Coverage Report
File Jws2Client.java
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52% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| Jws2Client | 54 | 93 | 53 |
Contributing tests
This file is covered by 110 tests.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 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. | |
| 11 | * | |
| 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. | |
| 16 | * | |
| 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. | |
| 20 | */ | |
| 21 | package jalview.ws.jws2; | |
| 22 | ||
| 23 | import java.awt.event.ActionEvent; | |
| 24 | import java.awt.event.ActionListener; | |
| 25 | import java.util.List; | |
| 26 | ||
| 27 | import javax.swing.JCheckBoxMenuItem; | |
| 28 | import javax.swing.JMenu; | |
| 29 | import javax.swing.JMenuItem; | |
| 30 | import javax.swing.event.MenuEvent; | |
| 31 | import javax.swing.event.MenuListener; | |
| 32 | ||
| 33 | import compbio.metadata.Argument; | |
| 34 | import jalview.api.AlignCalcWorkerI; | |
| 35 | import jalview.bin.Console; | |
| 36 | import jalview.gui.AlignFrame; | |
| 37 | import jalview.gui.Desktop; | |
| 38 | import jalview.gui.JvSwingUtils; | |
| 39 | import jalview.gui.WebserviceInfo; | |
| 40 | import jalview.gui.WsJobParameters; | |
| 41 | import jalview.util.MessageManager; | |
| 42 | import jalview.ws.jws2.dm.AAConSettings; | |
| 43 | import jalview.ws.jws2.dm.JabaWsParamSet; | |
| 44 | import jalview.ws.jws2.jabaws2.Jws2Instance; | |
| 45 | import jalview.ws.params.WsParamSetI; | |
| 46 | import jalview.ws.uimodel.AlignAnalysisUIText; | |
| 47 | ||
| 48 | /** | |
| 49 | * provides metadata for a jabaws2 service instance - resolves names, etc. | |
| 50 | * | |
| 51 | * @author JimP | |
| 52 | * | |
| 53 | */ | |
| 54 | public abstract class Jws2Client extends jalview.ws.WSClient | |
| 55 | { | |
| 56 | protected AlignFrame alignFrame; | |
| 57 | ||
| 58 | protected WsParamSetI preset; | |
| 59 | ||
| 60 | protected List<Argument> paramset; | |
| 61 | ||
| 62 | 0 |  public Jws2Client(AlignFrame _alignFrame, WsParamSetI preset, |
| 63 | List<Argument> arguments) | |
| 64 | { | |
| 65 | 0 | alignFrame = _alignFrame; |
| 66 | 0 | this.preset = preset; |
| 67 | 0 | if (preset != null) |
| 68 | { | |
| 69 | 0 | if (!((preset instanceof JabaPreset) |
| 70 | || preset instanceof JabaWsParamSet)) | |
| 71 | { | |
| 72 | /* | |
| 73 | * { this.preset = ((JabaPreset) preset).p; } else if (preset instanceof | |
| 74 | * JabaWsParamSet) { List<Argument> newargs = new ArrayList<Argument>(); | |
| 75 | * JabaWsParamSet pset = ((JabaWsParamSet) preset); for (Option opt : | |
| 76 | * pset.getjabaArguments()) { newargs.add(opt); } if (arguments != null | |
| 77 | * && arguments.size() > 0) { // merge arguments with preset's own | |
| 78 | * arguments. for (Argument opt : arguments) { newargs.add(opt); } } | |
| 79 | * paramset = newargs; } else { | |
| 80 | */ | |
| 81 | 0 | throw new Error(MessageManager.getString( |
| 82 | "error.implementation_error_can_only_instantiate_jaba_param_sets")); | |
| 83 | } | |
| 84 | } | |
| 85 | else | |
| 86 | { | |
| 87 | // just provided with a bunch of arguments | |
| 88 | 0 | this.paramset = arguments; |
| 89 | } | |
| 90 | } | |
| 91 | ||
| 92 | 0 | boolean processParams(Jws2Instance sh, boolean editParams) |
| 93 | { | |
| 94 | 0 | return processParams(sh, editParams, false); |
| 95 | } | |
| 96 | ||
| 97 | 0 | protected boolean processParams(Jws2Instance sh, boolean editParams, |
| 98 | boolean adjustingExisting) | |
| 99 | { | |
| 100 | ||
| 101 | 0 | if (editParams) |
| 102 | { | |
| 103 | 0 | if (sh.paramStore == null) |
| 104 | { | |
| 105 | 0 | sh.paramStore = new JabaParamStore(sh, |
| 106 | Desktop.getUserParameterStore()); | |
| 107 | } | |
| 108 | 0 | WsJobParameters jobParams = (preset == null && paramset != null |
| 109 | && paramset.size() > 0) | |
| 110 | ? new WsJobParameters(null, sh, null, paramset) | |
| 111 | : new WsJobParameters(sh, preset); | |
| 112 | 0 | if (adjustingExisting) |
| 113 | { | |
| 114 | 0 | jobParams.setName(MessageManager |
| 115 | .getString("label.adjusting_parameters_for_calculation")); | |
| 116 | } | |
| 117 | 0 | if (!jobParams.showRunDialog()) |
| 118 | { | |
| 119 | 0 | return false; |
| 120 | } | |
| 121 | 0 | WsParamSetI prset = jobParams.getPreset(); |
| 122 | 0 | if (prset == null) |
| 123 | { | |
| 124 | 0 | paramset = |
| 125 | /* JAL-3739 always take values from input form */ | |
| 126 | /* jobParams.isServiceDefaults() ? null : */ | |
| 127 | JabaParamStore.getJabafromJwsArgs(jobParams.getJobParams()); | |
| 128 | 0 | this.preset = null; |
| 129 | } | |
| 130 | else | |
| 131 | { | |
| 132 | 0 | this.preset = prset; // ((JabaPreset) prset).p; |
| 133 | 0 | paramset = null; // no user supplied parameters. |
| 134 | } | |
| 135 | } | |
| 136 | 0 | return true; |
| 137 | ||
| 138 | } | |
| 139 | ||
| 140 | 3031 | public Jws2Client() |
| 141 | { | |
| 142 | // anonymous constructor - used for headless method calls only | |
| 143 | } | |
| 144 | ||
| 145 | 2922 | protected WebserviceInfo setWebService(Jws2Instance serv, boolean b) |
| 146 | { | |
| 147 | // serviceHandle = serv; | |
| 148 | 2922 | String serviceInstance = serv.action; // serv.service.getClass().getName(); |
| 149 | 2922 | WebServiceName = serv.serviceType; |
| 150 | 2922 | WebServiceJobTitle = serv.getActionText(); |
| 151 | 2922 | WsURL = serv.hosturl; |
| 152 | 2922 | if (!b) |
| 153 | { | |
| 154 | 0 | return new WebserviceInfo(WebServiceJobTitle, |
| 155 | WebServiceJobTitle + " using service hosted at " | |
| 156 | + serv.hosturl + "\n" | |
| 157 | 0 | + (serv.description != null ? serv.description : ""), |
| 158 | false); | |
| 159 | } | |
| 160 | 2922 | return null; |
| 161 | } | |
| 162 | ||
| 163 | /* | |
| 164 | * Jws2Instance serviceHandle; (non-Javadoc) | |
| 165 | * | |
| 166 | * @see jalview.ws.WSMenuEntryProviderI#attachWSMenuEntry(javax.swing.JMenu, | |
| 167 | * jalview.gui.AlignFrame) | |
| 168 | * | |
| 169 | * @Override public void attachWSMenuEntry(JMenu wsmenu, AlignFrame | |
| 170 | * alignFrame) { if (serviceHandle==null) { throw new | |
| 171 | * Error("Implementation error: No service handle for this Jws2 service."); } | |
| 172 | * attachWSMenuEntry(wsmenu, serviceHandle, alignFrame); } | |
| 173 | */ | |
| 174 | /** | |
| 175 | * add the menu item for a particular jws2 service instance | |
| 176 | * | |
| 177 | * @param wsmenu | |
| 178 | * @param service | |
| 179 | * @param alignFrame | |
| 180 | */ | |
| 181 | abstract void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service, | |
| 182 | final AlignFrame alignFrame); | |
| 183 | ||
| 184 | 3031 | protected boolean registerAAConWSInstance(final JMenu wsmenu, |
| 185 | final Jws2Instance service, final AlignFrame alignFrame) | |
| 186 | { | |
| 187 | 3031 | final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; // |
| 188 | // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString()); | |
| 189 | 3031 | if (aaui == null) |
| 190 | { | |
| 191 | // not an instantaneous calculation GUI type service | |
| 192 | 2994 | return false; |
| 193 | } | |
| 194 | // create the instaneous calculation GUI bits and update state if existing | |
| 195 | // GUI elements already present | |
| 196 | ||
| 197 | 37 | JCheckBoxMenuItem _aaConEnabled = null; |
| 198 | 112 | for (int i = 0; i < wsmenu.getItemCount(); i++) |
| 199 | { | |
| 200 | 75 | JMenuItem item = wsmenu.getItem(i); |
| 201 | 75 | if (item instanceof JCheckBoxMenuItem |
| 202 | && item.getText().equals(aaui.getAAconToggle())) | |
| 203 | { | |
| 204 | 0 | _aaConEnabled = (JCheckBoxMenuItem) item; |
| 205 | } | |
| 206 | } | |
| 207 | // is there an aaCon worker already present - if so, set it to use the | |
| 208 | // given service handle | |
| 209 | { | |
| 210 | 37 | List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport() |
| 211 | .getCalcManager() | |
| 212 | .getRegisteredWorkersOfClass(aaui.getClient()); | |
| 213 | 35 | if (aaconClient != null && aaconClient.size() > 0) |
| 214 | { | |
| 215 | 0 | AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) aaconClient |
| 216 | .get(0); | |
| 217 | 0 | if (!worker.service.hosturl.equals(service.hosturl)) |
| 218 | { | |
| 219 | // javax.swing.SwingUtilities.invokeLater(new Runnable() | |
| 220 | { | |
| 221 | // @Override | |
| 222 | // public void run() | |
| 223 | { | |
| 224 | 0 | removeCurrentAAConWorkerFor(aaui, alignFrame); |
| 225 | 0 | buildCurrentAAConWorkerFor(aaui, alignFrame, service); |
| 226 | } | |
| 227 | } // ); | |
| 228 | } | |
| 229 | } | |
| 230 | } | |
| 231 | ||
| 232 | // is there a service already registered ? there shouldn't be if we are | |
| 233 | // being called correctly | |
| 234 | 35 | if (_aaConEnabled == null) |
| 235 | { | |
| 236 | 35 | final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem( |
| 237 | aaui.getAAconToggle()); | |
| 238 | ||
| 239 | 35 | aaConEnabled.setToolTipText( |
| 240 | JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip())); | |
| 241 | 35 | aaConEnabled.addActionListener(new ActionListener() |
| 242 | { | |
| 243 | 0 | @Override |
| 244 | public void actionPerformed(ActionEvent arg0) | |
| 245 | { | |
| 246 | 0 | List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport() |
| 247 | .getCalcManager() | |
| 248 | .getRegisteredWorkersOfClass(aaui.getClient()); | |
| 249 | 0 | if (aaconClient != null && aaconClient.size() > 0) |
| 250 | { | |
| 251 | 0 | removeCurrentAAConWorkerFor(aaui, alignFrame); |
| 252 | } | |
| 253 | else | |
| 254 | { | |
| 255 | 0 | buildCurrentAAConWorkerFor(aaui, alignFrame); |
| 256 | ||
| 257 | } | |
| 258 | } | |
| 259 | ||
| 260 | }); | |
| 261 | 35 | wsmenu.add(aaConEnabled); |
| 262 | 35 | final JMenuItem modifyParams = new JMenuItem( |
| 263 | aaui.getAAeditSettings()); | |
| 264 | 35 | modifyParams.setToolTipText(JvSwingUtils.wrapTooltip(true, |
| 265 | aaui.getAAeditSettingsTooltip())); | |
| 266 | 35 | modifyParams.addActionListener(new ActionListener() |
| 267 | { | |
| 268 | ||
| 269 | 0 | @Override |
| 270 | public void actionPerformed(ActionEvent arg0) | |
| 271 | { | |
| 272 | 0 | showAAConAnnotationSettingsFor(aaui, alignFrame); |
| 273 | } | |
| 274 | }); | |
| 275 | 35 | wsmenu.add(modifyParams); |
| 276 | 35 | wsmenu.addMenuListener(new MenuListener() |
| 277 | { | |
| 278 | ||
| 279 | 0 | @Override |
| 280 | public void menuSelected(MenuEvent arg0) | |
| 281 | { | |
| 282 | // TODO: refactor to the implementing class. | |
| 283 | 0 | if (alignFrame.getViewport().getAlignment().isNucleotide() |
| 284 | ? aaui.isNa() | |
| 285 | : aaui.isPr()) | |
| 286 | { | |
| 287 | 0 | aaConEnabled.setEnabled(true); |
| 288 | 0 | modifyParams.setEnabled(true); |
| 289 | } | |
| 290 | else | |
| 291 | { | |
| 292 | 0 | aaConEnabled.setEnabled(false); |
| 293 | 0 | modifyParams.setEnabled(false); |
| 294 | } | |
| 295 | 0 | List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport() |
| 296 | .getCalcManager() | |
| 297 | .getRegisteredWorkersOfClass(aaui.getClient()); | |
| 298 | 0 | if (aaconClient != null && aaconClient.size() > 0) |
| 299 | { | |
| 300 | 0 | aaConEnabled.setSelected(true); |
| 301 | } | |
| 302 | else | |
| 303 | { | |
| 304 | 0 | aaConEnabled.setSelected(false); |
| 305 | } | |
| 306 | } | |
| 307 | ||
| 308 | 0 | @Override |
| 309 | public void menuDeselected(MenuEvent arg0) | |
| 310 | { | |
| 311 | // TODO Auto-generated method stub | |
| 312 | ||
| 313 | } | |
| 314 | ||
| 315 | 0 | @Override |
| 316 | public void menuCanceled(MenuEvent arg0) | |
| 317 | { | |
| 318 | // TODO Auto-generated method stub | |
| 319 | ||
| 320 | } | |
| 321 | }); | |
| 322 | ||
| 323 | } | |
| 324 | 35 | return true; |
| 325 | } | |
| 326 | ||
| 327 | 0 | private static void showAAConAnnotationSettingsFor( |
| 328 | final AlignAnalysisUIText aaui, AlignFrame alignFrame) | |
| 329 | { | |
| 330 | /* | |
| 331 | * preferred settings Whether AACon is automatically recalculated Which | |
| 332 | * AACon server to use What parameters to use | |
| 333 | */ | |
| 334 | // could actually do a class search for this too | |
| 335 | 0 | AAConSettings fave = (AAConSettings) alignFrame.getViewport() |
| 336 | .getCalcIdSettingsFor(aaui.getCalcId()); | |
| 337 | 0 | if (fave == null) |
| 338 | { | |
| 339 | 0 | fave = createDefaultAAConSettings(aaui); |
| 340 | } | |
| 341 | 0 | new SequenceAnnotationWSClient(fave, alignFrame, true); |
| 342 | ||
| 343 | } | |
| 344 | ||
| 345 | 0 | private static void buildCurrentAAConWorkerFor( |
| 346 | final AlignAnalysisUIText aaui, AlignFrame alignFrame) | |
| 347 | { | |
| 348 | 0 | buildCurrentAAConWorkerFor(aaui, alignFrame, null); |
| 349 | } | |
| 350 | ||
| 351 | 0 | private static void buildCurrentAAConWorkerFor( |
| 352 | final AlignAnalysisUIText aaui, AlignFrame alignFrame, | |
| 353 | Jws2Instance service) | |
| 354 | { | |
| 355 | /* | |
| 356 | * preferred settings Whether AACon is automatically recalculated Which | |
| 357 | * AACon server to use What parameters to use | |
| 358 | */ | |
| 359 | 0 | AAConSettings fave = (AAConSettings) alignFrame.getViewport() |
| 360 | .getCalcIdSettingsFor(aaui.getCalcId()); | |
| 361 | 0 | if (fave == null) |
| 362 | { | |
| 363 | 0 | fave = createDefaultAAConSettings(aaui, service); |
| 364 | } | |
| 365 | else | |
| 366 | { | |
| 367 | 0 | if (service != null |
| 368 | && !fave.getService().hosturl.equals(service.hosturl)) | |
| 369 | { | |
| 370 | 0 | Console.debug("Changing AACon service to " + service.hosturl |
| 371 | + " from " + fave.getService().hosturl); | |
| 372 | 0 | fave.setService(service); |
| 373 | } | |
| 374 | } | |
| 375 | 0 | new SequenceAnnotationWSClient(fave, alignFrame, false); |
| 376 | } | |
| 377 | ||
| 378 | 0 | private static AAConSettings createDefaultAAConSettings( |
| 379 | AlignAnalysisUIText aaui) | |
| 380 | { | |
| 381 | 0 | return createDefaultAAConSettings(aaui, null); |
| 382 | } | |
| 383 | ||
| 384 | 0 | private static AAConSettings createDefaultAAConSettings( |
| 385 | AlignAnalysisUIText aaui, Jws2Instance service) | |
| 386 | { | |
| 387 | 0 | if (service != null) |
| 388 | { | |
| 389 | 0 | if (!service.serviceType.toString() |
| 390 | .equals(compbio.ws.client.Services.AAConWS.toString())) | |
| 391 | { | |
| 392 | 0 | Console.warn( |
| 393 | "Ignoring invalid preferred service for AACon calculations (service type was " | |
| 394 | + service.serviceType + ")"); | |
| 395 | 0 | service = null; |
| 396 | } | |
| 397 | else | |
| 398 | { | |
| 399 | // check service is actually in the list of currently avaialable | |
| 400 | // services | |
| 401 | 0 | if (!Jws2Discoverer.getDiscoverer().getServices().contains(service)) |
| 402 | { | |
| 403 | // it isn't .. | |
| 404 | 0 | service = null; |
| 405 | } | |
| 406 | } | |
| 407 | } | |
| 408 | 0 | if (service == null) |
| 409 | { | |
| 410 | // get the default service for AACon | |
| 411 | 0 | service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null, |
| 412 | aaui.getServiceType()); | |
| 413 | } | |
| 414 | 0 | if (service == null) |
| 415 | { | |
| 416 | // TODO raise dialog box explaining error, and/or open the JABA | |
| 417 | // preferences menu. | |
| 418 | 0 | throw new Error( |
| 419 | MessageManager.getString("error.no_aacon_service_found")); | |
| 420 | } | |
| 421 | 0 | return new AAConSettings(true, service, null, null); |
| 422 | } | |
| 423 | ||
| 424 | 0 | private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui, |
| 425 | AlignFrame alignFrame) | |
| 426 | { | |
| 427 | 0 | alignFrame.getViewport().getCalcManager() |
| 428 | .removeRegisteredWorkersOfClass(aaui.getClient()); | |
| 429 | } | |
| 430 | ||
| 431 | } |