+/*
+ * 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 jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.gui.Preferences;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+
public class PymolManager
{
private static final int RPC_REPLY_TIMEOUT_MS = 15000;
*/
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);
else if (os.startsWith("Windows"))
{
// todo Windows installation path(s)
+ for (String root : new String[]
+ {
+ String.format("%s\\AppData\\Local", System.getProperty("user.home")),
+ "\\Program Files", "C:\\Program Files", "\\Program Files (x86)",
+ "C:\\Program Files (x86)" })
+ {
+ for (String binary : new String [] {"PyMOLWinWithConsole.bat", "PyMOLWin.exe"})
+ {
+ pathList.add(String.format("%s\\Schrodinger\\PyMOL2\\%s", root, binary));
+ }
+ }
+
}
else if (os.startsWith("Mac"))
{
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
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);
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);
+ Console.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
+ 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;
}
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: ";
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()
}
} 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
}
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;
}
git://source.jalview.org / jalview.git / blobdiff