Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JabaWsServerQuery	45	71	22	0.00%	Show methods

Class JabaWsServerQuery

Class JabaWsServerQuery	Line # 45	Total Statements 71	Complexity 22	TOTAL Coverage 0.00%
isRunning() : boolean   isRunning() : boolean	5757	1.01	1.01	0.0 0.00%
setQuit(boolean) : void   setQuit(boolean) : void	6666	1.01	1.01	0.0 0.00%
JabaWsServerQuery(Jws2Discoverer,String)   JabaWsServerQuery(Jws2Discoverer,String)	7171	2.02	1.01	0.0 0.00%
run() : void   run() : void	9292	56.056	15.015	0.0 0.00%
isValidUrl(String) : boolean   isValidUrl(String) : boolean	238238	11.011	4.04	0.0 0.00%

 

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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		/**
22		*
23		*/
24		package jalview.ws.jws2;
25
26		import java.io.IOException;
27		import java.net.MalformedURLException;
28		import java.net.URL;
29		import java.util.HashSet;
30		import java.util.Set;
31
32		import compbio.data.msa.Category;
33		import compbio.data.msa.JABAService;
34		import compbio.ws.client.Jws2Client;
35		import compbio.ws.client.Services;
36		import jalview.bin.Console;
37		import jalview.util.HttpUtils;
38		import jalview.ws.jws2.jabaws2.Jws2Instance;
39		import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
40
41		/**
42		* @author JimP
43		*
44		*/
		0% Uncovered Elements: 96 (96) Complexity: 22 Complexity Density: 0.31
45		public class JabaWsServerQuery implements Runnable
46		{
47
48		Jws2Discoverer jws2Discoverer = null;
49
50		String jwsserver = null;
51
52		boolean quit = false, running = false;
53
54		/**
55		* @return the running
56		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	public boolean isRunning()...
58		{
59	0	return running;
60		}
61
62		/**
63		* @param quit
64		* the quit to set
65		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	public void setQuit(boolean quit)...
67		{
68	0	this.quit = quit;
69		}
70
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
71	0	public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server)...
72		{
73	0	this.jws2Discoverer = jws2Discoverer;
74	0	this.jwsserver = server;
75		}
76
77		Services[] JABAWS1SERVERS = new Services[] { Services.ClustalWS,
78		Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
79		Services.TcoffeeWS };
80
81		Services[] JABAWS2SERVERS = new Services[] { Services.ClustalWS,
82		Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
83		Services.TcoffeeWS, Services.AAConWS, Services.DisemblWS,
84		Services.GlobPlotWS, Services.IUPredWS, Services.JronnWS,
85		Services.RNAalifoldWS };
86
87		/*
88		* (non-Javadoc)
89		*
90		* @see java.lang.Runnable#run()
91		*/
		0% Uncovered Elements: 74 (74) Complexity: 15 Complexity Density: 0.27
92	0	@Override...
93		public void run()
94		{
95	0	running = true;
96	0	try
97		{
98		// TODO this test doesn't seem to attempt a connection - should it?
99		// would save a lot of failed tries with UnknownHostException
100	0	if (isValidUrl(jwsserver))
101		{
102	0	compbio.data.msa.RegistryWS registry = null;
103	0	Set svccategories = null;
104	0	boolean noservices = true;
105		// look for services
106	0	boolean jabasws2 = false;
107		// If we are dealing with a JABAWS2 service, then just go and ask the
108		// JABAWS 2 service registry
109	0	Set<Services> srv_set = new HashSet<Services>();
110
111	0	Set<Category> categories = Category.getCategories();
112	0	String svc_cat;
113
114	0	try
115		{
116		// JBPNote: why is RegistryWS in compbio.data.msa ?
117	0	registry = Jws2Client.connectToRegistry(jwsserver);
118	0	if (registry != null)
119		{
120		// jalview.bin.Console.errPrintln("Test Services Output\n"
121		// + registry.testAllServices());
122		// TODO: enumerate services and test those that haven't been tested
123		// in the last n-days/hours/etc.
124
125	0	jabasws2 = true;
126	0	srv_set = registry.getSupportedServices();
127
128		// dan test
129	0	jalview.bin.Console.outPrintln(
130		"registry.getSupportedServices: " + srv_set.toString());
131
132	0	svccategories = registry.getServiceCategories();
133
134		// dan test
135		// jalview.bin.Console.outPrintln("registry.getServiceCategories: "
136		// +
137		// svccategories.toString());
138
139		}
140		} catch (Exception ex)
141		{
142	0	jalview.bin.Console.errPrintln(
143		"Exception whilst trying to get at registry:");
144	0	ex.printStackTrace();
145		// if that failed, then we are probably working with a JABAWS1 server.
146		// in that case, look for each service endpoint
147	0	jalview.bin.Console.errPrintln("JWS2 Discoverer: " + jwsserver
148		+ " is a JABAWS1 server. Using hardwired list.");
149	0	for (Services srv : JABAWS1SERVERS)
150		{
151	0	srv_set.add(srv);
152		}
153		}
154
155	0	for (Category cat : categories)
156		{
157	0	for (Services srv : cat.getServices())
158		{
159	0	if (quit)
160		{
161	0	running = false;
162	0	return;
163		}
164	0	if (!srv_set.contains(srv))
165		{
166	0	continue;
167		}
168	0	JABAService service = null;
169	0	try
170		{
171	0	service = Jws2Client.connect(jwsserver, srv);
172		} catch (Exception e)
173		{
174	0	jalview.bin.Console.errPrintln("Jws2 Discoverer: Problem on "
175		+ jwsserver + " with service " + srv + ":\n"
176		+ e.getMessage());
177	0	if (!(e instanceof javax.xml.ws.WebServiceException))
178		{
179	0	e.printStackTrace();
180		}
181		// For moment, report service as a problem.
182	0	jws2Discoverer.addInvalidServiceUrl(jwsserver);
183		}
184	0	;
185	0	if (service != null
186		&& !Jws2InstanceFactory.ignoreService(srv.toString()))
187		{
188	0	noservices = false;
189	0	Jws2Instance svc = null;
190	0	if (registry != null)
191		{
192
193	0	String description = registry.getServiceDescription(srv);
194
195	0	svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
196		srv.toString(), cat.name, description, service);
197		}
198	0	if (svc == null)
199		{
200	0	svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
201		srv.toString(), cat.name,
202		"JABAWS 1 Alignment Service", service);
203		}
204	0	jws2Discoverer.addService(jwsserver, svc);
205		}
206
207		}
208		}
209
210	0	if (noservices)
211		{
212	0	jws2Discoverer.addUrlwithnoservices(jwsserver);
213		}
214		}
215		else
216		{
217	0	jws2Discoverer.addInvalidServiceUrl(jwsserver);
218	0	Console.warn("Ignoring invalid Jws2 service url " + jwsserver);
219		}
220		} catch (Exception e)
221		{
222	0	e.printStackTrace();
223	0	Console.warn("Exception when discovering Jws2 services.", e);
224	0	jws2Discoverer.addInvalidServiceUrl(jwsserver);
225		} catch (Error e)
226		{
227	0	Console.error("Exception when discovering Jws2 services.", e);
228	0	jws2Discoverer.addInvalidServiceUrl(jwsserver);
229		}
230	0	running = false;
231		}
232
233		/**
234		* Check if the URL is valid and responding.
235		*
236		* @return
237		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.36
238	0	private boolean isValidUrl(String server)...
239		{
240		// return Jws2Client.validURL(jwsserver); // checks syntax only
241	0	boolean result = false;
242	0	if (server != null)
243		{
244	0	try
245		{
246	0	URL url = new URL(server);
247	0	HttpUtils.openStream(url).close();
248	0	result = true;
249		} catch (MalformedURLException e)
250		{
251	0	jalview.bin.Console.errPrintln("Invalid server URL: " + server);
252	0	result = false;
253		} catch (IOException e)
254		{
255	0	jalview.bin.Console.errPrintln("Error connecting to server: "
256		+ server + ": " + e.toString());
257	0	result = false;
258		}
259		}
260	0	return result;
261		}
262
263		}