Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentServiceGuiHandler	37	139	53	0.00%	Show methods

Class AlignmentServiceGuiHandler

Class AlignmentServiceGuiHandler	Line # 37	Total Statements 139	Complexity 53	TOTAL Coverage 0.00%
AlignmentServiceGuiHandler(AlignmentAction,AlignFrame)   AlignmentServiceGuiHandler(AlignmentAction,AlignFrame)	5656	6.06	2.02	0.0 0.00%
taskStatusChanged(TaskI<AlignmentResult>,JobStatus) : void   taskStatusChanged(TaskI<AlignmentResult>,JobStatus) : void	6868	31.031	11.011	0.0 0.00%
taskStarted(TaskI<AlignmentResult>,List<? extends JobI>) : void   taskStarted(TaskI<AlignmentResult>,List<? extends JobI>) : void	112112	14.014	4.04	0.0 0.00%
taskCompleted(TaskI<AlignmentResult>,AlignmentResult) : void   taskCompleted(TaskI<AlignmentResult>,AlignmentResult) : void	134134	11.011	2.02	0.0 0.00%
displayResultsNewFrame(Alignment,List<AlignmentOrder>,HiddenColumns) : void   displayResultsNewFrame(Alignment,List<AlignmentOrder>,HiddenColumns) : void	155155	22.022	7.07	0.0 0.00%
addSortByMenuItems(AlignFrame,List<AlignmentOrder>) : void   addSortByMenuItems(AlignFrame,List<AlignmentOrder>) : void	196196	15.015	7.07	0.0 0.00%
taskException(TaskI<AlignmentResult>,Exception) : void   taskException(TaskI<AlignmentResult>,Exception) : void	225225	2.02	1.01	0.0 0.00%
subJobStatusChanged(TaskI<AlignmentResult>,JobI,JobStatus) : void   subJobStatusChanged(TaskI<AlignmentResult>,JobI,JobStatus) : void	232232	30.030	13.013	0.0 0.00%
subJobLogChanged(TaskI<AlignmentResult>,JobI,String) : void   subJobLogChanged(TaskI<AlignmentResult>,JobI,String) : void	271271	4.04	3.03	0.0 0.00%
subJobErrorLogChanged(TaskI<AlignmentResult>,JobI,String) : void   subJobErrorLogChanged(TaskI<AlignmentResult>,JobI,String) : void	282282	4.04	3.03	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ws2.gui;
2
3		import java.util.ArrayList;
4		import java.util.Arrays;
5		import java.util.BitSet;
6		import java.util.HashMap;
7		import java.util.LinkedHashMap;
8		import java.util.LinkedList;
9		import java.util.List;
10
11		import javax.swing.JInternalFrame;
12		import javax.swing.SwingUtilities;
13
14		import jalview.bin.Cache;
15		import jalview.bin.Console;
16		import jalview.datamodel.Alignment;
17		import jalview.datamodel.AlignmentI;
18		import jalview.datamodel.AlignmentOrder;
19		import jalview.datamodel.HiddenColumns;
20		import jalview.gui.AlignFrame;
21		import jalview.gui.Desktop;
22		import jalview.gui.JvOptionPane;
23		import jalview.gui.SplitFrame;
24		import jalview.gui.WebserviceInfo;
25		import jalview.util.ArrayUtils;
26		import jalview.util.MessageManager;
27		import jalview.util.Pair;
28		import jalview.ws2.actions.alignment.AlignmentAction;
29		import jalview.ws2.actions.alignment.AlignmentResult;
30		import jalview.ws2.actions.api.JobI;
31		import jalview.ws2.actions.api.TaskEventListener;
32		import jalview.ws2.actions.api.TaskI;
33		import jalview.ws2.api.JobStatus;
34		import jalview.ws2.api.WebService;
35		import jalview.ws2.helpers.WSClientTaskWrapper;
36
		0% Uncovered Elements: 191 (191) Complexity: 53 Complexity Density: 0.38
37		class AlignmentServiceGuiHandler
38		implements TaskEventListener<AlignmentResult>
39		{
40		private final WebService<?> service;
41
42		private final AlignFrame frame;
43
44		private WebserviceInfo infoPanel;
45
46		private String alnTitle; // title of the alignment used in new window
47
48		private JobI[] jobs = new JobI[0];
49
50		private int[] tabs = new int[0];
51
52		private int[] logOffset = new int[0];
53
54		private int[] errLogOffset = new int[0];
55
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
56	0	public AlignmentServiceGuiHandler(AlignmentAction action, AlignFrame frame)...
57		{
58	0	this.service = action.getWebService();
59	0	this.frame = frame;
60	0	String panelInfo = String.format("%s using service hosted at %s%n%s",
61		service.getName(), service.getUrl(), service.getDescription());
62	0	infoPanel = new WebserviceInfo(service.getName(), panelInfo, false);
63	0	String actionName = action.getName() != null ? action.getName() : "Alignment";
64	0	alnTitle = String.format("%s %s of %s", service.getName(), actionName,
65		frame.getTitle());
66		}
67
		0% Uncovered Elements: 31 (31) Complexity: 11 Complexity Density: 0.35
68	0	@Override...
69		public void taskStatusChanged(TaskI<AlignmentResult> source, JobStatus status)
70		{
71	0	switch (status)
72		{
73	0	case INVALID:
74	0	infoPanel.setVisible(false);
75	0	JvOptionPane.showMessageDialog(frame,
76		MessageManager.getString("info.invalid_msa_input_mininfo"),
77		MessageManager.getString("info.invalid_msa_notenough"),
78		JvOptionPane.INFORMATION_MESSAGE);
79	0	break;
80	0	case READY:
81	0	infoPanel.setthisService(new WSClientTaskWrapper(source));
82	0	infoPanel.setVisible(true);
83		// intentional no break
84	0	case SUBMITTED:
85	0	case QUEUED:
86	0	infoPanel.setStatus(WebserviceInfo.STATE_QUEUING);
87	0	break;
88	0	case RUNNING:
89	0	case UNKNOWN: // unsure what to do with unknown
90	0	infoPanel.setStatus(WebserviceInfo.STATE_RUNNING);
91	0	break;
92	0	case COMPLETED:
93	0	infoPanel.setProgressBar(
94		MessageManager.getString("status.collecting_job_results"),
95		jobs[0].getInternalId());
96	0	infoPanel.setStatus(WebserviceInfo.STATE_STOPPED_OK);
97	0	break;
98	0	case FAILED:
99	0	infoPanel.removeProgressBar(jobs[0].getInternalId());
100	0	infoPanel.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
101	0	break;
102	0	case CANCELLED:
103	0	infoPanel.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
104	0	break;
105	0	case SERVER_ERROR:
106	0	infoPanel.removeProgressBar(jobs[0].getInternalId());
107	0	infoPanel.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
108	0	break;
109		}
110		}
111
		0% Uncovered Elements: 20 (20) Complexity: 4 Complexity Density: 0.29
112	0	@Override...
113		public void taskStarted(TaskI<AlignmentResult> source, List<? extends JobI> subJobs)
114		{
115	0	jobs = subJobs.toArray(new JobI[0]);
116	0	tabs = new int[subJobs.size()];
117	0	logOffset = new int[subJobs.size()];
118	0	errLogOffset = new int[subJobs.size()];
119	0	for (int i = 0; i < subJobs.size(); i++)
120		{
121	0	JobI job = jobs[i];
122	0	int tabIndex = infoPanel.addJobPane();
123	0	tabs[i] = tabIndex;
124	0	infoPanel.setProgressName(String.format("region %d", i), tabIndex);
125	0	infoPanel.setProgressText(tabIndex, alnTitle + "\nJob details\n");
126		// jobs should not have states other than invalid or ready at this point
127	0	if (job.getStatus() == JobStatus.INVALID)
128	0	infoPanel.setStatus(tabIndex, WebserviceInfo.STATE_STOPPED_OK);
129	0	else if (job.getStatus() == JobStatus.READY)
130	0	infoPanel.setStatus(tabIndex, WebserviceInfo.STATE_QUEUING);
131		}
132		}
133
		0% Uncovered Elements: 13 (13) Complexity: 2 Complexity Density: 0.18
134	0	@Override...
135		public void taskCompleted(TaskI<AlignmentResult> source, AlignmentResult result)
136		{
137	0	SwingUtilities.invokeLater(() -> infoPanel.removeProgressBar(jobs[0].getInternalId()));
138	0	if (result == null)
139		{
140	0	SwingUtilities.invokeLater(infoPanel::setFinishedNoResults);
141	0	return;
142		}
143	0	infoPanel.showResultsNewFrame.addActionListener(evt -> {
144	0	var aln = result.getAlignment();
145		// copy alignment for each frame to have its own isntance
146	0	var alnCpy = new Alignment(aln);
147	0	alnCpy.setGapCharacter(aln.getGapCharacter());
148	0	alnCpy.setDataset(aln.getDataset());
149	0	displayResultsNewFrame(alnCpy, result.getAlignmentOrders(),
150		result.getHiddenColumns());
151		});
152	0	SwingUtilities.invokeLater(infoPanel::setResultsReady);
153		}
154
		0% Uncovered Elements: 32 (32) Complexity: 7 Complexity Density: 0.32
155	0	private void displayResultsNewFrame(Alignment aln,...
156		List<AlignmentOrder> alorders, HiddenColumns hidden)
157		{
158	0	AlignFrame newFrame = new AlignFrame(aln, hidden, AlignFrame.DEFAULT_WIDTH,
159		AlignFrame.DEFAULT_HEIGHT);
160	0	newFrame.getFeatureRenderer().transferSettings(
161		frame.getFeatureRenderer().getSettings());
162	0	if (alorders.size() > 0)
163		{
164	0	addSortByMenuItems(newFrame, alorders);
165		}
166
167	0	var requestingFrame = frame;
168	0	var splitContainer = requestingFrame.getSplitViewContainer();
169	0	if (splitContainer != null && splitContainer.getComplement(requestingFrame) != null)
170		{
171	0	AlignmentI complement = splitContainer.getComplement(requestingFrame);
172	0	String complementTitle = splitContainer.getComplementTitle(requestingFrame);
173	0	Alignment copyComplement = new Alignment(complement);
174	0	copyComplement.setGapCharacter(complement.getGapCharacter());
175	0	copyComplement.setDataset(complement.getDataset());
176	0	copyComplement.alignAs(aln);
177	0	if (copyComplement.getHeight() > 0)
178		{
179	0	newFrame.setTitle(alnTitle);
180	0	AlignFrame newFrame2 = new AlignFrame(copyComplement,
181		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
182	0	newFrame2.setTitle(complementTitle);
183	0	String linkedTitle = MessageManager.getString("label.linked_view_title");
184	0	JInternalFrame splitFrame = new SplitFrame(
185	0	aln.isNucleotide() ? newFrame : newFrame2,
186	0	aln.isNucleotide() ? newFrame2 : newFrame);
187	0	Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
188	0	return;
189		}
190		}
191		// no split frame or failed to create complementary alignment
192	0	Desktop.addInternalFrame(newFrame, alnTitle, AlignFrame.DEFAULT_WIDTH,
193		AlignFrame.DEFAULT_HEIGHT);
194		}
195
		0% Uncovered Elements: 25 (25) Complexity: 7 Complexity Density: 0.47
196	0	private void addSortByMenuItems(AlignFrame frame, List<AlignmentOrder> alorders)...
197		{
198	0	if (alorders.size() == 1)
199		{
200	0	frame.addSortByOrderMenuItem(service.getName() + " Ordering",
201		alorders.get(0));
202	0	return;
203		}
204	0	BitSet collected = new BitSet(alorders.size());
205	0	for (int i = 0, N = alorders.size(); i < N; i++)
206		{
207	0	if (collected.get(i))
208	0	continue;
209	0	var regions = new ArrayList<String>();
210	0	var order = alorders.get(i);
211	0	for (int j = i; j < N; j++)
212		{
213	0	if (!collected.get(j) && alorders.get(j).equals(order))
214		{
215	0	regions.add(Integer.toString(j + 1));
216	0	collected.set(j);
217		}
218		}
219	0	var orderName = String.format("%s Region %s Ordering",
220		service.getName(), String.join(",", regions));
221	0	frame.addSortByOrderMenuItem(orderName, order);
222		}
223		}
224
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
225	0	@Override...
226		public void taskException(TaskI<AlignmentResult> source, Exception e)
227		{
228	0	Console.error(String.format("Service %s raised an exception.", service.getName()), e);
229	0	infoPanel.appendProgressText(e.getMessage());
230		}
231
		0% Uncovered Elements: 34 (34) Complexity: 13 Complexity Density: 0.43
232	0	@Override...
233		public void subJobStatusChanged(TaskI<AlignmentResult> source, JobI job, JobStatus status)
234		{
235	0	int i = ArrayUtils.indexOf(jobs, job);
236	0	assert i >= 0 : "job does not exist";
237	0	if (i < 0)
238		// safeguard that should not happen irl
239	0	return;
240	0	int wsStatus;
241	0	switch (status)
242		{
243	0	case INVALID:
244	0	case COMPLETED:
245	0	wsStatus = WebserviceInfo.STATE_STOPPED_OK;
246	0	break;
247	0	case READY:
248	0	case SUBMITTED:
249	0	case QUEUED:
250	0	wsStatus = WebserviceInfo.STATE_QUEUING;
251	0	break;
252	0	case RUNNING:
253	0	case UNKNOWN:
254	0	wsStatus = WebserviceInfo.STATE_RUNNING;
255	0	break;
256	0	case FAILED:
257	0	wsStatus = WebserviceInfo.STATE_STOPPED_ERROR;
258	0	break;
259	0	case CANCELLED:
260	0	wsStatus = WebserviceInfo.STATE_CANCELLED_OK;
261	0	break;
262	0	case SERVER_ERROR:
263	0	wsStatus = WebserviceInfo.STATE_STOPPED_SERVERERROR;
264	0	break;
265	0	default:
266	0	throw new AssertionError("Non-exhaustive switch statement");
267		}
268	0	infoPanel.setStatus(tabs[i], wsStatus);
269		}
270
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
271	0	@Override...
272		public void subJobLogChanged(TaskI<AlignmentResult> source, JobI job, String log)
273		{
274	0	int i = ArrayUtils.indexOf(jobs, job);
275	0	assert i >= 0 : "job does not exist";
276	0	if (i < 0)
277		// safeguard that should never happen
278	0	return;
279	0	infoPanel.appendProgressText(tabs[i], log.substring(logOffset[i]));
280		}
281
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
282	0	@Override...
283		public void subJobErrorLogChanged(TaskI<AlignmentResult> source, JobI job, String log)
284		{
285	0	int i = ArrayUtils.indexOf(jobs, job);
286	0	assert i >= 0 : "job does not exist";
287	0	if (i < 0)
288		// safeguard that should never happen
289	0	return;
290	0	infoPanel.appendProgressText(tabs[i], log.substring(errLogOffset[i]));
291		}
292
293		}