Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/Query.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 package tax;
jpayne@68 2
jpayne@68 3 import java.io.IOException;
jpayne@68 4 import java.io.InputStream;
jpayne@68 5 import java.net.MalformedURLException;
jpayne@68 6 import java.net.URL;
jpayne@68 7 import java.util.Arrays;
jpayne@68 8 import java.util.Locale;
jpayne@68 9
jpayne@68 10 import shared.Shared;
jpayne@68 11 import shared.Timer;
jpayne@68 12
jpayne@68 13 public class Query {
jpayne@68 14
jpayne@68 15 /** For testing throughput */
jpayne@68 16 public static void main(String[] args){
jpayne@68 17
jpayne@68 18 // sun.net.http.errorstream.enableBuffering=true;
jpayne@68 19
jpayne@68 20 // System.setProperty("sun.net.http.errorstream.enableBuffering", "true");
jpayne@68 21 // System.setProperty("http.errorstream.enableBuffering", "true");
jpayne@68 22 ////// System.setProperty("", "");
jpayne@68 23 // System.setProperty("http.keepAlive", "true");
jpayne@68 24 // System.setProperty("http.maxConnections", "50");
jpayne@68 25 //// System.setProperty("", "");
jpayne@68 26 //// System.setProperty("", "");
jpayne@68 27 //
jpayne@68 28 // System.out.println("sun.net.http.errorstream.enableBuffering="+System.getProperty("sun.net.http.errorstream.enableBuffering"));
jpayne@68 29 // System.out.println("sun.net.http.errorstream.timeout="+System.getProperty("sun.net.http.errorstream.timeout"));
jpayne@68 30 // System.out.println("sun.net.http.errorstream.bufferSize="+System.getProperty("sun.net.http.errorstream.bufferSize"));
jpayne@68 31 // System.out.println("http.keepAlive="+System.getProperty("http.keepAlive"));
jpayne@68 32 // System.out.println("http.maxConnections="+System.getProperty("http.maxConnections"));
jpayne@68 33 // System.out.println(System.getProperties());
jpayne@68 34 // System.out.println("="+System.getProperty(""));
jpayne@68 35 // System.out.println("="+System.getProperty(""));
jpayne@68 36 // System.out.println("="+System.getProperty(""));
jpayne@68 37
jpayne@68 38 String x=args[0];
jpayne@68 39 int requests=(args.length>1 ? Integer.parseInt(args[1]) : 1);
jpayne@68 40
jpayne@68 41 Timer t=new Timer();
jpayne@68 42 Timer t2=new Timer();
jpayne@68 43 Timer t3=new Timer();
jpayne@68 44
jpayne@68 45 // URL url=toUrl(x);
jpayne@68 46 for(int i=0; i<requests; i++){
jpayne@68 47 String s=request(x);
jpayne@68 48 // System.out.println(s);
jpayne@68 49 if(i==0){t3.start();}
jpayne@68 50 //t2.stop("");
jpayne@68 51 //t2.start();
jpayne@68 52 }
jpayne@68 53
jpayne@68 54 t3.stop();
jpayne@68 55
jpayne@68 56 t.stop("Time: \t");
jpayne@68 57 double qps=requests*1000000000.0/(t.elapsed);
jpayne@68 58 System.err.println(String.format(Locale.ROOT, "Qps: \t%.2f", qps));
jpayne@68 59
jpayne@68 60 System.err.println("Time2: \t"+t3);
jpayne@68 61 double qps2=(requests-1)*1000000000.0/(t3.elapsed);
jpayne@68 62 System.err.println(String.format(Locale.ROOT, "Qps2: \t%.2f", qps2));
jpayne@68 63
jpayne@68 64 // System.out.println(s);
jpayne@68 65
jpayne@68 66 // BufferedReader reader;
jpayne@68 67 // try {
jpayne@68 68 // reader = new BufferedReader(new InputStreamReader(url.openStream(), "UTF-8"));
jpayne@68 69 //
jpayne@68 70 // for (String line; (line = reader.readLine()) != null;) {
jpayne@68 71 // System.out.println(line);
jpayne@68 72 // }
jpayne@68 73 //
jpayne@68 74 // } catch (UnsupportedEncodingException e) {
jpayne@68 75 // // TODO Auto-generated catch block
jpayne@68 76 // e.printStackTrace();
jpayne@68 77 // } catch (IOException e) {
jpayne@68 78 // // TODO Auto-generated catch block
jpayne@68 79 // e.printStackTrace();
jpayne@68 80 // }
jpayne@68 81 }
jpayne@68 82
jpayne@68 83 public static int[] getGi(String...args){
jpayne@68 84 return get("pt_gi", args);
jpayne@68 85 }
jpayne@68 86
jpayne@68 87 public static int[] getAccession(String...args){
jpayne@68 88 return get("pt_accession", args);
jpayne@68 89 }
jpayne@68 90
jpayne@68 91 public static int[] get(String type, String...args){
jpayne@68 92 String host=Shared.taxServer();
jpayne@68 93 StringBuilder sb=new StringBuilder(host.length()+32);
jpayne@68 94 sb.append(host);
jpayne@68 95 sb.append(type);
jpayne@68 96 sb.append('\t');
jpayne@68 97 String comma="";
jpayne@68 98 for(String arg : args){
jpayne@68 99 sb.append(comma);
jpayne@68 100 sb.append(arg);
jpayne@68 101 comma=",";
jpayne@68 102 }
jpayne@68 103 String result=request(sb.toString());
jpayne@68 104 String[] split=result.split(",");
jpayne@68 105 int[] ret=new int[split.length];
jpayne@68 106 for(int i=0; i<split.length; i++){
jpayne@68 107 ret[i]=Integer.parseInt(split[i]);
jpayne@68 108 }
jpayne@68 109 return ret;
jpayne@68 110 }
jpayne@68 111
jpayne@68 112 public static String request(String x){
jpayne@68 113 InputStream is=toStream(x);
jpayne@68 114 if(is==null){return null;}
jpayne@68 115 try {
jpayne@68 116 byte[] buffer=new byte[256];
jpayne@68 117 int count=is.read(buffer);
jpayne@68 118 int next=0;
jpayne@68 119 while(count>-1){
jpayne@68 120 next+=count;
jpayne@68 121 if(next>=buffer.length){
jpayne@68 122 buffer=Arrays.copyOf(buffer, buffer.length*2);
jpayne@68 123 }
jpayne@68 124 count=is.read(buffer, next, buffer.length-next);
jpayne@68 125 }
jpayne@68 126 is.close(); //TODO: Why am I not closing this stream?
jpayne@68 127 return new String(buffer, 0, next);
jpayne@68 128 } catch (IOException e) {
jpayne@68 129 // TODO Auto-generated catch block
jpayne@68 130 e.printStackTrace();
jpayne@68 131 }
jpayne@68 132 try {
jpayne@68 133 is.close();
jpayne@68 134 } catch (IOException e) {
jpayne@68 135 // TODO Auto-generated catch block
jpayne@68 136 e.printStackTrace();
jpayne@68 137 }
jpayne@68 138 return null;
jpayne@68 139 }
jpayne@68 140
jpayne@68 141 public static InputStream toStream(String x){
jpayne@68 142 URL url=null;
jpayne@68 143
jpayne@68 144 try {
jpayne@68 145 url = new URL(x);
jpayne@68 146 } catch (MalformedURLException e1) {
jpayne@68 147 // TODO Auto-generated catch block
jpayne@68 148 e1.printStackTrace();
jpayne@68 149 return null;
jpayne@68 150 }
jpayne@68 151
jpayne@68 152 try {
jpayne@68 153 InputStream is=url.openStream();
jpayne@68 154 return is;
jpayne@68 155 } catch (IOException e) {
jpayne@68 156 // TODO Auto-generated catch block
jpayne@68 157 e.printStackTrace();
jpayne@68 158 }
jpayne@68 159 return null;
jpayne@68 160 }
jpayne@68 161
jpayne@68 162 // public static URL toUrl(String x){
jpayne@68 163 // URL url=null;
jpayne@68 164 // try {
jpayne@68 165 // url = new URL(x);
jpayne@68 166 // } catch (MalformedURLException e1) {
jpayne@68 167 // // TODO Auto-generated catch block
jpayne@68 168 // e1.printStackTrace();
jpayne@68 169 // }
jpayne@68 170 //
jpayne@68 171 // return url;
jpayne@68 172 // }
jpayne@68 173 //
jpayne@68 174 // public static URLConnection toUrlConnection(URL url, String x){
jpayne@68 175 // URLConnection urlc=null;
jpayne@68 176 //
jpayne@68 177 // try {
jpayne@68 178 // urlc = url.openConnection();
jpayne@68 179 // } catch (IOException e) {
jpayne@68 180 // // TODO Auto-generated catch block
jpayne@68 181 // e.printStackTrace();
jpayne@68 182 // }
jpayne@68 183 // return urlc;
jpayne@68 184 // }
jpayne@68 185
jpayne@68 186 }