = new DefaultTreeListener();
    gp.setListener(dt);

    LOGGER.info("compile generic parser");
    try {
        gp.compile();
    } catch (CompilationException e) {
        LOGGER.error("cannot compile generic parser: {}", e.getMessage());
        System.exit(-1);
    }

    String fpfx = "";
    for (File of : od) {
        if (!of.exists() || !of.isDirectory()) {
            LOGGER.error("output directory does not exist or is not a " + "directory");
            System.exit(-1);
        }
        fpfx = of.getAbsolutePath();
    }

    Ast ast;
    for (File f : ins) {
        try {
            gp.parse(f);
        } catch (IllegalWorkflowException | FileNotFoundException e) {
            LOGGER.error(e.getMessage());
            System.exit(-1);
        }
        ast = dt.getAst();

        if (!fpfx.isEmpty()) {
            String of = fpfx + "/" + FilenameUtils.removeExtension(f.getName()) + ".dot";

            LOGGER.info("write file {}", of);

            try {
                FileUtils.writeStringToFile(new File(of), ast.toDot(), "UTF-8");
            } catch (IOException e) {
                LOGGER.error(e.getMessage());
                System.exit(-1);
            }
        } else {
            LOGGER.info("Tree for {} \n {}", f.getName(), ast.toDot());
        }
    }

    System.exit(0);
}

From source file:eu.fbk.dkm.sectionextractor.WikipediaSectionTitlesExtractor.java

public static void main(String args[]) throws IOException {

    CommandLineWithLogger commandLineWithLogger = new CommandLineWithLogger();
    commandLineWithLogger.addOption(OptionBuilder.withArgName("file").hasArg()
            .withDescription("wikipedia xml dump file").isRequired().withLongOpt("wikipedia-dump").create("d"));
    commandLineWithLogger.addOption(OptionBuilder.withArgName("file").hasArg().withDescription("Filter file")
            .withLongOpt("filter").create("f"));
    commandLineWithLogger.addOption(OptionBuilder.withArgName("dir").hasArg().withDescription("output file")
            .isRequired().withLongOpt("output-file").create("o"));
    commandLineWithLogger.addOption(OptionBuilder.withArgName("int").hasArg()
            .withDescription("max depth (default " + MAX_DEPTH + ")").withLongOpt("max-depth").create("m"));
    commandLineWithLogger.addOption(OptionBuilder.withArgName("int").hasArg()
            .withDescription("max num of sections").withLongOpt("max-num").create("n"));
    commandLineWithLogger.addOption(new Option("l", "print titles"));

    commandLineWithLogger.addOption(OptionBuilder.withArgName("int").hasArg()
            .withDescription(//from   w w w  .  jav a  2 s. c  o  m
                    "number of threads (default " + AbstractWikipediaXmlDumpParser.DEFAULT_THREADS_NUMBER + ")")
            .withLongOpt("num-threads").create("t"));
    commandLineWithLogger.addOption(OptionBuilder.withArgName("int").hasArg()
            .withDescription("number of pages to process (default all)").withLongOpt("num-pages").create("p"));
    commandLineWithLogger.addOption(OptionBuilder.withArgName("int").hasArg()
            .withDescription("receive notification every n pages (default "
                    + AbstractWikipediaExtractor.DEFAULT_NOTIFICATION_POINT + ")")
            .withLongOpt("notification-point").create("b"));

    CommandLine commandLine = null;
    try {
        commandLine = commandLineWithLogger.getCommandLine(args);
        PropertyConfigurator.configure(commandLineWithLogger.getLoggerProps());
    } catch (Exception e) {
        System.exit(1);
    }

    int numThreads = Integer.parseInt(commandLine.getOptionValue("num-threads",
            Integer.toString(AbstractWikipediaXmlDumpParser.DEFAULT_THREADS_NUMBER)));
    int numPages = Integer.parseInt(commandLine.getOptionValue("num-pages",
            Integer.toString(AbstractWikipediaExtractor.DEFAULT_NUM_PAGES)));
    int notificationPoint = Integer.parseInt(commandLine.getOptionValue("notification-point",
            Integer.toString(AbstractWikipediaExtractor.DEFAULT_NOTIFICATION_POINT)));

    int configuredDepth = Integer
            .parseInt(commandLine.getOptionValue("max-depth", Integer.toString(MAX_DEPTH)));
    int maxNum = Integer.parseInt(commandLine.getOptionValue("max-num", "0"));
    boolean printTitles = commandLine.hasOption("l");

    HashSet<String> pagesToConsider = null;
    String filterFileName = commandLine.getOptionValue("filter");
    if (filterFileName != null) {
        File filterFile = new File(filterFileName);
        if (filterFile.exists()) {
            pagesToConsider = new HashSet<>();
            List<String> lines = Files.readLines(filterFile, Charsets.UTF_8);
            for (String line : lines) {
                line = line.trim();
                if (line.length() == 0) {
                    continue;
                }

                line = line.replaceAll("\\s+", "_");

                pagesToConsider.add(line);
            }
        }
    }

    File outputFile = new File(commandLine.getOptionValue("output-file"));
    ExtractorParameters extractorParameters = new ExtractorParameters(
            commandLine.getOptionValue("wikipedia-dump"), outputFile.getAbsolutePath());

    WikipediaExtractor wikipediaPageParser = new WikipediaSectionTitlesExtractor(numThreads, numPages,
            extractorParameters.getLocale(), outputFile, configuredDepth, maxNum, printTitles, pagesToConsider);
    wikipediaPageParser.setNotificationPoint(notificationPoint);
    wikipediaPageParser.start(extractorParameters);

    logger.info("extraction ended " + new Date());

}

From source file:com.act.biointerpretation.BiointerpretationDriver.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*w  ww.  ja va2 s.c om*/
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(ReactionDesalter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    if (cl.hasOption(OPTION_CONFIGURATION_FILE)) {
        List<BiointerpretationStep> steps;
        File configFile = new File(cl.getOptionValue(OPTION_CONFIGURATION_FILE));
        if (!configFile.exists()) {
            String msg = String.format("Cannot find configuration file at %s", configFile.getAbsolutePath());
            LOGGER.error(msg);
            throw new RuntimeException(msg);
        }
        // Read the whole config file.
        try (InputStream is = new FileInputStream(configFile)) {
            steps = OBJECT_MAPPER.readValue(is, new TypeReference<List<BiointerpretationStep>>() {
            });
        } catch (IOException e) {
            LOGGER.error("Caught IO exception when attempting to read configuration file: %s", e.getMessage());
            throw e; // Crash after logging if the config file can't be read.
        }

        // Ask for explicit confirmation before dropping databases.
        LOGGER.info("Biointerpretation plan:");
        for (BiointerpretationStep step : steps) {
            crashIfInvalidDBName(step.getReadDBName());
            crashIfInvalidDBName(step.getWriteDBName());
            LOGGER.info("%s: %s -> %s", step.getOperation(), step.getReadDBName(), step.getWriteDBName());
        }
        LOGGER.warn("WARNING: each DB to be written will be dropped before the writing step commences");
        LOGGER.info("Proceed? [y/n]");
        String readLine;
        try (BufferedReader reader = new BufferedReader(new InputStreamReader(System.in))) {
            readLine = reader.readLine();
        }
        readLine.trim();
        if ("y".equalsIgnoreCase(readLine) || "yes".equalsIgnoreCase(readLine)) {
            LOGGER.info("Biointerpretation plan confirmed, commencing");
            for (BiointerpretationStep step : steps) {
                performOperation(step, true);
            }
            LOGGER.info("Biointerpretation plan completed");
        } else {
            LOGGER.info("Biointerpretation plan not confirmed, exiting");
        }
    } else if (cl.hasOption(OPTION_SINGLE_OPERATION)) {
        if (!cl.hasOption(OPTION_SINGLE_READ_DB) || !cl.hasOption(OPTION_SINGLE_WRITE_DB)) {
            String msg = "Must specify read and write DB names when performing a single operation";
            LOGGER.error(msg);
            throw new RuntimeException(msg);
        }
        BiointerpretationOperation operation;
        try {
            operation = BiointerpretationOperation.valueOf(cl.getOptionValue(OPTION_SINGLE_OPERATION));
        } catch (IllegalArgumentException e) {
            LOGGER.error("Caught IllegalArgumentException when trying to parse operation '%s': %s",
                    cl.getOptionValue(OPTION_SINGLE_OPERATION), e.getMessage());
            throw e; // Crash if we can't interpret the operation.
        }
        String readDB = crashIfInvalidDBName(cl.getOptionValue(OPTION_SINGLE_READ_DB));
        String writeDB = crashIfInvalidDBName(cl.getOptionValue(OPTION_SINGLE_WRITE_DB));

        performOperation(new BiointerpretationStep(operation, readDB, writeDB), false);
    } else {
        String msg = "Must specify either a config file or a single operation to perform.";
        LOGGER.error(msg);
        throw new RuntimeException(msg);
    }
}

From source file:co.cask.cdap.cli.CLIMain.java

public static void main(String[] args) {
    final PrintStream output = System.out;

    Options options = getOptions();/*from  w  ww.j  a va  2  s  .c o  m*/
    CLIMainArgs cliMainArgs = CLIMainArgs.parse(args, options);

    CommandLineParser parser = new BasicParser();
    try {
        CommandLine command = parser.parse(options, cliMainArgs.getOptionTokens());
        if (command.hasOption(HELP_OPTION.getOpt())) {
            usage();
            System.exit(0);
        }

        LaunchOptions launchOptions = LaunchOptions.builder()
                .setUri(command.getOptionValue(URI_OPTION.getOpt(), getDefaultURI().toString()))
                .setDebug(command.hasOption(DEBUG_OPTION.getOpt()))
                .setVerifySSL(parseBooleanOption(command, VERIFY_SSL_OPTION, DEFAULT_VERIFY_SSL))
                .setAutoconnect(parseBooleanOption(command, AUTOCONNECT_OPTION, DEFAULT_AUTOCONNECT)).build();

        String scriptFile = command.getOptionValue(SCRIPT_OPTION.getOpt(), "");
        boolean hasScriptFile = command.hasOption(SCRIPT_OPTION.getOpt());

        String[] commandArgs = cliMainArgs.getCommandTokens();

        try {
            ClientConfig clientConfig = ClientConfig.builder().setConnectionConfig(null).build();
            final CLIConfig cliConfig = new CLIConfig(clientConfig, output, new AltStyleTableRenderer());
            CLIMain cliMain = new CLIMain(launchOptions, cliConfig);
            CLI cli = cliMain.getCLI();

            cliMain.tryAutoconnect();

            CLIConnectionConfig connectionConfig = new CLIConnectionConfig(
                    cliConfig.getClientConfig().getConnectionConfig(), Id.Namespace.DEFAULT, null);
            cliMain.updateCLIPrompt(connectionConfig);

            if (hasScriptFile) {
                File script = cliMain.getFilePathResolver().resolvePathToFile(scriptFile);
                if (!script.exists()) {
                    output.println("ERROR: Script file '" + script.getAbsolutePath() + "' does not exist");
                    System.exit(1);
                }
                List<String> scriptLines = Files.readLines(script, Charsets.UTF_8);
                for (String scriptLine : scriptLines) {
                    output.print(cliMain.getPrompt(connectionConfig));
                    output.println(scriptLine);
                    cli.execute(scriptLine, output);
                    output.println();
                }
            } else if (commandArgs.length == 0) {
                cli.startInteractiveMode(output);
            } else {
                cli.execute(Joiner.on(" ").join(commandArgs), output);
            }
        } catch (Exception e) {
            e.printStackTrace(output);
        }
    } catch (ParseException e) {
        output.println(e.getMessage());
        usage();
    }
}

From source file:com.act.lcms.db.io.PrintConstructInfo.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*from   w  ww . j  a v a  2  s. co  m*/
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        return;
    }

    File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY));
    if (!lcmsDir.isDirectory()) {
        System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    try (DB db = DB.openDBFromCLI(cl)) {
        System.out.print("Loading/updating LCMS scan files into DB\n");
        ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir);

        String construct = cl.getOptionValue(OPTION_CONSTRUCT);
        List<LCMSWell> lcmsWells = LCMSWell.getInstance().getByConstructID(db, construct);
        Collections.sort(lcmsWells, new Comparator<LCMSWell>() {
            @Override
            public int compare(LCMSWell o1, LCMSWell o2) {
                return o1.getId().compareTo(o2.getId());
            }
        });

        Set<String> uniqueMSIDs = new HashSet<>();
        Map<Integer, Plate> platesById = new HashMap<>();

        System.out.format("\n\n-- Construct %s --\n\n", construct);

        List<ChemicalAssociatedWithPathway> pathwayChems = ChemicalAssociatedWithPathway.getInstance()
                .getChemicalsAssociatedWithPathwayByConstructId(db, construct);
        System.out.print("Chemicals associated with pathway:\n");
        System.out.format("  %-8s%-15s%-45s\n", "index", "kind", "chemical");
        for (ChemicalAssociatedWithPathway chem : pathwayChems) {
            System.out.format("  %-8d%-15s%-45s\n", chem.getIndex(), chem.getKind(), chem.getChemical());
        }

        System.out.print("\nLCMS wells:\n");
        System.out.format("  %-15s%-6s%-15s%-15s%-15s\n", "barcode", "well", "msid", "fed", "lcms_count");
        for (LCMSWell well : lcmsWells) {
            uniqueMSIDs.add(well.getMsid());

            Plate p = platesById.get(well.getPlateId());
            if (p == null) {
                // TODO: migrate Plate to be a subclass of BaseDBModel.
                p = Plate.getPlateById(db, well.getPlateId());
                platesById.put(p.getId(), p);
            }

            String chem = well.getChemical();
            List<ScanFile> scanFiles = ScanFile.getScanFileByPlateIDRowAndColumn(db, p.getId(),
                    well.getPlateRow(), well.getPlateColumn());

            System.out.format("  %-15s%-6s%-15s%-15s%-15d\n", p.getBarcode(), well.getCoordinatesString(),
                    well.getMsid(), chem == null || chem.isEmpty() ? "--" : chem, scanFiles.size());
            System.out.flush();
        }

        List<Integer> plateIds = Arrays.asList(platesById.keySet().toArray(new Integer[platesById.size()]));
        Collections.sort(plateIds);
        System.out.print("\nAppears in plates:\n");
        for (Integer id : plateIds) {
            Plate p = platesById.get(id);
            System.out.format("  %s: %s\n", p.getBarcode(), p.getName());
        }

        List<String> msids = Arrays.asList(uniqueMSIDs.toArray(new String[uniqueMSIDs.size()]));
        Collections.sort(msids);
        System.out.format("\nMSIDS: %s\n", StringUtils.join(msids, ", "));

        Set<String> availableNegativeControls = new HashSet<>();
        for (Map.Entry<Integer, Plate> entry : platesById.entrySet()) {
            List<LCMSWell> wells = LCMSWell.getInstance().getByPlateId(db, entry.getKey());
            for (LCMSWell well : wells) {
                if (!construct.equals(well.getComposition())) {
                    availableNegativeControls.add(well.getComposition());
                }
            }
        }

        // Print available standards for each step w/ plate barcodes and coordinates.
        System.out.format("\nAvailable Standards:\n");
        Map<Integer, Plate> plateCache = new HashMap<>();
        for (ChemicalAssociatedWithPathway chem : pathwayChems) {
            List<StandardWell> matchingWells = StandardWell.getInstance().getStandardWellsByChemical(db,
                    chem.getChemical());
            for (StandardWell well : matchingWells) {
                if (!plateCache.containsKey(well.getPlateId())) {
                    Plate p = Plate.getPlateById(db, well.getPlateId());
                    plateCache.put(p.getId(), p);
                }
            }
            Map<Integer, List<StandardWell>> standardWellsByPlateId = new HashMap<>();
            for (StandardWell well : matchingWells) {
                List<StandardWell> plateWells = standardWellsByPlateId.get(well.getPlateId());
                if (plateWells == null) {
                    plateWells = new ArrayList<>();
                    standardWellsByPlateId.put(well.getPlateId(), plateWells);
                }
                plateWells.add(well);
            }
            List<Pair<String, Integer>> plateBarcodes = new ArrayList<>(plateCache.size());
            for (Plate p : plateCache.values()) {
                if (p.getBarcode() == null) {
                    plateBarcodes.add(Pair.of("(no barcode)", p.getId()));
                } else {
                    plateBarcodes.add(Pair.of(p.getBarcode(), p.getId()));
                }
            }
            Collections.sort(plateBarcodes);
            System.out.format("  %s:\n", chem.getChemical());
            for (Pair<String, Integer> barcodePair : plateBarcodes) {
                // TODO: hoist this whole sorting/translation step into a utility class.
                List<StandardWell> wells = standardWellsByPlateId.get(barcodePair.getRight());
                if (wells == null) {
                    // Don't print plates that don't apply to this chemical, which can happen because we're caching the plates.
                    continue;
                }
                Collections.sort(wells, new Comparator<StandardWell>() {
                    @Override
                    public int compare(StandardWell o1, StandardWell o2) {
                        int c = o1.getPlateRow().compareTo(o2.getPlateRow());
                        if (c != 0)
                            return c;
                        return o1.getPlateColumn().compareTo(o2.getPlateColumn());
                    }
                });
                List<String> descriptions = new ArrayList<>(wells.size());
                for (StandardWell well : wells) {
                    descriptions.add(String.format("%s in %s%s", well.getCoordinatesString(), well.getMedia(),
                            well.getConcentration() == null ? ""
                                    : String.format(" c. %f", well.getConcentration())));
                }
                System.out.format("    %s: %s\n", barcodePair.getLeft(), StringUtils.join(descriptions, ", "));
            }
        }

        List<String> negativeControlStrains = Arrays
                .asList(availableNegativeControls.toArray(new String[availableNegativeControls.size()]));
        Collections.sort(negativeControlStrains);
        System.out.format("\nAvailable negative controls: %s\n", StringUtils.join(negativeControlStrains, ","));
        System.out.print("\n----------\n");
        System.out.print("\n\n");
    }
}

From source file:apps.LuceneIndexer.java

public static void main(String[] args) {
    Options options = new Options();

    options.addOption("i", null, true, "input file");
    options.addOption("o", null, true, "output directory");
    options.addOption("r", null, true, "optional output TREC-format QREL file");

    options.addOption("bm25_b", null, true, "BM25 parameter: b");
    options.addOption("bm25_k1", null, true, "BM25 parameter: k1");
    options.addOption("bm25fixed", null, false, "use the fixed BM25 similarity");

    Joiner commaJoin = Joiner.on(',');
    Joiner spaceJoin = Joiner.on(' ');

    options.addOption("source_type", null, true,
            "document source type: " + commaJoin.join(SourceFactory.getDocSourceList()));

    // If you increase this value, you may need to modify the following line in *.sh file
    // export MAVEN_OPTS="-Xms8192m -server"
    double ramBufferSizeMB = 1024 * 8; // 8 GB

    CommandLineParser parser = new org.apache.commons.cli.GnuParser();

    IndexWriter indexWriter = null;//from  www . j a va2  s .  c  om
    BufferedWriter qrelWriter = null;

    int docNum = 0;

    try {
        CommandLine cmd = parser.parse(options, args);

        String inputFileName = null, outputDirName = null, qrelFileName = null;

        if (cmd.hasOption("i")) {
            inputFileName = cmd.getOptionValue("i");
        } else {
            Usage("Specify 'input file'", options);
        }

        if (cmd.hasOption("o")) {
            outputDirName = cmd.getOptionValue("o");
        } else {
            Usage("Specify 'index directory'", options);
        }

        if (cmd.hasOption("r")) {
            qrelFileName = cmd.getOptionValue("r");
        }

        String sourceName = cmd.getOptionValue("source_type");

        if (sourceName == null)
            Usage("Specify document source type", options);

        if (qrelFileName != null)
            qrelWriter = new BufferedWriter(new FileWriter(qrelFileName));

        File outputDir = new File(outputDirName);
        if (!outputDir.exists()) {
            if (!outputDir.mkdirs()) {
                System.out.println("couldn't create " + outputDir.getAbsolutePath());
                System.exit(1);
            }
        }
        if (!outputDir.isDirectory()) {
            System.out.println(outputDir.getAbsolutePath() + " is not a directory!");
            System.exit(1);
        }
        if (!outputDir.canWrite()) {
            System.out.println("Can't write to " + outputDir.getAbsolutePath());
            System.exit(1);
        }

        boolean useFixedBM25 = cmd.hasOption("bm25fixed");

        float bm25_k1 = UtilConst.BM25_K1_DEFAULT, bm25_b = UtilConst.BM25_B_DEFAULT;

        if (cmd.hasOption("bm25_k1")) {
            try {
                bm25_k1 = Float.parseFloat(cmd.getOptionValue("bm25_k1"));
            } catch (NumberFormatException e) {
                Usage("Wrong format for 'bm25_k1'", options);
            }
        }

        if (cmd.hasOption("bm25_b")) {
            try {
                bm25_b = Float.parseFloat(cmd.getOptionValue("bm25_b"));
            } catch (NumberFormatException e) {
                Usage("Wrong format for 'bm25_b'", options);
            }
        }

        EnglishAnalyzer analyzer = new EnglishAnalyzer();
        FSDirectory indexDir = FSDirectory.open(Paths.get(outputDirName));
        IndexWriterConfig indexConf = new IndexWriterConfig(analyzer);

        /*
            OpenMode.CREATE creates a new index or overwrites an existing one.
            https://lucene.apache.org/core/6_0_0/core/org/apache/lucene/index/IndexWriterConfig.OpenMode.html#CREATE
        */
        indexConf.setOpenMode(OpenMode.CREATE);
        indexConf.setRAMBufferSizeMB(ramBufferSizeMB);

        System.out.println(String.format("BM25 parameters k1=%f b=%f ", bm25_k1, bm25_b));

        if (useFixedBM25) {
            System.out.println(String.format("Using fixed BM25Simlarity, k1=%f b=%f", bm25_k1, bm25_b));
            indexConf.setSimilarity(new BM25SimilarityFix(bm25_k1, bm25_b));
        } else {
            System.out.println(String.format("Using Lucene BM25Similarity, k1=%f b=%f", bm25_k1, bm25_b));
            indexConf.setSimilarity(new BM25Similarity(bm25_k1, bm25_b));
        }

        indexWriter = new IndexWriter(indexDir, indexConf);

        DocumentSource inpDocSource = SourceFactory.createDocumentSource(sourceName, inputFileName);
        DocumentEntry inpDoc = null;
        TextCleaner textCleaner = new TextCleaner(null);

        while ((inpDoc = inpDocSource.next()) != null) {
            ++docNum;

            Document luceneDoc = new Document();
            ArrayList<String> cleanedToks = textCleaner.cleanUp(inpDoc.mDocText);
            String cleanText = spaceJoin.join(cleanedToks);

            //        System.out.println(inpDoc.mDocId);
            //        System.out.println(cleanText);
            //        System.out.println("==============================");

            luceneDoc.add(new StringField(UtilConst.FIELD_ID, inpDoc.mDocId, Field.Store.YES));
            luceneDoc.add(new TextField(UtilConst.FIELD_TEXT, cleanText, Field.Store.YES));
            indexWriter.addDocument(luceneDoc);

            if (inpDoc.mIsRel != null && qrelWriter != null) {
                saveQrelOneEntry(qrelWriter, inpDoc.mQueryId, inpDoc.mDocId, inpDoc.mIsRel ? MAX_GRADE : 0);
            }
            if (docNum % 1000 == 0)
                System.out.println(String.format("Indexed %d documents", docNum));

        }

    } catch (ParseException e) {
        e.printStackTrace();
        Usage("Cannot parse arguments" + e, options);
    } catch (Exception e) {
        System.err.println("Terminating due to an exception: " + e);
        System.exit(1);
    } finally {
        System.out.println(String.format("Indexed %d documents", docNum));

        try {
            if (null != indexWriter)
                indexWriter.close();
            if (null != qrelWriter)
                qrelWriter.close();
        } catch (IOException e) {
            System.err.println("IO exception: " + e);
            e.printStackTrace();
        }
    }
}