X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestClient.java;h=ac1188d08aed6e92af2af5bd5500083796e0a64a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=df9050b2488572ca4f591a6e315d8bd3f705a0c1;hpb=3b12b9d08114c5acef7f8186f0cf79d235fe3416;p=jalview.git

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index df9050b..ac1188d 100644
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -1,3 +1,20 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
 /**
  * 
  */
@@ -5,6 +22,7 @@ package jalview.ws.rest;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.Collection;
 import java.util.Hashtable;
 import java.util.Vector;
 
@@ -14,10 +32,8 @@ import javax.swing.JOptionPane;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
-import com.sun.org.apache.bcel.internal.generic.ISHL;
-
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SequenceGroup;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
@@ -200,10 +216,14 @@ public class RestClient extends WSClient implements WSClientI,
    */
   jalview.io.packed.JalviewDataset jds;
 
+  /**
+   * informative name for results
+   */
+  public String viewTitle;
+
   protected void constructJob()
   {
     service.setInvolvesFlags();
-    
     // record all aspects of alignment view so we can merge back or recreate
     // later
     undoredo = av.getUndoRedoHash();
@@ -214,7 +234,7 @@ public class RestClient extends WSClient implements WSClientI,
      */
     boolean selExists = (av.getSelectionGroup() != null)
             && (av.getSelectionGroup().getSize() > 1);
-    // TODO: revise to full focus+context+dataset input data staging model
+    // TODO: JAL-715: refactor to alignViewport methods and revise to full focus+context+dataset input data staging model
     if (selExists)
     {
       if (service.partitiondata)
@@ -228,6 +248,7 @@ public class RestClient extends WSClient implements WSClientI,
                   av.hasHiddenColumns(), 
                   true, 
                   true);
+          viewTitle = "selected "+(av.hasHiddenColumns() ? "visible" : "") + " region of "+af.getTitle();
         }
         else
         {
@@ -239,7 +260,7 @@ public class RestClient extends WSClient implements WSClientI,
                   false, 
                   true);
         }
-        // TODO: verify that some kind of partition can be constructed from input
+        viewTitle = "select and unselected "+(av.hasHiddenColumns() ? "visible" : "") + " regions from "+af.getTitle();
       }
       else
       {
@@ -250,6 +271,7 @@ public class RestClient extends WSClient implements WSClientI,
                 av.hasHiddenColumns(), 
                 true, 
                 true);
+        viewTitle = "selected "+(av.hasHiddenColumns() ? "visible" : "") + " region of "+af.getTitle();
       }
     } else {
       // standard alignment view without selection present
@@ -259,6 +281,7 @@ public class RestClient extends WSClient implements WSClientI,
               av.hasHiddenColumns(), 
               false, 
               true);
+      viewTitle = ""+(av.hasHiddenColumns() ? "visible region of " : "") + af.getTitle();
     }
     
     RestJobThread jobsthread = new RestJobThread(this);
@@ -274,35 +297,37 @@ public class RestClient extends WSClient implements WSClientI,
     {
       // TODO: try to tell the user why the job couldn't be started.
       JOptionPane.showMessageDialog(Desktop.desktop,
-              "Unable to start web service analysis",
-              "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+              (jobsthread.hasWarnings() ? jobsthread.getWarnings() : "The Job couldn't be started. Please check your input, and the Jalview console for any warning messages."),
+              "Unable to start web service analysis", JOptionPane.WARNING_MESSAGE);
     }
   }
 
   public static RestClient makeShmmrRestClient()
   {
-    String action = "Analyse", description = "Sequence Harmony and Multi-Relief (UNSTABLE!)", name = "Sequence Harmony";
+    String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = "Multi-Harmony";
     Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
     jalview.ws.rest.params.JobConstant toolp;
     //toolp = new jalview.ws.rest.JobConstant("tool","jalview");
     //iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
-    iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
-    iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
-    iparams.put(toolp.token, toolp);
-    toolp = new jalview.ws.rest.params.JobConstant("blast","0");
-    iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
+    //iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
+    //iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
+    //iparams.put(toolp.token, toolp);
+    //toolp = new jalview.ws.rest.params.JobConstant("blast","0");
+    //iparams.put(toolp.token, toolp);
     
     jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
-    aliinput.token = "ali";//_file";
-    aliinput.writeAsFile=false;//true;
+    // SHMR server has a 65K limit for content pasted into the 'ali' parameter, so we always upload our files.
+    aliinput.token = "ali_file";//_file";
+    aliinput.writeAsFile=true;//true;
     //aliinput.token = "ali_file";
     //aliinput.writeAsFile=true;
     iparams.put(aliinput.token, aliinput);
     jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
-    sgroups.minsize=2;
+    sgroups.setMinsize(2);
+    sgroups.min=2;// need at least two group defined to make a partition
     iparams.put("groups", sgroups);
     sgroups.token = "groups";
     sgroups.sep = " ";
@@ -310,7 +335,7 @@ public class RestClient extends WSClient implements WSClientI,
             action,
             description,
             name,
-            "http://www.ibi.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
+            "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
             "?tool=jalview", iparams, true, false, '-');
     // a priori knowledge of the data returned from the service
     shmrService.addResultDatatype(JvDataType.ANNOTATION);
@@ -336,4 +361,92 @@ public class RestClient extends WSClient implements WSClientI,
     return true;
   }
 
+  protected static Vector<String> services=null;
+  public static final String RSBS_SERVICES="RSBS_SERVICES";
+  public static RestClient[] getRestClients()
+  {
+    if (services==null)
+    {
+      services = new Vector<String>();
+      try {
+      for (RestServiceDescription descr: RestServiceDescription.parseDescriptions(jalview.bin.Cache.getDefault(RSBS_SERVICES,makeShmmrRestClient().service.toString()))) 
+      {
+        services.add(descr.toString());
+      }
+      }
+      catch (Exception ex) {
+        System.err.println("Serious - RSBS descriptions in user preferences are corrupt!");
+        ex.printStackTrace();
+      }
+      
+    }
+    RestClient[] lst = new RestClient[services.size()];
+    int i=0;
+    for (String svc:services) {
+      lst[i++] = new RestClient(new RestServiceDescription(svc));
+    }
+    return lst;
+  }
+  public static void main(String args[])
+  {
+    try {
+      RestClient[] clients = getRestClients();
+      System.out.println("Got "+clients.length+" clients.");
+      int i=0;
+      Vector<String> urls=new Vector<String>();
+      for (RestClient cl:clients) {
+        System.out.println(""+(++i)+": "+cl.service.toString());
+        urls.add(cl.service.toString());
+      }
+      setRsbsServices(urls);
+      if (clients.length!=getRestClients().length)
+      {
+        System.err.println("Failed. Differing numbers of clients when stringified and parsed again.");
+      }
+      
+    } catch (Throwable x)
+    {
+      System.err.println("Failed. Unexpected exception.");
+      x.printStackTrace();
+    }
+  }
+  public String getAction()
+  {
+    return service.details.Action;
+  }
+
+  public RestServiceDescription getRestDescription()
+  {
+    return service;
+  }
+
+  public static Vector<String> getRsbsDescriptions()
+  {
+    Vector<String> rsbsDescrs = new Vector<String>();
+    for (RestClient rsbs:getRestClients())
+    {
+      rsbsDescrs.add(rsbs.getRestDescription().toString());
+    }
+    return rsbsDescrs;
+  }
+
+  public static void setRsbsServices(Vector<String> rsbsUrls)
+  {
+    if (rsbsUrls!=null)
+    {
+      // TODO: consider validating services ?
+      services = new Vector<String>(rsbsUrls);
+      StringBuffer sprop = new StringBuffer();
+      for (String s:services)
+      {
+        sprop.append(s);
+      }
+      Cache.setProperty(RSBS_SERVICES, sprop.toString());
+    } 
+    else
+    {
+      Cache.removeProperty(RSBS_SERVICES);
+    }
+  }
+
 }