JAL-3066 Move common web service methods to abstract SlivkaWSInstance

ServiceWithParameters and JalviewWebService overriden methods would be common to both Msa and Annotation services thus they are moved to the common abstract base class.

diff --git a/j11lib/slivka-client.jar b/j11lib/slivka-client.jar
index 12cc028..c990dd8 100644 (file)
Binary files a/j11lib/slivka-client.jar and b/j11lib/slivka-client.jar differ

diff --git a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
new file mode 100644 (file)
index 0000000..726b556
--- /dev/null
+++ b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
@@ -0,0 +1,95 @@
+package jalview.ws.slivkaws;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.ws.api.JobId;
+import jalview.ws.api.MultipleSequenceAlignmentI;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.InvalidArgumentException;
+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.HashMap;
+import java.util.List;
+
+import uk.ac.dundee.compbio.slivkaclient.FormField;
+import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
+
+public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
+{
+  SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service) {
+    super(client, service, "Alignment");
+  }
+
+  @Override
+  public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
+  {
+    StringBuilder builder = new StringBuilder();
+    for (SequenceI seq : toalign)
+    {
+      builder.append(">").append(seq.getName()).append("\n");
+      builder.append(seq.getSequence()).append("\n");
+    }
+    InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
+    RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
+    SlivkaForm form = service.getForm();
+    HashMap<String, String> values = new HashMap<>(list != null ? list.size() : 0);
+    if (list != null)
+    {
+      for (ArgumentI arg : list)
+      {
+        values.put(arg.getName(), arg.getValue());
+      }
+    }
+    for (FormField field : form.getFields())
+    {
+      switch (field.getType()) {
+      case FILE:
+        form.insert(field.getName(), file);
+        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())));
+      }
+    }
+    return new JobId(service.getName(), service.getName(), form.submit());
+  }
+
+  @Override
+  public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
+  {
+    List<RemoteFile> files;
+    try
+    {
+      files = client.getJobResults(jobId.getJobId());
+      for (RemoteFile f : files)
+      {
+        if (f.getMimeType().equals("application/clustal"))
+        {
+          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
+        }
+        else if (f.getMimeType().equals("application/fasta"))
+        {
+          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
+        }
+      }
+    } catch (IOException e)
+    {
+      throw new IOError(e);
+    }
+    return null;
+  }
+}

diff --git a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
index 009e388..54cfbc4 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
@@ -59,7 +59,7 @@ public class SlivkaWSDiscoverer
           }
           continue;
         }
-        SlivkaWSInstance instance = new SlivkaWSInstance(client, service);
+        SlivkaMsaServiceInstance instance = new SlivkaMsaServiceInstance(client, service);
         JMenuItem defaultEntry = new JMenuItem(String.format("%s with defaults", service.label));
         defaultEntry.addActionListener((ActionEvent evt) -> {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();

diff --git a/src/jalview/ws/slivkaws/SlivkaWSInstance.java b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
index 8bb554a..751637c 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@ -1,48 +1,33 @@
 package jalview.ws.slivkaws;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
 import jalview.gui.WebserviceInfo;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
 import jalview.ws.api.JalviewServiceEndpointProviderI;
-import jalview.ws.api.JobId;
-import jalview.ws.api.MultipleSequenceAlignmentI;
+import jalview.ws.api.JalviewWebServiceI;
 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.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.SlivkaClient;
-import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
 import uk.ac.dundee.compbio.slivkaclient.ValidationException;
 
-public class SlivkaWSInstance extends ServiceWithParameters
-    implements MultipleSequenceAlignmentI, JalviewServiceEndpointProviderI
+public abstract class SlivkaWSInstance extends ServiceWithParameters
+    implements JalviewServiceEndpointProviderI, JalviewWebServiceI
 {
-  private SlivkaClient client;
-  private SlivkaService service;
-  private SlivkaDatastore store = null;
+  protected final SlivkaClient client;
 
-  private EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
+  protected final SlivkaService service;
+
+  protected SlivkaDatastore store = null;
+
+  protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
   {
     stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
     stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
@@ -53,37 +38,33 @@ public class SlivkaWSInstance extends ServiceWithParameters
     stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
   }
 
-  SlivkaWSInstance(SlivkaClient client, SlivkaService service) {
-    super(service.getName(), "Alignment", service.getName(), "Slivka", client.getUrl().toString());
+  public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
+  {
+    super(service.getName(), action, service.getLabel(), "Slivka", client.getUrl().toString());
     this.client = client;
     this.service = service;
   }
 
   @Override
-  public void updateStatus(WsJob job)
+  public final void updateStatus(WsJob job)
   {
     try
     {
       job.setState(stateMap.get(client.getJobState(job.getJobId())));
     } catch (IOException e)
     {
-      throw new RuntimeException(e);
+      throw new IOError(e);
     }
   }
 
-  SlivkaService getService()
-  {
-    return service;
-  }
-
   @Override
-  public boolean updateJobProgress(WsJob job)
+  public final boolean updateJobProgress(WsJob job)
   {
     return false;
   }
 
   @Override
-  public boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
+  public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
   {
     if (_lex instanceof FormValidationException)
     {
@@ -102,81 +83,25 @@ public class SlivkaWSInstance extends ServiceWithParameters
   }
 
   @Override
-  public boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
+  public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
   {
+    // TODO
     return false;
   }
 
-  @Override
-  public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
-  {
-    StringBuilder builder = new StringBuilder();
-    for (SequenceI seq : toalign)
-    {
-      builder.append(">").append(seq.getName()).append("\n");
-      builder.append(seq.getSequence()).append("\n");
-    }
-    InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
-    RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
-    SlivkaForm form = service.getForm();
-    HashMap<String, String> values = new HashMap<>(list != null ? list.size() : 0);
-    if (list != null)
-    {
-      for (ArgumentI arg : list)
-      {
-        values.put(arg.getName(), arg.getValue());
-      }
-    }
-    for (FormField field : form.getFields())
-    {
-      switch (field.getType()) {
-      case FILE:
-        form.insert(field.getName(), file);
-        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())));
-      }
-    }
-    return new JobId(service.getName(), service.getName(), form.submit());
-  }
-
-  @Override
-  public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
+  final SlivkaService getService()
   {
-    List<RemoteFile> files;
-    try
-    {
-      files = client.getJobResults(jobId.getJobId());
-      for (RemoteFile f : files)
-      {
-        if (f.getMimeType().equals("application/clustal"))
-        {
-          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
-        }
-        else if (f.getMimeType().equals("application/fasta"))
-        {
-          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
-        }
-      }
-    } catch (IOException e)
-    {
-      throw new IOError(e);
-    }
-    return null;
+    return service;
   }
 
   @Override
-  public Object getEndpoint()
+  public final Object getEndpoint()
   {
     return this;
   }
 
   @Override
-  public void initParamStore(ParamManager userParameterStore)
+  public final void initParamStore(ParamManager userParameterStore)
   {
     if (store == null)
     {
@@ -197,8 +122,9 @@ public class SlivkaWSInstance extends ServiceWithParameters
   }
 
   @Override
-  public ParamDatastoreI getParamStore()
+  public final ParamDatastoreI getParamStore()
   {
     return store;
   }
+
 }