From 942bf94f9595a3b3755efd2574f235238bc3cdc1 Mon Sep 17 00:00:00 2001
From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Mon, 23 Sep 2019 16:01:54 +0100
Subject: [PATCH] JAL-3066 Annotation Service Instance stub

---
 .../slivkaws/SlivkaAnnotationServiceInstance.java  |   75 ++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java

diff --git a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
new file mode 100644
index 0000000..4d2c4fb
--- /dev/null
+++ b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
@@ -0,0 +1,75 @@
+package jalview.ws.slivkaws;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.ws.api.JobId;
+import jalview.ws.api.SequenceAnnotationServiceI;
+import jalview.ws.gui.AnnotationWsJob;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.WsParamSetI;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+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 SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
+{
+  public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
+  {
+    super(client, service, "Annotations");
+  }
+
+  @Override
+  public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
+  {
+    StringBuilder builder = new StringBuilder();
+    for (SequenceI seq : seqs)
+    {
+      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<>(paramset != null ? paramset.size() : 0);
+    if (paramset != null)
+    {
+      for (ArgumentI arg : paramset)
+      {
+        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 List<AlignmentAnnotation> getAlignmentAnnotation(AnnotationWsJob running,
+      SeqAnnotationServiceCalcWorker abstractJabaCalcWorker) throws Throwable
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+}
-- 
1.7.10.2