EDIT

minor

Add missing type information to UuidAndTitleCache object for search
results #5700

• fixes NPE

fix #5672

Merge branch 'hotfix/3.12.3' into develop

Conflicts:
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImpl.java
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceSearchTest.java

fix #5538

check for empty excludeUuid list

#4962 using LEFT FETCH JOIN for ranks and sec fixed problems and improves performance

organizing imports

Upgrade to hibernate 5 with persistence tests running #4716

#4313 implementing full stack of methods to expose TaxonNodeAgentRelations via remote controllers

#4962 commenting performance measure print-out via System.err

#4962 avoiding bean initialization in getChildNodesAtRank() as much as possible - performance improvement

#4313 relationship type as additinal filter option for TaxonNodeAgentRelation services

#4313 implementing full stack of methods to expose TaxonNodeAgentRelations throught the AgentController with filter options

fixing #4878

#4313 implementing full stack of methods to expose TaxonNodeAgentRelations via remote controllers

Revert "minor"

This reverts commit 64367d007ba404e037ccc2b6794b46c4f1f321bc.

minor

fixing getUUIDAndTitleCache for Classification and excluding taxa

fixing broken pager mechanism for listRankSpecificRootNodes() and improving test coverage

fix listRankSpecificRootNodes behavior for ranks in between and some
additional tests

add some tests for rankSpecificRootNodes, related to #2778

avoiding LEFT OUTER JOIN by splitting query in two

moving UuidAndTitleCache from model to persistence. #4799

added id to uuidAndTitleCache #4799 (bugfix)

added id to uuidAndTitleCache

delete the embedded class UuidAndTitleCacheOfAcceptedTaxon

fix search for common names in editor and minor

for infrageneric unranked rank adding unranked
fixing bug with deletion of names and homotypicalGroups

for testing

add taxonNode to session in countByIdentifier

improve byIdentifer service

missing persistence changes for findByIdentifier

latest changes for findByIdentifier service

changes in service layer for fixes in bulg editor and search for misapplied names and common names in editor

fix #4450

adapted tcs rdf and xml import, using apache jena for rdf import
tcs import for caryophylales
minor

minor

fixing #4273 (java.lang.ClassCastException in TaxonDaoHibernateImpl.countTaxaByCommonName() breaks taxon search) and most probably also other CommonName search related tickets

remove some comments and non-Javadocs

start bugfixing and refactoring sortindex handling in TaxonNode

adapt the service method loadChildNodesOfTaxonNode
with param recursive choose whether you get only the children of the node or the children of the children ...

Changed limits to INTEGER, so it is possible to nullify these parameters if needed

• show infraspecific taxa in Palmweb theme only if there are any
  • fixed output (taxon and NOT taxa if only one sub species present)

*added Test for service method: getTaxonOfAcceptedTaxaByClassification and countTaxonOfAcceptedTaxaByClassification
*fixed SQL Statement so it works with H2 DB

*added service layer method: countAllNodesForClassification
*improved performance CSVDemoExport

*Update of the CSVExport WS.
*fixed memory leak
*new service method to pull list of TaxonNode according to a given classification

add service to get all nodes of a classification

performance improvement for listChildNodes of a taxon

fixing #4112 (portal/taxon/{uuid}/accepted/{uuid} takes exceedingly much time in specific cases) and #2595 (portal/taxon/{uuid}/accepted/{uuid} producing too big data objects) this also solves the according issue mentioned in #3336 (Improve overall dataportal page loading performance)

implementing dao method listAcceptedTaxaFor, for #4112

fixing problems related to new taxon node structure

rootNode adaption for classification

revert r19380

change DescriptionBase.descriptionElements to DescriptionBase.elements #3841

fixed problem with deletion of nodes.

merging delete functionality into trunk

minor

implement sortIndex for TaxonNode and remove usedSynonym from addChildNode methods (#3508)

Merge trunk into CDM 3.3

workaround for the fact that hql is not able to parse boolean literals in the select list clause.

Improvements to TransmissionEngineDistribution, basic monitoring added and new service and dao methods for pageRankSpecificRootNodes()

Hibernate 4 migration. All test running except for SDDImport (Out of memory)

TaxonNodeServiceImpl : added clearing of relation sets
TaxonDaoHibernateImpl : added 'isOrphaned' field to hql query for building UuidAndTitleCache objects

calls to loadRankSpecificRootNodes() in tests and other classes adapted

loadRankSpecificRootNodes() extended, according test enabled and extended

fixing bug in getTaxonRelationships() for case directions = null

service for #3234 (implement cdm service method to collect SpecimensAndObservations via taxon)

adding method to find taxa by a list of given uuids

Implementations of functions which,

• find taxon names by title/uuid
• find taxons by uuid

bugfix for taxonDao.getAllRelationships

getAllRelationships reimplemented to match only relevant relationship classes,
Export generics include Transformer type

move inferred synonyms to service layer

fixing again the search for misapplied names. adapting the tests

Ticket #2648

fix for #2648

fixing bug in bugfix for #2648, also fixing tests

fixing bug in #2648: search for misapplied names implemented

bugfix (#2648)

test to reproduce bug in misapplied name search

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)

turning System.err into logger.debug

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

related to #2664 (Specimen maps are not shown in cyprus dev portal) - now the occurrence map is colored

inverse relations now are showing up, fixing #2609 (Implement Concept Relationships for Dataportal)

minor

bugfix for getAllRelationships()

minor

update taxon service (add some synonym delete functionality - still preliminary)

code cleaning

the query of prepareQuery always returns the type, if doNotReturnFullEntities is set

fixing #2274 ClassCastException in search

minor changes

remove import