Java tutorial
package uni.bielefeld.cmg.sparkhit.util; /** * Created by Liren Huang on 13/01/16. * * SparkHit * Copyright (c) 2015-2015: * Liren Huang <huanglr at cebitec.uni-bielefeld.de> * * SparkHit is free software: you can redistribute it and/or modify it * under the terms of the GNU General Public License as published by the Free * Software Foundation, either version 3 of the License, or (at your option) * any later version. * * This program is distributed in the hope that it will be useful, but WITHOU * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for * more details. * * You should have received a copy of the GNU General Public License along * with this program. If not, see <http://www.gnu.org/licenses/>. */ import org.apache.commons.cli.*; import java.io.File; import java.io.IOException; import java.util.HashMap; import java.util.Map; public class ParameterForScriptPiper { private String[] arguments; private InfoDumper info = new InfoDumper(); public ParameterForScriptPiper(String[] arguments) throws IOException, ParseException { this.arguments = arguments; } private static final Options parameter = new Options(); DefaultParam param = new DefaultParam(); /* parameter IDs */ private static final String INPUT_FASTQ = "fastq", INPUT_LINE = "line", FASTQ_FILTER = "filter", FASTA_CONVERT = "tofasta", LINE_FASTA = "linetofa", INPUT_TOOL = "tool", TOOL_PARAM = "toolparam", TOOL_DEPEND = "tooldepend", OUTPUT_LINE = "outfile", PARTITIONS = "partition", VERSION = "version", HELP2 = "h", HELP = "help"; private static final Map<String, Integer> parameterMap = new HashMap<String, Integer>(); public void putParameterID() { int o = 0; parameterMap.put(INPUT_FASTQ, o++); parameterMap.put(INPUT_LINE, o++); parameterMap.put(FASTQ_FILTER, o++); parameterMap.put(FASTA_CONVERT, o++); parameterMap.put(LINE_FASTA, o++); parameterMap.put(INPUT_TOOL, o++); parameterMap.put(TOOL_PARAM, o++); parameterMap.put(TOOL_DEPEND, o++); parameterMap.put(OUTPUT_LINE, o++); parameterMap.put(PARTITIONS, o++); parameterMap.put(VERSION, o++); parameterMap.put(HELP, o++); parameterMap.put(HELP2, o++); } public void addParameterInfo() { /* use Object parameter of Options class to store parameter information */ parameter.addOption(OptionBuilder.withArgName("input fastq file").hasArg() .withDescription( "Input spark hit result file in tabular format. Accept wild card, s3n schema, hdfs schema") .create(INPUT_FASTQ)); parameter.addOption(OptionBuilder.withArgName("input line file").hasArg() .withDescription("Input NGS data, line based text file format, one line per unit") .create(INPUT_LINE)); parameter.addOption(OptionBuilder.withArgName("filter input fastq").hasArg(false).withDescription( "Weather to filter input fastq file or not, default not (big data with small error, who knows)") .create(FASTQ_FILTER)); parameter.addOption(OptionBuilder.withArgName("convert to fasta").hasArg(false) .withDescription("Convert input fastq file to fasta before sending to external tool to process") .create(FASTA_CONVERT)); parameter.addOption(OptionBuilder.withArgName("line to fasta").hasArg(false) .withDescription("Convert input line file to fasta before sending to external tool to process") .create(LINE_FASTA)); parameter.addOption(OptionBuilder.withArgName("tool dependencies").hasArg().withDescription( "Use \"\" quotation to quote Dependencies for your tool. Or instead, put it in tool path in commandline logic. Default is NONE") .create(TOOL_DEPEND)); parameter.addOption(OptionBuilder.withArgName("external tool path").hasArg() .withDescription("Path to an external tool you want to use, a script or a tool") .create(INPUT_TOOL)); parameter.addOption(OptionBuilder.withArgName("external tool param").hasArg().withDescription( "Use \"\" quotation to quote Parameter for your tool, please exclude input and output for your tool as it should be STDIN and STDOUT for Spark Pipe. Please include reference and place it in the right position in your command line") .create(TOOL_PARAM)); parameter.addOption(OptionBuilder.withArgName("output file").hasArg() .withDescription("Output sequencing data directory").create(OUTPUT_LINE)); parameter.addOption(OptionBuilder.withArgName("re-partition num").hasArg().withDescription( "even the load of each task, 1 partition for a task or 4 partitions for a task is recommended. Default, not re-partition") .create(PARTITIONS)); parameter .addOption(OptionBuilder.hasArg(false).withDescription("show version information").create(VERSION)); parameter.addOption( OptionBuilder.hasArg(false).withDescription("print and show this information").create(HELP)); parameter.addOption(OptionBuilder.hasArg(false).withDescription("").create(HELP2)); } /* main method */ public DefaultParam importCommandLine() { /* Assigning Parameter ID to an ascending number */ putParameterID(); /* 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; } }