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

Example 76 with GnuParser

use of org.apache.commons.cli.GnuParser in project goci by EBISPOT.

the class ParentMappingApplication method parseArguments.

private static int parseArguments(String[] args) {
    CommandLineParser parser = new GnuParser();
    HelpFormatter help = new HelpFormatter();
    Options options = bindOptions();
    int parseArgs = 0;
    try {
        CommandLine cl = parser.parse(options, args, true);
        // check for mode help option
        if (cl.hasOption("")) {
            // print out mode help
            help.printHelp("mapper", options, true);
            parseArgs += 1;
        } else {
            // find -o option (for asserted output file)
            if (cl.hasOption("o")) {
                outputFile = new File(cl.getOptionValue("o"));
            } else {
                System.err.println("-o (output file) argument is required");
                help.printHelp("mapper", options, true);
                parseArgs += 2;
            }
        }
    } catch (ParseException e) {
        System.err.println("Failed to read supplied arguments");
        help.printHelp("mapper", options, true);
        parseArgs += 4;
    }
    return parseArgs;
}

Example 77 with GnuParser

use of org.apache.commons.cli.GnuParser in project goci by EBISPOT.

the class AssociationFilterApplication method parseArguments.

private static int parseArguments(String[] args) {
    CommandLineParser parser = new GnuParser();
    HelpFormatter help = new HelpFormatter();
    Options options = bindOptions();
    int parseArgs = 0;
    try {
        CommandLine cl = parser.parse(options, args, true);
        // check for mode help option
        if (cl.hasOption("")) {
            // print out mode help
            help.printHelp("filter", options, true);
            parseArgs += 1;
        } else {
            // find -o option (for asserted output file)
            if (cl.hasOption("o")) {
                outputFile = new File(cl.getOptionValue("o"));
            } else {
                System.err.println("-o (output file) argument is required");
                help.printHelp("filter", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("f")) {
                inputFile = new File(cl.getOptionValue("f"));
            } else {
                System.err.println("-f (input file) argument is required");
                help.printHelp("filter", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("p")) {
                prune = true;
            }
            if (cl.hasOption("t")) {
                threshold = Double.valueOf(cl.getOptionValue("t"));
            }
        }
    } catch (ParseException e) {
        System.err.println("Failed to read supplied arguments");
        help.printHelp("filter", options, true);
        parseArgs += 4;
    }
    return parseArgs;
}

Example 78 with GnuParser

use of org.apache.commons.cli.GnuParser in project goci by EBISPOT.

the class SnpListBuilderApp method parseArguments.

private static int parseArguments(String[] args) {
    CommandLineParser parser = new GnuParser();
    HelpFormatter help = new HelpFormatter();
    Options options = bindOptions();
    int parseArgs = 0;
    try {
        CommandLine cl = parser.parse(options, args, true);
        // check for mode help option
        if (cl.hasOption("")) {
            // print out mode help
            help.printHelp("publish", options, true);
            parseArgs += 1;
        } else {
            // find -o option (for asserted output file)
            if (cl.hasOption("o")) {
                outputFilePath = cl.getOptionValue("o");
            } else {
                System.err.println("-o (ontology output file) argument is required");
                help.printHelp("publish", options, true);
                parseArgs += 2;
            }
        }
    } catch (ParseException e) {
        System.err.println("Failed to read supplied arguments");
        help.printHelp("publish", options, true);
        parseArgs += 3;
    }
    return parseArgs;
}

Example 79 with GnuParser

use of org.apache.commons.cli.GnuParser in project goci by EBISPOT.

the class GOCIDataReleaseQCDriver method parseArguments.

private int parseArguments(String[] args) {
    CommandLineParser parser = new GnuParser();
    HelpFormatter help = new HelpFormatter();
    Options options = bindOptions();
    int parseArgs = 0;
    try {
        CommandLine cl = parser.parse(options, args, true);
        // check for mode help option
        if (cl.hasOption("")) {
            // print out mode help
            help.printHelp("qc", options, true);
            parseArgs += 1;
        } else {
            // find -o option (for asserted output file)
            if (cl.hasOption("a")) {
                this.opMode = OperationMode.ALL;
            } else if (cl.hasOption("k")) {
                this.opMode = OperationMode.KNOWLEDGE_BASE;
            } else if (cl.hasOption("e")) {
                this.opMode = OperationMode.SUMMARY_EMAIL;
            } else if (cl.hasOption("d")) {
                this.opMode = OperationMode.DIAGRAM;
            } else if (cl.hasOption("s")) {
                this.opMode = OperationMode.SOLR_INDEX;
            } else {
                System.err.println("-o (ontology output file) argument is required");
                help.printHelp("publish", options, true);
                parseArgs += 2;
            }
        }
    } catch (ParseException e) {
        System.err.println("Failed to read supplied arguments");
        help.printHelp("publish", options, true);
        parseArgs += 4;
    }
    return parseArgs;
}

Example 80 with GnuParser

use of org.apache.commons.cli.GnuParser in project goci by EBISPOT.

the class KBMetricsDriver method parseArguments.

private static int parseArguments(String[] args) {
    CommandLineParser parser = new GnuParser();
    HelpFormatter help = new HelpFormatter();
    Options options = bindOptions();
    int parseArgs = 0;
    try {
        CommandLine cl = parser.parse(options, args, true);
        // check for mode help option
        if (cl.hasOption("")) {
            // print out mode help
            help.printHelp("evaluate", options, true);
            parseArgs += 1;
        } else {
            System.out.println("Metrics will be calculated with the following options...");
            for (Option opt : cl.getOptions()) {
                System.out.println("\t" + opt.getLongOpt() + ": " + opt.getValue() + " (" + opt.getArgName() + ")");
            }
            if (cl.hasOption("efo")) {
                _efoLocation = new URL(cl.getOptionValue("efo"));
                System.out.println(_efoLocation);
            } else {
                System.err.println("-efo (EFO location) argument is required");
                help.printHelp("evaluate", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("gwas")) {
                _gwasSchemaLocation = new File(cl.getOptionValue("gwas")).toURI().toURL();
                System.out.println(_gwasSchemaLocation);
            } else {
                System.err.println("-gwas (GWAS Schema File) argument is required");
                help.printHelp("evaluate", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("kb")) {
                _kbLocation = new File(cl.getOptionValue("kb")).toURI().toURL();
                System.out.println(_kbLocation);
            } else {
                System.err.println("-kb (Knowledgebase File) argument is required");
                help.printHelp("evaluate", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("w")) {
                _watershedCutoff = Integer.parseInt(cl.getOptionValue("w"));
            //                    System.setProperty("watershed.cutoff", String.valueOf(_watershedCutoff));
            } else {
                System.err.println("-w (Watershed cutoff) argument is required");
                help.printHelp("evaluate", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("out")) {
                String outOpt = cl.getOptionValue("out");
                _out = new BufferedOutputStream(new FileOutputStream(new File(outOpt)));
            } else {
                System.out.println("No output file specified, report will be written to standard out");
                _out = System.out;
            }
        }
    } catch (ParseException e) {
        System.err.println("Failed to read supplied arguments (" + e.getMessage() + ")");
        help.printHelp("evaluate", options, true);
        parseArgs += 4;
    } catch (FileNotFoundException e) {
        System.err.println("Failed to read supplied arguments - file not found (" + e.getMessage() + ")");
        help.printHelp("evaluate", options, true);
        parseArgs += 5;
    } catch (MalformedURLException e) {
        System.err.println("Failed to read supplied arguments - a supplied argument was not a valid URL " + "(" + e.getMessage() + ")");
        help.printHelp("evaluate", options, true);
        parseArgs += 6;
    }
    return parseArgs;
}