Changeset 5060
- Timestamp:
- Aug 19, 2009, 9:02:11 AM (14 years ago)
- Location:
- trunk
- Files:
-
- 125 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/doc/src/docbook/appendix/incompatible.xml
r5027 r5060 99 99 org.hibernate.SessionException: proxies cannot be fetched by a stateless session 100 100 </code> 101 </para> 102 103 <bridgehead> 104 Re-attaching a detached item no longer assumes that it has been modified 105 </bridgehead> 106 107 <para> 108 The <code>DbControl.reattachItem(BasicItem)</code> method has been deprected 109 and replaced with <code>DbControl.reattachItem(BasicItem, boolean)</code>. 110 The boolean parameter is used to tell BASE if the item has been modified 111 or not while it was detached from the session. The previous behaviour of 112 <code>DbControl.reattachItem(BasicItem)</code> was equivalent to 113 <code>DbControl.reattachItem(BasicItem, true)</code>, but this is now 114 changed to <code>DbControl.reattachItem(BasicItem, false)</code> since 115 in most cases there are really no changes to the item. The problem with 116 the old behaviour was seen in the new (in BASE 2.13) change history 117 functionality which would create UPDATE events even when there was no 118 change. 101 119 </para> 102 120 -
trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/executors/DummyJobExecutor.java
r4512 r5060 123 123 } 124 124 dc = sc.newDbControl(); 125 dc.reattachItem(job );125 dc.reattachItem(job, false); 126 126 } 127 127 if (aborted) -
trunk/src/clients/migrate/net/sf/basedb/clients/migrate/SharedItemTransfer.java
r4889 r5060 109 109 @param worldAccess <code>int</code> Base 1 worldAccess value 110 110 */ 111 @SuppressWarnings("deprecation") 111 112 protected void chmod(DbControl dc, SharedItem item, int groupId, 112 113 int groupAccess, int worldAccess) -
trunk/src/clients/migrate/net/sf/basedb/clients/migrate/WellTransfer.java
r4889 r5060 108 108 } 109 109 110 @SuppressWarnings("deprecation") 110 111 private void annotateWellsForEachPlate() 111 112 { -
trunk/src/clients/web/net/sf/basedb/clients/web/Base.java
r5053 r5060 1300 1300 // reattached to the current session 1301 1301 Protocol p = newItem.getProtocol(); 1302 if (p != null) dc.reattachItem(p );1302 if (p != null) dc.reattachItem(p, false); 1303 1303 } 1304 1304 for (int i = 0; i < modifiedAnnotations.length; ++i) -
trunk/src/core/net/sf/basedb/core/DbControl.java
r5058 r5060 994 994 Reattach a detached item assuming that it has not been 995 995 updated while it was detached. 996 @ see #reattachItem(BasicItem, boolean)996 @deprecated Use {@link #reattachItem(BasicItem, boolean)} instead 997 997 */ 998 998 public void reattachItem(BasicItem item) … … 1012 1012 only be saved to the database if it is modified after the 1013 1013 reattachement 1014 @return The reattached item 1014 1015 @throws PermissionDeniedException If the logged in user doesn't have 1015 1016 read/write permission … … 1018 1019 @since 2.13 1019 1020 */ 1020 public void reattachItem(BasicItemitem, boolean updated)1021 public <T extends BasicItem> T reattachItem(T item, boolean updated) 1021 1022 throws PermissionDeniedException, ItemNotFoundException, BaseException 1022 1023 { … … 1055 1056 } 1056 1057 } 1058 return item; 1057 1059 } 1058 1060 -
trunk/src/core/net/sf/basedb/core/MultiPermissions.java
r4889 r5060 527 527 { 528 528 item.checkPermission(Permission.SET_PERMISSION); 529 dc.reattachItem(item );529 dc.reattachItem(item, false); 530 530 item.setItemKey(newItemKeys.get(item.getItemKey())); 531 531 item.setProjectKey(newProjectKeys.get(item.getProjectKey())); -
trunk/src/core/net/sf/basedb/core/ShareableUtil.java
r4889 r5060 174 174 175 175 BasicItem fromItem = (BasicItem)from; 176 if (fromItem.isDetached()) dc.reattachItem(fromItem );176 if (fromItem.isDetached()) dc.reattachItem(fromItem, false); 177 177 178 178 ItemKey itemKey = from.getItemKey(); -
trunk/src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java
r4516 r5060 391 391 for (BioAssay ba : bioAssaySubset) 392 392 { 393 dc.reattachItem(ba );393 dc.reattachItem(ba, false); 394 394 } 395 395 } -
trunk/src/plugins/core/net/sf/basedb/plugins/IntensityCalculatorPlugin.java
r4998 r5060 214 214 for (RawBioAssay rba : sources) 215 215 { 216 dc.reattachItem(rba );216 dc.reattachItem(rba, false); 217 217 } 218 218 -
trunk/src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java
r4776 r5060 282 282 for (Nameable item : selectedFilesAndDirs) 283 283 { 284 dc.reattachItem((BasicItem)item );284 dc.reattachItem((BasicItem)item, false); 285 285 Directory dir = null; 286 286 if (item.getType() == Item.FILE) -
trunk/src/plugins/core/net/sf/basedb/plugins/PlateFlatFileImporter.java
r4985 r5060 381 381 dc = sc.newDbControl(); 382 382 plates = new HashMap<String, Plate>(); 383 plateType = (PlateType)job.getValue("plateType"); 384 dc.reattachItem(plateType); 383 plateType = dc.reattachItem((PlateType)job.getValue("plateType"), false); 385 384 plateNamePrefix = (String)job.getValue("plateNamePrefix"); 386 385 if (plateNamePrefix == null) plateNamePrefix = ""; -
trunk/src/test/TestAnalyzePluginUtil.java
r4979 r5060 122 122 dc.commit(); 123 123 dc = TestUtil.getDbControl(); 124 dc.reattachItem(e );124 dc.reattachItem(e, false); 125 125 e.addRawBioAssay(rba); 126 126 } -
trunk/src/test/TestAnnotation.java
r4889 r5060 147 147 id = a.getId(); 148 148 dc = TestUtil.getDbControl(); 149 dc.reattachItem(a );149 dc.reattachItem(a, false); 150 150 write_item(0, a); 151 151 write("--Create annotation OK"); -
trunk/src/test/TestAnnotationType.java
r4889 r5060 151 151 dc.commit(); 152 152 dc = TestUtil.getDbControl(); 153 dc.reattachItem(at );153 dc.reattachItem(at, false); 154 154 id = at.getId(); 155 155 write_item(0, at); -
trunk/src/test/TestAnnotationTypeCategory.java
r4544 r5060 90 90 dc.commit(); 91 91 dc=TestUtil.getDbControl(); 92 dc.reattachItem(atgc );92 dc.reattachItem(atgc, false); 93 93 id=atgc.getId(); 94 94 write_item(id, atgc); -
trunk/src/test/TestAnyToAny.java
r5024 r5060 102 102 id = a.getId(); 103 103 dc = TestUtil.getDbControl(); 104 dc.reattachItem(a );104 dc.reattachItem(a, false); 105 105 write_item(0, a); 106 106 write("--Create any-to-any OK"); -
trunk/src/test/TestArrayBatch.java
r4889 r5060 169 169 id = ab.getId(); 170 170 dc = TestUtil.getDbControl(); 171 dc.reattachItem(ab );171 dc.reattachItem(ab, false); 172 172 write_item(0, ab); 173 173 write("--Create array batch OK"); -
trunk/src/test/TestArrayDesign.java
r5026 r5060 151 151 id = ad.getId(); 152 152 dc = TestUtil.getDbControl(); 153 dc.reattachItem(ad );153 dc.reattachItem(ad, false); 154 154 write_item(0, ad); 155 155 write("--Create array design OK"); -
trunk/src/test/TestArraySlide.java
r4889 r5060 89 89 id = as.getId(); 90 90 dc = TestUtil.getDbControl(); 91 dc.reattachItem(as );91 dc.reattachItem(as, false); 92 92 write_item(0, as); 93 93 write("--Create array slide OK"); -
trunk/src/test/TestBioAsssaySetExporter.java
r4931 r5060 269 269 id = rba.getId(); 270 270 dc = TestUtil.getDbControl(); 271 dc.reattachItem(rba );271 dc.reattachItem(rba, false); 272 272 write("--Create raw bioassay OK"); 273 273 } -
trunk/src/test/TestBioPlate.java
r4732 r5060 215 215 id = bp.getId(); 216 216 dc = TestUtil.getDbControl(); 217 dc.reattachItem(bp );217 dc.reattachItem(bp, false); 218 218 write_item(0, bp); 219 219 write("--Create bioplate OK"); -
trunk/src/test/TestClientDefaultSetting.java
r4889 r5060 71 71 id = cds.getId(); 72 72 dc = TestUtil.getDbControl(); 73 dc.reattachItem(cds );73 dc.reattachItem(cds, false); 74 74 write_item(0, cds); 75 75 write("--Create client default setting OK"); -
trunk/src/test/TestDirectory.java
r4889 r5060 95 95 id = d.getId(); 96 96 dc = TestUtil.getDbControl(); 97 dc.reattachItem(d );97 dc.reattachItem(d, false); 98 98 write_item(0, d); 99 99 write("--Create directory OK"); … … 128 128 id = sub.getId(); 129 129 dc = TestUtil.getDbControl(); 130 dc.reattachItem(sub );130 dc.reattachItem(sub, false); 131 131 write_item(0, sub); 132 132 write("--Create subdirectory OK"); -
trunk/src/test/TestExperiment.java
r4980 r5060 182 182 id = e.getId(); 183 183 dc = TestUtil.getDbControl(); 184 dc.reattachItem(e );184 dc.reattachItem(e, false); 185 185 write_item(0, e); 186 186 write("--Create experiment OK"); … … 643 643 id = root.getId(); 644 644 dc = TestUtil.getDbControl(); 645 dc.reattachItem(root );645 dc.reattachItem(root, false); 646 646 write_item(0, root); 647 647 write("--Create root bioassayset using calculator OK ("+numSpots+" spots inserted; "+time+" ms)"); … … 693 693 id = root.getId(); 694 694 dc = TestUtil.getDbControl(); 695 dc.reattachItem(root );695 dc.reattachItem(root, false); 696 696 write_item(0, root); 697 697 write("--Create root bioassayset using query OK ("+numSpots+" spots inserted; "+time+" ms)"); … … 744 744 id = root.getId(); 745 745 dc = TestUtil.getDbControl(); 746 dc.reattachItem(root );746 dc.reattachItem(root, false); 747 747 write_item(0, root); 748 748 write("--Create empty root bioassayset OK ("+numSpots+" spots inserted)"); … … 836 836 id = bas.getId(); 837 837 dc = TestUtil.getDbControl(); 838 dc.reattachItem(bas );838 dc.reattachItem(bas, false); 839 839 write_item(0, bas); 840 840 write("--Create file bioassayset OK ("+bas.getNumFileSpots()+" spots inserted)"); … … 917 917 id = bas.getId(); 918 918 dc = TestUtil.getDbControl(); 919 dc.reattachItem(bas );919 dc.reattachItem(bas, false); 920 920 write_item(0, bas); 921 921 write("--Create bioassayset OK ("+numSpots+" spots inserted)"); … … 982 982 id = bas.getId(); 983 983 dc = TestUtil.getDbControl(); 984 dc.reattachItem(bas );984 dc.reattachItem(bas, false); 985 985 write_item(0, bas); 986 986 write("--Create filtered bioassayset OK ("+numSpots+" spots inserted)"); … … 1074 1074 id = insertTo.getId(); 1075 1075 dc = TestUtil.getDbControl(); 1076 dc.reattachItem(insertTo );1076 dc.reattachItem(insertTo, false); 1077 1077 write_item(0, insertTo); 1078 1078 write("--Calculate spot extra values OK ("+numSpots+" values inserted)"); … … 1170 1170 id = bas.getId(); 1171 1171 dc = TestUtil.getDbControl(); 1172 dc.reattachItem(bas );1172 dc.reattachItem(bas, false); 1173 1173 write_item(0, bas); 1174 1174 write("--Calculate position extra values OK ("+numSpots+" values inserted)"); -
trunk/src/test/TestExtraValueType.java
r4889 r5060 77 77 id = evt.getId(); 78 78 dc = TestUtil.getDbControl(); 79 dc.reattachItem(evt );79 dc.reattachItem(evt, false); 80 80 write_item(0, evt); 81 81 write("--Create extra value type OK"); -
trunk/src/test/TestExtract.java
r4889 r5060 100 100 id = e.getId(); 101 101 dc = TestUtil.getDbControl(); 102 dc.reattachItem(e );102 dc.reattachItem(e, false); 103 103 write_item(0, e); 104 104 write("--Create extract OK"); … … 142 142 id = e.getId(); 143 143 dc = TestUtil.getDbControl(); 144 dc.reattachItem(e );144 dc.reattachItem(e, false); 145 145 write_item(0, e); 146 146 write("--Create pooled extract OK"); … … 324 324 eventId = bme.getId(); 325 325 dc = TestUtil.getDbControl(); 326 dc.reattachItem(bme );326 dc.reattachItem(bme, false); 327 327 write_item(0, bme, e); 328 328 write("--Add event for extract OK"); -
trunk/src/test/TestFile.java
r4889 r5060 116 116 id = file.getId(); 117 117 dc = TestUtil.getDbControl(); 118 dc.reattachItem(file );118 dc.reattachItem(file, false); 119 119 write_item(0, file); 120 120 write("--Create file OK"); … … 293 293 dc.commit(); 294 294 dc = TestUtil.getDbControl(); 295 dc.reattachItem(file );295 dc.reattachItem(file, false); 296 296 write_item(0, file); 297 297 write("--Update file OK"); -
trunk/src/test/TestHardware.java
r4889 r5060 86 86 id = hw.getId(); 87 87 dc = TestUtil.getDbControl(); 88 dc.reattachItem(hw );88 dc.reattachItem(hw, false); 89 89 write_item(0, hw); 90 90 write("--Create hardware OK"); -
trunk/src/test/TestHelp.java
r4889 r5060 86 86 id = h.getId(); 87 87 dc = TestUtil.getDbControl(); 88 dc.reattachItem(h );88 dc.reattachItem(h, false); 89 89 write_item(0, h); 90 90 write("--Create help OK"); -
trunk/src/test/TestHybridization.java
r4889 r5060 110 110 id = h.getId(); 111 111 dc = TestUtil.getDbControl(); 112 dc.reattachItem(h );113 dc.reattachItem(h.getCreationEvent() );112 dc.reattachItem(h, false); 113 dc.reattachItem(h.getCreationEvent(), false); 114 114 write_item(0, h); 115 115 write("--Create hybridization OK"); -
trunk/src/test/TestJob.java
r4930 r5060 200 200 id = job.getId(); 201 201 dc = TestUtil.getDbControl(); 202 dc.reattachItem(job );202 dc.reattachItem(job, false); 203 203 write_item(0, job); 204 204 write("--Create job OK"); -
trunk/src/test/TestJobAgent.java
r4514 r5060 267 267 dc.commit(); 268 268 dc = TestUtil.getDbControl(); 269 dc.reattachItem(settings );269 dc.reattachItem(settings, false); 270 270 write_item(0, settings); 271 271 write("--Create settings for job agent OK"); … … 356 356 id = job.getId(); 357 357 dc = TestUtil.getDbControl(); 358 dc.reattachItem(job );358 dc.reattachItem(job, false); 359 359 write_item(0, job, JobAgent.getById(dc, agentId).getSettings(plugin, true)); 360 360 write("--Create job OK"); -
trunk/src/test/TestLabeledExtract.java
r4889 r5060 103 103 id = le.getId(); 104 104 dc = TestUtil.getDbControl(); 105 dc.reattachItem(le );105 dc.reattachItem(le, false); 106 106 write_item(0, le); 107 107 write("--Create labeled extract OK"); … … 146 146 id = le.getId(); 147 147 dc = TestUtil.getDbControl(); 148 dc.reattachItem(le );148 dc.reattachItem(le, false); 149 149 write_item(0, le); 150 150 write("--Create pooled labeled extract OK"); … … 332 332 eventId = bme.getId(); 333 333 dc = TestUtil.getDbControl(); 334 dc.reattachItem(bme );334 dc.reattachItem(bme, false); 335 335 write_item(0, bme, le); 336 336 write("--Add event for labeled extract OK"); -
trunk/src/test/TestPlate.java
r4889 r5060 121 121 id = p.getId(); 122 122 dc = TestUtil.getDbControl(); 123 dc.reattachItem(p );123 dc.reattachItem(p, false); 124 124 write_item(0, p); 125 125 write("--Create plate OK"); … … 345 345 id = pe.getId(); 346 346 dc = TestUtil.getDbControl(); 347 dc.reattachItem(pe );347 dc.reattachItem(pe, false); 348 348 write_item(0, pe); 349 349 write("--Create event OK"); -
trunk/src/test/TestPlateMapping.java
r4889 r5060 118 118 id = pm.getId(); 119 119 dc = TestUtil.getDbControl(); 120 dc.reattachItem(pm );120 dc.reattachItem(pm, false); 121 121 write_item(0, pm); 122 122 write("--Create plate mapping OK"); … … 262 262 id = p.getId(); 263 263 dc = TestUtil.getDbControl(); 264 dc.reattachItem(p );264 dc.reattachItem(p, false); 265 265 TestPlate.write_item(0, p); 266 266 write("--Apply plate mapping OK"); -
trunk/src/test/TestPlateType.java
r4889 r5060 84 84 id = pt.getId(); 85 85 dc = TestUtil.getDbControl(); 86 dc.reattachItem(pt );86 dc.reattachItem(pt, false); 87 87 write_item(0, pt); 88 88 write("--Create plate type OK"); … … 222 222 id = pet.getId(); 223 223 dc = TestUtil.getDbControl(); 224 dc.reattachItem(pet );224 dc.reattachItem(pet, false); 225 225 write_item(0, pet); 226 226 write("--Create event type OK"); -
trunk/src/test/TestPlatform.java
r4514 r5060 317 317 id = v.getId(); 318 318 dc = TestUtil.getDbControl(); 319 dc.reattachItem(v );319 dc.reattachItem(v, false); 320 320 write_item(0, v); 321 321 write("--Create platform variant OK"); -
trunk/src/test/TestPluginConfiguration.java
r4889 r5060 85 85 id = pc.getId(); 86 86 dc = TestUtil.getDbControl(); 87 dc.reattachItem(pc );87 dc.reattachItem(pc, false); 88 88 write_item(0, pc); 89 89 write("--Create plugin configuration OK"); … … 205 205 206 206 dc = TestUtil.getDbControl(); 207 dc.reattachItem(pc );207 dc.reattachItem(pc, false); 208 208 209 209 List<?> value = pc.getParameterValues("oneString"); -
trunk/src/test/TestPluginType.java
r4889 r5060 73 73 id = pt.getId(); 74 74 dc = TestUtil.getDbControl(); 75 dc.reattachItem(pt );75 dc.reattachItem(pt, false); 76 76 write_item(0, pt); 77 77 write("--Create plugin type OK"); -
trunk/src/test/TestProtocol.java
r4889 r5060 89 89 id = p.getId(); 90 90 dc = TestUtil.getDbControl(); 91 dc.reattachItem(p );91 dc.reattachItem(p, false); 92 92 write_item(0, p); 93 93 write("--Create protocol OK"); … … 208 208 dc.commit(); 209 209 dc = TestUtil.getDbControl(); 210 dc.reattachItem(p );210 dc.reattachItem(p, false); 211 211 write_item(0, p); 212 212 write("--Deattach file OK"); … … 237 237 dc.commit(); 238 238 dc = TestUtil.getDbControl(); 239 dc.reattachItem(p );239 dc.reattachItem(p, false); 240 240 write_item(0, p); 241 241 write("--Attach file OK"); -
trunk/src/test/TestRawBioAssay.java
r5026 r5060 149 149 id = rba.getId(); 150 150 dc = TestUtil.getDbControl(); 151 dc.reattachItem(rba );151 dc.reattachItem(rba, false); 152 152 write_item(0, rba); 153 153 write("--Create raw bioassay OK"); -
trunk/src/test/TestSample.java
r4889 r5060 105 105 id = s.getId(); 106 106 dc = TestUtil.getDbControl(); 107 dc.reattachItem(s );107 dc.reattachItem(s, false); 108 108 write_item(0, s); 109 109 write("--Create sample OK"); … … 147 147 id = s.getId(); 148 148 dc = TestUtil.getDbControl(); 149 dc.reattachItem(s );149 dc.reattachItem(s, false); 150 150 write_item(0, s); 151 151 write("--Create pooled sample OK"); … … 328 328 eventId = bme.getId(); 329 329 dc = TestUtil.getDbControl(); 330 dc.reattachItem(bme );330 dc.reattachItem(bme, false); 331 331 write_item(0, bme, s); 332 332 write("--Add event for sample OK"); -
trunk/src/test/TestScan.java
r4889 r5060 93 93 id = s.getId(); 94 94 dc = TestUtil.getDbControl(); 95 dc.reattachItem(s );95 dc.reattachItem(s, false); 96 96 write_item(0, s); 97 97 write("--Create scan OK"); … … 257 257 dc.commit(); 258 258 dc = TestUtil.getDbControl(); 259 dc.reattachItem(img );259 dc.reattachItem(img, false); 260 260 write_item(0, img); 261 261 write("--Add image to scan OK"); -
trunk/src/test/TestSoftware.java
r4889 r5060 85 85 id = sw.getId(); 86 86 dc = TestUtil.getDbControl(); 87 dc.reattachItem(sw );87 dc.reattachItem(sw, false); 88 88 write_item(0, sw); 89 89 write("--Create software OK"); -
trunk/src/test/TestUnit.java
r4555 r5060 104 104 id = u.getId(); 105 105 dc = TestUtil.getDbControl(); 106 dc.reattachItem(u );106 dc.reattachItem(u, false); 107 107 write_item(0, u); 108 108 write("--Create unit OK"); -
trunk/src/test/TestUserClientSetting.java
r4889 r5060 74 74 id = ucs.getId(); 75 75 dc = TestUtil.getDbControl(); 76 dc.reattachItem(ucs );76 dc.reattachItem(ucs, false); 77 77 write_item(0, ucs); 78 78 write("--Create user client setting OK"); -
trunk/src/test/TestUserDefaultSetting.java
r4889 r5060 71 71 id = uds.getId(); 72 72 dc = TestUtil.getDbControl(); 73 dc.reattachItem(uds );73 dc.reattachItem(uds, false); 74 74 write_item(0, uds); 75 75 write("--Create user default setting OK"); -
trunk/src/test/net/sf/basedb/test/merge/MergeTest.java
r4915 r5060 198 198 { 199 199 TestUtil.write("--Creating features for array design: " + design.getName() + "\n"); 200 dc.reattachItem(design );200 dc.reattachItem(design, false); 201 201 FeatureBatcher batcher = design.getFeatureBatcher(FeatureIdentificationMethod.COORDINATES, null); 202 202 ReporterBatcher reporterBatcher = ReporterBatcher.getNew(dc); … … 235 235 { 236 236 TestUtil.write("--Creating data for raw bioassay: " + rba.getName() + "\n"); 237 dc.reattachItem(rba );237 dc.reattachItem(rba, false); 238 238 RawDataBatcher batcher = rba.getRawDataBatcher(null, null); 239 239 for (int block = 1; block <= 10; block++) -
trunk/src/test/net/sf/basedb/test/performance/RawDataTest.java
r4806 r5060 133 133 // Add raw bioassays to experiment 134 134 dc = TestUtil.getDbControl(); 135 dc.reattachItem(experiment );135 dc.reattachItem(experiment, false); 136 136 for (int i = 0; i < numIterations; i++) 137 137 { -
trunk/www/admin/annotationtypecategories/index.jsp
r4907 r5060 161 161 else 162 162 { 163 dc.reattachItem(annotationTypeCategory );163 dc.reattachItem(annotationTypeCategory, false); 164 164 message = "Annotation type category updated"; 165 165 } -
trunk/www/admin/annotationtypes/index.jsp
r4907 r5060 168 168 else 169 169 { 170 dc.reattachItem(annotationType );170 dc.reattachItem(annotationType, false); 171 171 message = "Annotation type updated"; 172 172 } -
trunk/www/admin/clients/help/index.jsp
r4889 r5060 130 130 else 131 131 { 132 dc.reattachItem(help );132 dc.reattachItem(help, false); 133 133 help.setExternalId(externalId); 134 134 message = "Help updated"; -
trunk/www/admin/clients/index.jsp
r4889 r5060 135 135 else 136 136 { 137 dc.reattachItem(client );137 dc.reattachItem(client, false); 138 138 client.setExternalId(Values.getStringOrNull(request.getParameter("external_id"))); 139 139 message = "Client application updated"; -
trunk/www/admin/datafiletypes/index.jsp
r4711 r5060 137 137 else 138 138 { 139 dc.reattachItem(fileType );139 dc.reattachItem(fileType, false); 140 140 message = "Data file type updated"; 141 141 } -
trunk/www/admin/extravaluetypes/index.jsp
r4510 r5060 136 136 else 137 137 { 138 dc.reattachItem(extraValueType );138 dc.reattachItem(extraValueType, false); 139 139 message = "Extra value type updated"; 140 140 } -
trunk/www/admin/filetypes/index.jsp
r4889 r5060 113 113 dc = sc.newDbControl(); 114 114 FileType fileType = (FileType)cc.getObject("item"); 115 dc.reattachItem(fileType );115 dc.reattachItem(fileType, false); 116 116 message = "File type updated"; 117 117 fileType.setName(Values.getStringOrNull(request.getParameter("name"))); -
trunk/www/admin/groups/index.jsp
r4906 r5060 167 167 else 168 168 { 169 dc.reattachItem(group );169 dc.reattachItem(group, false); 170 170 message = "Group updated"; 171 171 } -
trunk/www/admin/hardware/index.jsp
r4889 r5060 138 138 else 139 139 { 140 dc.reattachItem(hardware );140 dc.reattachItem(hardware, false); 141 141 message = "Hardware updated"; 142 142 } -
trunk/www/admin/hardwaretypes/index.jsp
r4907 r5060 154 154 else 155 155 { 156 dc.reattachItem(hardwareType );156 dc.reattachItem(hardwareType, false); 157 157 message = "Hardware type updated"; 158 158 } -
trunk/www/admin/jobagents/index.jsp
r4587 r5060 137 137 else 138 138 { 139 dc.reattachItem(agent );139 dc.reattachItem(agent, false); 140 140 agent.setExternalId(Values.getStringOrNull(request.getParameter("external_id"))); 141 141 message = "Job agent updated"; … … 176 176 else 177 177 { 178 dc.reattachItem(settings );178 dc.reattachItem(settings, false); 179 179 } 180 180 settings.setJarPath(Values.getStringOrNull(request.getParameter("jarPath."+pluginId))); -
trunk/www/admin/mimetypes/index.jsp
r4889 r5060 134 134 else 135 135 { 136 dc.reattachItem(mimeType );136 dc.reattachItem(mimeType, false); 137 137 message = "MIME type updated"; 138 138 } -
trunk/www/admin/news/index.jsp
r4889 r5060 143 143 news.setStartDate(startDate); 144 144 news.setNewsDate(newsDate); 145 dc.reattachItem(news );145 dc.reattachItem(news, false); 146 146 message = "News updated"; 147 147 } -
trunk/www/admin/platforms/index.jsp
r4906 r5060 168 168 else 169 169 { 170 dc.reattachItem(platform );170 dc.reattachItem(platform, false); 171 171 message = "Platform updated"; 172 172 } -
trunk/www/admin/platforms/variants/index.jsp
r4510 r5060 148 148 else 149 149 { 150 dc.reattachItem(variant );150 dc.reattachItem(variant, false); 151 151 platform = Platform.getById(dc, variant.getPlatform().getId()); 152 152 message = "Platform variant updated"; -
trunk/www/admin/pluginconfigurations/index.jsp
r4889 r5060 165 165 else 166 166 { 167 dc.reattachItem(configuration );167 dc.reattachItem(configuration, false); 168 168 message = "Configuration updated"; 169 169 } -
trunk/www/admin/plugindefinitions/index.jsp
r4936 r5060 310 310 else 311 311 { 312 dc.reattachItem(plugin );312 dc.reattachItem(plugin, false); 313 313 plugin.loadPluginInformation(jarPath, className, usePermissions == 2); 314 314 message = "Plugin updated"; … … 361 361 else 362 362 { 363 dc.reattachItem(settings );363 dc.reattachItem(settings, false); 364 364 } 365 365 settings.setJarPath(Values.getStringOrNull(request.getParameter("jarPath."+agentId))); -
trunk/www/admin/plugintypes/index.jsp
r4906 r5060 157 157 else 158 158 { 159 dc.reattachItem(pluginType );159 dc.reattachItem(pluginType, false); 160 160 pluginType.loadInterfaceInformation(jarPath, interfaceName); 161 161 message = "Plugin type updated"; -
trunk/www/admin/protocols/index.jsp
r4938 r5060 140 140 else 141 141 { 142 dc.reattachItem(protocol );142 dc.reattachItem(protocol, false); 143 143 message = "Protocol updated"; 144 144 } -
trunk/www/admin/protocoltypes/index.jsp
r4906 r5060 154 154 else 155 155 { 156 dc.reattachItem(protocolType );156 dc.reattachItem(protocolType, false); 157 157 message = "Protocol type updated"; 158 158 } -
trunk/www/admin/quantities/index.jsp
r4907 r5060 154 154 else 155 155 { 156 dc.reattachItem(quantity );156 dc.reattachItem(quantity, false); 157 157 message = "Quantity updated"; 158 158 } -
trunk/www/admin/quantities/units/index.jsp
r4889 r5060 129 129 else 130 130 { 131 dc.reattachItem(unit );131 dc.reattachItem(unit, false); 132 132 unit.setDisplaySymbol(displaySymbol); 133 133 message = "Unit updated"; -
trunk/www/admin/quota/index.jsp
r4889 r5060 135 135 else 136 136 { 137 dc.reattachItem(quota );137 dc.reattachItem(quota, false); 138 138 message = "Quota updated"; 139 139 } -
trunk/www/admin/quotatypes/index.jsp
r4889 r5060 113 113 dc = sc.newDbControl(); 114 114 QuotaType quotaType = (QuotaType)cc.getObject("item"); 115 dc.reattachItem(quotaType );115 dc.reattachItem(quotaType, false); 116 116 message = "Quota type updated"; 117 117 quotaType.setName(Values.getStringOrNull(request.getParameter("name"))); -
trunk/www/admin/reportertypes/index.jsp
r4889 r5060 132 132 else 133 133 { 134 dc.reattachItem(reporterType );134 dc.reattachItem(reporterType, false); 135 135 message = "Reporter type updated"; 136 136 } -
trunk/www/admin/roles/index.jsp
r4906 r5060 158 158 else 159 159 { 160 dc.reattachItem(role );160 dc.reattachItem(role, false); 161 161 message = "Role updated"; 162 162 } -
trunk/www/admin/software/index.jsp
r4889 r5060 138 138 else 139 139 { 140 dc.reattachItem(software );140 dc.reattachItem(software, false); 141 141 message = "Software updated"; 142 142 } -
trunk/www/admin/softwaretypes/index.jsp
r4907 r5060 135 135 dc = sc.newDbControl(); 136 136 SoftwareType softwareType = (SoftwareType)cc.getObject("item"); 137 dc.reattachItem(softwareType );137 dc.reattachItem(softwareType, false); 138 138 message = "Software type updated"; 139 139 softwareType.setName(Values.getStringOrNull(request.getParameter("name"))); -
trunk/www/admin/users/index.jsp
r4906 r5060 190 190 else 191 191 { 192 dc.reattachItem(user );192 dc.reattachItem(user, false); 193 193 oldLogin = user.getLogin(); 194 194 user.setLogin(login); -
trunk/www/biomaterials/bioplates/index.jsp
r5051 r5060 136 136 else 137 137 { 138 dc.reattachItem(bioPlate );138 dc.reattachItem(bioPlate, false); 139 139 message = "Bioplate updated"; 140 140 } -
trunk/www/biomaterials/bioplates/wells/index.jsp
r4864 r5060 128 128 dc = sc.newDbControl(); 129 129 BioWell biowell = (BioWell)cc.getObject("item"); 130 dc.reattachItem(biowell );130 dc.reattachItem(biowell, false); 131 131 MeasuredBioMaterial oldMbm = biowell.getBioMaterial(); 132 132 if (oldMbm != null) 133 133 { 134 dc.reattachItem(oldMbm );134 dc.reattachItem(oldMbm, false); 135 135 oldMbm.setBioWell(null); 136 136 } -
trunk/www/biomaterials/biosources/index.jsp
r4901 r5060 157 157 else 158 158 { 159 dc.reattachItem(bioSource );159 dc.reattachItem(bioSource, false); 160 160 message = "Biosource updated"; 161 161 } -
trunk/www/biomaterials/events/index.jsp
r4889 r5060 133 133 else 134 134 { 135 dc.reattachItem(event );135 dc.reattachItem(event, false); 136 136 message = "Event updated"; 137 137 } -
trunk/www/biomaterials/extracts/index.jsp
r4900 r5060 185 185 else 186 186 { 187 dc.reattachItem(extract );188 dc.reattachItem(extract.getCreationEvent() );187 dc.reattachItem(extract, false); 188 dc.reattachItem(extract.getCreationEvent(), false); 189 189 message = "Extract updated"; 190 190 } -
trunk/www/biomaterials/labeledextracts/index.jsp
r4901 r5060 191 191 else 192 192 { 193 dc.reattachItem(extract );194 dc.reattachItem(extract.getCreationEvent() );193 dc.reattachItem(extract, false); 194 dc.reattachItem(extract.getCreationEvent(), false); 195 195 message = "Labeled extract updated"; 196 196 if (labelId >= 0) // < 0 = denied or unchanged -
trunk/www/biomaterials/labels/index.jsp
r4889 r5060 136 136 else 137 137 { 138 dc.reattachItem(label );138 dc.reattachItem(label, false); 139 139 message = "Label updated"; 140 140 } -
trunk/www/biomaterials/lists/index.jsp
r4723 r5060 213 213 else 214 214 { 215 dc.reattachItem(list );215 dc.reattachItem(list, false); 216 216 message = "List updated"; 217 217 } … … 362 362 dc = sc.newDbControl(); 363 363 BioMaterialList bl = (BioMaterialList)cc.getObject("item"); 364 dc.reattachItem(bl );364 dc.reattachItem(bl, false); 365 365 366 366 String mergeType = request.getParameter("mergeType"); -
trunk/www/biomaterials/samples/index.jsp
r4901 r5060 182 182 else 183 183 { 184 dc.reattachItem(sample );185 dc.reattachItem(sample.getCreationEvent() );184 dc.reattachItem(sample, false); 185 dc.reattachItem(sample.getCreationEvent(), false); 186 186 message = "Sample updated"; 187 187 } -
trunk/www/common/annotations/index.jsp
r4510 r5060 61 61 Annotatable oldItem = (Annotatable)cc.getObject("item"); 62 62 Annotatable newItem = (Annotatable)itemType.getById(newDc, itemId); 63 oldDc.reattachItem((BasicItem)oldItem );63 oldDc.reattachItem((BasicItem)oldItem, false); 64 64 Base.updateAnnotations(newDc, oldItem, newItem, request); 65 65 oldDc.close(); -
trunk/www/common/anytoany/index.jsp
r4510 r5060 100 100 else 101 101 { 102 dc.reattachItem(anyToAny );102 dc.reattachItem(anyToAny, false); 103 103 message = "Any-to-any link updated"; 104 104 } -
trunk/www/common/import/select_plugin.jsp
r4889 r5060 174 174 { 175 175 lastPlugin = pd; 176 dc.reattachItem(pd );176 dc.reattachItem(pd, false); 177 177 boolean autoDetecting = !noAutodetect && pd.supports(autoDetectingType); 178 178 String supportsConfig = pd.supportsConfigurations() ? "true" : "false"; -
trunk/www/common/overview/info.jsp
r4840 r5060 317 317 { 318 318 Annotation a = (Annotation)item; 319 dc.reattachItem(a );319 dc.reattachItem(a, false); 320 320 annotations = Collections.singletonList(a); 321 321 try … … 337 337 { 338 338 annotatable = (Annotatable)parentItem; 339 dc.reattachItem((BasicItem)annotatable );339 dc.reattachItem((BasicItem)annotatable, false); 340 340 if (annotatable.isAnnotated()) 341 341 { … … 354 354 if (annotatable.isAnnotated()) 355 355 { 356 dc.reattachItem((BasicItem)annotatable );356 dc.reattachItem((BasicItem)annotatable, false); 357 357 358 358 // Load annotations & protocol parameters -
trunk/www/common/plugin/configure.jsp
r4889 r5060 92 92 PluginDefinition plugin = (PluginDefinition)sc.getSessionSetting("plugin.configure.plugin"); 93 93 Job job = (Job)sc.getSessionSetting("plugin.configure.job"); 94 dc.reattachItem(plugin );94 dc.reattachItem(plugin, false); 95 95 boolean configureByExample = false; 96 96 PluginConfiguration pluginConfig = (PluginConfiguration)sc.getSessionSetting("plugin.configure.config"); -
trunk/www/common/plugin/finish_job.jsp
r4537 r5060 64 64 { 65 65 Job job = (Job)sc.getSessionSetting("plugin.configure.job"); 66 dc.reattachItem(job );66 dc.reattachItem(job, false); 67 67 PluginDefinition plugin = job.getPluginDefinition(); 68 68 PluginConfiguration pluginConfig = job.getPluginConfiguration(); -
trunk/www/common/plugin/index.jsp
r4974 r5060 533 533 if (job.isInDatabase()) 534 534 { 535 dc.reattachItem(job );535 dc.reattachItem(job, false); 536 536 } 537 537 else -
trunk/www/common/plugin/select_plugin.jsp
r4889 r5060 165 165 { 166 166 lastPlugin = pd; 167 dc.reattachItem(pd );167 dc.reattachItem(pd, false); 168 168 String supportsConfig = pd.supportsConfigurations() ? "true" : "false"; 169 169 String requiresConfig = pd.requiresConfiguration() ? "true" : "false"; -
trunk/www/filemanager/directories/index.jsp
r5010 r5060 139 139 else 140 140 { 141 dc.reattachItem(directory );141 dc.reattachItem(directory, false); 142 142 message = "Directory updated"; 143 143 } -
trunk/www/filemanager/files/index.jsp
r4951 r5060 162 162 else 163 163 { 164 dc.reattachItem(file );164 dc.reattachItem(file, false); 165 165 message = "File updated"; 166 166 } -
trunk/www/filemanager/upload/upload.jsp
r4889 r5060 141 141 stopIfFileExists = !f.getName().equals(uploadedFile.getFilename()); 142 142 if (stopIfFileExists) fileExists = File.exists(dc, directory, uploadedFile.getFilename()); 143 dc.reattachItem(f );143 dc.reattachItem(f, false); 144 144 } 145 145 if (fileExists && stopIfFileExists) -
trunk/www/lims/arraybatches/index.jsp
r4889 r5060 143 143 else 144 144 { 145 dc.reattachItem(batch );145 dc.reattachItem(batch, false); 146 146 message = "Array batch updated"; 147 147 } -
trunk/www/lims/arraydesigns/index.jsp
r4901 r5060 183 183 else 184 184 { 185 dc.reattachItem(design );185 dc.reattachItem(design, false); 186 186 if (variant != null) 187 187 { … … 358 358 dc = sc.newDbControl(); 359 359 ArrayDesign design = (ArrayDesign)cc.getObject("item"); 360 dc.reattachItem(design );360 dc.reattachItem(design, false); 361 361 362 362 List<Plate> plates = new java.util.LinkedList<Plate>(); -
trunk/www/lims/arrayslides/index.jsp
r4889 r5060 147 147 else 148 148 { 149 dc.reattachItem(slide );149 dc.reattachItem(slide, false); 150 150 message = "Array slide updated"; 151 151 } -
trunk/www/lims/geometries/index.jsp
r4901 r5060 157 157 else 158 158 { 159 dc.reattachItem(geometry );159 dc.reattachItem(geometry, false); 160 160 message = "Plate geometry updated"; 161 161 } -
trunk/www/lims/platemappings/index.jsp
r4889 r5060 145 145 else 146 146 { 147 dc.reattachItem(mapping );147 dc.reattachItem(mapping, false); 148 148 message = "Plate mapping updated"; 149 149 } -
trunk/www/lims/plates/events/index.jsp
r4889 r5060 138 138 else 139 139 { 140 dc.reattachItem(event );140 dc.reattachItem(event, false); 141 141 message = "Event updated"; 142 142 } -
trunk/www/lims/plates/index.jsp
r4889 r5060 140 140 else 141 141 { 142 dc.reattachItem(plate );142 dc.reattachItem(plate, false); 143 143 message = "Plate updated"; 144 144 } -
trunk/www/lims/plates/wells/index.jsp
r4889 r5060 120 120 dc = sc.newDbControl(); 121 121 Well well = (Well)cc.getObject("item"); 122 dc.reattachItem(well );122 dc.reattachItem(well, false); 123 123 message = "Well updated"; 124 124 -
trunk/www/lims/platetypes/eventtypes/index.jsp
r4889 r5060 131 131 else 132 132 { 133 dc.reattachItem(eventType );133 dc.reattachItem(eventType, false); 134 134 message = "Event type updated"; 135 135 } -
trunk/www/lims/platetypes/index.jsp
r4901 r5060 162 162 else 163 163 { 164 dc.reattachItem(plateType );164 dc.reattachItem(plateType, false); 165 165 message = "Plate type updated"; 166 166 } -
trunk/www/my_base/projects/index.jsp
r4889 r5060 143 143 else 144 144 { 145 dc.reattachItem(project );145 dc.reattachItem(project, false); 146 146 message = "Project updated"; 147 147 } -
trunk/www/my_base/user/submit_user.jsp
r4889 r5060 66 66 } 67 67 User user = (User)sc.getSessionSetting("user"); 68 dc.reattachItem(user );68 dc.reattachItem(user, false); 69 69 70 70 // Contact information tab -
trunk/www/plugins/net/sf/basedb/plugins/jep_extra_value_calculator.jsp
r4917 r5060 73 73 dc = sc.newDbControl(); 74 74 Job job = (Job)sc.getSessionSetting("plugin.configure.job"); 75 dc.reattachItem(job );75 dc.reattachItem(job, false); 76 76 BioAssaySet source = null; 77 77 if (job != null) source = (BioAssaySet)job.getParameterValue("source"); -
trunk/www/plugins/net/sf/basedb/plugins/jep_filter.jsp
r4917 r5060 72 72 dc = sc.newDbControl(); 73 73 Job job = (Job)sc.getSessionSetting("plugin.configure.job"); 74 dc.reattachItem(job );74 dc.reattachItem(job, false); 75 75 BioAssaySet source = null; 76 76 source = (BioAssaySet)job.getParameterValue("source"); -
trunk/www/plugins/net/sf/basedb/plugins/jep_intensity_transformer.jsp
r4974 r5060 63 63 dc = sc.newDbControl(); 64 64 Job job = (Job)sc.getSessionSetting("plugin.configure.job"); 65 dc.reattachItem(job );65 dc.reattachItem(job, false); 66 66 BioAssaySet source = null; 67 67 source = (BioAssaySet)job.getParameterValue("source"); -
trunk/www/views/experiments/bioassays/index.jsp
r4978 r5060 136 136 if (ba != null) 137 137 { 138 dc.reattachItem(ba );138 dc.reattachItem(ba, false); 139 139 message = "Bioassay updated"; 140 140 ba.setName(Values.getStringOrNull(request.getParameter("name"))); -
trunk/www/views/experiments/bioassaysets/index.jsp
r4910 r5060 200 200 if (bas != null) 201 201 { 202 dc.reattachItem(bas );202 dc.reattachItem(bas, false); 203 203 message = "Bioassay set updated"; 204 204 bas.setName(Values.getStringOrNull(request.getParameter("name"))); -
trunk/www/views/experiments/index.jsp
r4889 r5060 149 149 else 150 150 { 151 dc.reattachItem(experiment );151 dc.reattachItem(experiment, false); 152 152 message = "Experiment updated"; 153 153 } -
trunk/www/views/experiments/spotdata/index.jsp
r4951 r5060 137 137 ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, subContext, pageContext, defaultContext); 138 138 dc = sc.newDbControl(); 139 if (bas != null) dc.reattachItem(bas );140 if (ba != null) dc.reattachItem(ba );139 if (bas != null) dc.reattachItem(bas, false); 140 if (ba != null) dc.reattachItem(ba, false); 141 141 final DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData(); 142 142 //cc.configureQuery(query, true); … … 150 150 ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, subContext, pageContext, defaultContext); 151 151 dc = sc.newDbControl(); 152 if (bas != null) dc.reattachItem(bas );153 if (ba != null) dc.reattachItem(ba );152 if (bas != null) dc.reattachItem(bas, false); 153 if (ba != null) dc.reattachItem(ba, false); 154 154 final DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData(); 155 155 cc.configureQuery(dc, query, Collections.singletonList("@id")); -
trunk/www/views/experiments/transformations/index.jsp
r4511 r5060 111 111 if (t != null) 112 112 { 113 dc.reattachItem(t );113 dc.reattachItem(t, false); 114 114 message = "Transformation updated"; 115 115 t.setName(Values.getStringOrNull(request.getParameter("name"))); -
trunk/www/views/formulas/index.jsp
r4935 r5060 142 142 else 143 143 { 144 dc.reattachItem(formula );144 dc.reattachItem(formula, false); 145 145 message = "Formula updated"; 146 146 } -
trunk/www/views/hybridizations/index.jsp
r4901 r5060 178 178 { 179 179 creationEvent = hyb.getCreationEvent(); 180 dc.reattachItem(hyb );181 dc.reattachItem(creationEvent );180 dc.reattachItem(hyb, false); 181 dc.reattachItem(creationEvent, false); 182 182 message = "Hybridization updated"; 183 183 } -
trunk/www/views/rawbioassays/index.jsp
r4901 r5060 273 273 else 274 274 { 275 dc.reattachItem(rba );275 dc.reattachItem(rba, false); 276 276 if (variant != null) 277 277 { -
trunk/www/views/reporterlists/index.jsp
r4889 r5060 223 223 else 224 224 { 225 dc.reattachItem(rl );225 dc.reattachItem(rl, false); 226 226 message = "Reporter list updated"; 227 227 } … … 375 375 dc = sc.newDbControl(); 376 376 ReporterList rl = (ReporterList)cc.getObject("item"); 377 dc.reattachItem(rl );377 dc.reattachItem(rl, false); 378 378 379 379 String mergeType = request.getParameter("mergeType"); -
trunk/www/views/scans/images/index.jsp
r4889 r5060 126 126 else 127 127 { 128 dc.reattachItem(image );128 dc.reattachItem(image, false); 129 129 message = "Image updated"; 130 130 } -
trunk/www/views/scans/index.jsp
r4901 r5060 162 162 else 163 163 { 164 dc.reattachItem(scan );164 dc.reattachItem(scan, false); 165 165 message = "Scan updated"; 166 166 }
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