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48 commits

Author SHA1 Message Date
j2blake
68b06322fb VIVO-906 Explicitly configure the SearchIndexExcluders and DocumentModifiers. 2014-11-13 17:18:13 -05:00
j2blake
78241be685 VIVO-906 Assemble application at runtime. 
Create an object to represent VitroHomeDirectory
Instantiate TripleSources, FileStorage, etc, based on the config file.
 2014-11-13 17:17:38 -05:00
j2blake
bb7ab3b2a3 VIVO-848 Move the FileStorage system behind an interface 
Add it to the Application framework, and do some cleanup.
 2014-08-14 16:55:46 -04:00
j2blake
423a57e47c VIVO-823 modify startup_listeners to match the changes in Vitro. 2014-07-22 15:04:01 -04:00
j2blake
cd355373a6 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 10:27:40 -04:00
j2blake
f4541133b6 VIVO-773 guard against RDB data that has not been migrated. 2014-06-09 15:38:20 -04:00
j2blake
8b33229fdd 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 18:26:31 -04:00
j2blake
939950dcd4 VIVO-769 Merge branch 'feature/orcid' into develop 2014-05-07 17:32:38 -04:00
j2blake
02bdddab23 VIVO-742 Many changes to remove "solr" from the code base. 
Comments, template names, Java classes, variables and method names (Java and JavaScript), etc.
 2014-04-23 14:20:22 -04:00
j2blake
711afa44fa VIVO-742 Rename some 'solr' packages. 2014-04-23 10:45:06 -04:00
j2blake
0d36fe58b8 VIVO-742 Setup the Application properly, and guard against NPEs 2014-04-22 15:15:20 -04:00
j2blake
cb204a3926 VIVO-742 Create SearchEngineSetup and SearchIndexerSetup 2014-04-22 15:15:09 -04:00
j2blake
96de00b737 Make DeveloperSettings a singleton, and other improvements. 
By making it a singleton, we do need an explicit Setup operation. However, it means that we can refer to the settings in client code that doesn’t have access to a request or to the ServletContext.

Other refactorings to simplify the logic or make it more scalable.
 2014-01-04 14:40:26 -05:00
brianjlowe
a7670f6c58 disabling sameAs reasoning by default 2013-12-04 16:32:26 -05:00
brianjlowe
77d1174135 resetting the order in startup_listeners to speed migration 2013-10-31 10:46:44 -04:00
brianjlowe
9089a58998 disabling obsolete reasoner plugins 2013-10-17 08:51:05 -04:00
brianjlowe
4047b4e8a9 data migration work 2013-09-20 15:42:17 -04:00
brianjlowe
5c14c1355d Merge commit '69a45e573a' into dev-isf 
Conflicts:
	productMods/WEB-INF/filegraph/tbox/geopolitical.tbox.ver1.1-11-18-11.owl
	productMods/WEB-INF/filegraph/tbox/isDefinedBy-1.5.owl
	productMods/WEB-INF/filegraph/tbox/scires-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-bibo-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-c4o-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-core-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-dcelements-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-dcterms-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-event-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-fabio-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-foaf-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-pws-1.5.owl
	productMods/WEB-INF/filegraph/tbox/vivo-skos-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/geopolitical.tbox.ver1.1-11-18-11.owl
	productMods/WEB-INF/ontologies/update/oldVersion/isDefinedBy-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/scires-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-bibo-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-c4o-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-core-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcelements-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcterms-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-event-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-fabio-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-foaf-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-pws-1.5.owl
	productMods/WEB-INF/ontologies/update/oldVersion/vivo-skos-1.5.owl
	productMods/templates/freemarker/body/partials/individual/individual-positions.ftl
	rdf/abox/filegraph/us-states.rdf
	rdf/tbox/filegraph/geopolitical.tbox.ver1.1-11-18-11.owl
	rdf/tbox/filegraph/isDefinedBy-1.5.owl
	rdf/tbox/filegraph/scires-1.5.owl
	rdf/tbox/filegraph/vivo-bibo-1.5.owl
	rdf/tbox/filegraph/vivo-c4o-1.5.owl
	rdf/tbox/filegraph/vivo-core-1.5.owl
	rdf/tbox/filegraph/vivo-dcelements-1.5.owl
	rdf/tbox/filegraph/vivo-dcterms-1.5.owl
	rdf/tbox/filegraph/vivo-event-1.5.owl
	rdf/tbox/filegraph/vivo-fabio-1.5.owl
	rdf/tbox/filegraph/vivo-foaf-1.5.owl
	rdf/tbox/filegraph/vivo-pws-1.5.owl
	rdf/tbox/filegraph/vivo-skos-1.5.owl
 2013-09-10 09:09:42 -04:00
j2blake
1994ab03a1 VIVO-274 move permission_config.n3 to rdf/auth/everytime 
Get rid of the PermissionSetsLoader, keep the smoke tests.
 2013-08-27 17:26:35 -04:00
j2blake
1c9f9f5f1a VIVO-246 Re-implement the FreemarkerConfiguration 
The Configuration must contain mutable information like the theme directory and the TemplateLoader. It must also be request-specific so it can have the correct Locale for language support. But we should only have one instance, so there is only one TemplateCache (alternatively, one TemplateCache per theme).

Previously, this was addressed by intercepting the Template processing and adding the request-based info to the Environment. However, this interception code needed to appear each time a Template was processed. This was sometimes overlooked, and at best introduced a bunch of duplicated code.

Instead, I extended the freemarker Configuration class to include a ThreadLocal that holds request-specific information.
 2013-08-08 13:23:40 -04:00
brianjlowe
4598aae578 work in progress on data migration and related changes for ISF properties 2013-08-05 16:46:25 -04:00
j2blake
1d16f165dc VIVO-213 smoke test to check JVM temp directory 
If it isn't set, if it isn't a directory, if we can't access it, if we can't create a temp file, complain.
 2013-07-17 13:01:33 -04:00
j2blake
463203a862 VIVO-82 Split WebappDaoSetup into ContentModelSetup and ModelMaker setup. 2013-05-16 16:43:13 -04:00
j2blake
a3bd67097b VIVO-12 NIHVIVO-4011 Provide config and GUI for selecting Locale 2013-01-24 16:14:45 -05:00
stellamit
117f634829 inactivating 1.5 data migration in trunk 2012-10-19 19:38:38 +00:00
stellamit
d1b2cabd52 NIHVIVO-3673 - updates for KB migration 2012-06-19 17:49:41 +00:00
brianjlowe
b3a1dcbcd3 updated startup_listeners.txt for rdf api 2012-06-13 18:45:17 +00:00
j2blake
7ed15e82b4 NIHVIVO-3774 Add startup smoke tests for the OpenSocial framework, if it is configured. 2012-06-08 16:16:31 +00:00
briancaruso
219ea3d0d5 Worked on refactoring the startup listeners NIHVIVO-3700. 2012-05-04 16:22:23 +00:00
j2blake
cfd3925317 NIHVIVO-2411 Create a mock implementation of the ShortViewService and incorporate it into the search page. Because this is a mock, it always uses the default short view, like before. There should be no difference for the end-user. 2012-04-25 19:32:45 +00:00
j2blake
1d2a9c9dca Stop using VivoPolicy to suppress add, edit, and delete links. Use a hard-coded list for now, while waiting for the application ontology. 2012-03-28 18:38:29 +00:00
j2blake
19f47459e0 NIHVIVO-3300 Placeholder images are configured by a properties file, which is loaded at startup. 2012-03-22 20:10:13 +00:00
j2blake
bb220015d7 NIHVIVO-3523 catch up with the trunk 2012-01-09 15:50:14 +00:00
j2blake
1a54405cf1 NIHVIVO-3523 Create the DisplayByRolePermission, so we can use the PermissionsPolicy instead of DisplayRestrictedDataByRoleLevelPolicy, and these display restrictions can be assigned to arbitrary PermissionSets. 2012-01-06 21:58:12 +00:00
stellamit
51c0b6ec96 ontology files generated from the newly created flora editing environment and renamed for 1.5. Also, commenting out the knowledgebaseupdate in startup_listeners.txt 2012-01-04 20:14:44 +00:00
j2blake
83c1d151ec NIHVIVO-3523 Rewrite the PermissionRegistry to be immutable, and to distribute BrokenPermissions when someone asks for a Permission that doesn't exist. 2011-12-19 21:19:54 +00:00
j2blake
353ffe1891 NIHVIVO-3523 For the first iteration, let's implement MANAGE_MENUS as a SimplePermission. This version still needs the loader and the policy and... 2011-12-18 00:02:23 +00:00
j2blake
c3d1d16d9b Create a smoke test to check the connection to Solr. 2011-11-23 21:53:51 +00:00
briancaruso
827ea6d7e9 Removing rdfs:label from search index document field ALLTEXT. Moving vivo specific DocumentModifiers out of vitro. NIHVIVO-2975 2011-11-01 16:19:02 +00:00
stellamit
db124422af NIHVIVO-3266 (list views for roles) NIHVIVO-3206 (data migration) 2011-10-28 21:42:25 +00:00
brianjlowe
f93b025963 NIHVIVO-3223 derive dc:creator for documents 2011-10-26 21:08:54 +00:00
brianjlowe
ffc5f98325 NIHVIVO-3221 derive dc:title for documents 2011-10-25 19:21:34 +00:00
stellamit
9813ea69f3 commenting out knowledge base update process 2011-10-17 16:13:27 +00:00
j2blake
adff0e9b9b Create basic smoke tests for startup; confirm that the home directory exists and is read/write; confirm that we can create a database connection. 2011-10-07 22:21:20 +00:00
j2blake
296b8285b4 NIHVIVO-1810 Change the way that the default theme and the list of available themes are handled. If the application is configured to use a theme that is not found, it will throw a warning on the StartupStatus and use the default theme instead. 2011-09-30 22:10:36 +00:00
j2blake
915e2259a7 NIHVIVO-336 Clean up some unused context listeners. 2011-09-28 16:20:33 +00:00
j2blake
fec264c952 NIHVIVO-336 Add the link to the Wiki page to the comments. 2011-09-26 21:15:54 +00:00
j2blake
60f418f299 NIHVIVO-336 Create a StartupManager to run all of the context listeners, and accumulate the results in a StartupStatus bean. 2011-09-20 21:13:07 +00:00