JAL-1601 Read full file before passing to FileParse

[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
index 36cc6c2..fccd876 100644 (file)
--- a/src/jalview/ws2/client/jpred4/JPred4WSClient.java
+++ b/src/jalview/ws2/client/jpred4/JPred4WSClient.java
@@ -1,5 +1,6 @@
 package jalview.ws2.client.jpred4;
 
+import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.util.List;
 
@@ -23,8 +24,14 @@ public class JPred4WSClient implements SecStructPredWebServiceClientI
 {
   final JPredClient client;
 
-  JPred4WSClient(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;
   }
 
@@ -44,13 +51,16 @@ public class JPred4WSClient implements SecStructPredWebServiceClientI
   public WebServiceJobHandle submit(List<SequenceI> sequences,
       List<ArgumentI> args, Credentials credentials) throws IOException
   {
-    var input = FileFormat.Fasta
-        .getWriter(null)
-        .print(sequences.toArray(SequenceI[]::new), false);
+    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(JPredRequest.Mode.MSA)
-        .format(JPredRequest.Format.FASTA)
+        .mode(mode)
+        .format(format)
         .input(input)
         .build();
     var jobId = client.submit(request);
@@ -63,6 +73,8 @@ public class JPred4WSClient implements SecStructPredWebServiceClientI
     var status = client.getStatus(job.getJobId());
     switch (status)
     {
+    case PENDING:
+      return JobStatus.QUEUED;
     case RUNNING:
       return JobStatus.RUNNING;
     case FINISHED:
@@ -96,20 +108,30 @@ public class JPred4WSClient implements SecStructPredWebServiceClientI
   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);
+    var stream = client.getResultStream(job.getJobId(), ResultTypes.PSIBLAST_ALIGN);
+    var buffer = new byte[2048];
+    var file = new ByteArrayOutputStream();
+    var len = 0;
+    while ((len= stream.read(buffer)) >= 0)
+      file.write(buffer, 0, len);
+    return new FastaFile(file.toString("UTF-8"), DataSourceType.PASTE);
   }
-  
+
   @Override
   public JPredFile getPredictionFile(WebServiceJobHandle job) throws IOException
   {
-    var url = client.getResultURL(job.getJobId(), ResultTypes.CONCISE);
-    return new JPredFile(url.toString(), DataSourceType.URL);
+    var stream = client.getResultStream(job.getJobId(), ResultTypes.CONCISE);
+    var buffer = new byte[2048];
+    var file = new ByteArrayOutputStream();
+    var len = 0;
+    while ((len= stream.read(buffer)) >= 0)
+      file.write(buffer, 0, len);
+    return new JPredFile(file.toString("UTF-8"), DataSourceType.PASTE);
   }
 }