EDIT

fixing testing context in persitence and fixing test

reverting last commit - will be committed again later

merging in git branch 'methodSecurityExpressions' and resolving conflict in SecurityTest.java

add methods for list/countTaxonDescriptionMedia

security stuff

harmonizing method names

ready to be reintegrated into trunk

fixing some test, but also ignoring some since i am running out of time - sorry for that

add html tagged full title

move inferred synonyms to service layer

add html tagged title cache generation for NonViralNames

tabs to spaces

remove imports

Merging r13268 through r14040 from trunk/cdmlib into branches/cdmlib-unitils3

all tests running sucessful, however unitil is still patched to not use jdbc batch mode

h2 as test alternative database & potentially fixing #2100 (Fix tests not running in suite)

bugfix for stateData.modifyingText (#2760)

fixing again the search for misapplied names. adapting the tests

test cases commented

Ticket #2648

more adapting xml datasources to unitils 3.3

ignoring test

test modified to reproduce bug in #2648 (search for misapplied names implemented)

adapting xml datasources to unitils 3.3

add a test for a search only for misapplied names

fix for #2648

update für andreas

fixing transaction problems

test to reproduce bug in #2648 (search for misapplied names implemented)

whitespace and minor changes

fixing bug associated with getTaxaByCommonName(); benchmarking taxa by common name hql vs lucene

hibernate fulltext search & refactoring getTaxaByName*() method headers

countTaxaByName harmonized with find method (replace Class <? extends TaxonBase> parameter with boolean parameters for synonyms, taxa and misapplied names)

changes for bugs and problems in search for misapplied names (#2648)

add includeEmpty vocs (#2704)

implement getTermVocabulariesByTermClasses also for subclasses (#2704)

adapt the search to be able to find misapplied names: to include misapplied names use the new configurator attribute doIncludeMisappliedNames

remove imports

added "hasMarker" to AnnotatableEntity

implemented tests for marker scope on descriptions

remove deprecated call for description.setAddSource

upgrading unitils to v3.2 (tests not yet working)

Implement correct mapping between TaxonNameBase and TypeDesignationBase and add delete method for type designations to NameService (#2396, #2647)

test for persisting description.scope

moving TaggedText classes and removing deprecated tagedName methods

cleaning up cache strategies

renamed getTaggedName -> getTaggedNameDeprecated

Refactoring nameCacheStrategy. Use same method for both caches (tagged + string)

change name of ReferencedMedia to ReferencedMediaBase (#2381)

added saveTypeDesignation Test (but is not running for some reason)

countByTitle() method for IIdentifiableService

splitting PolytomousKeyNodeService from PolytomousKeyService & more methods for IdentificationKeyService

further UserDao tests

first tests for list find methods for user and group services (#2283 and #2284).

minor

testGetTaxaByNameForEditor() added

minor changes

Reverting the RightsTerm -> RightsType change (see #1306). This is a model change and needs updates to the schema. We will transfer this into a branch.

comment syso's

created OccurrenceDaoHibernateImplTest class for #2232

minor

bugfix for descriptionBase.clone #2234

replace deprecated methods with new ones #2176

remove duplicate for Argentina

added a test case for polytomous keys

merge 3.0.2 to trunk

Implement all name relationships search

getting all SpecimenOrObservationBases for a Taxon

correcting utf8 chars

sdd import matches descriptions to existing taxa

re-integrating branches/cdmlib/oai-pmh up to revision 10059

merging /branches/cdmlib/SPRINT-Chichorieae1/ to trunk

ignoring test TaxonDaoHibernateImplTest.java

Merging cdmlib-persistence to trunk; pesi. Merge rev 8083-8429.

added a new method to IMediaService that will return the complete ImageInfo object and not just the metadata. Removed persistence layer from call stack of IMediaService methods that talk to ImageMetaData.

merging PESI brach into trunk

merge cate-development2 branch with trunk

bugfix for TaxonNode.getParent == null

removed System.err.println()

removed System.err.println()

preparing for hibernate-c3p0 & commenting out all System.err.println

minor

new test for the delete method of TaxonNameDao

#1390

Updated ICdmEntityDao replace(T x, T y) and refresh(T t, LockMode lockMode, List propertyPaths) and added methods to IAnnotationDao

Added an IIdentificationKeyDao to query across all identification key types

Refactored free text search to re-use the same code for all identifiable entities. Switched to StandardAnalyzer to include indexing of numbers. Removed redundant code from taxonDao.delete() method (as included entities deleted using hibernate's cascade method)

Refactored methods in VersionableDaoBase etc + added Query-By-Example for CdmEntityDaoBase

minor

revert the model changes...

rightsterm -> rightstype ticket #1306

test for getTaxaByCommonName added

Added methods and tests to recover changes to data

refactoring the references for imports...