Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/JAL-3066_Jalview_2...

[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 952aab6..8a16edb 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@ -2,6 +2,8 @@ package jalview.ws.slivkaws;
 
 import jalview.datamodel.SequenceI;
 import jalview.gui.WebserviceInfo;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
 import jalview.ws.api.JalviewServiceEndpointProviderI;
 import jalview.ws.api.JalviewWebServiceI;
 import jalview.ws.api.JobId;
@@ -13,10 +15,10 @@ import jalview.ws.params.ParamManager;
 import jalview.ws.params.WsParamSetI;
 
 import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
 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;
@@ -25,6 +27,7 @@ import java.util.Optional;
 import java.util.Set;
 
 import uk.ac.dundee.compbio.slivkaclient.FieldType;
+import uk.ac.dundee.compbio.slivkaclient.FileField;
 import uk.ac.dundee.compbio.slivkaclient.FormField;
 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
 import uk.ac.dundee.compbio.slivkaclient.JobState;
@@ -73,21 +76,34 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
           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())
+    for (FormField field : form.getFields())
     {
-      StringBuilder builder = new StringBuilder();
-      for (SequenceI seq : sequences)
+      if (field.getType() == FieldType.FILE)
       {
-        builder.append(">").append(seq.getName()).append("\n")
-                .append(seq.getSequence()).append("\n");
+        FormatAdapter fa = new FormatAdapter();
+        fa.setNewlineString("\r\n");
+        FileField fileField = (FileField) field;
+        FileFormat format;
+        switch (fileField.getMediaType())
+        {
+        case "application/pfam":
+          format = FileFormat.Pfam;
+          break;
+        case "application/stockholm":
+          format = FileFormat.Stockholm;
+          break;
+        default:
+        case "application/fasta":
+          format = FileFormat.Fasta;
+          break;
+        }
+        InputStream stream = new ByteArrayInputStream(
+            fa.formatSequences(format, sequences.toArray(new SequenceI[0]))
+                .getBytes());
+        RemoteFile rf = client.uploadFile(stream, "input",
+            fileField.getMediaType());
+        form.insert(field.getName(), rf);
       }
-      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)
     {
@@ -106,7 +122,7 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
         }
         else
         {
-          form.insert(fieldName, field.valueOf(arg.getValue()));
+          form.insert(fieldName, arg.getValue());
         }
       }
     }
@@ -130,44 +146,37 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
   {
     List<RemoteFile> files = client.getJobResults(job.getJobId());
     Optional<RemoteFile> logFile = files.stream()
-        .filter(f -> f.getLabel().equals("log")).findFirst();
+            .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;
+      ByteArrayOutputStream output = new ByteArrayOutputStream();
+      logFile.get().writeTo(output);
+      if (output.size() > job.getNextChunk())
+      {
+        newContent = true;
+        job.setStatus(output.toString("UTF-8"));
+        job.setnextChunk(output.size());
+      }
     }
     if (failedStates.contains(job.getJobState()))
     {
       Optional<RemoteFile> errLogFile = files.stream()
-          .filter(f -> f.getLabel().equals("error-log")).findFirst();
+              .filter(f -> f.getLabel().equals("error-log")).findFirst();
       if (errLogFile.isPresent())
       {
-        newContent |= appendJobStatus(job, errLogFile.get().getContent()) > 0;
+        ByteArrayOutputStream output = new ByteArrayOutputStream();
+        errLogFile.get().writeTo(output);
+        if (output.size() > 0)
+        {
+          newContent = true;
+          job.setStatus(job.getStatus() + "\n" + output.toString("UTF-8"));
+        }
       }
     }
     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
   public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
   {