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 9aae388..a21354e 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@ -1,20 +1,36 @@
 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;
+import java.io.InputStreamReader;
+import java.util.Arrays;
 import java.util.EnumMap;
+import java.util.HashSet;
+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;
 
@@ -30,13 +46,21 @@ 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);
   }
+  protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
+      WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
+      WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
+  ));
 
   public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
   {
@@ -45,6 +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)
   {
@@ -58,9 +126,46 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
   }
 
   @Override
-  public final boolean updateJobProgress(WsJob job)
+  public final boolean updateJobProgress(WsJob job) throws IOException
   {
-    return false;
+    List<RemoteFile> files = client.getJobResults(job.getJobId());
+    Optional<RemoteFile> logFile = files.stream()
+        .filter(f -> f.getLabel().equals("log")).findFirst();
+    boolean newContent = false;
+    if (logFile.isPresent())
+    {
+      InputStream stream = logFile.get().getContent();
+      long nextChunk = stream.skip(job.getNextChunk());
+      int len = appendJobStatus(job, stream);
+      job.setnextChunk(nextChunk + len);
+      newContent |= len > 0;
+    }
+    if (failedStates.contains(job.getJobState()))
+    {
+      Optional<RemoteFile> errLogFile = files.stream()
+          .filter(f -> f.getLabel().equals("error-log")).findFirst();
+      if (errLogFile.isPresent())
+      {
+        newContent |= appendJobStatus(job, errLogFile.get().getContent()) > 0;
+      }
+    }
+    return newContent;
+  }
+
+  private int appendJobStatus(WsJob job, InputStream stream) throws IOException
+  {
+    StringBuilder builder = new StringBuilder(job.getStatus());
+    InputStreamReader reader = new InputStreamReader(stream);
+    char[] buffer = new char[4096];
+    int chunkLen = 0;
+    int len = 0;
+    while ((len = reader.read(buffer)) != -1)
+    {
+      chunkLen += len;
+      builder.append(buffer, 0, len);
+    }
+    job.setStatus(builder.toString());
+    return chunkLen;
   }
 
   @Override