Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/shared/PreParser.java @ 68:5028fdace37b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
parents
children
rev   line source
jpayne@68 1 package shared;
jpayne@68 2
jpayne@68 3 import java.io.FileNotFoundException;
jpayne@68 4 import java.io.PrintStream;
jpayne@68 5 import java.util.ArrayList;
jpayne@68 6 import java.util.Arrays;
jpayne@68 7
jpayne@68 8 import fileIO.ByteFile1;
jpayne@68 9 import json.JsonObject;
jpayne@68 10 import stream.NullOutputStream;
jpayne@68 11
jpayne@68 12 /**
jpayne@68 13 * Pre-parses the command line to handle:
jpayne@68 14 * Leading hyphens
jpayne@68 15 * Java flags
jpayne@68 16 * Output stream redirection
jpayne@68 17 * Help/version information
jpayne@68 18 *
jpayne@68 19 * @author Brian Bushnell
jpayne@68 20 * @date November 28, 2017
jpayne@68 21 *
jpayne@68 22 */
jpayne@68 23 public class PreParser {
jpayne@68 24
jpayne@68 25 /**
jpayne@68 26 * Auxiliary constructor.
jpayne@68 27 * @param args Command line arguments
jpayne@68 28 * @param c Class object of the caller
jpayne@68 29 * @param printVersion True if the BBTools version should be printed to the screen
jpayne@68 30 */
jpayne@68 31 public PreParser(final String[] args_, final Class<?> c, boolean printVersion){
jpayne@68 32 this(args_, System.err, c, printVersion, true, true);
jpayne@68 33 }
jpayne@68 34
jpayne@68 35 /**
jpayne@68 36 * Auxiliary constructor.
jpayne@68 37 * @param args Command line arguments
jpayne@68 38 * @param defaultPrintStream Print stream that will be used if not overridden
jpayne@68 39 * @param c Class object of the caller
jpayne@68 40 * @param printVersion True if the BBTools version should be printed to the screen
jpayne@68 41 */
jpayne@68 42 public PreParser(final String[] args_, PrintStream defaultPrintStream, final Class<?> c, boolean printVersion){
jpayne@68 43 this(args_, defaultPrintStream, c, printVersion, true, true);
jpayne@68 44 }
jpayne@68 45
jpayne@68 46 /**
jpayne@68 47 * Primary constructor.
jpayne@68 48 * @param args0 Command line arguments
jpayne@68 49 * @param defaultPrintStream Print stream that will be used if not overridden
jpayne@68 50 * @param c Class object of the caller
jpayne@68 51 * @param printVersion True if the BBTools version should be printed to the screen
jpayne@68 52 * @param removeKnown Remove parameters from args that are parsed here
jpayne@68 53 * @param autoExit Exit if there is a version or help flag
jpayne@68 54 */
jpayne@68 55 public PreParser(final String[] args0, PrintStream defaultPrintStream, final Class<?> c, boolean printVersion, boolean removeKnown, boolean autoExit){
jpayne@68 56 original=args0;
jpayne@68 57 if(Shared.COMMAND_LINE==null){Shared.COMMAND_LINE=(original==null ? null : original.clone());}
jpayne@68 58 if(Shared.mainClass==null){Shared.mainClass=c;}
jpayne@68 59
jpayne@68 60 Parser.parseHelp(args0, autoExit);
jpayne@68 61
jpayne@68 62 String[] args=Parser.parseConfig(args0);
jpayne@68 63 this.config=(args!=args0);
jpayne@68 64
jpayne@68 65 final ArrayList<String> unknown=new ArrayList<String>(args.length);
jpayne@68 66 int removed=0, hyphens=0;
jpayne@68 67
jpayne@68 68 PrintStream outstream=((defaultPrintStream == null) ? System.err : defaultPrintStream);
jpayne@68 69 boolean help=false, jflag=false, json=false;
jpayne@68 70
jpayne@68 71 for(int i=0; i<args.length; i++){
jpayne@68 72 String s=args[i];
jpayne@68 73 boolean remove=false;
jpayne@68 74 if(Parser.isJavaFlag(s)){
jpayne@68 75 jflag=true;
jpayne@68 76 remove=true;
jpayne@68 77 }else if(s==null){
jpayne@68 78 remove=true;
jpayne@68 79 }else{
jpayne@68 80
jpayne@68 81 // while(a.charAt(0)=='-' && (a.indexOf('.')<0 || i>1 || !new File(a).exists())){a=a.substring(1);} //Another possibility
jpayne@68 82
jpayne@68 83 if(s.length()>0 && s.charAt(0)=='-'){
jpayne@68 84 int cnt=1;
jpayne@68 85 while(cnt<s.length() && s.charAt(cnt)=='-'){cnt++;}
jpayne@68 86 s=s.substring(cnt);
jpayne@68 87 hyphens+=cnt;
jpayne@68 88 args[i]=s;//Note that this mutates the original. Moral: Don't use hyphens.
jpayne@68 89 }
jpayne@68 90
jpayne@68 91 final String[] split=s.split("=");
jpayne@68 92 assert(split.length<3) : "To many '=' signs: "+s;
jpayne@68 93 assert(split!=null && split.length>0) : "Please do not put spaces around = symbols.\nSyntax is 'arg=value' with no spaces.";
jpayne@68 94 final String a=split[0].toLowerCase();
jpayne@68 95 String b=split.length>1 ? split[1] : null;
jpayne@68 96 if(b==null){
jpayne@68 97 //do nothing
jpayne@68 98 }else if("null".equalsIgnoreCase(b)){//Replace "null" with nothing
jpayne@68 99 b=null;
jpayne@68 100 args[i]=s=(a+"=");
jpayne@68 101 }
jpayne@68 102
jpayne@68 103 if(a.equals("outstream")){
jpayne@68 104 outstream=parseOutstream(b);
jpayne@68 105 remove=removeKnown;
jpayne@68 106 }else if(a.equals("json")){
jpayne@68 107 json=Parse.parseBoolean(b);
jpayne@68 108 }else if(a.equals("silent")){
jpayne@68 109 silent=Parse.parseBoolean(b);
jpayne@68 110 }else if(a.equals("printexecuting")){
jpayne@68 111 printExecuting=Parse.parseBoolean(b);
jpayne@68 112 remove=true;
jpayne@68 113 }else if(a.equals("metadatafile")){
jpayne@68 114 MetadataWriter.fnameStatic=b;
jpayne@68 115 remove=true;
jpayne@68 116 }else if(a.equals("bufferbf") || a.equals("bufferbf1")){//for testing
jpayne@68 117 ByteFile1.BUFFERED=Parse.parseBoolean(b);
jpayne@68 118 remove=true;
jpayne@68 119 }
jpayne@68 120 }
jpayne@68 121
jpayne@68 122 if(remove){removed++;}
jpayne@68 123 else{unknown.add(s);}
jpayne@68 124 }
jpayne@68 125 this.args=(removed==0 ? args : unknown.toArray(new String[0]));
jpayne@68 126 this.outstream=outstream;
jpayne@68 127 this.help=help;
jpayne@68 128 this.jflag=jflag;
jpayne@68 129 this.hyphens=hyphens;
jpayne@68 130 this.json=json;
jpayne@68 131
jpayne@68 132 if(json){
jpayne@68 133 jsonObject=new JsonObject();
jpayne@68 134 if(c!=null && printExecuting){jsonObject.add("commandLine", c.getName()+" "+Arrays.toString(original));}
jpayne@68 135 if(printVersion){jsonObject.add("version", Shared.BBMAP_VERSION_STRING);}
jpayne@68 136 jsonObject.add("memory", Shared.memTotal());
jpayne@68 137 jsonObject.add("assertions", Shared.EA());
jpayne@68 138 jsonObject.add("javaVersion", Shared.javaVersion);
jpayne@68 139 jsonObject.add("JVM_args", Shared.JVM_ARGS());
jpayne@68 140 }else if(!silent){
jpayne@68 141 if(c!=null && printExecuting){outstream.println("Executing "+c.getName()+" "+Arrays.toString(original));}
jpayne@68 142 if(printVersion){outstream.println("Version "+Shared.BBMAP_VERSION_STRING );}
jpayne@68 143 if(c!=null || printVersion){outstream.println();}
jpayne@68 144 }
jpayne@68 145 }
jpayne@68 146
jpayne@68 147 public static boolean isAmino(String[] args){
jpayne@68 148 boolean amino=false;
jpayne@68 149 for(String arg : args){
jpayne@68 150 if(arg!=null && arg.startsWith("amino")){
jpayne@68 151 final String[] split=arg.split("=");
jpayne@68 152 assert(split.length<3) : "To many '=' signs: "+arg;
jpayne@68 153 final String a=split[0].toLowerCase();
jpayne@68 154 String b=split.length>1 ? split[1] : null;
jpayne@68 155 if(a.equals("amino")){amino=Parse.parseBoolean(b);}
jpayne@68 156 }
jpayne@68 157 }
jpayne@68 158 return amino;
jpayne@68 159 }
jpayne@68 160
jpayne@68 161 public static int stripHyphens(String[] args){
jpayne@68 162 int stripped=0;
jpayne@68 163 for(int i=0; i<args.length; i++){
jpayne@68 164 String arg=args[i];
jpayne@68 165 if(Parser.isJavaFlag(arg)){
jpayne@68 166 //Do nothing
jpayne@68 167 }else if(arg.length()>0 && arg.charAt(0)=='-'){
jpayne@68 168 int cnt=1;
jpayne@68 169 while(cnt<arg.length() && arg.charAt(cnt)=='-'){cnt++;}
jpayne@68 170 arg=arg.substring(cnt);
jpayne@68 171 stripped+=cnt;
jpayne@68 172 }
jpayne@68 173 }
jpayne@68 174 return stripped;
jpayne@68 175 }
jpayne@68 176
jpayne@68 177 private static PrintStream parseOutstream(final String b) {
jpayne@68 178
jpayne@68 179 try {
jpayne@68 180 if(b==null || b.equalsIgnoreCase("null")){return new PrintStream(new NullOutputStream());}
jpayne@68 181 else if(b.equalsIgnoreCase("stdout") || b.startsWith("stdout.") || b.equals("System.out") || b.equalsIgnoreCase("sysout")){return System.out;}
jpayne@68 182 else if(b.equalsIgnoreCase("stderr") || b.startsWith("stderr.") || b.equals("System.err")){return System.err;}
jpayne@68 183 else{return new PrintStream(b);}
jpayne@68 184 } catch (FileNotFoundException e) {
jpayne@68 185 e.printStackTrace();
jpayne@68 186 }
jpayne@68 187 KillSwitch.kill("Unable to process argument outstream="+b);
jpayne@68 188 return null; //Unreachable
jpayne@68 189 }
jpayne@68 190
jpayne@68 191 public final String[] original;
jpayne@68 192 public final String[] args;
jpayne@68 193 public final PrintStream outstream;
jpayne@68 194 public final boolean help;
jpayne@68 195 public final boolean config;
jpayne@68 196 public final boolean jflag;
jpayne@68 197 public final boolean json;
jpayne@68 198 public final int hyphens;
jpayne@68 199 public JsonObject jsonObject;
jpayne@68 200
jpayne@68 201 public static boolean printExecuting=true;
jpayne@68 202 public static boolean silent=false;
jpayne@68 203
jpayne@68 204 }