1 package jalview.ws2.gui;
3 import static java.util.Objects.requireNonNullElse;
5 import java.util.ArrayList;
6 import java.util.Arrays;
7 import java.util.BitSet;
8 import java.util.HashMap;
9 import java.util.LinkedHashMap;
10 import java.util.LinkedList;
11 import java.util.List;
13 import javax.swing.JInternalFrame;
14 import javax.swing.SwingUtilities;
16 import jalview.bin.Cache;
17 import jalview.datamodel.Alignment;
18 import jalview.datamodel.AlignmentI;
19 import jalview.datamodel.AlignmentOrder;
20 import jalview.datamodel.HiddenColumns;
21 import jalview.gui.AlignFrame;
22 import jalview.gui.Desktop;
23 import jalview.gui.JvOptionPane;
24 import jalview.gui.SplitFrame;
25 import jalview.gui.WebserviceInfo;
26 import jalview.util.ArrayUtils;
27 import jalview.util.MessageManager;
28 import jalview.util.Pair;
29 import jalview.ws2.actions.alignment.AlignmentAction;
30 import jalview.ws2.actions.alignment.AlignmentResult;
31 import jalview.ws2.actions.api.JobI;
32 import jalview.ws2.actions.api.TaskEventListener;
33 import jalview.ws2.actions.api.TaskI;
34 import jalview.ws2.api.JobStatus;
35 import jalview.ws2.api.WebService;
36 import jalview.ws2.helpers.WSClientTaskWrapper;
38 class AlignmentServiceGuiHandler
39 implements TaskEventListener<AlignmentResult>
41 private final WebService<?> service;
43 private final AlignFrame frame;
45 private WebserviceInfo infoPanel;
47 private String alnTitle; // title of the alignment used in new window
49 private JobI[] jobs = new JobI[0];
51 private int[] tabs = new int[0];
53 private int[] logOffset = new int[0];
55 private int[] errLogOffset = new int[0];
57 public AlignmentServiceGuiHandler(AlignmentAction action, AlignFrame frame)
59 this.service = action.getWebService();
61 String panelInfo = String.format("%s using service hosted at %s%n%s",
62 service.getName(), service.getUrl(), service.getDescription());
63 infoPanel = new WebserviceInfo(service.getName(), panelInfo, false);
64 String actionName = requireNonNullElse(action.getName(), "Alignment");
65 alnTitle = String.format("%s %s of %s", service.getName(), actionName,
70 public void taskStatusChanged(TaskI<AlignmentResult> source, JobStatus status)
75 infoPanel.setVisible(false);
76 JvOptionPane.showMessageDialog(frame,
77 MessageManager.getString("info.invalid_msa_input_mininfo"),
78 MessageManager.getString("info.invalid_msa_notenough"),
79 JvOptionPane.INFORMATION_MESSAGE);
82 infoPanel.setthisService(new WSClientTaskWrapper(source));
83 infoPanel.setVisible(true);
84 // intentional no break
87 infoPanel.setStatus(WebserviceInfo.STATE_QUEUING);
90 case UNKNOWN: // unsure what to do with unknown
91 infoPanel.setStatus(WebserviceInfo.STATE_RUNNING);
94 infoPanel.setProgressBar(
95 MessageManager.getString("status.collecting_job_results"),
96 jobs[0].getInternalId());
97 infoPanel.setStatus(WebserviceInfo.STATE_STOPPED_OK);
100 infoPanel.removeProgressBar(jobs[0].getInternalId());
101 infoPanel.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
104 infoPanel.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
107 infoPanel.removeProgressBar(jobs[0].getInternalId());
108 infoPanel.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
114 public void taskStarted(TaskI<AlignmentResult> source, List<? extends JobI> subJobs)
116 jobs = subJobs.toArray(new JobI[0]);
117 tabs = new int[subJobs.size()];
118 logOffset = new int[subJobs.size()];
119 errLogOffset = new int[subJobs.size()];
120 for (int i = 0; i < subJobs.size(); i++)
123 int tabIndex = infoPanel.addJobPane();
125 infoPanel.setProgressName(String.format("region %d", i), tabIndex);
126 infoPanel.setProgressText(tabIndex, alnTitle + "\nJob details\n");
127 // jobs should not have states other than invalid or ready at this point
128 if (job.getStatus() == JobStatus.INVALID)
129 infoPanel.setStatus(tabIndex, WebserviceInfo.STATE_STOPPED_OK);
130 else if (job.getStatus() == JobStatus.READY)
131 infoPanel.setStatus(tabIndex, WebserviceInfo.STATE_QUEUING);
136 public void taskCompleted(TaskI<AlignmentResult> source, AlignmentResult result)
138 SwingUtilities.invokeLater(() -> infoPanel.removeProgressBar(jobs[0].getInternalId()));
141 SwingUtilities.invokeLater(infoPanel::setFinishedNoResults);
144 infoPanel.showResultsNewFrame.addActionListener(evt -> {
145 var aln = result.getAlignment();
146 // copy alignment for each frame to have its own isntance
147 var alnCpy = new Alignment(aln);
148 alnCpy.setGapCharacter(aln.getGapCharacter());
149 alnCpy.setDataset(aln.getDataset());
150 displayResultsNewFrame(alnCpy, result.getAlignmentOrders(),
151 result.getHiddenColumns());
153 SwingUtilities.invokeLater(infoPanel::setResultsReady);
156 private void displayResultsNewFrame(Alignment aln,
157 List<AlignmentOrder> alorders, HiddenColumns hidden)
159 AlignFrame newFrame = new AlignFrame(aln, hidden, AlignFrame.DEFAULT_WIDTH,
160 AlignFrame.DEFAULT_HEIGHT);
161 newFrame.getFeatureRenderer().transferSettings(
162 frame.getFeatureRenderer().getSettings());
163 if (alorders.size() > 0)
165 addSortByMenuItems(newFrame, alorders);
168 var requestingFrame = frame;
169 var splitContainer = requestingFrame.getSplitViewContainer();
170 if (splitContainer != null && splitContainer.getComplement(requestingFrame) != null)
172 AlignmentI complement = splitContainer.getComplement(requestingFrame);
173 String complementTitle = splitContainer.getComplementTitle(requestingFrame);
174 Alignment copyComplement = new Alignment(complement);
175 copyComplement.setGapCharacter(complement.getGapCharacter());
176 copyComplement.setDataset(complement.getDataset());
177 copyComplement.alignAs(aln);
178 if (copyComplement.getHeight() > 0)
180 newFrame.setTitle(alnTitle);
181 AlignFrame newFrame2 = new AlignFrame(copyComplement,
182 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
183 newFrame2.setTitle(complementTitle);
184 String linkedTitle = MessageManager.getString("label.linked_view_title");
185 JInternalFrame splitFrame = new SplitFrame(
186 aln.isNucleotide() ? newFrame : newFrame2,
187 aln.isNucleotide() ? newFrame2 : newFrame);
188 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
192 // no split frame or failed to create complementary alignment
193 Desktop.addInternalFrame(newFrame, alnTitle, AlignFrame.DEFAULT_WIDTH,
194 AlignFrame.DEFAULT_HEIGHT);
197 private void addSortByMenuItems(AlignFrame frame, List<AlignmentOrder> alorders)
199 if (alorders.size() == 1)
201 frame.addSortByOrderMenuItem(service.getName() + " Ordering",
205 BitSet collected = new BitSet(alorders.size());
206 for (int i = 0, N = alorders.size(); i < N; i++)
208 if (collected.get(i))
210 var regions = new ArrayList<String>();
211 var order = alorders.get(i);
212 for (int j = i; j < N; j++)
214 if (!collected.get(j) && alorders.get(j).equals(order))
216 regions.add(Integer.toString(j + 1));
220 var orderName = String.format("%s Region %s Ordering",
221 service.getName(), String.join(",", regions));
222 frame.addSortByOrderMenuItem(orderName, order);
227 public void taskException(TaskI<AlignmentResult> source, Exception e)
229 Cache.log.error(String.format("Service %s raised an exception.", service.getName()), e);
230 infoPanel.appendProgressText(e.getMessage());
234 public void taskRestarted(TaskI<AlignmentResult> source)
236 // alignment services are not restartable
240 public void subJobStatusChanged(TaskI<AlignmentResult> source, JobI job, JobStatus status)
242 int i = ArrayUtils.indexOf(jobs, job);
243 assert i >= 0 : "job does not exist";
245 // safeguard that should not happen irl
252 wsStatus = WebserviceInfo.STATE_STOPPED_OK;
257 wsStatus = WebserviceInfo.STATE_QUEUING;
261 wsStatus = WebserviceInfo.STATE_RUNNING;
264 wsStatus = WebserviceInfo.STATE_STOPPED_ERROR;
267 wsStatus = WebserviceInfo.STATE_CANCELLED_OK;
270 wsStatus = WebserviceInfo.STATE_STOPPED_SERVERERROR;
273 throw new AssertionError("Non-exhaustive switch statement");
275 infoPanel.setStatus(tabs[i], wsStatus);
279 public void subJobLogChanged(TaskI<AlignmentResult> source, JobI job, String log)
281 int i = ArrayUtils.indexOf(jobs, job);
282 assert i >= 0 : "job does not exist";
284 // safeguard that should never happen
286 infoPanel.appendProgressText(tabs[i], log.substring(logOffset[i]));
290 public void subJobErrorLogChanged(TaskI<AlignmentResult> source, JobI job, String log)
292 int i = ArrayUtils.indexOf(jobs, job);
293 assert i >= 0 : "job does not exist";
295 // safeguard that should never happen
297 infoPanel.appendProgressText(tabs[i], log.substring(errLogOffset[i]));