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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.BBTOOLS_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.BBTOOLS_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;
}
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