Coverage Report
File RestJob.java
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43% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| RestJob | 41 | 88 | 53 |
Contributing tests
This file is covered by 3 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.rest; | |
| 22 | ||
| 23 | import jalview.analysis.SeqsetUtils.SequenceInfo; | |
| 24 | import jalview.datamodel.AlignmentAnnotation; | |
| 25 | import jalview.datamodel.AlignmentI; | |
| 26 | import jalview.datamodel.AlignmentOrder; | |
| 27 | import jalview.datamodel.SequenceGroup; | |
| 28 | import jalview.datamodel.SequenceI; | |
| 29 | import jalview.io.packed.JalviewDataset; | |
| 30 | import jalview.ws.AWsJob; | |
| 31 | import jalview.ws.rest.params.Alignment; | |
| 32 | import jalview.ws.rest.params.SeqGroupIndexVector; | |
| 33 | ||
| 34 | import java.util.ArrayList; | |
| 35 | import java.util.Collection; | |
| 36 | import java.util.Hashtable; | |
| 37 | import java.util.Map; | |
| 38 | import java.util.Set; | |
| 39 | import java.util.Vector; | |
| 40 | ||
| 41 | public class RestJob extends AWsJob | |
| 42 | { | |
| 43 | ||
| 44 | // TODO: input alignmentview and other data for this job | |
| 45 | RestServiceDescription rsd; | |
| 46 | ||
| 47 | // boolean submitted; | |
| 48 | boolean gotresponse; | |
| 49 | ||
| 50 | boolean error; | |
| 51 | ||
| 52 | boolean waiting; | |
| 53 | ||
| 54 | boolean gotresult; | |
| 55 | ||
| 56 | Map<String, SequenceInfo> squniq; | |
| 57 | ||
| 58 | /** | |
| 59 | * dataset associated with this input data. | |
| 60 | */ | |
| 61 | AlignmentI dsForIO; | |
| 62 | ||
| 63 | AlignmentOrder inputOrder; | |
| 64 | ||
| 65 | /** | |
| 66 | * context of input data with respect to an AlignmentView's visible contigs. | |
| 67 | */ | |
| 68 | int[] origviscontig; | |
| 69 | ||
| 70 | private AlignmentI contextAl = null; | |
| 71 | ||
| 72 | /** | |
| 73 | * create a rest job using data bounded by the given start/end column. | |
| 74 | * | |
| 75 | * @param addJobPane | |
| 76 | * @param restJobThread | |
| 77 | * @param _input | |
| 78 | * @param viscontigs | |
| 79 | * visible contigs of an alignment view from which _input was derived | |
| 80 | */ | |
| 81 | 3 |  public RestJob(int jobNum, RestJobThread restJobThread, AlignmentI _input, |
| 82 | int[] viscontigs) | |
| 83 | { | |
| 84 | 3 | rsd = restJobThread.restClient.service; |
| 85 | 3 | jobnum = jobNum; |
| 86 | 3 | if (viscontigs != null) |
| 87 | { | |
| 88 | 2 | origviscontig = new int[viscontigs.length]; |
| 89 | 2 | System.arraycopy(viscontigs, 0, origviscontig, 0, viscontigs.length); |
| 90 | } | |
| 91 | // get sequences for the alignmentI | |
| 92 | // get groups trimmed to alignment columns | |
| 93 | // get any annotation trimmed to start/end columns, too. | |
| 94 | 3 | squniq = jalview.analysis.SeqsetUtils |
| 95 | .uniquify(_input.getSequencesArray(), true); | |
| 96 | // prepare input | |
| 97 | // form alignment+groups+annotation,preprocess and then record references | |
| 98 | // for formatters | |
| 99 | 3 | ArrayList<InputType> alinp = new ArrayList<InputType>(); |
| 100 | 3 | int paramsWithData = 0; |
| 101 | // TODO: JAL-715 - generalise the following validation logic for all | |
| 102 | // parameter types | |
| 103 | // we cheat for moment - since we know a-priori what data is available and | |
| 104 | // what inputs we have implemented so far | |
| 105 | 3 | for (Map.Entry<String, InputType> prm : rsd.inputParams.entrySet()) |
| 106 | { | |
| 107 | 6 | if (!prm.getValue().isConstant()) |
| 108 | { | |
| 109 | 6 | if (prm.getValue() instanceof Alignment) |
| 110 | { | |
| 111 | 3 | alinp.add(prm.getValue()); |
| 112 | } | |
| 113 | else | |
| 114 | { | |
| 115 | 3 | if (prm.getValue() instanceof SeqGroupIndexVector |
| 116 | && _input.getGroups() != null | |
| 117 | && _input.getGroups().size() >= -1 + prm.getValue().min) | |
| 118 | { | |
| 119 | // the test above is not rigorous but fixes JAL-1298, since | |
| 120 | // submission will fail if the partition set doesn't contain at | |
| 121 | // least one partition | |
| 122 | 3 | alinp.add(prm.getValue()); |
| 123 | } | |
| 124 | else | |
| 125 | { | |
| 126 | 0 | statMessage = ("Not enough groups defined on the alignment - need at least " |
| 127 | + prm.getValue().min); | |
| 128 | } | |
| 129 | } | |
| 130 | } | |
| 131 | else | |
| 132 | { | |
| 133 | 0 | paramsWithData++; |
| 134 | } | |
| 135 | } | |
| 136 | 3 | if ((paramsWithData + alinp.size()) == rsd.inputParams.size()) |
| 137 | { | |
| 138 | 3 | inputOrder = new AlignmentOrder(_input); |
| 139 | ? | if ((dsForIO = _input.getDataset()) == null) |
| 140 | { | |
| 141 | 2 | _input.setDataset(null); |
| 142 | } | |
| 143 | 3 | dsForIO = _input.getDataset(); |
| 144 | 3 | if (contextAl == null) |
| 145 | { | |
| 146 | 3 | contextAl = _input; |
| 147 | } | |
| 148 | 3 | setAlignmentForInputs(alinp, _input); |
| 149 | 3 | validInput = true; |
| 150 | } | |
| 151 | else | |
| 152 | { | |
| 153 | // not enough data, so we bail. | |
| 154 | 0 | validInput = false; |
| 155 | } | |
| 156 | } | |
| 157 | ||
| 158 | boolean validInput = false; | |
| 159 | ||
| 160 | 0 | @Override |
| 161 | public boolean hasResults() | |
| 162 | { | |
| 163 | 0 | return gotresult && (parsedResults ? validJvresults : true); |
| 164 | } | |
| 165 | ||
| 166 | 2 | @Override |
| 167 | public boolean hasValidInput() | |
| 168 | { | |
| 169 | 2 | return validInput; |
| 170 | } | |
| 171 | ||
| 172 | 1 | @Override |
| 173 | public boolean isRunning() | |
| 174 | { | |
| 175 | 1 | return running; // TODO: can we check the response body for status messages |
| 176 | // ? | |
| 177 | } | |
| 178 | ||
| 179 | 1 | @Override |
| 180 | public boolean isQueued() | |
| 181 | { | |
| 182 | 1 | return waiting; |
| 183 | } | |
| 184 | ||
| 185 | 1 | @Override |
| 186 | public boolean isFinished() | |
| 187 | { | |
| 188 | 1 | return resSet != null; |
| 189 | } | |
| 190 | ||
| 191 | 1 | @Override |
| 192 | public boolean isFailed() | |
| 193 | { | |
| 194 | // TODO logic for error | |
| 195 | 1 | return error; |
| 196 | } | |
| 197 | ||
| 198 | 1 | @Override |
| 199 | public boolean isBroken() | |
| 200 | { | |
| 201 | // TODO logic for error | |
| 202 | 1 | return error; |
| 203 | } | |
| 204 | ||
| 205 | 1 | @Override |
| 206 | public boolean isServerError() | |
| 207 | { | |
| 208 | // TODO logic for error | |
| 209 | 1 | return error; |
| 210 | } | |
| 211 | ||
| 212 | 1 | @Override |
| 213 | public boolean hasStatus() | |
| 214 | { | |
| 215 | 1 | return statMessage != null; |
| 216 | } | |
| 217 | ||
| 218 | protected String statMessage = null; | |
| 219 | ||
| 220 | public HttpResultSet resSet; | |
| 221 | ||
| 222 | 1 | @Override |
| 223 | public String getStatus() | |
| 224 | { | |
| 225 | 1 | return statMessage; |
| 226 | } | |
| 227 | ||
| 228 | 0 | @Override |
| 229 | public boolean hasResponse() | |
| 230 | { | |
| 231 | 0 | return statMessage != null || resSet != null; |
| 232 | } | |
| 233 | ||
| 234 | 0 | @Override |
| 235 | public void clearResponse() | |
| 236 | { | |
| 237 | // only clear the transient server response | |
| 238 | // statMessage=null; | |
| 239 | } | |
| 240 | ||
| 241 | /* | |
| 242 | * (non-Javadoc) | |
| 243 | * | |
| 244 | * @see jalview.ws.AWsJob#getState() | |
| 245 | */ | |
| 246 | 0 | @Override |
| 247 | public String getState() | |
| 248 | { | |
| 249 | // TODO generate state string - prolly should have a default abstract method | |
| 250 | // for this | |
| 251 | 0 | return "Job is clueless"; |
| 252 | } | |
| 253 | ||
| 254 | 1 | public String getPostUrl() |
| 255 | { | |
| 256 | ||
| 257 | // TODO Auto-generated method stub | |
| 258 | 1 | return rsd.postUrl; |
| 259 | } | |
| 260 | ||
| 261 | 1 | public Set<Map.Entry<String, InputType>> getInputParams() |
| 262 | { | |
| 263 | 1 | return rsd.inputParams.entrySet(); |
| 264 | } | |
| 265 | ||
| 266 | // return the URL that should be polled for this job | |
| 267 | 0 | public String getPollUrl() |
| 268 | { | |
| 269 | 0 | return rsd.getDecoratedResultUrl(jobId); |
| 270 | } | |
| 271 | ||
| 272 | /** | |
| 273 | * | |
| 274 | * @return the context for parsing results from service | |
| 275 | */ | |
| 276 | 0 | public JalviewDataset newJalviewDataset() |
| 277 | { | |
| 278 | 0 | if (context == null) |
| 279 | { | |
| 280 | 0 | context = new JalviewDataset(dsForIO, null, squniq, null); |
| 281 | 0 | if (contextAl != null) |
| 282 | { | |
| 283 | // TODO devise way of merging new annotation onto (identical) existing | |
| 284 | // annotation that was used as input | |
| 285 | // delete all input annotation | |
| 286 | 0 | if (contextAl.getAlignmentAnnotation() != null) |
| 287 | { | |
| 288 | 0 | for (AlignmentAnnotation alan : contextAl |
| 289 | .getAlignmentAnnotation()) | |
| 290 | { | |
| 291 | 0 | contextAl.deleteAnnotation(alan); |
| 292 | } | |
| 293 | } | |
| 294 | // TODO devise way of merging new groups onto (identical) existing | |
| 295 | // groups when they were used as input to service | |
| 296 | // delete all existing groups | |
| 297 | 0 | if (contextAl.getGroups() != null) |
| 298 | { | |
| 299 | 0 | contextAl.deleteAllGroups(); |
| 300 | } | |
| 301 | 0 | context.addAlignment(contextAl); |
| 302 | } | |
| 303 | ||
| 304 | } | |
| 305 | 0 | return context; |
| 306 | } | |
| 307 | ||
| 308 | /** | |
| 309 | * Extract list of sequence IDs for input parameter 'token' with given | |
| 310 | * molecule type | |
| 311 | * | |
| 312 | * @param token | |
| 313 | * @param type | |
| 314 | * @return | |
| 315 | */ | |
| 316 | 0 | public SequenceI[] getSequencesForInput(String token, |
| 317 | InputType.molType type) throws NoValidInputDataException | |
| 318 | { | |
| 319 | 0 | Object sgdat = inputData.get(token); |
| 320 | // can we form an alignment from this data ? | |
| 321 | 0 | if (sgdat == null) |
| 322 | { | |
| 323 | 0 | throw new NoValidInputDataException( |
| 324 | "No Sequence vector data bound to input '" + token | |
| 325 | + "' for service at " + rsd.postUrl); | |
| 326 | } | |
| 327 | 0 | if (sgdat instanceof AlignmentI) |
| 328 | { | |
| 329 | 0 | return ((AlignmentI) sgdat).getSequencesArray(); |
| 330 | } | |
| 331 | 0 | if (sgdat instanceof SequenceGroup) |
| 332 | { | |
| 333 | 0 | return ((SequenceGroup) sgdat).getSequencesAsArray(null); |
| 334 | } | |
| 335 | 0 | if (sgdat instanceof Vector) |
| 336 | { | |
| 337 | 0 | if (((Vector) sgdat).size() > 0 |
| 338 | && ((Vector) sgdat).get(0) instanceof SequenceI) | |
| 339 | { | |
| 340 | 0 | SequenceI[] sq = new SequenceI[((Vector) sgdat).size()]; |
| 341 | 0 | ((Vector) sgdat).copyInto(sq); |
| 342 | 0 | return sq; |
| 343 | } | |
| 344 | } | |
| 345 | 0 | throw new NoValidInputDataException( |
| 346 | "No Sequence vector data bound to input '" + token | |
| 347 | + "' for service at " + rsd.postUrl); | |
| 348 | } | |
| 349 | ||
| 350 | /** | |
| 351 | * binding between input data (AlignmentI, SequenceGroup, NJTree) and input | |
| 352 | * param names. | |
| 353 | */ | |
| 354 | private Hashtable<String, Object> inputData = new Hashtable<String, Object>(); | |
| 355 | ||
| 356 | /** | |
| 357 | * is the job fully submitted to server and apparently in progress ? | |
| 358 | */ | |
| 359 | public boolean running = false; | |
| 360 | ||
| 361 | /** | |
| 362 | * | |
| 363 | * @param itypes | |
| 364 | * @param al | |
| 365 | * - reference to object to be stored as input. Note - input data may | |
| 366 | * be modifed by formatter | |
| 367 | */ | |
| 368 | 4 | public void setAlignmentForInputs(Collection<InputType> itypes, |
| 369 | AlignmentI al) | |
| 370 | { | |
| 371 | 4 | for (InputType itype : itypes) |
| 372 | { | |
| 373 | 8 | if (!rsd.inputParams.values().contains(itype)) |
| 374 | { | |
| 375 | 0 | throw new IllegalArgumentException("InputType " + itype.getClass() |
| 376 | + " is not valid for service at " + rsd.postUrl); | |
| 377 | } | |
| 378 | 8 | if (itype instanceof AlignmentProcessor) |
| 379 | { | |
| 380 | 4 | ((AlignmentProcessor) itype).prepareAlignment(al); |
| 381 | } | |
| 382 | // stash a reference for recall when the alignment data is formatted | |
| 383 | 8 | inputData.put(itype.token, al); |
| 384 | } | |
| 385 | ||
| 386 | } | |
| 387 | ||
| 388 | /** | |
| 389 | * | |
| 390 | * @param token | |
| 391 | * @param type | |
| 392 | * @return alignment object bound to the given token | |
| 393 | * @throws NoValidInputDataException | |
| 394 | */ | |
| 395 | 4 | public AlignmentI getAlignmentForInput(String token, |
| 396 | InputType.molType type) throws NoValidInputDataException | |
| 397 | { | |
| 398 | 4 | Object al = inputData.get(token); |
| 399 | // can we form an alignment from this data ? | |
| 400 | 4 | if (al == null || !(al instanceof AlignmentI)) |
| 401 | { | |
| 402 | 0 | throw new NoValidInputDataException( |
| 403 | "No alignment data bound to input '" + token | |
| 404 | + "' for service at " + rsd.postUrl); | |
| 405 | } | |
| 406 | 4 | return (AlignmentI) al; |
| 407 | } | |
| 408 | ||
| 409 | /** | |
| 410 | * test to see if the job has data of type cl that's needed for the job to run | |
| 411 | * | |
| 412 | * @param cl | |
| 413 | * @return true or false | |
| 414 | */ | |
| 415 | 2 | public boolean hasDataOfType(Class cl) |
| 416 | { | |
| 417 | 2 | if (AlignmentI.class.isAssignableFrom(cl)) |
| 418 | { | |
| 419 | 2 | return true; |
| 420 | } | |
| 421 | // TODO: add more source data types | |
| 422 | ||
| 423 | 0 | return false; |
| 424 | } | |
| 425 | ||
| 426 | /** | |
| 427 | * context used to parse results from service | |
| 428 | */ | |
| 429 | JalviewDataset context = null; | |
| 430 | ||
| 431 | protected boolean parsedResults = false; | |
| 432 | ||
| 433 | protected boolean validJvresults = false; | |
| 434 | ||
| 435 | Object[] jvresultobj = null; | |
| 436 | ||
| 437 | /** | |
| 438 | * process the results obtained from the server into jalview datamodel objects | |
| 439 | * ready to be merged/added to the users' view. Use hasResults to test if | |
| 440 | * results were added to context. | |
| 441 | */ | |
| 442 | 0 | public void parseResultSet() throws Exception, Error |
| 443 | { | |
| 444 | 0 | if (!parsedResults) |
| 445 | { | |
| 446 | 0 | parsedResults = true; |
| 447 | 0 | jvresultobj = resSet.parseResultSet(); |
| 448 | 0 | validJvresults = true; |
| 449 | } | |
| 450 | } | |
| 451 | ||
| 452 | /** | |
| 453 | * | |
| 454 | * @return true if job has an input alignment and it was annotated when | |
| 455 | * results were parsed | |
| 456 | */ | |
| 457 | 0 | public boolean isInputContextModified() |
| 458 | { | |
| 459 | 0 | return contextAl != null && validJvresults |
| 460 | && context.getAl().get(0).isModified(); | |
| 461 | } | |
| 462 | ||
| 463 | /** | |
| 464 | * | |
| 465 | * @return true if the ID/metadata for the input sequences were saved and | |
| 466 | * sequence IDs renamed. | |
| 467 | */ | |
| 468 | 0 | public boolean isInputUniquified() |
| 469 | { | |
| 470 | // TODO Auto-generated method stub | |
| 471 | 0 | return false; |
| 472 | } | |
| 473 | ||
| 474 | /** | |
| 475 | * Return map between ordering of alignment submitted as input, and ordering | |
| 476 | * of alignment as provided by user | |
| 477 | * | |
| 478 | * @return int[sequence index in submitted data]==sequence index in input. | |
| 479 | */ | |
| 480 | 0 | public int[] getOrderMap() |
| 481 | { | |
| 482 | 0 | SequenceI[] contseq = contextAl.getSequencesArray(); |
| 483 | 0 | int map[] = new int[contseq.length]; |
| 484 | 0 | for (int i = 0; i < contseq.length; i++) |
| 485 | { | |
| 486 | // TODO: optimise for large N - build a lookup hash for IDs returning | |
| 487 | // order, and then lookup each sequ's original order | |
| 488 | 0 | map[i] = inputOrder.getOrder().indexOf(contseq[i]); |
| 489 | } | |
| 490 | 0 | return map; |
| 491 | } | |
| 492 | ||
| 493 | } |