Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JabawsServiceInstance	31	69	23	0.00%	Show methods

Class JabawsServiceInstance

Class JabawsServiceInstance	Line # 31	Total Statements 69	Complexity 23	TOTAL Coverage 0.00%
cancel(WsJob) : boolean   cancel(WsJob) : boolean	4242	2.02	1.01	0.0 0.00%
JabawsServiceInstance(Jws2Instance)   JabawsServiceInstance(Jws2Instance)	5454	2.02	1.01	0.0 0.00%
updateStatus(WsJob) : void   updateStatus(WsJob) : void	6060	2.02	1.01	0.0 0.00%
updateJobProgress(WsJob) : boolean   updateJobProgress(WsJob) : boolean	6767	20.020	7.07	0.0 0.00%
<init>, line 106()   <init>, line 106()	106106	9.09	1.01	0.0 0.00%
isPresetJob(WsJob) : boolean   isPresetJob(WsJob) : boolean	118118	1.01	1.01	0.0 0.00%
getServerPreset(WsJob) : Preset   getServerPreset(WsJob) : Preset	123123	1.01	2.02	0.0 0.00%
getJabaArguments(WsParamSetI) : List<Argument>   getJabaArguments(WsParamSetI) : List<Argument>	130130	6.06	3.03	0.0 0.00%
handleSubmitError(Throwable,WsJob,WebserviceInfo) : boolean   handleSubmitError(Throwable,WsJob,WebserviceInfo) : boolean	148148	19.019	4.04	0.0 0.00%
handleCollectionException(Exception,WsJob,WebserviceInfo) : boolean   handleCollectionException(Exception,WsJob,WebserviceInfo) : boolean	192192	7.07	2.02	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ws.jws2.jabaws2;
2
3		import jalview.bin.Cache;
4		import jalview.bin.Console;
5		import jalview.gui.WebserviceInfo;
6		import jalview.util.MessageManager;
7		import jalview.ws.gui.WsJob;
8		import jalview.ws.gui.WsJob.JobState;
9		import jalview.ws.jws2.JabaParamStore;
10		import jalview.ws.jws2.JabaPreset;
11		import jalview.ws.jws2.dm.JabaWsParamSet;
12		import jalview.ws.params.WsParamSetI;
13
14		import java.util.ArrayList;
15		import java.util.HashMap;
16		import java.util.List;
17		import java.util.Map;
18
19		import compbio.metadata.Argument;
20		import compbio.metadata.ChunkHolder;
21		import compbio.metadata.JobStatus;
22		import compbio.metadata.Preset;
23
24		/**
25		* Base class for JABAWS service instances. Provides helper methods for
26		* interfacing with Jalview.
27		*
28		* @author jprocter
29		*
30		*/
		0% Uncovered Elements: 101 (101) Complexity: 23 Complexity Density: 0.33
31		public class JabawsServiceInstance<T extends compbio.data.msa.JManagement>
32		implements
33		jalview.ws.api.JalviewWebServiceI, jalview.ws.api.CancellableI
34		{
35		/**
36		* our service instance handler generated by the discoverer
37		*/
38		Jws2Instance our;
39		protected T service;
40		protected Map<JobStatus, JobState> jwsState = new HashMap<>();
41
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
42	0	@Override...
43		public boolean cancel(WsJob job)
44		{
45	0	service.cancelJob(job.getJobId());
46		// if the Jaba server indicates the job can't be cancelled, its
47		// because its running on the server's local execution engine
48		// so we just close the window anyway.
49
50	0	return true;
51		}
52
53
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
54	0	public JabawsServiceInstance(Jws2Instance handle)...
55		{
56	0	our = handle;
57	0	service = (T) handle.service;
58		}
59
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
60	0	@Override...
61		public void updateStatus(WsJob job)
62		{
63	0	JobStatus jwsstatus = service.getJobStatus(job.getJobId());
64	0	job.setState(jwsState.get(jwsstatus));
65		}
66
		0% Uncovered Elements: 28 (28) Complexity: 7 Complexity Density: 0.35
67	0	@Override...
68		public boolean updateJobProgress(WsJob job) throws Exception
69		{
70	0	StringBuilder response = new StringBuilder(job.getStatus());
71	0	long lastchunk = job.getNextChunk();
72	0	if (lastchunk == -1)
73		{
74	0	Console.debug("No more status messages for job " + job.getJobId());
75	0	return false;
76		}
77	0	boolean changed = false;
78	0	do
79		{
80	0	ChunkHolder chunk = service.pullExecStatistics(job.getJobId(),
81		lastchunk);
82	0	if (chunk != null)
83		{
84	0	changed |= chunk.getChunk().length() > 0;
85	0	response.append(chunk.getChunk());
86	0	lastchunk = chunk.getNextPosition();
87	0	try
88		{
89	0	Thread.sleep(50);
90		} catch (InterruptedException x)
91		{
92		}
93	0	;
94		}
95	0	;
96	0	job.setnextChunk(lastchunk);
97	0	} while (lastchunk >= 0 && job.getNextChunk() != lastchunk);
98	0	if (job instanceof WsJob)
99		{
100		// TODO decide if WsJob will be the bean for all ng-webservices
101	0	job.setStatus(response.toString());
102		}
103	0	return changed;
104		}
105
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11
106	0	{...
107	0	jwsState.put(JobStatus.CANCELLED, JobState.CANCELLED);
108	0	jwsState.put(JobStatus.COLLECTED, JobState.FINISHED);
109	0	jwsState.put(JobStatus.FAILED, JobState.FAILED);
110	0	jwsState.put(JobStatus.FINISHED, JobState.FINISHED);
111	0	jwsState.put(JobStatus.PENDING, JobState.QUEUED);
112	0	jwsState.put(JobStatus.RUNNING, JobState.RUNNING);
113	0	jwsState.put(JobStatus.STARTED, JobState.RUNNING);
114	0	jwsState.put(JobStatus.SUBMITTED, JobState.SUBMITTED);
115	0	jwsState.put(JobStatus.UNDEFINED, JobState.UNKNOWN);
116		}
117
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
118	0	public boolean isPresetJob(WsJob job)...
119		{
120	0	return job.getPreset() != null && job.getPreset() instanceof JabaPreset;
121		}
122
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
123	0	public Preset getServerPreset(WsJob job)...
124		{
125	0	return (isPresetJob(job))
126		? ((JabaPreset) job.getPreset()).getJabaPreset()
127		: null;
128		}
129
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
130	0	public List<Argument> getJabaArguments(WsParamSetI preset)...
131		{
132	0	List<Argument> newargs = new ArrayList<>();
133	0	if (preset != null)
134		{
135	0	if (preset instanceof JabaWsParamSet)
136		{
137	0	newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
138		}
139		else
140		{
141	0	newargs.addAll(
142		JabaParamStore.getJabafromJwsArgs(preset.getArguments()));
143		}
144		}
145	0	return newargs;
146		}
147
		0% Uncovered Elements: 25 (25) Complexity: 4 Complexity Density: 0.21
148	0	@Override...
149		public boolean handleSubmitError(Throwable _lex, WsJob j,
150		WebserviceInfo wsInfo) throws Exception, Error
151		{
152	0	if (_lex instanceof compbio.metadata.UnsupportedRuntimeException)
153		{
154	0	wsInfo.appendProgressText(MessageManager.formatMessage(
155		"info.job_couldnt_be_run_server_doesnt_support_program",
156		new String[]
157		{ _lex.getMessage() }));
158	0	wsInfo.warnUser(_lex.getMessage(),
159		MessageManager.getString("warn.service_not_supported"));
160	0	wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
161	0	wsInfo.setStatus(j.getJobnum(),
162		WebserviceInfo.STATE_STOPPED_SERVERERROR);
163	0	return true;
164		}
165	0	if (_lex instanceof compbio.metadata.LimitExceededException)
166		{
167	0	wsInfo.appendProgressText(MessageManager.formatMessage(
168		"info.job_couldnt_be_run_exceeded_hard_limit", new String[]
169		{ _lex.getMessage() }));
170	0	wsInfo.warnUser(_lex.getMessage(),
171		MessageManager.getString("warn.input_is_too_big"));
172	0	wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
173	0	wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
174	0	return true;
175		}
176	0	if (_lex instanceof compbio.metadata.WrongParameterException)
177		{
178	0	wsInfo.warnUser(_lex.getMessage(),
179		MessageManager.getString("warn.invalid_job_param_set"));
180	0	wsInfo.appendProgressText(MessageManager.formatMessage(
181		"info.job_couldnt_be_run_incorrect_param_setting",
182		new String[]
183		{ _lex.getMessage() }));
184	0	wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
185	0	wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
186	0	return true;
187		}
188		// pass on to generic error handler
189	0	return false;
190		}
191
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
192	0	@Override...
193		public boolean handleCollectionException(Exception ex, WsJob msjob,
194		WebserviceInfo wsInfo)
195		{
196	0	if (ex instanceof compbio.metadata.ResultNotAvailableException)
197		{
198		// job has failed for some reason - probably due to invalid
199		// parameters
200	0	Console.debug(
201		"Results not available for finished job - marking as broken job.",
202		ex);
203	0	String status = msjob.getStatus();
204
205	0	msjob.setStatus(status
206		+ "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
207		+ ex.getLocalizedMessage());
208	0	msjob.setState(WsJob.JobState.BROKEN);
209	0	return true;
210		}
211	0	return false;
212		}
213		}