src/jalview/ws/Jemboss.java

   1 package jalview.ws;
   2
   3 /**
   4  * <p>Title: JalviewX</p>
   5  * <p>Description: Jalview Re-engineered</p>
   6  * <p>Copyright: Copyright (c) 2004</p>
   7  * <p>Company: Dundee University</p>
   8  * @author not attributable
   9  * @version 1.0
  10  * Commenced 14th January 2005, Jim Procter
  11  * Contains and depends on GPL-2 jemboss classes
  12  * see http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/index.html
  13  */
  14
  15 /**
  16  * Philosophy
  17  * Jemboss webservices are implemented here as re-entrant synchronous SOAP
  18  * exchanges. It is up to the user of the class whether these exchanges
  19  * are executed in their own thread to effect background processing
  20  * functionality.
  21  *
  22  * Things to do
  23  * Test threadability
  24  * Standardise the exceptions (currently errors are output on stdout)
  25  * Allow server configuration
  26  */
  27
  28 import java.net.*;
  29 import java.security.*;
  30 import java.util.*;
  31
  32 import ext.jemboss.*;
  33 import ext.jemboss.soap.*;
  34 import jalview.datamodel.*;
  35 import jalview.io.*;
  36
  37
  38 public class Jemboss
  39 {
  40   private static ext.jemboss.JembossParams vamsas_server;
  41
  42   public Jemboss()
  43   {
  44     // Set up default jalview-jemboss server properties
  45     //
  46     vamsas_server = new JembossParams();
  47     vamsas_server.setCurrentMode("interactive");
  48     System.out.println("Jemboss Server Init\n"
  49                        + vamsas_server.serverDescription()
  50                        + "\nUser Authorisation ? "
  51                        + vamsas_server.getUseAuth()
  52                        +"\n");
  53   }
  54
  55   /* public void updateServer(JembossParams props)
  56   {
  57     vamsas_server.updateJembossPropStrings (
  58       props.getEmbossEnvironmentArray());
  59   }
  60   */
  61     private Hashtable uniquify(SequenceI[] sequences) {
  62         // Generate a safely named sequence set and a hash to recover the sequence names
  63         Hashtable map = new Hashtable();
  64         for (int i=0; i<sequences.length; i++) {
  65             String safename = new String("Sequence"+i);
  66             map.put(safename, sequences[i].getName());
  67             sequences[i].setName(safename);
  68         }
  69         return map;
  70     }
  71
  72     private boolean deuniquify(Hashtable map, SequenceI[] sequences) {
  73         // recover unsafe sequence names for a sequence set
  74         boolean allfound=true;
  75         for (int i=0; i<sequences.length; i++) {
  76             if (map.containsKey(sequences[i].getName())) {
  77                 String unsafename = (String) map.get(sequences[i].getName());
  78                 sequences[i].setName(unsafename);
  79             } else {
  80                 allfound=false;
  81             }
  82         }
  83         return allfound;
  84     }
  85
  86   public SequenceI[] clustalW(SequenceI[] sequences)
  87   {
  88
  89     // Simplest client call - with gumph from jemboss.server.TestPrivateServer
  90     if (vamsas_server.getPublicSoapURL().startsWith("https"))
  91     {
  92       //SSL settings
  93       //    System.setProperty ("javax.net.debug", "all");
  94       com.sun.net.ssl.internal.ssl.Provider p =
  95           new com.sun.net.ssl.internal.ssl.Provider();
  96       Security.addProvider(p);
  97
  98       //have to do it this way to work with JNLP
  99       URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory()
 100       {
 101         public URLStreamHandler createURLStreamHandler(final String protocol)
 102         {
 103           if(protocol != null && protocol.compareTo("https") == 0)
 104           {
 105             return new com.sun.net.ssl.internal.www.protocol.https.Handler();
 106           }
 107           return null;
 108         }
 109       });
 110
 111       //location of keystore
 112       System.setProperty("javax.net.ssl.trustStore",
 113                          "resources/client.keystore");
 114
 115       String jembossClientKeyStore = System.getProperty("user.home") +
 116           "/.jembossClientKeystore";
 117
 118       try
 119       {
 120         new JembossJarUtil("resources/client.jar").writeByteFile(
 121       "client.keystore",jembossClientKeyStore);
 122         System.setProperty("javax.net.ssl.trustStore",
 123                            jembossClientKeyStore);
 124       }
 125       catch(Exception exp){}
 126
 127     }
 128
 129     Hashtable filesToMove = new Hashtable();
 130     String embossCommand = "emma -sequence jalseqs.fasta -auto";
 131     // Duplicate
 132     SequenceI[] myseq = new SequenceI[sequences.length];
 133     for (int i=0; i<sequences.length; i++) {
 134         myseq[i] = new Sequence(sequences[i]);
 135     }
 136     // Uniqueify, and
 137     Hashtable namemap = uniquify(myseq);
 138     // Load sequence file into hash
 139
 140     filesToMove.put("jalseqs.fasta",
 141                     jalview.io.FastaFile.print(myseq,124,false).getBytes());
 142
 143     if(vamsas_server.getUseAuth() == true)
 144       if(vamsas_server.getServiceUserName() == null)
 145         System.out.println("jalview.Jemboss: OOPS! Authentication required!");
 146
 147     // submit to private server
 148     try
 149     {
 150       JembossRun thisrun = new JembossRun(embossCommand,"",
 151                                           filesToMove,vamsas_server);
 152       Hashtable h = thisrun.hash();
 153       Enumeration enum = h.keys();
 154       // Find the alignment generated and parse it
 155       while (enum.hasMoreElements())
 156       {
 157         String thiskey = (String)enum.nextElement().toString();
 158         if (thiskey.endsWith(".aln"))
 159         {
 160           // FormatAdapter, and IdentifyFile use a protocol string
 161           // to work out what 'file' is - file/url/Alignmentasastring
 162           String alfile = h.get(thiskey).toString();
 163           String format = IdentifyFile.Identify(alfile, "Paste");
 164           SequenceI[] alignment = null;
 165
 166           if (FormatProperties.contains(format))
 167             alignment = FormatAdapter.read(alfile, "Paste", format);
 168           else
 169             System.out.println("jalview.Jemboss: Unknown format "+format+"\n");
 170           if (alignment == null)
 171             System.out.println("jalview.Jemboss: Couldn't read response:\n"
 172                                + alfile + "\n---EOF\n");
 173           else {
 174             if (!deuniquify(namemap, alignment)) {
 175                   System.out.println("jalview.Jemboss: Warning: Some of the "
 176                                      +"original sequence names have not been recovered!\n");
 177             }
 178             return alignment;
 179           }
 180         }
 181
 182       }
 183
 184     }
 185     catch (JembossSoapException eae)
 186     {
 187       System.out.println("jalview.Jemboss: SOAP ERROR :"+embossCommand
 188                          + "\n" + eae);
 189     }
 190     catch (Exception e) {
 191       System.out.println("jalview.Jemboss: Some other failure :\n"
 192                          +e.getMessage()+"\n");
 193     }
 194
 195     return null;
 196   }
 197 }
 198