2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ws.rest;
23 import jalview.bin.Cache;
24 import jalview.datamodel.AlignmentView;
25 import jalview.gui.AlignFrame;
26 import jalview.gui.AlignViewport;
27 import jalview.gui.AlignmentPanel;
28 import jalview.gui.Desktop;
29 import jalview.gui.JvOptionPane;
30 import jalview.gui.WebserviceInfo;
31 import jalview.io.packed.DataProvider.JvDataType;
32 import jalview.util.MessageManager;
33 import jalview.ws.WSClient;
34 import jalview.ws.WSClientI;
35 import jalview.ws.WSMenuEntryProviderI;
37 import java.awt.event.ActionEvent;
38 import java.awt.event.ActionListener;
39 import java.util.Hashtable;
40 import java.util.Vector;
42 import javax.swing.JMenu;
43 import javax.swing.JMenuItem;
44 import javax.swing.event.MenuEvent;
45 import javax.swing.event.MenuListener;
51 public class RestClient extends WSClient
52 implements WSClientI, WSMenuEntryProviderI
54 RestServiceDescription service;
56 public RestClient(RestServiceDescription rsd)
62 * parent alignframe for this job
67 * alignment view which provides data for job.
72 * get the alignFrame for the associated input data if it exists.
76 protected AlignFrame recoverAlignFrameForView()
78 return jalview.gui.Desktop.getAlignFrameFor(av);
81 public RestClient(RestServiceDescription service2, AlignFrame alignFrame)
83 this(service2, alignFrame, false);
86 boolean headless = false;
88 public RestClient(RestServiceDescription service2, AlignFrame alignFrame,
93 av = alignFrame.getViewport();
98 public void setWebserviceInfo(boolean headless)
100 WebServiceJobTitle = MessageManager
101 .formatMessage("label.webservice_job_title", new String[]
102 { service.details.Action, service.details.Name });
103 WebServiceName = service.details.Name;
104 WebServiceReference = "No reference - go to url for more info";
105 if (service.details.description != null)
107 WebServiceReference = service.details.description;
111 wsInfo = new WebserviceInfo(WebServiceJobTitle,
112 WebServiceName + "\n" + WebServiceReference, true);
113 wsInfo.setRenderAsHtml(true);
119 public boolean isCancellable()
121 // TODO define process for cancelling rsbws jobs
126 public boolean canMergeResults()
128 // TODO process service definition to identify if the results might be
130 // TODO: change comparison for annotation merge
135 public void cancelJob()
138 .errPrintln("Cannot cancel this job type: " + service);
142 public void attachWSMenuEntry(final JMenu wsmenu,
143 final AlignFrame alignFrame)
145 JMenuItem submit = new JMenuItem(service.details.Name);
146 submit.setToolTipText(MessageManager
147 .formatMessage("label.rest_client_submit", new String[]
148 { service.details.Action, service.details.Name }));
149 submit.addActionListener(new ActionListener()
153 public void actionPerformed(ActionEvent e)
155 new RestClient(service, alignFrame);
160 // TODO: menu listener should enable/disable entry depending upon selection
161 // state of the alignment
162 wsmenu.addMenuListener(new MenuListener()
166 public void menuSelected(MenuEvent e)
168 // TODO Auto-generated method stub
173 public void menuDeselected(MenuEvent e)
175 // TODO Auto-generated method stub
180 public void menuCanceled(MenuEvent e)
182 // TODO Auto-generated method stub
191 * record of initial undoredo hash for the alignFrame providing data for this
194 long[] undoredo = null;
197 * Compare the original input data to the data currently presented to the
198 * user. // LOGIC: compare undo/redo - if same, merge regardless (coping with
199 * any changes in hidden columns as normal) // if different undo/redo then
200 * compare region that was submitted // if same, then merge as before, if
201 * different then prompt user to open a new window.
205 protected boolean isAlignmentModified()
207 if (undoredo == null || av == null || av.getAlignment() == null)
209 // always return modified if we don't have access to live GUI elements
213 if (av.isUndoRedoHashModified(undoredo))
215 // alignment has been modified in some way.
218 // TODO: look deeper into modification of selection state, etc that may
219 // affect RestJobThread.realiseResults(boolean merge);
225 * TODO: combine to form a dataset+alignment+annotation context
227 AlignmentView _input;
232 jalview.io.packed.JalviewDataset jds;
235 * informative name for results
237 public String viewTitle;
239 protected void constructJob()
241 service.setInvolvesFlags();
242 // record all aspects of alignment view so we can merge back or recreate
244 undoredo = av.getUndoRedoHash();
246 * delete ? Vector sgs = av.getAlignment().getGroups(); if (sgs!=null) {
247 * _sgs = new SequenceGroup[sgs.size()]; sgs.copyInto(_sgs); } else { _sgs =
248 * new SequenceGroup[0]; }
250 boolean selExists = (av.getSelectionGroup() != null)
251 && (av.getSelectionGroup().getSize() > 1);
252 // TODO: JAL-715: refactor to alignViewport methods and revise to full
253 // focus+context+dataset input data staging model
256 if (service.partitiondata)
258 if (av.getAlignment().getGroups() != null
259 && av.getAlignment().getGroups().size() > 0)
261 // intersect groups with selected region
262 _input = new AlignmentView(av.getAlignment(),
263 av.getAlignment().getHiddenColumns(),
264 av.getSelectionGroup(), av.hasHiddenColumns(), true,
266 viewTitle = MessageManager.formatMessage(
267 "label.select_visible_region_of", new String[]
268 { (av.hasHiddenColumns()
269 ? MessageManager.getString("label.visible")
275 // use selected region to partition alignment
276 _input = new AlignmentView(av.getAlignment(),
277 av.getAlignment().getHiddenColumns(),
278 av.getSelectionGroup(), av.hasHiddenColumns(), false,
281 viewTitle = MessageManager.formatMessage(
282 "label.select_unselect_visible_regions_from", new String[]
283 { (av.hasHiddenColumns()
284 ? MessageManager.getString("label.visible")
290 // just take selected region intersection
291 _input = new AlignmentView(av.getAlignment(),
292 av.getAlignment().getHiddenColumns(),
293 av.getSelectionGroup(), av.hasHiddenColumns(), true, true);
294 viewTitle = MessageManager.formatMessage(
295 "label.select_visible_region_of", new String[]
296 { (av.hasHiddenColumns()
297 ? MessageManager.getString("label.visible")
304 // standard alignment view without selection present
305 _input = new AlignmentView(av.getAlignment(),
306 av.getAlignment().getHiddenColumns(), null,
307 av.hasHiddenColumns(), false, true);
309 + (av.hasHiddenColumns()
310 ? (new StringBuffer(" ")
311 .append(MessageManager
312 .getString("label.visible_region_of"))
318 RestJobThread jobsthread = new RestJobThread(this);
320 if (jobsthread.isValid())
322 setWebserviceInfo(headless);
325 wsInfo.setthisService(this);
326 jobsthread.setWebServiceInfo(wsInfo);
332 // TODO: try to tell the user why the job couldn't be started.
333 JvOptionPane.showMessageDialog(Desktop.desktop,
334 (jobsthread.hasWarnings() ? jobsthread.getWarnings()
335 : MessageManager.getString(
336 "label.job_couldnt_be_started_check_input")),
338 .getString("label.unable_start_web_service_analysis"),
339 JvOptionPane.WARNING_MESSAGE);
343 public static RestClient makeShmmrRestClient()
345 String action = "Analysis",
346 description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)",
347 name = MessageManager.getString("label.multiharmony");
348 Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
349 jalview.ws.rest.params.JobConstant toolp;
350 // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
351 // iparams.put(toolp.token, toolp);
352 // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
353 // iparams.put(toolp.token, toolp);
355 // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
356 // iparams.put(toolp.token, toolp);
357 // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
358 // iparams.put(toolp.token, toolp);
359 // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
360 // iparams.put(toolp.token, toolp);
362 jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
363 // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
364 // so we always upload our files.
365 aliinput.token = "ali_file";
366 aliinput.writeAsFile = true;
367 iparams.put(aliinput.token, aliinput);
368 jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
369 sgroups.setMinsize(2);
370 sgroups.min = 2;// need at least two group defined to make a partition
371 iparams.put("groups", sgroups);
372 sgroups.token = "groups";
374 RestServiceDescription shmrService = new RestServiceDescription(action,
376 "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview", // ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
377 "?tool=jalview", iparams, true, false, '-');
378 // a priori knowledge of the data returned from the service
379 shmrService.addResultDatatype(JvDataType.ANNOTATION);
380 return new RestClient(shmrService);
383 public AlignmentPanel recoverAlignPanelForView()
385 AlignmentPanel[] aps = Desktop
386 .getAlignmentPanels(av.getSequenceSetId());
387 for (AlignmentPanel alp : aps)
397 public boolean isShowResultsInNewView()
399 // TODO make this a property of the service
403 protected static Vector<String> services = null;
405 public static final String RSBS_SERVICES = "RSBS_SERVICES";
407 public static RestClient[] getRestClients()
409 if (services == null)
411 services = new Vector<String>();
414 for (RestServiceDescription descr : RestServiceDescription
415 .parseDescriptions(Cache.getDefault(RSBS_SERVICES,
416 makeShmmrRestClient().service.toString())))
418 services.add(descr.toString());
420 } catch (Exception ex)
422 jalview.bin.Console.errPrintln(
423 "Serious - RSBS descriptions in user preferences are corrupt!");
424 ex.printStackTrace();
428 RestClient[] lst = new RestClient[services.size()];
430 for (String svc : services)
432 lst[i++] = new RestClient(new RestServiceDescription(svc));
437 public String getAction()
439 return service.details.Action;
442 public RestServiceDescription getRestDescription()
447 public static Vector<String> getRsbsDescriptions()
449 Vector<String> rsbsDescrs = new Vector<String>();
450 for (RestClient rsbs : getRestClients())
452 rsbsDescrs.add(rsbs.getRestDescription().toString());
457 public static void setRsbsServices(Vector<String> rsbsUrls)
459 if (rsbsUrls != null)
461 // TODO: consider validating services ?
462 services = new Vector<String>(rsbsUrls);
463 StringBuffer sprop = new StringBuffer();
464 for (String s : services)
468 Cache.setProperty(RSBS_SERVICES, sprop.toString());
472 Cache.removeProperty(RSBS_SERVICES);