Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AWSThread	43	79	31	0.270491827%	Show methods

Class AWSThread

Class AWSThread	Line # 43	Total Statements 79	Complexity 31	TOTAL Coverage 0.270491827%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	124124	32.032	11.011	0.22727273 0.2272727322.7%
start() : void   start() : void	108108	10.010	2.02	0.41666666 0.4166666641.7%
updateGlobalStatus(JobStateSummary) : void   updateGlobalStatus(JobStateSummary) : void	200200	11.011	6.06	0.0 0.00%
interrupt() : void   interrupt() : void	229229	1.01	1.01	0.0 0.00%
propagateDatasetMappings(Alignment) : void   propagateDatasetMappings(Alignment) : void	264264	8.08	5.05	0.0 0.00%
getGapChar() : char   getGapChar() : char	289289	1.01	1.01	0.0 0.00%
AWSThread(AlignFrame,WebserviceInfo,AlignmentView,String,String)   AWSThread(AlignFrame,WebserviceInfo,AlignmentView,String,String)	307307	2.02	1.01	0.0 0.00%
AWSThread(AlignFrame,WebserviceInfo,AlignmentView,String)   AWSThread(AlignFrame,WebserviceInfo,AlignmentView,String)	326326	13.013	3.03	0.88235295 0.8823529588.2%
getRequestingAlignFrame() : AlignFrame   getRequestingAlignFrame() : AlignFrame	349349	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.04918033	jalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbsjalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbs	1PASS

 

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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		package jalview.ws;
22
23		import jalview.bin.Console;
24		import jalview.datamodel.AlignedCodonFrame;
25		import jalview.datamodel.Alignment;
26		import jalview.datamodel.AlignmentI;
27		import jalview.datamodel.AlignmentView;
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.AlignFrame;
30		import jalview.gui.WebserviceInfo;
31		import jalview.util.MessageManager;
32		import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
33
34		import java.util.ArrayList;
35		import java.util.List;
36
37		import static java.lang.String.format;
38
39		import java.awt.event.ActionEvent;
40		import java.awt.event.ActionListener;
41		import javax.swing.Timer;
42
		27% Uncovered Elements: 89 (122) Complexity: 31 Complexity Density: 0.39
43		public abstract class AWSThread
44		{
45
46		private javax.swing.Timer timer;
47
48		/**
49		* view that this job was associated with
50		*/
51		protected AlignmentI currentView = null;
52
53		/**
54		* feature settings from view that job was associated with
55		*/
56		protected FeatureRendererSettings featureSettings = null;
57
58		/**
59		* metadata about this web service
60		*/
61		protected WebserviceInfo wsInfo = null;
62
63		/**
64		* original input data for this job
65		*/
66		protected AlignmentView input = null;
67
68		/**
69		* dataset sequence relationships to be propagated onto new results
70		*/
71		protected List<AlignedCodonFrame> codonframe = null;
72
73		/**
74		* are there jobs still running in this thread.
75		*
76		* fixme: initialize with an empty array?
77		*/
78		protected boolean jobComplete = false;
79
80		/**
81		* one or more jobs being managed by this thread.
82		*/
83		protected AWsJob[] jobs = null;
84
85		/**
86		* full name of service
87		*/
88		protected String WebServiceName = null;
89
90		protected char defGapChar = '-';
91
92		/**
93		* header prepended to all output from job
94		*/
95		protected String OutputHeader;
96
97		/**
98		* only used when reporting a web service out of memory error - the job ID
99		* will be concatenated to the URL
100		*/
101		protected String WsUrl = null;
102
103		/*
104		* The AlignFrame from which the service was requested.
105		*/
106		private AlignFrame alignFrame;
107
		41.7% Uncovered Elements: 7 (12) Complexity: 2 Complexity Density: 0.2
108	1	public void start()...
109		{
110	1	if (jobs == null)
111		{
112	0	jobComplete = true;
113	0	Console.debug(
114		"WebServiceJob poll loop finished with no jobs created.");
115	0	wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
116	0	wsInfo.appendProgressText(
117		MessageManager.getString("info.no_jobs_ran"));
118	0	wsInfo.setFinishedNoResults();
119	0	return;
120		}
121	1	timer = new Timer(5000, new ActionListener()
122		{
123
		22.7% Uncovered Elements: 34 (44) Complexity: 11 Complexity Density: 0.34
124	1	@Override...
125		public void actionPerformed(ActionEvent e)
126		{
127
128	1	JobStateSummary jstate = new JobStateSummary();
129	1	for (final AWsJob job : jobs)
130		{
131	1	if (!job.submitted && job.hasValidInput())
132		{
133	1	StartJob(job);
134		}
135	1	Console.debug(format(
136	1	"Job %s is %ssubmitted", job, job.submitted ? "" : "not "));
137	1	if (job.submitted && !job.subjobComplete)
138		{
139	0	Console.debug(format(
140		"Polling Job %s Result state was:%s(ServerError=%b)",
141		job, job.getState(), job.isServerError()));
142	0	try
143		{
144	0	pollJob(job);
145	0	if (!job.hasResponse())
146	0	throw new Exception("Timed out when communicating with server. Try again later.");
147		else
148	0	Console.debug(format("Job %s Result state:%s(ServerError=%b)",
149		job, job.getState(), job.isServerError()));
150		} catch (Exception exc)
151		{
152		// Deal with Transaction exceptions
153	0	wsInfo.appendProgressText(job.jobnum, MessageManager
154		.formatMessage("info.server_exception", WebServiceName,
155		exc.getMessage()));
156		// always output the exception's stack trace to the log
157	0	Console.warn(format("%s job(%s) Server exception.",
158		WebServiceName, job.jobnum));
159	0	exc.printStackTrace();
160
161	0	if (job.allowedServerExceptions > 0)
162		{
163	0	job.allowedServerExceptions--;
164		}
165		else
166		{
167	0	Console.warn(format("Dropping job %s %s", job, job.jobId));
168	0	job.subjobComplete = true;
169	0	wsInfo.setStatus(job.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
170		}
171		} catch (OutOfMemoryError oomerror)
172		{
173	0	jobComplete = true;
174	0	job.subjobComplete = true;
175	0	job.clearResponse();
176	0	wsInfo.setStatus(job.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
177	0	Console.error(format("Out of memory when retrieving Job %s id:%s/%s",
178		job, WsUrl, job.jobId), oomerror);
179	0	new jalview.gui.OOMWarning("retrieving result for " + WebServiceName, oomerror);
180	0	System.gc();
181		}
182		}
183	1	jstate.updateJobPanelState(wsInfo, OutputHeader, job);
184		}
185		// Decide on overall state based on collected jobs[] states
186	0	updateGlobalStatus(jstate);
187	0	if (jobComplete)
188		{
189	0	timer.stop();
190		// jobs should never be null at this point
191	0	parseResult(); // tidy up and make results available to user
192
193		}
194		}
195		});
196	1	timer.setInitialDelay(0);
197	1	timer.start();
198		}
199
		0% Uncovered Elements: 21 (21) Complexity: 6 Complexity Density: 0.55
200	0	protected void updateGlobalStatus(JobStateSummary jstate)...
201		{
202	0	if (jstate.running > 0)
203		{
204	0	wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
205		}
206	0	else if (jstate.queuing > 0)
207		{
208	0	wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
209		}
210		else
211		{
212	0	jobComplete = true;
213	0	if (jstate.finished > 0)
214		{
215	0	wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
216		}
217	0	else if (jstate.error > 0)
218		{
219	0	wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
220		}
221	0	else if (jstate.serror > 0)
222		{
223	0	wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
224		}
225		}
226		}
227
228
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
229	0	public void interrupt()...
230		{
231	0	timer.stop();
232		}
233
234		/**
235		* query web service for status of job. on return, job.result must not be null
236		* - if it is then it will be assumed that the job status query timed out and
237		* a server exception will be logged.
238		*
239		* @param job
240		* @throws Exception
241		* will be logged as a server exception for this job
242		*/
243		public abstract void pollJob(AWsJob job) throws Exception;
244
245		/**
246		* submit job to web service
247		*
248		* @param job
249		*/
250		public abstract void StartJob(AWsJob job);
251
252		/**
253		* process the set of AWsJob objects into a set of results, and tidy up.
254		*/
255		public abstract void parseResult();
256
257		/**
258		* helper function to conserve dataset references to sequence objects returned
259		* from web services 1. Propagates AlCodonFrame data from
260		* <code>codonframe</code> to <code>al</code> TODO: refactor to datamodel
261		*
262		* @param al
263		*/
		0% Uncovered Elements: 14 (14) Complexity: 5 Complexity Density: 0.62
264	0	public void propagateDatasetMappings(Alignment al)...
265		{
266	0	if (codonframe != null)
267		{
268	0	SequenceI[] alignment = al.getSequencesArray();
269	0	for (int sq = 0; sq < alignment.length; sq++)
270		{
271	0	for (AlignedCodonFrame acf : codonframe)
272		{
273	0	final SequenceI seq = alignment[sq];
274	0	if (acf != null && acf.involvesSequence(seq))
275		{
276	0	al.addCodonFrame(acf);
277	0	break;
278		}
279		}
280		}
281		}
282		}
283
284
285		/**
286		*
287		* @return gap character to use for any alignment generation
288		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
289	0	public char getGapChar()...
290		{
291	0	return defGapChar;
292		}
293
294		/**
295		*
296		* @param alignFrame
297		* reference for copying mappings across
298		* @param wsinfo
299		* gui attachment point
300		* @param input
301		* input data for the calculation
302		* @param webServiceName
303		* name of service
304		* @param wsUrl
305		* url of the service being invoked
306		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
307	0	public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,...
308		AlignmentView input, String webServiceName, String wsUrl)
309		{
310	0	this(alignFrame, wsinfo, input, wsUrl);
311	0	WebServiceName = webServiceName;
312		}
313
314		/**
315		* Extracts additional info from alignment view's context.
316		*
317		* @param alframe
318		* - reference for copying mappings and display styles across
319		* @param wsinfo2
320		* - gui attachment point - may be null
321		* @param alview
322		* - input data for the calculation
323		* @param wsurl2
324		* - url of the service being invoked
325		*/
		88.2% Uncovered Elements: 2 (17) Complexity: 3 Complexity Density: 0.23
326	2	public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,...
327		AlignmentView alview, String wsurl2)
328		{
329	2	super();
330	2	this.alignFrame = alframe;
331	2	currentView = alframe.getCurrentView().getAlignment();
332	2	featureSettings = alframe.getFeatureRenderer().getSettings();
333	2	defGapChar = alframe.getViewport().getGapCharacter();
334	2	this.wsInfo = wsinfo2;
335	2	this.input = alview;
336	2	WsUrl = wsurl2;
337	2	if (alframe != null)
338		{
339	2	List<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
340		.getCodonFrames();
341	2	if (cf != null)
342		{
343	2	codonframe = new ArrayList<>();
344	2	codonframe.addAll(cf);
345		}
346		}
347		}
348
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
349	0	protected AlignFrame getRequestingAlignFrame()...
350		{
351	0	return this.alignFrame;
352		}
353		}