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3628 commits

Author SHA1 Message Date
grahamtriggs
c8818932a4 [VIVO-1031] Minor cleanup 2015-10-31 22:19:27 +00:00
grahamtriggs
a5084a614c Remove last use of graph wrapper from reinferencer 2015-10-31 19:01:51 +00:00
grahamtriggs
25874449dd Replace the other instance where the reinferencer was going through a serialisation that could easily be a direct write into a model. 2015-10-31 14:41:56 +00:00
grahamtriggs
1832bba831 [VIVO-1031] Minor improvements to remove RDFServiceGraph usage from reinferencer. 2015-10-31 14:13:44 +00:00
grahamtriggs
5d6f4dada7 [VIVO-1031] Small caching layer in the ABoxRecomputer to reduce overhead of continually querying for the same type information. 2015-10-31 12:46:45 +00:00
grahamtriggs
3bff514d97 Remove redundant stream object 2015-10-30 16:20:29 +00:00
grahamtriggs
c0f482344d [VIVO-1068] Hide SPARQL Query Builder 2015-10-23 16:30:33 +01:00
grahamtriggs
efd431a332 Minor code cleanup 2015-10-23 15:26:18 +01:00
grahamtriggs
31898440f3 [VIVO-1115] Pass properties from the config to enable AltMetric badges 2015-10-22 15:27:05 +01:00
grahamtriggs
acae9bbf94 [VIVO-1079] Fix debugging problem when not using constructed models 2015-10-20 10:40:55 +01:00
grahamtriggs
34d78a9463 [VIVO-1031] Use consumer interface for most ResultSets 2015-10-19 17:16:09 +01:00
grahamtriggs
39b0d2e6bd [VIVO-1031] Add methods to process construct / select queries without buffering / translating through streams. 2015-10-17 22:03:12 +01:00
grahamtriggs
db0bb6a5e6 [VIVO-1031] Always execute SDB queries against the dataset and not the default model 2015-10-15 22:58:48 +01:00
grahamtriggs
83404c2c80 [VIVO-1075] Get Literal and Integer from count RDFNode rather than a toString/parseInt which fails if there is a type present. 2015-10-14 07:54:48 +01:00
grahamtriggs
2f6489610c [VIVO-1031] Rework the resolve faux properties method so that it is much faster for logged in users. 2015-10-14 07:43:40 +01:00
grahamtriggs
f37f115160 [VIVO-1031] HTML sanitisation is slow - for now, replace AntiSamy with simple RegEx of JavaScript patterns for significant boost. Will add full sanitisation to the input later. 2015-10-09 10:34:23 +01:00
grahamtriggs
b64b87ee1a Fix incorrect parameter order 2015-10-06 11:38:51 +01:00
grahamtriggs
7fbaf1cadc Pause counting to avoid problems of overlapping pause / unpauses, add event to notify of the intention to rebuild the index, so that overhead of tracking unnecessary indexing can be reduced 2015-10-03 08:44:26 +01:00
grahamtriggs
656488b958 [VIVO-1031] Shave off 2/3rds of time required to check if any triples exist by using Jena API instead of SPARQL ASK 2015-09-29 21:59:01 +01:00
grahamtriggs
15cd6a8ac0 [VIVO-1031] Improve logged in performance by handling a bulk of faux properties statements at once, rather than one-by-one. 2015-09-29 17:02:50 +01:00
grahamtriggs
4883621236 [VIVO-1059] Improve bind parameter method in SparqlQueryDataGetter so that variables with a common root are bound correctly - e.g. binding ?individual won't match ?individualURI 
(Does not use full set of allowed Sparql characters, but should catch all commonly used cases)
 2015-09-25 22:16:41 +01:00
Tim Worrall
937a3abca5 No Jira issue. When a person has no webpages, the group_concat in the query resulted in a non-empty result set: one that had no values but was nonetheless not empty. Added a check to see if the node was null. 2015-08-25 10:56:59 -04:00
Stephan Zednik
5ed701be79 simplified getConfigFromSession logic with ternary operator 2015-08-17 00:05:49 -06:00
Tim Worrall
3fdc17d16d No Jira issue. Add tooltips to object property labels by pulling in the public description of th eproperty. 2015-07-10 12:21:14 -04:00
Jim Blake
f993cf85ab Guard against accidental blanks in developer.properties 2015-06-09 11:36:15 -04:00
hudajkhan
5db470d307 VIVO-1032 retrieve whether or not property is a faux property 2015-05-26 19:58:31 -04:00
Jim Blake
2058fbf2a6 VIVO-1026 Back off to an older version of HttpClient 
OWLAPI 4.0.1 uses HttpClient 4.2.5, and we were getting a class-version conflict in some contexts.
 2015-05-03 17:38:38 -04:00
Jim Blake
0b79dfdf01 VIVO-1025 Improvements to the Virtuoso driver. 2015-04-27 14:45:14 -04:00
Jim Blake
c7979c05a7 VIVO-1018 RiotReader.createIteratorTriples() assumes an ASCII stream, so we need a different method. 2015-04-22 15:34:06 -04:00
Jim Blake
c623e32cff VIVO-1017 Fix stupid mistake from VIVO-1015 
When the variables were given meaningful names, it became obvious that I was checking
the wrong one to see whether it was a faux property.
 2015-04-15 11:13:27 -04:00
Jim Blake
c8eca40385 VIVO-1015 fix the redundancy check for restricted properties. 
Now that we have faux properties, we consider two object properties to be different if they have different ranges.
However, an object property with a restriction appears to have a different range from its base property, but is
considered to be the same property. Fix this.
 2015-04-13 16:25:25 -04:00
Jim Blake
dc726d2600 VIVO-1016 Avoid crashing on ABox.isEmpty() 
1) Don't ask whether the ABox is empty, if you don't need to
2) If you must ask, ask the graph of the base model, to avoid SDB layers
3) change contains() to use SELECT instead of ASK, because SDB implements ASK very poorly.
 2015-04-13 10:25:58 -04:00
Tim Worrall
d8aaecd4fd No Jira issue. Fixed a null pointer exception when I data property has no rangeDatatypeUri. 2015-04-08 16:15:59 -04:00
Tim Worrall
0c5d69e25e Related to VIVO-921. Server-side validation for default data property form. 2015-04-07 14:00:30 -04:00
Tim Worrall
a32ee20a40 VIVO-921: some additional validation work as well as dislaying an indicator when a data property has been ingested in an invalid format. 2015-04-06 14:48:05 -04:00
Jim Blake
ced99d7703 Improve some error handling to clean up the catalina log. 2015-04-02 17:05:47 -04:00
Jim Blake
6aa29378e5 No Jira issue. Print a better message when a SPARQL Query won't parse. 2015-04-01 18:07:07 -04:00
Tim Worrall
c47964fbde VIVO-921: widget-ized the data property form. Dates, ints, integers, floats, uris and booleans no longer use tinyMCE. 2015-04-01 12:48:15 -04:00
Jim Blake
c69138b737 VIVO-1009 Tweak the handling of TDB transactions. 2015-03-31 17:38:53 -04:00
Jim Blake
12ccf8ed9e VIVO-1008 Refine the mime type: if no extension, then HTML 
When behind Apache, some HTML pages were coming out as text/plain
 2015-03-31 13:30:04 -04:00
Jim Blake
afde710d9a Merge branch 'develop' of git+ssh://github.com/vivo-project/Vitro into develop 2015-03-30 16:36:33 -04:00
Jim Blake
b0b6e9dbc9 VIVO-1009 Use ModelMakerWithPersistenEmptyModels so new models show up. 
With ListCachingModelMaker, the filegraph models did not show up until you started VIVO for a second time.
Also, models that you create by the SPARQL Update API are not evident until restarting.
This fixes that.
 2015-03-30 16:36:11 -04:00
hudajkhan
0e54b7bb43 Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop 2015-03-30 16:24:29 -04:00
hudajkhan
a133ed206e Enabling more general exception to be logged and caught in makeIndividual method 2015-03-30 16:24:12 -04:00
Jim Blake
abf3d00996 VIVO-1009 Apply the UNION content models at the proper level. 
The ContentTripleSourceTDB and ContentTripleSourceSPARQL need to have union models on the
short-term OntModelCache. But they shouldn't be required to add them. They should be added to the
long-term OntModelCache and let ContentTripleSourceSDB override them when it overrides the long-term models.
 2015-03-30 13:47:31 -04:00
Jim Blake
6981838348 VIVO-1009 Rely less on JenaDataSourceSetupBase.isFirstStartup() 
In general, we can read firsttime files iff a model is empty. This provides more flexibility than relying on isFirstStartup().
However, the KnowledgeBaseUpdater still relies on isFirstStartup(), so we need to be sure that we set it when appropriate.
 2015-03-30 11:40:02 -04:00
Jim Blake
0362770961 VIVO-1009 TDB is based on transactions. Handle them correctly. 2015-03-30 11:01:07 -04:00
Tim Worrall
0a78ab5687 VIVO-919 and VIVO-1007: added the max password length to login widget class and also corrected the variable reference in the template for the minimum length (was minimumLength not minimumPasswordLength). 2015-03-27 16:05:42 -04:00
Jim Blake
8e429ca878 VIVO-1008 Don't override the mime type if the servlet container can provide it. 
In CharsetEncodingFilter, check to see whether the servlet container knows the mime type,
before forcing it to "text/html;charset=UTF-8"
 2015-03-27 15:38:38 -04:00
Jim Blake
94c190896e VIVO-941 Add debug statements and clean up compiler warnings. 2015-03-25 15:12:50 -04:00