--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/shared/MetadataWriter.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,115 @@
+package shared;
+
+import java.net.InetAddress;
+import java.net.UnknownHostException;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+
+import fileIO.ReadWrite;
+import json.JsonObject;
+
+public class MetadataWriter {
+	
+	public static void write(String fname, long readsIn, long basesIn, long readsOut, long basesOut, boolean append){
+		if(fname==null){fname=fnameStatic;}
+		if(fname==null){return;}
+		fnameStatic=null;
+		final String s;
+		if(jsonMode){
+			s=toJson(readsIn, basesIn, readsOut, basesOut);
+		}else{
+			s=toTsv(readsIn, basesIn, readsOut, basesOut);
+		}
+		ReadWrite.writeStringInThread(s, fname, append);
+	}
+	
+	public static String toTsv(long readsIn, long basesIn, long readsOut, long basesOut){
+		Map<String,String> env=System.getenv();
+		StringBuilder sb=new StringBuilder();
+		
+		sb.append("Time\t").append(new Date()).append('\n');
+		try {
+			sb.append("Host\t").append(InetAddress.getLocalHost().getHostName()).append('\n');
+		} catch (UnknownHostException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		sb.append("BBToolsVersion\t").append(Shared.BBMAP_VERSION_STRING).append('\n');
+		sb.append("JavaVersion\t").append(Shared.javaVersion).append('\n');
+		sb.append("Command\t").append(Shared.fullCommandline()).append('\n');
+		String script=commandToShellscript(Shared.fullCommandline());
+		if(script!=null){sb.append("Script\t").append(script).append('\n');}
+		sb.append("ReadsIn\t").append(readsIn).append('\n');
+		sb.append("BasesIn\t").append(basesIn).append('\n');
+		sb.append("ReadsOut\t").append(readsOut).append('\n');
+		sb.append("BasesOut\t").append(basesOut).append('\n');
+		return sb.toString();
+	}
+	
+	public static String toJson(long readsIn, long basesIn, long readsOut, long basesOut){
+		Map<String,String> env=System.getenv();
+		JsonObject jo=new JsonObject();
+		
+		jo.add("Time", new Date().toString());
+		try {
+			jo.add("Host", InetAddress.getLocalHost().getHostName());
+		} catch (UnknownHostException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+//		jo.add("Host", env.get("HOSTNAME"));
+//		assert(false) : env;InetAddress.getLocalHost().getHostName()
+		jo.add("BBToolsVersion", Shared.BBMAP_VERSION_STRING);
+		jo.add("JavaVersion", Shared.javaVersion);
+		jo.add("Command", Shared.fullCommandline());
+		String script=commandToShellscript(Shared.fullCommandline());
+		if(script!=null){jo.add("Script", script);}
+		jo.add("ReadsIn", readsIn);
+		jo.add("BasesIn", basesIn);
+		jo.add("ReadsOut", readsOut);
+		jo.add("BasesOut", basesOut);
+		return jo.toString();
+	}
+	
+	private static String commandToShellscript(String command) {
+		if(command==null) {return null;}
+		final HashMap<String, String> map=shellMap();
+		String[] split=command.split(" ");
+		int pos=0;
+		for(pos=0; pos<split.length; pos++){
+			if(map.containsKey(split[pos])){
+				split[pos]=map.get(split[pos]);
+				break;
+			}
+		}
+		if(pos>=split.length){return null;}
+		StringBuilder sb=new StringBuilder();
+		for(; pos<split.length; pos++){
+			sb.append(split[pos]);
+			sb.append(' ');
+		}
+		sb.setLength(sb.length()-1);
+		return sb.toString();
+	}
+	
+	/** Anything in this map will have the command line translated
+	 * to the equivalent shell script command for the "Script" key */
+	private static HashMap<String, String> shellMap(){
+		HashMap<String, String> map=new HashMap<String, String>();
+		map.put("bloom.BloomFilterCorrectorWrapper", "bbcms.sh");
+		map.put("jgi.ReformatReads", "reformat.sh");
+		map.put("jgi.FungalRelease", "fungalrelease.sh");
+		map.put("jgi.MakeLengthHistogram", "readlength.sh");
+		map.put("jgi.AssemblyStats2", "stats.sh");
+		map.put("jgi.BBDuk", "bbduk.sh");
+		map.put("assemble.Tadpole", "tadpole.sh");
+		map.put("sketch.SendSketch", "sendsketch.sh");
+		map.put("clump.Clumpify", "clumpify.sh");
+		return map;
+	}
+	
+	public static String fnameStatic;
+	public static boolean jsonMode=true;
+	
+}