From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Thu, 14 Mar 2024 11:59:48 +0000 (+0100)
Subject: Merge branch 'JAL-1601-direct-jpred4-rest-service' into development/Release_2_12_Branch
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fdevelopment%2FRelease_2_12_Branch;hp=b8c0c4d78deccb7901d905a248aba47ea1c87a6a;p=jalview.git

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

diff --git a/j11lib/jpred-client-1.0-SNAPSHOT.jar b/j11lib/jpred-client-1.0-SNAPSHOT.jar
index 0e7aacf..0c9557b 100644
Binary files a/j11lib/jpred-client-1.0-SNAPSHOT.jar and b/j11lib/jpred-client-1.0-SNAPSHOT.jar differ
diff --git a/src/jalview/ws2/client/jpred4/JPred4WSClient.java b/src/jalview/ws2/client/jpred4/JPred4WSClient.java
index 3782723..fccd876 100644
--- 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;
 
@@ -113,14 +114,24 @@ public class JPred4WSClient implements SecStructPredWebServiceClientI
   @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);
   }
 }
diff --git a/utils/jalviewjs/libjs/jpred-client-site.zip b/utils/jalviewjs/libjs/jpred-client-site.zip
index 0142933..021d332 100644
Binary files a/utils/jalviewjs/libjs/jpred-client-site.zip and b/utils/jalviewjs/libjs/jpred-client-site.zip differ