From 9c7418155500b39b96d2d6f92d9ce12012b58622 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 19 May 2020 11:50:41 +0100
Subject: [PATCH] JAL-3624 use temp file for SIFT download in JS, correct
 unmarshalling

---
 src/jalview/ws/sifts/SiftsClient.java |   79 ++++++++++++++++++++-------------
 1 file changed, 48 insertions(+), 31 deletions(-)

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index d065666..4fb9ca9 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -20,28 +20,6 @@
  */
 package jalview.ws.sifts;
 
-import jalview.analysis.AlignSeq;
-import jalview.analysis.scoremodels.ScoreMatrix;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.DBRefEntryI;
-import jalview.api.SiftsClientI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.io.StructureFile;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
-import jalview.util.Comparison;
-import jalview.util.DBRefUtils;
-import jalview.util.Format;
-import jalview.xml.binding.sifts.Entry;
-import jalview.xml.binding.sifts.Entry.Entity;
-import jalview.xml.binding.sifts.Entry.Entity.Segment;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
-
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -67,10 +45,33 @@ import java.util.TreeMap;
 import java.util.zip.GZIPInputStream;
 
 import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
 import javax.xml.bind.Unmarshaller;
 import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamReader;
 
+import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.DBRefEntryI;
+import jalview.api.SiftsClientI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.Format;
+import jalview.util.Platform;
+import jalview.xml.binding.sifts.Entry;
+import jalview.xml.binding.sifts.Entry.Entity;
+import jalview.xml.binding.sifts.Entry.Entity.Segment;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
 import mc_view.Atom;
 import mc_view.PDBChain;
 
@@ -187,7 +188,8 @@ public class SiftsClient implements SiftsClientI
       XMLStreamReader streamReader = XMLInputFactory.newInstance()
               .createXMLStreamReader(gzis);
       Unmarshaller um = jc.createUnmarshaller();
-      return (Entry) um.unmarshal(streamReader);
+      JAXBElement<Entry> jbe = um.unmarshal(streamReader, Entry.class);
+      return jbe.getValue();
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -299,21 +301,36 @@ public class SiftsClient implements SiftsClientI
     }
     String siftFile = pdbId + ".xml.gz";
     String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
-    String downloadedSiftsFile = SiftsSettings.getSiftDownloadDirectory()
-            + siftFile;
-    File siftsDownloadDir = new File(
-            SiftsSettings.getSiftDownloadDirectory());
-    if (!siftsDownloadDir.exists())
+    
+    /*
+     * Download the file from URL to either
+     * Java: directory of cached downloaded SIFTS files
+     * Javascript: temporary 'file' (in-memory cache)
+     */
+    File downloadTo = null;
+    if (Platform.isJS())
+    {
+      downloadTo = File.createTempFile(siftFile, ".xml.gz");
+    }
+    else
     {
-      siftsDownloadDir.mkdirs();
+      downloadTo = new File(
+              SiftsSettings.getSiftDownloadDirectory() + siftFile);
+      File siftsDownloadDir = new File(
+              SiftsSettings.getSiftDownloadDirectory());
+      if (!siftsDownloadDir.exists())
+      {
+        siftsDownloadDir.mkdirs();
+      }
     }
+
     // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
     // long now = System.currentTimeMillis();
     URL url = new URL(siftsFileFTPURL);
     URLConnection conn = url.openConnection();
     InputStream inputStream = conn.getInputStream();
     FileOutputStream outputStream = new FileOutputStream(
-            downloadedSiftsFile);
+            downloadTo);
     byte[] buffer = new byte[BUFFER_SIZE];
     int bytesRead = -1;
     while ((bytesRead = inputStream.read(buffer)) != -1)
@@ -324,7 +341,7 @@ public class SiftsClient implements SiftsClientI
     inputStream.close();
     // System.out.println(">>> File downloaded : " + downloadedSiftsFile
     // + " took " + (System.currentTimeMillis() - now) + "ms");
-    return new File(downloadedSiftsFile);
+    return downloadTo;
   }
 
   /**
-- 
1.7.10.2