2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.ws.rest;
21 import java.awt.event.ActionEvent;
22 import java.awt.event.ActionListener;
23 import java.util.Hashtable;
24 import java.util.Vector;
26 import javax.swing.JMenu;
27 import javax.swing.JMenuItem;
28 import javax.swing.JOptionPane;
29 import javax.swing.event.MenuEvent;
30 import javax.swing.event.MenuListener;
32 import jalview.bin.Cache;
33 import jalview.datamodel.AlignmentView;
34 import jalview.gui.AlignFrame;
35 import jalview.gui.AlignViewport;
36 import jalview.gui.AlignmentPanel;
37 import jalview.gui.Desktop;
38 import jalview.gui.WebserviceInfo;
39 import jalview.io.packed.DataProvider.JvDataType;
40 import jalview.ws.WSClient;
41 import jalview.ws.WSClientI;
42 import jalview.ws.WSMenuEntryProviderI;
48 public class RestClient extends WSClient implements WSClientI,
51 RestServiceDescription service;
53 public RestClient(RestServiceDescription rsd)
59 * parent alignframe for this job
64 * alignment view which provides data for job.
69 * get the alignFrame for the associated input data if it exists.
73 protected AlignFrame recoverAlignFrameForView()
75 return jalview.gui.Desktop.getAlignFrameFor(av);
78 public RestClient(RestServiceDescription service2, AlignFrame alignFrame)
80 this(service2, alignFrame, false);
82 boolean headless = false;
83 public RestClient(RestServiceDescription service2, AlignFrame alignFrame, boolean nogui)
87 av = alignFrame.getViewport();
92 public void setWebserviceInfo(boolean headless)
94 WebServiceJobTitle = service.details.Action + " using "
95 + service.details.Name;
96 WebServiceName = service.details.Name;
97 WebServiceReference = "No reference - go to url for more info";
98 if (service.details.description != null)
100 WebServiceReference = service.details.description;
104 wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
105 + WebServiceReference);
106 wsInfo.setRenderAsHtml(true);
112 public boolean isCancellable()
114 // TODO define process for cancelling rsbws jobs
119 public boolean canMergeResults()
121 // TODO process service definition to identify if the results might be
123 // TODO: change comparison for annotation merge
128 public void cancelJob()
130 System.err.println("Cannot cancel this job type: " + service);
134 public void attachWSMenuEntry(final JMenu wsmenu,
135 final AlignFrame alignFrame)
137 JMenuItem submit = new JMenuItem(service.details.Name);
138 submit.setToolTipText(service.details.Action + " using "
139 + service.details.Name);
140 submit.addActionListener(new ActionListener()
144 public void actionPerformed(ActionEvent e)
146 new RestClient(service, alignFrame);
151 // TODO: menu listener should enable/disable entry depending upon selection
152 // state of the alignment
153 wsmenu.addMenuListener(new MenuListener()
157 public void menuSelected(MenuEvent e)
159 // TODO Auto-generated method stub
164 public void menuDeselected(MenuEvent e)
166 // TODO Auto-generated method stub
171 public void menuCanceled(MenuEvent e)
173 // TODO Auto-generated method stub
182 * record of initial undoredo hash for the alignFrame providing data for this
185 long[] undoredo = null;
188 * Compare the original input data to the data currently presented to the
189 * user. // LOGIC: compare undo/redo - if same, merge regardless (coping with
190 * any changes in hidden columns as normal) // if different undo/redo then
191 * compare region that was submitted // if same, then merge as before, if
192 * different then prompt user to open a new window.
196 protected boolean isAlignmentModified()
198 if (undoredo == null || av == null || av.getAlignment() == null)
200 // always return modified if we don't have access to live GUI elements
204 if (av.isUndoRedoHashModified(undoredo))
206 // alignment has been modified in some way.
209 // TODO: look deeper into modification of selection state, etc that may
210 // affect RestJobThread.realiseResults(boolean merge);
216 * TODO: combine to form a dataset+alignment+annotation context
218 AlignmentView _input;
223 jalview.io.packed.JalviewDataset jds;
226 * informative name for results
228 public String viewTitle;
229 protected void constructJob()
231 service.setInvolvesFlags();
232 // record all aspects of alignment view so we can merge back or recreate
234 undoredo = av.getUndoRedoHash();
236 * delete ? Vector sgs = av.getAlignment().getGroups(); if (sgs!=null) {
237 * _sgs = new SequenceGroup[sgs.size()]; sgs.copyInto(_sgs); } else { _sgs =
238 * new SequenceGroup[0]; }
240 boolean selExists = (av.getSelectionGroup() != null)
241 && (av.getSelectionGroup().getSize() > 1);
242 // TODO: JAL-715: refactor to alignViewport methods and revise to full
243 // focus+context+dataset input data staging model
246 if (service.partitiondata)
248 if (av.getAlignment().getGroups() != null
249 && av.getAlignment().getGroups().size() > 0)
251 // intersect groups with selected region
252 _input = new AlignmentView(av.getAlignment(),
253 av.getColumnSelection(), av.getSelectionGroup(),
254 av.hasHiddenColumns(), true, true);
255 viewTitle = "selected "
256 + (av.hasHiddenColumns() ? "visible" : "")
257 + " region of " + af.getTitle();
261 // use selected region to partition alignment
262 _input = new AlignmentView(av.getAlignment(),
263 av.getColumnSelection(), av.getSelectionGroup(),
264 av.hasHiddenColumns(), false, true);
266 viewTitle = "select and unselected "
267 + (av.hasHiddenColumns() ? "visible" : "")
268 + " regions from " + af.getTitle();
272 // just take selected region intersection
273 _input = new AlignmentView(av.getAlignment(),
274 av.getColumnSelection(), av.getSelectionGroup(),
275 av.hasHiddenColumns(), true, true);
276 viewTitle = "selected " + (av.hasHiddenColumns() ? "visible" : "")
277 + " region of " + af.getTitle();
282 // standard alignment view without selection present
283 _input = new AlignmentView(av.getAlignment(),
284 av.getColumnSelection(), null, av.hasHiddenColumns(), false,
286 viewTitle = "" + (av.hasHiddenColumns() ? "visible region of " : "")
290 RestJobThread jobsthread = new RestJobThread(this);
292 if (jobsthread.isValid())
294 setWebserviceInfo(headless);
296 wsInfo.setthisService(this);
297 jobsthread.setWebServiceInfo(wsInfo);
303 // TODO: try to tell the user why the job couldn't be started.
307 (jobsthread.hasWarnings() ? jobsthread.getWarnings()
308 : "The Job couldn't be started. Please check your input, and the Jalview console for any warning messages."),
309 "Unable to start web service analysis",
310 JOptionPane.WARNING_MESSAGE);
314 public static RestClient makeShmmrRestClient()
316 String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = "Multi-Harmony";
317 Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
318 jalview.ws.rest.params.JobConstant toolp;
319 // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
320 // iparams.put(toolp.token, toolp);
321 // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
322 // iparams.put(toolp.token, toolp);
324 // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
325 // iparams.put(toolp.token, toolp);
326 // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
327 // iparams.put(toolp.token, toolp);
328 // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
329 // iparams.put(toolp.token, toolp);
331 jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
332 // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
333 // so we always upload our files.
334 aliinput.token = "ali_file";
335 aliinput.writeAsFile = true;
336 iparams.put(aliinput.token, aliinput);
337 jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
338 sgroups.setMinsize(2);
339 sgroups.min = 2;// need at least two group defined to make a partition
340 iparams.put("groups", sgroups);
341 sgroups.token = "groups";
343 RestServiceDescription shmrService = new RestServiceDescription(
347 "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
348 "?tool=jalview", iparams, true, false, '-');
349 // a priori knowledge of the data returned from the service
350 shmrService.addResultDatatype(JvDataType.ANNOTATION);
351 return new RestClient(shmrService);
354 public AlignmentPanel recoverAlignPanelForView()
356 AlignmentPanel[] aps = Desktop
357 .getAlignmentPanels(av.getSequenceSetId());
358 for (AlignmentPanel alp : aps)
368 public boolean isShowResultsInNewView()
370 // TODO make this a property of the service
374 protected static Vector<String> services = null;
376 public static final String RSBS_SERVICES = "RSBS_SERVICES";
378 public static RestClient[] getRestClients()
380 if (services == null)
382 services = new Vector<String>();
385 for (RestServiceDescription descr : RestServiceDescription
386 .parseDescriptions(jalview.bin.Cache.getDefault(
388 makeShmmrRestClient().service.toString())))
390 services.add(descr.toString());
392 } catch (Exception ex)
395 .println("Serious - RSBS descriptions in user preferences are corrupt!");
396 ex.printStackTrace();
400 RestClient[] lst = new RestClient[services.size()];
402 for (String svc : services)
404 lst[i++] = new RestClient(new RestServiceDescription(svc));
409 public static void main(String args[])
413 RestClient[] clients = getRestClients();
414 System.out.println("Got " + clients.length + " clients.");
416 Vector<String> urls = new Vector<String>();
417 for (RestClient cl : clients)
419 System.out.println("" + (++i) + ": " + cl.service.toString());
420 urls.add(cl.service.toString());
422 setRsbsServices(urls);
423 if (clients.length != getRestClients().length)
426 .println("Failed. Differing numbers of clients when stringified and parsed again.");
429 } catch (Throwable x)
431 System.err.println("Failed. Unexpected exception.");
436 public String getAction()
438 return service.details.Action;
441 public RestServiceDescription getRestDescription()
446 public static Vector<String> getRsbsDescriptions()
448 Vector<String> rsbsDescrs = new Vector<String>();
449 for (RestClient rsbs : getRestClients())
451 rsbsDescrs.add(rsbs.getRestDescription().toString());
456 public static void setRsbsServices(Vector<String> rsbsUrls)
458 if (rsbsUrls != null)
460 // TODO: consider validating services ?
461 services = new Vector<String>(rsbsUrls);
462 StringBuffer sprop = new StringBuffer();
463 for (String s : services)
467 Cache.setProperty(RSBS_SERVICES, sprop.toString());
471 Cache.removeProperty(RSBS_SERVICES);