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

Example 51 with ParseException

use of org.apache.commons.cli.ParseException in project athenz by yahoo.

the class InstanceClientRegister method parseCommandLine.

private static CommandLine parseCommandLine(String[] args) {
    Options options = new Options();
    Option domain = new Option("d", "domain", true, "domain name");
    domain.setRequired(true);
    options.addOption(domain);
    Option service = new Option("s", "service", true, "service name");
    service.setRequired(true);
    options.addOption(service);
    Option provider = new Option("p", "provider", true, "provider name");
    provider.setRequired(true);
    options.addOption(provider);
    Option instance = new Option("i", "instance", true, "instance id");
    instance.setRequired(true);
    options.addOption(instance);
    Option dnsSuffix = new Option("dns", "dnssuffix", true, "provider dns suffix");
    dnsSuffix.setRequired(true);
    options.addOption(dnsSuffix);
    Option providerKey = new Option("pk", "providerkey", true, "provider private key path");
    providerKey.setRequired(true);
    options.addOption(providerKey);
    Option keyId = new Option("pkid", "providerkeyid", true, "provider private key identifier");
    keyId.setRequired(true);
    options.addOption(keyId);
    Option instanceKey = new Option("ik", "instancekey", true, "instance private key path");
    instanceKey.setRequired(true);
    options.addOption(instanceKey);
    Option ztsUrl = new Option("z", "ztsurl", true, "ZTS Server url");
    ztsUrl.setRequired(true);
    options.addOption(ztsUrl);
    CommandLineParser parser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        formatter.printHelp("instance-client", options);
        System.exit(1);
    }
    return cmd;
}

Example 52 with ParseException

use of org.apache.commons.cli.ParseException in project pentaho-platform by pentaho.

the class CommandLineProcessor method performDatasourceImport.

/**
 * @throws ParseException
 * @throws IOException
 */
private void performDatasourceImport() throws ParseException, IOException {
    String contextURL = getOptionValue(INFO_OPTION_URL_NAME, true, false);
    String filePath = getOptionValue(INFO_OPTION_FILEPATH_NAME, true, false);
    String datasourceType = getOptionValue(INFO_OPTION_DATASOURCE_TYPE_NAME, true, false);
    String overwrite = getOptionValue(INFO_OPTION_OVERWRITE_NAME, false, true);
    /*
     * wrap in a try/finally to ensure input stream is closed properly
     */
    try {
        initRestService();
        File file = new File(filePath);
        if (datasourceType != null) {
            if (datasourceType.equals(DatasourceType.ANALYSIS.name())) {
                performAnalysisDatasourceImport(contextURL, file, overwrite);
            } else if (datasourceType.equals(DatasourceType.METADATA.name())) {
                performMetadataDatasourceImport(contextURL, file, overwrite);
            }
        }
    } catch (Exception e) {
        System.err.println(e.getMessage());
        log.error(e.getMessage());
    }
}

Example 53 with ParseException

use of org.apache.commons.cli.ParseException in project hmftools by hartwigmedical.

the class BreakPointInspectorApplication method main.

public static void main(final String... args) throws IOException {
    final AnalysisBuilder analysisBuilder = new AnalysisBuilder();
    final Options options = createOptions();
    try {
        final CommandLine cmd = createCommandLine(options, args);
        final String refPath = cmd.getOptionValue(REF_PATH);
        final String refSlicePath = cmd.getOptionValue(REF_SLICE);
        final String tumorPath = cmd.getOptionValue(TUMOR_PATH);
        final String tumorSlicePath = cmd.getOptionValue(TUMOR_SLICE);
        final String vcfPath = cmd.getOptionValue(VCF);
        if (cmd.hasOption(PROXIMITY)) {
            analysisBuilder.setRange(Integer.parseInt(cmd.getOptionValue(PROXIMITY, "500")));
        }
        if (cmd.hasOption(CONTAMINATION)) {
            analysisBuilder.setContaminationFraction(Float.parseFloat(cmd.getOptionValue(CONTAMINATION, "0")));
        }
        if (refPath == null || tumorPath == null || vcfPath == null) {
            printHelpAndExit(options);
            return;
        }
        final File tumorBAM = new File(tumorPath);
        final SamReader tumorReader = SamReaderFactory.makeDefault().open(tumorBAM);
        final File refBAM = new File(refPath);
        final SamReader refReader = SamReaderFactory.makeDefault().open(refBAM);
        final File vcfFile = new File(vcfPath);
        final VCFFileReader vcfReader = new VCFFileReader(vcfFile, false);
        final List<String> samples = vcfReader.getFileHeader().getGenotypeSamples();
        if (samples.size() != 2) {
            System.err.println("could not determine tumor and sample from VCF");
            System.exit(1);
            return;
        }
        TSVOutput.PrintHeaders();
        final Analysis analysis = analysisBuilder.setRefReader(refReader).setTumorReader(tumorReader).createAnalysis();
        final List<QueryInterval> combinedQueryIntervals = Lists.newArrayList();
        final Map<String, VariantContext> variantMap = new HashMap<>();
        final List<VariantContext> variants = Lists.newArrayList();
        for (VariantContext variant : vcfReader) {
            variantMap.put(variant.getID(), variant);
            final VariantContext mateVariant = variant;
            if (variant.hasAttribute("MATEID")) {
                variant = variantMap.get(variant.getAttributeAsString("MATEID", ""));
                if (variant == null) {
                    continue;
                }
            }
            final String location = variant.getContig() + ":" + Integer.toString(variant.getStart());
            final Location location1 = Location.parseLocationString(location, tumorReader.getFileHeader().getSequenceDictionary());
            final Range uncertainty1 = extractCIPOS(variant);
            final List<Integer> CIEND = variant.getAttributeAsIntList("CIEND", 0);
            Range uncertainty2 = CIEND.size() == 2 ? new Range(CIEND.get(0), CIEND.get(1)) : null;
            final boolean IMPRECISE = variant.hasAttribute("IMPRECISE");
            HMFVariantType svType;
            final Location location2;
            switch(variant.getStructuralVariantType()) {
                case INS:
                    svType = HMFVariantType.INS;
                    location2 = location1.set(variant.getAttributeAsInt("END", 0));
                    break;
                case INV:
                    if (variant.hasAttribute("INV3")) {
                        svType = HMFVariantType.INV3;
                    } else if (variant.hasAttribute("INV5")) {
                        svType = HMFVariantType.INV5;
                    } else {
                        System.err.println(variant.getID() + " : expected either INV3 or INV5 flag");
                        continue;
                    }
                    location2 = location1.add(Math.abs(variant.getAttributeAsInt("SVLEN", 0)));
                    break;
                case DEL:
                    svType = HMFVariantType.DEL;
                    location2 = location1.add(Math.abs(variant.getAttributeAsInt("SVLEN", 0)));
                    break;
                case DUP:
                    svType = HMFVariantType.DUP;
                    location2 = location1.add(Math.abs(variant.getAttributeAsInt("SVLEN", 0)));
                    break;
                case BND:
                    // process the breakend string
                    final String call = variant.getAlternateAllele(0).getDisplayString();
                    final String[] leftSplit = call.split("\\]");
                    final String[] rightSplit = call.split("\\[");
                    if (leftSplit.length >= 2) {
                        location2 = Location.parseLocationString(leftSplit[1], tumorReader.getFileHeader().getSequenceDictionary());
                        if (leftSplit[0].length() > 0) {
                            svType = HMFVariantType.INV3;
                            uncertainty2 = Range.invert(uncertainty1);
                        } else {
                            svType = HMFVariantType.DUP;
                            uncertainty2 = uncertainty1;
                        }
                    } else if (rightSplit.length >= 2) {
                        location2 = Location.parseLocationString(rightSplit[1], tumorReader.getFileHeader().getSequenceDictionary());
                        if (rightSplit[0].length() > 0) {
                            svType = HMFVariantType.DEL;
                            uncertainty2 = uncertainty1;
                        } else {
                            svType = HMFVariantType.INV5;
                            uncertainty2 = Range.invert(uncertainty1);
                        }
                    } else {
                        System.err.println(variant.getID() + " : could not parse breakpoint");
                        continue;
                    }
                    if (IMPRECISE) {
                        uncertainty2 = extractCIPOS(mateVariant);
                    }
                    break;
                default:
                    System.err.println(variant.getID() + " : UNEXPECTED SVTYPE=" + variant.getStructuralVariantType());
                    continue;
            }
            final HMFVariantContext ctx = new HMFVariantContext(variant.getID(), location1, location2, svType, IMPRECISE);
            ctx.Filter.addAll(variant.getFilters().stream().filter(s -> !s.startsWith("BPI")).collect(Collectors.toSet()));
            ctx.Uncertainty1 = uncertainty1;
            ctx.Uncertainty2 = ObjectUtils.firstNonNull(uncertainty2, fixup(uncertainty1, IMPRECISE, svType == HMFVariantType.INV3 || svType == HMFVariantType.INV5));
            ctx.HomologySequence = variant.getAttributeAsString("HOMSEQ", "");
            if (variant.hasAttribute("LEFT_SVINSSEQ") && variant.hasAttribute("RIGHT_SVINSSEQ")) {
                ctx.InsertSequence = variant.getAttributeAsString("LEFT_SVINSSEQ", "") + "..." + variant.getAttributeAsString("RIGHT_SVINSSEQ", "");
            } else {
                ctx.InsertSequence = variant.getAttributeAsString("SVINSSEQ", "");
            }
            ctx.BND = variant.getStructuralVariantType() == StructuralVariantType.BND;
            switch(ctx.Type) {
                case INS:
                case DEL:
                    ctx.OrientationBP1 = 1;
                    ctx.OrientationBP2 = -1;
                    break;
                case INV3:
                    ctx.OrientationBP1 = 1;
                    ctx.OrientationBP2 = 1;
                    break;
                case INV5:
                    ctx.OrientationBP1 = -1;
                    ctx.OrientationBP2 = -1;
                    break;
                case DUP:
                    ctx.OrientationBP1 = -1;
                    ctx.OrientationBP2 = 1;
                    break;
            }
            final StructuralVariantResult result = analysis.processStructuralVariant(ctx);
            combinedQueryIntervals.addAll(asList(result.QueryIntervals));
            TSVOutput.print(variant, ctx, result);
            final BiConsumer<VariantContext, Boolean> vcfUpdater = (v, swap) -> {
                final Set<String> filters = v.getCommonInfo().getFiltersMaybeNull();
                if (filters != null) {
                    filters.clear();
                }
                // we will map BreakpointError to a flag
                if (result.Filters.contains(Filter.Filters.BreakpointError.toString())) {
                    v.getCommonInfo().putAttribute("BPI_AMBIGUOUS", true, true);
                } else {
                    v.getCommonInfo().addFilters(result.Filters);
                }
                if (result.Filters.isEmpty()) {
                    final List<Double> af = asList(result.AlleleFrequency.getLeft(), result.AlleleFrequency.getRight());
                    v.getCommonInfo().putAttribute(AlleleFrequency.VCF_INFO_TAG, swap ? Lists.reverse(af) : af, true);
                }
                if (result.Breakpoints.getLeft() != null) {
                    v.getCommonInfo().putAttribute(swap ? "BPI_END" : "BPI_START", result.Breakpoints.getLeft().Position, true);
                }
                if (result.Breakpoints.getRight() != null) {
                    v.getCommonInfo().putAttribute(swap ? "BPI_START" : "BPI_END", result.Breakpoints.getRight().Position, true);
                }
                // remove CIPOS / CIEND when we have an insert sequence
                if (!v.hasAttribute("IMPRECISE") && v.hasAttribute("SVINSSEQ")) {
                    v.getCommonInfo().removeAttribute("CIPOS");
                    v.getCommonInfo().removeAttribute("CIEND");
                }
                variants.add(v);
            };
            vcfUpdater.accept(variant, false);
            if (mateVariant != variant) {
                vcfUpdater.accept(mateVariant, true);
            }
        }
        // TODO: update START, END with BPI values and save Manta values in new attributes
        final String vcfOutputPath = cmd.getOptionValue(VCF_OUT);
        if (vcfOutputPath != null) {
            final VCFHeader header = vcfReader.getFileHeader();
            header.addMetaDataLine(new VCFInfoHeaderLine("BPI_START", 1, VCFHeaderLineType.Integer, "BPI adjusted breakend location"));
            header.addMetaDataLine(new VCFInfoHeaderLine("BPI_END", 1, VCFHeaderLineType.Integer, "BPI adjusted breakend location"));
            header.addMetaDataLine(new VCFInfoHeaderLine("BPI_AMBIGUOUS", 0, VCFHeaderLineType.Flag, "BPI could not determine the breakpoints, inspect manually"));
            header.addMetaDataLine(new VCFHeaderLine("bpiVersion", BreakPointInspectorApplication.class.getPackage().getImplementationVersion()));
            Filter.UpdateVCFHeader(header);
            AlleleFrequency.UpdateVCFHeader(header);
            // setup VCF
            final VariantContextWriter writer = new VariantContextWriterBuilder().setReferenceDictionary(header.getSequenceDictionary()).setOutputFile(vcfOutputPath).build();
            writer.writeHeader(header);
            // write variants
            variants.sort(new VariantContextComparator(header.getSequenceDictionary()));
            variants.forEach(writer::add);
            writer.close();
        }
        final QueryInterval[] optimizedIntervals = QueryInterval.optimizeIntervals(combinedQueryIntervals.toArray(new QueryInterval[combinedQueryIntervals.size()]));
        if (tumorSlicePath != null) {
            writeToSlice(tumorSlicePath, tumorReader, optimizedIntervals);
        }
        if (refSlicePath != null) {
            writeToSlice(refSlicePath, refReader, optimizedIntervals);
        }
        refReader.close();
        tumorReader.close();
    } catch (ParseException e) {
        printHelpAndExit(options);
        System.exit(1);
    }
}

Example 54 with ParseException

use of org.apache.commons.cli.ParseException in project hmftools by hartwigmedical.

the class ConfigSupplier method createSomaticConfig.

@NotNull
private static SomaticConfig createSomaticConfig(@NotNull CommandLine cmd, @NotNull Options opt) throws ParseException {
    final Optional<File> file;
    if (cmd.hasOption(SOMATIC_VARIANTS)) {
        final String somaticFilename = cmd.getOptionValue(SOMATIC_VARIANTS);
        final File somaticFile = new File(somaticFilename);
        if (!somaticFile.exists()) {
            printHelp(opt);
            throw new ParseException("Unable to read somatic variants from: " + somaticFilename);
        }
        file = Optional.of(somaticFile);
    } else {
        file = Optional.empty();
    }
    return ImmutableSomaticConfig.builder().file(file).minTotalVariants(defaultIntValue(cmd, SOMATIC_MIN_TOTAL, SOMATIC_MIN_TOTAL_DEFAULT)).minPeakVariants(defaultIntValue(cmd, SOMATIC_MIN_PEAK, SOMATIC_MIN_PEAK_DEFAULT)).build();
}

Example 55 with ParseException

use of org.apache.commons.cli.ParseException in project hmftools by hartwigmedical.

the class ConfigSupplier method createBAFConfig.

@NotNull
private static BAFConfig createBAFConfig(@NotNull final CommandLine cmd, Options opt, @NotNull final CommonConfig config) throws ParseException {
    if (cmd.hasOption(BAF)) {
        final String filename = cmd.getOptionValue(BAF);
        final File file = new File(filename);
        if (!file.exists()) {
            printHelp(opt);
            throw new ParseException("Unable to read bafs from: " + filename);
        }
        return ImmutableBAFConfig.builder().bafFile(file).build();
    }
    final String amberBaf = AmberBAFFile.generateAmberFilename(config.amberDirectory(), config.tumorSample());
    final File amberFile = new File(amberBaf);
    if (amberFile.exists()) {
        return ImmutableBAFConfig.builder().bafFile(amberFile).build();
    }
    printHelp(opt);
    throw new ParseException("Baf file " + amberBaf + " not found. Please supply -baf argument.");
}