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3385 commits

Author SHA1 Message Date
Jim Blake
f690bf0235 VIVO-801 Bug fix: user a consistent spelling for tdbModels directory. 2014-06-19 11:11:18 -04:00
Tim Worrall
6ddb6336ca Merge branch 'maint-rel-1.7' of https://github.com/vivo-project/Vitro into maint-rel-1.7 2014-06-18 14:24:44 -04:00
Tim Worrall
8fc32d28ed VIVO-799: only display individuals with rdfs labels in custom form picklists 2014-06-18 14:24:32 -04:00
Jim Blake
7e514f3cfd VIVO-797 Handle both types of file size exceptions. 
Could be either FileSizeLimitExceededException or SizeLimitExceededException.
 2014-06-17 12:05:52 -04:00
Jim Blake
a086957046 Fix licensing issues. 2014-06-14 11:32:48 -04:00
Jim Blake
3e72fda9a6 VIVO-668 Increase the timeout interval when waiting for the search index. 2014-06-14 11:05:32 -04:00
Jim Blake
4edd490fbb Improve thread safety. 
Also, correct a spelling error.
 2014-06-14 11:04:18 -04:00
Jim Blake
338dd6344a VIVO-773 create BulkUpdatingModel and OntModel as decorators. 
Clean up the code, and no need to copy from Jena source files.
 2014-06-13 16:07:56 -04:00
Jim Blake
ea9d1e739d VIVO 746, at startup, remove obsolete Permissions from the user accounts model. 
Also, get rid of UpdatePermissionSetUris, which supported the transition from 1.4 to 1.5.
 2014-06-13 10:27:25 -04:00
Jim Blake
81733d305d VIVO-773 Add a Context to RDFServiceDatasetGraph. 
Every attempt at SPARQL Update fails because RDFServiceDatasetGraph.getContext() returns null.
I see that DatasetGraphBase just creates an empty Context on instantiation, so now RDFServiceDatasetGraph
does the same, and the problem goes away.
 2014-06-13 10:24:21 -04:00
Jim Blake
c1e4b36cf2 VIVO-773 remove references to IRI-0.8 library. 
Converted to 0.9.6
 2014-06-12 16:16:41 -04:00
Jim Blake
efcc677d96 Document the improvements to the developer panel 2014-06-11 17:50:47 -04:00
Jim Blake
66fbf81034 Merge commit 'a83c1e5e4f' into feature/TDBfromRDB2 2014-06-11 16:50:58 -04:00
brianjlowe
a83c1e5e4f fix to KnowledgeBaseUpdater's avoidance of triggering unnecessary recomputes 2014-06-11 15:41:14 -04:00
brianjlowe
cfada56e31 change to prevent foreground recompute when only annotations are updated 2014-06-11 15:36:35 -04:00
Jim Blake
7cf03661d4 VIVO-773 guard against RDB data that has not been migrated. 2014-06-09 15:37:54 -04:00
Jim Blake
ae6a2a7251 VIVO-719 Improve the user interface 2014-06-09 15:14:16 -04:00
Jim Blake
be11b190bc VIVO-719 Don't use streaming unless required. 
At some point we need to find out who is not closing connections.
 2014-06-07 13:47:34 -04:00
Jim Blake
21a3c242df VIVO-719 Add some log statements so we can follow the progress. 2014-06-06 22:02:44 -04:00
Jim Blake
c05a3a857a VIVO-719 Fix an error in the JSON parsing. 2014-06-06 17:46:50 -04:00
Jim Blake
aa1df06ac2 VIVO-719 Add "bucketing" to optimize the restore. 2014-06-06 17:05:51 -04:00
Jim Blake
4809fcb37e VIVO-719 Create the first attempt at restore. 2014-06-06 15:27:17 -04:00
Jim Blake
a7915785f4 VIVO-719 Create the dump/restore tool - no restore yet. 2014-06-05 15:58:06 -04:00
Jim Blake
2ea6a5d8cb VIVO-719 Create a method on RDFService for a streaming SELECT query. 
By passing an OutputStream to the method, we don't buffer the entire response into memory.
 2014-06-05 15:57:01 -04:00
Jim Blake
0cd42e211e VIVO-773 Remove "connectDB" function of advanced data tools. 
It was tied up with RDB. It could have been converted, but there was little interest.
 2014-06-02 17:57:06 -04:00
Jim Blake
3a2930cdc6 VIVO-773 Update the JENA libraries and adjust to the changes 
Replace the JAR files with more current ones.
Add a one-line change to BaseInfGraph (from the Jena source), so it will work with Pellet 2.3.1
Adjust all implementations of Graph to include new methods and remove old ones.
Add annotations and generics to reduce compiler warnings.
Remove all dependencies on RDB, which is no longer supported.
   This requires considerable refactoring of JenaIngestController, RDFUploadController, listModels.jsp
Refactor the ModelMaker uses
   Remove VitroJenaModelMaker,
   Revise VitroInterceptingModelMaker to be configurable for Config or Content models
Add debug logging code to ModelChangeImpl ChangeSetImpl, RDFServiceJena.
Add TDB support: RDFServiceFactoryTDB, RDFServiceTDB
   Refactor RDFServiceJena and RDFServiceSDB so much of the code can be reused by RDFServiceTDB
Accomodate two RDFService instances - one for Configuration models and one for Content models.
   Changes to RDFServiceUtils, RDFServiceSetup
   Configuration models use TDB directory in Vitro home directory
Handle bulk updating:
   Jena has deprecated bulk operations, and their models classes no longer use the bulk updaters
   Create a VitroModelFactory to use instead of the ModelFactory, when bulk updating is required.
   Create adapter classes: BulkUpdatingModel, BulkUpdatingOntModel, AbstractModelDecorator
Make the configuration model setup algorithms uniform
   Combine ApplicationModelSetup and UserModelSetup into ConfigurationModelsSetup
 2014-06-01 18:23:21 -04:00
Tim Worrall
03c87f49a4 VIVO-752: display most specific type in picklists where the list contains indivduals of different classes. 2014-05-30 11:12:53 -04:00
Jim Blake
1ec5d1dec7 Close request-based WebappDaoFactory instances. 2014-05-28 13:20:26 -04:00
brianjlowe
25e8d41e52 Removing obsolete namespace listener to avoid memory leak if WebappDaoFactories are unclosed 2014-05-28 10:49:00 -04:00
Jim Blake
fc66530304 VIVO-773 create and use VitroInterceptingModelMaker 
It provides access to the "pseudo-models": UNION_FULL, BASE_FULL, and INFERRED_FULL.
It also intercepts access to the memory-mapped models, returning a reference to the in-memory version.
 2014-05-21 16:07:17 -04:00
Jim Blake
216a43de10 VIVO-773 create and use VitroInterceptingModelMaker 
It provides access to the "pseudo-models": UNION_FULL, BASE_FULL, and INFERRED_FULL.
It also intercepts access to the memory-mapped models, returning a reference to the in-memory version.
 2014-05-21 16:00:34 -04:00
Jim Blake
c44df14ec1 VIVO-773 continue clean up of model makers 2014-05-21 13:08:36 -04:00
Jim Blake
68cfef81cd VIVO-773 clean up the structure of the model makers 2014-05-21 11:34:46 -04:00
Jim Blake
4ffb7bce87 Refactor SearchEngine logging for the Developer Panel 2014-05-19 11:07:52 -04:00
Jim Blake
c77241e251 VIVO-659 Move the location of "Startup Status" on the Site Admin page. 2014-05-09 17:30:26 -04:00
brianjlowe
710844a2fb eliminating Sesame dependencies 2014-05-09 15:47:04 -04:00
Jim Blake
a29b61d277 VIVO-284 ServletContext.getRealPath() requires an absolute path. 2014-05-08 16:30:32 -04:00
Jim Blake
2cd3f36db0 VIVO-769 Merge branch 'feature/orcid' into develop 
Conflicts:
	webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/PrimitiveRdfEdit.java
	webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/FreemarkerHttpServlet.java
 2014-05-07 17:31:44 -04:00
Jim Blake
d3fe9d082e Upgrade HttpClient libraries from 3.1 to 4.3.2 2014-05-07 17:07:39 -04:00
Jim Blake
10d692d411 VIVO-734 implement listrdf by delegating to SparqlQueryApiExecutor. 
It formerly retrieved the data from Solr.
 2014-05-06 15:09:27 -04:00
Jim Blake
6178aa0347 Add SearchEngine logging to the Developer Panel 2014-05-05 16:53:36 -04:00
Jim Blake
06a3acaaa0 Fix typo in logging format. 2014-05-01 15:33:09 -04:00
hudajkhan
431a3c179f adding jar file to distribution for solr 2014-05-01 14:27:01 -04:00
Jim Blake
dfbd3bb552 VIVO-758 move methods to where they are used. 2014-04-28 12:48:37 -04:00
Jim Blake
d506e5ce25 Merge branch 'develop' into feature/requestedActions 2014-04-28 12:02:43 -04:00
Jim Blake
9a8c378732 VIVO-761 Unit tests and clean-up 2014-04-28 11:59:05 -04:00
Jim Blake
20ba75d1d2 VIVO-761 Clean up some logic, remove some obsolete classes. 2014-04-25 16:08:38 -04:00
Jim Blake
78fe1bbb41 VIVO-761 Take advantage of the changes to simplify some logic. 2014-04-25 15:30:43 -04:00
Jim Blake
4baad05643 VIVO-761 Use RequestedAction instead of Actions 
Modify VitroHttpServlet, similar classes, and all subclasses to use RequestedAction instead of Actions. Modify PolicyHelper also.
 2014-04-25 14:39:17 -04:00
Jim Blake
b642f30391 VIVO-742 Fix an issue with SearchInputDocument.addField() 
Behavior should be that if a field with the same name already exists on the document, then the new values are added, and the new boost is factored in.
 2014-04-24 16:49:58 -04:00