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Author SHA1 Message Date
Jim Blake
f389d320ed VIVO-898 Call removedStatements.add(), not removedStatements.remove() 
Also, in RefactorOperationController, edit events must be fired against the base model, not against the ontModel itself.
Also, add some debugging statements.
 2015-03-24 12:21:51 -04:00
Tim Worrall
ba56c3de06 No Jira issue. Removed superfluous colon from the end of a message. 2015-03-23 10:49:36 -04:00
Jim Blake
cf5a56d8e8 VIVO-1004 Treat an accept header of application/ld+json as equivalent to application/json 
This is a minimal fix. It doesn't take related issues into account. It also doesn't attempt to
clean up the logic in IndividualController, or to deal with the fact that much of this logic is
repeated around the application.
 2015-03-20 17:21:08 -04:00
Jim Blake
a909cda3ee Merge branch 'develop' of git+ssh://github.com/vivo-project/Vitro into develop 2015-03-20 15:37:11 -04:00
Jim Blake
5476ba66e1 V IVO-989 Don't show a property twice just because its range is a blank node. 2015-03-20 15:37:03 -04:00
Jim Blake
abea644f46 Ignore markdown files in RDF directories. 
People want to document the RDF directories (such as rdf/abox/filegraph) by adding README.md files
Such files produce either a warning or an exception, depending on the directory and who is reading.
Modify to ignore any file with a .md extension.
 2015-03-20 15:34:53 -04:00
Tim Worrall
8f7a9beea5 class hierarchy was throwing a null pointer exception when the all classes option was selected 2015-03-20 15:33:22 -04:00
Tim Worrall
ed0b7f0f0d VIVO-998: the label will no longer be rendered on the page, leaving the name field. 2015-03-19 12:49:55 -04:00
Tim Worrall
4e09f96548 VIVO-999: when showing the list of classes that have a restriction on a property, hide the display option select and add class button. When no classes, diplay a message to tht effect. 2015-03-17 16:47:53 -04:00
Tim Worrall
f078bc4931 VIVO-970: language changes that coincide with the previous js change. 2015-03-16 13:01:05 -04:00
Tim Worrall
61e95b7d4e VIVO-970: add display limit to the object property control panel 2015-03-16 11:42:29 -04:00
Tim Worrall
5664be4a43 VIVO-970: needed to break out the more/less javascript toggle into a separate file. 2015-03-16 11:02:33 -04:00
Jim Blake
4b0cdadb0d VIVO-958 Accommodate a migration directly from 1.5 data to 1.8 
Move data directory from ontologies/update to version-specific directory ontologies/update17to18
Create ontologies/update15to16 and ontologies/update16to17 from previous update data directories.

Revise UpdateKnowledgeBase to accept the data directory as a parameter instead of having it hard-coded.
Create classes like Release18Migrator that will call UpdateKnowledgeBase with the appropriate directory, and do other release-specific migration tasks.

Make corresponding changes in startup_listeners.txt
 2015-03-13 12:15:25 -04:00
Tim Worrall
d6a17ef0b6 No Jira issue. Minor 18n change: moved an entry from vivo to vitro and modified an existing entry. 2015-03-11 15:25:35 -04:00
Jim Blake
f29b8c781a Correct a copy/paste error in static utility method. Also, add another utility method. 2015-03-10 13:30:53 -04:00
Jim Blake
e818f1ab24 VIVO-986 Limit the concatenation of string values to ALLTEXT and ALLTEXTUNSTEMMED 2015-03-09 16:32:12 -04:00
Jim Blake
32979536e6 VIVO-987 Properly shutdown the TripleSource instances. 
When shutting down a ContentTripleSourceSDB instance, attempt to deregister the JDBC driver.
Also, attempt to shut down the AbandonedConnectionCleanupThread.
Each of these produce warning messages if not shut down.
 2015-03-09 16:01:48 -04:00
Jim Blake
3b57db938f VIVO-986 Concatenate string values in search records for better snippets. 
Concatenated values are separated by a single space. Non-string values are not affected.
 2015-03-09 12:11:44 -04:00
Jim Blake
37a08c5dcf VIVO-976 The property is appearing twice in the list - remove one of them. 
For some reason, the property shows up once with a domain of OWL:Thing, and once with a domain of a blank node.
Treat them as equivalent and the problem disappears.
 2015-03-04 14:36:31 -05:00
Jim Blake
e3859b7863 ContentTripleSourceVirtuoso does not inherit annotated methods. 2015-03-02 16:24:58 -05:00
Jim Blake
f775a725de VIVO-982 ExcludeNonFlagVitro is redundant 2015-03-02 13:29:36 -05:00
Jim Blake
89c6627340 VIVO-946 VIVO-984 Hack out a way of properly filtering faux properties. 2015-03-02 13:23:28 -05:00
Jim Blake
ecbda5be7b VIVO-946 remove vestigial method: ObjectPropertyDao.getStatementsUsingObjectProperty() 2015-03-02 11:34:48 -05:00
Jim Blake
31eb5d73f4 VIVO-946 bug fix - thread pool is not idle if the queue is not empty. 
The active count might be zero if work units have been queued but not started.
 2015-03-02 11:33:27 -05:00
Jim Blake
7414084fee VIVO-981 An indexing task must never return null status. 2015-02-27 15:22:38 -05:00
Jim Blake
2b83e30866 VIVO-869 More formal coordination between startup(), pause(), and unpause(). 
Fix an oversight where the listener was still starting in paused state.
 2015-02-25 17:38:54 -05:00
Jim Blake
5c1944f508 VIVO-925 When creating class or properties, permit URIs that are already in use... 
...as long as they aren't already declared as things, classes or properties
 2015-02-25 15:42:07 -05:00
Jim Blake
837d2afdad VIVO-978 clarify the instructions for alternative triple stores 2015-02-23 13:34:06 -05:00
Jim Blake
a7a894606b VIVO-978 Move developer.properties into the config sub-directory. 2015-02-23 12:16:18 -05:00
Jim Blake
31c10db442 VIVO-978 move applicationSetup.n3 to example.applicationSetup.n3 and add comments. 2015-02-23 11:13:27 -05:00
Jim Blake
d82889d192 VIVO-914 path to TDB content directory may be absolute or relative to Vitro home directory 2015-02-23 11:08:55 -05:00
Jim Blake
ab60341355 VIVO-907 Handle RDFService quirks for TDB and Virtuoso 
Modify signature for isEquivalentGraph() - might throw RDFServiceException
Modify RDFServiceTDB to work around the nonNegativeIntegerBug
Implement toString() for the entire RDFServiceImpl hierarchy
Parameterize ContentTripleSourceSPARQL.createRDFService() so ContentTripleSourceVirtuoso can override it.
Create ContentTripleSourceVirtuoso and RDFServiceVirtuoso, to work around the nonNegativeInteger bug
   and the "INSERT DATA" problem.
 2015-02-17 16:29:04 -05:00
Jim Blake
066d013360 Modifications to https://github.com/vivo-project/Vitro/pull/14 
Restore pause logic to IndexingChangeListener.
Adjust comments, remove compiler warnings and vestigial code items, rename method.
 2015-02-17 12:08:09 -05:00
Jim Blake
680953115f Merge branch 'grahamtriggs-gt-defer-and-reader' into develop 2015-02-17 12:05:39 -05:00
Jim Blake
383598ba77 Merge pull request #15 from grahamtriggs/log4j-fix 
Update log4j.properties
 2015-02-17 10:03:41 -05:00
Jim Blake
73bb8a472d Merge branch 'gt-defer-and-reader' of https://github.com/grahamtriggs/Vitro into grahamtriggs-gt-defer-and-reader 2015-02-16 16:03:56 -05:00
Jim Blake
e2912bd79e VIVO-909 add isEquivalentGraph() to the RDFService interface. 
Moves the test for isIsomorpic() to within the RDFService implementation,
so we can handle the "broken" cases like Virtuoso and TDB. This way seems
to be cleaner than the TripleStoreQuirks approach that I was fooling around with.
 2015-02-16 14:32:57 -05:00
Jim Blake
13334cdc80 Merge branch 'develop' into feature/enhancedRdfService 2015-02-16 12:22:20 -05:00
Jim Blake
cca747f86f VIVO-974 Replace streaming variant of sparqlSelectQuery() with serializeGraph() and serializeAll() 2015-02-16 12:21:18 -05:00
Tim Worrall
36ef3b2572 Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop 2015-02-16 11:03:34 -05:00
Tim Worrall
0a516b0a01 VIVO-970: added domain and range display limit fields to object property editing form. The display is now used with the 'more...' link on profile pages. 2015-02-16 11:03:29 -05:00
Jim Blake
b59d755007 VIVO-974 Modify dump-restore to use only N-Quads format. 2015-02-16 10:39:23 -05:00
grahamtriggs
8144f46386 Update log4j.properties 
Add org.apache.jena.riot to log4j, as the packages moved in 2.10.x
 2015-02-16 09:48:15 +00:00
Graham Triggs
64680d22b0 Defer tasks by passing passing in a reference for obtaining the config at runtime, rather than at creation, allowing tasks to be deferred during startup. 2015-02-15 15:09:03 +00:00
Graham Triggs
2bde98e3df Simplify Listener, allowing tasks to be submitted to the Indexer even when paused 2015-02-15 13:32:16 +00:00
Graham Triggs
aedfb7280f Merge branch 'develop' of https://github.com/vivo-project/Vitro into search-deferrable-task 2015-02-14 10:53:04 +00:00
Jim Blake
46b075464c VIVO-869 Remove "memory leak" in indexing listener. 
Not really a leak, just holding on to references longer than necessary, reducing the scalability.
 2015-02-13 10:03:16 -05:00
Graham Triggs
999fb5e1f9 Don't queue indexing tasks for the ABoxRecomputer 2015-02-13 12:10:41 +00:00
Graham Triggs
45b753119d Create deferrable task for search tasks, allowing them to be created even when the searchindexer has not been start / initialized. 
Clear the deferred queue when scheduling the tasks.
 2015-02-13 06:56:55 +00:00
Tim Worrall
823133688a VIVO-962: <p> tags were getting stripped out when they shouldn't have been. 2015-02-12 11:10:37 -05:00