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5067 commits

Author SHA1 Message Date
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
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
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
brianjlowe
86d4ed6506 Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop 2015-02-11 16:50:41 +02:00
brianjlowe
e74f65350f fix to ABoxRecomputer's test for whether sameAs reasoning is enabled 2015-02-11 16:49:30 +02:00
Jim Blake
34b01ee198 VIVO-869 More formal coordination between startup(), pause(), and unpause(). 
Fix an oversight in 9f9cea06e3
 2015-02-10 16:54:51 -05:00
Jim Blake
e78b020cb5 VIVO-948 remove the sdb/metadata models. 2015-02-10 16:36:35 -05:00
Tim Worrall
9072d436e5 Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop 2015-02-10 16:34:47 -05:00
Tim Worrall
83b6458fe3 VIVO-928: added microformats to non persons. Typing goes two levels down in some cases for organizations. Some info content entities covered, though many types not covered by schema.org 2015-02-10 16:34:32 -05:00
Jim Blake
9cf0233d81 VIVO-845 move vitroSearchProhibited.n3 to rdf/display/everytime 2015-02-10 15:23:42 -05:00
Jim Blake
afeba916d8 Merge pull request #11 from nateprewitt/develop 
removed extra } from title attributes in vitro templates
 2015-02-10 14:58:05 -05:00
Jim Blake
505ca41179 Merge pull request #8 from lawlesst/develop 
SPARQL update API comments in permission_config.n3
 2015-02-10 14:57:09 -05:00
hudajkhan
f9361f4cd6 VIVO-957 updating to utilize subclass variable which is now most specific type 2015-02-10 14:23:50 -05:00
Nate Prewitt
76668990c4 removed extra } from title attributes in vitro templates 2015-02-10 12:10:28 -07:00
Tim Worrall
b21cd24489 VIVO-904: the display limit annotation on data and faux properties now determines when the more... link is employed for one of these properties. Regular object properties will have a default limit of 5. Also, the add statement link is no longer suppressed when the display limit is reached. 2015-02-09 15:54:11 -05:00
hudajkhan
ed9b82258d VIVO-957 updating so most specific types are retrieved for the object uri instead of any string comparison or subclass comparison through the dao 2015-02-07 14:08:25 -05:00
Jim Blake
9f9cea06e3 VIVO-869 More formal coordination between startup(), pause(), and unpause(). 2015-02-07 13:13:48 -05:00
Jim Blake
b213718a72 VIVO-869 A full re-inference invokes a full re-index. 
IndexingChangeListener is also modified to listen for the beginning of a re-index, and discard any changes it has accumulated.
 2015-02-06 15:51:29 -05:00
Jim Blake
d25176298d VIVO-869 Drastically simplify the search configuration. 
Create LabelsAcrossContextNodes to replace AdditionalURIsForContextNodes. It's more configurable.
Create SelectQueryUriFinder to replace AdditionalUrisForVCards. It's more configurable.
Rename SimpleSparqlQueryDocumentModifier to SelectQueryDocumentModifier, to conform.
Radically simplify the VIVO search configuration, omitting all special cases except those for VCards.
 2015-02-06 15:22:42 -05:00
hudajkhan
8e97ff3678 VIVO-957 error, updating subclass sorting method for object, using superclasses of classes instead of just comparing whether classes are subclasses of each other 2015-02-03 15:25:18 -05:00
Jim Blake
a829de7923 VIVO-950, a null range is like a range of Owl:Thing 2015-02-02 16:05:51 -05:00
Jim Blake
474b984bed VIVO-950 When looking up FauxProperties, use an unfiltered WebappDaoFactory. 2015-02-02 11:44:11 -05:00
Tim Worrall
49de7204d6 no Jira issue. Search index template file was missing a closing div tag. 2015-01-30 12:06:26 -05:00
Tim Worrall
3b85239642 Related to VIVO-954. Added handling of null vClass for odd objects like \'count per year\' 2015-01-30 11:33:17 -05:00
hudajkhan
9297c90946 reasoner error occurring with n3 files that contain [ a owl:Axiom, etc.] statements, read in as empty axiom statements 2015-01-29 12:54:39 -05:00
Tim Worrall
2433f8b7a1 no jira issue: subclass headings were not getting removed correctly when all pubs were hidden and user has no editing privileges. 2015-01-28 13:17:18 -05:00
Jim Blake
7f61b39311 VIVO-869 Don't enter duplicate class group URIs in the search document. 2015-01-28 10:56:37 -05:00
Jim Blake
b3564e31bd VIVO-869 Cleanup: Committer, shorter event type, ALLTEXTUNSTEMMED, et. al. 
Get rid of the SearchIndexerSetup.Committer listener class. This functionality becomes internal to UpdateUrisTask.
Use shorter names for Event.Type values, so the display will be more compact.
ALLTEXTUNSTEMMED is not automatically populated from ALLTEXT, so change the default target field on
    SimpleSparqlQueryDocumentModifier to include both of them.
Trivial cleanup in UpdateDocumentWorkUnit.
Create StackTraceLayout, a simple Log4J layout that will print the stack trace for each call.
    Used for diagnosing the source of uninformative log messages.
 2015-01-26 10:18:02 -05:00
Jim Blake
de5b80bf75 VIVO-869 ABoxRecomputer should pause the SearchIndexer during a rebuild. 2015-01-22 15:49:08 -05:00
Tim Worrall
ccb2063aa4 Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop 2015-01-22 15:02:35 -05:00
Tim Worrall
d932703360 added a check to ensure that debug is enabled before a logging statement is processed. Also implemented the ToString.ontModelToString() method. 2015-01-22 15:02:15 -05:00
Jim Blake
db6893666d VIVO-870 Move VivoAgentContextNodeFields into the configuration. 
Delete VivoAgentContextNodeFields and its tests and the data files for the tests.
This is the last subclass of ContextNodeFields, so delete that, too.
 2015-01-22 13:10:45 -05:00
Jim Blake
989ae261ca VIVO-870 Add thread pool size to the search indexer setup. 2015-01-21 12:41:20 -05:00
Jim Blake
2fbf467ab4 Merge branch 'feature/searchIndexerTry' into develop 2015-01-21 12:32:48 -05:00
Ted Lawless
5488b30d99 Fixes ETag quoting and strips white space from generated Etag. 2015-01-21 12:31:33 -05:00
Jim Blake
d382e0efd6 VIVO-869 Don't submit updates while indexer is paused. 
When the pause flag is set, the IndexingChangeListener will continue to accumulate changes even if there
are gaps in the stream. The listener will not submit a task until the indexer is unpaused.
 2015-01-21 12:30:44 -05:00
Jim Blake
7d16e10357 VIVO-945 Produce more concise log messages when a failure is caused by shutdown. 2015-01-20 18:08:52 -05:00
Jim Blake
d5a497774e VIVO-869 Don't operate on null URIs. 
If a UriFinder finds a null URI, issue a warning message. If a null URI is submitted to UpdateUrisTask, ignore it.
 2015-01-20 17:22:43 -05:00
Jim Blake
d37c41cf65 VIVO-869 Improve throttling for indexing tasks. 
Start the implementation in "paused" state, so tasks submitted before startup() are queued.
Increase the time interval on IndexingChangeListener, so we get larger batches.
Change the RejectedExecutionHandler on the pool to CallerRunsPolicy,
   so if there is no available thread for a work unit then the thread of the task itself will run it.
 2015-01-20 17:21:09 -05:00
Jim Blake
fcfd2e7be6 VIVO-869 The display should not barf if no IndexHistory is present. 2015-01-20 16:09:53 -05:00
Jim Blake
83a5523ace VIVO-869 Improve the display 
Show exclusions count as separate from deletions count.
When there is an error on the Ajax call, display the error status and stop asking for refreshes.
When a rebuild is requested, redirect to just status, so refreshing the page would not request another rebuild.
 2015-01-20 14:06:11 -05:00
Jim Blake
78491234db VIVO-871 Improve performance when reading object properties. 
Also, improve display.
 2015-01-20 10:25:55 -05:00
Jim Blake
56a640fe44 VIVO-870 Make the number of threads configurable. 
Also, clean up the shutdown process and some comments.
 2015-01-18 18:45:14 -05:00
Jim Blake
8c3e06fc78 VIVO-870 Move the DocumentModifiers into the configuration. 2015-01-16 16:52:52 -05:00
Jim Blake
4fac4b7576 VIVO-870 Start moving DocumentModifiers into the configuration. 
Create the SimpleSparqlQueryDocumentModifier.
Use it to replace VivoISFGrantFields and VivoInformationResourceContextNodeFields.
 2015-01-16 11:46:58 -05:00