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     System.out.println("Jemboss Server Init\n"
  48                        + vamsas_server.serverDescription()
  49                        + "\nUser Authorisation ? "
  50                        + vamsas_server.getUseAuth()
  51                        +"\n");
  52   }
  53
  54   /* public void updateServer(JembossParams props)
  55   {
  56     vamsas_server.updateJembossPropStrings (
  57       props.getEmbossEnvironmentArray());
  58   }
  59   */
  60
  61   public SequenceI[] clustalW(SequenceI[] sequences)
  62   {
  63
  64     // Simplest client call - with gumph from jemboss.server.TestPrivateServer
  65     if (vamsas_server.getPublicSoapURL().startsWith("https"))
  66     {
  67       //SSL settings
  68       //    System.setProperty ("javax.net.debug", "all");
  69       com.sun.net.ssl.internal.ssl.Provider p =
  70           new com.sun.net.ssl.internal.ssl.Provider();
  71       Security.addProvider(p);
  72
  73       //have to do it this way to work with JNLP
  74       URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory()
  75       {
  76         public URLStreamHandler createURLStreamHandler(final String protocol)
  77         {
  78           if(protocol != null && protocol.compareTo("https") == 0)
  79           {
  80             return new com.sun.net.ssl.internal.www.protocol.https.Handler();
  81           }
  82           return null;
  83         }
  84       });
  85
  86       //location of keystore
  87       System.setProperty("javax.net.ssl.trustStore",
  88                          "resources/client.keystore");
  89
  90       String jembossClientKeyStore = System.getProperty("user.home") +
  91           "/.jembossClientKeystore";
  92
  93       try
  94       {
  95         new JembossJarUtil("resources/client.jar").writeByteFile(
  96       "client.keystore",jembossClientKeyStore);
  97         System.setProperty("javax.net.ssl.trustStore",
  98                            jembossClientKeyStore);
  99       }
 100       catch(Exception exp){}
 101
 102     }
 103
 104     Hashtable filesToMove = new Hashtable();
 105     String embossCommand = "emma -sequence jalseqs.fasta -auto";
 106     // Load sequence file into hash
 107     filesToMove.put("jalseqs.fasta",
 108                     jalview.io.FastaFile.print(sequences,124,false).getBytes());
 109
 110     if(vamsas_server.getUseAuth() == true)
 111       if(vamsas_server.getServiceUserName() == null)
 112         System.out.println("jalview.Jemboss: OOPS! Authentication required!");
 113
 114     // submit to private server
 115     try
 116     {
 117       JembossRun thisrun = new JembossRun(embossCommand,"",
 118                                           filesToMove,vamsas_server);
 119       Hashtable h = thisrun.hash();
 120       Enumeration enum = h.keys();
 121       // Find the alignment generated and parse it
 122       while (enum.hasMoreElements())
 123       {
 124         String thiskey = (String)enum.nextElement().toString();
 125         if (thiskey.endsWith(".aln"))
 126         {
 127           // FormatAdapter, and IdentifyFile use a protocol string
 128           // to work out what 'file' is - file/url/Alignmentasastring
 129           String alfile = h.get(thiskey).toString();
 130           String format = IdentifyFile.Identify(alfile, "Paste");
 131           SequenceI[] alignment = null;
 132
 133           if (FormatProperties.contains(format))
 134             alignment = FormatAdapter.read(alfile, "Paste", format);
 135           else
 136             System.out.println("jalview.Jemboss: Unknown format "+format+"\n");
 137           if (alignment == null)
 138             System.out.println("jalview.Jemboss: Couldn't read response:\n"
 139                                + alfile + "\n---EOF\n");
 140           else
 141             return alignment;
 142         }
 143
 144       }
 145
 146     }
 147     catch (JembossSoapException eae)
 148     {
 149       System.out.println("jalview.Jemboss: SOAP ERROR :"+embossCommand
 150                          + "\n" + eae);
 151     }
 152     catch (Exception e) {
 153       System.out.println("jalview.Jemboss: Some other failure :\n"
 154                          +e.getMessage()+"\n");
 155     }
 156
 157     return null;
 158   }
 159 }
 160