From 6e0685c38078ddcf959db75d001f8c92b114c8ae Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 30 Apr 2020 11:47:39 +0100
Subject: [PATCH] JAL-3551 tidied error handling for HTTP request

---
 src/jalview/ext/pymol/PymolManager.java |   59 ++++++++++++++++++-------------
 1 file changed, 34 insertions(+), 25 deletions(-)

diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index ad44677..f410b54 100644
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -1,22 +1,23 @@
 package jalview.ext.pymol;
 
-import jalview.bin.Cache;
-import jalview.gui.Preferences;
-import jalview.structure.StructureCommand;
-import jalview.structure.StructureCommandI;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
+import java.net.HttpURLConnection;
+import java.net.SocketException;
 import java.net.URL;
-import java.net.URLConnection;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
 
+import jalview.bin.Cache;
+import jalview.gui.Preferences;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+
 public class PymolManager
 {
   private static final int RPC_REPLY_TIMEOUT_MS = 15000;
@@ -120,11 +121,12 @@ public class PymolManager
     String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort;
     PrintWriter out = null;
     BufferedReader in = null;
-    List<String> result = new ArrayList<>();
+    List<String> result = getReply ? new ArrayList<>() : null;
+
     try
     {
       URL realUrl = new URL(rpcUrl);
-      URLConnection conn = realUrl.openConnection();
+      HttpURLConnection conn = (HttpURLConnection) realUrl.openConnection();
       conn.setRequestProperty("accept", "*/*");
       conn.setRequestProperty("content-type", "text/xml");
       conn.setDoOutput(true);
@@ -132,31 +134,38 @@ public class PymolManager
       out = new PrintWriter(conn.getOutputStream());
       out.print(postBody);
       out.flush();
-      in = new BufferedReader(new InputStreamReader(conn.getInputStream()));
-      String line;
-      while ((line = in.readLine()) != null)
+      int rc = conn.getResponseCode();
+      if (rc != HttpURLConnection.HTTP_OK)
       {
-        result.add(line);
+        Cache.log.error(
+                String.format("Error status from %s: %d", rpcUrl, rc));
+        return result;
       }
+
+      InputStream inputStream = conn.getInputStream();
+      if (getReply)
+      {
+        in = new BufferedReader(new InputStreamReader(inputStream));
+        String line;
+        while ((line = in.readLine()) != null)
+        {
+          result.add(line);
+        }
+      }
+    } catch (SocketException e)
+    {
+      // thrown when 'quit' command is sent to PyMol
+      Cache.log.warn(String.format("Request to %s returned %s", rpcUrl,
+              e.toString()));
     } catch (Exception e)
     {
       e.printStackTrace();
     } finally
     {
-      try
-      {
-        if (out != null)
-        {
-          out.close();
-        }
-        if (in != null)
-        {
-          in.close();
-        }
-      } catch (IOException ex)
+      if (out != null)
       {
-        ex.printStackTrace();
-        }
+        out.close();
+      }
     }
     return result;
   }
-- 
1.7.10.2