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

Example 41 with Option

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

the class GOCIDataPublisherDriver method bindOptions.

private static Options bindOptions() {
    Options options = new Options();
    // help
    Option helpOption = new Option("h", "help", false, "Print the help");
    options.addOption(helpOption);
    // add output file arguments
    Option outputFileOption = new Option("o", "output", true, "The output file to write the published ontology to");
    outputFileOption.setArgName("file");
    outputFileOption.setRequired(true);
    options.addOption(outputFileOption);
    Option pvalueFilterOption = new Option("p", "pvalue", true, "The minimum p-value on which to filter the knowledge base, in format nE-x, e.g. 5E-8");
    options.addOption(pvalueFilterOption);
    Option dateFilterOption = new Option("d", "date", true, "The date on which to filter the knowledge base, in format YYYY-MM-DD");
    options.addOption(dateFilterOption);
    return options;
}

Example 42 with Option

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

the class AssociationFilterApplication method bindOptions.

private static Options bindOptions() {
    Options options = new Options();
    // help
    Option helpOption = new Option("h", "help", false, "Print the help");
    options.addOption(helpOption);
    // add output file arguments
    Option outputFileOption = new Option("o", "output", true, "The output file to write the filtered list to");
    outputFileOption.setArgName("output");
    outputFileOption.setRequired(true);
    options.addOption(outputFileOption);
    Option inOption = new Option("f", "file", true, "Input file - file where data to be filtered can be found");
    inOption.setArgName("file");
    inOption.setRequired(true);
    options.addOption(inOption);
    Option pruneOption = new Option("p", "prune", false, "Prune output - removes associations with p-value < 1E-5 from the result output");
    pruneOption.setRequired(false);
    options.addOption(pruneOption);
    Option thresholdOption = new Option("t", "threshold", true, "Filter only associations below the provided threshold. If no threshold is provided, the default of 1e-5 will be used.");
    thresholdOption.setRequired(false);
    options.addOption(thresholdOption);
    return options;
}

Example 43 with Option

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

the class GOCIDataReleaseQCDriver method bindOptions.

private static Options bindOptions() {
    Options options = new Options();
    // help
    Option helpOption = new Option("h", "help", false, "Print the help");
    options.addOption(helpOption);
    // add output file arguments
    Option allQCOption = new Option("a", "all", false, "Run the full QC pipeline");
    options.addOption(allQCOption);
    Option emailOption = new Option("e", "email", false, "Check the most recently published studies and email them out");
    options.addOption(emailOption);
    Option knowledgeBaseOption = new Option("k", "knowledgebase", false, "Run knowledge base QC tasks");
    options.addOption(knowledgeBaseOption);
    Option diagramOption = new Option("d", "diagram", false, "Run diagram QC tasks");
    options.addOption(diagramOption);
    Option solrOption = new Option("s", "solr", false, "Run Solr QC tasks");
    options.addOption(solrOption);
    return options;
}

Example 44 with Option

use of org.apache.commons.cli.Option 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;
}

Example 45 with Option

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

the class ImportExportApplication method bindOptions.

private Options bindOptions() {
    Options options = new Options();
    // help
    Option helpOption = new Option("h", "help", false, "Print the help");
    options.addOption(helpOption);
    // options are...
    // -n --ncbi        (write out NCBI export file)
    // -d --download    (write out downloads file)
    // -f --file        (file to load in)
    // -o --out         (file to write out to)
    // -a --download_alt  (write out alternative downloads file)
    // -s --stats       (write out catalog meta data)
    // add input options
    OptionGroup modeGroup = new OptionGroup();
    modeGroup.setRequired(true);
    Option ncbiOption = new Option("n", "ncbi", false, "NCBI - generate an export of the GWAS catalog to send to the NCBI for mapping");
    ncbiOption.setRequired(false);
    modeGroup.addOption(ncbiOption);
    Option downloadOption = new Option("d", "download", false, "Download - generate an export of the GWAS catalog suitable for download");
    downloadOption.setRequired(false);
    modeGroup.addOption(downloadOption);
    Option downloadAltOption = new Option("a", "download_alt", false, "Download alternative - generate an export of the GWAS catalog, including ontology mappings, suitable for download");
    downloadAltOption.setRequired(false);
    modeGroup.addOption(downloadAltOption);
    Option statsOption = new Option("s", "stats", false, "Stats - generate the meta data for the GWAS Catalog published content");
    statsOption.setRequired(false);
    modeGroup.addOption(statsOption);
    options.addOptionGroup(modeGroup);
    // add input file arguments
    OptionGroup fileGroup = new OptionGroup();
    fileGroup.setRequired(true);
    Option inOption = new Option("f", "file", true, "Input file - file where the NCBI mapped data can be found");
    inOption.setArgName("file");
    inOption.setRequired(false);
    fileGroup.addOption(inOption);
    // add output file arguments
    Option outOption = new Option("o", "out", true, "Output file - file to write the chosen data export to");
    outOption.setArgName("file");
    outOption.setRequired(false);
    fileGroup.addOption(outOption);
    options.addOptionGroup(fileGroup);
    return options;
}