From 1150d64d19f544a302de4a581e1a7979d04bb820 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 24 Nov 2005 12:14:53 +0000
Subject: [PATCH] New EBI WS implementation

---
 src/jalview/io/EBIFetchClient.java  |    1 +
 src/jalview/io/WSWUBlastClient.java |  103 ++++++++++++++++-------------------
 2 files changed, 49 insertions(+), 55 deletions(-)

diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index c1a0302..0012ffe 100755
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -147,6 +147,7 @@ public class EBIFetchClient
       File outFile = null;
       try{
         outFile = File.createTempFile("jalview", ".xml");
+        outFile.deleteOnExit();
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
         int index=0;
         while( index < data.length )
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index e6800bc..0906d12 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -31,6 +31,7 @@ import javax.swing.*;
 import javax.xml.namespace.QName;
 import jalview.analysis.AlignSeq;
 
+import uk.ac.ebi.www.*;
 
 /**
  * DOCUMENT ME!
@@ -57,8 +58,13 @@ public class WSWUBlastClient
         this.ap = ap;
         this.al = al;
         output.setText(
-            "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +
-            "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");
+            "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
+            +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
+            +"\n\nRunning WSWUBlast at EBI."
+            +"\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
+            +"\nSOAP-based services provided by the European Bioinformatics Institute."
+            +"\nNucleic Acids Res. 33(1):W25-W28 (2005));");
+
         Desktop.addInternalFrame(output,
             "BLASTing for unidentified sequences ", 800, 300);
 
@@ -89,7 +95,7 @@ public class WSWUBlastClient
         String data;
         String id2;
         int maxFound = 90;
-        StringBuffer buffer = new StringBuffer("\n\n" + seq.getShortName() + " :");
+        StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
 
         while (st.hasMoreTokens())
         {
@@ -238,26 +244,23 @@ public class WSWUBlastClient
             {
                 try
                 {
-                    Call call = (Call) new Service().createCall();
-                    call.setTargetEndpointAddress(new java.net.URL(
-                            "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
-                    call.setOperationName(new QName("WSWUBlast", "polljob"));
-
-                    Object object = (String) call.invoke(new Object[]
-                            {
-                                jobid, "xml"
-                            });
-
-                    if(object instanceof String)
-                    {
-                      parseResult(sequence, (String)object);
+                  WSWUBlastService service =  new WSWUBlastServiceLocator();
+                  WSWUBlast wublast = service.getWSWUBlast();
+                  WSFile[] results = wublast.getResults(jobid);
+
+                  if(results!=null)
+                  {
+                      String result = new String(wublast.poll(jobid, "tooloutput"));
+                      parseResult(sequence, result);
                       jobComplete = true;
                       jobsRunning--;
-                    }
-
-                    Thread.sleep(5000);
-
-                    System.out.println("WSWuBlastClient: I'm alive "+sequence.getShortName()+" "+jobid); // log.debug
+                  }
+                  else
+                  {
+                    Thread.sleep(10000);
+                    System.out.println("WSWuBlastClient: I'm alive " +
+                                       sequence.getName() + " " + jobid); // log.debug
+                  }
                 }
                 catch (Exception ex)
                 {
@@ -267,46 +270,36 @@ public class WSWUBlastClient
 
         void StartJob()
         {
-            HashMap params = new HashMap();
-            params.put("database", "uniprot");
-            params.put("sensitivity", "low");
-            params.put("sort", "totalscore");
-            params.put("matrix", "pam10");
-            params.put("program", "blastp");
-            params.put("alignments", "5");
-            params.put("type", "xml");
-            params.put("async", "true");
-
-            byte[] seqbytes = AlignSeq.extractGaps("-. ",
-                                                  sequence.getSequence()).getBytes();
-
-            try
-            {
-                Call call = (Call) new Service().createCall();
-                call.setTargetEndpointAddress(new java.net.URL(
-                        "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
-                call.setOperationName(new QName("WSWUBlast", "doWUBlast"));
-
-                Object object = call.invoke(new Object[]
-                        {
-                            params, seqbytes
-                        });
+          InputParams params = new InputParams();
 
-                if(object instanceof byte[])
-                  jobid = new String( (byte[])object);
+          params.setProgram("blastp");
+          params.setDatabase("uniprot");
+          params.setMatrix("pam10");
 
-                else
-                {
-                  jobComplete = true;
-                  jobsRunning--;
-                  parseResult(sequence, (String)object);
-                }
+          params.setNumal(5);
+          params.setSensitivity("low");
+          params.setSort("totalscore");
+          params.setOutformat("txt");
+          params.setAsync(true);
 
+            try
+            {
+              Data inputs[] = new Data[1];
+              Data input= new Data();
+              input.setType("sequence");
+              input.setContent(AlignSeq.extractGaps("-. ",sequence.getSequence()));
+              inputs[0]=input;
+
+              WSWUBlastService service = new WSWUBlastServiceLocator();
+              WSWUBlast wublast = service.getWSWUBlast();
+              jobid = wublast.runWUBlast(params, inputs);
             }
             catch (Exception exp)
             {
-                System.err.println("WSWUBlastClient error:\n" + exp.toString());
-                exp.printStackTrace();
+              jobComplete = true;
+              jobsRunning--;
+              System.err.println("WSWUBlastClient error:\n" + exp.toString());
+              exp.printStackTrace();
             }
         }
     }
-- 
1.7.10.2