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44 commits

Author SHA1 Message Date
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
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
Jim Blake
4405d76683 VIVO-44 Add some JARs and update others, to serve the updated SolrJ client. 2014-05-15 18:10:40 -04:00
Jim Blake
356b17f9a0 Upgrade to latest MySQL driver. 2014-05-15 14:45:55 -04:00
Jim Blake
c47b2ea3cc VIVO-44 Upgrade SolrJ client libraries. 2014-05-15 14:32:44 -04:00
brianjlowe
710844a2fb eliminating Sesame dependencies 2014-05-09 15:47:04 -04:00
j2blake
d932f851e9 Convert from HttpClient 3.1 to HttpClient 4.3 2014-03-05 18:32:36 -05:00
j2blake
1d7812ed28 First cut of Orcid Integration is working 2014-02-26 14:58:18 -05:00
hudajkhan
5e369a751f new versions of jar files for sparql query json ld also used in vivo semantic search 2013-12-04 13:31:05 -05:00
Brian Caruso
7129912e43 Adding unit tests, adding easymock library, Fixed problem with URIs with localnames that start with a digit. VIVO-13 2013-08-30 14:19:13 -04:00
Brian Caruso
50945d5af1 Adding JSON-LD to SPARQL form. Adding jsonld-java libraries. VIVO-255 2013-08-27 15:10:34 -04:00
j2blake
c00fefacfe Changes to the SolrSetup class require access to the newer HttpClient libraries 
VIVO-161 VIVO-43
 2013-07-24 11:49:56 -04:00
Brian Caruso
be734aa293 adding files that were missed from branch 2013-07-10 15:30:38 -04:00
Brian Caruso
1d5f53ab78 Adding solr client libraries to test task. 
Removing old version of solrj from lib
Adding new version of solrj to lib
 2013-07-09 11:39:00 -04:00
brianjlowe
d7551ae44c C3P0 library for connection pool 2012-08-30 18:08:41 +00:00
brianjlowe
e2438d404d NIHVIVO-3828 allows update and graph URI retrieval for non-Sesame SPARQL endpoints and NIHVIVO-3850 fixes IllegalStateException when downloading unmergeable statements 2012-06-28 19:58:31 +00:00
brianjlowe
cead502f89 SDB implementation of RDF API (and merge from trunk) 2012-06-04 21:09:36 +00:00
brianjlowe
58e2441a6c Sesame library update and SparqlGraph for RDF API work 2012-03-08 19:19:24 +00:00
tworrall
9f0d886d99 these three jar files are need with the antysamy jar 2012-01-11 16:19:51 +00:00
j2blake
f50f8eb919 NIHVIVO-2774 Remove JARs that we don't seem to be using. 2011-10-20 21:50:47 +00:00
cappadona
8095541706 NIHVIVO-352 Applied Miles' patch for search snippets. 2011-07-18 16:26:53 +00:00
ryounes
6083deeaf7 NIHVIVO-2775 Remove Lucene controllers, libraries, and all references to Lucene throughout the code. 2011-07-13 15:19:52 +00:00
briancaruso
22427f694f Adding render time filtering of script elements to avoid javascript based security exploits. NIHVIVO-2678 2011-07-11 23:14:55 +00:00
brianjlowe
6e4fcedb6c NIHVIVO-2317 NIHVIVO-2318 removing vitro namespace properties from editing and various Java classes and interfaces 2011-07-05 19:14:16 +00:00
ryounes
6fc85c2595 NIHVIVO-2623 Upgrade to Freemarker 2.3.18 2011-05-25 20:08:35 +00:00
ryounes
dcc316f9dd NIHVIVO-2437 Remove unneeded library 2011-05-16 22:27:41 +00:00
ryounes
265a86019c NIHVIVO-2437 Upgrade to Solr 3.1 2011-05-16 21:58:24 +00:00
brianjlowe
2f132d6290 NIHVIVO-2576 addresses issue with db connections closed by MySQL not being returned to the pool 2011-04-29 16:55:58 +00:00
ryounes
3ba088e8e9 Update org.apache.commons.io library 2011-04-26 23:16:12 +00:00
briancaruso
543c1cd945 Adding solr indexing prototype 2011-04-11 17:21:38 +00:00
ryounes
e9e069fb94 Upgrading to apache commons lang version 2.6 2011-04-05 14:50:22 +00:00
j2blake
c0aa6cdbf0 JAXEN is no longer used. 2011-03-24 15:50:38 +00:00
cdtank
43c1c6707e 1. Adding the TDB 0.8.7 (compatible with current hena/sdb libs) library. 2011-03-16 16:06:15 +00:00
bkoniden
801d789696 Upgraded lucene-2.4-*.jar to lucene-2.9.3-*.jar. Upgraded solr-1.0.jar to apache-solr-core-1.4.1.jar. Removed LuceneHighlighter and SimpleLuceneHighlighter as they are not used anymore. Made minor changes to the way Query is parsed in PagedSearchController. The query now uses a MultiFieldQueryParser that searches the query against ALLTEXT, NAME and TYPE fields in the search index. 2011-03-14 13:41:16 +00:00
bjl23
0dc6abfe61 latest releases of Jena, ARQ, SDB, and Pellet libraries 2010-11-05 17:45:57 +00:00
jeb228
85f3fa25fa NIHVIVO-817 Use Java Advanced Imaging library to crop and scale images instead of javax.imageio 2010-07-15 20:05:41 +00:00
cdtank
94755a7f73 1. Refactored/Cleaned the front-end for the co-author vis. 
2. Added Gson library for making use of json. 
3. Added capability to send information in json format. We will use this especially in getting non-specific information on the fly about an individual.
 2010-06-29 22:07:55 +00:00
cdtank
25e534e23f 1. Added code related to Visualization Framework. 
2. Added code related to Person Publication count visualization.
3. Added code related to College Publication count visualization.
4. Added code related to PDF Report visualization.
 2010-06-21 21:44:26 +00:00
jeb228
21d1d96df4 Upgrade to servlet 2.5, since we have agreed to support nothing prior to Tomcat 6.0 2010-05-27 18:38:27 +00:00
bdc34
ce73b46c96 Removing AXIS web services. NIHVIVO-415 2010-05-19 19:54:00 +00:00
rjy7
a0c93fda6d Move FreeMarker templates, controllers, setup, and library upgrades into trunk. Not used to generate any pages or templates yet (except a couple of hidden pages that are only available through the url). 2010-05-11 20:37:48 +00:00
bjl23
e06c6d0cba fixing initial classgroup 2010-03-13 01:01:43 +00:00
jeb228
9a4a38b7c7 NIHVIVO-62 Removed json.jar instead of the source files, since it's easier to determine the provenance of the source. 2010-02-05 15:32:28 +00:00
jeb228
4f2e303079 Improve output: distinguish between failed assertions (failures) and unexpected exceptions (errors), and print a filtered stack trace for any exception. 2010-01-29 22:13:57 +00:00