jpayne@68: package shared;
jpayne@68: 
jpayne@68: import java.io.FileNotFoundException;
jpayne@68: import java.io.PrintStream;
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.Arrays;
jpayne@68: 
jpayne@68: import fileIO.ByteFile1;
jpayne@68: import json.JsonObject;
jpayne@68: import stream.NullOutputStream;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Pre-parses the command line to handle:
jpayne@68:  * Leading hyphens
jpayne@68:  * Java flags
jpayne@68:  * Output stream redirection
jpayne@68:  * Help/version information
jpayne@68:  * 
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date November 28, 2017
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class PreParser {
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Auxiliary constructor.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 * @param c Class object of the caller
jpayne@68: 	 * @param printVersion True if the BBTools version should be printed to the screen
jpayne@68: 	 */
jpayne@68: 	public PreParser(final String[] args_, final Class<?> c, boolean printVersion){
jpayne@68: 		this(args_, System.err, c, printVersion, true, true);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Auxiliary constructor.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 * @param defaultPrintStream Print stream that will be used if not overridden
jpayne@68: 	 * @param c Class object of the caller
jpayne@68: 	 * @param printVersion True if the BBTools version should be printed to the screen
jpayne@68: 	 */
jpayne@68: 	public PreParser(final String[] args_, PrintStream defaultPrintStream, final Class<?> c, boolean printVersion){
jpayne@68: 		this(args_, defaultPrintStream, c, printVersion, true, true);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Primary constructor.
jpayne@68: 	 * @param args0 Command line arguments
jpayne@68: 	 * @param defaultPrintStream Print stream that will be used if not overridden
jpayne@68: 	 * @param c Class object of the caller
jpayne@68: 	 * @param printVersion True if the BBTools version should be printed to the screen
jpayne@68: 	 * @param removeKnown Remove parameters from args that are parsed here
jpayne@68: 	 * @param autoExit Exit if there is a version or help flag
jpayne@68: 	 */
jpayne@68: 	public PreParser(final String[] args0, PrintStream defaultPrintStream, final Class<?> c, boolean printVersion, boolean removeKnown, boolean autoExit){
jpayne@68: 		original=args0;
jpayne@68: 		if(Shared.COMMAND_LINE==null){Shared.COMMAND_LINE=(original==null ? null : original.clone());}
jpayne@68: 		if(Shared.mainClass==null){Shared.mainClass=c;}
jpayne@68: 		
jpayne@68: 		Parser.parseHelp(args0, autoExit);
jpayne@68: 		
jpayne@68: 		String[] args=Parser.parseConfig(args0);
jpayne@68: 		this.config=(args!=args0);
jpayne@68: 		
jpayne@68: 		final ArrayList<String> unknown=new ArrayList<String>(args.length);
jpayne@68: 		int removed=0, hyphens=0;
jpayne@68: 
jpayne@68: 		PrintStream outstream=((defaultPrintStream == null) ? System.err : defaultPrintStream);
jpayne@68: 		boolean help=false, jflag=false, json=false;
jpayne@68: 		
jpayne@68: 		for(int i=0; i<args.length; i++){
jpayne@68: 			String s=args[i];
jpayne@68: 			boolean remove=false;
jpayne@68: 			if(Parser.isJavaFlag(s)){
jpayne@68: 				jflag=true;
jpayne@68: 				remove=true;
jpayne@68: 			}else if(s==null){
jpayne@68: 				remove=true;
jpayne@68: 			}else{
jpayne@68: 				
jpayne@68: //				while(a.charAt(0)=='-' && (a.indexOf('.')<0 || i>1 || !new File(a).exists())){a=a.substring(1);} //Another possibility
jpayne@68: 				
jpayne@68: 				if(s.length()>0 && s.charAt(0)=='-'){
jpayne@68: 					int cnt=1;
jpayne@68: 					while(cnt<s.length() && s.charAt(cnt)=='-'){cnt++;}
jpayne@68: 					s=s.substring(cnt);
jpayne@68: 					hyphens+=cnt;
jpayne@68: 					args[i]=s;//Note that this mutates the original.  Moral:  Don't use hyphens.
jpayne@68: 				}
jpayne@68: 				
jpayne@68: 				final String[] split=s.split("=");
jpayne@68: 				assert(split.length<3) : "To many '=' signs: "+s;
jpayne@68: 				assert(split!=null && split.length>0) : "Please do not put spaces around = symbols.\nSyntax is 'arg=value' with no spaces.";
jpayne@68: 				final String a=split[0].toLowerCase();
jpayne@68: 				String b=split.length>1 ? split[1] : null;
jpayne@68: 				if(b==null){
jpayne@68: 					//do nothing
jpayne@68: 				}else if("null".equalsIgnoreCase(b)){//Replace "null" with nothing
jpayne@68: 					b=null;
jpayne@68: 					args[i]=s=(a+"=");
jpayne@68: 				}
jpayne@68: 				
jpayne@68: 				if(a.equals("outstream")){
jpayne@68: 					outstream=parseOutstream(b);
jpayne@68: 					remove=removeKnown;
jpayne@68: 				}else if(a.equals("json")){
jpayne@68: 					json=Parse.parseBoolean(b);
jpayne@68: 				}else if(a.equals("silent")){
jpayne@68: 					silent=Parse.parseBoolean(b);
jpayne@68: 				}else if(a.equals("printexecuting")){
jpayne@68: 					printExecuting=Parse.parseBoolean(b);
jpayne@68: 					remove=true;
jpayne@68: 				}else if(a.equals("metadatafile")){
jpayne@68: 					MetadataWriter.fnameStatic=b;
jpayne@68: 					remove=true;
jpayne@68: 				}else if(a.equals("bufferbf") || a.equals("bufferbf1")){//for testing
jpayne@68: 					ByteFile1.BUFFERED=Parse.parseBoolean(b);
jpayne@68: 					remove=true;
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			if(remove){removed++;}
jpayne@68: 			else{unknown.add(s);}
jpayne@68: 		}
jpayne@68: 		this.args=(removed==0 ? args : unknown.toArray(new String[0]));
jpayne@68: 		this.outstream=outstream;
jpayne@68: 		this.help=help;
jpayne@68: 		this.jflag=jflag;
jpayne@68: 		this.hyphens=hyphens;
jpayne@68: 		this.json=json;
jpayne@68: 		
jpayne@68: 		if(json){
jpayne@68: 			jsonObject=new JsonObject();
jpayne@68: 			if(c!=null && printExecuting){jsonObject.add("commandLine", c.getName()+" "+Arrays.toString(original));}
jpayne@68: 			if(printVersion){jsonObject.add("version", Shared.BBMAP_VERSION_STRING);}
jpayne@68: 			jsonObject.add("memory", Shared.memTotal());
jpayne@68: 			jsonObject.add("assertions", Shared.EA());
jpayne@68: 			jsonObject.add("javaVersion", Shared.javaVersion);
jpayne@68: 			jsonObject.add("JVM_args", Shared.JVM_ARGS());
jpayne@68: 		}else if(!silent){
jpayne@68: 			if(c!=null && printExecuting){outstream.println("Executing "+c.getName()+" "+Arrays.toString(original));}
jpayne@68: 			if(printVersion){outstream.println("Version "+Shared.BBMAP_VERSION_STRING );}
jpayne@68: 			if(c!=null || printVersion){outstream.println();}
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static boolean isAmino(String[] args){
jpayne@68: 		boolean amino=false;
jpayne@68: 		for(String arg : args){
jpayne@68: 			if(arg!=null && arg.startsWith("amino")){
jpayne@68: 				final String[] split=arg.split("=");
jpayne@68: 				assert(split.length<3) : "To many '=' signs: "+arg;
jpayne@68: 				final String a=split[0].toLowerCase();
jpayne@68: 				String b=split.length>1 ? split[1] : null;
jpayne@68: 				if(a.equals("amino")){amino=Parse.parseBoolean(b);}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return amino;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static int stripHyphens(String[] args){
jpayne@68: 		int stripped=0;
jpayne@68: 		for(int i=0; i<args.length; i++){
jpayne@68: 			String arg=args[i];
jpayne@68: 			if(Parser.isJavaFlag(arg)){
jpayne@68: 				//Do nothing
jpayne@68: 			}else if(arg.length()>0 && arg.charAt(0)=='-'){
jpayne@68: 				int cnt=1;
jpayne@68: 				while(cnt<arg.length() && arg.charAt(cnt)=='-'){cnt++;}
jpayne@68: 				arg=arg.substring(cnt);
jpayne@68: 				stripped+=cnt;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return stripped;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static PrintStream parseOutstream(final String b) {
jpayne@68: 		
jpayne@68: 		try {
jpayne@68: 			if(b==null || b.equalsIgnoreCase("null")){return new PrintStream(new NullOutputStream());}
jpayne@68: 			else if(b.equalsIgnoreCase("stdout") || b.startsWith("stdout.") || b.equals("System.out") || b.equalsIgnoreCase("sysout")){return System.out;}
jpayne@68: 			else if(b.equalsIgnoreCase("stderr") || b.startsWith("stderr.") || b.equals("System.err")){return System.err;}
jpayne@68: 			else{return new PrintStream(b);}
jpayne@68: 		} catch (FileNotFoundException e) {
jpayne@68: 			e.printStackTrace();
jpayne@68: 		}
jpayne@68: 		KillSwitch.kill("Unable to process argument outstream="+b);
jpayne@68: 		return null; //Unreachable
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public final String[] original;
jpayne@68: 	public final String[] args;
jpayne@68: 	public final PrintStream outstream;
jpayne@68: 	public final boolean help;
jpayne@68: 	public final boolean config;
jpayne@68: 	public final boolean jflag;
jpayne@68: 	public final boolean json;
jpayne@68: 	public final int hyphens;
jpayne@68: 	public JsonObject jsonObject; 
jpayne@68: 
jpayne@68: 	public static boolean printExecuting=true;
jpayne@68: 	public static boolean silent=false;
jpayne@68: 	
jpayne@68: }