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 jalview.io.*;
  29 import jalview.datamodel.*;
  30 import ext.jemboss.*;
  31 import ext.jemboss.soap.*;
  32 import java.io.*;
  33 import java.net.*;
  34 import java.util.Hashtable;
  35 import java.util.Enumeration;
  36 import java.security.Security;
  37
  38
  39 public class Jemboss
  40 {
  41   private static ext.jemboss.JembossParams vamsas_server;
  42
  43   public Jemboss()
  44   {
  45     // Set up default jalview-jemboss server properties
  46     //
  47     vamsas_server = new JembossParams();
  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
  62   public SequenceI[] clustalW(SequenceI[] sequences)
  63   {
  64
  65     // Simplest client call - with gumph from jemboss.server.TestPrivateServer
  66     if (vamsas_server.getPublicSoapURL().startsWith("https"))
  67     {
  68       //SSL settings
  69       //    System.setProperty ("javax.net.debug", "all");
  70       com.sun.net.ssl.internal.ssl.Provider p =
  71           new com.sun.net.ssl.internal.ssl.Provider();
  72       Security.addProvider(p);
  73
  74       //have to do it this way to work with JNLP
  75       URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory()
  76       {
  77         public URLStreamHandler createURLStreamHandler(final String protocol)
  78         {
  79           if(protocol != null && protocol.compareTo("https") == 0)
  80           {
  81             return new com.sun.net.ssl.internal.www.protocol.https.Handler();
  82           }
  83           return null;
  84         }
  85       });
  86
  87       //location of keystore
  88       System.setProperty("javax.net.ssl.trustStore",
  89                          "resources/client.keystore");
  90
  91       String jembossClientKeyStore = System.getProperty("user.home") +
  92           "/.jembossClientKeystore";
  93
  94       try
  95       {
  96         new JembossJarUtil("resources/client.jar").writeByteFile(
  97       "client.keystore",jembossClientKeyStore);
  98         System.setProperty("javax.net.ssl.trustStore",
  99                            jembossClientKeyStore);
 100       }
 101       catch(Exception exp){}
 102
 103     }
 104
 105     Hashtable filesToMove = new Hashtable();
 106     String embossCommand = "emma -sequence jalseqs.fasta -auto";
 107     // Load sequence file into hash
 108     filesToMove.put("jalseqs.fasta",
 109                     jalview.io.FastaFile.print(sequences,124,false).getBytes());
 110
 111     if(vamsas_server.getUseAuth() == true)
 112       if(vamsas_server.getServiceUserName() == null)
 113         System.out.println("jalview.Jemboss: OOPS! Authentication required!");
 114
 115     // submit to private server
 116     try
 117     {
 118       JembossRun thisrun = new JembossRun(embossCommand,"",
 119                                           filesToMove,vamsas_server);
 120       Hashtable h = thisrun.hash();
 121       Enumeration enum = h.keys();
 122       // Find the alignment generated and parse it
 123       while (enum.hasMoreElements())
 124       {
 125         String thiskey = (String)enum.nextElement().toString();
 126         if (thiskey.endsWith(".aln"))
 127         {
 128           // FormatAdapter, and IdentifyFile use a protocol string
 129           // to work out what 'file' is - file/url/Alignmentasastring
 130           String alfile = h.get(thiskey).toString();
 131           String format = IdentifyFile.Identify(alfile, "Paste");
 132           SequenceI[] alignment = null;
 133
 134           if (FormatProperties.contains(format))
 135             alignment = FormatAdapter.read(alfile, "Paste", format);
 136           else
 137             System.out.println("jalview.Jemboss: Unknown format "+format+"\n");
 138           if (alignment == null)
 139             System.out.println("jalview.Jemboss: Couldn't read response:\n"
 140                                + alfile + "\n---EOF\n");
 141           else
 142             return alignment;
 143         }
 144
 145       }
 146
 147     }
 148     catch (JembossSoapException eae)
 149     {
 150       System.out.println("jalview.Jemboss: SOAP ERROR :"+embossCommand
 151                          + "\n" + eae);
 152     }
 153     catch (Exception e) {
 154       System.out.println("jalview.Jemboss: Some other failure :\n"
 155                          +e.getMessage()+"\n");
 156     }
 157
 158     return null;
 159   }
 160 }
 161