List of usage examples for org.apache.commons.cli OptionBuilder withValueSeparator
public static OptionBuilder withValueSeparator(char sep)
sep as a means to separate argument values. From source file:org.dspace.app.mediafilter.MediaFilterCLITool.java
public static void main(String[] argv) throws Exception { // set headless for non-gui workstations System.setProperty("java.awt.headless", "true"); // create an options object and populate it CommandLineParser parser = new PosixParser(); int status = 0; Options options = new Options(); options.addOption("v", "verbose", false, "print all extracted text and other details to STDOUT"); options.addOption("q", "quiet", false, "do not print anything except in the event of errors."); options.addOption("f", "force", false, "force all bitstreams to be processed"); options.addOption("i", "identifier", true, "ONLY process bitstreams belonging to identifier"); options.addOption("m", "maximum", true, "process no more than maximum items"); options.addOption("h", "help", false, "help"); //create a "plugin" option (to specify specific MediaFilter plugins to run) OptionBuilder.withLongOpt("plugins"); OptionBuilder.withValueSeparator(','); OptionBuilder.withDescription("ONLY run the specified Media Filter plugin(s)\n" + "listed from '" + MEDIA_FILTER_PLUGINS_KEY + "' in dspace.cfg.\n" + "Separate multiple with a comma (,)\n" + "(e.g. MediaFilterManager -p \n\"Word Text Extractor\",\"PDF Text Extractor\")"); Option pluginOption = OptionBuilder.create('p'); pluginOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args options.addOption(pluginOption);//from ww w . ja v a 2s. co m //create a "skip" option (to specify communities/collections/items to skip) OptionBuilder.withLongOpt("skip"); OptionBuilder.withValueSeparator(','); OptionBuilder.withDescription( "SKIP the bitstreams belonging to identifier\n" + "Separate multiple identifiers with a comma (,)\n" + "(e.g. MediaFilterManager -s \n 123456789/34,123456789/323)"); Option skipOption = OptionBuilder.create('s'); skipOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args options.addOption(skipOption); boolean isVerbose = false; boolean isQuiet = false; boolean isForce = false; // default to not forced String identifier = null; // object scope limiter int max2Process = Integer.MAX_VALUE; Map<String, List<String>> filterFormats = new HashMap<>(); CommandLine line = null; try { line = parser.parse(options, argv); } catch (MissingArgumentException e) { System.out.println("ERROR: " + e.getMessage()); HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(1); } if (line.hasOption('h')) { HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(0); } if (line.hasOption('v')) { isVerbose = true; } isQuiet = line.hasOption('q'); if (line.hasOption('f')) { isForce = true; } if (line.hasOption('i')) { identifier = line.getOptionValue('i'); } if (line.hasOption('m')) { max2Process = Integer.parseInt(line.getOptionValue('m')); if (max2Process <= 1) { System.out.println("Invalid maximum value '" + line.getOptionValue('m') + "' - ignoring"); max2Process = Integer.MAX_VALUE; } } String filterNames[] = null; if (line.hasOption('p')) { //specified which media filter plugins we are using filterNames = line.getOptionValues('p'); if (filterNames == null || filterNames.length == 0) { //display error, since no plugins specified System.err.println("\nERROR: -p (-plugin) option requires at least one plugin to be specified.\n" + "(e.g. MediaFilterManager -p \"Word Text Extractor\",\"PDF Text Extractor\")\n"); HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(1); } } else { //retrieve list of all enabled media filter plugins! filterNames = DSpaceServicesFactory.getInstance().getConfigurationService() .getArrayProperty(MEDIA_FILTER_PLUGINS_KEY); } MediaFilterService mediaFilterService = MediaFilterServiceFactory.getInstance().getMediaFilterService(); mediaFilterService.setForce(isForce); mediaFilterService.setQuiet(isQuiet); mediaFilterService.setVerbose(isVerbose); mediaFilterService.setMax2Process(max2Process); //initialize an array of our enabled filters List<FormatFilter> filterList = new ArrayList<FormatFilter>(); //set up each filter for (int i = 0; i < filterNames.length; i++) { //get filter of this name & add to list of filters FormatFilter filter = (FormatFilter) CoreServiceFactory.getInstance().getPluginService() .getNamedPlugin(FormatFilter.class, filterNames[i]); if (filter == null) { System.err.println( "\nERROR: Unknown MediaFilter specified (either from command-line or in dspace.cfg): '" + filterNames[i] + "'"); System.exit(1); } else { filterList.add(filter); String filterClassName = filter.getClass().getName(); String pluginName = null; //If this filter is a SelfNamedPlugin, //then the input formats it accepts may differ for //each "named" plugin that it defines. //So, we have to look for every key that fits the //following format: filter.<class-name>.<plugin-name>.inputFormats if (SelfNamedPlugin.class.isAssignableFrom(filter.getClass())) { //Get the plugin instance name for this class pluginName = ((SelfNamedPlugin) filter).getPluginInstanceName(); } //Retrieve our list of supported formats from dspace.cfg //For SelfNamedPlugins, format of key is: // filter.<class-name>.<plugin-name>.inputFormats //For other MediaFilters, format of key is: // filter.<class-name>.inputFormats String[] formats = DSpaceServicesFactory.getInstance().getConfigurationService() .getArrayProperty(FILTER_PREFIX + "." + filterClassName + (pluginName != null ? "." + pluginName : "") + "." + INPUT_FORMATS_SUFFIX); //add to internal map of filters to supported formats if (ArrayUtils.isNotEmpty(formats)) { //For SelfNamedPlugins, map key is: // <class-name><separator><plugin-name> //For other MediaFilters, map key is just: // <class-name> filterFormats.put(filterClassName + (pluginName != null ? MediaFilterService.FILTER_PLUGIN_SEPARATOR + pluginName : ""), Arrays.asList(formats)); } } //end if filter!=null } //end for //If verbose, print out loaded mediafilter info if (isVerbose) { System.out.println("The following MediaFilters are enabled: "); Iterator<String> i = filterFormats.keySet().iterator(); while (i.hasNext()) { String filterName = i.next(); System.out.println("Full Filter Name: " + filterName); String pluginName = null; if (filterName.contains(MediaFilterService.FILTER_PLUGIN_SEPARATOR)) { String[] fields = filterName.split(MediaFilterService.FILTER_PLUGIN_SEPARATOR); filterName = fields[0]; pluginName = fields[1]; } System.out.println(filterName + (pluginName != null ? " (Plugin: " + pluginName + ")" : "")); } } mediaFilterService.setFilterFormats(filterFormats); //store our filter list into an internal array mediaFilterService.setFilterClasses(filterList); //Retrieve list of identifiers to skip (if any) String skipIds[] = null; if (line.hasOption('s')) { //specified which identifiers to skip when processing skipIds = line.getOptionValues('s'); if (skipIds == null || skipIds.length == 0) { //display error, since no identifiers specified to skip System.err.println("\nERROR: -s (-skip) option requires at least one identifier to SKIP.\n" + "Make sure to separate multiple identifiers with a comma!\n" + "(e.g. MediaFilterManager -s 123456789/34,123456789/323)\n"); HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(0); } //save to a global skip list mediaFilterService.setSkipList(Arrays.asList(skipIds)); } Context c = null; try { c = new Context(); // have to be super-user to do the filtering c.turnOffAuthorisationSystem(); // now apply the filters if (identifier == null) { mediaFilterService.applyFiltersAllItems(c); } else // restrict application scope to identifier { DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(c, identifier); if (dso == null) { throw new IllegalArgumentException("Cannot resolve " + identifier + " to a DSpace object"); } switch (dso.getType()) { case Constants.COMMUNITY: mediaFilterService.applyFiltersCommunity(c, (Community) dso); break; case Constants.COLLECTION: mediaFilterService.applyFiltersCollection(c, (Collection) dso); break; case Constants.ITEM: mediaFilterService.applyFiltersItem(c, (Item) dso); break; } } c.complete(); c = null; } catch (Exception e) { status = 1; } finally { if (c != null) { c.abort(); } } System.exit(status); }
From source file:org.dspace.app.mediafilter.MediaFilterManager.java
public static void main(String[] argv) throws Exception { // set headless for non-gui workstations System.setProperty("java.awt.headless", "true"); // create an options object and populate it CommandLineParser parser = new PosixParser(); int status = 0; Options options = new Options(); options.addOption("v", "verbose", false, "print all extracted text and other details to STDOUT"); options.addOption("q", "quiet", false, "do not print anything except in the event of errors."); options.addOption("f", "force", false, "force all bitstreams to be processed"); options.addOption("n", "noindex", false, "do NOT update the search index after filtering bitstreams"); options.addOption("i", "identifier", true, "ONLY process bitstreams belonging to identifier"); options.addOption("m", "maximum", true, "process no more than maximum items"); options.addOption("h", "help", false, "help"); //create a "plugin" option (to specify specific MediaFilter plugins to run) OptionBuilder.withLongOpt("plugins"); OptionBuilder.withValueSeparator(','); OptionBuilder.withDescription("ONLY run the specified Media Filter plugin(s)\n" + "listed from '" + MEDIA_FILTER_PLUGINS_KEY + "' in dspace.cfg.\n" + "Separate multiple with a comma (,)\n" + "(e.g. MediaFilterManager -p \n\"Word Text Extractor\",\"PDF Text Extractor\")"); Option pluginOption = OptionBuilder.create('p'); pluginOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args options.addOption(pluginOption);// ww w . j a v a 2s . c o m //create a "skip" option (to specify communities/collections/items to skip) OptionBuilder.withLongOpt("skip"); OptionBuilder.withValueSeparator(','); OptionBuilder.withDescription( "SKIP the bitstreams belonging to identifier\n" + "Separate multiple identifiers with a comma (,)\n" + "(e.g. MediaFilterManager -s \n 123456789/34,123456789/323)"); Option skipOption = OptionBuilder.create('s'); skipOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args options.addOption(skipOption); CommandLine line = null; try { line = parser.parse(options, argv); } catch (MissingArgumentException e) { System.out.println("ERROR: " + e.getMessage()); HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(1); } if (line.hasOption('h')) { HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(0); } if (line.hasOption('v')) { isVerbose = true; } isQuiet = line.hasOption('q'); if (line.hasOption('n')) { updateIndex = false; } if (line.hasOption('f')) { isForce = true; } if (line.hasOption('i')) { identifier = line.getOptionValue('i'); } if (line.hasOption('m')) { max2Process = Integer.parseInt(line.getOptionValue('m')); if (max2Process <= 1) { System.out.println("Invalid maximum value '" + line.getOptionValue('m') + "' - ignoring"); max2Process = Integer.MAX_VALUE; } } String filterNames[] = null; if (line.hasOption('p')) { //specified which media filter plugins we are using filterNames = line.getOptionValues('p'); if (filterNames == null || filterNames.length == 0) { //display error, since no plugins specified System.err.println("\nERROR: -p (-plugin) option requires at least one plugin to be specified.\n" + "(e.g. MediaFilterManager -p \"Word Text Extractor\",\"PDF Text Extractor\")\n"); HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(1); } } else { //retrieve list of all enabled media filter plugins! String enabledPlugins = ConfigurationManager.getProperty(MEDIA_FILTER_PLUGINS_KEY); filterNames = enabledPlugins.split(",\\s*"); } //initialize an array of our enabled filters List<FormatFilter> filterList = new ArrayList<FormatFilter>(); //set up each filter for (int i = 0; i < filterNames.length; i++) { //get filter of this name & add to list of filters FormatFilter filter = (FormatFilter) PluginManager.getNamedPlugin(FormatFilter.class, filterNames[i]); if (filter == null) { System.err.println( "\nERROR: Unknown MediaFilter specified (either from command-line or in dspace.cfg): '" + filterNames[i] + "'"); System.exit(1); } else { filterList.add(filter); String filterClassName = filter.getClass().getName(); String pluginName = null; //If this filter is a SelfNamedPlugin, //then the input formats it accepts may differ for //each "named" plugin that it defines. //So, we have to look for every key that fits the //following format: filter.<class-name>.<plugin-name>.inputFormats if (SelfNamedPlugin.class.isAssignableFrom(filter.getClass())) { //Get the plugin instance name for this class pluginName = ((SelfNamedPlugin) filter).getPluginInstanceName(); } //Retrieve our list of supported formats from dspace.cfg //For SelfNamedPlugins, format of key is: // filter.<class-name>.<plugin-name>.inputFormats //For other MediaFilters, format of key is: // filter.<class-name>.inputFormats String formats = ConfigurationManager.getProperty(FILTER_PREFIX + "." + filterClassName + (pluginName != null ? "." + pluginName : "") + "." + INPUT_FORMATS_SUFFIX); //add to internal map of filters to supported formats if (formats != null) { //For SelfNamedPlugins, map key is: // <class-name><separator><plugin-name> //For other MediaFilters, map key is just: // <class-name> filterFormats.put( filterClassName + (pluginName != null ? FILTER_PLUGIN_SEPARATOR + pluginName : ""), Arrays.asList(formats.split(",[\\s]*"))); } } //end if filter!=null } //end for //If verbose, print out loaded mediafilter info if (isVerbose) { System.out.println("The following MediaFilters are enabled: "); Iterator<String> i = filterFormats.keySet().iterator(); while (i.hasNext()) { String filterName = i.next(); System.out.println("Full Filter Name: " + filterName); String pluginName = null; if (filterName.contains(FILTER_PLUGIN_SEPARATOR)) { String[] fields = filterName.split(FILTER_PLUGIN_SEPARATOR); filterName = fields[0]; pluginName = fields[1]; } System.out.println(filterName + (pluginName != null ? " (Plugin: " + pluginName + ")" : "")); } } //store our filter list into an internal array filterClasses = (FormatFilter[]) filterList.toArray(new FormatFilter[filterList.size()]); //Retrieve list of identifiers to skip (if any) String skipIds[] = null; if (line.hasOption('s')) { //specified which identifiers to skip when processing skipIds = line.getOptionValues('s'); if (skipIds == null || skipIds.length == 0) { //display error, since no identifiers specified to skip System.err.println("\nERROR: -s (-skip) option requires at least one identifier to SKIP.\n" + "Make sure to separate multiple identifiers with a comma!\n" + "(e.g. MediaFilterManager -s 123456789/34,123456789/323)\n"); HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(0); } //save to a global skip list skipList = Arrays.asList(skipIds); } Context c = null; try { c = new Context(); // have to be super-user to do the filtering c.turnOffAuthorisationSystem(); // now apply the filters if (identifier == null) { applyFiltersAllItems(c); } else // restrict application scope to identifier { DSpaceObject dso = HandleManager.resolveToObject(c, identifier); if (dso == null) { throw new IllegalArgumentException("Cannot resolve " + identifier + " to a DSpace object"); } switch (dso.getType()) { case Constants.COMMUNITY: applyFiltersCommunity(c, (Community) dso); break; case Constants.COLLECTION: applyFiltersCollection(c, (Collection) dso); break; case Constants.ITEM: applyFiltersItem(c, (Item) dso); break; } } // update search index? if (updateIndex) { if (!isQuiet) { System.out.println("Updating search index:"); } DSIndexer.setBatchProcessingMode(true); try { DSIndexer.updateIndex(c); } finally { DSIndexer.setBatchProcessingMode(false); } } c.complete(); c = null; } catch (Exception e) { status = 1; } finally { if (c != null) { c.abort(); } } System.exit(status); }
From source file:org.dspace.papaya.mediafilter.PapayaMediaFilterManager.java
public static void main(String[] argv) throws Exception { // set headless for non-gui workstations System.setProperty("java.awt.headless", "true"); // create an options object and populate it CommandLineParser parser = new PosixParser(); int status = 0; Options options = new Options(); options.addOption("v", "verbose", false, "print all extracted text and other details to STDOUT"); options.addOption("q", "quiet", false, "do not print anything except in the event of errors."); options.addOption("f", "force", false, "force all bitstreams to be processed"); options.addOption("i", "identifier", true, "ONLY process bitstreams belonging to identifier"); options.addOption("m", "maximum", true, "process no more than maximum items"); options.addOption("h", "help", false, "help"); //create a "plugin" option (to specify specific MediaFilter plugins to run) OptionBuilder.withLongOpt("plugins"); OptionBuilder.withValueSeparator(','); OptionBuilder.withDescription("ONLY run the specified Media Filter plugin(s)\n" + "listed from '" + MEDIA_FILTER_PLUGINS_KEY + "' in dspace.cfg.\n" + "Separate multiple with a comma (,)\n" + "(e.g. MediaFilterManager -p \n\"Word Text Extractor\",\"PDF Text Extractor\")"); Option pluginOption = OptionBuilder.create('p'); pluginOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args options.addOption(pluginOption);/*w ww .j a va 2 s . c om*/ //create a "skip" option (to specify communities/collections/items to skip) OptionBuilder.withLongOpt("skip"); OptionBuilder.withValueSeparator(','); OptionBuilder.withDescription( "SKIP the bitstreams belonging to identifier\n" + "Separate multiple identifiers with a comma (,)\n" + "(e.g. MediaFilterManager -s \n 123456789/34,123456789/323)"); Option skipOption = OptionBuilder.create('s'); skipOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args options.addOption(skipOption); CommandLine line = null; try { line = parser.parse(options, argv); } catch (MissingArgumentException e) { System.out.println("ERROR: " + e.getMessage()); HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(1); } if (line.hasOption('h')) { HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(0); } if (line.hasOption('v')) { isVerbose = true; } isQuiet = line.hasOption('q'); if (line.hasOption('f')) { isForce = true; } if (line.hasOption('i')) { identifier = line.getOptionValue('i'); } if (line.hasOption('m')) { max2Process = Integer.parseInt(line.getOptionValue('m')); if (max2Process <= 1) { System.out.println("Invalid maximum value '" + line.getOptionValue('m') + "' - ignoring"); max2Process = Integer.MAX_VALUE; } } String filterNames[] = null; if (line.hasOption('p')) { //specified which media filter plugins we are using filterNames = line.getOptionValues('p'); if (filterNames == null || filterNames.length == 0) { //display error, since no plugins specified System.err.println("\nERROR: -p (-plugin) option requires at least one plugin to be specified.\n" + "(e.g. MediaFilterManager -p \"Word Text Extractor\",\"PDF Text Extractor\")\n"); HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(1); } } else { //retrieve list of all enabled media filter plugins! String enabledPlugins = ConfigurationManager.getProperty(MEDIA_FILTER_PLUGINS_KEY); filterNames = enabledPlugins.split(",\\s*"); } //initialize an array of our enabled filters List<FormatFilter> filterList = new ArrayList<FormatFilter>(); //set up each filter for (int i = 0; i < filterNames.length; i++) { //get filter of this name & add to list of filters FormatFilter filter = (FormatFilter) PluginManager.getNamedPlugin(FormatFilter.class, filterNames[i]); if (filter == null) { System.err.println( "\nERROR: Unknown MediaFilter specified (either from command-line or in dspace.cfg): '" + filterNames[i] + "'"); System.exit(1); } else { filterList.add(filter); String filterClassName = filter.getClass().getName(); String pluginName = null; //If this filter is a SelfNamedPlugin, //then the input formats it accepts may differ for //each "named" plugin that it defines. //So, we have to look for every key that fits the //following format: filter.<class-name>.<plugin-name>.inputFormats if (SelfNamedPlugin.class.isAssignableFrom(filter.getClass())) { //Get the plugin instance name for this class pluginName = ((SelfNamedPlugin) filter).getPluginInstanceName(); } //Retrieve our list of supported formats from dspace.cfg //For SelfNamedPlugins, format of key is: // filter.<class-name>.<plugin-name>.inputFormats //For other MediaFilters, format of key is: // filter.<class-name>.inputFormats String formats = ConfigurationManager.getProperty(FILTER_PREFIX + "." + filterClassName + (pluginName != null ? "." + pluginName : "") + "." + INPUT_FORMATS_SUFFIX); //add to internal map of filters to supported formats if (formats != null) { //For SelfNamedPlugins, map key is: // <class-name><separator><plugin-name> //For other MediaFilters, map key is just: // <class-name> filterFormats.put( filterClassName + (pluginName != null ? FILTER_PLUGIN_SEPARATOR + pluginName : ""), Arrays.asList(formats.split(",[\\s]*"))); } } //end if filter!=null } //end for //If verbose, print out loaded mediafilter info if (isVerbose) { System.out.println("The following MediaFilters are enabled: "); Iterator<String> i = filterFormats.keySet().iterator(); while (i.hasNext()) { String filterName = i.next(); System.out.println("Full Filter Name: " + filterName); String pluginName = null; if (filterName.contains(FILTER_PLUGIN_SEPARATOR)) { String[] fields = filterName.split(FILTER_PLUGIN_SEPARATOR); filterName = fields[0]; pluginName = fields[1]; } System.out.println(filterName + (pluginName != null ? " (Plugin: " + pluginName + ")" : "")); } } //store our filter list into an internal array filterClasses = (FormatFilter[]) filterList.toArray(new FormatFilter[filterList.size()]); //Retrieve list of identifiers to skip (if any) String skipIds[] = null; if (line.hasOption('s')) { //specified which identifiers to skip when processing skipIds = line.getOptionValues('s'); if (skipIds == null || skipIds.length == 0) { //display error, since no identifiers specified to skip System.err.println("\nERROR: -s (-skip) option requires at least one identifier to SKIP.\n" + "Make sure to separate multiple identifiers with a comma!\n" + "(e.g. MediaFilterManager -s 123456789/34,123456789/323)\n"); HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("MediaFilterManager\n", options); System.exit(0); } //save to a global skip list skipList = Arrays.asList(skipIds); } Context c = null; try { c = new Context(); // have to be super-user to do the filtering c.turnOffAuthorisationSystem(); // now apply the filters if (identifier == null) { applyFiltersAllItems(c); } else // restrict application scope to identifier { DSpaceObject dso = HandleManager.resolveToObject(c, identifier); if (dso == null) { throw new IllegalArgumentException("Cannot resolve " + identifier + " to a DSpace object"); } switch (dso.getType()) { case Constants.COMMUNITY: applyFiltersCommunity(c, (Community) dso); break; case Constants.COLLECTION: applyFiltersCollection(c, (Collection) dso); break; case Constants.ITEM: applyFiltersItem(c, (Item) dso); break; } } c.complete(); c = null; } catch (Exception e) { status = 1; } finally { if (c != null) { c.abort(); } } System.exit(status); }
From source file:org.lib4j.cli.Options.java
public static Options parse(final Cli binding, final Class<?> mainClass, final String[] args) { final Set<String> requiredNames = new HashSet<>(); final Map<String, String> nameToAltName = new HashMap<>(); final org.apache.commons.cli.Options apacheOptions = new org.apache.commons.cli.Options(); apacheOptions.addOption(null, "help", false, "Print help and usage."); short argumentsMinOccurs = 0; short argumentsMaxOccurs = 0; final Cli.Arguments cliArguments; if (binding != null) { cliArguments = binding.getArguments(); if (cliArguments != null) { argumentsMinOccurs = cliArguments.getMinOccurs(); argumentsMaxOccurs = "unbounded".equals(cliArguments.getMaxOccurs()) ? Short.MAX_VALUE : Short.parseShort(cliArguments.getMaxOccurs()); if (argumentsMaxOccurs < argumentsMinOccurs) { logger.error("minOccurs > maxOccurs on <arguments> element"); System.exit(1);//from w w w .j av a 2 s. com } } if (binding.getOption() != null) { for (final Cli.Option option : binding.getOption()) { final Cli.Option.Name optionName = option.getName(); final String longName = optionName.getLong() == null ? null : optionName.getLong(); final String shortName = optionName.getShort() == null ? null : optionName.getShort(); final String name = longName != null ? longName : shortName; if (longName == null && shortName == null) { logger.error("both [long] and [short] option names are null in cli spec"); System.exit(1); } nameToAltName.put(name, shortName != null ? shortName : longName); OptionBuilder.withLongOpt(name == longName ? longName : null); // Record which options are required if (option.getArgument() != null) { final Cli.Option.Argument argument = option.getArgument(); final boolean isRequired = Use.REQUIRED == argument.getUse(); if (isRequired) { OptionBuilder.isRequired(); requiredNames.add(longName); } final int maxOccurs = argument.getMaxOccurs() == null ? 1 : "unbounded".equals(argument.getMaxOccurs()) ? Integer.MAX_VALUE : Integer.parseInt(argument.getMaxOccurs()); if (maxOccurs == 1) { if (isRequired) OptionBuilder.hasArgs(1); else OptionBuilder.hasOptionalArgs(1); } else if (maxOccurs == Integer.MAX_VALUE) { if (isRequired) OptionBuilder.hasArgs(); else OptionBuilder.hasOptionalArgs(); } else { if (isRequired) OptionBuilder.hasArgs(maxOccurs); else OptionBuilder.hasOptionalArgs(maxOccurs); } final char valueSeparator = argument.getValueSeparator() != null ? argument.getValueSeparator().charAt(0) : ' '; OptionBuilder .withArgName(formatArgumentName(argument.getLabel(), maxOccurs, valueSeparator)); OptionBuilder.withValueSeparator(valueSeparator); if (option.getDescription() == null) { logger.error("missing <description> for " + name + " option"); System.exit(1); } final StringBuilder description = new StringBuilder(option.getDescription()); if (option.getArgument().getDefault() != null) description.append("\nDefault: ").append(option.getArgument().getDefault()); OptionBuilder.withDescription(description.toString()); } apacheOptions.addOption(OptionBuilder.create(shortName)); } } } else { cliArguments = null; } final Map<String, Option> optionsMap = new HashMap<>(); final Set<String> specifiedLongNames; CommandLine commandLine = null; if (args != null && args.length != 0) { specifiedLongNames = new HashSet<>(); final CommandLineParser parser = new PosixParser(); do { try { commandLine = parser.parse(apacheOptions, args); } catch (final UnrecognizedOptionException e) { if (e.getMessage().startsWith("Unrecognized option: ")) { final String unrecognizedOption = e.getMessage().substring(21); logger.error("Unrecognized option: " + unrecognizedOption); for (int i = 0; i < args.length; i++) if (args[i].equals(unrecognizedOption)) args[i] = "--help"; } else { throw new IllegalArgumentException(e); } } catch (final org.apache.commons.cli.ParseException e) { Options.trapPrintHelp(apacheOptions, cliArguments, null, System.err); } } while (commandLine == null); } else { specifiedLongNames = null; } final Collection<String> arguments = commandLine != null ? commandLine.getArgList() : null; if (arguments != null && arguments.size() > 0) { if (argumentsMaxOccurs < arguments.size() || arguments.size() < argumentsMinOccurs) { Options.trapPrintHelp(apacheOptions, cliArguments, null, System.err); } } else if (argumentsMinOccurs > 0) { Options.trapPrintHelp(apacheOptions, cliArguments, null, System.err); } if (commandLine != null) { for (final org.apache.commons.cli.Option option : commandLine.getOptions()) { specifiedLongNames.add(option.getLongOpt()); if ("help".equals(option.getLongOpt())) Options.trapPrintHelp(apacheOptions, cliArguments, null, System.out); final String optionName = option.getLongOpt() != null ? option.getLongOpt() : option.getOpt(); optionsMap.put(optionName, option.getValue() != null ? new Option(optionName, option.getValueSeparator(), option.getValues()) : new Option(optionName, option.getValueSeparator(), "true")); } } // See if some arguments are missing if (requiredNames.size() != 0) { if (specifiedLongNames != null) requiredNames.removeAll(specifiedLongNames); if (requiredNames.size() != 0) { final StringBuilder builder = new StringBuilder(); for (final String longName : requiredNames) { final String shortName = nameToAltName.get(longName); if (shortName.equals(longName)) builder.append("\nMissing argument: -").append(shortName); else builder.append("\nMissing argument: -").append(shortName).append(",--").append(longName); } Options.trapPrintHelp(apacheOptions, cliArguments, builder.substring(1), System.out); } } // Include default values for options that are not specified if (binding.getOption() != null) { for (final Cli.Option option : binding.getOption()) { if (option.getArgument() != null && option.getArgument().getDefault() != null) { final String optionName = option.getName().getLong() != null ? option.getName().getLong() : option.getName().getShort(); if (!optionsMap.containsKey(optionName)) { final String valueSeparator = option.getArgument().getValueSeparator(); final String defaultValue = option.getArgument().getDefault(); optionsMap.put(optionName, valueSeparator != null ? new Option(optionName, valueSeparator.charAt(0), defaultValue) : new Option(optionName, defaultValue)); } } } } // Check pattern for specified and default options if (binding.getOption() != null) { final StringBuilder builder = new StringBuilder(); for (final Cli.Option option : binding.getOption()) { if (option.getArgument() != null && option.getArgument().getPattern() != null) { final String optionName = option.getName().getLong() != null ? option.getName().getLong() : option.getName().getShort(); final Option opt = optionsMap.get(optionName); if (opt != null) { for (final String value : opt.getValues()) { if (!value.matches(option.getArgument().getPattern())) { if (option.getName().getLong() == null || option.getName().getShort() == null) builder.append("\nIncorrect argument form: -").append(optionName); else builder.append("\nIncorrect argument form: -") .append(option.getName().getShort()).append(",--") .append(option.getName().getLong()); builder.append(' ').append(value).append("\n Required: ") .append(option.getArgument().getPattern()); } } } } } if (builder.length() > 0) Options.trapPrintHelp(apacheOptions, cliArguments, builder.substring(1), System.out); } return new Options(mainClass, args, optionsMap.values(), arguments == null || arguments.size() == 0 ? null : arguments.toArray(new String[arguments.size()])); }
From source file:org.libx4j.cli.Options.java
public static Options parse(final cli_cli binding, final Class<?> mainClass, final String[] args) throws OptionsException { final Set<String> requiredNames = new HashSet<String>(); final Map<String, String> nameToAltName = new HashMap<String, String>(); final org.apache.commons.cli.Options apacheOptions = new org.apache.commons.cli.Options(); apacheOptions.addOption(null, "help", false, "Print help and usage."); int argumentsMinOccurs = 0; int argumentsMaxOccurs = 0; final cli_cli._arguments cliArguments; if (binding != null) { cliArguments = binding._arguments(0); if (!cliArguments.isNull()) { argumentsMinOccurs = cliArguments._minOccurs$().text(); argumentsMaxOccurs = "unbounded".equals(cliArguments._maxOccurs$().text()) ? Integer.MAX_VALUE : Integer.parseInt(cliArguments._maxOccurs$().text()); if (argumentsMaxOccurs < argumentsMinOccurs) { logger.error("minOccurs > maxOccurs on <arguments> element"); System.exit(1);//ww w.j a v a 2s . c o m } } if (binding._option() != null) { for (final cli_cli._option option : binding._option()) { final cli_cli._option._name optionName = option._name(0); final String longName = optionName._long$().isNull() ? null : optionName._long$().text(); final String shortName = optionName._short$().isNull() ? null : optionName._short$().text(); final String name = longName != null ? longName : shortName; if (longName == null && shortName == null) { logger.error("both [long] and [short] option names are null in cli spec"); System.exit(1); } nameToAltName.put(name, shortName != null ? shortName : longName); OptionBuilder.withLongOpt(name == longName ? longName : null); // Record which options are required if (option._argument() != null && option._argument().size() != 0) { final cli_cli._option._argument argument = option._argument(0); final boolean isRequired = $cli_use.required.text().equals(argument._use$().text()); if (isRequired) { OptionBuilder.isRequired(); requiredNames.add(longName); } final int maxOccurs = argument._maxOccurs$().isNull() ? 1 : "unbounded".equals(argument._maxOccurs$().text()) ? Integer.MAX_VALUE : Integer.parseInt(argument._maxOccurs$().text()); if (maxOccurs == 1) { if (isRequired) OptionBuilder.hasArgs(1); else OptionBuilder.hasOptionalArgs(1); } else if (maxOccurs == Integer.MAX_VALUE) { if (isRequired) OptionBuilder.hasArgs(); else OptionBuilder.hasOptionalArgs(); } else { if (isRequired) OptionBuilder.hasArgs(maxOccurs); else OptionBuilder.hasOptionalArgs(maxOccurs); } final char valueSeparator = argument._valueSeparator$().text() != null ? argument._valueSeparator$().text().charAt(0) : ' '; OptionBuilder.withArgName( formatArgumentName(argument._label$().text(), maxOccurs, valueSeparator)); OptionBuilder.withValueSeparator(valueSeparator); if (option._description(0).isNull()) { logger.error("missing <description> for " + name + " option"); System.exit(1); } final StringBuilder description = new StringBuilder(option._description(0).text()); if (!option._argument(0)._default$().isNull()) description.append("\nDefault: ").append(option._argument(0)._default$().text()); OptionBuilder.withDescription(description.toString()); } apacheOptions.addOption(OptionBuilder.create(shortName)); } } } else { cliArguments = null; } final Map<String, Option> optionsMap = new HashMap<String, Option>(); final Set<String> specifiedLongNames; CommandLine commandLine = null; if (args != null && args.length != 0) { specifiedLongNames = new HashSet<String>(); final CommandLineParser parser = new PosixParser(); do { try { commandLine = parser.parse(apacheOptions, args); } catch (final UnrecognizedOptionException e) { if (e.getMessage().startsWith("Unrecognized option: ")) { final String unrecognizedOption = e.getMessage().substring(21); logger.error("Unrecognized option: " + unrecognizedOption); for (int i = 0; i < args.length; i++) if (args[i].equals(unrecognizedOption)) args[i] = "--help"; } else { throw new OptionsException(e); } } catch (final org.apache.commons.cli.ParseException e) { Options.trapPrintHelp(apacheOptions, cliArguments, null, System.err); } } while (commandLine == null); } else { specifiedLongNames = null; } final Collection<String> arguments = commandLine != null ? commandLine.getArgList() : null; if (arguments != null && arguments.size() > 0) { if (argumentsMaxOccurs < arguments.size() || arguments.size() < argumentsMinOccurs) { Options.trapPrintHelp(apacheOptions, cliArguments, null, System.err); } } else if (argumentsMinOccurs > 0) { Options.trapPrintHelp(apacheOptions, cliArguments, null, System.err); } if (commandLine != null) { for (final org.apache.commons.cli.Option option : commandLine.getOptions()) { specifiedLongNames.add(option.getLongOpt()); if ("help".equals(option.getLongOpt())) Options.trapPrintHelp(apacheOptions, cliArguments, null, System.out); final String optionName = option.getLongOpt() != null ? option.getLongOpt() : option.getOpt(); optionsMap.put(optionName, option.getValue() != null ? new Option(optionName, option.getValueSeparator(), option.getValues()) : new Option(optionName, option.getValueSeparator(), "true")); } } // See if some arguments are missing if (requiredNames.size() != 0) { if (specifiedLongNames != null) requiredNames.removeAll(specifiedLongNames); if (requiredNames.size() != 0) { final StringBuilder builder = new StringBuilder(); for (final String longName : requiredNames) { final String shortName = nameToAltName.get(longName); if (shortName.equals(longName)) builder.append("\nMissing argument: -").append(shortName); else builder.append("\nMissing argument: -").append(shortName).append(",--").append(longName); } Options.trapPrintHelp(apacheOptions, cliArguments, builder.substring(1), System.out); } } // Include default values for options that are not specified if (binding._option() != null) { for (final cli_cli._option option : binding._option()) { if (!option._argument(0)._default$().isNull()) { final String optionName = !option._name(0)._long$().isNull() ? option._name(0)._long$().text() : option._name(0)._short$().text(); if (!optionsMap.containsKey(optionName)) { final String valueSeparator = option._argument(0)._valueSeparator$().text(); final String defaultValue = option._argument(0)._default$().text(); optionsMap.put(optionName, valueSeparator != null ? new Option(optionName, valueSeparator.charAt(0), defaultValue) : new Option(optionName, defaultValue)); } } } } // Check pattern for specified and default options if (binding._option() != null) { final StringBuilder builder = new StringBuilder(); for (final cli_cli._option option : binding._option()) { if (!option._argument(0)._pattern$().isNull()) { final String optionName = !option._name(0)._long$().isNull() ? option._name(0)._long$().text() : option._name(0)._short$().text(); final Option opt = optionsMap.get(optionName); if (opt != null) { for (final String value : opt.getValues()) { if (!value.matches(option._argument(0)._pattern$().text())) { if (option._name(0)._long$().isNull() || option._name(0)._short$().isNull()) builder.append("\nIncorrect argument form: -").append(optionName); else builder.append("\nIncorrect argument form: -") .append(option._name(0)._short$().text()).append(",--") .append(option._name(0)._long$().text()); builder.append(" ").append(value).append("\n Required: ") .append(option._argument(0)._pattern$().text()); } } } } } if (builder.length() > 0) Options.trapPrintHelp(apacheOptions, cliArguments, builder.substring(1), System.out); } return new Options(mainClass, args, optionsMap.values(), arguments == null || arguments.size() == 0 ? null : arguments.toArray(new String[arguments.size()])); }
From source file:org.neovera.jdiablo.internal.OptionAnnotatedProperty.java
@SuppressWarnings("static-access") public org.apache.commons.cli.Option getCliOption() { if (_cliOption != null) { return _cliOption; } else {/*from w w w . ja v a 2 s. co m*/ Option option = getOption(); OptionBuilder builder = OptionBuilder.withDescription(option.description()); if (StringUtils.isNotBlank(option.argName())) { builder = builder.withArgName(option.argName()); } if (option.args() != 0) { builder = builder.hasArgs(option.args()); } if (option.hasArgs()) { builder = builder.hasArgs(); } if (StringUtils.isNotBlank(option.longOption())) { builder = builder.withLongOpt(option.longOption()); } if (option.optionalArgs() != 0) { builder = builder.hasOptionalArgs(option.optionalArgs()); } if (option.required() && !getOptionProperty().isOptionNotRequiredOverride()) { builder = builder.isRequired(); } if (option.valueSeparator() != ' ') { builder = builder.withValueSeparator(option.valueSeparator()); } setCliOption(builder.create(option.shortOption())); return getCliOption(); } }
From source file:org.nuunframework.cli.NuunCliPlugin.java
private Option createOptionFromField(Field field) { Option option = null;//w w w.j ava 2 s . c om // Cli Option Builder is completly static :-/ // so we synchronized it ... synchronized (OptionBuilder.class) { // reset the builder creating a dummy option OptionBuilder.withLongOpt("dummy"); OptionBuilder.create(); // NuunOption nuunOption = field.getAnnotation(NuunOption.class); if (nuunOption == null) { for (Annotation anno : field.getAnnotations()) { if (AssertUtils.hasAnnotationDeep(anno.annotationType(), NuunOption.class)) { nuunOption = AssertUtils.annotationProxyOf(NuunOption.class, anno); break; } } } // longopt if (!Strings.isNullOrEmpty(nuunOption.longOpt())) { OptionBuilder.withLongOpt(nuunOption.longOpt()); } // description if (!Strings.isNullOrEmpty(nuunOption.description())) { OptionBuilder.withDescription(nuunOption.description()); } // required OptionBuilder.isRequired((nuunOption.required())); // arg OptionBuilder.hasArg((nuunOption.arg())); // args if (nuunOption.args()) { if (nuunOption.numArgs() > 0) { OptionBuilder.hasArgs(nuunOption.numArgs()); } else { OptionBuilder.hasArgs(); } } // is optional if (nuunOption.optionalArg()) { OptionBuilder.hasOptionalArg(); } // nuun OptionBuilder.withValueSeparator(nuunOption.valueSeparator()); // opt if (!Strings.isNullOrEmpty(nuunOption.opt())) { option = OptionBuilder.create(nuunOption.opt()); } else { option = OptionBuilder.create(); } } return option; }
From source file:org.openscience.jmol.app.Jmol.java
public static void main(String[] args) { Dialog.setupUIManager();/* w w w.j av a 2 s. c o m*/ Jmol jmol = null; String modelFilename = null; String scriptFilename = null; Options options = new Options(); options.addOption("b", "backgroundtransparent", false, GT._("transparent background")); options.addOption("h", "help", false, GT._("give this help page")); options.addOption("n", "nodisplay", false, GT._("no display (and also exit when done)")); options.addOption("c", "check", false, GT._("check script syntax only")); options.addOption("i", "silent", false, GT._("silent startup operation")); options.addOption("l", "list", false, GT._("list commands during script execution")); options.addOption("o", "noconsole", false, GT._("no console -- all output to sysout")); options.addOption("t", "threaded", false, GT._("independent commmand thread")); options.addOption("x", "exit", false, GT._("exit after script (implicit with -n)")); OptionBuilder.withLongOpt("script"); OptionBuilder.withDescription("script file to execute"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("s")); OptionBuilder.withLongOpt("menu"); OptionBuilder.withDescription("menu file to use"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("m")); OptionBuilder.withArgName(GT._("property=value")); OptionBuilder.hasArg(); OptionBuilder.withValueSeparator(); OptionBuilder.withDescription(GT._("supported options are given below")); options.addOption(OptionBuilder.create("D")); OptionBuilder.withLongOpt("geometry"); // OptionBuilder.withDescription(GT._("overall window width x height, e.g. {0}", "-g512x616")); OptionBuilder.withDescription(GT._("window width x height, e.g. {0}", "-g500x500")); OptionBuilder.withValueSeparator(); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("g")); OptionBuilder.withLongOpt("quality"); // OptionBuilder.withDescription(GT._("overall window width x height, e.g. {0}", "-g512x616")); OptionBuilder.withDescription(GT._( "JPG image quality (1-100; default 75) or PNG image compression (0-9; default 2, maximum compression 9)")); OptionBuilder.withValueSeparator(); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("q")); OptionBuilder.withLongOpt("write"); OptionBuilder .withDescription(GT._("{0} or {1}:filename", new Object[] { "CLIP", "GIF|JPG|JPG64|PNG|PPM" })); OptionBuilder.withValueSeparator(); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("w")); int startupWidth = 0, startupHeight = 0; CommandLine line = null; try { CommandLineParser parser = new PosixParser(); line = parser.parse(options, args); } catch (ParseException exception) { System.err.println("Unexpected exception: " + exception.toString()); } if (line.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Jmol", options); // now report on the -D options System.out.println(); System.out.println(GT._("For example:")); System.out.println(); System.out.println("Jmol -ions myscript.spt -w JPEG:myfile.jpg > output.txt"); System.out.println(); System.out.println(GT._("The -D options are as follows (defaults in parenthesis):")); System.out.println(); System.out.println(" cdk.debugging=[true|false] (false)"); System.out.println(" cdk.debug.stdout=[true|false] (false)"); System.out.println(" display.speed=[fps|ms] (ms)"); System.out.println(" JmolConsole=[true|false] (true)"); System.out.println(" jmol.logger.debug=[true|false] (false)"); System.out.println(" jmol.logger.error=[true|false] (true)"); System.out.println(" jmol.logger.fatal=[true|false] (true)"); System.out.println(" jmol.logger.info=[true|false] (true)"); System.out.println(" jmol.logger.logLevel=[true|false] (false)"); System.out.println(" jmol.logger.warn=[true|false] (true)"); System.out.println(" plugin.dir (unset)"); System.out.println(" user.language=[CA|CS|DE|EN|ES|FR|NL|PT|TR] (EN)"); System.exit(0); } args = line.getArgs(); if (args.length > 0) { modelFilename = args[0]; } // Process more command line arguments // these are also passed to viewer String commandOptions = ""; //silent startup if (line.hasOption("i")) { commandOptions += "-i"; isSilent = Boolean.TRUE; } // transparent background if (line.hasOption("b")) { commandOptions += "-b"; } // independent command thread if (line.hasOption("t")) { commandOptions += "-t"; } //list commands during script operation if (line.hasOption("l")) { commandOptions += "-l"; } //output to sysout if (line.hasOption("o")) { commandOptions += "-o"; haveConsole = Boolean.FALSE; } //no display (and exit) if (line.hasOption("n")) { // this ensures that noDisplay also exits commandOptions += "-n-x"; haveDisplay = Boolean.FALSE; } //check script only if (line.hasOption("c")) { commandOptions += "-c"; } //run script if (line.hasOption("s")) { commandOptions += "-s"; scriptFilename = line.getOptionValue("s"); } //menu file if (line.hasOption("m")) { menuFile = line.getOptionValue("m"); } //exit when script completes (or file is read) if (line.hasOption("x")) { commandOptions += "-x"; } String imageType_name = null; //write image to clipboard or image file if (line.hasOption("w")) { imageType_name = line.getOptionValue("w"); } Dimension size; try { String vers = System.getProperty("java.version"); if (vers.compareTo("1.1.2") < 0) { System.out.println("!!!WARNING: Swing components require a " + "1.1.2 or higher version VM!!!"); } size = historyFile.getWindowSize(JMOL_WINDOW_NAME); if (size != null && haveDisplay.booleanValue()) { startupWidth = size.width; startupHeight = size.height; } //OUTER window dimensions /* if (line.hasOption("g") && haveDisplay.booleanValue()) { String geometry = line.getOptionValue("g"); int indexX = geometry.indexOf('x'); if (indexX > 0) { startupWidth = parseInt(geometry.substring(0, indexX)); startupHeight = parseInt(geometry.substring(indexX + 1)); } } */ Point b = historyFile.getWindowBorder(JMOL_WINDOW_NAME); //first one is just approximate, but this is set in doClose() //so it will reset properly -- still, not perfect //since it is always one step behind. if (b == null) border = new Point(12, 116); else border = new Point(b.x, b.y); //note -- the first time this is run after changes it will not work //because there is a bootstrap problem. int width = -1; int height = -1; int quality = 75; //INNER frame dimensions if (line.hasOption("g")) { String geometry = line.getOptionValue("g"); int indexX = geometry.indexOf('x'); if (indexX > 0) { width = Parser.parseInt(geometry.substring(0, indexX)); height = Parser.parseInt(geometry.substring(indexX + 1)); //System.out.println("setting geometry to " + geometry + " " + border + " " + startupWidth + startupHeight); } if (haveDisplay.booleanValue()) { startupWidth = width + border.x; startupHeight = height + border.y; } } if (line.hasOption("q")) quality = Parser.parseInt(line.getOptionValue("q")); if (imageType_name != null) commandOptions += "-w\1" + imageType_name + "\t" + width + "\t" + height + "\t" + quality + "\1"; if (startupWidth <= 0 || startupHeight <= 0) { startupWidth = 500 + border.x; startupHeight = 500 + border.y; } JFrame jmolFrame = new JFrame(); Point jmolPosition = historyFile.getWindowPosition(JMOL_WINDOW_NAME); if (jmolPosition != null) { jmolFrame.setLocation(jmolPosition); } //now pass these to viewer jmol = getJmol(jmolFrame, startupWidth, startupHeight, commandOptions); // Open a file if one is given as an argument -- note, this CAN be a script file if (modelFilename != null) { jmol.viewer.openFile(modelFilename); jmol.viewer.getOpenFileError(); } // OK, by now it is time to execute the script if (scriptFilename != null) { report("Executing script: " + scriptFilename); if (haveDisplay.booleanValue()) jmol.splash.showStatus(GT._("Executing script...")); jmol.viewer.evalFile(scriptFilename); } } catch (Throwable t) { System.out.println("uncaught exception: " + t); t.printStackTrace(); } if (haveConsole.booleanValue()) { Point location = jmol.frame.getLocation(); size = jmol.frame.getSize(); // Adding console frame to grab System.out & System.err consoleframe = new JFrame(GT._("Jmol Java Console")); consoleframe.setIconImage(jmol.frame.getIconImage()); try { final ConsoleTextArea consoleTextArea = new ConsoleTextArea(); consoleTextArea.setFont(java.awt.Font.decode("monospaced")); consoleframe.getContentPane().add(new JScrollPane(consoleTextArea), java.awt.BorderLayout.CENTER); if (Boolean.getBoolean("clearConsoleButton")) { JButton buttonClear = new JButton(GT._("Clear")); buttonClear.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { consoleTextArea.setText(""); } }); consoleframe.getContentPane().add(buttonClear, java.awt.BorderLayout.SOUTH); } } catch (IOException e) { JTextArea errorTextArea = new JTextArea(); errorTextArea.setFont(java.awt.Font.decode("monospaced")); consoleframe.getContentPane().add(new JScrollPane(errorTextArea), java.awt.BorderLayout.CENTER); errorTextArea.append(GT._("Could not create ConsoleTextArea: ") + e); } Dimension consoleSize = historyFile.getWindowSize(CONSOLE_WINDOW_NAME); Point consolePosition = historyFile.getWindowPosition(CONSOLE_WINDOW_NAME); if ((consoleSize != null) && (consolePosition != null)) { consoleframe.setBounds(consolePosition.x, consolePosition.y, consoleSize.width, consoleSize.height); } else { consoleframe.setBounds(location.x, location.y + size.height, size.width, 200); } Boolean consoleVisible = historyFile.getWindowVisibility(CONSOLE_WINDOW_NAME); if ((consoleVisible != null) && (consoleVisible.equals(Boolean.TRUE))) { consoleframe.show(); } } }
From source file:org.openscience.jvxl.Jvxl.java
public static void main(String[] args) { boolean blockData = false; int fileIndex = Integer.MAX_VALUE; String inputFile = null;// w w w. ja va 2s . com String mapFile = null; String outputFile = null; float cutoff = Float.NaN; boolean isPositiveOnly = false; P4 plane = null; boolean bicolor = false; boolean reverseColor = false; float min = Float.NaN; float max = Float.NaN; Options options = new Options(); options.addOption("h", "help", false, "give this help page"); /* * examples: * * jvxl ch3cl-density.cub --min=0.0 --max=0.2 --map ch3cl-esp.cub * jvxl ethene-HOMO.cub --bicolor --output ethene.jvxl * jvxl d_orbitals.jvxl --index 2 --phase yz * jvxl d_orbitals.jvxl --map sets * jvxl --plane xy --min=0.0 --max=0.2 --map data/ch3cl-density.cub */ // file options options.addOption("B", "blockdata", false, "multiple cube data are in blocks, not interspersed"); options.addOption("P", "progressive", false, "create JVXL+ progressive X low-to-high format"); OptionBuilder.withLongOpt("file"); OptionBuilder.withDescription("file containing surface data"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("f")); OptionBuilder.withLongOpt("index"); OptionBuilder.withDescription("index of surface in file (starting with 1)"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("i")); OptionBuilder.withLongOpt("plane"); OptionBuilder.withDescription("plane: x, y, z, xy, xz, yz, z2, x2-y2, or {a,b,c,d}"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("p")); OptionBuilder.withLongOpt("map"); OptionBuilder.withDescription("file containing data to map onto the surface or \"sets\""); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("m")); OptionBuilder.withLongOpt("output"); OptionBuilder.withDescription("JVXL output file"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("o")); // surface options OptionBuilder.withLongOpt("cutoff"); OptionBuilder.withDescription("isosurface cutoff value"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("c")); // color mapping options options.addOption("b", "bicolor", false, "bicolor map (orbital)"); options.addOption("r", "reversecolor", false, "reverse color"); OptionBuilder.withLongOpt("colorScheme"); OptionBuilder.withDescription("VRML color scheme: bw, wb, roygb, bgyor, rwb, bwr, low, high"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("s")); OptionBuilder.withLongOpt("phase"); OptionBuilder.withDescription("color by phase: x, y, z, xy, xz, yz, z2, x2-y2"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("F")); OptionBuilder.withLongOpt("min"); OptionBuilder.withDescription("color absolute minimum value"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("n")); OptionBuilder.withLongOpt("max"); OptionBuilder.withDescription("color absolute maximum value"); OptionBuilder.withValueSeparator('='); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create("x")); CommandLine line = null; try { CommandLineParser parser = new PosixParser(); line = parser.parse(options, args); } catch (ParseException exception) { Logger.error("Unexpected exception: " + exception.toString()); } if (line.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Jvxl", options); return; } args = line.getArgs(); if (args.length > 0) { inputFile = args[0]; } // files blockData = (line.hasOption("B")); if (line.hasOption("i")) { fileIndex = PT.parseInt(line.getOptionValue("i")); } if (line.hasOption("f")) { inputFile = line.getOptionValue("f"); } if (line.hasOption("m")) { mapFile = line.getOptionValue("m"); } if (line.hasOption("p")) { plane = getPlane(line.getOptionValue("p")); if (plane == null) { Logger.error("invalid plane"); return; } Logger.info("using plane " + plane); if (mapFile == null) mapFile = inputFile; if (inputFile == null) inputFile = mapFile; } if (line.hasOption("o")) { outputFile = line.getOptionValue("o"); } else { outputFile = inputFile; if (outputFile.indexOf(".") < 0) outputFile += "."; String sIndex = (fileIndex == Integer.MAX_VALUE ? "" : "_" + fileIndex); if (sIndex.length() == 0 && outputFile.indexOf(".jvxl") >= 0) sIndex += "_new"; outputFile = outputFile.substring(0, outputFile.lastIndexOf(".")) + sIndex + ".jvxl"; } // Process more command line arguments // these are also passed to vwr bicolor = (line.hasOption("b")); reverseColor = (line.hasOption("r")); if (bicolor && mapFile != null) { Logger.warn("--map option ignored; incompatible with --bicolor"); mapFile = null; } if (line.hasOption("c")) { String s = line.getOptionValue("c"); if (s.indexOf("+") == 0) { isPositiveOnly = true; s = s.substring(1); } cutoff = PT.parseFloat(s); } if (line.hasOption("n")) { if (bicolor) Logger.warn("--min option ignored; incompatible with --bicolor"); else min = PT.parseFloat(line.getOptionValue("n")); } if (line.hasOption("x")) { if (bicolor) Logger.warn("--max option ignored; incompatible with --bicolor"); else max = PT.parseFloat(line.getOptionValue("x")); } // if (line.hasOption("P")) { // phase = line.getOptionValue("P"); // } boolean progressive = line.hasOption("P"); // compose the surface SurfaceGenerator sg = new SurfaceGenerator(null, null, null, null); // input file sg.version = VERSION; if (blockData) sg.setProp("blockData", Boolean.TRUE, null); if (!Float.isNaN(cutoff)) sg.setProp(isPositiveOnly ? "cutoffPositive" : "cutoff", Float.valueOf(cutoff), null); if (bicolor) sg.setProp("sign", null, null); if (reverseColor) sg.setProp("reverseColor", null, null); //if (phase != null) //sg.setProp("phase", phase); if (progressive) sg.setProp("progressive", null, null); if (plane != null) sg.setProp("plane", plane, null); else { if (fileIndex != Integer.MAX_VALUE) sg.setProp("fileIndex", Integer.valueOf(fileIndex), null); Object t = FileReader.getBufferedReaderOrErrorMessageFromName(inputFile); if (t instanceof String) { Logger.error((String) t); return; } BufferedReader br = (BufferedReader) t; sg.setProp("readFile", br, null); try { br.close(); } catch (Exception e) { // } } sg.setProp("title", line.toString(), null); //color scheme is only for VMRL //if (colorScheme != null) { // ColorEncoder ce = new ColorEncoder(null); // ce.setColorScheme(colorScheme, false); // sg.setProp("colorScheme", ce); // } if (!Float.isNaN(min)) sg.setProp("red", Float.valueOf(min), null); if (!Float.isNaN(max)) sg.setProp("blue", Float.valueOf(max), null); if (mapFile != null) { Object t = FileReader.getBufferedReaderOrErrorMessageFromName(mapFile); if (t instanceof String) { Logger.error((String) t); return; } BufferedReader br2 = (BufferedReader) t; sg.setProp("mapColor", br2, null); try { br2.close(); } catch (Exception e) { // } } writeFile(outputFile, (String) sg.getProperty("jvxlFileData", 0)); Logger.info((String) sg.getProperty("jvxlFileInfo", 0)); Logger.info("\ncreated " + outputFile); }
From source file:org.psystems.dicomweb.Dcm2DcmCopy.java
private static CommandLine parse(String[] args) { Options opts = new Options(); opts.addOption(null, "no-fmi", false, "Encode result without File Meta Information. At default, " + " File Meta Information is included."); opts.addOption("e", "explicit", false, "Encode result with Explicit VR Little Endian Transfer Syntax. " + "At default, Implicit VR Little Endian is used."); opts.addOption("b", "big-endian", false, "Encode result with Explicit VR Big Endian Transfer Syntax. " + "At default, Implicit VR Little Endian is used."); opts.addOption("z", "deflated", false, "Encode result with Deflated Explicit VR Little Endian Syntax. " + "At default, Implicit VR Little Endian is used."); OptionBuilder.withArgName("[seq/]attr=value"); OptionBuilder.hasArgs(2);// www . ja va 2s. c o m OptionBuilder.withValueSeparator('='); OptionBuilder.withDescription( "specify value to set in the output stream. Currently only works when transcoding images."); opts.addOption(OptionBuilder.create("s")); opts.addOption("t", "syntax", true, "Encode result with the specified transfer syntax - recodes" + " the image typically."); OptionBuilder.withArgName("KB"); OptionBuilder.hasArg(); OptionBuilder.withDescription("transcoder buffer size in KB, 1KB by default"); OptionBuilder.withLongOpt("buffer"); opts.addOption(OptionBuilder.create(null)); opts.addOption("h", "help", false, "print this message"); opts.addOption("V", "version", false, "print the version information and exit"); CommandLine cl = null; try { cl = new PosixParser().parse(opts, args); } catch (ParseException e) { exit("dcm2dcm: " + e.getMessage()); throw new RuntimeException("unreachable"); } if (cl.hasOption('V')) { Package p = Dcm2DcmCopy.class.getPackage(); System.out.println("dcm2dcm v" + p.getImplementationVersion()); System.exit(0); } if (cl.hasOption('h') || cl.getArgList().size() < 2) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(USAGE, DESCRIPTION, opts, EXAMPLE); System.exit(0); } return cl; }