X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fpymol%2FPymolManager.java;h=e10fc9d6fb543d714f651604e19926d86f2483ad;hp=ad44677762a45f144bf2dc6b2107efd941bc550b;hb=cea2941f089e7d7a8dd94d4478ed711255eba75b;hpb=42f4227ed213d422a87d3b22fc9e85d14ffaf53f

diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index ad44677..e10fc9d 100644
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -1,21 +1,44 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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 java.util.Locale;
+
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.gui.Preferences;
+import jalview.structure.StructureCommandI;
+import jalview.util.Platform;
 
 public class PymolManager
 {
@@ -42,20 +65,33 @@ public class PymolManager
    */
   public static List<String> getPymolPaths()
   {
+    return getPymolPaths(System.getProperty("os.name"));
+  }
+
+  /**
+   * Returns a list of paths to try for the PyMOL executable. Any user
+   * preference is placed first, otherwise 'standard' paths depending on the
+   * operating system.
+   * 
+   * @param os
+   *          operating system as reported by environment variable
+   *          {@code os.name}
+   * @return
+   */
+  protected static List<String> getPymolPaths(String os)
+  {
     List<String> pathList = new ArrayList<>();
-  
-    String userPath = Cache
-            .getDefault(Preferences.PYMOL_PATH, null);
+
+    String userPath = Cache.getDefault(Preferences.PYMOL_PATH, null);
     if (userPath != null)
     {
-      pathList.add(0, userPath);
+      pathList.add(userPath);
     }
-  
+
     /*
      * add default installation paths
      */
     String pymol = "PyMOL";
-    String os = System.getProperty("os.name");
     if (os.startsWith("Linux"))
     {
       pathList.add("/usr/local/pymol/bin/" + pymol);
@@ -65,7 +101,23 @@ public class PymolManager
     }
     else if (os.startsWith("Windows"))
     {
-      // todo Windows installation path(s)
+      for (String root : new String[] {
+          String.format("%s\\AppData\\Local",
+                  System.getProperty("user.home")), // default user path
+          "\\ProgramData", "C:\\ProgramData", // this is the default install
+                                              // path "for everyone"
+          System.getProperty("user.home"), "\\Program Files",
+          "C:\\Program Files", "\\Program Files (x86)",
+          "C:\\Program Files (x86)" })
+      {
+        for (String path : new String[] { "Schrodinger\\PyMOL2", "PyMOL" })
+        {
+          for (String binary : new String [] {"PyMOLWinWithConsole.bat", "Scripts\\pymol.exe", "PyMOLWin.exe"})
+          {
+            pathList.add(String.format("%s\\%s\\%s", root, path, binary));
+          }
+        }
+      }
     }
     else if (os.startsWith("Mac"))
     {
@@ -93,17 +145,6 @@ public class PymolManager
     return launched;
   }
 
-  public void exitPymol()
-  {
-    if (isPymolLaunched() && pymolProcess != null)
-    {
-      sendCommand(new StructureCommand("quit"), false);
-    }
-    pymolProcess = null;
-    // currentModelsMap.clear();
-    this.pymolXmlRpcPort = 0;
-  }
-
   /**
    * Sends the command to Pymol; if requested, tries to get and return any
    * replies, else returns null
@@ -120,11 +161,12 @@ 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 +174,46 @@ 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)
+      {
+        Console.error(
+                String.format("Error status from %s: %d", rpcUrl, rc));
+        return result;
+      }
+
+      InputStream inputStream = conn.getInputStream();
+      if (getReply)
       {
-        result.add(line);
+        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
+      Console.warn(String.format("Request to %s returned %s", rpcUrl,
+              e.toString()));
     } catch (Exception e)
     {
       e.printStackTrace();
     } finally
     {
-      try
+      if (out != null)
       {
-        if (out != null)
-        {
-          out.close();
-        }
-        if (in != null)
-        {
-          in.close();
-        }
-      } catch (IOException ex)
+        out.close();
+      }
+      if (Console.isTraceEnabled())
       {
-        ex.printStackTrace();
+        Console.trace("Sent: " + command.toString());
+        if (result != null)
+        {
+          Console.trace("Received: " + result);
         }
+      }
     }
     return result;
   }
@@ -188,13 +245,13 @@ public class PymolManager
     return sb.toString();
   }
 
-  public boolean launchPymol()
+  public Process launchPymol()
   {
     // todo pull up much of this
     // Do nothing if already launched
     if (isPymolLaunched())
     {
-      return true;
+      return pymolProcess;
     }
 
     String error = "Error message: ";
@@ -214,27 +271,42 @@ public class PymolManager
         }
         List<String> args = new ArrayList<>();
         args.add(pymolPath);
+        
+        // Windows PyMOLWin.exe needs an extra argument
+        if (Platform.isWin() && pymolPath.toLowerCase(Locale.ROOT).endsWith("\\pymolwin.exe"))
+        {
+          args.add("+2");
+        }
         args.add("-R"); // https://pymolwiki.org/index.php/RPC
         ProcessBuilder pb = new ProcessBuilder(args);
+        Console.debug("Running PyMOL as "+String.join(" ", pb.command()));
         pymolProcess = pb.start();
         error = "";
         break;
       } catch (Exception e)
       {
-        // pPymol could not be started using this path
+        // Pymol could not be started using this path
         error += e.getMessage();
       }
     }
-    if (error.length() == 0)
+
+    if (pymolProcess != null)
     {
       this.pymolXmlRpcPort = getPortNumber();
-      System.out.println(
-              "PyMOL XMLRPC started on port " + pymolXmlRpcPort);
-      return (pymolXmlRpcPort > 0);
+      if (pymolXmlRpcPort > 0)
+      {
+        Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
+      }
+      else
+      {
+        error += "Failed to read PyMOL XMLRPC port number";
+        Console.error(error);
+        pymolProcess.destroy();
+        pymolProcess = null;
+      }
     }
 
-    // logger.warn(error);
-    return false;
+    return pymolProcess;
   }
 
   private int getPortNumber()
@@ -272,9 +344,8 @@ public class PymolManager
       }
     } catch (Exception e)
     {
-      System.err.println(
-              "Failed to get REST port number from " + responses + ": "
-              + e.getMessage());
+      Console.error("Failed to get REST port number from " + responses
+              + ": " + e.getMessage());
       // logger.error("Failed to get REST port number from " + responses + ": "
       // + e.getMessage());
     } finally
@@ -288,10 +359,10 @@ public class PymolManager
     }
     if (port == 0)
     {
-      System.err.println("Failed to start PyMOL with XMLRPC, response was: "
+      Console.error("Failed to start PyMOL with XMLRPC, response was: "
               + responses);
     }
-    System.err.println("PyMOL started with XMLRPC on port " + port);
+    Console.info("PyMOL started with XMLRPC on port " + port);
     return port;
   }