List of usage examples for org.apache.commons.lang3 BooleanUtils toBoolean
public static boolean toBoolean(final String str, final String trueString, final String falseString)
Converts a String to a Boolean throwing an exception if no match found.
BooleanUtils.toBoolean("true", "true", "false") = true BooleanUtils.toBoolean("false", "true", "false") = false From source file:com.omertron.bgg.model.OwnerStatus.java
public void setOwn(String own) { this.own = BooleanUtils.toBoolean(own, "1", "0"); }
From source file:com.omertron.bgg.model.OwnerStatus.java
public void setPreviouslyOwned(String previouslyOwned) { this.previouslyOwned = BooleanUtils.toBoolean(previouslyOwned, "1", "0"); }
From source file:com.omertron.bgg.model.OwnerStatus.java
public void setForTrade(String forTrade) { this.forTrade = BooleanUtils.toBoolean(forTrade, "1", "0"); }
From source file:com.omertron.bgg.model.OwnerStatus.java
public void setWant(String want) { this.want = BooleanUtils.toBoolean(want, "1", "0"); }
From source file:com.omertron.bgg.model.OwnerStatus.java
public void setWantToPlay(String wantToPlay) { this.wantToPlay = BooleanUtils.toBoolean(wantToPlay, "1", "0"); }
From source file:com.omertron.bgg.model.OwnerStatus.java
public void setWantToBuy(String wantToBuy) { this.wantToBuy = BooleanUtils.toBoolean(wantToBuy, "1", "0"); }
From source file:com.dsh105.nexus.command.module.admin.ChannelCommand.java
@Override public boolean onCommand(CommandPerformEvent event) { if (event.getArgs().length < 1 || event.getArgs().length > 3) { event.errorWithPing("Please specify both a channel and a command to disable ({0}).", event.getCommandPrefix() + event.getCommand() + " <channel> <command>"); return true; }/*w w w .j a v a 2 s . c o m*/ String channel = event.getArgs()[0]; ChannelConfig channelConfig = Nexus.getInstance().getChannelConfiguration().getChannel(channel); if (channelConfig == null) { event.errorWithPing("Commands cannot be disabled in a channel I am not present in ({0}).", channel); return true; } channel = channelConfig.getChannelName(); if (event.getArgs().length == 1) { ArrayList<String> disabledCommands = channelConfig.getDisabledCommands(); if (disabledCommands.isEmpty()) { event.respondWithPing("All commands are enabled in {0}.", channel); } else { event.respondWithPing("Disabled commands in {0}: " + StringUtil.join(disabledCommands, ", "), channel); } return true; } String command = event.getArgs()[1]; if (!command.equalsIgnoreCase("ALL")) { // Check if the command is valid CommandModule module = event.getManager().getModuleFor(command); if (module == null) { event.errorWithPing("{0} is not a valid command! Use {1} for help info.", command, event.getCommandPrefix() + "help"); return true; } command = module.info().command(); } if (event.getArgs().length == 3) { boolean enable = BooleanUtils.toBoolean(event.getArgs()[2], "enable", "disable"); channelConfig.setCommandStatus(command, enable); event.respondWithPing("{0} " + (enable ? "enabled" : "disabled") + " in {1}.", (command.equalsIgnoreCase("ALL") ? "All commands" : event.getCommandPrefix() + command), channel); return true; } if (command.equalsIgnoreCase("ALL")) { event.errorWithPing("Please use {0} to see if a command is disabled in a channel.", event.getCommandPrefix() + event.getCommand() + "<channel> <command>"); } boolean enabled = channelConfig.isEnabled(command); event.respondWithPing("{0} is currently " + (enabled ? "enabled" : "disabled") + " in {1}.", command, channel); return true; }
From source file:com.omertron.bgg.model.OwnerStatus.java
public void setPreordered(String preordered) { this.preordered = BooleanUtils.toBoolean(preordered, "1", "0"); }
From source file:ca.on.oicr.pde.workflows.GATKGenotypeGVCFsWorkflow.java
@Override public void buildWorkflow() { final String binDir = this.getWorkflowBaseDir() + "/bin/"; final Boolean manualOutput = BooleanUtils.toBoolean(getProperty("manual_output"), "true", "false"); final String queue = getOptionalProperty("queue", ""); final String java = getProperty("java"); final String gatk = getOptionalProperty("gatk_jar", binDir); final String gatkKey = getProperty("gatk_key"); final String identifier = getProperty("identifier"); final String refFasta = getProperty("ref_fasta"); final Double standCallConf = Double.valueOf(getProperty("stand_call_conf")); final Double standEmitConf = Double.valueOf(getProperty("stand_emit_conf")); final String dbsnpVcf = getOptionalProperty("gatk_dbsnp_vcf", null); final Integer gatkGenotypeGvcfsXmx = Integer.parseInt(getProperty("gatk_genotype_gvcfs_xmx")); final String gatkGenotypeGvcfsParams = getOptionalProperty("gatk_genotype_gvcfs_params", null); final Integer gatkCombineGVCFsXmx = Integer.parseInt(getProperty("gatk_combine_gvcfs_xmx")); final Integer gatkOverhead = Integer.parseInt(getProperty("gatk_sched_overhead_mem")); final Integer maxGenotypeGVCFsInputFiles = Integer .parseInt(getProperty("gatk_genotype_gvcfs_max_input_files")); final Integer maxCombineGVCFsInputFiles = Integer .parseInt(getProperty("gatk_combine_gvcfs_max_input_files")); final List<String> chrSizesList = Arrays.asList(StringUtils.split(getProperty("chr_sizes"), ",")); final Set<String> chrSizes = new LinkedHashSet<>(chrSizesList); if (chrSizes.size() != chrSizesList.size()) { throw new RuntimeException("Duplicate chr_sizes detected."); }/* w ww .j a va2 s. co m*/ // one chrSize record is required, null will result in no parallelization if (chrSizes.isEmpty()) { chrSizes.add(null); } List<Pair<String, Job>> combineGvcfs = batchGVCFs(inputFiles, maxGenotypeGVCFsInputFiles, maxCombineGVCFsInputFiles, java, gatkCombineGVCFsXmx, gatkOverhead, tmpDir, gatk, gatkKey, tmpGVCFsDir, refFasta, queue); //use linked hashmap to keep "pairs" in sort order determined by chr_sizes LinkedHashMap<String, Pair<GenotypeGVCFs, Job>> vcfs = new LinkedHashMap<>(); for (String chrSize : chrSizes) { //GATK Genotype VCFs( https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.php ) GenotypeGVCFs.Builder genotypeGvcfsBuilder = new GenotypeGVCFs.Builder(java, gatkGenotypeGvcfsXmx + "g", tmpDir, gatk, gatkKey, dataDir) .setReferenceSequence(refFasta) .setOutputFileName( identifier + (chrSize != null ? "." + chrSize.replace(":", "-") : "") + ".raw") .addInterval(chrSize).setStandardCallConfidence(standCallConf) .setStandardEmitConfidence(standEmitConf).setDbsnpFilePath(dbsnpVcf) .setExtraParameters(gatkGenotypeGvcfsParams); for (String f : getLeftCollection(combineGvcfs)) { genotypeGvcfsBuilder.addInputFile(f); } GenotypeGVCFs genotypeGvcfsCommand = genotypeGvcfsBuilder.build(); Job genotypeGvcfsJob = getWorkflow().createBashJob("GATKGenotypeGVCFs") .setMaxMemory(Integer.toString((gatkGenotypeGvcfsXmx + gatkOverhead) * 1024)).setQueue(queue); genotypeGvcfsJob.getCommand().setArguments(genotypeGvcfsCommand.getCommand()); // add parents, null if provision file in, not null if parent is a combine gvcf job for (Job j : getRightCollection(combineGvcfs)) { if (j != null) { genotypeGvcfsJob.addParent(j); } } if (vcfs.put(chrSize, Pair.of(genotypeGvcfsCommand, genotypeGvcfsJob)) != null) { throw new RuntimeException("Unexpected state: duplicate vcf."); } } if (vcfs.size() > 1) { //GATK CatVariants ( https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_CatVariants.php ) CatVariants.Builder catVariantsBuilder = new CatVariants.Builder(java, gatkCombineGVCFsXmx + "g", tmpDir, gatk, gatkKey, dataDir).setReferenceSequence(refFasta) //individual vcf files sorted by genotype gvcfs; order of input vcf concatenation is determined by chr_sizes order (assumed to be sorted) .disableSorting().setOutputFileName(identifier + ".raw"); for (GenotypeGVCFs cmd : getLeftCollection(vcfs.values())) { catVariantsBuilder.addInputFile(cmd.getOutputFile()); } CatVariants catVariantsCommand = catVariantsBuilder.build(); Job combineGVCFsJob = getWorkflow().createBashJob("GATKCombineGVCFs") .setMaxMemory(Integer.toString((gatkCombineGVCFsXmx + gatkOverhead) * 1024)).setQueue(queue); combineGVCFsJob.getParents().addAll(getRightCollection(vcfs.values())); combineGVCFsJob.getCommand().setArguments(catVariantsCommand.getCommand()); combineGVCFsJob.addFile( createOutputFile(catVariantsCommand.getOutputFile(), "application/vcf-gz", manualOutput)); combineGVCFsJob.addFile( createOutputFile(catVariantsCommand.getOutputIndex(), "application/tbi", manualOutput)); } else if (vcfs.size() == 1) { Pair<GenotypeGVCFs, Job> p = Iterables.getOnlyElement(vcfs.values()); GenotypeGVCFs cmd = p.getLeft(); Job genotypeGvcfsJob = p.getRight(); genotypeGvcfsJob.addFile(createOutputFile(cmd.getOutputFile(), "application/vcf-gz", manualOutput)); genotypeGvcfsJob.addFile(createOutputFile(cmd.getOutputIndex(), "application/tbi", manualOutput)); } else { throw new RuntimeException("Unexpected state: No VCFs"); } }
From source file:ca.on.oicr.pde.workflows.GATKHaplotypeCallerWorkflow.java
@Override public void buildWorkflow() { final String binDir = this.getWorkflowBaseDir() + "/bin/"; final Boolean manualOutput = BooleanUtils.toBoolean(getProperty("manual_output"), "true", "false"); final String queue = getOptionalProperty("queue", ""); final String java = getProperty("java"); final String gatk = getOptionalProperty("gatk_jar", binDir); final String gatkKey = getProperty("gatk_key"); final String identifier = getProperty("identifier"); final String refFasta = getProperty("ref_fasta"); final String dbsnpVcf = getProperty("gatk_dbsnp_vcf"); final Integer intervalPadding = hasPropertyAndNotNull("interval_padding") ? Integer.parseInt(getProperty("interval_padding")) : null;// ww w .j a v a 2s .co m final Integer downsamplingCoverage = hasPropertyAndNotNull("downsampling_coverage") ? Integer.parseInt(getProperty("downsampling_coverage")) : null; final String downsamplingType = getOptionalProperty("downsampling_type", null); final Integer gatkHaplotypeCallerThreads = Integer.parseInt(getProperty("gatk_haplotype_caller_threads")); final Integer gatkHaplotypeCallerXmx = Integer.parseInt(getProperty("gatk_haplotype_caller_xmx")); final Integer gatkCombineGVCFsXmx = Integer.parseInt(getProperty("gatk_combine_gvcfs_xmx")); final Integer gatkOverhead = Integer.parseInt(getProperty("gatk_sched_overhead_mem")); final String haplotypeCallerParams = getOptionalProperty("gatk_haplotype_caller_params", null); final List<String> intervalFilesList = Arrays .asList(StringUtils.split(getOptionalProperty("interval_files", ""), ",")); final Set<String> intervalFiles = new HashSet<>(intervalFilesList); if (intervalFiles.size() != intervalFilesList.size()) { throw new RuntimeException("Duplicate interval_files detected"); } final Set<String> chrSizes; if (hasProperty("chr_sizes")) { //chr_sizes has been set List<String> chrSizesList = Arrays.asList(StringUtils.split(getProperty("chr_sizes"), ",")); chrSizes = new HashSet<>(chrSizesList); if (chrSizes.size() != chrSizesList.size()) { throw new RuntimeException("Duplicate chr_sizes detected."); } } else if (!intervalFiles.isEmpty()) { //chr_sizes not set, interval_files has been set - use interval files to calculate chrSizes try { chrSizes = BEDFileUtils.getChromosomes(intervalFiles); } catch (IOException ioe) { throw new RuntimeException(ioe); } } else { //chr_sizes and interval_files not set - can not calculate chrSizes chrSizes = new HashSet<>(); } // one chrSize record is required, null will result in no parallelization if (chrSizes.isEmpty()) { chrSizes.add(null); } Map<String, Pair<HaplotypeCaller, Job>> gvcfs = new HashMap<>(); for (String chrSize : chrSizes) { //GATK Haplotype Caller ( https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php ) HaplotypeCaller haplotypeCallerCommand = new HaplotypeCaller.Builder(java, Integer.toString(gatkHaplotypeCallerXmx) + "g", tmpDir, gatk, gatkKey, dataDir) .setInputBamFiles(inputBamFiles).setReferenceSequence(refFasta) .setDbsnpFilePath(dbsnpVcf).addInterval(chrSize).addIntervalFiles(intervalFiles) .setIntervalPadding(intervalPadding) .setDownsamplingCoverageThreshold(downsamplingCoverage) .setDownsamplingType(downsamplingType) .setOutputFileName( identifier + (chrSize != null ? "." + chrSize.replace(":", "-") : "")) .setNumCpuThreadsPerDataThread(gatkHaplotypeCallerThreads) .setExtraParameters(haplotypeCallerParams).build(); Job haplotypeCallerJob = this.getWorkflow().createBashJob("GATKHaplotypeCaller") .setMaxMemory(Integer.toString((gatkHaplotypeCallerXmx + gatkOverhead) * 1024)).setQueue(queue); haplotypeCallerJob.getCommand().setArguments(haplotypeCallerCommand.getCommand()); if (gvcfs.put(chrSize, Pair.of(haplotypeCallerCommand, haplotypeCallerJob)) != null) { throw new RuntimeException("Unexpected state: Duplicate key."); } } if (gvcfs.size() > 1) { //GATK CatVariants ( https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_CatVariants.php ) CatVariants.Builder catVariantsBuilder = new CatVariants.Builder(java, Integer.toString(gatkCombineGVCFsXmx) + "g", tmpDir, gatk, gatkKey, dataDir) .setReferenceSequence(refFasta).setOutputFileName(identifier); for (HaplotypeCaller hc : getLeftCollection(gvcfs.values())) { catVariantsBuilder.addInputFile(hc.getOutputFile()); } CatVariants catvariantsCommand = catVariantsBuilder.build(); Job combineGVCFsJob = getWorkflow().createBashJob("GATKCombineGVCFs") .setMaxMemory(Integer.toString((gatkCombineGVCFsXmx + gatkOverhead) * 1024)).setQueue(queue); combineGVCFsJob.getParents().addAll(getRightCollection(gvcfs.values())); combineGVCFsJob.getCommand().setArguments(catvariantsCommand.getCommand()); combineGVCFsJob.addFile( createOutputFile(catvariantsCommand.getOutputFile(), "application/g-vcf-gz", manualOutput)); combineGVCFsJob.addFile( createOutputFile(catvariantsCommand.getOutputIndex(), "application/tbi", manualOutput)); } else if (gvcfs.size() == 1) { Pair<HaplotypeCaller, Job> p = Iterables.getOnlyElement(gvcfs.values()); HaplotypeCaller hcCmd = p.getLeft(); Job hcJob = p.getRight(); hcJob.addFile(createOutputFile(hcCmd.getOutputFile(), "application/g-vcf-gz", manualOutput)); hcJob.addFile(createOutputFile(hcCmd.getOutputIndex(), "application/tbi", manualOutput)); } else { throw new RuntimeException("Unexpected state: No GVCFs"); } }