2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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
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 java.util.ArrayList;
24 import java.util.Collection;
25 import java.util.Hashtable;
28 import java.util.Vector;
30 import jalview.datamodel.AlignmentAnnotation;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.AlignmentOrder;
33 import jalview.datamodel.SequenceGroup;
34 import jalview.datamodel.SequenceI;
35 import jalview.io.packed.JalviewDataset;
36 import jalview.ws.AWsJob;
37 import jalview.ws.rest.params.Alignment;
38 import jalview.ws.rest.params.SeqGroupIndexVector;
40 public class RestJob extends AWsJob
43 // TODO: input alignmentview and other data for this job
44 RestServiceDescription rsd;
58 * dataset associated with this input data.
62 AlignmentOrder inputOrder;
65 * context of input data with respect to an AlignmentView's visible contigs.
69 private AlignmentI contextAl = null;
72 * create a rest job using data bounded by the given start/end column.
75 * @param restJobThread
78 * visible contigs of an alignment view from which _input was derived
80 public RestJob(int jobNum, RestJobThread restJobThread,
81 AlignmentI _input, int[] viscontigs)
83 rsd = restJobThread.restClient.service;
85 if (viscontigs != null)
87 origviscontig = new int[viscontigs.length];
88 System.arraycopy(viscontigs, 0, origviscontig, 0, viscontigs.length);
90 // get sequences for the alignmentI
91 // get groups trimmed to alignment columns
92 // get any annotation trimmed to start/end columns, too.
93 squniq = jalview.analysis.SeqsetUtils.uniquify(_input.getSequencesArray(), true);
95 // form alignment+groups+annotation,preprocess and then record references
97 ArrayList<InputType> alinp = new ArrayList<InputType>();
98 int paramsWithData = 0;
99 // TODO: JAL-715 - generalise the following validation logic for all parameter types
100 // we cheat for moment - since we know a-priori what data is available and
101 // what inputs we have implemented so far
102 for (Map.Entry<String, InputType> prm : rsd.inputParams.entrySet())
104 if (!prm.getValue().isConstant())
106 if (prm.getValue() instanceof Alignment)
108 alinp.add(prm.getValue());
112 if (prm.getValue() instanceof SeqGroupIndexVector
113 && _input.getGroups() != null
114 && _input.getGroups().size() >= -1 + prm.getValue().min)
116 // the test above is not rigorous but fixes JAL-1298, since submission will fail if the partition set doesn't contain at least one partition
117 alinp.add(prm.getValue());
121 statMessage = ("Not enough groups defined on the alignment - need at least " + prm
131 if ((paramsWithData + alinp.size()) == rsd.inputParams.size())
133 inputOrder = new AlignmentOrder(_input);
134 if ((dsForIO = _input.getDataset()) == null)
136 _input.setDataset(null);
138 dsForIO = _input.getDataset();
139 if (contextAl == null)
143 setAlignmentForInputs(alinp, _input);
148 // not enough data, so we bail.
153 boolean validInput = false;
156 public boolean hasResults()
158 return gotresult && (parsedResults ? validJvresults : true);
162 public boolean hasValidInput()
168 public boolean isRunning()
170 return running; // TODO: can we check the response body for status messages
175 public boolean isQueued()
181 public boolean isFinished()
183 return resSet != null;
187 public boolean isFailed()
189 // TODO logic for error
194 public boolean isBroken()
196 // TODO logic for error
201 public boolean isServerError()
203 // TODO logic for error
208 public boolean hasStatus()
210 return statMessage != null;
213 protected String statMessage = null;
215 public HttpResultSet resSet;
218 public String getStatus()
224 public boolean hasResponse()
226 return statMessage != null || resSet != null;
230 public void clearResponse()
232 // only clear the transient server response
239 * @see jalview.ws.AWsJob#getState()
242 public String getState()
244 // TODO generate state string - prolly should have a default abstract method
246 return "Job is clueless";
249 public String getPostUrl()
252 // TODO Auto-generated method stub
256 public Set<Map.Entry<String, InputType>> getInputParams()
258 return rsd.inputParams.entrySet();
261 // return the URL that should be polled for this job
262 public String getPollUrl()
264 return rsd.getDecoratedResultUrl(jobId);
269 * @return the context for parsing results from service
271 public JalviewDataset newJalviewDataset()
275 context = new JalviewDataset(dsForIO, null, squniq, null);
276 if (contextAl != null)
278 // TODO devise way of merging new annotation onto (identical) existing
279 // annotation that was used as input
280 // delete all input annotation
281 if (contextAl.getAlignmentAnnotation() != null)
283 for (AlignmentAnnotation alan : contextAl
284 .getAlignmentAnnotation())
286 contextAl.deleteAnnotation(alan);
289 // TODO devise way of merging new groups onto (identical) existing
290 // groups when they were used as input to service
291 // delete all existing groups
292 if (contextAl.getGroups() != null)
294 contextAl.deleteAllGroups();
296 context.addAlignment(contextAl);
304 * Extract list of sequence IDs for input parameter 'token' with given
311 public SequenceI[] getSequencesForInput(String token,
312 InputType.molType type) throws NoValidInputDataException
314 Object sgdat = inputData.get(token);
315 // can we form an alignment from this data ?
318 throw new NoValidInputDataException(
319 "No Sequence vector data bound to input '" + token
320 + "' for service at " + rsd.postUrl);
322 if (sgdat instanceof AlignmentI)
324 return ((AlignmentI) sgdat).getSequencesArray();
326 if (sgdat instanceof SequenceGroup)
328 return ((SequenceGroup) sgdat).getSequencesAsArray(null);
330 if (sgdat instanceof Vector)
332 if (((Vector) sgdat).size() > 0
333 && ((Vector) sgdat).get(0) instanceof SequenceI)
335 SequenceI[] sq = new SequenceI[((Vector) sgdat).size()];
336 ((Vector) sgdat).copyInto(sq);
340 throw new NoValidInputDataException(
341 "No Sequence vector data bound to input '" + token
342 + "' for service at " + rsd.postUrl);
346 * binding between input data (AlignmentI, SequenceGroup, NJTree) and input
349 private Hashtable<String, Object> inputData = new Hashtable<String, Object>();
352 * is the job fully submitted to server and apparently in progress ?
354 public boolean running = false;
360 * - reference to object to be stored as input. Note - input data may
361 * be modifed by formatter
363 public void setAlignmentForInputs(Collection<InputType> itypes,
366 for (InputType itype : itypes)
368 if (!rsd.inputParams.values().contains(itype))
370 throw new IllegalArgumentException("InputType " + itype.getClass()
371 + " is not valid for service at " + rsd.postUrl);
373 if (itype instanceof AlignmentProcessor)
375 ((AlignmentProcessor) itype).prepareAlignment(al);
377 // stash a reference for recall when the alignment data is formatted
378 inputData.put(itype.token, al);
387 * @return alignment object bound to the given token
388 * @throws NoValidInputDataException
390 public AlignmentI getAlignmentForInput(String token,
391 InputType.molType type) throws NoValidInputDataException
393 Object al = inputData.get(token);
394 // can we form an alignment from this data ?
395 if (al == null || !(al instanceof AlignmentI))
397 throw new NoValidInputDataException(
398 "No alignment data bound to input '" + token
399 + "' for service at " + rsd.postUrl);
401 return (AlignmentI) al;
405 * test to see if the job has data of type cl that's needed for the job to run
408 * @return true or false
410 public boolean hasDataOfType(Class cl)
412 if (AlignmentI.class.isAssignableFrom(cl))
416 // TODO: add more source data types
422 * context used to parse results from service
424 JalviewDataset context = null;
426 protected boolean parsedResults = false;
428 protected boolean validJvresults = false;
430 Object[] jvresultobj = null;
433 * process the results obtained from the server into jalview datamodel objects
434 * ready to be merged/added to the users' view. Use hasResults to test if
435 * results were added to context.
437 public void parseResultSet() throws Exception, Error
441 parsedResults = true;
442 jvresultobj = resSet.parseResultSet();
443 validJvresults = true;
449 * @return true if job has an input alignment and it was annotated when
450 * results were parsed
452 public boolean isInputContextModified()
454 return contextAl != null && validJvresults
455 && context.getAl().get(0).isModified();
460 * @return true if the ID/metadata for the input sequences were saved and
461 * sequence IDs renamed.
463 public boolean isInputUniquified()
465 // TODO Auto-generated method stub
470 * Return map between ordering of alignment submitted as input, and ordering
471 * of alignment as provided by user
473 * @return int[sequence index in submitted data]==sequence index in input.
475 public int[] getOrderMap()
477 SequenceI[] contseq = contextAl.getSequencesArray();
478 int map[] = new int[contseq.length];
479 for (int i = 0; i < contseq.length; i++)
481 // TODO: optimise for large N - build a lookup hash for IDs returning
482 // order, and then lookup each sequ's original order
483 map[i] = inputOrder.getOrder().indexOf(contseq[i]);