--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/TaxClient.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,254 @@
+package tax;
+
+import java.io.PrintStream;
+import java.util.ArrayList;
+
+import server.PercentEncoding;
+import server.ServerTools;
+import shared.Parse;
+import shared.PreParser;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import structures.ByteBuilder;
+import structures.StringNum;
+
+public class TaxClient {
+	
+	public static void main(String[] args){
+		Timer t=new Timer();
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, null, false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+
+		ArrayList<Integer> gi=new ArrayList<Integer>();
+		ArrayList<String> acc=new ArrayList<String>();
+		ArrayList<String> name=new ArrayList<String>();
+		ArrayList<String> header=new ArrayList<String>();
+		
+		boolean slow=true;
+		
+		//Parse each argument
+		for(int i=0; i<args.length; i++){
+			String arg=args[i];
+			
+			//Break arguments into their constituent parts, in the form of "a=b"
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			
+			if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+			}else if(a.equals("name") || a.equals("names")){
+				if(b!=null){
+					for(String s : b.split(",")){
+						name.add(s);
+					}
+				}
+			}else if(a.equals("gi")){
+				if(b!=null){
+					for(String s : b.split(",")){
+						gi.add(Integer.parseInt(s));
+					}
+				}
+			}else if(a.equals("accession")){
+				if(b!=null){
+					for(String s : b.split(",")){
+						acc.add(s);
+					}
+				}
+			}else if(a.equals("header")){
+				if(b!=null){
+					for(String s : b.split(",")){
+						header.add(s);
+					}
+				}
+			}else if(a.equals("slow")){
+				slow=Parse.parseBoolean(b);
+			}else if(a.equals("fast")){
+				slow=!Parse.parseBoolean(b);
+			}else if(a.equals("parse_flag_goes_here")){
+				long fake_variable=Parse.parseKMG(b);
+				//Set a variable here
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+			}
+		}
+		
+		if(slow){
+			for(String s : name){
+				outstream.println(s+"\t"+nameToTaxid(s));
+			}
+			for(Integer s : gi){
+				outstream.println(s+"\t"+giToTaxid(s));
+			}
+			for(String s : acc){
+				outstream.println(s+"\t"+accessionToTaxid(s));
+			}
+		}else{
+			if(name.size()>0){
+				int[] ids=nameToTaxidArray(name);
+				for(int i=0; i<ids.length; i++){
+					outstream.println(name.get(i)+"\t"+ids[i]);
+				}
+			}
+			if(gi.size()>0){
+				int[] ids=giToTaxidArray(gi);
+				for(int i=0; i<ids.length; i++){
+					outstream.println(gi.get(i)+"\t"+ids[i]);
+				}
+			}
+			if(acc.size()>0){
+				int[] ids=accessionToTaxidArray(acc);
+				for(int i=0; i<ids.length; i++){
+					outstream.println(acc.get(i)+"\t"+ids[i]);
+				}
+			}
+		}
+		
+		t.stopAndPrint();
+	}
+	
+	public static int accessionToTaxid(String accession){
+		String s=sendAndReceive("pt/accession/",accession);
+		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
+		return Integer.parseInt(s);
+	}
+	
+	public static int accessionToTaxidSpecificServer(String path, String accession){
+		String s=sendAndReceiveSpecificServer(path,"pt/accession/",accession);
+		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
+		return Integer.parseInt(s);
+	}
+	
+	public static int giToTaxid(int gi){
+		String s=sendAndReceive("pt/gi/",Integer.toString(gi));
+		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
+		return Integer.parseInt(s);
+	}
+	
+	public static int nameToTaxid(String name){
+		String s=sendAndReceive("pt/name/",name.replace(' ', '_'));
+		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
+		return Integer.parseInt(s);
+	}
+	
+	public static int headerToTaxid(String header){
+		String s=sendAndReceive("pt/name/",header);
+		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return -1;}
+		return Integer.parseInt(s);
+	}
+	
+	
+	public static int[] accessionToTaxidArray(String accession){
+		String s=sendAndReceive("pt/accession/",accession);
+//		System.err.println("Sent "+accession+"\nReceived "+s);
+		return splitOutput(s);
+	}
+	
+	public static int[] giToTaxidArray(String gi){
+		String s=sendAndReceive("pt/gi/",gi);
+		return splitOutput(s);
+	}
+	
+	public static int[] nameToTaxidArray(String name){
+		String s=sendAndReceive("pt/name/",name.replace(' ', '_'));
+		return splitOutput(s);
+	}
+	
+	public static int[] headerToTaxidArray(String header){
+		String s=sendAndReceive("pt/header/",header);
+		return splitOutput(s);
+	}
+	
+	
+	public static int[] accessionToTaxidArray(ArrayList<String> accession){
+		String s=sendAndReceive("pt/accession/",fuse(accession));
+		return splitOutput(s);
+	}
+	
+	public static int[] giToTaxidArray(ArrayList<Integer> gi){
+		String s=sendAndReceive("pt/gi/",fuse(gi));
+		return splitOutput(s);
+	}
+	
+	public static int[] nameToTaxidArray(ArrayList<String> name){
+		String s=sendAndReceive("pt/name/",fuse(name).replace(' ', '_'));
+		return splitOutput(s);
+	}
+	
+	public static int[] headerToTaxidArray(ArrayList<String> header){
+		String s=sendAndReceive("pt/header/",fuse(header));
+		return splitOutput(s);
+	}
+	
+	private static final int[] splitOutput(String s){
+		if(s==null || s.length()<1 || !Tools.isDigitOrSign(s.charAt(0))){return null;}
+		String[] split=s.split(",");
+		int[] ret=new int[split.length];
+		for(int i=0; i<split.length; i++){
+			ret[i]=Integer.parseInt(split[i]);
+		}
+		return ret;
+	}
+	
+	private static final String sendAndReceive(String prefix, String message){
+		String path=Shared.taxServer();
+		return sendAndReceiveSpecificServer(path, prefix, message);
+	}
+	
+	private static final String sendAndReceiveSpecificServer(String path, String prefix, String message){
+		String response=null;
+		for(int i=0, millis=200; i<12 && (response==null || response.length()==0); i++) {
+			if(i>0){
+				System.err.println("Null response, retrying after "+millis+" ms.");
+				try {
+					Thread.sleep(millis);
+				} catch (InterruptedException e) {
+					e.printStackTrace();
+				}
+				millis*=2;
+			}
+			response=sendAndReceiveOnceSpecificServer(path, prefix, message);
+		}
+		return response;
+	}
+	
+	private static String sendAndReceiveOnce(String prefix, String message){
+		String path=Shared.taxServer();
+		return sendAndReceiveOnceSpecificServer(path, prefix, message);
+	}
+	
+	private static String sendAndReceiveOnceSpecificServer(String path, String prefix, String message){
+		final String response;
+		if(message.length()<2000){//NERSC Apache limit is around 8kb
+			message=prefix+PercentEncoding.symbolToCode(message);
+			ByteBuilder bb=ServerTools.readPage(path+message, false);
+			response=(bb==null ? null : bb.toString());
+			//			System.err.println("S&R1 send:\n"+path+message);
+			//			System.err.println("S&R1 receive:\n"+response);
+		}else{
+			StringNum sn=ServerTools.sendAndReceive((prefix+message).getBytes(), path+"$POST");
+			response=sn.s;
+			//			System.err.println("S&R2: "+message+"\n"+path+"$POST");
+		}
+		return response;
+	}
+	
+	private static String fuse(ArrayList<?> list){
+		if(list==null || list.size()<0){return null;}
+		StringBuilder sb=new StringBuilder();
+		for(Object s : list){
+			sb.append(s).append(',');
+		}
+		sb.setLength(sb.length()-1);
+		return sb.toString();
+	}
+	
+	public static PrintStream outstream=System.err;
+	public static boolean verbose=false;
+	
+}