Alexander Oppermann [Fri, 11 Apr 2014 12:56:24 +0000 (12:56 +0000)]
Added missing sort to method listTaxonChildNodeOf via comparator
Cherian Mathew [Thu, 10 Apr 2014 14:20:15 +0000 (14:20 +0000)]
ignore tests for release
Alexander Oppermann [Thu, 10 Apr 2014 14:19:40 +0000 (14:19 +0000)]
*added Test for service method: getTaxonOfAcceptedTaxaByClassification and countTaxonOfAcceptedTaxaByClassification
*fixed SQL Statement so it works with H2 DB
edit-jenkins [Thu, 10 Apr 2014 13:51:08 +0000 (13:51 +0000)]
[maven-release-plugin] prepare for next development iteration
edit-jenkins [Thu, 10 Apr 2014 13:51:05 +0000 (13:51 +0000)]
[maven-release-plugin] prepare release cdmlib-parent-3.3.2
Alexander Oppermann [Thu, 10 Apr 2014 12:51:15 +0000 (12:51 +0000)]
*added service layer method: countAllNodesForClassification
*improved performance CSVDemoExport
Andreas Müller [Thu, 10 Apr 2014 12:17:49 +0000 (12:17 +0000)]
log childIndex is null
Andreas Müller [Thu, 10 Apr 2014 12:16:48 +0000 (12:16 +0000)]
fix logging for taxa used multiple times in addParentChild
Alexander Oppermann [Thu, 10 Apr 2014 09:26:30 +0000 (09:26 +0000)]
*Update of the CSVExport WS.
*fixed memory leak
*new service method to pull list of TaxonNode according to a given classification
Andreas Müller [Wed, 9 Apr 2014 15:35:22 +0000 (15:35 +0000)]
new doubtful relationships for BM import
Andreas Müller [Wed, 9 Apr 2014 15:29:29 +0000 (15:29 +0000)]
handle inverse and doubtful taxon relations in Berlin Model import
Andreas Müller [Wed, 9 Apr 2014 14:36:12 +0000 (14:36 +0000)]
change log4j properties
Andreas Müller [Wed, 9 Apr 2014 14:27:53 +0000 (14:27 +0000)]
fix GeoServiceTest
Cherian Mathew [Wed, 9 Apr 2014 14:27:35 +0000 (14:27 +0000)]
DatabaseServiceHibernateImpl : added important fixme
CdmPersistentDataSource : clean up
CdmPersistentXMLSource : added context path enum for remoting
CdmApplicationUtils : variable change
Andreas Müller [Wed, 9 Apr 2014 12:43:42 +0000 (12:43 +0000)]
fix country mapping
Andreas Kohlbecker [Wed, 9 Apr 2014 09:09:01 +0000 (09:09 +0000)]
loading annotations with distribution elements - #3348 (should annotations always be returned for cdm instances? [DISCUSS])
Andreas Kohlbecker [Tue, 8 Apr 2014 15:05:38 +0000 (15:05 +0000)]
reverting r20536 , related to #4174 (simple search for Micrasterias* causes LazyInitializationException)
Andreas Kohlbecker [Tue, 8 Apr 2014 15:05:33 +0000 (15:05 +0000)]
fixing #4174 (simple search for Micrasterias* causes LazyInitializationException)
Katja Luther [Tue, 8 Apr 2014 12:24:15 +0000 (12:24 +0000)]
add service to get all nodes of a classification
Andreas Müller [Tue, 8 Apr 2014 10:44:22 +0000 (10:44 +0000)]
remove isFigure from getImageMedia
Andreas Kohlbecker [Mon, 7 Apr 2014 15:06:47 +0000 (15:06 +0000)]
fixing TYPEDESIGNATION_INIT_STRATEGY to avoid LIEs
Andreas Kohlbecker [Mon, 7 Apr 2014 15:06:43 +0000 (15:06 +0000)]
fixing NAMERELATIONSHIP_INIT_STRATEGY to avoid LIEs
Andreas Kohlbecker [Mon, 7 Apr 2014 14:17:24 +0000 (14:17 +0000)]
fixing #4176 (Dataportal shows wrong symbols for non-symmetric taxon relationships)
Cherian Mathew [Fri, 4 Apr 2014 15:38:05 +0000 (15:38 +0000)]
added comments / javadoc
Andreas Kohlbecker [Fri, 4 Apr 2014 10:30:04 +0000 (10:30 +0000)]
fixing bug in NameServiceImpl (toNameRelations never could be listed) #4175 (some name relations (basionym) missing)
Cherian Mathew [Fri, 4 Apr 2014 10:25:58 +0000 (10:25 +0000)]
adding temprary workaround for implementing remote controller
Andreas Kohlbecker [Fri, 4 Apr 2014 09:23:29 +0000 (09:23 +0000)]
extending the title and name cache auto initializer by relationsFromThisName - #4174 (simple search for Micrasterias* causes LazyInitializationException)
Andreas Kohlbecker [Fri, 4 Apr 2014 09:23:24 +0000 (09:23 +0000)]
logging json serialization
Cherian Mathew [Fri, 4 Apr 2014 08:21:08 +0000 (08:21 +0000)]
TestDatabase / CdmPersistentDataSourceTest / CdmApplicationUtils : updated as per Cdm Source refactoring
ICdmDataSource : moved generic methods to super interface ICdmSource
CdmPersistentDataSource : refactored by spliting the utility part to CdmPersistentXMLUtils and the jDom elementpart to CdmXMLPersistentSource
CdmDataSourceBase : implementing databse check methods
Cherian Mathew [Fri, 4 Apr 2014 08:16:44 +0000 (08:16 +0000)]
added extra checks when parsing jdbc connection url
Cherian Mathew [Fri, 4 Apr 2014 08:07:24 +0000 (08:07 +0000)]
moved pretty format from CdmPersistentDataSource to XmlHelp
Cherian Mathew [Fri, 4 Apr 2014 08:05:32 +0000 (08:05 +0000)]
New classes / interface to refactor the CdmDataSource object to be more generic to allow for remoting sources
ICdmSource / CdmSource : Base class / interface which represent any CDM Source
ICdmPersistentSource : interface which represents a persistent cdm source
CdmPersistentXMLSource : class which represents a cdm persistent source in the form of a jDom xml element
Cherian Mathew [Fri, 4 Apr 2014 07:58:51 +0000 (07:58 +0000)]
CdmPersistentSourceUtils : new class which contains all functionality to manage the persistent cdm sources config (taken from CdmPersistentDataSource)
CdmSourceException : wraps around exceptions when interacting with the Cdm Sources
Andreas Kohlbecker [Thu, 3 Apr 2014 16:47:36 +0000 (16:47 +0000)]
fixing #4172 (NPE in ext/edit/mapServiceParameters/taxonOccurrencesFor/{uuid})
Cherian Mathew [Thu, 3 Apr 2014 13:58:49 +0000 (13:58 +0000)]
updated IPrimer service settings
Cherian Mathew [Thu, 3 Apr 2014 13:57:45 +0000 (13:57 +0000)]
added methods to get schema version and check if db is empty
house-keeping and adding javadoc
Patric Plitzner [Wed, 2 Apr 2014 09:35:28 +0000 (09:35 +0000)]
- added service method to retrieve a map of SingleReads and their "hosting" Sequences
Andreas Kohlbecker [Tue, 1 Apr 2014 15:22:02 +0000 (15:22 +0000)]
fixing initstrategy for #3182 (roteliste: categorical data does not show up)
Patric Plitzner [Tue, 1 Apr 2014 06:50:25 +0000 (06:50 +0000)]
- added two NewInstance() methods to Amplification
- added getUuidAndDescriptions to IAmplificationService and DAO
Katja Luther [Mon, 31 Mar 2014 10:25:31 +0000 (10:25 +0000)]
add tests for treeIndex and deletion of nodes
Patric Plitzner [Mon, 31 Mar 2014 09:52:29 +0000 (09:52 +0000)]
- bundled services for molecular data in one package
- added more tests
Alexander Oppermann [Mon, 31 Mar 2014 08:25:42 +0000 (08:25 +0000)]
Generate CSV file from pojo
Alexander Oppermann [Mon, 31 Mar 2014 08:24:12 +0000 (08:24 +0000)]
Generate CSV file from pojo
Patric Plitzner [Mon, 31 Mar 2014 08:08:46 +0000 (08:08 +0000)]
- added IAmplificationService and ISequenceService
- added service methods to move derivates from one to another
- added test for move method
Andreas Kohlbecker [Sat, 29 Mar 2014 20:50:59 +0000 (20:50 +0000)]
performance improvement for listChildNodes of a taxon
Andreas Kohlbecker [Fri, 28 Mar 2014 17:39:15 +0000 (17:39 +0000)]
fixing #4168 (performance problem with DescriptionListPortalController.getDescriptionElementsForTaxon())
edit-jenkins [Fri, 28 Mar 2014 08:53:38 +0000 (08:53 +0000)]
[maven-release-plugin] prepare for next development iteration
edit-jenkins [Fri, 28 Mar 2014 08:53:32 +0000 (08:53 +0000)]
[maven-release-plugin] prepare release cdmlib-parent-3.3.1
p.kelbert [Thu, 27 Mar 2014 14:27:44 +0000 (14:27 +0000)]
debug collection and institution for excel import
Andreas Kohlbecker [Thu, 27 Mar 2014 12:51:48 +0000 (12:51 +0000)]
cdmlib part for #3766 (Check if specimenOrObservation.kindOfUnit is shown correctly in data portal)
Andreas Kohlbecker [Thu, 27 Mar 2014 12:34:53 +0000 (12:34 +0000)]
adding missing statisticalValues.* to init strategy. fixes #4165 (algaterra: values of specimen descriptions not shown)
Andreas Kohlbecker [Thu, 27 Mar 2014 12:02:54 +0000 (12:02 +0000)]
cdmlib part of #3576 (Adapt CdmServer and Dataportal to new naming of CategoricalData.stateData)
Andreas Kohlbecker [Thu, 27 Mar 2014 12:02:51 +0000 (12:02 +0000)]
lowering log level
Andreas Kohlbecker [Thu, 27 Mar 2014 12:02:48 +0000 (12:02 +0000)]
renaming protected setter to setStateData, see #2923 (Rename CategoricalData.states collection to stateData)
Alexander Oppermann [Thu, 27 Mar 2014 11:08:57 +0000 (11:08 +0000)]
deactivated controller due to urgent release and unfinished business with a serious memory leak
Patric Plitzner [Wed, 26 Mar 2014 14:36:54 +0000 (14:36 +0000)]
- added moveSequence() and moveDerivate() to occurrence service
Patric Plitzner [Wed, 26 Mar 2014 09:14:52 +0000 (09:14 +0000)]
- replaced BasicHttpParams with the default params of DefaultHttpClient (SyncBasicHttpParams) which are already initialised with default values
Andreas Kohlbecker [Wed, 26 Mar 2014 08:40:31 +0000 (08:40 +0000)]
solving TODO: using AbstractPagerImpl.hasResultsInRange() in dao method
Andreas Kohlbecker [Wed, 26 Mar 2014 08:40:27 +0000 (08:40 +0000)]
missing @Override
Andreas Kohlbecker [Wed, 26 Mar 2014 08:40:24 +0000 (08:40 +0000)]
contoller methods with return type List should always return a list, even if it is empty
Andreas Kohlbecker [Tue, 25 Mar 2014 22:44:50 +0000 (22:44 +0000)]
removing the deprecated method TaxonPortalController.doGetNameTypeDesignations() for #2280 (Stop using portal/taxon//bin/zsh/nameTypeDesignations)
Patric Plitzner [Tue, 25 Mar 2014 16:01:19 +0000 (16:01 +0000)]
- added removeSingleRead() method to Amplification
Andreas Kohlbecker [Tue, 25 Mar 2014 15:31:24 +0000 (15:31 +0000)]
fixing #4151 (AdvancedBeanInitializer causes problems when initializing taxonnode hierarchies)
Patric Plitzner [Mon, 24 Mar 2014 13:22:42 +0000 (13:22 +0000)]
- added timeout parameter to isServiceAvailable() method
Andreas Kohlbecker [Fri, 21 Mar 2014 20:19:48 +0000 (20:19 +0000)]
avoiding recurive calls, replaced by while loop
Andreas Kohlbecker [Fri, 21 Mar 2014 16:55:32 +0000 (16:55 +0000)]
avoiding NPE
Andreas Kohlbecker [Thu, 20 Mar 2014 15:43:35 +0000 (15:43 +0000)]
bug fix: list and page REST services must return List or page objects, not ModelAndView
Alexander Oppermann [Thu, 20 Mar 2014 14:29:56 +0000 (14:29 +0000)]
checklist webservice optimized
*integrated a ModelAndView for file downloads
*integerated a ProgressMonitor for csv export
*export is threaded
*extended ProgressMonitor with origin property
Andreas Kohlbecker [Thu, 20 Mar 2014 13:56:00 +0000 (13:56 +0000)]
adating test to modified number of taxa
Andreas Kohlbecker [Thu, 20 Mar 2014 13:29:10 +0000 (13:29 +0000)]
refactoring taxon controllers and thus solving #2595 (portal/taxon/{uuid}/accepted/{uuid} producing too big data objects)
Katja Luther [Thu, 20 Mar 2014 12:50:06 +0000 (12:50 +0000)]
#4114 sort order in taxon navigator and adding that autonyms could be whether infraspecific or infrageneric (Art. 22.3 and 26.3)
Andreas Kohlbecker [Thu, 20 Mar 2014 12:31:10 +0000 (12:31 +0000)]
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)
Andreas Kohlbecker [Thu, 20 Mar 2014 12:31:01 +0000 (12:31 +0000)]
implementing dao method listAcceptedTaxaFor, for #4112
Cherian Mathew [Thu, 20 Mar 2014 11:12:10 +0000 (11:12 +0000)]
added containsValue method to retrieve value object for maps
p.kelbert [Thu, 20 Mar 2014 10:42:53 +0000 (10:42 +0000)]
remove link to the apt file for the documentation. ie, there is no external documentation yet
p.kelbert [Thu, 20 Mar 2014 10:26:02 +0000 (10:26 +0000)]
add occurrence controler for the occurrence web-service
p.kelbert [Thu, 20 Mar 2014 10:22:47 +0000 (10:22 +0000)]
add new method for getting specimen and observation
p.kelbert [Thu, 20 Mar 2014 10:20:14 +0000 (10:20 +0000)]
add new webservice for exporting occurrences for a specific taxon uuid
definition in xml files (web-inf)
p.kelbert [Thu, 20 Mar 2014 10:19:36 +0000 (10:19 +0000)]
add new webservice for exporting occurrences for a specific taxon uuid
Andreas Kohlbecker [Wed, 19 Mar 2014 15:31:58 +0000 (15:31 +0000)]
fixing #4148 (problems with simple search)
Andreas Kohlbecker [Wed, 19 Mar 2014 10:40:01 +0000 (10:40 +0000)]
updating site doc by adding maven memory requirements and mentioning the requirement for maven 3
Andreas Kohlbecker [Mon, 17 Mar 2014 22:03:12 +0000 (22:03 +0000)]
cdmlib part of fix #4121 (Changing password does not work)
Andreas Kohlbecker [Mon, 17 Mar 2014 22:03:09 +0000 (22:03 +0000)]
additional method required to avoid problems which where due to a fix for ticket #3822 (see related commit for taxeditor)
Katja Luther [Mon, 17 Mar 2014 12:30:15 +0000 (12:30 +0000)]
fix compareTo for IdentifiableEntity
Patric Plitzner [Mon, 17 Mar 2014 08:58:41 +0000 (08:58 +0000)]
- renamed method
Patric Plitzner [Mon, 17 Mar 2014 08:36:17 +0000 (08:36 +0000)]
- added reference to trac ticket
Patric Plitzner [Mon, 17 Mar 2014 07:53:54 +0000 (07:53 +0000)]
- made default constructor protected due to a hibernate problem (see https://stackoverflow.com/questions/
7273125/hibernate-envers-and-javassist-enhancement-failed-exception)
Patric Plitzner [Mon, 17 Mar 2014 07:52:42 +0000 (07:52 +0000)]
- fixed a bug in the automated setting of the string length
Patric Plitzner [Mon, 17 Mar 2014 07:51:06 +0000 (07:51 +0000)]
- added javadoc
Patric Plitzner [Mon, 17 Mar 2014 07:50:19 +0000 (07:50 +0000)]
- added test for baseUnit() method
Patric Plitzner [Mon, 17 Mar 2014 07:44:46 +0000 (07:44 +0000)]
- added IPrimerService and IPrimerDao with the corresponding implementations
- interface supports the retrieval of UuidAndTitleCache lists for all primers in the DB
Alexander Oppermann [Mon, 17 Mar 2014 07:19:16 +0000 (07:19 +0000)]
Removed Java 1.7 specific function due to backwards compatability
Andreas Müller [Sat, 15 Mar 2014 09:21:54 +0000 (09:21 +0000)]
fix missing idInVocabulary for countries; implement country mapping for EditGeoService (#3452, #3651)
Andreas Müller [Sat, 15 Mar 2014 01:36:29 +0000 (01:36 +0000)]
fix missing idInVocabulary for countries; implement country mapping for EditGeoService (#3452, #3651)
Andreas Müller [Fri, 14 Mar 2014 20:54:57 +0000 (20:54 +0000)]
minor
Andreas Müller [Fri, 14 Mar 2014 20:52:26 +0000 (20:52 +0000)]
add NomStatus vocabulary for ICZN #4085
Andreas Müller [Fri, 14 Mar 2014 20:46:05 +0000 (20:46 +0000)]
latest changes to Specimen Excel Import
Andreas Müller [Fri, 14 Mar 2014 19:46:02 +0000 (19:46 +0000)]
Added IsoParaType to SpecimenTypeDesignationStatus
Andreas Müller [Fri, 14 Mar 2014 19:39:15 +0000 (19:39 +0000)]
Added IsoParaType to SpecimenTypeDesignationStatus
Andreas Müller [Fri, 14 Mar 2014 16:46:00 +0000 (16:46 +0000)]
fix compilation bug in MarkupTransformer