JAL-6386 update slivka client for j2s compatibility

[jalview.git] / src / jalview / ws / slivkaws / SlivkaWSInstance.java

diff --git a/src/jalview/ws/slivkaws/SlivkaWSInstance.java b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
index a5c809f..a21354e 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@ -1,13 +1,18 @@
 package jalview.ws.slivkaws;
 
+import jalview.datamodel.SequenceI;
 import jalview.gui.WebserviceInfo;
 import jalview.ws.api.JalviewServiceEndpointProviderI;
 import jalview.ws.api.JalviewWebServiceI;
+import jalview.ws.api.JobId;
 import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.gui.WsJob;
+import jalview.ws.params.ArgumentI;
 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;
@@ -19,10 +24,13 @@ import java.util.List;
 import java.util.Optional;
 import java.util.Set;
 
+import uk.ac.dundee.compbio.slivkaclient.FieldType;
+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;
 
@@ -38,9 +46,13 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
   protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
   {
     stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
+    stateMap.put(JobState.REJECTED, WsJob.JobState.INVALID);
+    stateMap.put(JobState.ACCEPTED, WsJob.JobState.QUEUED);
     stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
     stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
     stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
+    stateMap.put(JobState.INTERRUPED, WsJob.JobState.CANCELLED);
+    stateMap.put(JobState.DELETED, WsJob.JobState.CANCELLED);
     stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
     stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
     stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
@@ -57,6 +69,50 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
     this.service = service;
   }
 
+  protected final JobId submit(List<SequenceI> sequences,
+          WsParamSetI preset, List<ArgumentI> args) throws Throwable
+  {
+    SlivkaForm form = service.getForm();
+    Optional<FormField> inputField = form.getFields().stream()
+            .filter(f -> f.getType() == FieldType.FILE).findFirst();
+    if (inputField.isPresent())
+    {
+      StringBuilder builder = new StringBuilder();
+      for (SequenceI seq : sequences)
+      {
+        builder.append(">").append(seq.getName()).append("\n")
+                .append(seq.getSequence()).append("\n");
+      }
+      InputStream stream = new ByteArrayInputStream(
+              builder.toString().getBytes());
+      RemoteFile file = client.uploadFile(stream, "input.fa",
+              "application/fasta");
+      form.insert(inputField.get().getName(), file);
+    }
+    if (args != null)
+    {
+      for (ArgumentI arg : args)
+      {
+        // multiple choice field names are name$number to avoid duplications
+        // the number is stripped here
+        String fieldName = arg.getName().split("\\$", 2)[0];
+        FormField field = form.getField(fieldName);
+        if (field.getType() == FieldType.BOOLEAN)
+        {
+          form.insert(fieldName,
+                  (arg.getValue() != null && !arg.getValue().isBlank())
+                          ? true
+                          : false);
+        }
+        else
+        {
+          form.insert(fieldName, arg.getValue());
+        }
+      }
+    }
+    return new JobId(service.getName(), service.getName(), form.submit());
+  }
+
   @Override
   public final void updateStatus(WsJob job)
   {