jpayne@68: package tax;
jpayne@68: 
jpayne@68: import java.io.PrintStream;
jpayne@68: import java.util.ArrayList;
jpayne@68: 
jpayne@68: import server.PercentEncoding;
jpayne@68: import server.ServerTools;
jpayne@68: import shared.Parse;
jpayne@68: import shared.PreParser;
jpayne@68: import shared.Shared;
jpayne@68: import shared.Timer;
jpayne@68: import shared.Tools;
jpayne@68: import structures.ByteBuilder;
jpayne@68: import structures.StringNum;
jpayne@68: 
jpayne@68: public class TaxClient {
jpayne@68: 	
jpayne@68: 	public static void main(String[] args){
jpayne@68: 		Timer t=new Timer();
jpayne@68: 		{//Preparse block for help, config files, and outstream
jpayne@68: 			PreParser pp=new PreParser(args, null, false);
jpayne@68: 			args=pp.args;
jpayne@68: 			outstream=pp.outstream;
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		ArrayList<Integer> gi=new ArrayList<Integer>();
jpayne@68: 		ArrayList<String> acc=new ArrayList<String>();
jpayne@68: 		ArrayList<String> name=new ArrayList<String>();
jpayne@68: 		ArrayList<String> header=new ArrayList<String>();
jpayne@68: 		
jpayne@68: 		boolean slow=true;
jpayne@68: 		
jpayne@68: 		//Parse each argument
jpayne@68: 		for(int i=0; i<args.length; i++){
jpayne@68: 			String arg=args[i];
jpayne@68: 			
jpayne@68: 			//Break arguments into their constituent parts, in the form of "a=b"
jpayne@68: 			String[] split=arg.split("=");
jpayne@68: 			String a=split[0].toLowerCase();
jpayne@68: 			String b=split.length>1 ? split[1] : null;
jpayne@68: 			
jpayne@68: 			if(a.equals("verbose")){
jpayne@68: 				verbose=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("name") || a.equals("names")){
jpayne@68: 				if(b!=null){
jpayne@68: 					for(String s : b.split(",")){
jpayne@68: 						name.add(s);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}else if(a.equals("gi")){
jpayne@68: 				if(b!=null){
jpayne@68: 					for(String s : b.split(",")){
jpayne@68: 						gi.add(Integer.parseInt(s));
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}else if(a.equals("accession")){
jpayne@68: 				if(b!=null){
jpayne@68: 					for(String s : b.split(",")){
jpayne@68: 						acc.add(s);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}else if(a.equals("header")){
jpayne@68: 				if(b!=null){
jpayne@68: 					for(String s : b.split(",")){
jpayne@68: 						header.add(s);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}else if(a.equals("slow")){
jpayne@68: 				slow=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("fast")){
jpayne@68: 				slow=!Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("parse_flag_goes_here")){
jpayne@68: 				long fake_variable=Parse.parseKMG(b);
jpayne@68: 				//Set a variable here
jpayne@68: 			}else{
jpayne@68: 				outstream.println("Unknown parameter "+args[i]);
jpayne@68: 				assert(false) : "Unknown parameter "+args[i];
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(slow){
jpayne@68: 			for(String s : name){
jpayne@68: 				outstream.println(s+"\t"+nameToTaxid(s));
jpayne@68: 			}
jpayne@68: 			for(Integer s : gi){
jpayne@68: 				outstream.println(s+"\t"+giToTaxid(s));
jpayne@68: 			}
jpayne@68: 			for(String s : acc){
jpayne@68: 				outstream.println(s+"\t"+accessionToTaxid(s));
jpayne@68: 			}
jpayne@68: 		}else{
jpayne@68: 			if(name.size()>0){
jpayne@68: 				int[] ids=nameToTaxidArray(name);
jpayne@68: 				for(int i=0; i<ids.length; i++){
jpayne@68: 					outstream.println(name.get(i)+"\t"+ids[i]);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			if(gi.size()>0){
jpayne@68: 				int[] ids=giToTaxidArray(gi);
jpayne@68: 				for(int i=0; i<ids.length; i++){
jpayne@68: 					outstream.println(gi.get(i)+"\t"+ids[i]);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			if(acc.size()>0){
jpayne@68: 				int[] ids=accessionToTaxidArray(acc);
jpayne@68: 				for(int i=0; i<ids.length; i++){
jpayne@68: 					outstream.println(acc.get(i)+"\t"+ids[i]);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		t.stopAndPrint();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int accessionToTaxid(String accession){
jpayne@68: 		String s=sendAndReceive("pt/accession/",accession);
jpayne@68: 		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
jpayne@68: 		return Integer.parseInt(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int accessionToTaxidSpecificServer(String path, String accession){
jpayne@68: 		String s=sendAndReceiveSpecificServer(path,"pt/accession/",accession);
jpayne@68: 		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
jpayne@68: 		return Integer.parseInt(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int giToTaxid(int gi){
jpayne@68: 		String s=sendAndReceive("pt/gi/",Integer.toString(gi));
jpayne@68: 		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
jpayne@68: 		return Integer.parseInt(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int nameToTaxid(String name){
jpayne@68: 		String s=sendAndReceive("pt/name/",name.replace(' ', '_'));
jpayne@68: 		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
jpayne@68: 		return Integer.parseInt(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int headerToTaxid(String header){
jpayne@68: 		String s=sendAndReceive("pt/name/",header);
jpayne@68: 		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
jpayne@68: 		return Integer.parseInt(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	
jpayne@68: 	public static int[] accessionToTaxidArray(String accession){
jpayne@68: 		String s=sendAndReceive("pt/accession/",accession);
jpayne@68: //		System.err.println("Sent "+accession+"\nReceived "+s);
jpayne@68: 		return splitOutput(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int[] giToTaxidArray(String gi){
jpayne@68: 		String s=sendAndReceive("pt/gi/",gi);
jpayne@68: 		return splitOutput(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int[] nameToTaxidArray(String name){
jpayne@68: 		String s=sendAndReceive("pt/name/",name.replace(' ', '_'));
jpayne@68: 		return splitOutput(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int[] headerToTaxidArray(String header){
jpayne@68: 		String s=sendAndReceive("pt/header/",header);
jpayne@68: 		return splitOutput(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	
jpayne@68: 	public static int[] accessionToTaxidArray(ArrayList<String> accession){
jpayne@68: 		String s=sendAndReceive("pt/accession/",fuse(accession));
jpayne@68: 		return splitOutput(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int[] giToTaxidArray(ArrayList<Integer> gi){
jpayne@68: 		String s=sendAndReceive("pt/gi/",fuse(gi));
jpayne@68: 		return splitOutput(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int[] nameToTaxidArray(ArrayList<String> name){
jpayne@68: 		String s=sendAndReceive("pt/name/",fuse(name).replace(' ', '_'));
jpayne@68: 		return splitOutput(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int[] headerToTaxidArray(ArrayList<String> header){
jpayne@68: 		String s=sendAndReceive("pt/header/",fuse(header));
jpayne@68: 		return splitOutput(s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static final int[] splitOutput(String s){
jpayne@68: 		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return null;}
jpayne@68: 		String[] split=s.split(",");
jpayne@68: 		int[] ret=new int[split.length];
jpayne@68: 		for(int i=0; i<split.length; i++){
jpayne@68: 			ret[i]=Integer.parseInt(split[i]);
jpayne@68: 		}
jpayne@68: 		return ret;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static final String sendAndReceive(String prefix, String message){
jpayne@68: 		String path=Shared.taxServer();
jpayne@68: 		return sendAndReceiveSpecificServer(path, prefix, message);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static final String sendAndReceiveSpecificServer(String path, String prefix, String message){
jpayne@68: 		String response=null;
jpayne@68: 		for(int i=0, millis=200; i<12 && (response==null || response.length()==0); i++) {
jpayne@68: 			if(i>0){
jpayne@68: 				System.err.println("Null response, retrying after "+millis+" ms.");
jpayne@68: 				try {
jpayne@68: 					Thread.sleep(millis);
jpayne@68: 				} catch (InterruptedException e) {
jpayne@68: 					e.printStackTrace();
jpayne@68: 				}
jpayne@68: 				millis*=2;
jpayne@68: 			}
jpayne@68: 			response=sendAndReceiveOnceSpecificServer(path, prefix, message);
jpayne@68: 		}
jpayne@68: 		return response;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static String sendAndReceiveOnce(String prefix, String message){
jpayne@68: 		String path=Shared.taxServer();
jpayne@68: 		return sendAndReceiveOnceSpecificServer(path, prefix, message);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static String sendAndReceiveOnceSpecificServer(String path, String prefix, String message){
jpayne@68: 		final String response;
jpayne@68: 		if(message.length()<2000){//NERSC Apache limit is around 8kb
jpayne@68: 			message=prefix+PercentEncoding.symbolToCode(message);
jpayne@68: 			ByteBuilder bb=ServerTools.readPage(path+message, false);
jpayne@68: 			response=(bb==null ? null : bb.toString());
jpayne@68: 			//			System.err.println("S&R1 send:\n"+path+message);
jpayne@68: 			//			System.err.println("S&R1 receive:\n"+response);
jpayne@68: 		}else{
jpayne@68: 			StringNum sn=ServerTools.sendAndReceive((prefix+message).getBytes(), path+"$POST");
jpayne@68: 			response=sn.s;
jpayne@68: 			//			System.err.println("S&R2: "+message+"\n"+path+"$POST");
jpayne@68: 		}
jpayne@68: 		return response;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static String fuse(ArrayList<?> list){
jpayne@68: 		if(list==null || list.size()<0){return null;}
jpayne@68: 		StringBuilder sb=new StringBuilder();
jpayne@68: 		for(Object s : list){
jpayne@68: 			sb.append(s).append(',');
jpayne@68: 		}
jpayne@68: 		sb.setLength(sb.length()-1);
jpayne@68: 		return sb.toString();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static PrintStream outstream=System.err;
jpayne@68: 	public static boolean verbose=false;
jpayne@68: 	
jpayne@68: }