Examples with DefaultParser org.apache.commons.cli.DefaultParser used on opensource projects

Example 91 with DefaultParser

use of org.apache.commons.cli.DefaultParser in project MassBank-web by MassBank.

the class Validator method main.

public static void main(String[] arguments) {
    // load version and print
    final Properties properties = new Properties();
    try {
        properties.load(ClassLoader.getSystemClassLoader().getResourceAsStream("project.properties"));
    } catch (IOException e) {
        e.printStackTrace();
        System.exit(1);
    }
    System.out.println("Validator version: " + properties.getProperty("version"));
    // parse command line
    Options options = new Options();
    options.addOption(null, "db", false, "also read record from database and compare with original Record; Developer Feature!");
    options.addOption(null, "legacy", false, "less strict mode for legacy records with minor problems.");
    options.addOption(null, "online", false, "also do online checks, like PubChem CID check.");
    CommandLine cmd = null;
    try {
        cmd = new DefaultParser().parse(options, arguments);
    } catch (ParseException e) {
        // oops, something went wrong
        System.err.println("Parsing command line failed. Reason: " + e.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("Validator [OPTIONS] <FILE|DIR> [<FILE|DIR> ...]", options);
        System.exit(1);
    }
    if (cmd.getArgList().size() == 0) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("Validator [OPTIONS] <FILE|DIR> [<FILE|DIR> ...]", options);
        System.exit(1);
    }
    if (cmd.hasOption("legacy"))
        System.out.println("Validation mode: legacy");
    // find all files in arguments and all *.txt files in directories and subdirectories
    // specified in arguments
    List<File> recordfiles = new ArrayList<>();
    for (String argument : cmd.getArgList()) {
        File argumentf = new File(argument);
        if (argumentf.isFile() && FilenameUtils.getExtension(argument).equals("txt")) {
            recordfiles.add(argumentf);
        } else if (argumentf.isDirectory()) {
            recordfiles.addAll(FileUtils.listFiles(argumentf, new String[] { "txt" }, true));
        } else {
            logger.warn("Argument " + argument + " could not be processed.");
        }
    }
    if (recordfiles.size() == 0) {
        logger.error("No files found for validation.");
        System.exit(1);
    }
    // validate all files
    logger.trace("Validating " + recordfiles.size() + " files");
    AtomicBoolean haserror = new AtomicBoolean(false);
    AtomicBoolean doDatbase = new AtomicBoolean(cmd.hasOption("db"));
    AtomicBoolean legacyMode = new AtomicBoolean(cmd.hasOption("legacy"));
    AtomicBoolean onlineMode = new AtomicBoolean(cmd.hasOption("online"));
    List<String> accessions = recordfiles.parallelStream().map(filename -> {
        String recordString;
        String accession = null;
        logger.info("Working on " + filename + ".");
        try {
            recordString = FileUtils.readFileToString(filename, StandardCharsets.UTF_8);
            if (hasNonStandardChars(recordString)) {
                logger.warn("Check " + filename + ".");
            }
            ;
            // basic validation
            Set<String> config = new HashSet<String>();
            if (legacyMode.get())
                config.add("legacy");
            if (onlineMode.get())
                config.add("online");
            Record record = validate(recordString, "", config);
            if (record == null) {
                logger.error("Error in \'" + filename + "\'.");
                haserror.set(true);
            } else // additional tests
            {
                logger.trace("validation passed for " + filename);
                // compare ACCESSION with filename
                accession = record.ACCESSION();
                if (!accession.equals(FilenameUtils.getBaseName(filename.toString()))) {
                    logger.error("Error in \'" + filename.getName().toString() + "\'.");
                    logger.error("ACCESSION \'" + record.ACCESSION() + "\' does not match filename \'" + filename.getName().toString() + "\'");
                    haserror.set(true);
                }
                // validate correct serialization: String <-> (String -> Record class -> String)
                String recordStringFromRecord = record.toString();
                int position = StringUtils.indexOfDifference(new String[] { recordString, recordStringFromRecord });
                if (position != -1) {
                    logger.error("Error in \'" + filename + "\'.");
                    logger.error("File content differs from generated record string.\nThis might be a code problem. Please Report!");
                    String[] tokens = recordStringFromRecord.split("\\n");
                    int line = 0, col = 0, offset = 0;
                    for (String token : tokens) {
                        offset = offset + token.length() + 1;
                        if (position < offset) {
                            col = position - (offset - (token.length() + 1));
                            logger.error("Error in line " + (line + 1) + ".");
                            logger.error(tokens[line]);
                            StringBuilder error_at = new StringBuilder(StringUtils.repeat(" ", col));
                            error_at.append('^');
                            logger.error(error_at);
                            haserror.set(true);
                            break;
                        }
                        line++;
                    }
                }
                // validate correct serialization with db: String <-> (db -> Record class -> String)
                if (doDatbase.get()) {
                    Record recordDatabase = null;
                    try {
                        DatabaseManager dbMan = new DatabaseManager("MassBank");
                        recordDatabase = dbMan.getAccessionData(record.ACCESSION());
                        dbMan.closeConnection();
                    } catch (SQLException | ConfigurationException e) {
                        e.printStackTrace();
                        System.exit(1);
                    }
                    if (recordDatabase == null) {
                        String errormsg = "retrieval of '" + record.ACCESSION() + "' from database failed";
                        logger.error(errormsg);
                        System.exit(1);
                    }
                    String recordStringFromDB = recordDatabase.toString();
                    position = StringUtils.indexOfDifference(new String[] { recordString, recordStringFromDB });
                    if (position != -1) {
                        logger.error("Error in \'" + filename + "\'.");
                        logger.error("File content differs from generated record string from database content.\nThis might be a code problem. Please Report!");
                        String[] tokens = recordStringFromDB.split("\\n");
                        int line = 0, col = 0, offset = 0;
                        for (String token : tokens) {
                            offset = offset + token.length() + 1;
                            if (position < offset) {
                                col = position - (offset - (token.length() + 1));
                                logger.error("Error in line " + (line + 1) + ".");
                                logger.error(tokens[line]);
                                StringBuilder error_at = new StringBuilder(StringUtils.repeat(" ", col));
                                error_at.append('^');
                                logger.error(error_at);
                                haserror.set(true);
                                break;
                            }
                            line++;
                        }
                    }
                }
            }
        } catch (IOException e) {
            e.printStackTrace();
            System.exit(1);
        }
        return accession;
    }).filter(Objects::nonNull).collect(Collectors.toList());
    // check duplicates
    Set<String> duplicates = new LinkedHashSet<String>();
    Set<String> uniques = new HashSet<String>();
    for (String c : accessions) {
        // System.out.println(c);
        if (!uniques.add(c)) {
            duplicates.add(c);
        }
    }
    if (duplicates.size() > 0) {
        logger.error("There are duplicates in all accessions:");
        logger.error(duplicates.toString());
        haserror.set(true);
    }
    // return 1 if there were errors
    if (haserror.get())
        System.exit(1);
    else
        System.exit(0);
}

Example 92 with DefaultParser

use of org.apache.commons.cli.DefaultParser in project streaming-samples by ashvina.

the class TopologyArgParser method parseOptions.

private void parseOptions(String[] args) throws Exception {
    Options options = new Options();
    compNames.stream().forEach(comp -> {
        options.addOption(Option.builder(comp).desc("instance count for component: " + comp).hasArg().build());
    });
    options.addOption(Option.builder("workers").desc("number of workers").hasArg().required().build());
    CommandLineParser parser = new DefaultParser();
    CommandLine cmd = parser.parse(options, args);
    compNames.stream().filter(comp -> cmd.hasOption(comp)).forEach(comp -> compCounts.put(comp, getIntValue(cmd, comp)));
    numWorkers = getIntValue(cmd, "workers");
}

Example 93 with DefaultParser

use of org.apache.commons.cli.DefaultParser in project java-docs-samples by GoogleCloudPlatform.

the class Inspect method main.

// [END dlp_inspect_bigquery]
/**
 * Command line application to inspect data using the Data Loss Prevention API. Supported data
 * formats: string, file, text file on GCS, BigQuery table, and Datastore entity
 */
public static void main(String[] args) throws Exception {
    OptionGroup optionsGroup = new OptionGroup();
    optionsGroup.setRequired(true);
    Option stringOption = new Option("s", "string", true, "inspect string");
    optionsGroup.addOption(stringOption);
    Option fileOption = new Option("f", "file path", true, "inspect input file path");
    optionsGroup.addOption(fileOption);
    Option gcsOption = new Option("gcs", "Google Cloud Storage", false, "inspect GCS file");
    optionsGroup.addOption(gcsOption);
    Option datastoreOption = new Option("ds", "Google Datastore", false, "inspect Datastore kind");
    optionsGroup.addOption(datastoreOption);
    Option bigqueryOption = new Option("bq", "Google BigQuery", false, "inspect BigQuery table");
    optionsGroup.addOption(bigqueryOption);
    Options commandLineOptions = new Options();
    commandLineOptions.addOptionGroup(optionsGroup);
    Option minLikelihoodOption = Option.builder("minLikelihood").hasArg(true).required(false).build();
    commandLineOptions.addOption(minLikelihoodOption);
    Option maxFindingsOption = Option.builder("maxFindings").hasArg(true).required(false).build();
    commandLineOptions.addOption(maxFindingsOption);
    Option infoTypesOption = Option.builder("infoTypes").hasArg(true).required(false).build();
    infoTypesOption.setArgs(Option.UNLIMITED_VALUES);
    commandLineOptions.addOption(infoTypesOption);
    Option includeQuoteOption = Option.builder("includeQuote").hasArg(true).required(false).build();
    commandLineOptions.addOption(includeQuoteOption);
    Option bucketNameOption = Option.builder("bucketName").hasArg(true).required(false).build();
    commandLineOptions.addOption(bucketNameOption);
    Option gcsFileNameOption = Option.builder("fileName").hasArg(true).required(false).build();
    commandLineOptions.addOption(gcsFileNameOption);
    Option datasetIdOption = Option.builder("datasetId").hasArg(true).required(false).build();
    commandLineOptions.addOption(datasetIdOption);
    Option tableIdOption = Option.builder("tableId").hasArg(true).required(false).build();
    commandLineOptions.addOption(tableIdOption);
    Option projectIdOption = Option.builder("projectId").hasArg(true).required(false).build();
    commandLineOptions.addOption(projectIdOption);
    Option topicIdOption = Option.builder("topicId").hasArg(true).required(false).build();
    commandLineOptions.addOption(topicIdOption);
    Option subscriptionIdOption = Option.builder("subscriptionId").hasArg(true).required(false).build();
    commandLineOptions.addOption(subscriptionIdOption);
    Option datastoreNamespaceOption = Option.builder("namespace").hasArg(true).required(false).build();
    commandLineOptions.addOption(datastoreNamespaceOption);
    Option datastoreKindOption = Option.builder("kind").hasArg(true).required(false).build();
    commandLineOptions.addOption(datastoreKindOption);
    CommandLineParser parser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd;
    try {
        cmd = parser.parse(commandLineOptions, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        formatter.printHelp(Inspect.class.getName(), commandLineOptions);
        System.exit(1);
        return;
    }
    Likelihood minLikelihood = Likelihood.valueOf(cmd.getOptionValue(minLikelihoodOption.getOpt(), Likelihood.LIKELIHOOD_UNSPECIFIED.name()));
    int maxFindings = Integer.parseInt(cmd.getOptionValue(maxFindingsOption.getOpt(), "0"));
    boolean includeQuote = Boolean.parseBoolean(cmd.getOptionValue(includeQuoteOption.getOpt(), "true"));
    String projectId = cmd.getOptionValue(projectIdOption.getOpt(), ServiceOptions.getDefaultProjectId());
    String topicId = cmd.getOptionValue(topicIdOption.getOpt());
    String subscriptionId = cmd.getOptionValue(subscriptionIdOption.getOpt());
    List<InfoType> infoTypesList = Collections.emptyList();
    if (cmd.hasOption(infoTypesOption.getOpt())) {
        infoTypesList = new ArrayList<>();
        String[] infoTypes = cmd.getOptionValues(infoTypesOption.getOpt());
        for (String infoType : infoTypes) {
            infoTypesList.add(InfoType.newBuilder().setName(infoType).build());
        }
    }
    // string inspection
    if (cmd.hasOption("s")) {
        String val = cmd.getOptionValue(stringOption.getOpt());
        inspectString(val, minLikelihood, maxFindings, infoTypesList, includeQuote, projectId);
    } else if (cmd.hasOption("f")) {
        String filePath = cmd.getOptionValue(fileOption.getOpt());
        inspectFile(filePath, minLikelihood, maxFindings, infoTypesList, includeQuote, projectId);
    // gcs file inspection
    } else if (cmd.hasOption("gcs")) {
        String bucketName = cmd.getOptionValue(bucketNameOption.getOpt());
        String fileName = cmd.getOptionValue(gcsFileNameOption.getOpt());
        inspectGcsFile(bucketName, fileName, minLikelihood, infoTypesList, maxFindings, topicId, subscriptionId, projectId);
    // datastore kind inspection
    } else if (cmd.hasOption("ds")) {
        String namespaceId = cmd.getOptionValue(datastoreNamespaceOption.getOpt(), "");
        String kind = cmd.getOptionValue(datastoreKindOption.getOpt());
        // use default project id when project id is not specified
        inspectDatastore(projectId, namespaceId, kind, minLikelihood, infoTypesList, maxFindings, topicId, subscriptionId);
    } else if (cmd.hasOption("bq")) {
        String datasetId = cmd.getOptionValue(datasetIdOption.getOpt());
        String tableId = cmd.getOptionValue(tableIdOption.getOpt());
        // use default project id when project id is not specified
        inspectBigquery(projectId, datasetId, tableId, minLikelihood, infoTypesList, maxFindings, topicId, subscriptionId);
    }
}

Example 94 with DefaultParser

use of org.apache.commons.cli.DefaultParser in project java-docs-samples by GoogleCloudPlatform.

the class Redact method main.

// [END dlp_redact_image]
/**
 * Command line application to redact strings, images using the Data Loss Prevention API.
 */
public static void main(String[] args) throws Exception {
    Options commandLineOptions = new Options();
    Option minLikelihoodOption = Option.builder("minLikelihood").hasArg(true).required(false).build();
    commandLineOptions.addOption(minLikelihoodOption);
    Option infoTypesOption = Option.builder("infoTypes").hasArg(true).required(false).build();
    infoTypesOption.setArgs(Option.UNLIMITED_VALUES);
    commandLineOptions.addOption(infoTypesOption);
    Option inputFilePathOption = Option.builder("f").hasArg(true).longOpt("inputFilePath").required(false).build();
    commandLineOptions.addOption(inputFilePathOption);
    Option outputFilePathOption = Option.builder("o").hasArg(true).longOpt("outputFilePath").required(false).build();
    commandLineOptions.addOption(outputFilePathOption);
    Option projectIdOption = Option.builder("projectId").hasArg(true).required(false).build();
    CommandLineParser parser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd;
    try {
        cmd = parser.parse(commandLineOptions, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        formatter.printHelp(Redact.class.getName(), commandLineOptions);
        System.exit(1);
        return;
    }
    List<InfoType> infoTypesList = new ArrayList<>();
    String[] infoTypes = cmd.getOptionValues(infoTypesOption.getOpt());
    if (infoTypes != null) {
        for (String infoType : infoTypes) {
            infoTypesList.add(InfoType.newBuilder().setName(infoType).build());
        }
    }
    Likelihood minLikelihood = Likelihood.valueOf(cmd.getOptionValue(minLikelihoodOption.getOpt(), Likelihood.LIKELIHOOD_UNSPECIFIED.name()));
    String inputFilePath = cmd.getOptionValue(inputFilePathOption.getOpt());
    String outputFilePath = cmd.getOptionValue(outputFilePathOption.getOpt());
    String projectId = cmd.getOptionValue(projectIdOption.getOpt(), ServiceOptions.getDefaultProjectId());
    redactImage(inputFilePath, minLikelihood, infoTypesList, outputFilePath, projectId);
}

Example 95 with DefaultParser

use of org.apache.commons.cli.DefaultParser in project java-docs-samples by GoogleCloudPlatform.

the class Triggers method main.

// [END dlp_delete_trigger]
/**
 * Command line application to crate, list and delete triggers.
 */
public static void main(String[] args) throws Exception {
    OptionGroup optionsGroup = new OptionGroup();
    optionsGroup.setRequired(true);
    Option createTriggerOption = new Option("c", "create", false, "Create trigger to scan a GCS bucket");
    optionsGroup.addOption(createTriggerOption);
    Option listTriggersOption = new Option("l", "list", false, "List triggers");
    optionsGroup.addOption(listTriggersOption);
    Option deleteTriggerOption = new Option("d", "delete", false, "Delete trigger");
    optionsGroup.addOption(deleteTriggerOption);
    Options commandLineOptions = new Options();
    commandLineOptions.addOptionGroup(optionsGroup);
    Option bucketNameOption = Option.builder("bucketName").hasArg(true).required(false).build();
    commandLineOptions.addOption(bucketNameOption);
    Option gcsFileNameOption = Option.builder("fileName").hasArg(true).required(false).build();
    commandLineOptions.addOption(gcsFileNameOption);
    Option minLikelihoodOption = Option.builder("minLikelihood").hasArg(true).required(false).build();
    commandLineOptions.addOption(minLikelihoodOption);
    Option maxFindingsOption = Option.builder("maxFindings").hasArg(true).required(false).build();
    commandLineOptions.addOption(maxFindingsOption);
    Option infoTypesOption = Option.builder("infoTypes").hasArg(true).required(false).build();
    infoTypesOption.setArgs(Option.UNLIMITED_VALUES);
    commandLineOptions.addOption(infoTypesOption);
    Option projectIdOption = Option.builder("projectId").hasArg(true).required(false).build();
    commandLineOptions.addOption(projectIdOption);
    Option triggerIdOption = Option.builder("triggerId").hasArg(true).required(false).build();
    commandLineOptions.addOption(triggerIdOption);
    Option displayNameOption = Option.builder("displayName").hasArg(true).required(false).build();
    commandLineOptions.addOption(displayNameOption);
    Option descriptionOption = Option.builder("description").hasArg(true).required(false).build();
    commandLineOptions.addOption(descriptionOption);
    Option scanPeriodOption = Option.builder("scanPeriod").hasArg(true).required(false).build();
    commandLineOptions.addOption(scanPeriodOption);
    CommandLineParser parser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd;
    try {
        cmd = parser.parse(commandLineOptions, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        formatter.printHelp(DeIdentification.class.getName(), commandLineOptions);
        System.exit(1);
        return;
    }
    String projectId = cmd.getOptionValue(projectIdOption.getOpt(), ServiceOptions.getDefaultProjectId());
    if (cmd.hasOption("c")) {
        Likelihood minLikelihood = Likelihood.valueOf(cmd.getOptionValue(minLikelihoodOption.getOpt(), Likelihood.LIKELIHOOD_UNSPECIFIED.name()));
        int maxFindings = Integer.parseInt(cmd.getOptionValue(maxFindingsOption.getOpt(), "0"));
        String triggerId = cmd.getOptionValue(triggerIdOption.getOpt());
        String displayName = cmd.getOptionValue(displayNameOption.getOpt(), "");
        String description = cmd.getOptionValue(descriptionOption.getOpt(), "");
        String bucketName = cmd.getOptionValue(bucketNameOption.getOpt());
        String fileName = cmd.getOptionValue(gcsFileNameOption.getOpt());
        int scanPeriod = Integer.valueOf(cmd.getOptionValue(scanPeriodOption.getOpt()));
        List<InfoType> infoTypesList = new ArrayList<>();
        if (cmd.hasOption(infoTypesOption.getOpt())) {
            infoTypesList = new ArrayList<>();
            String[] infoTypes = cmd.getOptionValues(infoTypesOption.getOpt());
            for (String infoType : infoTypes) {
                infoTypesList.add(InfoType.newBuilder().setName(infoType).build());
            }
        }
        createTrigger(triggerId, displayName, description, bucketName, fileName, scanPeriod, infoTypesList, minLikelihood, maxFindings, projectId);
    } else if (cmd.hasOption("l")) {
        // list triggers
        listTriggers(projectId);
    } else if (cmd.hasOption("d")) {
        String triggerId = cmd.getOptionValue(triggerIdOption.getOpt());
        deleteTrigger(projectId, triggerId);
    }
}