Example usage for org.apache.commons.cli PosixParser parse

Introduction

In this page you can find the example usage for org.apache.commons.cli PosixParser parse.

Prototype

public CommandLine parse(Options options, String[] arguments, Properties properties) throws ParseException 

Source Link

Document

Parse the arguments according to the specified options and properties.

Usage

From source file:uni.bielefeld.cmg.sparkhit.util.ParameterForScriptPiper.java

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();/*from w w  w .  ja  v a  2s .  co  m*/

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printScriptPiperHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printScriptPiperHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_FASTQ)) != null) {
            param.inputFqPath = value;
        } else if ((value = cl.getOptionValue(INPUT_LINE)) != null) {
            param.inputFqLinePath = value;
            param.inputFqPath = value;
        } else {
            help.printScriptPiperHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            help.printScriptPiperHelp();
            info.readMessage("Output file not set with -outfile options");
            info.screenDump();
            System.exit(0);
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

        if (cl.hasOption(FASTQ_FILTER)) {
            param.filterFastq = true;
        }

        if (cl.hasOption(FASTA_CONVERT)) {
            param.filterToFasta = true;
        }

        if (cl.hasOption(LINE_FASTA)) {
            param.lineToFasta = true;
        }

        if ((value = cl.getOptionValue(INPUT_TOOL)) != null) {
            param.tool = value;
            info.readParagraphedMessages("External tool locate at : \n\t" + param.tool
                    + "\nplease ensure that all nodes have such tools in the same path.\nOr it is located in a shared file system.\nOr use a Docker container");
            info.screenDump();
        } else {
            help.printScriptPiperHelp();
            info.readMessage("External tool path have not been set with parameter -tool");
            info.screenDump();
            System.exit(0);
        }

        if ((value = cl.getOptionValue(TOOL_DEPEND)) != null) {
            param.toolDepend = value;
            info.readParagraphedMessages("External tool Dependencies : \n\t" + param.toolDepend + "\n");
            info.screenDump();
        } else {
            info.readMessage(
                    "External tool dependencies have not been set, will run with tool build-in Interpreter");
            info.screenDump();
        }

        if ((value = cl.getOptionValue(TOOL_PARAM)) != null) {
            param.toolParam = value;
            info.readParagraphedMessages("External tool parameter : \n\t" + param.toolParam
                    + "\nThe entire command looks like : \n\t" + param.toolDepend + " " + param.tool + " "
                    + param.toolParam);
            info.screenDump();
            info.readParagraphedMessages("Final external command is : \n\t" + param.toolDepend + " "
                    + param.tool + " " + param.toolParam);
            info.screenDump();
        } else {
            info.readMessage("External tool parameter have not been set, will run with its default parameter");
            info.screenDump();
        }

        // param.bestNas = (param.alignLength * param.readIdentity) / 100;
        // param.bestKmers = param.alignLength - (param.alignLength - param.bestNas) * 4 - 3;

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.ParameterForVariantCaller.java

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();/*ww w.  ja v  a  2 s. c o m*/

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printScriptPiperHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printScriptPiperHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_LIST)) != null) {
            param.inputList = value;
        } else {
            help.printScriptPiperHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            help.printScriptPiperHelp();
            info.readMessage("Output file not set with -outfile options");
            info.screenDump();
            System.exit(0);
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

        if ((value = cl.getOptionValue(INPUT_TOOL)) != null) {
            param.tool = value.replaceAll("\"", "");
            info.readParagraphedMessages("External tool locate at : \n\t" + param.tool
                    + "\nplease ensure that all nodes have such tools in the same path.\nOr it is located in a shared file system.\nOr use a Docker container");
            info.screenDump();
        } else {
            help.printScriptPiperHelp();
            info.readMessage("External tool path have not been set with parameter -tool");
            info.screenDump();
            System.exit(0);
        }

        if ((value = cl.getOptionValue(TOOL_DEPEND)) != null) {
            param.toolDepend = value.replaceAll("\"", "");
            info.readParagraphedMessages("External tool Dependencies : \n\t" + param.toolDepend + "\n");
            info.screenDump();
        } else {
            info.readMessage(
                    "External tool dependencies have not been set, will run with tool build-in Interpreter");
            info.screenDump();
        }

        if ((value = cl.getOptionValue(TOOL_PARAM)) != null) {
            param.toolParam = value.replaceAll("\"", "");
            info.readParagraphedMessages("External tool parameter : \n\t" + param.toolParam
                    + "\nThe entire command looks like : \n\t" + param.toolDepend + " " + param.tool + " "
                    + param.toolParam);
            info.screenDump();
            info.readParagraphedMessages("Final external command is : \n\t" + param.toolDepend + " "
                    + param.tool + " " + param.toolParam);
            info.screenDump();
        } else {
            info.readMessage("External tool parameter have not been set, will run with its default parameter");
            info.screenDump();
        }

        // param.bestNas = (param.alignLength * param.readIdentity) / 100;
        // param.bestKmers = param.alignLength - (param.alignLength - param.bestNas) * 4 - 3;

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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