Create generic msa service instance

diff --git a/j11lib/slivka-client.jar b/j11lib/slivka-client.jar
index 7c00c7c..9efae32 100644 (file)
Binary files a/j11lib/slivka-client.jar and b/j11lib/slivka-client.jar differ

diff --git a/src/jalview/ws/slivkaws/SlivkaDatastore.java b/src/jalview/ws/slivkaws/SlivkaDatastore.java
index 24d11c7..ef10006 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaDatastore.java
+++ b/src/jalview/ws/slivkaws/SlivkaDatastore.java
@@ -8,14 +8,14 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
-import uk.ac.dundee.compbio.slivkaclient.Service;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
 
 public class SlivkaDatastore implements ParamDatastoreI
 {
   private SlivkaParamSet defaultPreset;
   private List<WsParamSetI> presets = new ArrayList<>();
 
-  SlivkaDatastore(Service service) throws IOException {
+  SlivkaDatastore(SlivkaService service) throws IOException {
     defaultPreset = new SlivkaParamSet(service);
     presets.add(defaultPreset);
   }

diff --git a/src/jalview/ws/slivkaws/SlivkaParamSet.java b/src/jalview/ws/slivkaws/SlivkaParamSet.java
index 7feb2f1..86755cb 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaParamSet.java
+++ b/src/jalview/ws/slivkaws/SlivkaParamSet.java
@@ -18,19 +18,20 @@ import uk.ac.dundee.compbio.slivkaclient.DecimalField;
 import uk.ac.dundee.compbio.slivkaclient.Form;
 import uk.ac.dundee.compbio.slivkaclient.FormField;
 import uk.ac.dundee.compbio.slivkaclient.IntegerField;
-import uk.ac.dundee.compbio.slivkaclient.Service;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
 import uk.ac.dundee.compbio.slivkaclient.TextField;
 
 
 
 public class SlivkaParamSet implements WsParamSetI
 {
-  private Service service;
+  private SlivkaService service;
   private List<ArgumentI> args = new ArrayList<>();
 
-  SlivkaParamSet(Service service) throws IOException {
+  SlivkaParamSet(SlivkaService service) throws IOException {
     this.service = service;
-    Form form = service.getForm();
+    SlivkaForm form = service.getForm();
     for (FormField field : form.getFields())
     {
       ArgumentI arg;

diff --git a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
index dfa3d89..2d46c9f 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
@@ -6,6 +6,7 @@ import jalview.ws.WSMenuEntryProviderI;
 import jalview.ws.jws2.MsaWSClient;
 
 import java.awt.event.ActionEvent;
+import java.io.IOError;
 import java.io.IOException;
 import java.net.URISyntaxException;
 
@@ -19,7 +20,6 @@ public class SlivkaWSDiscoverer
 {
   private static SlivkaWSDiscoverer instance = null;
   private SlivkaClient client;
-  private ClustaloWS clustalo;
 
   private SlivkaWSDiscoverer() {
     try
@@ -29,7 +29,6 @@ public class SlivkaWSDiscoverer
     {
       throw new RuntimeException(e);
     }
-    clustalo = new ClustaloWS(client);
   }
 
   public static SlivkaWSDiscoverer getInstance()
@@ -45,38 +44,93 @@ public class SlivkaWSDiscoverer
   {
     JMenu submenu = new JMenu("Slivka");
 
-    JMenuItem noParamMenuItem = new JMenuItem("ClustalO with defaults");
-    noParamMenuItem.addActionListener((ActionEvent e) -> {
-      AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-      if (msa != null)
+    {
+      // clustalo menu entry
+      JMenuItem noParamMenuItem = new JMenuItem("ClustalO with defaults");
+      SlivkaWSInstance clustalo;
+      try
+      {
+        clustalo = new SlivkaWSInstance(client, client.getService("clustalo"));
+      } catch (IOException e)
       {
-        new MsaWSClient(
-            clustalo, alignFrame.getTitle(), msa, false, true,
-            alignFrame.getViewport().getAlignment().getDataset(),
-            alignFrame);
+        throw new IOError(e);
       }
-    });
-    submenu.add(noParamMenuItem);
+      noParamMenuItem.addActionListener((ActionEvent e) -> {
+        AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+        if (msa != null)
+        {
+          new MsaWSClient(
+              clustalo, alignFrame.getTitle(), msa, false, true, alignFrame.getViewport().getAlignment().getDataset(),
+              alignFrame
+          );
+        }
+      });
+      submenu.add(noParamMenuItem);
 
-    JMenuItem parametrisedMenuItem = new JMenuItem("ClustalO with custom parameters");
-    parametrisedMenuItem.addActionListener((ActionEvent evt) -> {
-      AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-      if (msa != null)
+      JMenuItem parametrisedMenuItem = new JMenuItem("ClustalO with custom parameters");
+      parametrisedMenuItem.addActionListener((ActionEvent evt) -> {
+        AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+        if (msa != null)
+        {
+          try
+          {
+            SlivkaParamSet paramSet = new SlivkaParamSet(clustalo.getService());
+            new MsaWSClient(
+                clustalo, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
+                alignFrame.getViewport().getAlignment().getDataset(), alignFrame
+            );
+          } catch (IOException e)
+          {
+            e.printStackTrace();
+          }
+        }
+      });
+      submenu.add(parametrisedMenuItem);
+    }
+
+    {
+      // clustalw2 menu entry
+      JMenuItem noParamMenuItem = new JMenuItem("ClustalW2 with defaults");
+      SlivkaWSInstance clustalo;
+      try
       {
-        try
+        clustalo = new SlivkaWSInstance(client, client.getService("clustalw"));
+      } catch (IOException e)
+      {
+        throw new IOError(e);
+      }
+      noParamMenuItem.addActionListener((ActionEvent e) -> {
+        AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+        if (msa != null)
         {
-          SlivkaParamSet paramSet = new SlivkaParamSet(clustalo.getService());
           new MsaWSClient(
-              clustalo, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
-              alignFrame.getViewport().getAlignment().getDataset(), alignFrame
+              clustalo, alignFrame.getTitle(), msa, false, true, alignFrame.getViewport().getAlignment().getDataset(),
+              alignFrame
           );
-        } catch (IOException e)
+        }
+      });
+      submenu.add(noParamMenuItem);
+
+      JMenuItem parametrisedMenuItem = new JMenuItem("ClustalW2 with custom parameters");
+      parametrisedMenuItem.addActionListener((ActionEvent evt) -> {
+        AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+        if (msa != null)
         {
-          e.printStackTrace();
+          try
+          {
+            SlivkaParamSet paramSet = new SlivkaParamSet(clustalo.getService());
+            new MsaWSClient(
+                clustalo, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
+                alignFrame.getViewport().getAlignment().getDataset(), alignFrame
+            );
+          } catch (IOException e)
+          {
+            e.printStackTrace();
+          }
         }
-      }
-    });
-    submenu.add(parametrisedMenuItem);
+      });
+      submenu.add(parametrisedMenuItem);
+    }
 
     wsmenu.add(submenu);
   }

diff --git a/src/jalview/ws/slivkaws/ClustaloWS.java b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
similarity index 71%
rename from src/jalview/ws/slivkaws/ClustaloWS.java
rename to src/jalview/ws/slivkaws/SlivkaWSInstance.java
index 6a2dae6..d5456a6 100644 (file)
--- a/src/jalview/ws/slivkaws/ClustaloWS.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@ -12,32 +12,34 @@ import jalview.ws.api.MultipleSequenceAlignmentI;
 import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.gui.WsJob;
 import jalview.ws.params.ArgumentI;
+import jalview.ws.params.InvalidArgumentException;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.ParamManager;
 import jalview.ws.params.WsParamSetI;
 
 import java.io.ByteArrayInputStream;
+import java.io.IOError;
 import java.io.IOException;
 import java.io.InputStream;
+import java.rmi.ServerError;
 import java.util.EnumMap;
 import java.util.HashMap;
 import java.util.List;
 
-import uk.ac.dundee.compbio.slivkaclient.FieldType;
-import uk.ac.dundee.compbio.slivkaclient.Form;
 import uk.ac.dundee.compbio.slivkaclient.FormField;
 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
 import uk.ac.dundee.compbio.slivkaclient.JobState;
 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
-import uk.ac.dundee.compbio.slivkaclient.Service;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
 import uk.ac.dundee.compbio.slivkaclient.ValidationException;
 
-public class ClustaloWS extends ServiceWithParameters
+public class SlivkaWSInstance extends ServiceWithParameters
     implements MultipleSequenceAlignmentI, JalviewServiceEndpointProviderI
 {
   private SlivkaClient client;
-  private Service service;
+  private SlivkaService service;
   private SlivkaDatastore store = null;
 
   private EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
@@ -51,19 +53,10 @@ public class ClustaloWS extends ServiceWithParameters
     stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
   }
 
-
-  ClustaloWS(SlivkaClient client)
-  {
-    super("ClustalO", "Alignment", "ClustalO", "Slivka", client.getUrl().toString());
-
+  SlivkaWSInstance(SlivkaClient client, SlivkaService service) {
+    super(service.getName(), "Alignment", service.getName(), "Slivka", client.getUrl().toString());
     this.client = client;
-    try
-    {
-      this.service = client.getService("clustalo");
-    } catch (IOException e)
-    {
-      throw new RuntimeException(e);
-    }
+    this.service = service;
   }
 
   @Override
@@ -78,7 +71,7 @@ public class ClustaloWS extends ServiceWithParameters
     }
   }
 
-  Service getService()
+  SlivkaService getService()
   {
     return service;
   }
@@ -92,6 +85,19 @@ public class ClustaloWS extends ServiceWithParameters
   @Override
   public boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
   {
+    if (_lex instanceof FormValidationException)
+    {
+      FormValidationException formError = (FormValidationException) _lex;
+      String[] messages = new String[formError.getErrors().size()];
+      int i = 0;
+      for (ValidationException e : formError.getErrors())
+      {
+        messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
+      }
+      j.setState(WsJob.JobState.INVALID);
+      j.setStatus(String.join(", ", messages));
+      return true;
+    }
     return false;
   }
 
@@ -102,8 +108,7 @@ public class ClustaloWS extends ServiceWithParameters
   }
 
   @Override
-  public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list)
-      throws IOException
+  public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
   {
     StringBuilder builder = new StringBuilder();
     for (SequenceI seq : toalign)
@@ -113,7 +118,7 @@ public class ClustaloWS extends ServiceWithParameters
     }
     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
     RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
-    Form form = service.getForm();
+    SlivkaForm form = service.getForm();
     HashMap<String, String> values = new HashMap<>(list != null ? list.size() : 0);
     if (list != null)
     {
@@ -124,49 +129,49 @@ public class ClustaloWS extends ServiceWithParameters
     }
     for (FormField field : form.getFields())
     {
-      if (field.getType() == FieldType.FILE)
-      {
+      switch (field.getType()) {
+      case FILE:
         form.insert(field.getName(), file);
-      } else
-      {
+        break;
+      case BOOLEAN:
+        String value = values.get(field.getName());
+        form.insert(field.getName(), (value != null && !value.isBlank()) ? true : false);
+        break;
+      default:
         form.insert(field.getName(), field.valueOf(values.get(field.getName())));
       }
     }
-    try
-    {
-      return new JobId("clustalo", "clustalo", form.submit());
-    } catch (FormValidationException e)
-    {
-      for (ValidationException ve : e.getErrors())
-      {
-        System.out.format("%s: %s%n", ve.getField().getName(), ve.getMessage());
-      }
-      return null;
-    }
+    return new JobId(service.getName(), service.getName(), form.submit());
   }
 
   @Override
-  public AlignmentI getAlignmentFor(JobId jobId)
+  public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
   {
     List<RemoteFile> files;
     try
     {
       files = client.getJobResults(jobId.getJobId());
-      for (RemoteFile f: files) {
+      for (RemoteFile f : files)
+      {
         if (f.getMimeType().equals("application/clustal"))
         {
           return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
         }
       }
-    } catch (IOException e1)
+    } catch (IOException e)
     {
-      // TODO Auto-generated catch block
-      e1.printStackTrace();
+      throw new IOError(e);
     }
     return null;
   }
 
   @Override
+  public Object getEndpoint()
+  {
+    return this;
+  }
+
+  @Override
   public void initParamStore(ParamManager userParameterStore)
   {
     if (store == null)
@@ -176,7 +181,7 @@ public class ClustaloWS extends ServiceWithParameters
         store = new SlivkaDatastore(service);
       } catch (IOException e)
       {
-        throw new RuntimeException(e);
+        throw new IOError(e);
       }
     }
   }
@@ -192,10 +197,4 @@ public class ClustaloWS extends ServiceWithParameters
   {
     return store;
   }
-
-  @Override
-  public Object getEndpoint()
-  {
-    return this;
-  }
 }