Merge branch 'JAL-1601-direct-jpred4-rest-service' into development/Release_2_12_Branch

[jalview.git] / src / jalview / ws2 / client / jpred4 / JPred4WSClient.java

diff --git a/src/jalview/ws2/client/jpred4/JPred4WSClient.java b/src/jalview/ws2/client/jpred4/JPred4WSClient.java
new file mode 100644 (file)
index 0000000..3782723
--- /dev/null
+++ b/src/jalview/ws2/client/jpred4/JPred4WSClient.java
@@ -0,0 +1,126 @@
+package jalview.ws2.client.jpred4;
+
+import java.io.IOException;
+import java.util.List;
+
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
+import jalview.io.DataSourceType;
+import jalview.io.FastaFile;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.io.JPredFile;
+import jalview.ws.params.ArgumentI;
+import jalview.ws2.api.Credentials;
+import jalview.ws2.api.JobStatus;
+import jalview.ws2.api.WebServiceJobHandle;
+import jalview.ws2.client.api.SecStructPredWebServiceClientI;
+import uk.ac.dundee.compbio.jpred.JPredClient;
+import uk.ac.dundee.compbio.jpred.JPredRequest;
+import uk.ac.dundee.compbio.jpred.ResultTypes;
+
+public class JPred4WSClient implements SecStructPredWebServiceClientI
+{
+  final JPredClient client;
+
+  private final JPredRequest.Mode mode;
+
+  private final JPredRequest.Format format;
+
+  JPred4WSClient(JPredClient client, boolean msaMode)
+  {
+    this.mode = msaMode ? JPredRequest.Mode.MSA : JPredRequest.Mode.SINGLE;
+    this.format = msaMode ? JPredRequest.Format.FASTA : JPredRequest.Format.SEQ;
+    this.client = client;
+  }
+
+  @Override
+  public String getUrl()
+  {
+    return client.getURL().toString();
+  }
+
+  @Override
+  public String getClientName()
+  {
+    return "jpred4";
+  }
+
+  @Override
+  public WebServiceJobHandle submit(List<SequenceI> sequences,
+      List<ArgumentI> args, Credentials credentials) throws IOException
+  {
+    var input = mode == JPredRequest.Mode.MSA
+        ? FileFormat.Fasta
+            .getWriter(null)
+            .print(sequences.toArray(new SequenceI[sequences.size()]), false)
+        : sequences.get(0).getSequenceAsString();
+
+    JPredRequest request = JPredRequest
+        .newBuilder()
+        .mode(mode)
+        .format(format)
+        .input(input)
+        .build();
+    var jobId = client.submit(request);
+    return new WebServiceJobHandle(getClientName(), "jpred4", getUrl(), jobId);
+  }
+
+  @Override
+  public JobStatus getStatus(WebServiceJobHandle job) throws IOException
+  {
+    var status = client.getStatus(job.getJobId());
+    switch (status)
+    {
+    case PENDING:
+      return JobStatus.QUEUED;
+    case RUNNING:
+      return JobStatus.RUNNING;
+    case FINISHED:
+      return JobStatus.COMPLETED;
+    case NO_JOB:
+      return JobStatus.SERVER_ERROR;
+    case MALFORMED:
+      return JobStatus.INVALID;
+    case NOT_EXIST:
+      return JobStatus.SERVER_ERROR;
+    default:
+      return JobStatus.UNKNOWN;
+    }
+  }
+
+  @Override
+  public String getLog(WebServiceJobHandle job) throws IOException
+  {
+    var stream = client.getResultStream(job.getJobId(), ResultTypes.LOG);
+    // FIXME: potential OOM
+    return new String(stream.readAllBytes());
+  }
+
+  @Override
+  public String getErrorLog(WebServiceJobHandle job) throws IOException
+  {
+    return "";
+  }
+
+  @Override
+  public void cancel(WebServiceJobHandle job)
+      throws IOException, UnsupportedOperationException
+  {
+
+  }
+
+  @Override
+  public AlignFile getAlignmentFile(WebServiceJobHandle job) throws IOException
+  {
+    var url = client.getResultURL(job.getJobId(), ResultTypes.PSIBLAST_ALIGN);
+    return new FastaFile(url.toString(), DataSourceType.URL);
+  }
+
+  @Override
+  public JPredFile getPredictionFile(WebServiceJobHandle job) throws IOException
+  {
+    var url = client.getResultURL(job.getJobId(), ResultTypes.CONCISE);
+    return new JPredFile(url.toString(), DataSourceType.URL);
+  }
+}