Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PymolManager	21	109	34	0.1962025319.6%	Show methods

Class PymolManager

Class PymolManager	Line # 21	Total Statements 109	Complexity 34	TOTAL Coverage 0.1962025319.6%
getPymolPaths() : List<String>   getPymolPaths() : List<String>	4444	1.01	1.01	0.0 0.00%
getPymolPaths(String) : List<String>   getPymolPaths(String) : List<String>	5959	14.014	5.05	0.90909094 0.9090909490.9%
isPymolLaunched() : boolean   isPymolLaunched() : boolean	9292	6.06	3.03	0.0 0.00%
sendCommand(StructureCommandI,boolean) : List<String>   sendCommand(StructureCommandI,boolean) : List<String>	119119	30.030	8.08	0.0 0.00%
getPostRequest(StructureCommandI) : String   getPostRequest(StructureCommandI) : String	182182	7.07	2.02	1.0 1.0100%
launchPymol() : Process   launchPymol() : Process	203203	27.027	6.06	0.0 0.00%
getPortNumber() : int   getPortNumber() : int	260260	24.024	9.09	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.1329114	jalview.ext.pymol.PymolManagerTest.testGetPymolPathsjalview.ext.pymol.PymolManagerTest.testGetPymolPaths	1PASS
	0.06329114	jalview.ext.pymol.PymolManagerTest.testGetPostRequestjalview.ext.pymol.PymolManagerTest.testGetPostRequest	1PASS

 

Source view

1		package jalview.ext.pymol;
2
3		import java.io.BufferedReader;
4		import java.io.File;
5		import java.io.IOException;
6		import java.io.InputStream;
7		import java.io.InputStreamReader;
8		import java.io.PrintWriter;
9		import java.net.HttpURLConnection;
10		import java.net.SocketException;
11		import java.net.URL;
12		import java.nio.file.Paths;
13		import java.util.ArrayList;
14		import java.util.List;
15
16		import jalview.bin.Cache;
17		import jalview.gui.Preferences;
18		import jalview.structure.StructureCommand;
19		import jalview.structure.StructureCommandI;
20
		19.6% Uncovered Elements: 127 (158) Complexity: 34 Complexity Density: 0.31
21		public class PymolManager
22		{
23		private static final int RPC_REPLY_TIMEOUT_MS = 15000;
24
25		private static final int CONNECTION_TIMEOUT_MS = 100;
26
27		private static final String POST1 = "<methodCall><methodName>";
28
29		private static final String POST2 = "</methodName><params>";
30
31		private static final String POST3 = "</params></methodCall>";
32
33		private Process pymolProcess;
34
35		private int pymolXmlRpcPort;
36
37		/**
38		* Returns a list of paths to try for the PyMOL executable. Any user
39		* preference is placed first, otherwise 'standard' paths depending on the
40		* operating system.
41		*
42		* @return
43		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
44	0	public static List<String> getPymolPaths()...
45		{
46	0	return getPymolPaths(System.getProperty("os.name"));
47		}
48
49		/**
50		* Returns a list of paths to try for the PyMOL executable. Any user
51		* preference is placed first, otherwise 'standard' paths depending on the
52		* operating system.
53		*
54		* @param os
55		* operating system as reported by environment variable
56		* {@code os.name}
57		* @return
58		*/
		90.9% Uncovered Elements: 2 (22) Complexity: 5 Complexity Density: 0.36
59	4	protected static List<String> getPymolPaths(String os)...
60		{
61	4	List<String> pathList = new ArrayList<>();
62
63	4	String userPath = Cache
64		.getDefault(Preferences.PYMOL_PATH, null);
65	4	if (userPath != null)
66		{
67	0	pathList.add(userPath);
68		}
69
70		/*
71		* add default installation paths
72		*/
73	4	String pymol = "PyMOL";
74	4	if (os.startsWith("Linux"))
75		{
76	1	pathList.add("/usr/local/pymol/bin/" + pymol);
77	1	pathList.add("/usr/local/bin/" + pymol);
78	1	pathList.add("/usr/bin/" + pymol);
79	1	pathList.add(System.getProperty("user.home") + "/opt/bin/" + pymol);
80		}
81	3	else if (os.startsWith("Windows"))
82		{
83		// todo Windows installation path(s)
84		}
85	2	else if (os.startsWith("Mac"))
86		{
87	1	pathList.add("/Applications/PyMOL.app/Contents/MacOS/" + pymol);
88		}
89	4	return pathList;
90		}
91
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
92	0	public boolean isPymolLaunched()...
93		{
94		// TODO pull up generic methods for external viewer processes
95	0	boolean launched = false;
96	0	if (pymolProcess != null)
97		{
98	0	try
99		{
100	0	pymolProcess.exitValue();
101		// if we get here, process has ended
102		} catch (IllegalThreadStateException e)
103		{
104		// ok - not yet terminated
105	0	launched = true;
106		}
107		}
108	0	return launched;
109		}
110
111		/**
112		* Sends the command to Pymol; if requested, tries to get and return any
113		* replies, else returns null
114		*
115		* @param command
116		* @param getReply
117		* @return
118		*/
		0% Uncovered Elements: 40 (40) Complexity: 8 Complexity Density: 0.27
119	0	public List<String> sendCommand(StructureCommandI command,...
120		boolean getReply)
121		{
122	0	String postBody = getPostRequest(command);
123		// System.out.println(postBody);// debug
124	0	String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort;
125	0	PrintWriter out = null;
126	0	BufferedReader in = null;
127	0	List<String> result = getReply ? new ArrayList<>() : null;
128
129	0	try
130		{
131	0	URL realUrl = new URL(rpcUrl);
132	0	HttpURLConnection conn = (HttpURLConnection) realUrl.openConnection();
133	0	conn.setRequestProperty("accept", "*/*");
134	0	conn.setRequestProperty("content-type", "text/xml");
135	0	conn.setDoOutput(true);
136	0	conn.setDoInput(true);
137	0	out = new PrintWriter(conn.getOutputStream());
138	0	out.print(postBody);
139	0	out.flush();
140	0	int rc = conn.getResponseCode();
141	0	if (rc != HttpURLConnection.HTTP_OK)
142		{
143	0	Cache.log.error(
144		String.format("Error status from %s: %d", rpcUrl, rc));
145	0	return result;
146		}
147
148	0	InputStream inputStream = conn.getInputStream();
149	0	if (getReply)
150		{
151	0	in = new BufferedReader(new InputStreamReader(inputStream));
152	0	String line;
153	0	while ((line = in.readLine()) != null)
154		{
155	0	result.add(line);
156		}
157		}
158		} catch (SocketException e)
159		{
160		// thrown when 'quit' command is sent to PyMol
161	0	Cache.log.warn(String.format("Request to %s returned %s", rpcUrl,
162		e.toString()));
163		} catch (Exception e)
164		{
165	0	e.printStackTrace();
166		} finally
167		{
168	0	if (out != null)
169		{
170	0	out.close();
171		}
172		}
173	0	return result;
174		}
175
176		/**
177		* Builds the body of the XML-RPC format POST request to execute the command
178		*
179		* @param command
180		* @return
181		*/
		100% Uncovered Elements: 0 (9) Complexity: 2 Complexity Density: 0.29
182	2	static String getPostRequest(StructureCommandI command)...
183		{
184	2	StringBuilder sb = new StringBuilder(64);
185	2	sb.append(POST1).append(command.getCommand()).append(POST2);
186	2	if (command.hasParameters())
187		{
188	1	for (String p : command.getParameters())
189		{
190		/*
191		* for now assuming all are string - <string> element is optional
192		* refactor in future if other data types needed
193		* https://www.tutorialspoint.com/xml-rpc/xml_rpc_data_model.htm
194		*/
195	2	sb.append("<parameter><value>").append(p)
196		.append("</value></parameter>");
197		}
198		}
199	2	sb.append(POST3);
200	2	return sb.toString();
201		}
202
		0% Uncovered Elements: 35 (35) Complexity: 6 Complexity Density: 0.22
203	0	public Process launchPymol()...
204		{
205		// todo pull up much of this
206		// Do nothing if already launched
207	0	if (isPymolLaunched())
208		{
209	0	return pymolProcess;
210		}
211
212	0	String error = "Error message: ";
213	0	for (String pymolPath : getPymolPaths())
214		{
215	0	try
216		{
217		// ensure symbolic links are resolved
218	0	pymolPath = Paths.get(pymolPath).toRealPath().toString();
219	0	File path = new File(pymolPath);
220		// uncomment the next line to simulate Pymol not installed
221		// path = new File(pymolPath + "x");
222	0	if (!path.canExecute())
223		{
224	0	error += "File '" + path + "' does not exist.\n";
225	0	continue;
226		}
227	0	List<String> args = new ArrayList<>();
228	0	args.add(pymolPath);
229	0	args.add("-R"); // https://pymolwiki.org/index.php/RPC
230	0	ProcessBuilder pb = new ProcessBuilder(args);
231	0	pymolProcess = pb.start();
232	0	error = "";
233	0	break;
234		} catch (Exception e)
235		{
236		// Pymol could not be started using this path
237	0	error += e.getMessage();
238		}
239		}
240
241	0	if (pymolProcess != null)
242		{
243	0	this.pymolXmlRpcPort = getPortNumber();
244	0	if (pymolXmlRpcPort > 0)
245		{
246	0	Cache.log.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
247		}
248		else
249		{
250	0	error += "Failed to read PyMOL XMLRPC port number";
251	0	Cache.log.error(error);
252	0	pymolProcess.destroy();
253	0	pymolProcess = null;
254		}
255		}
256
257	0	return pymolProcess;
258		}
259
		0% Uncovered Elements: 36 (36) Complexity: 9 Complexity Density: 0.38
260	0	private int getPortNumber()...
261		{
262		// TODO pull up most of this!
263	0	int port = 0;
264	0	InputStream readChan = pymolProcess.getInputStream();
265	0	BufferedReader lineReader = new BufferedReader(
266		new InputStreamReader(readChan));
267	0	StringBuilder responses = new StringBuilder();
268	0	try
269		{
270	0	String response = lineReader.readLine();
271	0	while (response != null)
272		{
273	0	responses.append("\n" + response);
274		// expect: xml-rpc server running on host localhost, port 9123
275	0	if (response.contains("xml-rpc"))
276		{
277	0	String[] tokens = response.split(" ");
278	0	for (int i = 0; i < tokens.length - 1; i++)
279		{
280	0	if ("port".equals(tokens[i]))
281		{
282	0	port = Integer.parseInt(tokens[i + 1]);
283	0	break;
284		}
285		}
286		}
287	0	if (port > 0)
288		{
289	0	break; // hack for hanging readLine()
290		}
291	0	response = lineReader.readLine();
292		}
293		} catch (Exception e)
294		{
295	0	Cache.log.error("Failed to get REST port number from " + responses
296		+ ": " + e.getMessage());
297		// logger.error("Failed to get REST port number from " + responses + ": "
298		// + e.getMessage());
299		} finally
300		{
301	0	try
302		{
303	0	lineReader.close();
304		} catch (IOException e2)
305		{
306		}
307		}
308	0	if (port == 0)
309		{
310	0	Cache.log.error("Failed to start PyMOL with XMLRPC, response was: "
311		+ responses);
312		}
313	0	Cache.log.error("PyMOL started with XMLRPC on port " + port);
314	0	return port;
315		}
316
317		}