Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PymolManager	44	122	38	0.1977401119.8%	Show methods

Class PymolManager

Class PymolManager	Line # 44	Total Statements 122	Complexity 38	TOTAL Coverage 0.1977401119.8%
getPymolPaths() : List<String>   getPymolPaths() : List<String>	6767	1.01	1.01	0.0 0.00%
getPymolPaths(String) : List<String>   getPymolPaths(String) : List<String>	8282	18.018	5.05	0.9230769 0.923076992.3%
isPymolLaunched() : boolean   isPymolLaunched() : boolean	131131	6.06	3.03	0.0 0.00%
sendCommand(StructureCommandI,boolean) : List<String>   sendCommand(StructureCommandI,boolean) : List<String>	158158	34.034	10.010	0.0 0.00%
getPostRequest(StructureCommandI) : String   getPostRequest(StructureCommandI) : String	230230	7.07	2.02	1.0 1.0100%
launchPymol() : Process   launchPymol() : Process	251251	32.032	8.08	0.0 0.00%
getPortNumber() : int   getPortNumber() : int	319319	24.024	9.09	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.14124294	jalview.ext.pymol.PymolManagerTest.testGetPymolPathsjalview.ext.pymol.PymolManagerTest.testGetPymolPaths	1PASS
	0.056497175	jalview.ext.pymol.PymolManagerTest.testGetPostRequestjalview.ext.pymol.PymolManagerTest.testGetPostRequest	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.ext.pymol;
22
23		import java.io.BufferedReader;
24		import java.io.File;
25		import java.io.IOException;
26		import java.io.InputStream;
27		import java.io.InputStreamReader;
28		import java.io.PrintWriter;
29		import java.net.HttpURLConnection;
30		import java.net.SocketException;
31		import java.net.URL;
32		import java.nio.file.Paths;
33		import java.util.ArrayList;
34		import java.util.List;
35		import java.util.Locale;
36
37		import jalview.bin.Cache;
38		import jalview.bin.Console;
39		import jalview.gui.Preferences;
40		import jalview.structure.StructureCommandI;
41		import jalview.util.HttpUtils;
42		import jalview.util.Platform;
43
		19.8% Uncovered Elements: 142 (177) Complexity: 38 Complexity Density: 0.31
44		public class PymolManager
45		{
46		private static final int RPC_REPLY_TIMEOUT_MS = 15000;
47
48		private static final int CONNECTION_TIMEOUT_MS = 100;
49
50		private static final String POST1 = "<methodCall><methodName>";
51
52		private static final String POST2 = "</methodName><params>";
53
54		private static final String POST3 = "</params></methodCall>";
55
56		private Process pymolProcess;
57
58		private int pymolXmlRpcPort;
59
60		/**
61		* Returns a list of paths to try for the PyMOL executable. Any user
62		* preference is placed first, otherwise 'standard' paths depending on the
63		* operating system.
64		*
65		* @return
66		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	public static List<String> getPymolPaths()...
68		{
69	0	return getPymolPaths(System.getProperty("os.name"));
70		}
71
72		/**
73		* Returns a list of paths to try for the PyMOL executable. Any user
74		* preference is placed first, otherwise 'standard' paths depending on the
75		* operating system.
76		*
77		* @param os
78		* operating system as reported by environment variable
79		* {@code os.name}
80		* @return
81		*/
		92.3% Uncovered Elements: 2 (26) Complexity: 5 Complexity Density: 0.28
82	4	protected static List<String> getPymolPaths(String os)...
83		{
84	4	List<String> pathList = new ArrayList<>();
85
86	4	String userPath = Cache.getDefault(Preferences.PYMOL_PATH, null);
87	4	if (userPath != null)
88		{
89	0	pathList.add(userPath);
90		}
91
92		/*
93		* add default installation paths
94		*/
95	4	String pymol = "PyMOL";
96	4	if (os.startsWith("Linux"))
97		{
98	1	pathList.add("/usr/local/pymol/bin/" + pymol);
99	1	pathList.add("/usr/local/bin/" + pymol);
100	1	pathList.add("/usr/bin/" + pymol);
101	1	pathList.add(System.getProperty("user.home") + "/opt/bin/" + pymol);
102		}
103	3	else if (os.startsWith("Windows"))
104		{
105	1	for (String root : new String[] {
106		String.format("%s\\AppData\\Local",
107		System.getProperty("user.home")), // default user path
108		"\\ProgramData", "C:\\ProgramData", // this is the default install
109		// path "for everyone"
110		System.getProperty("user.home"), "\\Program Files",
111		"C:\\Program Files", "\\Program Files (x86)",
112		"C:\\Program Files (x86)" })
113		{
114	8	for (String path : new String[] { "Schrodinger\\PyMOL2", "PyMOL" })
115		{
116	16	for (String binary : new String[] { "PyMOLWinWithConsole.bat",
117		"Scripts\\pymol.exe", "PyMOLWin.exe" })
118		{
119	48	pathList.add(String.format("%s\\%s\\%s", root, path, binary));
120		}
121		}
122		}
123		}
124	2	else if (os.startsWith("Mac"))
125		{
126	1	pathList.add("/Applications/PyMOL.app/Contents/MacOS/" + pymol);
127		}
128	4	return pathList;
129		}
130
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
131	0	public boolean isPymolLaunched()...
132		{
133		// TODO pull up generic methods for external viewer processes
134	0	boolean launched = false;
135	0	if (pymolProcess != null)
136		{
137	0	try
138		{
139	0	pymolProcess.exitValue();
140		// if we get here, process has ended
141		} catch (IllegalThreadStateException e)
142		{
143		// ok - not yet terminated
144	0	launched = true;
145		}
146		}
147	0	return launched;
148		}
149
150		/**
151		* Sends the command to Pymol; if requested, tries to get and return any
152		* replies, else returns null
153		*
154		* @param command
155		* @param getReply
156		* @return
157		*/
		0% Uncovered Elements: 48 (48) Complexity: 10 Complexity Density: 0.29
158	0	public List<String> sendCommand(StructureCommandI command,...
159		boolean getReply)
160		{
161	0	String postBody = getPostRequest(command);
162		// jalview.bin.Console.outPrintln(postBody);// debug
163	0	String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort;
164	0	PrintWriter out = null;
165	0	BufferedReader in = null;
166	0	List<String> result = getReply ? new ArrayList<>() : null;
167
168	0	try
169		{
170	0	URL realUrl = new URL(rpcUrl);
171	0	HttpURLConnection conn = (HttpURLConnection) HttpUtils
172		.openConnection(realUrl);
173	0	conn.setRequestProperty("accept", "*/*");
174	0	conn.setRequestProperty("content-type", "text/xml");
175	0	conn.setDoOutput(true);
176	0	conn.setDoInput(true);
177	0	out = new PrintWriter(conn.getOutputStream());
178	0	out.print(postBody);
179	0	out.flush();
180	0	int rc = conn.getResponseCode();
181	0	if (rc != HttpURLConnection.HTTP_OK)
182		{
183	0	Console.error(
184		String.format("Error status from %s: %d", rpcUrl, rc));
185	0	return result;
186		}
187
188	0	InputStream inputStream = conn.getInputStream();
189	0	if (getReply)
190		{
191	0	in = new BufferedReader(new InputStreamReader(inputStream));
192	0	String line;
193	0	while ((line = in.readLine()) != null)
194		{
195	0	result.add(line);
196		}
197		}
198		} catch (SocketException e)
199		{
200		// thrown when 'quit' command is sent to PyMol
201	0	Console.warn(String.format("Request to %s returned %s", rpcUrl,
202		e.toString()));
203		} catch (Exception e)
204		{
205	0	e.printStackTrace();
206		} finally
207		{
208	0	if (out != null)
209		{
210	0	out.close();
211		}
212	0	if (Console.isTraceEnabled())
213		{
214	0	Console.trace("Sent: " + command.toString());
215	0	if (result != null)
216		{
217	0	Console.trace("Received: " + result);
218		}
219		}
220		}
221	0	return result;
222		}
223
224		/**
225		* Builds the body of the XML-RPC format POST request to execute the command
226		*
227		* @param command
228		* @return
229		*/
		100% Uncovered Elements: 0 (9) Complexity: 2 Complexity Density: 0.29
230	2	static String getPostRequest(StructureCommandI command)...
231		{
232	2	StringBuilder sb = new StringBuilder(64);
233	2	sb.append(POST1).append(command.getCommand()).append(POST2);
234	2	if (command.hasParameters())
235		{
236	1	for (String p : command.getParameters())
237		{
238		/*
239		* for now assuming all are string - <string> element is optional
240		* refactor in future if other data types needed
241		* https://www.tutorialspoint.com/xml-rpc/xml_rpc_data_model.htm
242		*/
243	2	sb.append("<parameter><value>").append(p)
244		.append("</value></parameter>");
245		}
246		}
247	2	sb.append(POST3);
248	2	return sb.toString();
249		}
250
		0% Uncovered Elements: 42 (42) Complexity: 8 Complexity Density: 0.25
251	0	public Process launchPymol()...
252		{
253		// todo pull up much of this
254		// Do nothing if already launched
255	0	if (isPymolLaunched())
256		{
257	0	return pymolProcess;
258		}
259
260	0	String error = "Error message: ";
261	0	for (String pymolPath : getPymolPaths())
262		{
263	0	Console.debug("Using '" + pymolPath + "' to look for Pymol");
264	0	try
265		{
266		// ensure symbolic links are resolved
267	0	pymolPath = Paths.get(pymolPath).toRealPath().toString();
268	0	File path = new File(pymolPath);
269		// uncomment the next line to simulate Pymol not installed
270		// path = new File(pymolPath + "x");
271	0	if (!path.canExecute())
272		{
273	0	Console.debug("Cannot execute " + path.toString());
274	0	error += "File '" + path + "' does not exist.\n";
275	0	continue;
276		}
277	0	List<String> args = new ArrayList<>();
278	0	args.add(pymolPath);
279
280		// Windows PyMOLWin.exe needs an extra argument
281	0	if (Platform.isWin() && pymolPath.toLowerCase(Locale.ROOT)
282		.endsWith("\\pymolwin.exe"))
283		{
284	0	args.add("+2");
285		}
286	0	args.add("-R"); // https://pymolwiki.org/index.php/RPC
287	0	ProcessBuilder pb = new ProcessBuilder(args);
288	0	Console.debug("Running PyMOL with '"
289		+ String.join(" ", pb.command()) + "'");
290	0	pymolProcess = pb.start();
291	0	error = "";
292	0	break;
293		} catch (Exception e)
294		{
295		// Pymol could not be started using this path
296	0	error += e.getMessage();
297		}
298		}
299
300	0	if (pymolProcess != null)
301		{
302	0	this.pymolXmlRpcPort = getPortNumber();
303	0	if (pymolXmlRpcPort > 0)
304		{
305	0	Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
306		}
307		else
308		{
309	0	error += "Failed to read PyMOL XMLRPC port number";
310	0	Console.error(error);
311	0	pymolProcess.destroy();
312	0	pymolProcess = null;
313		}
314		}
315
316	0	return pymolProcess;
317		}
318
		0% Uncovered Elements: 36 (36) Complexity: 9 Complexity Density: 0.38
319	0	private int getPortNumber()...
320		{
321		// TODO pull up most of this!
322	0	int port = 0;
323	0	InputStream readChan = pymolProcess.getInputStream();
324	0	BufferedReader lineReader = new BufferedReader(
325		new InputStreamReader(readChan));
326	0	StringBuilder responses = new StringBuilder();
327	0	try
328		{
329	0	String response = lineReader.readLine();
330	0	while (response != null)
331		{
332	0	responses.append("\n" + response);
333		// expect: xml-rpc server running on host localhost, port 9123
334	0	if (response.contains("xml-rpc"))
335		{
336	0	String[] tokens = response.split(" ");
337	0	for (int i = 0; i < tokens.length - 1; i++)
338		{
339	0	if ("port".equals(tokens[i]))
340		{
341	0	port = Integer.parseInt(tokens[i + 1]);
342	0	break;
343		}
344		}
345		}
346	0	if (port > 0)
347		{
348	0	break; // hack for hanging readLine()
349		}
350	0	response = lineReader.readLine();
351		}
352		} catch (Exception e)
353		{
354	0	Console.error("Failed to get REST port number from " + responses
355		+ ": " + e.getMessage());
356		// logger.error("Failed to get REST port number from " + responses + ": "
357		// + e.getMessage());
358		} finally
359		{
360	0	try
361		{
362	0	lineReader.close();
363		} catch (IOException e2)
364		{
365		}
366		}
367	0	if (port == 0)
368		{
369	0	Console.error("Failed to start PyMOL with XMLRPC, response was: "
370		+ responses);
371		}
372	0	Console.info("PyMOL started with XMLRPC on port " + port);
373	0	return port;
374		}
375
376		}