Example usage for org.apache.commons.cli2 CommandLine getValues

Introduction

In this page you can find the example usage for org.apache.commons.cli2 CommandLine getValues.

Prototype

List getValues(final Option option);

Source Link

Document

Retrieves the Argument values associated with the specified Option

Usage

From source file:org.mzd.shap.spring.cli.ExportData.java

@Override
@SuppressWarnings("unchecked")
public void execute(String[] args) {
    try {//from  w ww  .j  av a2s.  c o  m
        CommandLine cl = getApp().parseArguments(args);

        String[] xmlPath = { "datasource-context.xml", "service-context.xml", "orm-context.xml" };

        getApp().startApplication(xmlPath, true);

        // Target
        DomainTarget target = null;
        if (cl.hasOption(SAMPLE_ID)) {
            target = DomainTarget.SAMPLE;
        } else if (cl.hasOption(SEQUENCE_ID)) {
            target = DomainTarget.SEQUENCE;
        } else if (cl.hasOption(FEATURE_ID)) {
            target = DomainTarget.FEATURE;
        } else if (cl.hasOption(REF_BY_ASSOC)) {
            target = DomainTarget.DEFERRED;
        }

        // Taxonomy filter
        List<Taxonomy> excludedTaxa = new ArrayList<Taxonomy>();
        if (cl.hasOption(TAXON)) {
            for (Object obj : cl.getValues(TAXON)) {
                try {
                    excludedTaxa.add(Taxonomy.valueOf(((String) obj).toUpperCase()));
                } catch (IllegalArgumentException ex) {
                    throw new ApplicationException("Unknown taxon name [" + obj + "]", ex);
                }
            }
        }

        // Source
        List<String> idList = null;
        if (cl.hasOption(LIST)) {
            idList = cl.getValues(LIST);
        } else if (cl.hasOption(INPUT_FILE)) {
            idList = readIdFile((File) cl.getValue(INPUT_FILE));
        }

        // Destination
        File outputFile = (File) cl.getValue(OUTPUT_FILE);
        if (outputFile.exists()) {
            throw new IOException("Output file [" + outputFile.getPath() + "] already exists");
        }

        // Format
        if (cl.hasOption(ANNOTATION)) {
            writeAnnotation(target, idList, excludedTaxa, outputFile);
        } else if (cl.hasOption(FASTA)) {
            writeFasta(target, cl.hasOption(FASTA_FEATURES), cl.hasOption(FEATURE_TRANSLATE),
                    cl.hasOption(FASTA_LONG_HEADER), idList, excludedTaxa, outputFile);
        } else if (cl.hasOption(GENBANK)) {
            writeGenbank(target, idList, excludedTaxa, outputFile);
        }
        //         else if (cl.hasOption(HISTOGRAM)) {
        //            writeHistogram(
        //                  target, 
        //                  (String)cl.getValue(HISTOGRAM_ANNOTATOR), 
        //                  idList, 
        //                  (Double)cl.getValue(HISTOGRAM_CONFIDENCE), 
        //                  excludedTaxa, 
        //                  outputFile);
        //         }
    } catch (Throwable t) {
        System.err.println(t.getMessage());
        System.exit(1);
    }
}

---

From source file:org.mzd.shap.spring.cli.ImportData.java

@Override
public void execute(String[] args) {
    try {//from   w ww.  ja  v a 2  s .  com
        CommandLine cl = getApp().parseArguments(args);

        String[] xmlPath = { "datasource-context.xml", "service-context.xml", "orm-context.xml" };

        getApp().startApplication(xmlPath, true);

        // Add an observer to show simply progress activity.
        this.dataAdminService = (DataAdminService) getApp().getContext().getBean("dataAdminService");

        if (cl.hasOption(SET_COVERAGE)) {
            String projectName = (String) cl.getValue(PROJECT);
            String sampleName = (String) cl.getValue(SAMPLE);
            File inputFile = (File) cl.getValue(SET_COVERAGE);
            setCoverage(projectName, sampleName, inputFile);
        } else if (cl.hasOption(IMPORT_SEQUENCE)) {
            String projectName = (String) cl.getValue(PROJECT);
            String sampleName = (String) cl.getValue(SAMPLE);
            File inputFile = (File) cl.getValue(IMPORT_SEQUENCE);
            getDataAdminService().addSequencesFromFasta(projectName, sampleName, inputFile);
        } else if (cl.hasOption(ADD_PROJECT)) {
            String projectName = (String) cl.getValue(PROJECT);
            String description = CommandLineApplication.concatenateValues(cl.getValues(DESCRIPTION));
            System.out.println("Adding project [" + projectName + "] [" + description + "]");
            getDataAdminService().addProject(projectName, description);
        } else if (cl.hasOption(ADD_SAMPLE)) {
            String sampleName = (String) cl.getValue(SAMPLE);
            String projectName = (String) cl.getValue(PROJECT);
            String description = CommandLineApplication.concatenateValues(cl.getValues(DESCRIPTION));
            System.out.println(
                    "Adding sample [" + sampleName + "] [" + description + "] to [" + projectName + "]");
            getDataAdminService().addSample(projectName, sampleName, description);
        } else if (cl.hasOption(ADD_SEQUENCE)) {
            String sampleName = (String) cl.getValue(SAMPLE);
            String projectName = (String) cl.getValue(PROJECT);
            String sequenceName = (String) cl.getValue(SEQUENCE);
            String description = CommandLineApplication.concatenateValues(cl.getValues(DESCRIPTION));
            System.out.println("Adding container sequence [" + sequenceName + "] [" + description + "] to ["
                    + projectName + "," + sampleName + "]");
            getDataAdminService().addSequence(projectName, sampleName, sequenceName, description);
        } else if (cl.hasOption(IMPORT_SEQUENCE_XML)) {
            String sampleName = (String) cl.getValue(SAMPLE);
            String projectName = (String) cl.getValue(PROJECT);
            String detectorName = (String) cl.getValue(DETECTOR);
            File inputFile = (File) cl.getValue(IMPORT_SEQUENCE_XML);
            System.out.println("Importing sequences from XML to [" + projectName + "," + sampleName
                    + "] registered to detector [" + detectorName + "]");
            getDataAdminService().addSequencesFromXml(projectName, sampleName, detectorName, inputFile);
        } else if (cl.hasOption(IMPORT_FEATURE_XML)) {
            String sampleName = (String) cl.getValue(SAMPLE);
            String projectName = (String) cl.getValue(PROJECT);
            String sequenceName = (String) cl.getValue(SEQUENCE);
            String detectorName = (String) cl.getValue(DETECTOR);
            File inputFile = (File) cl.getValue(IMPORT_FEATURE_XML);
            System.out.println("Importing features from XML to [" + projectName + "," + sampleName + ","
                    + sequenceName + "] " + "registered to detector [" + detectorName + "]");
            getDataAdminService().addFeaturesFromXml(projectName, sampleName, sequenceName, detectorName,
                    inputFile);
        } else if (cl.hasOption(REMOVE_SEQUENCE)) {
            File inputFile = (File) cl.getValue(REMOVE_SEQUENCE);
            removeSequence(inputFile);
        } else if (cl.hasOption(REMOVE_FEATURE)) {
            File inputFile = (File) cl.getValue(REMOVE_FEATURE);
            removeFeature(inputFile);
        }
    } catch (Throwable t) {
        System.err.println(t.getMessage());
        System.exit(1);
    }
}

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