Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
DatastoreItem | 45 | 130 | 69 |
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.io.vamsas; | |
22 | ||
23 | import java.util.Enumeration; | |
24 | import java.util.Hashtable; | |
25 | import java.util.IdentityHashMap; | |
26 | import java.util.Vector; | |
27 | ||
28 | import jalview.bin.Console; | |
29 | import jalview.io.VamsasAppDatastore; | |
30 | import jalview.log.JLoggerLog4j; | |
31 | import jalview.util.MessageManager; | |
32 | import uk.ac.vamsas.client.IClientDocument; | |
33 | import uk.ac.vamsas.client.Vobject; | |
34 | import uk.ac.vamsas.client.VorbaId; | |
35 | import uk.ac.vamsas.objects.core.Entry; | |
36 | import uk.ac.vamsas.objects.core.Provenance; | |
37 | import uk.ac.vamsas.objects.core.Seg; | |
38 | ||
39 | /** | |
40 | * Holds all the common machinery for binding objects to vamsas objects | |
41 | * | |
42 | * @author JimP | |
43 | * | |
44 | */ | |
45 | public abstract class DatastoreItem | |
46 | { | |
47 | /** | |
48 | * | |
49 | */ | |
50 | Entry provEntry = null; | |
51 | ||
52 | IClientDocument cdoc; | |
53 | ||
54 | Hashtable vobj2jv; | |
55 | ||
56 | IdentityHashMap jv2vobj; | |
57 | ||
58 | boolean tojalview = false; | |
59 | ||
60 | /** | |
61 | * shared log instance | |
62 | */ | |
63 | protected static JLoggerLog4j log = JLoggerLog4j | |
64 | .getLogger(DatastoreItem.class); | |
65 | ||
66 | /** | |
67 | * note: this is taken verbatim from jalview.io.VamsasAppDatastore | |
68 | * | |
69 | * @return the Vobject bound to Jalview datamodel object | |
70 | */ | |
71 | 0 | protected Vobject getjv2vObj(Object jvobj) |
72 | { | |
73 | 0 | if (jv2vobj.containsKey(jvobj)) |
74 | { | |
75 | 0 | return cdoc.getObject((VorbaId) jv2vobj.get(jvobj)); |
76 | } | |
77 | 0 | if (Console.isDebugEnabled()) |
78 | { | |
79 | 0 | Console.debug( |
80 | "Returning null VorbaID binding for jalview object " + jvobj); | |
81 | } | |
82 | 0 | return null; |
83 | } | |
84 | ||
85 | /** | |
86 | * | |
87 | * @param vobj | |
88 | * @return Jalview datamodel object bound to the vamsas document object | |
89 | */ | |
90 | 0 | protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj) |
91 | { | |
92 | 0 | if (vobj2jv == null) |
93 | 0 | return null; |
94 | 0 | VorbaId id = vobj.getVorbaId(); |
95 | 0 | if (id == null) |
96 | { | |
97 | 0 | id = cdoc.registerObject(vobj); |
98 | 0 | Console.debug( |
99 | "Registering new object and returning null for getvObj2jv"); | |
100 | 0 | return null; |
101 | } | |
102 | 0 | if (vobj2jv.containsKey(vobj.getVorbaId())) |
103 | { | |
104 | 0 | return vobj2jv.get(vobj.getVorbaId()); |
105 | } | |
106 | 0 | return null; |
107 | } | |
108 | ||
109 | /** | |
110 | * note: this is taken verbatim from jalview.io.VamsasAppDatastore with added | |
111 | * call to updateRegistryEntry | |
112 | * | |
113 | * @param jvobj | |
114 | * @param vobj | |
115 | */ | |
116 | 0 | protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj) |
117 | { | |
118 | 0 | VorbaId id = vobj.getVorbaId(); |
119 | 0 | if (id == null) |
120 | { | |
121 | 0 | id = cdoc.registerObject(vobj); |
122 | 0 | if (id == null || vobj.getVorbaId() == null |
123 | || cdoc.getObject(id) != vobj) | |
124 | { | |
125 | 0 | Console.error("Failed to get id for " |
126 | 0 | + (vobj.isRegisterable() ? "registerable" |
127 | : "unregisterable") | |
128 | + " object " + vobj); | |
129 | } | |
130 | } | |
131 | 0 | if (vobj2jv.containsKey(vobj.getVorbaId()) |
132 | && !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) | |
133 | { | |
134 | 0 | Console.debug( |
135 | "Warning? Overwriting existing vamsas id binding for " | |
136 | + vobj.getVorbaId(), | |
137 | new Exception(MessageManager.getString( | |
138 | "exception.overwriting_vamsas_id_binding"))); | |
139 | } | |
140 | 0 | else if (jv2vobj.containsKey(jvobj) |
141 | && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId())) | |
142 | { | |
143 | 0 | Console.debug( |
144 | "Warning? Overwriting existing jalview object binding for " | |
145 | + jvobj, | |
146 | new Exception(MessageManager.getString( | |
147 | "exception.overwriting_jalview_id_binding"))); | |
148 | } | |
149 | /* | |
150 | * Cache.error("Attempt to make conflicting object binding! "+vobj+" id " | |
151 | * +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+" | |
152 | * already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to | |
153 | * bindjvvobj")); } | |
154 | */ | |
155 | // we just update the hash's regardless! | |
156 | 0 | Console.debug("Binding " + vobj.getVorbaId() + " to " + jvobj); |
157 | 0 | vobj2jv.put(vobj.getVorbaId(), jvobj); |
158 | // JBPNote - better implementing a hybrid invertible hash. | |
159 | 0 | jv2vobj.put(jvobj, vobj.getVorbaId()); |
160 | 0 | if (jvobj == this.jvobj || vobj == this.vobj) |
161 | { | |
162 | 0 | updateRegistryEntry(jvobj, vobj); |
163 | } | |
164 | } | |
165 | ||
166 | /** | |
167 | * update the vobj and jvobj references and the registry entry for this | |
168 | * datastore object called by bindjvvobj and replacejvobjmapping | |
169 | */ | |
170 | 0 | private void updateRegistryEntry(Object jvobj, Vobject vobj) |
171 | { | |
172 | 0 | if (this.jvobj != null && this.vobj != null) |
173 | { | |
174 | 0 | Console.debug("updating dsobj registry. (" + this.getClass().getName() |
175 | + ")"); | |
176 | } | |
177 | 0 | this.jvobj = jvobj; |
178 | 0 | this.vobj = vobj; |
179 | 0 | dsReg.registerDsObj(this); |
180 | } | |
181 | ||
182 | /** | |
183 | * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID | |
184 | * binding tables note: originally taken verbatim from | |
185 | * jalview.io.VamsasAppDatastore with added call to updateRegistryEntry | |
186 | * | |
187 | * @param oldjvobject | |
188 | * @param newjvobject | |
189 | * (may be null to forget the oldjvobject's document mapping) | |
190 | * | |
191 | */ | |
192 | 0 | protected void replaceJvObjMapping(Object oldjvobject, Object newjvobject) |
193 | { | |
194 | 0 | Object vobject = jv2vobj.remove(oldjvobject); |
195 | 0 | if (vobject == null) |
196 | { | |
197 | 0 | throw new Error(MessageManager.formatMessage( |
198 | "error.implementation_error_old_jalview_object_not_bound", | |
199 | new String[] | |
200 | { oldjvobject.toString() })); | |
201 | } | |
202 | 0 | if (newjvobject != null) |
203 | { | |
204 | 0 | jv2vobj.put(newjvobject, vobject); |
205 | 0 | vobj2jv.put(vobject, newjvobject); |
206 | 0 | updateRegistryEntry(newjvobject, vobj); |
207 | } | |
208 | } | |
209 | ||
210 | 0 | public DatastoreItem() |
211 | { | |
212 | 0 | super(); |
213 | } | |
214 | ||
215 | 0 | public DatastoreItem(VamsasAppDatastore datastore) |
216 | { | |
217 | 0 | this(); |
218 | 0 | initDatastoreItem(datastore); |
219 | // TODO Auto-generated constructor stub | |
220 | } | |
221 | ||
222 | /** | |
223 | * construct and initialise datastore object and retrieve object bound to | |
224 | * vobj2 and validate it against boundType | |
225 | * | |
226 | * @param datastore2 | |
227 | * @param vobj2 | |
228 | * @param boundType | |
229 | */ | |
230 | 0 | public DatastoreItem(VamsasAppDatastore datastore2, Vobject vobj2, |
231 | Class boundType) | |
232 | { | |
233 | 0 | this(datastore2); |
234 | 0 | vobj = vobj2; |
235 | 0 | jvobj = getvObj2jv(vobj2); |
236 | 0 | tojalview = true; |
237 | 0 | if (jvobj != null && !(boundType.isAssignableFrom(jvobj.getClass()))) |
238 | { | |
239 | 0 | throw new Error(MessageManager.formatMessage( |
240 | "error.implementation_error_vamsas_doc_class_should_bind_to_type", | |
241 | new String[] | |
242 | { vobj.getClass().toString(), boundType.toString(), | |
243 | jvobj.getClass().toString() })); | |
244 | } | |
245 | 0 | dsReg.registerDsObj(this); |
246 | } | |
247 | ||
248 | /** | |
249 | * construct and initialise datastore object and retrieve document object | |
250 | * bound to Jalview object jvobj2 and validate it against boundType | |
251 | * | |
252 | * @param datastore2 | |
253 | * the datastore | |
254 | * @param jvobj2 | |
255 | * the jalview object | |
256 | * @param boundToType | |
257 | * - the document object class that the bound object should be | |
258 | * assignable from | |
259 | */ | |
260 | 0 | public DatastoreItem(VamsasAppDatastore datastore2, Object jvobj2, |
261 | Class boundToType) | |
262 | { | |
263 | 0 | this(datastore2); |
264 | 0 | jvobj = jvobj2; |
265 | 0 | tojalview = false; |
266 | 0 | vobj = getjv2vObj(jvobj); |
267 | 0 | if (vobj != null && !(boundToType.isAssignableFrom(vobj.getClass()))) |
268 | { | |
269 | 0 | throw new Error(MessageManager.formatMessage( |
270 | "error.implementation_error_vamsas_doc_class_should_bind_to_type", | |
271 | new String[] | |
272 | { jvobj2.getClass().toString(), boundToType.toString(), | |
273 | vobj.getClass().toString() })); | |
274 | } | |
275 | 0 | dsReg.registerDsObj(this); |
276 | } | |
277 | ||
278 | /** | |
279 | * create a new vobj to be added to the document for the jalview object jvobj | |
280 | * (jvobj!=null, vobj==null) | |
281 | */ | |
282 | public abstract void addToDocument(); | |
283 | ||
284 | /** | |
285 | * handle a conflict where both an existing vobj has been updated and a local | |
286 | * jalview object has been updated. This method is only called from doSync, | |
287 | * when an incoming update from the vamsas session conflicts with local | |
288 | * modifications made by the Jalview user. (jvobj!=null, vobj!=null) | |
289 | */ | |
290 | public abstract void conflict(); | |
291 | ||
292 | /** | |
293 | * update an existing vobj in the document with the data and settings from | |
294 | * jvobj (jvobj!=null, vobj!=null) | |
295 | */ | |
296 | public abstract void updateToDoc(); | |
297 | ||
298 | /** | |
299 | * update the local jalview object with the data from an existing vobj in the | |
300 | * document (jvobj!=null, vobj!=null) | |
301 | */ | |
302 | public abstract void updateFromDoc(); | |
303 | ||
304 | /** | |
305 | * create a new local jvobj bound to the vobj in the document. (jvobj==null, | |
306 | * vobj!=null) | |
307 | */ | |
308 | public abstract void addFromDocument(); | |
309 | ||
310 | boolean addtodoc = false, conflicted = false, updated = false, | |
311 | addfromdoc = false, success = false; | |
312 | ||
313 | private boolean updatedtodoc; | |
314 | ||
315 | private boolean updatedfromdoc; | |
316 | ||
317 | /** | |
318 | * Sync jalview to document. Enact addToDocument, conflict or update dependent | |
319 | * on existence of a vobj bound to the local jvobj. | |
320 | */ | |
321 | 0 | protected void doSync() |
322 | { | |
323 | 0 | dsReg.registerDsObj(this); |
324 | 0 | if (vobj == null) |
325 | { | |
326 | 0 | log.debug("adding new vobject to document."); |
327 | 0 | addtodoc = true; |
328 | 0 | addToDocument(); |
329 | } | |
330 | else | |
331 | { | |
332 | 0 | if (vobj.isUpdated()) |
333 | { | |
334 | 0 | log.debug("Handling update conflict for existing bound vobject."); |
335 | 0 | conflicted = true; |
336 | 0 | conflict(); |
337 | } | |
338 | else | |
339 | { | |
340 | 0 | log.debug("updating existing vobject in document."); |
341 | 0 | updatedtodoc = true; |
342 | 0 | updateToDoc(); |
343 | } | |
344 | } | |
345 | // no exceptions were encountered... | |
346 | 0 | success = true; |
347 | } | |
348 | ||
349 | /** | |
350 | * Update jalview from document. enact addFromDocument if no local jvobj | |
351 | * exists, or update iff jvobj exists and the vobj.isUpdated() flag is set. | |
352 | */ | |
353 | 0 | protected void doJvUpdate() |
354 | { | |
355 | 0 | dsReg.registerDsObj(this); |
356 | 0 | if (jvobj == null) |
357 | { | |
358 | 0 | log.debug("adding new vobject to Jalview from Document"); |
359 | 0 | addfromdoc = true; |
360 | 0 | addFromDocument(); |
361 | } | |
362 | else | |
363 | { | |
364 | 0 | if (vobj.isUpdated()) |
365 | { | |
366 | 0 | log.debug("updating Jalview from existing bound vObject"); |
367 | 0 | updatedfromdoc = true; |
368 | 0 | updateFromDoc(); |
369 | } | |
370 | } | |
371 | } | |
372 | ||
373 | VamsasAppDatastore datastore = null; | |
374 | ||
375 | /** | |
376 | * object in vamsas document | |
377 | */ | |
378 | protected Vobject vobj = null; | |
379 | ||
380 | /** | |
381 | * local jalview object | |
382 | */ | |
383 | protected Object jvobj = null; | |
384 | ||
385 | protected DatastoreRegistry dsReg; | |
386 | ||
387 | 0 | public void initDatastoreItem(VamsasAppDatastore ds) |
388 | { | |
389 | 0 | datastore = ds; |
390 | 0 | dsReg = ds.getDatastoreRegisty(); |
391 | 0 | initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(), |
392 | ds.getVamsasObjectBinding(), ds.getJvObjectBinding()); | |
393 | } | |
394 | ||
395 | 0 | private void initDatastoreItem(Entry provEntry, IClientDocument cdoc, |
396 | Hashtable vobj2jv, IdentityHashMap jv2vobj) | |
397 | { | |
398 | 0 | this.provEntry = provEntry; |
399 | 0 | this.cdoc = cdoc; |
400 | 0 | this.vobj2jv = vobj2jv; |
401 | 0 | this.jv2vobj = jv2vobj; |
402 | } | |
403 | ||
404 | 0 | protected boolean isModifiable(String modifiable) |
405 | { | |
406 | 0 | return modifiable == null; // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS) |
407 | } | |
408 | ||
409 | 0 | protected Vector getjv2vObjs(Vector alsq) |
410 | { | |
411 | 0 | Vector vObjs = new Vector(); |
412 | 0 | Enumeration elm = alsq.elements(); |
413 | 0 | while (elm.hasMoreElements()) |
414 | { | |
415 | 0 | vObjs.addElement(getjv2vObj(elm.nextElement())); |
416 | } | |
417 | 0 | return vObjs; |
418 | } | |
419 | ||
420 | // utility functions | |
421 | /** | |
422 | * get start<end range of segment, adjusting for inclusivity flag and | |
423 | * polarity. | |
424 | * | |
425 | * @param visSeg | |
426 | * @param ensureDirection | |
427 | * when true - always ensure start is less than end. | |
428 | * @return int[] { start, end, direction} where direction==1 for range running | |
429 | * from end to start. | |
430 | */ | |
431 | 0 | public int[] getSegRange(Seg visSeg, boolean ensureDirection) |
432 | { | |
433 | 0 | boolean incl = visSeg.getInclusive(); |
434 | // adjust for inclusive flag. | |
435 | 0 | int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of |
436 | // region. | |
437 | 0 | int start = visSeg.getStart() + (incl ? 0 : pol); |
438 | 0 | int end = visSeg.getEnd() + (incl ? 0 : -pol); |
439 | 0 | if (ensureDirection && pol == -1) |
440 | { | |
441 | // jalview doesn't deal with inverted ranges, yet. | |
442 | 0 | int t = end; |
443 | 0 | end = start; |
444 | 0 | start = t; |
445 | } | |
446 | 0 | return new int[] { start, end, pol < 0 ? 1 : 0 }; |
447 | } | |
448 | ||
449 | /** | |
450 | * provenance bits | |
451 | */ | |
452 | 0 | protected jalview.datamodel.Provenance getJalviewProvenance( |
453 | Provenance prov) | |
454 | { | |
455 | // TODO: fix App and Action entries and check use of provenance in jalview. | |
456 | 0 | jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance(); |
457 | 0 | for (int i = 0; i < prov.getEntryCount(); i++) |
458 | { | |
459 | 0 | jprov.addEntry(prov.getEntry(i).getUser(), |
460 | prov.getEntry(i).getAction(), prov.getEntry(i).getDate(), | |
461 | prov.getEntry(i).getId()); | |
462 | } | |
463 | ||
464 | 0 | return jprov; |
465 | } | |
466 | ||
467 | /** | |
468 | * | |
469 | * @return default initial provenance list for a Jalview created vamsas | |
470 | * object. | |
471 | */ | |
472 | 0 | Provenance dummyProvenance() |
473 | { | |
474 | 0 | return dummyProvenance(null); |
475 | } | |
476 | ||
477 | 0 | protected Entry dummyPEntry(String action) |
478 | { | |
479 | 0 | Entry entry = new Entry(); |
480 | 0 | entry.setApp(this.provEntry.getApp()); |
481 | 0 | if (action != null) |
482 | { | |
483 | 0 | entry.setAction(action); |
484 | } | |
485 | else | |
486 | { | |
487 | 0 | entry.setAction("created."); |
488 | } | |
489 | 0 | entry.setDate(new java.util.Date()); |
490 | 0 | entry.setUser(this.provEntry.getUser()); |
491 | 0 | return entry; |
492 | } | |
493 | ||
494 | 0 | protected Provenance dummyProvenance(String action) |
495 | { | |
496 | 0 | Provenance prov = new Provenance(); |
497 | 0 | prov.addEntry(dummyPEntry(action)); |
498 | 0 | return prov; |
499 | } | |
500 | ||
501 | 0 | protected void addProvenance(Provenance p, String action) |
502 | { | |
503 | 0 | p.addEntry(dummyPEntry(action)); |
504 | } | |
505 | ||
506 | /** | |
507 | * @return true if jalview was being updated from the vamsas document | |
508 | */ | |
509 | 0 | public boolean isTojalview() |
510 | { | |
511 | 0 | return tojalview; |
512 | } | |
513 | ||
514 | /** | |
515 | * @return true if addToDocument() was called. | |
516 | */ | |
517 | 0 | public boolean isAddtodoc() |
518 | { | |
519 | 0 | return addtodoc; |
520 | } | |
521 | ||
522 | /** | |
523 | * @return true if conflict() was called | |
524 | */ | |
525 | 0 | public boolean isConflicted() |
526 | { | |
527 | 0 | return conflicted; |
528 | } | |
529 | ||
530 | /** | |
531 | * @return true if updateFromDoc() was called | |
532 | */ | |
533 | 0 | public boolean isUpdatedFromDoc() |
534 | { | |
535 | 0 | return updatedfromdoc; |
536 | } | |
537 | ||
538 | /** | |
539 | * @return true if updateToDoc() was called | |
540 | */ | |
541 | 0 | public boolean isUpdatedToDoc() |
542 | { | |
543 | 0 | return updatedtodoc; |
544 | } | |
545 | ||
546 | /** | |
547 | * @return true if addFromDocument() was called. | |
548 | */ | |
549 | 0 | public boolean isAddfromdoc() |
550 | { | |
551 | 0 | return addfromdoc; |
552 | } | |
553 | ||
554 | /** | |
555 | * @return true if object sync logic completed normally. | |
556 | */ | |
557 | 0 | public boolean isSuccess() |
558 | { | |
559 | 0 | return success; |
560 | } | |
561 | ||
562 | /** | |
563 | * @return the vobj | |
564 | */ | |
565 | 0 | public Vobject getVobj() |
566 | { | |
567 | 0 | return vobj; |
568 | } | |
569 | ||
570 | /** | |
571 | * @return the jvobj | |
572 | */ | |
573 | 0 | public Object getJvobj() |
574 | { | |
575 | 0 | return jvobj; |
576 | } | |
577 | ||
578 | 0 | public boolean docWasUpdated() |
579 | { | |
580 | 0 | return (this.addtodoc || this.updated) && this.success; |
581 | } | |
582 | ||
583 | 0 | public boolean jvWasUpdated() |
584 | { | |
585 | 0 | return (success); // TODO : Implement this properly! |
586 | } | |
587 | ||
588 | } |