Commit graph

4986 commits

Author SHA1 Message Date
Jim Blake
dad574d33a Merge branch 'develop' into feature/elk 2014-12-11 16:24:52 -05:00
Jim Blake
f339f1864f VIVO-863 get rid of GuardAgainstUnmigratedRDB
It was only useful for the transition from 1.6 to 1.7, and it was a problem when someone used a triple-store other than SDB.
2014-12-11 16:12:42 -05:00
Jim Blake
73b76a6e90 VIVO-933 Read PropertyConfig.n3 into an existing model, just once. 2014-12-11 15:51:59 -05:00
Jim Blake
d48d6f63ec Merge branch 'develop' into feature/fauxEditing 2014-12-10 17:41:37 -05:00
Jim Blake
481d3fc1d8 VIVO-695 VIVO-699 Refactor and optimize the PropertyRestrictionBean
Formerly the PropertyRestrictionPolicyHelper.
2014-12-10 17:39:06 -05:00
hudajkhan
05fe47e50a needed access to rdfservice in nyccsc 2014-12-10 12:36:37 -05:00
Tim Worrall
da9e244c18 Merge branch 'feature/fauxEditing' of https://github.com/vivo-project/Vitro into feature/fauxEditing 2014-12-09 13:16:57 -05:00
Tim Worrall
ee8300dccc No Jira issue. Faux property listing was not displaying all cases of a property where the labels were the same but the domains were different. 2014-12-09 13:16:20 -05:00
Jim Blake
5a54fa171b VIVO-825 do not allow access to APIs if the account is not in a valid state.
Before testing the password, test that the account is well-formed: first name, last name, email.
After testing the password, check to see whether a password change is required.
2014-12-09 12:26:49 -05:00
Jim Blake
ec36574041 VIVO-774 fix a unit test that was broken by faux property refactoring. 2014-12-09 11:41:26 -05:00
Jim Blake
875ba66a46 Merge branch 'develop' into feature/fauxEditing 2014-12-08 15:55:32 -05:00
Jim Blake
d1b07bcffc VIVO-766 This comparator is invalid under Java 8.
Because subclass/superclass is only a partial ordering, this breaks the contract for Comparator,
and throws an IllegalArgumentException under Java 8. In particular, for classes sub, super and other,
we have sub=other, sub<super, which should imply other<super, but instead other=super.

As far as I can determine, this sort is never used anyway, so there should be no impact in removing it.
PropertyInstanceDaoJena sorts these results again before using them, as does GroupedPropertyList.
2014-12-08 15:31:10 -05:00
Jim Blake
14d1cdb5bf VIVO-766 Java 8 writes prefixes in a different order.
Probably due to a change in the algorithm for HashMap, or something similar.
This test expected a particular string in response, but Java 7 and Java 8 returned two different, but equivalent, strings.
Modify it so it will accept @prefix or xmlns: specifications in any order.
2014-12-08 15:28:21 -05:00
Jim Blake
3b508a6c97 VIVO-766 Java 8 handles no-argument constructors differently.
Claims that a non-static inner class has no no-argument constructors.
2014-12-08 15:25:59 -05:00
Jim Blake
75fff3ee54 Remove call to deprecated JUmitMatchers method. 2014-12-08 11:25:34 -05:00
Jim Blake
4b71c1d6bb VIVO-778 Refactor the connections to the TBox reasoner.
Replace PelletListener with a TBoxReasonerModule in the Application.
   The reasoner will be accessible only through here, not as a context attribute or through the WebappDaoFactory.
Split out the initialization of the TBox reasoner from SimpleReasonerSetup.
Break out the filtering of TBox changes into a ConfiguredReasonerListener.
Refactor the threading logic into a BasicTBoxReasonerDriver.
   Add a factory for creating VitroBackgroundThreads in an Executor.
Isolate the actual reasoner into a TBoxReasoner implementation. In this case, PelletTBoxReasoner.
Combine the consistency flag, error flag, explanation, and running status into one TBoxReasonerStatus object.
2014-12-08 10:54:07 -05:00
Tim Worrall
b8cb95d252 VIVO-922: updates for new faux listing functionality. New controller, template and js file, updated web.xml and site admin page, and updates to the all.properties 2014-12-05 16:57:09 -05:00
Jim Blake
1c66271101 VIVO-778 Restructure the driver and connect the plumbing properly.
Replace PelletListener with BasicTBoxReasonerDriver, and associated classes.
Run the background thread from an ExecutorService.
Since nobody was using the FOREGROUND flag, and since its logic was flawed, skip it.

Make TBoxReasonerModule a module on the Application. Make the reasoner status available through the module.
Initialize it in startup_listeners.txt
Create a concrete class for PelletTBoxReasonerModule, and configure it in applicationSetup.n3

Get rid of PelletReasonerSetup.

Make it so the ExecutorService in BasicTBoxReasonerDriver uses a VitroBackgroundThread.,
2014-12-03 18:01:37 -05:00
Jim Blake
fb97bae6af VIVO-778 Connect the plumbing properly.
Make TBoxReasonerModule a module on the Application. Make the reasoner status available through the module.
Initialize it in startup_listeners.txt
Create a concrete class for PelletTBoxReasonerModule, and configure it in applicationSetup.n3

Get rid of PelletReasonerSetup.

Make it so the ExecutorService in BasicTBoxReasonerDriver uses a VitroBackgroundThread.,
2014-12-03 16:36:26 -05:00
Jim Blake
3d65a708b7 VIVO-778 Some renaming and moving. 2014-12-03 10:44:28 -05:00
Jim Blake
0c46f1d14e VIVO-778 Let the listener hold the change set. 2014-12-03 10:40:55 -05:00
Jim Blake
6bb8987d9d VIVO-778 Accumulate the TBox changes in a change set object. 2014-12-03 10:18:03 -05:00
Jim Blake
24bce9ff67 VIVO-778 Wild restructuring
Create TBoxChanges, createTBoxReasonerDriver, delete PelletListener, deal with repercussions all over.
2014-12-03 09:46:25 -05:00
Jim Blake
4e15695281 VIVO-778 Break out just the task of building the pattern list. 2014-12-02 14:22:58 -05:00
Jim Blake
d513dcf9ae VIVO-778 Break out just the task of syncing the inference model to the reasoner model. 2014-12-02 14:22:34 -05:00
Jim Blake
370df0b7ec VIVO-778 Extract ConfiguredReasonerListener from PelletListener.
Separate the filtered listener from the reasoner driver.
2014-11-26 16:31:07 -05:00
Jim Blake
85b9067eee VIVO-778 Separate PelletReasonerSetup from SimpleReasonerSetup. 2014-11-26 16:30:57 -05:00
Jim Blake
10e081c378 VIVO-778 Clean up ObjectPropertyStatementPattern
Rename to ReasonerStatementPattern, move to a new package and refactor.
2014-11-26 16:30:45 -05:00
Jim Blake
21727afd13 VIVO-778 Extract ConfiguredReasonerListener from PelletListener.
Separate the filtered listener from the reasoner driver.
2014-11-26 16:29:59 -05:00
Jim Blake
e0abd88ac2 BOGUS - add a TBoxReasonerSmokeTest at startup to insure that the generated inferences don't change by my actions. 2014-11-26 11:38:13 -05:00
Jim Blake
ac5c73ef42 VIVO-778 Separate PelletReasonerSetup from SimpleReasonerSetup. 2014-11-26 11:25:42 -05:00
Jim Blake
468a7214fe VIVO-778 Clean up ObjectPropertyStatementPattern
Rename to ReasonerStatementPattern, move to a new package and refactor.
2014-11-26 11:16:17 -05:00
Tim Worrall
4da345d843 Merge branch 'feature/fauxEditing' of https://github.com/vivo-project/Vitro into feature/fauxEditing 2014-11-20 10:58:04 -05:00
Tim Worrall
6e212e2889 VIVO-724: minor clean up of verbose property display. 2014-11-20 10:57:46 -05:00
Jim Blake
e79ace9d55 VIVO-774 Show correct property name
Also, pre-populate the custom entry generator if the base property has one.
2014-11-19 17:03:13 -05:00
Jim Blake
474b0abb44 VIVO-774 Fix display of unpopulated properties
Unpopulated properties with no domain URI were not recognized as faux properties
Use the faux property display name instead of the base property name.
2014-11-19 15:55:56 -05:00
Jim Blake
dfb9b7517e VIVO-774 When merging property lists, distinguish faux property from its base.
Merging list of populated properties with all possible properties,
   we don't want to consider two properties equivalent just on the basis of base URI and label (domainPublic)
Why was this previously considered to be a good thing?
2014-11-19 12:13:19 -05:00
Jim Blake
ef6f92539f Merge branch 'develop' into feature/fauxEditing 2014-11-18 11:56:52 -05:00
Tim Worrall
adf04bd2be VIVO-900: on data property hierarchy, range class should be range data type 2014-11-18 10:56:02 -05:00
Tim Worrall
3cc87ba0c6 VIVO-916: fix menu item title so that it includes the linkText variable 2014-11-18 10:22:13 -05:00
Tim Worrall
9ce4b1e275 some very minor jsp cleanup 2014-11-18 10:10:22 -05:00
Jim Blake
61eb57ca5d VIVO-907 Create the TripleStoreQuirks interface
Use it to handle the odd behavior that a particular triple store might have.
In this case, the odd behavior is that TDB mangles XMLSchema#nonNegativeInteger to XMLSchema#integer in literal types.
2014-11-17 13:21:36 -05:00
Jim Blake
546e27c15a VIVO-907 Migrate away from ModelMaker interface.
Use RDFService instead.
2014-11-17 13:18:13 -05:00
Jim Blake
3022155988 VIVO-906 fix bug with multiple closures on content RDFService.
DocumentModifiers were calling close().
2014-11-14 15:33:05 -05:00
Jim Blake
1e6b66a12c VIVO-906 Explicitly configure the SearchIndexExcluders and DocumentModifiers. 2014-11-13 17:14:42 -05:00
Jim Blake
ebb31eb081 VIVO-906 Assemble application at runtime.
Create an object to represent VitroHomeDirectory
Instantiate TripleSources, FileStorage, etc, based on the config file.
2014-11-13 17:11:11 -05:00
Jim Blake
e3dca6a699 VIVO-906 Create the TripleSource hierarchy.
SingleSourceDataStructuresProvider becomes TripleSource
DataStructuresProvider becomes CombinedTripleSource
2014-11-13 17:06:05 -05:00
Jim Blake
d18c9a38ca Stop 'deprecated' messages from JUnit imports. 2014-11-09 16:22:25 -05:00
Jim Blake
2fa9583569 Merge branch 'develop' into feature/fauxEditing
Conflicts:
	webapp/src/edu/cornell/mannlib/vitro/webapp/utils/configuration/ConfigurationBeanLoader.java
	webapp/src/edu/cornell/mannlib/vitro/webapp/utils/configuration/ConfigurationRdfParser.java
	webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/Critical.java
2014-11-09 16:14:48 -05:00
Jim Blake
72b86bd4d5 Improve handling of critical sections
Use LockableOntModel, etc., instead of Critical.
2014-11-09 16:05:06 -05:00