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CDM Platform Roadmap Archive

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Current Roadmap

see CdmPlatformRoadmap

CDM Platform 5.11 (released Nov 15th, 2019)

Issues: 39

Downloads: Ask the edit team for backups of this version

What's new?

  • - Data Model
    • Added count parameter for statics during data aggregation of categorical (structured descriptive) data
    • Added ORCID identifier to persons
    • Added CDM source links (sources may link to other information in the same CDM instance)
  • - Data Portal
    • Fixed polytomous key display for key parts linked from multiple places
    • Fix label formatting for specimen with missing collection identifier in specimen tables
    • Fixing problem with names having multiple nomenclatural status
  • - Import/Export
    • ABCD:
      • Fix collector and field number handling for derived units missing this data (but available in field unit record)
  • - CDM Library
    • Better parsing for infrageneric autonyms with authors
    • Imporved distribution and descriptive data aggregation
  • - CDM Server
    • Fix memory leaks
  • - TaxEditor
    • Taxon search: new filter to search only for published taxa
    • Terms:
      • Tree editor for Named Areas, Ranks and Distribution Status available (to define user defined term collections and orders, including cross-vocabulary collections) - usage of such collections will be implemented in future releases
    • Taxon/Name details view
      • Nomenclatural code edition editable for rule considered (nomenclatural status and name relationships)
      • Rule considered and nomenclatural code editon visibility configurable (serverside and local)
      • Minor changes in ordering of misapplied name details view
    • Person details view
      • ORCID editable
    • Taxon navigator:
      • Taxon node doubtful flag editable via context menu
      • Rename view to "Taxon Navigator" (regression in one of the last releases)
      • Refresh problem after editing classfication label or adding child taxon to classification
      • Rename open-in for Taxon Node (Wizard) to ... Dialogue
      • Reorder and rename import menu (items)
    • Import/Export:
      • Multiple fixes for file based ABCD import
      • Fix for DwC-A export
    • Factual Data View
      • Visibility of "modifier" and "modifying text" is configurable now
    • Distribution Editor
      • Default source also used when creating an additional source for an existing source
    • User administration
      • Better error handling for user and group names with not allowed characters

# Subject Status
  cdm 4 Collapse all/Expand all
8466 Delete FeatureTree tables Closed
8625 Add count parameter to StateData Closed
8628 Add ORCID as person identifier Closed
8673 Allow OriginalSource to link to other CDM objects Closed
  cdm-dataportal 3 Collapse all/Expand all
8610 tagged_text_extract_nomstatus() fails handling more than one status Closed
8596 Add a list of descriptions to the taxon page Closed
8622 Missing specimen Identifier leads to empty brackets in portal Closed
  cdmadapter 2 Collapse all/Expand all
8533 missing collector and fieldnumber in abcd import Closed
8632 ABCD retrieves DNA Sample from Biocase Provider even if it is not selected in the import configuration Closed
  cdmlib 3 Collapse all/Expand all
8253 Authors for genus autonyms Closed
8651 Unify description aggregation methods (distribution and structured descriptive data) Closed
8676 TaxonDaoHibernateImpl.countTaxaByName misses parameter authorship Closed
  cdmlib-remote 1 Collapse all/Expand all
8570 PolytomousKeyNode.otherNode missing in REST service response Closed
  cdmserver 2 Collapse all/Expand all
8674 configure cdm-server docker image to run with jemalloc Closed
5048 cdm-server causes unusual high native memory consumption for jvm Closed
  taxeditor 24 Collapse all/Expand all
8653 NullPointerException (NPE) when focusing Taxion Name Editor Resolved
7143 Finish not enabled when unprotecting titleCache in new Person dialog Closed
7457 E+M: Allow filtering for only published in search Closed
8685 Exception when calling DwC-A Export Closed
8410 Add nomenclatural code edition to ruleConsidered in TaxEditor Closed
8470 Handle username constraints in user and group editing Closed
8568 improve performance for term and vocabulary preference pages Closed
8572 Rule considered configurable Closed
8581 Naming inconsitency: Taxon Navigator or Taxonomic Tree? Closed
8582 Taxon Navigator: Classification label not refreshed & new taxa not visible Closed
8613 For distribution editor default reference should be used also when new source is created Closed
8584 Appended phrase should be shown on top level for misapplied names Closed
8609 Rename Taxon Node context menu entry Open in .. -> Taxon Node Wizard Closed
8642 Add tree editor for rank, NamedArea and PresenceAbsence Closed
8664 SQLGrammarException when opening Specimen selection Closed
8667 Make Person.orcid editable in TaxEditor Closed
8630 ClassCastException when ABCD import has finished Closed
8631 ABCD import fails to put new taxa into the classification, create mediaspecimens, etc Closed
8648 Simplify name details view configuration Closed
8634 NullPointerException (NPE) in PreferencesUtil.getLocalAbcdImportConfigurator() on starting ABCD import Closed
7019 sort import menu Closed
8226 make modifiers for description elements configurable Closed
8486 Indicating doubtful state in navigator and add set-doubtful to Set-Flags menu Closed
8652 disentangle confusion when connecting to development cdm instance fails Closed

CDM Platform 5.10 (released Sep 23rd, 2019)

Issues: 30

Downloads: Ask the edit team for backups of this version

What's new?

  • - Data Portal
    • Taxon section in name page can be suppressed via settings.
    • Bug fix of a regression related to the display of DOIs and publication reference links.
  • - Import/Export
    • CDM light export:
      • type designation export differs between textual and specimen type designation
    • Biocase search:
      • add possibility to search for Higher Taxon
  • - CDM Library
    • Bugfixes and code maintenance
      • Providing the default user role USER_MANAGER to all databases.
  • - TaxEditor
    • Bugfix for swap taxon and synonym
    • Further improvements to preference handling
    • Search dialogue for distribution areas works with abbreviations
    • Old taxeditor documentation made available.
  • - Web editor (Phycobank registration UI)
    • Name relations and nomencaltural status now offering fields to mention the nomenclatural code edition.
    • Layout and user experience (UX) issues in the UI have been solved (#8014, #8342, #8377).
    • Fixing important bug to prevent data loss and corruption (#8462, #8527)

# Subject Status
  cdm-dataportal 3 Collapse all/Expand all
8504 Name page: allow hiding the Taxon section via settings Closed
8565 external links and dois no longer showing up Closed
8594 registration search results page showing: cdm_compose_url(): missing pathParameter 0 for !uri_pattern Closed
  cdm-vaadin 8 Collapse all/Expand all
8014 Label wording im UI Name Editor Closed
8342 shift field Field number Closed
8376 RegistrationWorkingsetEditor: prevent clicking any futher buttons after the openting of a popup editor has been triggered Closed
8408 add nomenclatural code select to NomenclaturalStatusRow Closed
8409 add nomenclatural code select to NameRelationField Closed
8377 TypeDesignationsEditors: Delete must not be allowe before the workingset is saved Closed
8462 NoSuchElementException accessing Optional<RegistrationDTO> in RegistrationWorkingsetPresenter.findRegistrationInContext() Closed
8527 TaxonNameEdior: 'Validations' and 'Orthographocal corrections' are lost when editor is saved a second time Closed
  cdmlib 6 Collapse all/Expand all
8517 SpecimenOrObservation: data from protected titleCache missig in portal pages Resolved
8519 ROLE_USER_MANAGER missing in FirstDataInserter Closed
8505 ConfigFileUtil: turn all spring bean methods into not statical methods. Closed
8513 CdmUtils: remove MUST_EXIST_FILE and getResourceFolderSeperator() Closed
8425 FieldUnitDTO: remove taxonRelatedDerivedUnits Closed
8456 FieldUnitDTO: remove newInstanceMethod Closed
  cdmlib-remote 1 Collapse all/Expand all
8538 add text_l10n for TextualTypeDesignation.text to web service respones Closed
  taxeditor 12 Collapse all/Expand all
7321 multi-language textfields should not show empty text when there is text Closed
8034 Recently used references shows all references Closed
8092 set default for term and vocabulary selection preferences in selection wizard Closed
8123 Make available features a DB preference Closed
8489 Further issues for DB preferences Resolved
8335 Store character matrix table state as DB preference Closed
8386 Disable admin menu when not logged into a DB Closed
8488 Characters can not be added to feature trees Closed
8382 Local Supplemental Data Source Preferences should reflect the state of admin preferences Closed
8539 Add IndividualsAssociation when adding specimens to the character matrix Closed
8564 Link to PlatformDocumentation wiki page Closed
8350 Search dialog for named areas should work with abbreviations Closed

CDM Platform 5.9 (released Aug 29th, 2019)

Issues: 51

Downloads: TaxEditor, CDM Server, Data Portal

What's new?

  • - Data Model
    • Term structure improved to allow all types of relations between terms and to allow vocabulary independent term collections/graphs (partly implemented in TaxEditor)
    • Add state vocabulary for presence/absence of a biological structure
    • Improve structure for inapplicableIf handling in character trees used for descriptive data matrices/datasets and for indentification keys
    • Improve authority handling in data model (preparation only)
    • Allow certain patterns only as usernames (Latin letters, numbers, '_', '.' are allowed)
    • Doubtful (placement) flag for taxon nodes
    • List of nomenclatural code editions (e.g. Melbourne Code) additional to rule considered in nomenclatural status, name relationship and hybrid relationship
    • Fields added to allow externally managed terms and vocabularies (not yet in TaxEditor)
    • Fields for textual/verbatim type designation information
    • Possibility to add fixed markers/types to a description (e.g. to mark a description as a computed/aggregated description which should not be editable)
  • - Data Portal
    • Adapted to term structure changes in the data model.
    • Improved ordering of type designations in the name and taxon pages.
    • Harmonization and improvement of the specimen display in various parts of the portal, including better intra portal linking.
    • Performance improvement regarding to type designations.
    • Auto-zooming of maps has been fixed for different map projections.
    • Improved layout of the registration page to clearly show the nomenclatural act.
    • Classification tree horizontally automatically scrolls to active entry.
  • - Import/Export
    • CDM light export:
      • add textual/verbatim type designations
      • some minor adaptations
  • - CDM Library
    • Fix and improve polytomous key generation (to be used from descriptive data set, experimental feature)
    • Multiple improvements and bug fixes to web services
  • - TaxEditor
    • Add textual/verbatim type designations to details view
    • Use feature states for applicability of term nodes
    • Improvement and harmonization of serverside and local preferences
    • Update name in source data when changing an accepted taxon into a synonym (configurable)
    • Allow setPublish for subtree to include misapplied names, pro parte synonyms and exclude hybrids
    • Seperate term tree editor for each term type available
    • Warning if misapplied names or pro parte synonyms are used/linked from more then 1 other taxon.
    • Bugs.
      • fixed term order of term trees

# Subject Status
  cdm 12 Collapse all/Expand all
7099 Make CdmAuthority a persistable class Resolved
8429 Rename DeterminationEvent_Reference.setOfReferences_id Resolved
8180 Add property term "Presence/Absence" to CDM default terms Closed
4884 Update Reference_AUD.refType to allow NULL Closed
8441 Add FeatureState class Closed
8442 Add fields to handle external terms to DefinedTermBase or TermBase Closed
8454 Only allow certain patterns as username and groupname Closed
7470 Verbatim type designation information Closed
7957 Add types for taxon description (as EnumSet) Closed
8281 Doubtful flag for TaxonNode Closed
8398 Add nomenclatural code edition to ruleConsidered Closed
3972 Strictly validate username to not null and not empty Closed
  cdm-dataportal 11 Collapse all/Expand all
8502 taxa with doubtful flag lack proper formatting Resolved
8166 Adapt dataportal to term structure changes Closed
8402 ordering typedesignations in name and taxon page Closed
8418 specimens and occurrence links must not have a target=_blank attribute Closed
8406 specimens and occurrence code cleaning and harmonization Closed
8415 use /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup to speed up type designation retrieval Closed
8440 specimen accession numbers link to specimen page Closed
8430 maps zoom to wrong bbox with some layers Closed
8448 Maps settings > Bounding box inconsistent Closed
8449 improve layout of registration page to clearly show the nomencaltural act Closed
8495 classification tree horizontally scrolls to active entrty Closed
  cdmlib 8 Collapse all/Expand all
8437 ITermTreeService provides a list method which supports filtering by TermTree.termType, Resolved
3472 Update name in source data when changing an accepted taxon into a synonym Closed
7450 Allow setPublish for subtree to include misapplied names and pro parte synonyms Closed
8422 Make PolytomousKeyGenerator work (correctly) Closed
8482 java.lang.IllegalArgumentException: Collection is empty in DescriptionType.includesType(DescriptionType.java:151) Closed
8426 IndexOutOfBoundsException during serialization of RegistrationWorkingSet Closed
8404 Add update step list within updaters Closed
8446 Allow setPublish for subtree to filter for hybrids Closed
  cdmlib-remote 5 Collapse all/Expand all
8390 implement /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup Closed
8395 NullPointerException (NPE) in NameCatalogueController Closed
8434 Change FeatureTree contollers to TermTree controllers Closed
8414 occurrence controller code cleaning and harmonization Closed
8436 featureTree/* services should filter the termTrees by the TermType Feature Closed
  taxeditor 15 Collapse all/Expand all
8526 Swap synonym with accepted taxon does not work Resolved
8532 common name language selection is not selected Resolved
8389 Correct handling of default values with allowOverride=false Resolved
8135 Implement verbatim type information in TaxEditor Closed
8282 Implement placementDoubtful in TaxEditor Closed
8334 Move sources for type designations to details view Closed
8385 Open issues in DB preferences Closed
7597 Aggregate and persist descriptions on taxon level Closed
8235 Create separate menu for term tree editors for each term tree type Closed
8444 Show warning if misapplied names / pro parte synonyms are used more then once Closed
8475 Adapt applicable state detail view elements to FeatureState Closed
8480 Use DescriptionTypes for matrix descriptions Closed
8485 Add column groups to character matrix Closed
8447 Adapt setPublishForSubtree to new parameters for pro parte, misapplications and hybrids Closed
8465 Term nodes order in term trees is ignored in term tree editor Closed

CDM Platform 5.8 (released on Jul 19th, 2019)

Issues: 68

Downloads: Ask the edit team for backups of this version

What's new?

  • - Model
    • cm added as measurment unit
  • - Data Portal
    • Improvements to the media page related to source references and the media title
    • Name page shows more information: name relations, type designation with specimen map, related taxa, nomenclatural acts (registrations)
      • The automatic redirect behavior to the taxon page is now configurable
    • Registration search:
      • Support for filtering by references
      • Improved search by type designation status and name
    • Registration page:
      • Subheadline to show the type of the nomenclatural event
    • General layout improvements
      • Links to reference pages as unobtrusive icon link
    • Maps:
    • User interface to search the Unified Taxonomic Information Service (UTIS)
    • Bugfixes related to
      • Name relations
      • Nomenclatural status
      • Type designations
  • - CDM Server
    • improved error detection when failing to start
  • - TaxEditor
    • improved deduplication for references in name editor (hotfix 5.7.3)
    • handling of preferences improved
      • consistent model to always allow default and specific values and to handle override more intuitive
      • area specific status list preferences for distribution data
      • status list serverside preferences for distribution data handled in details view
      • ranks as serverside preferences
      • nomenclatural status as serverside preferences
      • visibility of fields Source.idInSource and Source.IdNamespace as preferences
    • CDMlight export
      • includes excluded flag and excluded notes
      • sortindex for taxa added
      • improvements in ABCD import
    • Terms allow adding media in term editor
    • Media:
      • media loaded asynchronously to improve performance (has open issues)
    • Bugs
      • exception/freezing when opening name in source search dialogue (hotfix 5.7.3)
      • recognize again the previous state (opened sections) of details view and supplemental data view (hotfix 5.7.3)
      • refresh in name bulk editor after search (hotfix 5.7.3)
  • - Web editor (Phycobank registration UI)
    • Registration list view with reference filter
    • Curators and admins can edit arbitrary Annotations (Notes)
    • Bugfixes related to
      • user permissions
      • ...

# Subject Status
  cdm 1 Collapse all/Expand all
8286 Add cm as unit term to CDM Closed
  cdm-dataportal 26 Collapse all/Expand all
8182 show blast search result In Progress
6316 display source references of media objects in media page Closed
5857 show nomenclatural status for for representations of TaxonName Closed
6380 typedesignations missing in homotypic group Closed
7620 RegistrationSearch implemented with Reference filter Closed
7966 Registration search simplify type select options Closed
8016 Registration page: subheadline with event type Closed
8318 TaxonName processing for taggedFullTitle Closed
8245 Improve representation of DescriptionElementBase.timeperiod Closed
8347 point map zooms to wrong area when using sphericalMercator maps like OpenTopo OSM etc. Closed
8352 name page: show nomenclatorical acts Closed
8366 Same typedesignation display for registration page as in name page Closed
8388 UTIS search block Closed
8320 Links to reference page as appendend icon instead of having the whole citation as link Closed
8321 Namepage shows wrong taxa as related to the name Closed
8351 name page: show type designations with map Closed
8368 problems in compose_cdm_specimen_or_observation_tree_entry() Closed
8370 feature blocks created by compose_description_element_individuals_association() are broken Closed
8304 Name page redirects to according taxon depending on query parameter Feedback
4177 display of name relationships in synonymy broken Closed
7975 Implement a block to display name relations Closed
8306 Registration page links to registered taxon name Closed
8108 Name page shows complete name information (I) Closed
6709 Do not show UUID on media page Closed
5855 potential improvements in settings for name relationship types Closed
8280 polyfills folder check in zen_dataportal/theme-settings.php fails when portal is installed in subfolder Closed
  cdm-vaadin 6 Collapse all/Expand all
8167 Permission denied for Submitter when adding section to newly created journal Resolved
8345 RegistrationListView: filter option for publication Closed
8346 Curators and admins can edit arbitrary Annotations (Notes) Closed
8278 LazyInitializationException (LIE) in ReferenceEllypsisCaptionGenerator Closed
8284 starting a registration for an existing name causes the name editor to pop up in read only mode Closed
8279 ClassCastException in CdmUserHelper.user() Closed
  cdmadapter 5 Collapse all/Expand all
6627 Remaining cdm light issues Resolved
8273 abcd import: check for all specimen for DNA in DNABank Feedback
8264 excluded and excluded notes in cdmlight export Closed
8322 add sortindex to cdm light export Resolved
8344 cdm light export: add dummy line in simpla facts table Feedback
  cdmlib 14 Collapse all/Expand all
7932 Implement subject resolver for CdmPreferences In Progress
8062 Make default preferences deletable serverside In Progress
7433 new service method to get specimen by genetic AccessionNumber Resolved
7904 DerivedUnitFacadeFieldUnitCacheStrategy.getCollectorAndFieldNumber() creates temporary Team objects which can not be garbage collected. Feedback
7902 Allow default values for PreferencePredicates Closed
7296 externalize redmine api key Closed
7829 Improve deduplication of parsed names and references Closed
8314 TaxonName provides the FullTitleCache as TaggedText Closed
8354 taxonomic registration search by name finds also typifications for this name Closed
8369 SpecimenTypeDesignationDTO can not be serialized to JSON Closed
8330 RegistrationDao search method Closed
8365 DerivedUnitFacadeCacheStrategy should remove collection codes from accession numbers Closed
8257 Remove factory methods for term node creation Closed
8287 RegistrationServiceImpl.page( .... Collection<UUID> typeDesignationStatusUuids ... ) fails when NULL and UUIDs are passed Closed
  cdmlib-remote 2 Collapse all/Expand all
7621 registration search also covers typified names Closed
8319 NomenclaturalStatus webservice implemented Closed
  cdmserver 1 Collapse all/Expand all
5774 cdmserver misses to detect some errors in failed instances Closed
  taxeditor 13 Collapse all/Expand all
7920 Possibility to define area specific status selection Feedback
8293 Distribution preferences for details view should be serverside preferences Feedback
8045 Improve handling of default values and override in local preferences Feedback
8088 Open taxon node wizard issues Feedback
8256 Show all status preferences as table Feedback
8294 Make display of ID in source and ID Namespace configurable Closed
8129 Load images asynchronously in media details view Closed
8260 Details and Supplemental Data View do not save the expansion state of sections Closed
8283 Allow adding media to terms in taxeditor Closed
8332 Excel matrix exports only the visible rows Closed
8333 Show modifiers for states in Character Matrix Closed
8058 Further issues for (local) preferences Feedback
8323 Make nom.status and rank lists a CdmPreference Feedback

CDM Platform 5.7 (released on May 6th, 2019)

Issues: 21

Downloads: Ask the edit team for backups of this version

What's new?

  • - Data Portal
    • Bugfix for setting the feature tree for the general page
  • - TaxEditor
    • some urgent bugfixes for character matrix editing
    • possibility to define area specific distribution status for distribution editor (UI for setting this preference is still missing)
    • some bugfixes
  • - Web editor (Phycobank registration UI)
    • All comboboxes for references are making use of the ellypsed reference labels
    • The TaxonNamePopeditor now supports editing the nomenclatural status
    • Name type status filter in registration search simplified
    • and some bugfixes

# Subject Status
  cdm-vaadin 8 Collapse all/Expand all
8252 reference ellypsis must not be applied to all reference types Closed
8250 ReferenceEditor: inReference must not be required for type book Closed
8246 TaxonNamePopupEditor can not be canceled Closed
8220 incomplete creation of blocking registration in case of registering existing name which misses the nomenclatural reference Closed
8215 User demand: sorting order in reference editor Closed
8209 use ellypsed references for all reference comboboxes Resolved
8193 TaxonNamePopupEditor: add select form element for Nomenclatural status Closed
7965 Registration search simplify type select options Closed
  cdmlib 2 Collapse all/Expand all
8189 Allow configuration of 'user.home' via the spring environment Closed
7953 Book in BookSeries: incomplete titleCache misses series title Feedback
  cdmlib-remote 1 Collapse all/Expand all
8251 LazyInitializationException (LIE) in featureTree webservice Closed
  taxeditor 10 Collapse all/Expand all
8349 NPE in ParseHandler when parsing name without nomencl reference Closed
8316 Endless loop when editing name in source of distribution Feedback
8315 Parsing existing references with inReferences changes the inReference Closed
8267 common name preference saving does not work correctly Closed
8266 local preference is not evaluated for distribution editor status Closed
8265 Referencing objects view does not work for term editor Closed
8263 Improve performance of term editor Resolved
8258 Default Feature Tree contains name features and features Closed
8241 Rename FeatureTreeEditor to TermTreeEditor Closed
8229 reload of the bulkeditor does not work correctly Closed

CDM Platform 5.6 (released on Apr 12th, 2019)

Issues: 67

Downloads: Ask the edit team for backups of this version

What's new?

  • Data Model
    • feature trees have been refactored to typified Term trees which support any type of terms
    • added term types to term vocabularies
    • added structure, property and regional modifier as new term types
  • - Data Portal
    • added time period for description elements in data portals
    • improve user profile settigs in cdm_dataportal
    • harmonize registrationId links and make testing easier
    • improve image gallery settings labeling
  • - Import/Export
    • name facts added to cdm light export
  • - TaxEditor
    • term editor
      • add "plural" to representations
      • new term editor for structures, properties, regional modifers
    • feature/term tree editor
      • feature trees became more generic and support all types of terms (not yet fully available in editor)
      • restrict editor according to typified term trees
    • name editor
      • creating duplicates of specimen type designations
    • update of open data after updating subtree operations (update publish flag and update sec reference)
    • user selection dialogs for group members filter out already added users
    • name facts now editable, when selecting name in details view and in name bulk editor
    • sources can be added to type designations
    • Bugs
      • changing of title cache of a factual data set was not possible
      • selection dialogs for teams or persons did not filter out institutes
      • insufficient rights lead to missing focus in name editor
      • fixed title cache issues for taxon descriptions
  • - Web editor (Phycobank registration UI)
    • User friendly message when accessing editors with unsufficient permissions (#8218)
    • Registry curator can unlock a published registration for minor changes (#8192)
    • Solving a major performance problem related to uninomial und specific epithet comboboxes (#8176)
    • Better lables for popup editors breadcrumbs (#7962)
    • ReferenceEditor: optional validation for completenes of Partial values in datePublished (#7968)
    • Create blocking relations for un-registered names which are to be used in nomenclatural acts (#8050)
    • TaxonNamePopEditor: name part field visibility not correct for all ranks (#7963)
    • ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic and NULL (#8149)
    • ReferencePopupEditor: When coming from NameEdior editing of the inreference should not be blocked (#8191)
    • Bugfixes:
      • Fixing enabled state of edit buttons in combobox widgets (#8217)
      • Solving multiple problems related to problems with hibernate session an transaction handling
      • Problem with inserting a section - inReference is "lost" (#8097)
      • Error saving name type designation editor due to problem in poupeditor context (#8099)

# Subject Status
  cdm 2 Collapse all/Expand all
8190 Default FeatureTree throws exception Closed
8162 Move term related classes from model.common to model.term Closed
  cdm-dataportal 5 Collapse all/Expand all
8106 improve image gallery settings labeling Closed
8093 harmonize registrationId links and make tesing easier Closed
5699 user profile settigs in cdm_dataportal module done wrong Closed
3747 Check if time period is handled correctly for description elements in data portals Closed
3616 Show DescriptionElementBase.timeperiod in Dataportals Closed
  cdm-vaadin 23 Collapse all/Expand all
8218 Show appropriate error message when accessing RegistrationWorkingsetEditor without sufficient permissions Closed
8217 ToManyRelatedEntitiesComboboxSelect edit button not enabled Closed
8214 WeaklyRelatedEntityCombobox is not validated Closed
8213 MySQLSyntaxErrorException with 'Submitter' user acessing view registration#!regStart Closed
8194 LazyInitializationException (LIE) on deleting the nomenclatural referenz (Section) of a Name Closed
8192 The curator must be able to unlock a published registration for edition Closed
8191 ReferencePopupEditor: When coming from NameEdior editing of the inreference should not be blocked Closed
8188 Allow configuring hibernate properties via properties file Closed
8184 SpecimenTypedesignationEditor: add new specimen broken Chrome browser Closed
8176 WeaklyRelatedEntityCombobox is slow Closed
8160 CdmBeanItemContainerFactory as readonly service bean Closed
8158 cascade="all-delete-orphan" problem when .... Closed
8149 ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic and NULL Closed
8107 NPE when throwing PopupEditorException in AbstractPopupEditor Closed
8099 Error saving name type designation editor due to problem in poupeditor context Closed
8097 Problem with inserting a section - inReference is "lost" Closed
8075 multiple cascade all-delete-orphan exceptions related to DefinedTermBase.representations Closed
8065 HibernateException: corrupt session problem breaks SpecimenTypeDesignationworkingsetEditor type designation table Closed
8050 Create blocking registrations for un-registered names which are to be used in nomenclatural acts Closed
7968 ReferenceEditor: optional validation for completenes of Partial values in datePublished Closed
7963 TaxonNamePopEditor: name part field visibility not correct for all ranks Closed
7962 PopupEditors: *DTO in context 'breadcrumbs' to be transformed into more humane labels Closed
7881 reference selection combobox broken after error in ... Closed
  cdmadapter 1 Collapse all/Expand all
8175 add name facts to cdm light export Closed
  cdmlib 6 Collapse all/Expand all
8171 javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource fails to cache the connection which and leaves it unclosed Closed
8153 Adapt cdmlib to FeatureNode/FeatureTree model changes Closed
8104 TaxonName.getLastNamePart erroneously renamed .getFamiliyNamePart Closed
7896 NPE, NullPointerException in RelationshipTermBase Closed
7106 avoid factory.openSession() in CdmRepository Closed
615 remove suns repository Closed
  cdmlib-remote 2 Collapse all/Expand all
8173 spring profile remoting enabled by default Closed
8096 Implement CacheUpdater as long running task with correct progress monitoring Closed
  taxeditor 28 Collapse all/Expand all
8234 Move description elements issues Closed
8228 refresh of details for same object in different bulk editors does not work Closed
8225 Deleting one of two type designations removes both Closed
8223 Urgent TaxonNode wizard issues Resolved
8222 Deleting a type designation from a name is directly persisted Closed
8211 Trigger new search when clicking on identifier search Closed
8200 Changing title(cache) for factual data set not possible Closed
8197 Deleting Media from Image Gallery View does not make view dirty Closed
8151 after creating a new synonym and pasting a name string the default string is not removed Closed
8150 Allow editing the representation label of characters in details view Closed
8148 Login Dialog cuts off information Closed
8147 Add "plural" to representation detail element Closed
8146 Adapt taxeditor UI to structure and property term type Closed
8143 It is possible to open multiple instances of the login dialog Closed
8136 Implement sources for type designations in TaxEditor Closed
8124 Activate Name Facts in Taxeditor Closed
8121 Allow selecting structural/property modifiers when creating a character Closed
8115 NPE when moving factual data Closed
8111 User selection dialog for groups does not filter out existing users Closed
8011 Implement term search view Closed
7923 Add context menu and drag'n'drop to CharacterEditor Closed
7865 Remaining factual data view label issues Resolved
7541 Insufficient rights lead to missing focus in name editor Closed
7515 TypeDesignationStatusComparator to sort by vocabulary first and then by term order Resolved
7428 Open issues for updating open data while subtree is updated Closed
6413 [DISCUSS] How to create type duplicates (e.g. isotypes) for a taxon name Closed
4545 Implement TeamOrPersonBaseSelectionDialog Closed
3836 Implement modifiers and modifying text for Description Elements in TaxEditor Closed

CDM Platform 5.5 (released on Feb 14th, 2019)

Issues: 122

Downloads: TaxEditor, CDM Server, Data Portal

What's new?

  • - Data Model
    • removed/added some attributes from certain attribute types (e.g. removed date published and authorship from journals and print series, added ISBN to Proceedings)
  • - CDM Server
    • Available as docker container
  • - Import/Export
    • taxon (tree)index added to CDMlight export
  • - Dataportal
    • improved registration page, now showing the complete nomenclatural act data and registration metadata
      • human feedback to users in case a registration is not public or does not exist
    • improved diplay of type designations
    • improved display of registrations in lists like in search results and reference page
    • reference page shows name relations
    • details page for field units improved
    • some bugs fixed
  • - TaxEditor
    • Distribution editor
      • use new table frame work (so called NAT tables), offering improved usabilty and functionality like filtering, column freezing etc
      • improved area selection dialog
      • bug fixes
    • Preferences
      • new menu structure for local preferences (not fully completed yet)
      • serverside preferences and local preferenced unsing same user interface pages
      • translation to German completed
      • improved handling of "(allow) override" functionality
      • improved handling of default values
      • (the last 2 will be further developed into 1 system with one of the next releases)
    • References
      • DOI available as attribute
      • warning for multiple usage of references also in details view (not only in editing dialog)
      • improved attribute selection for specific reference types (see data model section above)
    • Rights&Roles
      • Role "remoting" added, only users belonging to a group with role remoting are allowed to open data in TaxEditor
    • Term editor
      • performance improved
      • 2nd symbol for terms available
      • Bugs/exceptions when moving or adding terms fixed
    • Feature tree editor
      • drag&drop from (feature) term editor available
      • Right click menu added (replacement for buttons)
      • copy&paste added (for the rare case that a feature should be reused within the tree)
    • Name editor
      • invalid designations available similar to pro parte synonyms and misapplied names (formatting not yet correct)
    • Description/Character Editor (experimental, multiple improvements)
    • Taxon node wizard improved
    • Automated deduplication of references and authors works also for new taxon dialog (before it worked only in name editor)
    • Bugs
      • Improved (title)cache updating
      • Empty dialog for File -> New -> Reference -> Change reference type fixed
      • Some exceptions thrown in term editor fixed
      • sometimes invisible deduplication icons fixed in bulk editor
      • handling of deleting new+unsaved records fixed in bulk editor
  • - Web editor (Phycobank registration UI)
    • Reference editor
      • Reference editor: Label In proceedings in InProceedings missing
      • ReferencePopupEditor: saving a newly created inreference is not refreshing the inrefernce field with the new entity
      • ReferencePopupEditor: apply sensible reference type pre-set for in references
      • ReferenceEditor: filter inReferences by applicable reference type
      • ReferenceEditor misses institution, organization and school fields
    • TaxonNameEditor:
      • Entering data for name parts (genus, specific epithet) is now required
      • Exclude current name from name relationship comboboxes
      • orthographic name correction available
    • Registration start view:
      • Reference combobox to offer two search modes
      • Exclude irrelevant reference types from list of existing publications
    • Registration Workingset Editor
      • A couple of severe bugs fixed
      • realiably setting registration date when status is set to PUBLISHED
    • Registration search
      • Registration items in list view is using the wrong button icons for blocking regs and validation errors
    • SpecimenTypeDesignationEditor
      • Display of altitude fixed and also a related problem when saving
      • GeoLocationField uses OpenTopoMap
      • Collection date supports timespans
      • Improved user feedback
      • Geolocation
        • Suopport for reference systems
        • Map shows error radius
    • cdmlib-vaadin UI widgets
      • Reference combobox options with ellypsed reference titles
      • ToOneRelatedEntityCombobox validation fixed, layout problems solved
      • PopupEditors notify user on editor changes and allow the user choose from discard or save in a dialog
      • PopupEditors show editor context information as 'breadcrumbs' in the header or toolbar.
    • Label improvements
    • Permission and security improvements
    • Performance improvements
    • Classification fragments are managed in a non cyclic directed graph, this mainly improves the search capabilities
      • Automatic management of the graph during editing of RegistrationStatusFieldInstantiator
    • Bugs fixed:
      • Massive memory consumption problem solved
      • Multiple representations problems fixed
      • LazyInitializationExceptions fixed
      • Fixing problems with possibly corrupted hiberante sessions
    • Complete removal of the rejected messaging prototype implementation

# Subject Status
  cdm 6 Collapse all/Expand all
8030 Cache updater service methods externalized and base class specific Closed
7930 Remove DOI from journals, print series and person communications Closed
7918 Revision of reference type specific properties Closed
7915 Remove date published from journals and print series Closed
7914 Add ISBN to IProceedings Closed
7913 Remove authorship from IJournal and IPrintSeries Closed
  cdm-dataportal 13 Collapse all/Expand all
8076 implement test for typified name for registration page Closed
8074 Registration page has fatal error when registration identifier in url path is ivalid Closed
8073 Registration page: show typified name for registrations covering typifications only Closed
8056 WSOD in cdm_dataportal/search/results/taxon Closed
8051 improve display of registration items lists Closed
8048 Selenium test for Registration page Closed
7977 Registration page layout improved Closed
7974 Layout for Registration date Closed
7947 registration page shows name relations Closed
7927 Registration not found, Portal handling registrations in preparation Closed
7907 Annotations in Reference page do not respect the annotation settings Closed
7616 reference page: show name types Closed
7564 remove Phycobank - Registration data - block and other outdated registration code Closed
  cdm-vaadin 45 Collapse all/Expand all
8090 Reference editor: Label In proceedings in InProceedings missing Closed
8072 Registration items in list view is using the wrong button icons for blocking regs and validation errors Closed
8071 ReferencePopupEditor: saving a newly created inreference is not refreshing the inrefernce field with the new entity Closed
8070 ReferencePopupEditor: apply sensible reference type pre-set for in references Closed
8069 RegistrationUI: remove all messaging related code and message indicators from all views Closed
8064 NPE in AbstractHibernateTaxonGraphProcessor.assureSingleTaxon() on saving new name for new registration with new genus Closed
8063 multiple representations problem wirth collector being author of the registration citation Closed
8059 NPE when adding existing but un-registered name to workingset Closed
8039 NPE when creating new name in unsaved NameTypeDesignation for exising name in workingset which has no registration yet Closed
8031 Cannot add existing name to blank workingset Closed
8013 LazyInitializationException (LIE) in RegistrationDTO.makeBibliographicCitationStrings Closed
7995 Registration.registrationDate not set when status is set PUBLISHED Closed
7956 RegistrationWorkingsetEditor refresh problem after saving TaxonNameEditor Closed
7951 Reference Combobox option titles can be too long causing the select box to extend too much Closed
7950 ToOneRelatedEntityCombobox: add new button "jumpes" to the right when hovering the mouse over Closed
7949 New Registration: Reference combobox to offer two search modes Closed
7946 RegistrationStatusFieldInstantiator must set status value internally before adding the ValueChangedListener Closed
7944 TaxonNamePopEditor: name part fields are required Closed
7942 SpecimenTypeDesignationEditor: Explanation on why editor can not be saved without type designation Closed
7937 TaxoNamePopupEditor: Exclude current name from name relationship comboboxes Closed
7925 AbstractPopupEditor: exception handling in save method is incomplete Closed
7919 GeoLocationField uses OpenTopoMap Closed
7916 SpecimenTypeDesignationEditor: Map shows error radius Closed
7910 TeamOrPersonField: readonly exception on bindig data Closed
7908 Redmine communication hub slows down RegistrationWorkingSets Closed
7906 AbstractPopupEditor: Notify user on editor changes and provide options to choose from discard or save Closed
7905 NPE in InstitutionEditorPresenter Closed
7900 Excessive heap consuption in RegistrationWorkingsetEditor with big workingsets Closed
7899 enable orthographic name correction in Vaadin Closed
7893 RegistrationWorkingsetEditor: canceling new name editor leaves the new name button disabled Closed
7892 RegistrationWorkingsetEditor: LIE creating new name for book section Closed
7888 TypeSpecimenEditor: Collection date should be timespan Closed
7878 Edit CollectionCode not saved Closed
7870 RegistrationWorkingsetEditor: Internal error on clicking "new name" Closed
7867 FieldGroup$BindException: The given field is not part of this FieldBinder in TeamOrPersonField Closed
7866 Phycobank UI further label improvements Closed
7846 PopupEditors show editor context information as 'breadcrumbs' in the header or toolbar. Closed
7833 submitters can access see any registration in any RegistrationWorkingSet Rejected
7718 New Registration: Exclude irrelevant reference types from list of existing publications Closed
7639 SpecimenTypeDesignationEditor: Altitude not saved and displayed properly Closed
7559 possibly corrupted hiberante session after previous error on saving editor Closed
7481 ReferenceEditor: filter inReferences by applicable reference type Closed
7480 ReferenceEditor misses institution, organization and school fields Closed
7245 validation of ToOneRelatedEntityCombobox not working Closed
7218 SpecimenTypedesignationsWorkingsetEditor: support for Reference system Closed
  cdmadapter 1 Collapse all/Expand all
7903 Add treeIndex with rank to cdm light export Resolved
  cdmlib 6 Collapse all/Expand all
8066 CdmUserHelper.createAuthorityFor() causes flush of pending transactions Closed
7939 TaxonNodeDTO need sortIndex of Rank Closed
7901 Make PreferencePredicates an interface to allow multiple implementations (e.g. for client apps, for grouping, for data type specific instances, etc.) Closed
7874 TeamOrPersonBase entity can become unusable due to replacement of the title caches on using getters Closed
7600 public setters for entity collections Closed
7217 SpecimenTypedesignationsWorkingsetEditor: Longitute Latitude fields allow values in degrees minutes seconds formats Closed
  cdmlib-remote 4 Collapse all/Expand all
8042 UI is too restricted for users with right Project Manager Closed
7978 registration search result ordered by identifier descending Closed
7972 explicitly allow disallow access to HTTP Invoker endpoints (/remoting/**) Resolved
7924 LazyInitializationException (LIE) in taxon/{uuid}/synonymy.json when used with subtree filter Closed
  cdmserver 1 Collapse all/Expand all
6522 package cdm-server in docker container Closed
  data 1 Collapse all/Expand all
7811 Import higher classifications Resolved
  taxeditor 45 Collapse all/Expand all
8041 PatternSyntaxException in FeatureTreeSelectionDialog Closed
8037 "Detail" is not saved in taxon node wizard Closed
8032 NPE when editing Local Prefs -> Factual Data Closed
8026 details view is empty for some references in bulk editor Closed
7999 Allow override does not work correctly for distribution areas Closed
7998 Store newly created Characters in selected vocabulary Closed
7993 Display "Access Denied" dialog in case the remoting service responds with status code = 4xx Closed
7985 Remove Print Series from InProceedings, use "Proceedings" Closed
7954 protected vs. unproteced caches in TaxEditor Closed
7941 Deduplication does not work in new taxon dialog Closed
7940 "New" menu in navigator not available for certain users Feedback
7934 sometimes the signs for deduplication are not shown Closed
7933 Adding a new Term to the "Country" vocabulary leads to corrupt data Closed
7931 add symbol2 to term detailsview Closed
7929 after delete of not persisted object in bulkeditor the object is still in bulkeditor list Closed
7912 Enhance checkbox tree viewer Closed
7887 Use DTOs in term editor Closed
7880 Implement centralized preference default loading strategy Closed
7877 Form elements disappear in reference dialog after changing the reference type Closed
7875 Add multiple area selection to descriptive data set editor Closed
7873 Implement copy&paste for feature nodes in feature tree editor Closed
7871 Open character matrix as singleton Closed
7869 Run gfbio term service requests as background tasks Closed
7868 Allow creating a new vocabulary in vocabulary selection dialog Closed
7856 Allow local override for distribution vocabularies Closed
7854 Open issues in TaxDistributionEditor Closed
7850 Further problems with term editor Duplicate
7849 Improve DB Preferences handling and saving in TaxEditor Closed
7847 Use separate column for row state instead of symbol in titleCache column Closed
7836 ClassCastException when invoking cdm light export with wrong selection Closed
7806 GfBio Term Search issues Closed
7794 Update TaxonNodeWizard Closed
7761 Invalid designations should be displayed like misapplied names in name editor Closed
7746 NPE when deleting volatile DescriptionBase Closed
7737 Reference Details view does NOT give a multiple usage warning Closed
7680 Refactor TaxonNodeDetailElement Closed
7668 NPE when changing author Closed
7649 Term editor loads/saves extremely slow Closed
7367 Deleting a term in the term editor does not update the UI Closed
7163 Restructure preferences Closed
6951 Drag and drop does not update term hierarchy in the UI Closed
6806 Add context menu to FeatureTreeEditor Closed
6805 Implement drag and drop from Term Editor (Feature) to FeatureTreeEditor Closed
5926 Update labels in TermEditor for Vocabularies Closed
4227 handle generated resources in eclipse workspace Feedback

CDM Platform 5.4 (released on Oct 25th, 2018)

Issues: 54

Downloads: Ask the edit team for backups of this version

What's new?

  • Documentation

    • online webservice documentation was broken since 5.3. Fixed.

  • Dataportal

    • display of related taxa (misapplied names, pro parte synonyms, concept relations)
      • sort order
      • hyperlink to related taxa was missing
      • further links (???)
    • phycobank/name registration related
      • search via taxon graph (#7835)
      • improvements on name registration page
      • hide unpublished names, types and registrations (#7723)

  • TaxEditor

    • restart menu available
    • distribution editor
      • further improvements, now it is not an experimental feature anymore (but still has some open issues, we recommend to contact us before using)
      • improved area selection (still some issues)
      • predefined source selection
      • support supplemental data
      • support various symbols/labels for areas and status
    • performance
      • faster loading of details view and other views (open issues exist)
      • faster creation of factual data view right click menu
    • bulk editor
      • multiple columns available for display and sorting
      • symbol indicating deduplication status
    • navigator
      • set excluded and unplaced via right click menu
    • name relationships allow reverse direction
    • hybrid flags enabled/disabled rank specific
    • determination events can now have sources
    • factual data
      • improved labels for descriptions including sources
      • available common name references can be explicitly marked
      • reference search on alternative identifiers possible parallel to title (cache) search
      • add sources to descriptions when creating them (explicit menu item)
      • reorder menu ("new" on top, ...)
      • available distribution area vocabularies and status and common name areas definable via DB preferences
    • further database sided preferences implemented (there are still some bugs, we recommend contacting us before using DB sided preferences)
      • exclude specimen, media, import/exports, multiple classification functionality
      • further attributes for simplified name details view
      • distribution area vocabulary selection
      • distribution status selection
      • checklist perspective as start perspective
      • simplify sources view (hide IdInSource and IdNamespace)
    • client side (local) preferences stored database specific
      • if users use multiple databases client side preferences often need to be different depending on the database in use; now also client side preferences are stored for each database and not for the complete TaxEditor installation anymore (only valid for newly changed preferences)
    • NOTE: preference handling (server and client side) still has some severe open issues, we will try to work on them for the next release, so we recommend to handle with care until then
    • bugs:
      • taxon node editor does not allow editing existing taxon data anymore, only taxon node data
      • right click menu sometimes does not show up in name editor
      • exceptions when editing terms in term editor
      • freezing login dialog if no connection established
      • exception after saving bulk editor
      • exception during specimen search in bulk editor
      • exception when canceling "move elements" in factual data view

  • Browser Editor (Vaadin)

    • performance
      • big workingsets in the RegistrationWorkingSetEditor are loading much faster now. This improvement also has positive effects on other editors (#7785)
    • usability
      • multiple classifications and classification fragments can be merged into a common taxon graph structure. This graph first of all allows searching names by higher ranked names. Edits of names are automatically tracked in the graph. (#7834)
      • New mode for the TaxonNameEditor: VALIDATE_AGAINST_HIGHER_NAME_PART. This mode requires that a higher name must exising in the data base before it can be used as name part. (#7783, #7648, #7831, #7830, 7845)
      • improving some labels in the UI
    • bugs
      • memory issues (#7036, #7036)
      • problem with session attributes in different CDM Instances

# Subject Status
  cdm-dataportal 4 Collapse all/Expand all
7835 taxonGraph search block implemented Closed
7788 Registration page shows registration date and office Closed
7778 identifier links missing in taxon relations footnotes Closed
7723 PhycoBank unpublished data must not be visible in Portal Closed
  cdm-vaadin 16 Collapse all/Expand all
7855 PersonField modifies the nomenclaturalTitle forcing users to have the UPDATE permission even if the person was not edited or readonly Closed
7845 NamePopupEditor new Genus button should clear the genus name field in the new editor Closed
7842 TaxonNamePopEditor: adding new name as replaced synonym to name with basionym causes NonUniqueObjectException Closed
7831 VALIDATE_AGAINST_HIGHER_NAME_PART specific epithet name is not exluded when changing species to subspecies Closed
7830 VALIDATE_AGAINST_HIGHER_NAME_PART specific epithet is not being reset to testfield on rank changes Closed
7824 PopupViewRegistration not removing registered views causes memleak Closed
7814 Section in Name and section in Basionym, usability Closed
7785 CdmUserHelper caches permission information Closed
7783 NamePopupEditor new buttons for genus and species Closed
7777 NPE on login attempt after logout Closed
7648 Create taxonrelation to genus or species when subordinate names are created Resolved
7630 blocking registration relations get lost after saving adding a typedesignation to a newly created "typification only" registration Closed
7594 RegistrationWorkingsetEditor click on new serveral times Closed
7222 Phycobank UI improve labels Closed
7047 Vaadin UI and View scope beans are not always destroyed correctly Closed
7036 correctly release vaadin view resources when the browser windows has been closed Closed
  cdmlib 5 Collapse all/Expand all
7834 taxonGraph search listing all included names implemented Closed
7818 TaxonRelationshipsDTOTest leaves test environment in unpredictable state Feedback
7795 untilis xml DataSets creation without "[NULL]" values Closed
7776 Add source of descriptive data set to SpecimenDescriptions added to it Resolved
7767 Incorrect handling of secundum detail reference in formatter Closed
  cdmlib-remote 2 Collapse all/Expand all
7784 deduplicate and harmonize ClassificationController methods Closed
7779 swagger UI broken after springfox-swagger2 upgrade Closed
  taxeditor 27 Collapse all/Expand all
7911 Changing areas in Distribution Editor yields to wrong column labels Worksforme
7886 Divide local preferences to db dependend local preferences Closed
7883 IndexOutOfBoundsException in TermComboElement Closed
7844 LoginDialog freezes Taxeditor if no connection can be established Closed
7838 Optimize details view creation for section expansion Closed
7827 LazyInitializationException when saving term editor (named areas) Closed
7826 NPE after saving groupbulkeditor Closed
7810 DB preference to make Specimen editors visible Closed
7809 Improve namerelationship handling in editor Feedback
7793 Master ticket for E+M editor issues Closed
7792 Rendering of context menu of factual data view is super slow Closed
7775 Factual Data label issue Closed
7773 when changing rank the hybrid section is empty Closed
7674 Show taxon descriptions in character matrix editor Closed
7660 Indicate the row state in a NAT table via symbols Closed
7502 Add further columns to bulk editor Closed
7424 right click menu does not show up in name editor Closed
7345 [E+M] Common name references selectable in TaxEditor Closed
7283 Improvements for alternative identifier search Resolved
7236 Make available distribution status a database preference for TaxEditor distribution editor Closed
7235 Make available area vocabularies a database preference for TaxEditor distribution editor Closed
7063 Improve the area selection wizard for distribution editor Closed
6159 improve distribution editor in TaxEditor Closed
3989 [DISCUSS] Allow defining the vocabularies to be offered in the select dialogs Resolved
3276 NPE for "Move Elements" context menu option Closed
2444 Disable binom and trinom hybrid flag when epithets are not available Closed
2406 DeterminationEventElement is lacking references Closed

CDM Platform 5.3 (released on Sep 17th, 2018)

Downloads: Ask the edit team for backups of this version

Issues: 51

What's new?

  • General

    • Allow handling "continued" for reference date published for dates like 2017+
    • Allow filtering some webservices on taxonomic subtrees

  • Dataportal

    • Creation of data portals with a filter on taxonomic subtrees (e.g. families)
    • Formatting of misapplied names and invalid designations refactored (and hopefully improved)
    • Improved advanced search on taxa with geo-filter, * on start does work now, but still remaining issues for searches including * and whitespace
    • Improved handling of specimen with protected cache
    • Tree View for specimen data (still experimental)
    • Bugs
      • Fix for aggregated images not being shown anymore
      • Fix empty bibliography sections
      • Fix disabling of determination keys block in tab-less taxon pages

  • Export

    • Improved handling for types in CDM light export

  • TaxEditor

    • "Continued" for date published (see General section) available in TaxEditor
    • External links for sources (not yet implemented in data portal)
    • Label changes
    • Consistent handling of Description and DescriptionElement sources
    • Warning if Media are linked multiple times
    • Improved synchronization between views when moving factual data
    • Improved formatting of misapplied names and pro parte synonyms (synchronized with formatting in data portal)
    • Ordering misapplications with defined alphabetic order
    • Editing of supplemental data for descriptive data sets
    • Specimen Tree Editor collapsable and expandable
    • Bugs
      • Protected cache handling in details view for References
      • Exception when deleting a polytomous key
      • Dialog to avoid creating users with duplicated usernames
      • Exception when trying to create a new datasource

  • Browser Editor (Vaadin)

    • Reference editor offers field for adding notes
    • Multiple important bug fixes to increase the overall stability and reliance of the registration system
      • Preventing from creation of empty registrations
      • Problem with inserting several new authors into a new author team solved
      • Memory leak eliminated

# Subject Status
  cdm-dataportal 7 Collapse all/Expand all
7759 classification subtreefilter settings in portal Closed
7720 use new taxonRelationshipsDTO webservice for all taxon relations Closed
7691 Empty "Bibliography" section Closed
7686 Specimen title cache issues in data portal specimen table Closed
7658 use new taxon relationship DTO webservice in portal Closed
7294 keys block can not be disabled in tabless taxon page Closed
6289 “Back to images” link as “Back to taxon page” when in table-less mode Closed
  cdm-vaadin 11 Collapse all/Expand all
7742 vaadin view presenters not disposing ehcaches and object references in event bus which can cause memory leaks Closed
7722 NamePopupEditor: validation not working for rank genus Closed
7712 PhycoBank UI Reference detail size Closed
7702 corrupted hibernate session after previous error during save operation Closed
7676 Suchfunktionalität in Registration UI Dateneingabe Closed
7641 Reference editor: Error when incerting several new authors into a new author team Closed
7624 Note field for Reference in Vaadin Closed
7622 RegistrationWorkingsetEditor: navigating to other pages with fresh registrations leaves empty registrations in the system Closed
7585 RegistrationCuratorRoleProbe does not only check the ROLE_CURATION Closed
7582 prevent from creating empty registrations Duplicate
7560 LazyInitializationException (LIE) saving TaxonNamePopupEditor caused during hibernate.search indexing Worksforme
  cdmadapter 1 Collapse all/Expand all
7700 use TypeDesignationSetManager for creating typedesignation string in cdmlightExport Closed
  cdmlib 7 Collapse all/Expand all
7764 Fix classification and synonym bug in taxon name freetext search Closed
7757 Replace deprecated hibernate @Index annotation Closed
7756 org.hibernate.QueryException in portal/taxon/{uuid}/subtree/media.json webservice related to relation direction param in prepareTaxonRelationshipQuery() Feedback
7687 NPE in TypeDesignationSetManager Closed
7644 Add "continued" flag to (Verbatim)Timeperiod Closed
7553 move TypeDesignationSetManagerIT to cdmlib Closed
5868 re-establish support for wildcard at start of query string (includes the query string '*' ) Feedback
  cdmlib-remote 1 Collapse all/Expand all
7745 Subtree filter for dataportal services Closed
  taxeditor 24 Collapse all/Expand all
7753 use TaxonRelationshipFormatter for MAN and pro parte synonyms in name editor Closed
7738 NPE for cancel in Use existing media dialog of specimen tree editor Closed
7728 NPE in wizard when changing type of reference Closed
7726 Change label of "Abbrev. Title Cache" to "Nomenclatural Cache" in details view for references Closed
7717 Implement "continued" in TimePeriod UI Closed
7715 Description sources should be handled same as DescriptionElement Closed
7706 Warning for reused Media is missing Closed
7698 CCE when creating new datasource Closed
7667 NoHttpResponseException for large queries in bulk editor Feedback
7665 ConcurrentModificationException when closing Editor Closed
7575 Implement advanced quantitative cell editor Closed
7509 Aggregate and persist specimen character data from character matrix Closed
7500 Can't open both related accepted taxa of reused MAN Closed
7484 Protected titleCache handling not correct in Reference detail view Closed
7415 Implement ExternalLinks for OriginalSources in TaxEditor Closed
7412 Allow editing supplemental data for DescriptiveDataSets Closed
7371 Deleting Polytomous Key throws NPE Closed
7362 Implement view for Gfbio terminology service Closed
6850 NPE when clearing label of "kind of" term in TermEditor Closed
6742 IAE when using "Link with taxon selection" in Specimen-Editor Closed
6559 Order misapplied names in name editor Closed
6475 Make specimen tree editor collapsable and expandable Closed
4573 Handle duplicate username, group or grantedAuthority correctly Closed
3535 Automatically update descriptive view if content changed Closed

CDM Platform 5.2 (released on Aug 17th, 2018)

Downloads: Ask the edit team for backups of this version

Issues: 76

What's new?

  • General

    • Some improvements for ABCD import
    • Some minor improvements for CDM light export
    • New webservice for formatted taxon relationships (misapplications, pro parte synonyms, concept relationships) - available in data portal in next version

  • Dataportal

    • Reference page
      • proper formatting of taxon names in registration summary
      • proper handling of date published without end date
    • Specimen tab
      • remove "associated with" in compressed table
      • correct handling of freetext in altitude, distance to gorund and watersurface in default specimen table
      • correct handling of missing values for numeric values (do not show 0 anymore) in default specimen table
    • Name Registration
      • TBC

  • TaxEditor

    • Bulk editor
      • improve new implementation with so called NAT tables
      • asynchronous loading of data for large datasets
    • specimen
      • remaining issues for determinations in details view
    • Bugs
      • Taxa, being misapplied names or pro parte synonyms elsewhere, always show misapplied name details view
      • specimen server preferences are not saved
      • exception handling for media with corrupted metadata
      • exception out of bounds exception after deleting record in bulk editor
      • problems with progress monitor for setting publish flag for subtree (maybe some issues open)
      • dragging a misapplication on itself throws exception
      • multiple representations exception when adding annotation in bulk editor
    • experimental features
      • data aggregation in character matrix
      • improved workflow for editing descriptive data

  • Browser Editor (Vaadin)

    • TBC: name registration issues

# Subject Status
  cdm-dataportal 14 Collapse all/Expand all
7615 Registrations not searchable in the PhycoBank portal Closed
7611 media types with media uris are clickable Closed
7605 harmonize cdm_tagged_text_to_markup() with tagged text strategy in cdmlib Closed
7602 reference page: proper formating of taxonnames in registration summries Closed
7601 date published time period in reference page shows 'to' even if end date is missing Closed
7596 PhycoBank Portal - Formatting Closed
7595 PhycoBank Portal - Order Reference name Closed
7592 Search Button PhycoBank Test Closed
7562 Specimen table "Associated with" taxon is irritating and needs to be removed, replaced Closed
7552 use TaggedText.entityReference to add style and uuid to html tags Closed
7496 TaxonNodes in cdm_taxontree can either link to taxon or reference search result pages Closed
7495 Registration page implemented Closed
7494 RegistrationSearch implemented Closed
6563 Display altitude, distance to Ground and watersurface correct handling of freetext Closed
  cdm-vaadin 29 Collapse all/Expand all
7629 creating a typification only registration should not be possible if the names protologue is in the current workingset Closed
7628 Create registration for existing name (typification only) creates two registratios Closed
7617 Specimen TypesDesignations Editor - aus dem Editor heraus neu angelegter CollectionCode nicht auswählbar Closed
7591 Vaadin Layout Reference new Closed
7588 ToOneRelatedEntityCombobox: edit button must not be enabled when value is null Closed
7586 com.vaadin.data.Property$ReadOnlyException on opening TypeSpecimenWorkingsetEditor Closed
7583 NPE on logout in registration list view Closed
7574 IllegalStateException: Multiple representations ... when saving ReferenceEditor with in Reference ... Closed
7573 CollectionPopEditor superCollection only visible for advanced users Closed
7572 SpecimenTypeDesignationEditor: Collection combobox shows collection.code and collection.institution Closed
7571 Collection editor has field to select and edit the institution Closed
7570 Institution editor implemented Closed
7569 SpecimenTypeDesignationEditor: Typedesignations should be ordered Closed
7568 SpecimenTypeDesignationEditor: Collector Field not following the readonly state of the editor. Closed
7566 TeamOrPersonField: some Persons can not be selected Closed
7557 TaxonNamePopEditor: com.vaadin.data.Property$ReadOnlyException on saving a sub popup editor Closed
7554 TeamOrPersonField: removing existing team and adding new team leaves nested components buttons in disabled state Closed
7547 ToManyRelatedEntitiesComboboxSelect buttons enabled even if the containig editor is readOnly Closed
7546 Better guidance for users when creating registrations for exising names Closed
7545 IllegalStateException: Multiple representations ... when saving first typeDesignation for name less Registration Closed
7535 TeamOrPersonField: remove OK button an select the chosen enitity immediately Closed
7534 registration list filters preserved in session Closed
7533 add typeStatus filter to registration list Closed
7528 Allow changing the Registration status in the RegistrationWorkingsetEditor Closed
7524 TaxonNameEditor blocks entering new names for genera Closed
7361 Consistent UI concept for create, new, add, remove, delete, edit buttons Closed
7358 Show warning when browser history back is used while popup editors are open Closed
7274 GrantedAuthorityRevokingRegistrationUpdateLister: add the exception handling for failing flush or commit Closed
7131 Registrations ListView has pager to browse the whole result set Closed
  cdmadapter 1 Collapse all/Expand all
7643 cdmlight export: for bibliographic short citation use the freetext of the date as default Closed
  cdmlib 13 Collapse all/Expand all
7608 TypeDesignationSetManager: string representations for media types are missing Closed
7607 TypeDesignationSetManager: remove brackets from type representations Closed
7590 findByTitleWithRestrictions allows combining Restrictions by OR Closed
7555 TaxonServiceImpl.findTaxaAndNames() broken for cichoriae searching for "Lapsana communis" Closed
7551 TypeDesignationSetManager provides summary as TaggedText Closed
7550 Move UserHelper from cdm-vaadin into cdmlib Closed
7542 Move synonym of homotypical group to taxon does not move the homotypical group correctly Closed
7531 PermissionDeniedException on flushing registration with modified status even if the user has the required authority Closed
7527 CdmEntityDaoBase.*ByParam() public and also available in the service layer Closed
7525 IdentifiableServiceBase findByTitle(), and listByTitle() methods support cdm Restrictions and Criteria Closed
7429 Improve parsing and formatting for VerbatimTimePeriod Closed
6695 module cdmlib/services should not be an osgi bundle Closed
6682 Formatter and DTO for taxon relationships (e.g. misapplied names) Closed
  cdmlib-remote 4 Collapse all/Expand all
7578 preseve null values in all mesurements during serialization of webservice responses Closed
7561 OccurrencePortalController and FieldUnitDTO should not allow passing the determintation, associated name as argument Closed
7348 RegistrationDTO webservices implemented Closed
6967 RegistrationController identifier endpoints implemented Closed
  taxeditor 15 Collapse all/Expand all
7681 Update date field when editing parse field in TimePeriodElement Closed
7679 NPE when creating root child in classification Closed
7677 Nomenclatural Status is always set to nom illeg in details view Closed
7647 accepted taxa also used as MAN or Pro Parte Synonym are displayed as MAN in details view Closed
7645 specimen admin preferences are not saved Closed
7638 problem with media data missing meta data Resolved
7614 IndexOutOfBoundsException after deleting in bulkeditor Closed
7603 Changing a user group does not work as expected Closed
7576 Set Publish Flag for Subtree Dialog - Problems with Progressmonitor Closed
7549 Show tooltip for data aggregation in character matrix Closed
7544 Dragging a misapplication onto itself throws an exception in name editor Closed
7518 remaining issues for usage of NatTable for bulkeditor Closed
7505 IllegalStateException: Multiple representations problem when adding Annotation to name in NameBulkEditor Closed
7418 remaining specimen determination details view issues Closed
6321 Implement parallel loading + progress bar for loading objects into the bulk editor Closed

CDM Platform 5.1 (released on Jun 27th, 2018)

Downloads: TaxEditor, CDM Server, Data Portal

Issues: 43

What's new?

  • General

    • update script to model 5.0 fixed for PostGreSQL databases
    • freetext search indexing fixed after change in misapplied names
    • term related webservices include language information

  • Dataportal

    • Withheld taxa with publish=false from dataportal results (not yet implemented for freetext search on factual data)
    • External Links fixed
    • Default visibility for pro parte and partial synonyms and misapplied names
    • Find pro parte and partial synonyms in search
    • Creation date for media visible

  • TaxEditor

    • Recently used references list for reference search dialog (bibliographic references only)
    • Find pro parte and partial synonyms in search
    • Default value for taxon publish flag configurable (true, false, inherit)
    • Allow multiple selections for moving taxa
    • Progress monitoring for moving taxa
    • Default nomenclatural status is nom. illeg.
    • Further support for eclipse4
    • Bulk editor
      • change table type (using so called NAT tables now, which are more powerful)
      • sorting for columns by clicking on column headers
      • multi select for deduplication more user friendly
    • Bugs
      • fixed lazy loading exception for misapplied names with type specimen
      • incorrect title cache creation for persons with protected title cache
      • new team member added to the end of the list now
      • some File->New dialogues fixed

  • Browser Editor (Vaadin)

    • Improved consistency in taxon names by restricting the higher name parts like genus name or species epithet to names which are already known to the system. (#7364)
    • Support for validations and replaced synonyms in the TaxonNameEditor
    • Login dialog can be submitted by pressing the enter key
    • Fields visibility in the ReferenceEditor adapts to the Reference type
    • A Field for editorial notes is now available in TaxonName , NameType and SpecimenType editors
    • Bugs
      • Readonly state problems fixed
      • Fixing incomplete terms

# Subject Status
  cdm 2 Collapse all/Expand all
7469 Updated script for individualCount column type in Postgres Closed
7468 Updated script for mediaCreated does not work for PostGreSQL Closed
  cdm-dataportal 3 Collapse all/Expand all
7451 ExternalLinks [ext-links]: update search urls Closed
7417 Make pro parte and partial synonym relationships always visible in data portals Closed
6659 Show mediaCreated in dataportal Closed
  cdm-vaadin 14 Collapse all/Expand all
7498 ClassCastException on saving popup editor for validated name Closed
7482 TaxonNameEditor relpacedSynonym not set after adding or editing the related name Closed
7477 TeamOrPersonField: ToManyRelatedEntitiesListSelect blocks removing new entries Closed
7476 RegistrationWorkingSetEditor: existing name combobox broken after saving a popup editor Closed
7475 error when saving Reference editor with new empty Person in Team when OK or NEW was not pressed Closed
7461 Add oder by ISSN an ISBN to the PagingProvider for all Reference comboboxes Closed
7458 Note field for TaxonName , NameType and SpecimenType editors Closed
7453 Registration Workingsets inconsistent for registrations for sections of publications Closed
7386 TaxonNamePopEditor: com.vaadin.data.Property$ReadOnlyException on saving a basionym Closed
7364 TaxonNameEditor supports editing of a validated name Closed
7338 Validate taxon name against the higher taxon name Closed
7313 eu.etaxonomy.cdm.dataInserter.RegistrationRequiredDataInserter add all terms to vocabulary Closed
7257 Activate Enter key to send login in vaadin login Closed
7223 ReferenceEditor: disable fields depending on the Reference type Closed
  cdmlib 7 Collapse all/Expand all
7486 Fulltext taxon and name search not correct for Synonym based queries Closed
7478 Fix pro parte synonym search Resolved
7467 taxon name parts lookup method with support for wildcard searches Closed
7445 Empty term uri and isoXXX fields should be null Closed
7340 OderedVocabularies are initialised with DefinedTerms Closed
5477 lucene index not updated in all cases after Taxon.addMisappliedName Closed
4101 Default value for publish bit of new taxa must be configurable via DB preferences Closed
  cdmlib-remote 2 Collapse all/Expand all
7508 Add language information to term representations Closed
3560 Withheld unpublished taxa from webservice used in E+M dataportal Resolved
  data 1 Collapse all/Expand all
7092 Adapt dates in Nicks images after mediaCreated became TimePeriod Resolved
  taxeditor 14 Collapse all/Expand all
7499 NPE when trying to open a taxon which belongs to 2 taxon nodes and cancel Closed
7472 lazy loading exception for MAN with type specimen Closed
7464 make move Taxonnodes a longrunning task Closed
7463 Move taxonnodes should be available for multiple selection Closed
7452 TitleCache is not correctly set for new Person Closed
7439 Use NatTable for BulkEditor Closed
7430 New team members should be added at the end of the member list Closed
7422 Set nom. illeg as default in NomenclaturalStatusType ComboBox Closed
7227 New name bulk editor shows all menu entries Worksforme
7010 Adapt handlers for multiple selection in e4 views Closed
6598 Migrate commands and handlers Closed
4363 Show more informative message for unsupported specimen structures in specimen bulk editor Closed
4362 Some File->New dialogs do not work Closed
3984 Easier reference selection - recently used references Closed

CDM Platform 5.0 (released on May 16th, 2018)

Issues: 123

What's new?

  • General

    • Project Website (cybertaxonomy.org) migrated to Drupal 8
    • Demo servers renamed to demo I and demo II
    • Improved performance for saving

  • Model

    • Micrometer added to measurement units
    • Person last name and first name renamed to given name and family name
    • Add second under definable symbol to defined terms (e.g. for better representations of distribution status)
    • Change type of Media.mediaCreated from DateTime (single date) to TimePeriod (start and end time, freetext, ...)
    • Allow time for TimePeriod (before only dates were handled) - not yet handled in TaxEditor
    • Support for zoological in-Authors
    • Add verbatim date to publication date of references
    • Individual count for occurrence data changed from numbers to text
    • Added external links to sources (not yet supported in TaxEditor)
    • Rename "WorkingSet" to "DescriptiveDataSet" and make it a so called identifiable entity (=> some further attributes like sources, extensions, ...)
    • Added nomen oblitum to zoological name status vocabulary

  • TaxEditor

    • Further migration to Eclipse4 (e4) => migration finished now except for some open issues.
    • Hardcoded update sites to avoid problems with automated TaxEditor update in future (and for development)
    • Download site shows version number and release date
    • Name editor
      • Specimen Type Designation ordered by type
      • Pro parte and partial synonyms handled similar to misapplied names (internally handled as concept relationships)
      • Allow editing pro parte and partial misapplied names
    • References
      • Reference search via alternative identifiers available
      • References have verbatim date
    • Media representations have fixed order (by creation date in database)
    • Allow opening gathering events from referencing objects view
    • New Dialog for editing server based preferences, including some more preferences (but still incomplete)
    • Deleting names and taxa for specimen determinations
    • Usage view migrated to e4 and fully functional again
    • Taxon navigator
      • fully refactored underlying data model
      • improve performance
      • refresh mechanism improved for changes elsewhere
      • Progress monitor and cancel for set secundum for subtree (not yet available for set publish for subtree)
    • Feature tree editor
      • Multi-language support for feature tree editor
      • Details view and supplemental data view for feature tree/nodes
    • Rights&Roles: drag&drop for rights on features in rights editor
    • Facts
      • Fact label in fact view truncated and line breaks removed
      • Fact have a time scope now in facts details view
    • Refresh:
      • Taxon navigator after changes to taxa, names or sort order
      • Name editors with specimen types after a specimen has been deleted
      • Name editor after selecting a new taxon for a misapplied name
      • Name relationships and similar data in details view after selecting a new name for a taxon
      • Open taxa refreshed after setting secundum or publish flag for subtree
      • Refresh reference title cache after changing in-reference title in edit dialog
    • Renaming:
      • Person: lastname => family name; firstname => other/given name
      • Specimen Bulk Editor => Specimen Editor (List) and Derivative Editor => Sepcimen Editor (Tree)
      • Working Set Editor => Descriptive Data Editor
    • Distribution Editor
      • Available areas as server based preferences
      • Area selection dialog improved
      • some further bug fixes (still some open)
    • Bug fixes:
      • Selection of nomenclatural code in "new taxon" dialog
      • Accepted taxon and new synonym disappear after creating homotypic synonym
      • Right click menus in name editor
      • correct handling of doubtful in misapplied names
      • Missing labels for gathering events in referencing objects view
      • dirty flag after number recomputation in polytomous key
      • saving of preferences only after pressing "Finish" button
      • Exception after selecting a team after team has been merged in bulk editor
      • Show only accepted taxa for concept relationship taxon selection and polytomous key taxon selection
      • Exception when searching for "?" in Taxon search dialog
      • Exception when creating the first node in polytomous key
      • To many menu entries in a fresh name bulk editor
      • Do not allow self-referencing name relationships
      • Remove "open in ... referencing objects view" where not appropriate
      • Refresh issues for details and supplemental data view
      • Exception when deleting a type specimen
      • Excluded and excluded note notupdated in taxon node wizard
      • Removing country not possible in specimen editors
      • Dirty flag handling when deleting a synonym in name editor
      • Term could be opened multiple times for same term type, now they are singletons
      • Remove old data when again parsing a time period

  • Browser Editor (Vaadin)

    • Many improvements in name registration editor
    • Help for distribution editor
    • Sorting of areas in area selection dialog

# Subject Status
  cdm 17 Collapse all/Expand all
7405 Rename WorkingSet to DescriptiveDataSet Closed
7384 Order SpecimenTypeDesignationStatus according to new order in vocabulary Closed
7334 Make pro parte and partial synonyms real concept relationships Closed
7285 Edaphobase import: implement ranks Cohort, Hyporder Closed
7277 Add micrometer to MeasurmentUnit Closed
7238 Rename lastName and firstName Closed
7144 Add country as level to all areas of type Country. Closed
7109 Rename nom. valid to nom. val. Closed
7096 Add second symbol attribute to DefinedTermBase Resolved
7074 Use TimePeriod for Media.mediaCreated Closed
6943 Allow zoological in-Authors in taxon names Closed
6879 Update uuid and name for admin user group Closed
6752 Add verbatimDate Closed
6720 Make individualCount a string Closed
6699 Delete term version from CdmMetaData Closed
6588 Add URL and URL comment to OriginalSource / ExternalLink Closed
2335 Make WorkingSet IdentifiableEntity Closed
  cdm-vaadin 24 Collapse all/Expand all
7425 Implement VerbatimTimeField for cdm-vaadin and use this in the ReferencePopupEditor Closed
7387 TaxonNamePopEditor: ConstraintViolationException on saving a basionym Closed
7385 TaxonNameEditor adapt field visibility to rank Closed
7382 SpecimenTypedesignationsWorkingsetEditor blocks saving as long as typeDesignations are missing Closed
7381 LIE (LazyInitializationException) when saving SpecimenTypeDesignationWorkingsetEditor for Registration with existing name Closed
7366 TeamOrPersonField readonly if users lacks edit permissions Closed
7365 enable CdmPopupEditors to operate on CdmDecoratorDTOs Closed
7363 TaxonNameEditor supports replaced synonyms Duplicate
7359 cdm popuop editors in readonly mode if the user is not permitted to edit Closed
7355 TaxonNamePopupEditor: newly created nomenclatural reference should be selected immediately Closed
7353 SpecimenTypedesignationsWorkingsetEditor: error on saving after changing kindOfUnit Closed
7350 Collection date is not being saved Closed
7349 RegistrationPopupEditor fails saving new References with new Team with 2 new memers Closed
7344 TaxonNamesEditor to fill authorship fields automatically if nomref and basionym are set? Closed
7343 PersonField allows editing the nomenclaturalTitle Closed
7337 creating of new NameTypeDesignation for empty registration ends up without typified name Closed
7333 LIE when creating registration for existing name Closed
7322 registration workingset editor handles multiple different submitters correctly Closed
7314 support for dot and comma in Georeferenz, Error radius, Altitude, Distance to ... Closed
7269 Use redmine as message hub for submitter curator communication Closed
7249 NameTypeDesignationEditor delete not working Closed
7244 DistributionStatus editor help Resolved
7241 Missing rights are not correctly indicated in Vaadin distribution editor - flexible vaadin errorhandler is needed Closed
6707 transient properties managed by ToManyRelatedEntitiesListSelect are not updated on save Duplicate
  cdmlib 10 Collapse all/Expand all
7392 Remove Cascade from relations Closed
7390 possible permission clash when adding basionym Duplicate
7368 cdm entities report persistence state Closed
7360 users NOT having DELETE are permitted to delete References Closed
7354 DerivedUnitConverter handles associated SpecimenTypeDesignation correctly Closed
7323 RegistrationVoter ignores uuid if propery given Closed
7308 Add nomen oblitum to zoological taxon name status Closed
7289 hibernate warning HHH90000003 pollutes log files Closed
7287 Unit tests using the DefaultTermInitializer break subsequent integration tests in the suite Closed
7209 use git repos instead of svn in all pom.xml Closed
  data 1 Collapse all/Expand all
7374 Set titleCache of feature trees to protected as long as i18n support does not yet exist. Closed
  documentation 3 Collapse all/Expand all
7001 Show date and/or version-number on taxeditor download site Closed
6572 Adapt/Add Wiki pages for e4 development Closed
6158 Update EDIT documentation from svn to git Closed
  taxeditor 68 Collapse all/Expand all
7421 Implement verbatim date for references in TaxEditor Closed
7411 adapt mediaCreated in taxeditor to timePeriod Closed
7399 Adding taxon nodes to working sets leads to MultipleRepresentationException Closed
7395 Selection of nomenclatural code does not work in new taxon dialog Closed
7393 Fix regressions resulting from cascade removal from relationships in TaxEditor Closed
7379 right click menu of accepted taxa should not show "change to" Closed
7378 doubtful in misapplied names incorrect Closed
7336 Implement partial misapplied names in TaxEditor Closed
7335 Allow editing of pro parte and partial synonyms in the same way as misapplied names in the NameEditor Closed
7329 Unify naming for both specimen editors (bulk and hierarchy) Closed
7328 Add label provider for GatheringEvent in referencing objects view Closed
7326 NPE when setting focus on specimen in Specimen Editor (hierarchy) Closed
7325 Taxeditor uses CdmTransientEntityCacher from cdmlib-cache Closed
7324 Add "Open in.." for GatheringEvents in ReferencingObjectsView Closed
7320 dirty flag is not set when clicking "Erneuere Knoten" in Polytomous Keynode editor Closed
7312 some preferences are saved immediately, cancel has no effect Closed
7307 Synonyms should not be shown when creating a new concept relation Closed
7301 Refresh open name editors when deleting specimen used in type designation Worksforme
7300 NPE when selecting team member after merge in bulkeditor Closed
7295 When creating homotypic synonym the accepted taxon and new synonym are not shown anymore Closed
7292 TaxonSelectionDialog throws error when searching for '?' Closed
7291 PolytomousKey Node should not allow to search for synonym Closed
7290 Creating the first node in a new polytomous key throws NPE Closed
7284 Multiple taxeditor jars created in p2 update for a single jenkins build Resolved
7282 Still remaining feature tree editor issues Closed
7279 p2 sites are extremely huge Closed
7268 Re-implement own preference dialog Closed
7239 Rename last name by family name and first name by "Other/given names" Closed
7230 Refresh in name editor does not work if using "reuse taxon" in Misapplied Name View (e4) Closed
7226 Name relationship Dialog shows same name Closed
7215 Implement pro parte misapplied names in TaxEditor Closed
7102 Enable EDIT and DELETE for specimen determinations Closed
7079 P2 updates not found Closed
7065 When updating a subtree the affected and opened taxa are not updated in name editor this needs to be handled Closed
7031 Open in referencing objects view must not show "Open in referencing Objects" Closed
7009 Replace part descriptor IDs in open handler with AppModel constants Closed
6973 Refreshing details and supplemental view Closed
6931 Migrate uses view Closed
6925 Migrate general framework Closed
6913 Remove e3 parts and dependencies Closed
6909 Migrate taxon navigator Closed
6838 Implement i18n for FeatureTreeEditor Closed
6804 Order areas in Distribution Selection Editor Resolved
6779 Allow drag&drop for features in GrantedAuthority editor Closed
6769 Usages can not be created anymore in usage perspective Closed
6746 Implement DetailsView and show SupplementalDataView for Feature Tree and FeatureNode Closed
6668 NPE in DetailsView when deleting a type specimen Closed
6568 Migrate perspectives Closed
6565 [MASTER] Eclipse 4 Migration Closed
6533 New taxon wizard does not refresh is excluded and excluded note information Closed
6526 Show types in correct order Closed
6455 Remove not possible for country in field/derived unit details view Closed
6437 Always update titleCache for nomenclatural reference Closed
6389 Returning a Map in cdmlib leads to data loss Closed
6330 Defined sort order for Mediarepresentations Closed
6318 Truncate TextData in FactualData View Closed
6219 Deleting synonym is persisted immediately, but the editor is set dirty Closed
5783 Rename demo instances back to demo I and demo II Closed
5696 When selecting a new name for a given taxon the name relationships are not updated Closed
5687 search for alternative identifiers Closed
5637 Selecting a new name for a taxon does not update the details view Closed
5193 Changing the name of a taxon does not refresh the taxon navigator Worksforme
4136 authorship part of names not being refreshed in taxon navigator Closed
4048 Changing the name in free text editor does not refresh the taxon navigator view Worksforme
3746 Implement time period scope for description elements in TaxEditor Closed
3161 Term Editors are no singletons Closed
2450 DateTime field - Old values do not get deleted if you enter a new value to the parse field Closed
2380 TaxonNavigator should work with DTO objects instead of full blown cdm instances Closed

CDM Platform 4.14 (released on Feb 15th, 2018)

Issues: 26

What's new?

  • General / Model

    • Export:
      • CSV_Print and CDM light: Progress monitor added (hopefully also fixes the problem of failing long running exports)

  • TaxEditor

    • Distribution Editor
      • Bugfix: Status not deletable
      • Natural sorting of areas
    • Feature Tree editor: several bugfixes
    • Rights Editor:
      • Allow Drag&Drop
    • Taxon Navigator:
      • Handling of excluded and unplaced (move to the end and use icon)
    • Bugs
      • Protected Cache for person editing not working
      • Opening a type specimen from referencing objects view throws an exception

  • Dataportal

    • Bugfix: Misapplied name search not working

  • Browser Editor (Vaadin)

    • Registration UI completed

# Subject Status
  cdm-dataportal 2 Collapse all/Expand all
6679 search for misapplied names in portal does not work Closed
6075 harmonize ' Enable auto-suggest' option with existing code Closed
  cdm-vaadin 12 Collapse all/Expand all
7247 TypeDesignationSetManager must not bundle NameTypes in workingset Closed
7246 ToOneRelatedEntityReloader.valueChange() not triggered after editing bean chosen in ToOneRelatedEntityCombobox or ToManyRelatedEntitiesComboboxSelect Closed
7240 Rename last name by family name and first name by "Other/given names" Closed
7231 replace the SpringApplicationBus by Vaadin4Spring Event Bus in scoped contexts Closed
7229 obsolte code in AbstractEditorPresenter.onEditorDeleteEvent? Closed
7224 PersonField: implement support for 'initials' field Closed
7207 TeamOrPersonField and PersonField comboboxSelect is configurable to use different cache types Closed
7195 RegistrationWorkingsetEditor creates blocking relations for new basionym names Closed
7174 SpecimenTypeDesignationWorkingsetEditor image reference add and edit problems Closed
6811 View and according Presenter are initialized 3x Closed
6740 Popup Editor for NameTypeDesignation Closed
6562 vaadin mvp framwork presenters without view Closed
  cdmlib 2 Collapse all/Expand all
7262 add progress monitor to csv print export and cdm light export Closed
7250 add null checks to TeamDefaultCacheStrategy Closed
  data 1 Collapse all/Expand all
7252 createdby_id often is null Closed
  taxeditor 9 Collapse all/Expand all
7263 Protected title cache for persons does not work Closed
7237 Status are not deletable in TaxEditor distribution status Closed
7234 Make areas in TaxEditor distribution editor sortable Closed
7076 Add Nebula CompositeTable as direct dependency Closed
7030 Opening referenced object of type designation throws NPE Closed
7013 NonUniqueObjectException for setSecundumReferenceForSubtree Closed
6786 Remaining feature tree editor issues Closed
6751 After shutdown error message in log file Worksforme
6547 Implement excluded and unplaced in taxon navigator Closed

CDM Platform 4.13 (released on Feb 1st, 2018)

Issues: 63

What's new?

  • General / Model

    • Export:
      • DwC-A and CDM light: Add rank and area filter (not yet available in TaxEditor)
    • Added pro parte misapplied name relationship (not yet fully supported by TaxEditor and Dataportal)
    • Bugs:
      • DwC-A Export did use incorrect file endings
      • DwC-A Export include headers fixed

  • TaxEditor

    • Exports
      • DwC-A and CDM light: allow filtering for published taxa/synonyms only
      • DwC-A: filtering on single taxa
    • Performance
      • After selecting an area in area search dialog
    • Security:
      • Allow to fully forget "remembered" password
    • Taxon Navigator:
      • Consistent delete dialog for single nodes and nodes with children
      • Set for Subtree functionality: change of data synchronized with open name editors (still some open issues)
    • Search Dialogues:
      • Taxon search: Allow sorting by rank, too
    • Bugs
      • Fix in Caching mechanism: hopefully fixes many of the "multiple representations" exceptions
      • Bulk Editor
        • Set focus to newly created record
        • Exceptions when using wildcards for user and group search
      • TaxonNavigator:
        • ClassCast exceptions when synchronizing with NameEditor
        • Failing behavior after an exception
      • Default Classification for "Move factual data" dialogue
    • Character data editing (experimental)
      • New character matrix editor (only available as experimental feature)

  • Dataportal

    • FSI Viewer for media did not work for Chrome and other browsers anymore

  • Browser Editor (Vaadin)

    • Many improvements in name registration editor (not yet publicly available)

# Subject Status
  cdm 2 Collapse all/Expand all
7158 Add pro parte misapplied name to the concept relationship types Resolved
7114 DerivedUnitConverter.convertTo() creates duplicate entities Closed
  cdm-dataportal 1 Collapse all/Expand all
7164 fsi viewer no longer works in chrome browser Closed
  cdm-vaadin 26 Collapse all/Expand all
7206 CdmEntityCache not correctly updating with entitiy graphs loaded afterwards Closed
7205 use edit and create button for basionyms in the TaxonNamePopupEditor Closed
7204 ToManyRelatedEntitiesListSelect with edit and create button Closed
7197 system-admin autheticated through RunAsAuthenticator can stay authenticated after RuntimeException Closed
7194 NoSuchElementException in LazyComboBox used in ToOneRelatedEntityCombobox Closed
7187 ReferenceEditor: saving with DOI casues exception Closed
7182 ToOneRelatedEntityCombobox implement setReadOnly() Closed
7181 TeamOrPersonField implement setReadOnly() Closed
7176 published=false for Taxon where the according TaxonName is associated with an unpublished Registration Resolved
7172 creating Sections must be disallowd in StartRegistrationViewBean Closed
7171 TaxonNameEditor: mode which only allows adding nomenclatory references which are sub references of the current one Closed
7170 TaxonNameEditor: option to suppress CombinationAuthorshipField & BasionymAuthorship when it contains no data Closed
7169 RegistrationWorkingSet class must use the in-reference as base citation in case a Section is used as nomenclatural reference. Closed
7154 CdmEntityCache can update cached entities Closed
7150 GrantedAuthorities & PermissionVoter for Cdm Collection type Closed
7149 Collection Editor implemented Closed
7148 GrantedAuthorityRevokingRegistrationUpdateLister: delete orphan references to GrantedAuthorityImpl in User and Group Closed
7135 TeamOrPersonField allows selecting from existing Persons and Teams Closed
7132 allow opening editors for name and typedesignations in readonly mode Closed
7130 Registrations ListView allows filtering the list of registrations Closed
7103 verify, fix, improve SpecimenTypeDesignationWorkingSetServiceImpl delete functions Closed
7082 Implement integration test for the SpecimenTypeDesignationWorkingsetEditorPresenter Closed
7070 Registration workingset support for sections Closed
6871 TaxonNameEditor modes for basionym, replaced synonym and validation Closed
6867 explicitely assign and revoke UPDATE & DELETE permission per enitity in the registration workflow Closed
6796 PersonField: add UI Element to choose from existing Persons Closed
  cdmadapter 3 Collapse all/Expand all
7216 Import pteridophyta for Cuba checklist Resolved
7180 cdm light export optionally filters by published flag Closed
6984 withHeader is not yet working in DwC-A export Closed
  cdmlib 11 Collapse all/Expand all
7219 CacheLoader.loadRecursive() fails handling proxy objects correctly Closed
7212 CacheLoader replaces loaded entities with uninitialized proxies Resolved
7201 [DISCUSS] Should we remove created comparison from CdmBase.equals? Closed
7175 DwC-A export optionally filters by published flag Closed
7173 RegistrationDao supports sections Closed
7166 Implement area filter for TaxonNodeFilter Closed
7165 Extend TaxonNodeFilter with rank filtering Closed
7161 DwC-A meta.xml file csv file references invalid Closed
7160 DwC-A meta.xml file has wrong file extension Closed
7137 Registration Identifier minter implemented Closed
7077 INameService.deleteTypeDesignation(TaxonName name, TypeDesignationBase typeDesignation) should delete the type designation also from Registrations Closed
  data 1 Collapse all/Expand all
7055 automatic creation of registrations from name extension only for latest reference Closed
  taxeditor 19 Collapse all/Expand all
7228 Add concept and referencing objects view to supplemental view layer stack Closed
7196 Check existing data when adding specimens to CharacterMatrix Closed
7188 namedArea selection dialog needs too long to set the selected area Closed
7183 Creating a new reference in bulk editor the focus is not set to the newly created entity Feedback
7153 Implement possibility to "logout" completely from TaxEditor Closed
7146 ClassCastException when clicking on synchronize button Closed
7128 NPE in selection dialog Closed
7127 dangling metacharacter exception in selection dialog Closed
7111 synchronize button does not work as expected Closed
7095 Implement Character Matrix Closed
7086 Implement WorkingSet Editor Closed
7078 sort result in taxon selection dialog Closed
7069 Delete taxon node should have consistent configuration Closed
7068 Move factual data to a new taxon should use same classification as default Closed
7008 Migrate export wizards Closed
6800 Allow all filters for DwCA export in TaxEditor Feedback
6762 Implement Character Editor Closed
6728 Changing author data when editing a reference does neither update the reference titleCache nor the author label Closed
6538 Add perspectives for working character data/matrix Closed

CDM Platform 4.12 (released on Dec 5th, 2017)

Issues: 25

What's new?

  • General / Model

    • Better support for SQL Server (not yet ready)
    • Tropicos import (not yet available through TaxEditor)

  • TaxEditor

    • Search Dialogs fully refactored
      • improve performance
      • improve usability (filter button, new record buttons)
      • fix bugs (multiple representation exceptions)
      • migration to eclipse4
    • Specimen Editor
      • edit & delete buttons added to specimen determinations
    • Name Parser
      • better recognition of reference duplicates
      • remove empty spaces in nomenclatural author names
    • bug fixes
      • exception when reusing taxon names
      • widget is disposed exceptions
      • multiple representation exceptions in bulk editor and specimen tree editor
      • refresh of taxon title after taxon/synonym swap
      • ask for saving when closing workbench

  • Browser Editor (Vaadin)

    • Distribution Editor
      • Ordering of areas by vocabulary defined order
      • German translation

# Subject Status
  cdm-dataportal 1 Collapse all/Expand all
7108 supress unwanted sourcetypes in handle_annotations_and_sources() Closed
  cdm-vaadin 5 Collapse all/Expand all
7636 remove obsolete code which dissociates removed TypeDesignations from Registrations Closed
7115 Order distribution areas by vocabulary order in distribution editor Closed
7097 Internationalization for distribution editor Resolved
7083 Implement URI form element for SpecimenTypeDesignationDTOs Closed
7059 use kindOfUnit for TypeDesisgnations instead of DerivationEvent type Closed
  cdmadapter 1 Collapse all/Expand all
6965 Tropicos Import Closed
  cdmlib 6 Collapse all/Expand all
7121 adapt remaining UuidAndTitleCache methods to use filter Closed
7094 Remove empty spaces in nomencl. title of persons Closed
7080 Fix matching for empty time periods Closed
6955 NamedAreaSelection Dialog needs to be adapted to filtered getUuidAndTitleCache loading Closed
6780 ConversationHolder isTransactionActive() returns true even if the transaction is completed Closed
4957 MS SQL Server not functional as it does not allow more than 2100 parameters Closed
  taxeditor 12 Collapse all/Expand all
7126 supplemental data view shows the last selected name data when scrolling down in details view Closed
7125 widgetIsDisposed exceptions when clicking in another part Closed
7124 Avoiding multiple repesentation exceptions by removing the conversation from selection dialogs Closed
7123 Multiple Represenation Exception in Derivate View and bulk editor Closed
7122 titlecache of the taxon is not updated when swap accepted taxon and synonym Closed
7120 implement new buttons for selection dialogs Closed
7119 implement filter button for selection dialogs Closed
7118 migrate selection dialogs Closed
7117 Some bugs in Misapplied Name View after e4 migration Closed
7098 reuse name does not work Closed
7073 add extension to a name does not result in a dirty state Closed
6763 Editors do not ask for saving when closing the workbench Closed

CDM Platform 4.11 (released on Nov 11th, 2017)

Issues: 40

What's new?

  • General / Model

    • Some minor improvements in the rights&roles module

  • DataPortal

    • Display name registration metadata in footnotes

  • TaxEditor

    • Eclipse3->Eclipse4 migration
      • migration
        • Editors: name editor, bulk editors, group authority editor
        • Views: search result, concept graph
        • Modules: molecular module, polytomous key module
        • Dialogues: preferences, import wizards and views,
        • others: taxon navigator, main menu, theme
      • bugfixes for bugs that came with the previous migration
    • Distribution editor: add possibility to add references to distributions (first version)
    • some improvements for the import/export wizard (e.g. order of configuration pages)
    • Setting publish flag for a classification subtree
    • Media View shows preview (first version, needs to be switched on in preferences)
    • Performance improvements (details view rendering, combo boxes, name editor focus)
    • Bugs
      • rank selection did not work if ranks were sorted naturally
      • drag&drop for classifications in navigator disabled
      • exception when switching type of description element in details view
      • size of search field to small
      • multiple minor issues

  • Browser Editor (Vaadin)

    • Distribution editor fixed and improved (ready for use in production)
    • Name Registration
      • Rights&Roles for Registrations
      • RegistrationUI: Buttons only enabled if the user has according permissions
      • phycobankID links only active when status is PUBLISHED
      • minor bug fixes

# Subject Status
  cdm-dataportal 1 Collapse all/Expand all
6985 display Registration metadata in footnotes Closed
  cdm-vaadin 9 Collapse all/Expand all
7053 TeamOrPersonField disabled state inconsistent Closed
7046 replace open session per view pattern by DTO strategy Closed
7028 make available distribution status configurable in vaadin distribution editor Closed
7026 RegistrationVoter evaluates CdmAuthorities with RegistrationStatus properties Closed
6999 RegistrationUI: Enable, disable editor buttons according to the users permission to edit or delete the according cdm entity Closed
6997 RegistrationUI: Show authenticated user in toolbar with option to logout Closed
6995 Show phycobankIDs in Workingset editor Closed
6994 phycobankID links only active when status is PUBLISHED Closed
6802 Selection of distribution in Vaadin distribution editor does throw LIE Closed
  cdmadapter 1 Collapse all/Expand all
6953 use taxonNodeOutStreamPartitioner in CdmLightExport Closed
  cdmlib 4 Collapse all/Expand all
7027 GrantedAuthorityImpl.authority entities inconsistent Closed
7021 CREATE permission not sufficient to save new TaxonName entity Resolved
7018 implement a CdmPermissionVoter and default authorities for SpecimenOrObservationBase Closed
7016 implement a CdmPermissionVoter for TypeDesignations Rejected
  cdmlib-remote 1 Collapse all/Expand all
6987 LIE during name catalogue service call processing Closed
  taxeditor 24 Collapse all/Expand all
7088 Media can not be saved in TaxEditor Closed
7062 combo box for hierarchically sorted ranks select wrong terms Closed
7056 Media View should show Preview Resolved
7044 Migrate theme Closed
7041 D&D for classifications should not be possible and corrupts data Closed
7011 Migrate group authority editor Closed
7006 Migrate preferences Closed
7005 Migrate import wizards Closed
7000 clicking in specimen details of bulk editor results in an empty details view Closed
6998 Potential NPE with endless loop when switching type of description element in details view Closed
6990 Migrate search result view Closed
6989 Migrate concept graph view Closed
6974 improve the io wizards Resolved
6932 Migrate bulk editor Closed
6924 Taxon name incorrect after swap synonym with accepted taxon Worksforme
6921 Migrate data import views Closed
6914 exception in bulk editor after search Closed
6908 Migrate polytomous key module Closed
6902 Migrate molecular module Closed
6862 Supplemental data view is grey when editing images in specimen tree editor Worksforme
6622 Migrate remaining main menu items Closed
6595 Migrate name editor Closed
6569 Remove unused application model from taxeditor.application Closed
4155 Implement handler (IHandler) to trigger recursive setting of the publish bit on a taxon subtree Closed

CDM Platform 4.10 (released on Sept 15th, 2017)

Issues: 56

What's new?

  • General / Model

    • Allow recursive setting of publish flag (not yet available in TaxEditor)
    • Fix usage of country label in specimen title cache

  • Rights&Roles

    • Role group "Admin" as standard group to all CDM instances
    • Fix rights checking for editing of persons and teams

  • DataPortal

    • Fix selection of best matching image representation for profile picture and overlay images
    • Fix bug with links to synonyms in tabbed view with no explicit synonym tab

  • TaxEditor

    • New download site available
    • Eclipse3->Eclipse4 migration
      • Views: Details, Conceptrelations, Referencing objects, datasource, factual data, supplemental data, media
      • Editors: terms
    • Misapplication editing improved, also reusability of misapplied name taxa
    • Automated updating fixed
    • Export:
      • CDM light and DwC-A export for taxonomic subtrees (e.g. families, genus, ...)
      • Progress monitor for DwC-A export
      • DwC-A exports higher classification for each taxon
      • Fix DwC-A export not stored in selected file
    • Allow scientific name editing for bacterial, fungi, cultivar plants and undefined codes (non viral names)
    • Add Person, team and specimen cache updating
    • Specimen
      • Add Life-form to field unit and kind-of-unit, lifestage and sex to derived units (specimen)
    • Performance
      • Improve performance when first loading selection dialog for named area (still needs further improvement)
      • View refresh faster (still needs further improvement)
    • Bugs
      • Exception during drag&drop in taxon navigator
      • Editing Rights&Roles throws exception
      • Deleting media leads to inconsistent data
      • Move description to other taxon command fails in factual data view
      • Sorting of ranks not configurable anymore
      • Duplicate menu in search result view
      • Handling of with time zones for date time editing (image created, ...)

  • Documentation

    • Fix OAIPMH swagger documentation

  • Vaadin

    • Registration UI prototype

# Subject Status
  cdm-dataportal 5 Collapse all/Expand all
6969 Use media representation which best fits the available size for taxon profile picture Closed
6959 Block to display Registration metadata Closed
6877 links to synonyms not working when portal in tabbed mode without separate synonymy part/tab Closed
6815 OriginalSource idNamespace + idInSource default separator should be whitespace Closed
6684 Use media representation which best fits the available viewport size for the Image Overlay Closed
  cdm-vaadin 5 Collapse all/Expand all
6855 TeamOrPersonField allows adding Persons and Team for users with unsufficient authorities Closed
6852 GrantedAuthorities and permission Groups for Phycobank Closed
6846 layout component sizing probelms in worflow view Closed
6843 resize problems of Popup editors when clicking contained elements Closed
6810 View for starting new registrations implemented Closed
  cdmadapter 3 Collapse all/Expand all
6968 Unexpected error in CDM light when exporting Individuals Association with no unit attached Closed
6933 Add possibility to export only families or other part of the tree in CDM light and DwC-A export Closed
6880 Allow removing auditing from imports Closed
  cdmlib 8 Collapse all/Expand all
6957 Implement cache strategy for viral names Closed
6856 Add group Admin to standard FirstDataInserter Closed
6851 Use country label instead of description in specimen cache strategy Closed
6842 NPE in Registration constructor when name is null Closed
6721 Show kindOfUnit, Sex and Lifestage also for DerivedUnits in DUFacade Closed
6654 implement a CdmPermissionVoter for Registrations Closed
6630 Unify TaxonName cache strategies Closed
3740 Allow recursively setting the publish bit for TaxonBase Closed
  cdmlib-remote 3 Collapse all/Expand all
6964 Registration webservices implemented Closed
6948 OAIPMH service broken by NPE with verb=ListIdentifiers & set=taxon Closed
6836 Swagger documentation for OAIPMH broken Closed
  documentation 1 Collapse all/Expand all
6812 Improve TaxEditor download site Feedback
  taxeditor 31 Collapse all/Expand all
6961 Drag&Drop for taxon nodes throws NPE when hovering Classification Closed
6958 The description of the referencing objects view is missing in e4 Closed
6949 The Media details view does not show the full image Closed
6926 First call of NamedAreaSelectionDialog needs too much time Closed
6923 move description to other taxon command fails in factual data view Closed
6922 Migrate term editor Closed
6919 Unprotected titleCache field is still grayed Closed
6918 Rank is always sorted by label Closed
6915 Delete does not work in media view for taxon Closed
6912 Migrate datasources view Closed
6911 Migrate concept view Closed
6910 Migrate referencing objects view Closed
6907 Migrate factual data view Closed
6906 Migrate media view Closed
6905 Migrate supplemental data view Closed
6894 NPE when trying drag&drop a Classification to the GrantedAuthority editor Closed
6875 Duplicate menu in search result view Closed
6860 Use consistent calendar system for date picker Closed
6828 SpecimenOrObservation and Person/Team missing in Cache updater Closed
6809 Name Editor throws double selection change events Closed
6801 DwCA Export is not stored at expected place Closed
6799 Implement progress monitor for DwC A export Closed
6797 Use short sec citation for misapplied name in NameEditor Resolved
6789 Remaining issues for misapplied name details view Closed
6781 Automatic update does not work anymore for TaxEditor Closed
6730 Deleting media leads to inconsistent data Feedback
6722 Make Life-form available via DerivedUnitFacade Closed
6693 Implement missing nomenclatural codes for name detail element Closed
6692 Make name types changeable Closed
6597 Migrate Details View Closed
6347 Improve layout for navigator sorttype selection Closed

CDM Platform 4.9 (released on July 20th, 2017)

Issues: 20

What's new?

  • General / Model

    • Framework for csv imports implemented

  • DataPortal

    • In tabbed version it is now possible to show the synonymy on the general page
    • Feature block items "glue" is now configurable
    • Media:
      • image viewer uses best quality media representation now
      • "show captions under thumbnails" is now evaluated
      • "back to image" improved
    • Specimen table:
      • uses country label instead of full description (not yet fixed for titlecache, will come in 4.10)
      • collection date shows up now
      • label for specimen in collection simplified
      • preferred stable URI shows up as text, not only link
    • Bugs:
      • map did not show point data, when some specimen where not georeferenced
      • bounding box for maps did not work correctly

  • TaxEditor

    • Feature tree editor
      • allows drag&drop from term editor
      • uses context menu
    • Restore
      • restoring views after restart/reconnect works now on a per instance level when using multiple instances of the TaxEditor on the same computer, leading to less exceptions
    • Taxon Navigator
      • Linking taxa opened in NameEditor with taxa in navigator works now (was fixed in 4.8 but not mentioned there)
    • Experimental
      • Allow handling terms as "kind-of"
    • Bugs
      • details view for taxon relationships fixed
    • Logging
      • human readable labels for datasources when logging datasource issues

  • Vaadin

    • Generic MVP (Model View Presenter) framework with support for the CDM library

# Subject Status
  cdm-dataportal 9 Collapse all/Expand all
6837 Use country label instead of description for specimen table Closed
6831 glue for feature block items configurable Closed
6822 Media settings: "Show captions under thumbnails" has no effect on the Image Viewer Closed
6820 Settings option to place the synonymy at the top of the general page and to supress the according tab. Closed
6817 Media page: "Back to Image" only shown when the HTTP referrer is a cdm_dataportal page Closed
6816 [Dataportal] Specimen table issues Closed
6703 Improve title handling for media in dataportal Closed
6683 Use best quality media representation in image viewer on media page Closed
6608 Setting the 'Bounding box' for the OSM layer no longer works Closed
  cdm-vaadin 1 Collapse all/Expand all
6687 Multiple representations of the same entity merge problem Closed
  cdmadapter 2 Collapse all/Expand all
6793 Implement simple Csv import framework Resolved
6286 Import Flora Hellenica Resolved
  cdmlib 2 Collapse all/Expand all
6825 Specimen map shows point data only if ALL field units are georeferenced Closed
6790 IO class hierarchie creates problems in IDE Closed
  taxeditor 6 Collapse all/Expand all
6897 i18n Messages.java files are missing in the build version Closed
6848 Add context menu option to add "kind of" term to TermEditor Closed
6847 Change location of workbench.xmi to taxeditor installation folder Closed
6808 New misapplied name details view destroyed old concept relationship details view Closed
6787 NPE when opening Specimen Tree Editor Closed
6421 Document workaround for user.home location problem in Windows Closed

CDM Platform 4.8 (released on July 6th, 2017)

NOTES for TaxEditor users

  • The automated update via Help->Search for Updates does not seem to work for this version. Please download the TaxEditor from https://dev.e-taxonomy.eu/download/taxeditor/stable/ . Contact us if you encounter problems.
  • It may happen that the right click menu in the Specimen Tree Editor does not appear. In this case please delete the following file: {user}.cdmLibrary.metadata.plugins\org.eclipse.e4.workbench\workbench.xmi

What's new?

  • General / Model

    • Classes for name and type registration added
    • Unify taxon name class (will allow changing name types like changing a botanical name into a zoological name) and simplifies development
    • Person: initials added
    • Reference: type Website: accessed (date) field added
    • References: attributes added to allow usage sharing references by multiple instances
    • Remove unique index on rights (e.g. copyright) to make it reusable
    • Added "Exact Value" to statistical measures for quantitative data
    • Improved reporting for schema updates

  • DataPortal

    • Position of protologue icon moved directly behind nomenclatural reference (was behind status before, misleading because status can have its own reference)
    • Additional base maps for the map viewer: Stamen terrain, OpenTopoMap
    • In cases where images are available in multiple qualities the DataPortal now chooses the quality which is most appropriate for the current display situation.

  • Imports / Exports

    • DwC-A (Darwin Core Archive) export for taxa fixed, improved and available via webservices
    • Improved reporting for imports and exports

  • Vaadin Based Applications

    • MVP framework with popup editor support which integrates into the the spring framework
    • Prototype implementation of the Phycobank (registry for algal nomenclatural acts)

  • TaxEditor

    • Misapplications:
      • err. sec. references editable
      • improved formatting in name editor, especially for names having an author and a nom.ref., this allows better reusing of names
    • Person "initials" editable and used for better reference formatting (initials behind family name)
    • Feature Tree Editor: moved from preferences to main menu (together with term editor), and did some improvements
    • Website "accessed" editable and integrated in formatting
    • Media: "media created" editable
    • Specimen Tree Editor migrated to only use Eclipse4 functionality now (all other editors still use a compatibility layer component)
    • Markers set to true by default
    • Parser
      • Autonym hybirds parsable
    • Bugs:
      • Delete was not successful, but did not show an exception
      • Some menu items were duplicated
      • Incorrect user management when changing password
      • Setting of kind-of-unit for specimen
      • Restoring of views after restart or reconnect

# Subject Status
  cdm 19 Collapse all/Expand all
6717 Rename taxonNameBaseTitleCacheIndex and taxonNameBaseNameCacheIndex Closed
6663 Add required attributes to Reference to include externally managed references Closed
6661 Add initials to Person Closed
6660 Remove unique index from Rights MN tables Closed
6618 Add link to Structure, Property, Method(?) and Type(?) Closed
6617 Add "Exact Value" to StatisticalMeasure Closed
6535 MetaDataPropertyName from number to string in DB Closed
6529 Extend WorkingSet to allow a more fine grained definiton of taxon set Closed
6472 Include keys as target for IntextReferences Closed
6368 Merge all TaxonNameBase classes, remove DTYPE, rename table Closed
6367 Make NomenclaturalCode an attribute ("type") of TaxonNameBase Closed
6361 [MASTER] Merge all TaxonName classes into 1 class Closed
6340 Update script for nomenclatural status types Closed
6258 Add Registration to cdm model Closed
5817 Rename RelationshipTermBase_inverseRepresentation Closed
5258 Accessed field for WebPages Closed
5149 Remove UNIQUE index on Sequence_Reference.citations_id column Closed
3734 Stop separating term and schema update Closed
2949 Simplify TaxonName classes Duplicate
  cdm-dataportal 4 Collapse all/Expand all
6702 Post release 4.8.0 tasks Rejected
6700 Adapt dataportal to TaxonName model changes Closed
6653 add more base maps to the data portal Closed
6651 the protologue icon should be shown directly after the nomenclatural reference Closed
  cdm-vaadin 5 Collapse all/Expand all
6759 better theming of the on/off SwitchButton which is used in SwitchableTextField component Closed
6758 remove Registration type icons Closed
6724 Popup Editor for SpecimenTypeDesignation Workingsets Closed
6719 Compact display of TypeDesignations in RegistrationItems with edit button per fieldUnit Closed
6673 conceptual problems with vaadin Popup editor presenters (AbstractEditorPresenter) Closed
  cdmadapter 2 Collapse all/Expand all
6754 Adapt DwcA Export to CDM light export strategy Closed
6517 Stable IDs in Edaphobase at least for example taxa Resolved
  cdmlib 11 Collapse all/Expand all
6750 DerivedUnitConverter which can convert DerivedUnits <--> MediaSpecimen Closed
6725 Bug in DU facade for setting / retrieving kind of unit Closed
6689 Implement SchemaUpdateResult instead of boolean Resolved
6671 Remove generics from TaxonName Closed
6662 Adapt person formatting, set initials behind lastname Closed
6656 Make autonym hybrids parsable Closed
6612 Implement dao and service class for Registrations Closed
6504 Bibliographic references should not start with firstname. Closed
6240 maven javadoc plugin fails with java 1.8 Closed
6138 fix test testNoRecursiveChangeEvents() in DerivedUnitFacadeTest Closed
3665 Further implementation of original spelling name caching Closed
  cdmlib-remote 2 Collapse all/Expand all
6755 Make DwcA export available for annosys via web services Closed
6502 LIE during request to portal/classification/{uuid}/pathFrom/{taxonNodeUUID}/toRa nk/{rankUuid} Closed
  data 1 Collapse all/Expand all
6226 Delete orphaned key nodes Closed
  taxeditor 27 Collapse all/Expand all
6795 Invoke selection change event when setting focus to specimen editor Closed
6785 Editors should be able to have multiple instances Closed
6783 Menu item for editing right is missing Closed
6776 Restored Specimen Editor does not load conversation => NPE Closed
6773 Changing pwd as admin changes the user Closed
6749 No media is created for new mediaSpecimen Closed
6748 Linking between derivate view and facts/media view Closed
6747 Media and Facts view is inactive for specimen editor Closed
6743 Translation missing for Specimen-Editor context menu Closed
6733 NPE when trying to open Derivative Editor Closed
6726 NPE in FactualDataView and feature selection does not show any entries in Factual Data View Closed
6711 Make initials editable in TaxEditor Closed
6694 Migrate FeatureTreeEditor Closed
6681 Correct formatting for misapplied names in name editor Closed
6669 Duplicate menu items in several views and editor Closed
6666 Exception in SearchResultView when starting the Taxeditor Closed
6664 Deleting often does not succeed without throwing an exception Closed
6658 Make mediaCreated editable in Media view Closed
6607 Implement WebSite.accessed in TaxEditor Closed
6596 Migrate specimen editor Closed
6527 Refactor delete configurator for media Closed
6473 Marker by default should be true Closed
6446 Merge botanical and zoological names into TaxonNameBase in external applications Closed
6445 Remove occurrence of NonViralName in external applications (TaxEditor etc.) Closed
6418 Status line does not update after completing the update of the referencing objects view Worksforme
6390 Details view for misapplied names Closed
3866 Link Taxon Editor name to the taxon in the taxon navigator Closed

CDM Platform 4.7 (released on May 16th, 2017)

What's new?

  • General / Model

    • The main change in Version 4.7 is the upgrade of the TaxEditor from Eclipse 3.7 to Eclipse 4.6 (Neon). This upgrade will ease development in future. To make the TaxEditor running under e4.6 several adaptations had to be made.
      • IMPORTANT: Due to the upgrade it might happen that during the first opening an error shows up. If this happens CLOSE and REOPEN the editor.
      • IMPORTANT: Due to the upgrade the default update mechanism for the TaxEditor will not work. Instead you need to install it from scratch (download from https://dev.e-taxonomy.eu/download/taxeditor/stable/ and unzip into any folder).
    • A new import and export framework has been established. It is meant for more feedback and reporting during the imports. Currently it is used only experimentally for the new "Excel Distribution Update" import (experimental feature), and partly for the new "CDM light (csv)" export (also experimental in the current state).
    • New identifier types for botanical names added: IPNI, Tropicos, WFO (World Flora Online)
    • Improved handling of hybrids
    • Automatic basionym recognition (not yet available in TaxEditor)

  • DataPortal

    • Allow multiple layers in maps (option to define a wms overlay layer for the openlayers map viewer)
    • Bugfix for fast moving maps while padding

  • Imports / Exports

    • Improved Import- and Export framework for better report resulting (existing imports/exports still need to be adapted to the new framework)
    • New: "CDM light (csv)" export - a CSV export that exports all CDM data for a single classification in csv format
    • New: RIS Reference import - e.g. to import reference data from Endnote via RIS format (still experimental, some attributes are not yet handled)
    • New: "Excel Distribution Update" added (still experimental, please contact us, if you want to use it)
    • New: Multilingual Term Representation import (not yet available in TaxEditor)
    • New: Identifier import (not yet available in TaxEditor)
    • Updated: ABCD Import
      • possibility to import all siblings of a specimen derived from a culture.
      • better handling of media data, identifications, gathering events

  • TaxEditor

    • Upgrade to Eclipse 4.6
    • Improved Parser
    • Parse "sp. nov." and similar names
    • Improved handling for original spellings (further improvements needed)
    • Prefill nomenclatural reference selection dialog if taxon name author is given
    • Selected items removed from selection dialog
    • Server-side preference for frequently used biocase providers added (ABCD import)
    • Improved search behavior in Specimen Hierarchy Editor
    • Some improvements for the Alignement Editor integration
    • Rank list for create new name in bulk editor sorted
    • Improvements for specimen search/import:
      • better parsing of results to display scientific name, collection etc
      • add possibility to configure the import in result view
      • possibility to set the name of the import reference
    • Bug fixes:
      • Delete synonyms in Name Editor with supplemental data attached
      • Delete synonyms in bulk editor
      • Exception when switching to simple name details view
      • Empty reference dialog after changing reference type
      • Incorrect data when editing a new nomenclatural reference for a new name
      • Exception ("multiple representations") when adding name relationships

  • Vaadin Applications

# Subject Status
  cdm 2 Collapse all/Expand all
6531 Add WFO Name Identifier to Identifier Types Closed
6515 Add Tropicos and IPNI Name Identifer Closed
  cdm-dataportal 4 Collapse all/Expand all
6614 cdm_taxontree: plus/minus/loading gifs not correctly loaded Closed
6573 Option to define a wms overlay layer for the openlayers map viewer Closed
6442 Feature block settings: margins for data in block level elements Feedback
6303 distribution map is moving too fast Closed
  cdm-vaadin 2 Collapse all/Expand all
6628 require vaadin UIs to be explicitely enabled per cdm-webapp instance Closed
5285 Use Vaadin Spring Add-on Closed
  cdmadapter 8 Collapse all/Expand all
6636 First version of RIS reference import (e.g. for Endnote import) Resolved
6542 Import identifier for Nepenthaceae names Resolved
6541 Implement ImportResult Resolved
6524 Distribtion Update for Fauna Europaea Closed
6519 Implement ExportResult Resolved
6509 Implement Representation csv import Resolved
6314 CDM light (csv) export implemented Closed
6166 In ABCD import also import all siblings of a culture or tissue sample Closed
  cdmlib 6 Collapse all/Expand all
6578 Implement name cache for hybrid formulas Resolved
6577 Make sp. nov. parsable Closed
6576 Implement operation that guesses all basionyms for a syonymy Closed
6511 Handling of objects being referenced in a InTextReference during deleting Rejected
6281 delete synonym with annotations throws exception Closed
6078 import of references in specimen search Resolved
  taxeditor 28 Collapse all/Expand all
6640 Integrate RIS Import in taxEditor Resolved
6639 Context menu of Specimen Editor is missing entries Closed
6620 [MASTER] Critical Eclipse 4 bugs Closed
6619 Integrate Excel distribution import into taxeditor Resolved
6604 NPE when having simple details view switched on Closed
6587 Wrong order of "Window" menu Closed
6586 Duplicate menu items in name editor context menu Closed
6584 Remove annotation and Editor navigation from perspectives/toolbar Closed
6582 status bar not completely visible Closed
6579 user and usergroup menu item is missing Closed
6570 rank list should be sorted Closed
6566 Migrate main menu Closed
6558 Some menu items are missing Closed
6556 After restart of the editor the previous views show errors Rejected
6553 eclipse 4 problem while creating controls for name editor Closed
6552 Remove "Run" menu from editor Closed
6550 ArrayIndexOutOfBoundsException when opening a taxon with double click from the navigator Closed
6549 ClassCastException when adding a new synonym in name editor Closed
6540 After changing type of reference the dialog is empty Closed
6539 Build problems for taxeditor post 4.6 release Closed
6530 After editing a nomenclatural reference of a new created name some information is lost Closed
6489 Selection dialogs should not show the already selected elements for Synonym and TaxonNode operations Closed
6480 Re-saved by cascade in specimen bulk editor Feedback
6399 Add admin property frequently used biocase provider Closed
6385 Specimen Editor should handle new search same as bulk editor Closed
6088 New reproducable multiple representations exception for name relationships Closed
4452 p2 update problem with nebula compositetable dependency Closed
3533 Prefill nomenclatural reference information if possible Resolved

CDM Platform 4.6 (released on March 13th, 2017)

What's new?

  • General / Model

    • Full migration to Java 8
    • Improved import functionality for IPNI Names (not yet available in TaxEditor)
    • Improved handling for intext references (references within a text) including support for deduplication (intext references are not yet editable in TaxEditor or visible in DataPortal)
    • Bugfix in permission handling for rights and roles
    • Prepare for simplifying names module
    • Formatting
      • Specimen: Use barcode or catalogue number if accession number is not available
      • References:
      • #5834
      • #6449 References with protected titleCache
      • #3532 Nomenclatural reference null for database

  • CDM Server

    • Improved caching for multiple instances
    • Improved authentication / security

  • DataPortal

    • Authentication for triggering freetext index creation
    • Bugs:
      • Wildcard search in advanced search #6354
      • Missing data of marked descriptions
      • "Usage" data not shown anymore
    • Remove "sensu" from misapplication footnotes
    • Formatting:
      • Improved formatting for media data

  • TaxEditor

    • Main menu
      • Move user and user groups to Admin menu
      • Move Specimen hierarchy editor to (bulk) editor menu
    • Selection dialogs
      • Restrict selections of in-references to the respective reference type
    • Referencing objects view
      • Improved performance and loading in background
      • Fixed some bugs throwing exceptions
    • Taxon navigator
      • Set secundum for subtree (including synonyms)
    • Specimen editor:
      • Improved performance for counting results
      • Improved labeling if some data is missing
    • Rights (e.g. copyright) implemented as reusable record
    • Improved Internationalization
      • More terms/sentences translated to German
      • Preparation for Spanish translation
    • Improved handling for protected caches
    • Parser improvements
      • Names
      • Coordinates
        • lat/long with English apostrophs
    • Bugs
      • Exceptions after changing password
      • Field unit title cache not filled correctly #4390
      • Exceptions when deleting misapplications
      • Exceptions when entering dates and altitudes
      • Exceptions when deleting empty name in name editor
      • Exceptions when adding types to a taxon name
      • Exceptions when deleting persons/teams
      • Exceptions in datasource view
      • Exceptions when deleting recently created media
      • Exceptions when editing rights for a user group
      • Avoid creation of dummy terms
    • #6408 NPE in AbcdParseUtility

  • Web Editor

    • New architecture for future developments

# Subject Status
  cdm-dataportal 7 Collapse all/Expand all
6432 Apply CSS only to non-admin pages Closed
6431 php INFO 'warnings' in fauna europeae taxon page Closed
6392 selenium tests for palmweb uses data Closed
6382 option to supply user credentials in the admin setting for the freetext index triggers Closed
6375 footnotes on sensu references must not be prefixed with 'sensu' Closed
6374 Uses no longer shown in palmweb portal broken Closed
6349 Fix media description handling Closed
  cdmadapter 1 Collapse all/Expand all
6440 Improve IPNI Name Service Closed
  cdmlib 26 Collapse all/Expand all
6496 Pages not shown in biblographic reference of articles Closed
6459 Implement deduplication for IntextReferences Closed
6439 Add (Heft xxx) as part of volume to name parser Closed
6419 CdmApplicationDefaultConfiguration should be named CdmRepository Closed
6405 CdmPermissionVoter handles merged and separate CdmAuthorities the same Closed
6381 Specimen titleCache should include barcode or catalogue number if accession number not exists Closed
6369 Create interfaces for TaxonName types Closed
6366 Merge cultivar names into TaxonNameBase Closed
6365 Merge botanical and zoological names into TaxonNameBase Closed
6364 Merge viral names and bacterial names into TaxonNameBase Closed
6363 Implement validation rules for all names according to their code Closed
6362 Remove occurrence of NonViralName in code Closed
6360 Move NonViralName functionality to TaxonNameBase Closed
6354 Advanced search: non phrase search with wildcard broken Closed
6311 Refactor IdentifiableEntity.compareTo method Rejected
6111 invalid SQL (MySQLSyntaxErrorException) during call to CdmEntityDaoBase.list() Closed
6076 Specimen biocase search should work on observations Closed
5983 Better parsing of hybrid names Closed
5924 Change password leads to bad credentials Closed
5848 Problem with writing ehCache folder on network drive using UNC path (net.sf.ehcache.CacheException) Closed
5834 Show volume etc. for generic references Closed
5554 Allow parsing of lat/long with different minute/second characters Closed
4390 Titlecache of field unit does not update when changing field unit data via derived unit facade Closed
4232 Check all Comparators for fulfilling the Comparator contract Closed
2501 Remove redundant SDD import class Closed
922 Implement compareTo method in IdentifiableEntity properly Closed
  cdmlib-remote 3 Collapse all/Expand all
6398 portal/taxon/{uuid}/descriptions.json with markerType-filter returns no data Closed
6393 manage/* web service can be used by ajax requests Closed
2939 ehcache diskStore conflict? Closed
  devOps 1 Collapse all/Expand all
6255 jenkins job cdm-webapp-HFX-FINISH fails due to merge conflict Closed
  platform 1 Collapse all/Expand all
6401 Update working environment to jdk 1.8 Closed
  taxeditor 30 Collapse all/Expand all
6497 "Open in bulkeditor" does not show up in SearchResultView Closed
6488 Always show some label text in the specimen editor even when no information is available Closed
6483 Restructure "Show view" and bulk editor menu Closed
6479 Class Cast Exception when trying to delete a misapplication Closed
6477 Show collection name in specimen editor if no collection code exists Closed
6466 IndexOutOfBoundsException when entering month Closed
6454 NumberWithLabelElement.getFloat and .getInteger should return null Closed
6453 Deleting text from min/max fields throws NPE Closed
6449 Nomenclatural references with protected titleCache are not shown correctly in name editor Closed
6433 NPE in PartialElement Closed
6424 Empty name creates problem/NPE in name editor Closed
6408 NPE in AbcdParseUtility Closed
6388 Duplicate entry exception when adding types to a taxon Closed
6376 NPE when deduplicating agent Closed
6372 NPE when using ShowView - Datasource Closed
6336 NPE when deleting recently created media Closed
6322 In the specimen editor showing the warning for long loading times already has a long loading time Closed
6315 Implement setSecundumForSubtree in TaxEditor Closed
6309 Creating an existing user throws exception Closed
6308 Add configuration dialog for the deletion of synonyms in name editor Closed
6304 Deleting of Person used as user does not work Closed
6300 DataIntegrityViolationException when saving a type Closed
6262 Implement Rights reusable in TaxEditor Closed
6214 Add project specific preferences to CdmPreference menu Closed
5691 Referencing objects view makes editor inresponsive if an object references many objects Closed
5216 Changing the CRUD flags of an existing GrantedAuthority in the CdmAuthorityEditorInput causes an MySQLIntegrityConstraintViolationException Closed
3737 Protected caches for taxa and names behave inconsistent Closed
3603 Remove creation of dummy DefinedTerm when creating new Term related entities Closed
3532 Nomenclatural reference null for database Closed
1606 Restrict filtered selection of in references to the respective reference types Closed

CDM Platform 4.5 (released on January 19th, 2017)

What's new?

  • General / Model

    • Possibility to set secundum reference for subtrees (implementation in TaxEditor still missing)

  • DataPortal

    • Search
      • Advanced search for taxa allows wildcards and some further bugs fixed
      • Remove duplicates for common name search #6296
      • Allow hiding classification information
    • Improved display of media in image galleries and media pages
      • Display of descriptions
      • Display of rights (e.g. copyright)
      • Display of sources
      • Fix media representations (e.g. thumbnails) display on media page
    • Taxon page
    • Labels of tabs customizable
    • Bugfixes for exceptions

  • TaxEditor

    • Repair method for corrupted CDM instances
    • Polytomous Keys
    • Allow inserting nodes at the beginning or in between
    • other bugfixes
    • Media
    • Allow configurable delete in MediaView and bulk editor
    • Fix save for reused Media
    • Zoological nomenclatural status not shown anymore for botanical names (not yet the other way round)
    • Order in supplemental data view changed (types that are used more often were moved up)
    • Improve order of type selection for sources/references
    • Disallow self-referencing name relations
    • Make details view empty if no selection exists
    • Term editor menu structured
    • Further Bugfixes
      • selectable terms for stage and preservation method fixed
      • delete for references fixed
      • delete of unsaved taxon descriptions fixed
      • selecting taxon node with '?' fixed
      • missing ampersand in some labels fixed
      • exception during creation of new taxon fixed

# Subject Status
  cdm-dataportal 13 Collapse all/Expand all
6430 proxy_content not returning data Closed
6397 palmweb: various feature blocks missing Closed
6301 Display of sources for images Closed
6292 IAPT-Data Registration date Closed
6291 allow hiding the classification information from the search results Closed
6290 style Phycobank registration data in tabular style Closed
6288 harmonize CommonName feature block elements Closed
6278 add sec reference as class attribute to all taxon markup Closed
6275 Phycobank - DataPortal: display registration data stored in name extension Closed
6260 media page: rights stored in the cdm are not displayed Closed
6259 Media page problems with multiple media representations Closed
4490 Make the label of the taxon page tabs customizable for portal admins Closed
4223 Advanced search returns unexpected results Closed
  cdmlib 6 Collapse all/Expand all
6296 Simple search for common names returns duplicates Resolved
6283 Exceptions when editing polytomous key Closed
6274 add update of childrenCount cache in repair method Closed
6190 remove svn property place holder in first line of code Closed
4766 Repair Methods for the cdm instance Closed
3465 Function to copy secundum reference of a given taxon node to all it's children Closed
  cdmlib-remote 10 Collapse all/Expand all
6373 LIE during request to /portal/descriptionElement/byTaxon Closed
6339 frontendBaseUrl parameter not longer working in web services Closed
6323 LIE during request to name_catalogue/taxon.json Closed
6317 LIE during request to portal/taxon/find.json Closed
6268 descriptions missing in media service responses Closed
6261 NPE while processing /portal/media/{uuid}/sources in BaseController Closed
6249 better logging strategy Closed
6248 allow machine clients to access /manage/* OAuth2 protected web services Closed
6227 LIE during request to derivedUnitFacade/{uuid}/collectingareas Closed
4377 LazyInitializationException (LIE) related to Team.teamMembers when calling portal/taxon.json Closed
  taxeditor 15 Collapse all/Expand all
6342 Exception when searching for '?' in TaxonNodeSelectionDialog Closed
6334 Deleting unsaved TaxonDescription does not work Closed
6333 add existing media to a taxon description is not persisted Resolved
6307 Logfile/exception dialog should show connected datasource Closed
6299 Error when deleting reference in bulk editor Feedback
6295 NPE when creating a new taxon Closed
5922 Change order in supplemental data view Closed
5714 In Original Source Type dropdown show Primary Taxonomic Source first Closed
5698 Ampersand (&) is not shown in labels for NameRelationships in details view Closed
5671 Name selection should not allow self referencing name relationships Feedback
5474 TermEditor menu should be more structured Resolved
5365 Add delete configurator to Media View image gallery Feedback
5055 Integrate Luna installation instruction into standard installation instructions Closed
4246 Allow inserting a new node at the beginning or somewhere else in the Polytomous Key tree Closed
2957 running maven site:site for Taxonomic Editor fails Closed

CDM Platform 4.4 (released on December 5th, 2016)

What's new?

  • General / Model
    • Distribution status terms of several CDM instance have been unified and some new status were added to the CDM distribution status base vocabulary; default symbols used in condensed distribution strings were updated
    • Simplification: Synonyms belong to max. 1 accepted taxon now (before they could belong to multiple taxa, this was used for pro parte synonyms, which will be handled as taxon concept relationships in future, but with special user interface functionality similar to misapplied names)
    • Support for locally overriding database specific preferences (currently only implemented for preference "nomenclautral code", will be more in next version)
    • Symbol for congruence concept relationships changed
    • Unplaced and excluded attribute moved from taxon to taxon within classification ("taxon node"), including multi-lingual note field to document why a taxon is excluded
    • Improved support for Java 8
  • DataPortal
    • Security
      • Allow dataportal to show content only to logged in users (further improvements have bee investigated and will be implemented soon)
    • Maps
      • Allow distribution (area based) and occurrence (point based) data to show up on the same taxon page (better support for tabless taxon pages)
      • Improved support for Google Maps
      • Support for distribution maps if no distribution data is available (Fauna Europaea request)
    • Performance
      • Improved performance for synonymies
    • Formatting:
      • Improved formatting for specimen title
      • Improved display for specimen altitude
      • Display of "extensions" added to specimen and others
      • Display of "additional areas" (sub-country level) added to specimen
      • Bugfix for lectotype references
      • Bugfix for feature "Citation" showing up as footnote only
      • Suppress display of protologues if URL is missing
    • General Improvements
      • Improved breadcrumb navigation for desktop and mobile devices
      • Flexible handling and placing of "back to search button"
      • Persistent stable Identifier ("CETAF" identifier) clickable now in default specimen view
    • Bugfixes:
      • Area selection widget fixed in advanced search
      • Fix for missing sensu on misapplications with sensu reference missing an author
  • TaxEditor
    • Allow editing of default color for distribution status in term editor (Presence-Absence-Term) -> the color is used e.g. for maps in the dataportal
    • New Admin menu for general admins and project admins, currently used only for setting the database preferences
    • Improved support for deleting names, taxa, persons/teams, factual data and terms in bulk editor, name editor, factual data view and term editor, including bugfixes
    • Remember filter on selection dialog for named areas more individually (named areas are used at different places - distribution, specimen country, common name language area, geoscopes, ...)
    • Prevent users from unwanted updates on shared data: a red warning is shown in dialogs now if a shared resource is edited (currently implemented only for reference editing)
    • Preference to choose available fields for taxon details view (most fields can be selected individually now; in next version this may become a database specific preference)
    • Flags for unplaced and excluded moved from taxon details view to taxon node assistant (right click in taxon navigator -> open in -> taxon node assistant)
    • Excluded note (s.a.) available in taxon node assistant
    • Improved handling of orphaned taxa and synonyms
    • Nomenclatural status selection box shows abbreviated labels now
    • User interface for import configurations improved
    • Bugfixes:
      • Critical fix for a bug that prevented to correctly install the TaxEditor on computer for the first time
      • Exception when editing empty term / vocabulary labels
      • New references could not be found in selection dialog
      • Exception when editing taxon interactions (e.g. parasites) in factual data view
    • Some minor issues

  • Browser Editor (Vaadin)

    • Simple and easy to use distribution editor is now functional (was prototype only before)
    • Architectural improvements

  • Webservices (machine readable services)

    • Add full entity to findByMarker and findByIdentifier webservice result (fix for non functional "includeEntitiy" parameter)
    • OAuth2 authorization available
    • Securing critical web services with authentication. The '/manage/' web services now require authentication.
    • Some improvements for project specific webservices
      • Sorting by length on name search
      • Return pure names for taxonomic group search
      • Grouping by taxonomic groups
      • Add taxon parent to taxonInContext webservice result
    • bugfix for name catalogue taxon search
    • New services returning pure titleCaches and uuids with titleCache

# Subject Status
  architecture 1 Collapse all/Expand all
6206 Vaadin view fail with: Failed to load the bootstrap javascript Closed
  cdm 11 Collapse all/Expand all
6089 Remove taxonomicParentCache and taxonomicChildrenCount from Taxon Closed
5981 Add abbreviation to Rank "Cultivar" Closed
5974 Remove synonym relationships Closed
5970 Implement allowOverride in CdmPreference Closed
5952 Second cache field for specimen (identityCache) Closed
5921 Change symbol for congruence relationship. Closed
5875 Add isDefault flag to DescriptionBase Closed
5778 Update symbols for PresenceAbsenceTerms in existing databases Closed
5634 Excluded note for excluded taxa /taxon nodes Closed
3925 Unplaced and excluded to TaxonNode Closed
3658 Update Nomenclatural code for datasources Closed
  cdm-dataportal 16 Collapse all/Expand all
6201 Adapt dataportal to the new synonym datamodel Closed
6130 Areafilter widget broken Closed
6115 protect cdm content by drupal permission Closed
6114 Regression of #4379: Citations only consist of footnotes if bibliography block is enabled Closed
6110 Use https for map service calls when the portal is access via https Closed
5956 Improve functionality and UX for (children display in) breadcrumb navigation - 2 Feedback
5948 supress protologue icon if according media uri is missing Closed
5943 back to search button/link should go into a drupal block Closed
5938 distribution and specimen maps can not be used on the same page Closed
5844 Make stable identifier clickable in default specimen tab Closed
5676 Sensu does not show up if no author exists for secundum reference Feedback
5047 option to show empty distribution maps Duplicate
3650 allow supressing empty distribution and specimen maps Closed
3226 openlayers map google baselayers: api keys rejected Closed
3061 Lecototype typeReference not rendered correctly Closed
2985 Improve Specimen details display Closed
  cdm-vaadin 1 Collapse all/Expand all
6131 Vaadin DistributionEditor TODOS Closed
  cdmadapter 1 Collapse all/Expand all
6077 Import of gathering images Closed
  cdmlib 8 Collapse all/Expand all
6244 Sortindex problems in complex operations like swap synonym and accepted and others Closed
6220 Improve definition of orphaned taxon and synonym Feedback
6120 Cleanup uuidAndTitleCache methods Closed
6118 evaluate spring-security-auth2 and spring-cloud-security as a framework for OAuth2 Closed
6099 Duration of save is increasing Closed
6023 configuration problems with maven-antrun-plugin Closed
5862 Spring needs online resources during launch Closed
4965 unsupported method getDatabase() in WrappedCdmDataSource breaks forceSchemaUpdate Closed
  cdmlib-remote 11 Collapse all/Expand all
6236 Add alphabetic length ordering in name search Closed
6211 massive heap consumption by service endpoint /portal/taxon/{uuid}/synonymy Closed
6135 Remove authors from Taxonomische Großgruppe Closed
6134 Allow grouping by Taxonomische Großgruppe Closed
6133 Improve Rank Webservice Closed
6128 Include authorship in taxon search web service Closed
6127 NPE in NameCatalogue Controller on name_catalogue/taxon Closed
6122 add titleCache service Closed
6119 Implement uuidAndTitleCache remote services Resolved
6072 Implement getTaxonomicGroups for Edaphobase Closed
4594 RL Webservice 7: Return taxa by Identifier Resolved
  data 3 Collapse all/Expand all
6071 Handle Taxonomische Großgruppen correctly in Edaphobase Closed
5976 Update sortIndex for potential nullValue sortIndexes Closed
5826 Clean up names with empty name descriptions Closed
  devOps 1 Collapse all/Expand all
6224 cdm-webapp is not using current version of cdmlib-remote-webapp.war Closed
  taxeditor 27 Collapse all/Expand all
6218 NPE when editing term vocabulary label Closed
6216 Allow changing of defaultColor for PresenceAbsenceTerm Closed
6215 NPE when opening preferences with no DB connection Closed
6209 NPE in DatasourceView Closed
6199 Excluded note for excluded taxon nodes in TaxEdtior Closed
6198 Remove synonym relationships in TaxEditor Closed
6197 Move excluded and unplaced from Taxon to TaxonNode in TaxEditor Closed
6174 LIE when deleting new name Closed
6129 After creating a new Reference in selection dialog, it could not be found in the selection dialog Closed
6105 Make CdmPreferences editable in separate view Resolved
6058 Store NamedArea dialog filters more individually Closed
6050 provide the possibility to choose the fields of the simple details view for names Feedback
5972 Prevent user from unwanted author and reference updates Feedback
5971 Implement database wide CdmPreference writing Closed
5891 Taxon appended phrase should not allow empty string Closed
5888 Deleting factual data does not work (dirty flag not set) Closed
5870 NPE when trying to open a synonym (or taxon) that has been deleted Closed
5841 Creating a new alternative in PolytomousKey Editor should set focus to new PKNode Closed
5800 Remove "Taxonomically Included In" from list of concept relationship types Closed
5693 Deleting a synonym only deletes the synonym relation Closed
5692 Delete a person within the bulk editor deletes the person even if not saved Closed
5680 Out-of-Memory when editing TaxonInteraction Closed
5660 Rename Name Relationship to Name Relationships in Name Details View Closed
4945 Right click menu for polytomous key node list view needs correct enabling Feedback
4461 Ordering in datasources view fails Closed
3573 Improve EDITOR import UI configuration panel Closed
1362 Version number should be located at one place Rejected

CDM Platform 4.3 (released on September 26th, 2016)

What's new?

  • General

    • Improved handling of notho ranks
    • Some new/fixed machine readable web-services

  • DataPortal

    • Advanced Search: Distributions marked as absent are no longer displayed in search result
    • Advanced search: Area filter is now sorted
    • Breadcrumb navigation fixed for Internet Explorer / MS Edge
    • Fix some links to images

  • TaxEditor

    • Bugfix for user defined order in taxon navigator
    • ABCD import improved
    • Name Parser improved
    • Checklist/Distribution Editor:
      • Renamed to Distribution Editor
      • Fixe some bugs (but it still has status experimental; opening is now available via standard open in menu)
    • Referencing objects view:
      • available for relationships (name relationship, concept relationship, etc.)
      • minor bugfix
    • Name author search works on nomenclatural title and standard title
    • Nomenclatural reference search works on abbreviated title and standard title
    • Expansion state of the details view and the supplemental data view is now remembered (e.g. if you close all sections in the name details view except for the name relationships the next time when you enter the name details view it will remember this state and only the name relationship section will be open)
    • Filtering for area selection fixed (also last filter is remembered now)
    • The preferred nomenclatural code can now be stored as a database wide variable instead of a local variable. This way projects can define there own settings. This implementation is a first implementation and prototype for the general availability of project settings.
    • Underlying link for the automated update has been fixed
    • Infraspecific epithet editing now available for species (all codes) and infraspecific ranks (zoology)
    • Reusing of names and taxa fixed
    • Bulk editor
      • auto-focus on search
      • new search allows not to save now
      • Concept relationship editor view now available also from taxon bulk editor
    • Search
      • Search results allow opening in different target views (e.g. name editor, bulk editor) via right click menu
    • Correct handling of secundum reference for newly created taxa
    • Delete for type designations fixed
    • Term editor
      • Language dependent representations for terms are now deletable if more than 1 representation exists
      • Non English default representation shows up correctly
      • #6101
    • Details view
      • Horizontal scrolling removed where possible
    • Some bugfixes
      • "multipe representations" exception
      • focus issue for protected title caches

# Subject Status
  cdm-dataportal 2 Collapse all/Expand all
6087 Top level items not sorted in tree of advanced search areaFilter widget Closed
6054 classification breadcrumb navigation broken in IE and MS Edge Closed
  cdmlib 6 Collapse all/Expand all
6086 Percentage value in ProgressMonitor accuratly rounded Closed
6060 Name parser fails parsing author names with - U+002D HYPHEN-MINUS Closed
6057 Name parser fails parsing author names with ` U+0060 GRAVE ACCENT Closed
6045 NPE when using TaxonNaturalComparator Closed
6032 Name parser support for hybrid ranks Rejected
6030 Name parser support for genus hybrids Closed
  cdmlib-remote 3 Collapse all/Expand all
6073 Fix groupByHigherTaxon webservice Closed
6066 Edaphobase DTO for getChildrenTaxaOfId Closed
6065 Edaphobase DTO for getTaxonById Closed
  taxeditor 11 Collapse all/Expand all
6101 NPE when having multiple lanugage support disabled Closed
6084 NPE when opening the checklist editor with no areas selected in preferences Closed
6082 Local managed server in Taxeditor fails during start Closed
6062 NPE in RefencingObjects for TaxonNameDescription Closed
6061 Add titlecache to nom author search Closed
6059 Save expand state more individually Closed
6056 Checklist Editor does not close session Closed
6049 Improve (area) filter handling for selection dialogs Closed
5982 editing the protected titleCache set sometimes the focus to the name editor Closed
5969 Implement CdmPreference reading for database preferences Closed
5616 Add the"Open in..." menu to taxon search Closed

CDM Platform 4.2 (released on July 6th, 2016)

What's new?

  • General

    • Some new terms: feature "Notes", nomenclatural status "ined." and taxon relationships "unclear" and "not yet worked on"
    • Improved aggregation for distribution data (transmission engine)
    • Improved multi-language support
    • Some new machine readable web-services

  • DataPortal

    • Improved usability of breadcrumb navigation
    • minor formatting issues
    • geo filtered search fixed
    • support for taxon secundum micro reference
    • Display of children on "General" tab (first version, block needs to be switched on)
    • Spanish translation for Dataportal module

  • TaxEditor

    • Improved performance for selection boxes
    • Fix bugs in feature tree editing
    • Support for species with infrageneric epithet
    • Multi-language editing for terms
    • "Open in ... bulk editor" for taxon navigator and referencing objects view
    • Support for "additional identifiers" in supplemental data view
    • Improved taxon name and reference parsing
    • Nomenclatural reference parser uses abbrev title
    • Improved "Changed Password" functionality
    • Improved session handling for bulk editor searches (fixing unexpected results and memory effects)
    • Ordering in specimen derivative editor
    • Improved labels in referencing objects view for specimen determinations and taxa in classifications (taxon nodes)
    • bug fixes

Milestones and tickets

# Subject Status
  cdm-dataportal 3 Collapse all/Expand all
5911 deploy spanisch translation with the cdm_dataportal module Closed
5903 serve fontawesome icons directly from the portal (prevents users from being tracked by google) Closed
5861 Taxon appended phrase must not be in italics Closed
  cdmlib 2 Collapse all/Expand all
5177 improve perfomance of TransmissionEngineDistribution Closed
4366 Transmissionengine Distribution: implement rules for source references Duplicate

CDM Platform 4.1 (released on June 1st, 2016)

What's new?

  • General

    • Support for persistent stable identifiers (e.g. "CETAF Identifiers")
    • Support for secundum micro reference

  • DataPortal

    • Breadcrumb navigation shows child taxa
    • Changing to breadcrumb navigation and removing tree navigation improves performance of data portals significantly

  • TaxEditor

    • "Standalone" functionality removed
    • Connection to datasources is now only possible via remoting" functionality introduced in "v3.12
    • Datasource was adapted to only support editing user defined datasources (connect to "localhost mgd." server) and to create a new database schema in such datasources if they are still empty
    • Search for nomenclatural authors works on abbrev. title now
    • Labels for referencing objects improved
    • Some major bugs fixed that lead to error messages when saving taxa
    • Bugfix for "unavailable" authors after creation of new authors
    • Symbols for distribution strings and concept relationships editable
    • Error handling for connection process
    • Performance for save improved
    • Couple of minor bug fixes

Milestones and tickets

# Subject Status
  cdmlib 2 Collapse all/Expand all
5833 Implement single cache strategy for references Closed
1815 setInReference needs to reset the title cache Closed

CDM Platform 4.0 (released on May 3rd, 2016)

What's new?

  • Upgrades to all underlying software libraries

    • Full Java 8 support (Downloading TaxEditor JRE version not necessary anymore)
    • Improved freetext indexing (faster and more stable) and search support
    • Improved webservice documentation

  • DataPortal

    • Breadcrumb menu for higher taxonomy
    • Clickable list of all parent taxa of a given taxon shown in 1 line
    • Needs to be switched on by dataportal admin
    • Improved multi-language support
    • Improved support for taxon concepts, misapplied names and doubtful taxa formatting
    • Maps
    • Animated "Hourglass" while loading maps
    • Improved stability for distribution and occurrence maps
    • Improved display of textual distributions for hierarchically ordered distributions
    • Faster loading of the most important base layers through the new EDIT MapProxy
    • Condensed distribution string configurable and improved
    • Support for hierarchical feature trees for factual data
    • Improved display of reference pages (e.g. )
    • Specimen linking to associated taxa
    • Improved error and warning messages
    • Bugfixes
    • Fix display of taxon interactions
    • Fix name page display

Examples for many of the new features (like breadcrumb menu, multi-language support and condensed distribution strings) can be found at (e.g. http://portal.cybertaxonomy.org/flora-cuba/ )

  • TaxEditor

    • Improvements to the name and coordinate parsers
    • Ordering of sources (according to rules described in #3185)
    • Editing supplemental data for type designations and name relationships
    • New generic "Open in ..." right mouse click menu
    • Available servers configurable
    • Renaming Descriptions to Factual data finalized
    • Many bugfixes to stabilize existing functionality
    • PolytomousKey editing and deleting
    • Creation of new terms
    • ...

  • Data Model (CDM)

    • Preferred persistent identifiers for specimen
    • Symbols for condensed distribution strings and concept relationships
    • Secundum micro reference for taxa

Milestones and tickets

# Subject Status
  cdm 1 Collapse all/Expand all
5662 New nomenclatural status nom. cons. des. Closed
  cdm-dataportal 5 Collapse all/Expand all
5697 Show name conserved against as [non xxx] Closed
5683 loading animation for open layers map viewer Closed
5647 Aggregate misapplied names with multiple sensu references Closed
5492 Doubtful synonyms and misapplied names to be displayed correctly Closed
5491 Implement name phrase correctly for misapplied names Closed
  cdmlib 1 Collapse all/Expand all
4716 Other dependencies to be updated Closed
  taxeditor 2 Collapse all/Expand all
5346 Allow 3 ways of ordering in Taxon Navigator Resolved
5289 trying to delete an already deleted object leads to not correctly handled exception Closed

CDM Platform 3.12 - Hotfixes (released on February 15th, 2016)

This is a pure bugfix release for Release 3.12 with no new functionality. It handles 1 issues.

Milestones and tickets

# Category Subject Status Target version
5581 cdmlib Specimen title cache does not show up correctly after editing Closed Release 3.12 - Hotfixes

CDM Platform 3.12 (released on December 21st, 2015)

Note: Version 3.9, 3.10 and 3.11 were minor releases mostly for development reasons and were not published

Version 3.12 handles 6 issues.

What's new?

  • DataPortal

    • Taxon experts can now be displayed in a new tab of the taxon pages.
    • Maps adapted to different screen size. Openlayers try to adapt to the screen size and the map aspect ratio can be set instead of fixed width and height (#5385)
    • MapProxy established (#5023): Background layers for the maps can now be retrieved via the Cybertaxonomy MapProxy The layers served through the map proxy are delivered much faster and availability problems of some map server are circumvented this way. It is therefore highly recommended to use the map proxy versions of the base layers instead of the original ones so far a map proxy version is available. You may want to adapt the Geo & Map settings in your dataportal accordingly.

  • Taxonomic Editor

    • Support for remote access without using ulteo (or any other virtual desktop)
    • most important new feature,
    • to be accessed via 'Connect' in the editors 'File' menu
    • old access via 'Datasource View' still possible if direct database access exists, but deprecated and will be removed in a future version
    • Remote Editor How To
    • Derivative (specimen tree) view improved
    • unified search and editing view
    • a couple of new features
    • some bugfixes
    • now considered as stable
    • Java JRE bundled with Editor (2 versions are now available for each platform, 1 without java bundled, 1 with java(jre) bundled)
    • ABCD Import improved
    • LSIDs for scientific names editable
    • Ordering of terms
    • Deleting concept relationships
    • Scopes for polytomous keys
    • Deletes in bulk editor configurable
    • Common name and scientific name search made consistent
    • Feedback for impossible deletes improved
    • Image shown also in simple media view
    • Bugfixes
    • switch synonym to misapplied name
    • deleting terms
    • moving descriptions
    • deleting taxa being used in multiple classifications
    • incorrect behavior when pressing cancel in popups
    • delete specimen media
    • merging 2 persons
    • convert person to team
    • many minor bugfixes

Milestones and tickets

# Category Subject Status Target version
5286 cdm-dataportal seemingly duplicate distributions Closed Release 3.12
5250 taxeditor Derivate search is slow Resolved Release 3.12
5104 cdmlib prevent MarkerTypes from being deleted when there are Marker entities using that type Closed Release 3.12
4962 cdmlib improve portal/classification/{taxon_uuid}/childNodesAt/{rank_uuid} web service Resolved Release 3.12
4944 taxeditor "Protected" indication for references needs to be improved Resolved Release 3.12
3742 cdm-dataportal Display altitude, distance to Ground and watersurface correctly in dataportal Closed Release 3.12

CDM Platform 3.8 (released on September 10th, 2015)

What's new?

  • DataPortal

    • Simple search runs by default on the selected single classification, *IMPORTANT! * If your portal has multiple classifications, You may check the according settings option in the cdm_dataportal/settings/layout/search admin page.
    • Distribiution maps show circles as symbols for areas which are too tiny to see the colored area.
    • Option to display the so called sec reference for the taxa in all parts of the DataPortal. This can be configured via the name render template settings in admin/config/cdm_dataportal/settings/layout

  • Editor

    • LibrAlign editor is now available for single read alignment (experimental feature)
    • Media can be opened in external browser by button click.
    • Allow searching for uuid in bulk editors
    • Taxon can now be edited and deleted when a PolytomousKeyNode is not a leaf
    • Improved error handling
    • Layout improved for error messages

Milestones and tickets

# Subject Status
  cdmlib-remote 2 Collapse all/Expand all
5040 Allow transmission engine webservice to define area level Closed
3904 EuroMed: Implement filtering rules for distributions Closed

CDM Platform 3.7 (released on July 19th, 2015)

What's new?

  • Editor-Features:

    • Team convertable to persons and vice versa (Bulkeditor)
    • Name parser allows comma separated authors and improved handling for et al. authors
    • Datasource view is loading faster in datasource view (not after selecting a datasource)
    • ABCD import: import for DNA (ABCD-DNA) and associated units
    • Usergroups deletable (Rights&Roles)
    • Vocabularies can be ordered
    • Improved error handling for media URIs including bugfixes
    • Resizing of user dialogs improved if content changes (e.g. reference type changes)
    • Text cells selectable in referencing objects view
    • Media attached to description elements allow simple / advanced view switch

  • Editor-Bugs:

    • Fix duplicated team members when editing a team
    • Fix ignored title cache protectedion for taxa
    • Fix show abbreviated author in taxon name author fields
    • Other (minor) bugfixes

  • DataPortal

    • Optional switch on/off taxon profile picture placeholder
    • New API hook in the Drupal module cdm_dataportal allow developers to flexibly modify the content of feature blocks shown on the taxon general page.
    • Distribution areas show distributions status on mouse over (not yet working in hierarchic distribution display)
    • Condensed distribution string in Euro+Med style available
    • Multiple bug fixes regarding distribution filtering
    • Display later homonym information for accepted names

Milestones and tickets

# Subject Status
  cdm-dataportal 1 Collapse all/Expand all
3907 EuroMed: implement condensed "status" string of distribution information Closed
  taxeditor 1 Collapse all/Expand all
4908 adding convert Team to Person and Person to Team to the bulk editor Closed

CDM Platform 3.6 (released on June 4th, 2015)

What's new?

  • Editor:

    • improved handling for persons and teams (deduplication, conversion, et al., create, imroved parsing for teams (still open issues), ...)
    • improved handling for categorical and quantitative data (allow features to define supported vocabularies)
    • add id to search results (optional feature)
    • improved dialog for data delete
    • entering new taxa improved (prefill fields, focus on OK, etc.)
    • menus cleaned up
    • show hybrid formula flag
    • improve bulk editor search behavior
    • improve behavior for protected fields
    • Improved ABCD import

  • CDM Server and Dataportal

    • a couple of performance improvements
    • display of scaled images fixed in the zen base theme
    • CDM model:
    • allow Subtree(TaxonNode) - Agent relationships
    • add cutting of edges in SingleReadAlignment
    • added "et al." attribute to teams
    • cardinality improved for categorical data and statistical data and for supported vocabulary relation of features

Milestones and tickets

[[[TicketQuery(milestone=Release|3.6.0 |cdm_dataportal RELEASE 3.6.0 |cdm-server RELEASE 3.6.0 |cdmlib RELEASE 3.6.0 |TaxEditor RELEASE 3.6.0 |CDM UML 3.6 ,group=milestone)]]]

CDM Platform 3.5.1 (released on May 4th, 2015)

What's new?

  • Web editor

    • Browser based editing for distribution data
    • Browser based editing for concept relationships / experimental

  • Taxonomic Editor

    • Bundled deploy of Editor with java
    • Searching for common names and pure name in Editor
    • Metadata editing for classifications
    • Automated creation of missing taxa (e.g. genuses) in hierarchy
    • Improved reusability of taxon names and media
    • Support for hybrid formula parsing

  • DataPortal

    • Improved area filter for advanced search in dataportals
    • Quantitative data display in dataportal (e.g. altitudes)
    • improvement in dataportal base layout for smartphones and other small displays

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.5.1 |cdm-server RELEASE 3.5.1 |cdmlib RELEASE 3.5.1 |TaxEditor RELEASE 3.5.1 ,group=milestone)]]]

CDM Platform 3.5.0 (released on Mar. 24th, 2015)

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.5.0 |cdm-server RELEASE 3.5.0 |cdmlib RELEASE 3.5.0 |TaxEditor RELEASE 3.5.0|CDM UML 3.5 ,group=milestone)]]]

CDM Platform 3.4.0 (released on Dec. 16th, 2014)

What's new?

  • DataPortal

    • A new and much more beautiful icon set for icons which are used for example at the protologue links.
    • Better support for media on mobile devices
    • Improved handling for footnotes, annotations and bibliogaphie

  • Taxonomic Editor

    • NEW Checklist perspective
    • NEW Checklist Editor - simple edit distribution status in a excel like table view
    • fixed display issues for default languages
    • DetailsView
    • support for editing molecular data (tissue sample, dna sample, sequence, single read, amplification)
    • in DerivateEditor
    • SampleDesignation for tissue and dna samples
    • publish bit for specimens
    • show taxon associations (individuals associations and type designations) for specimen (customizable in preferences)
    • show collecting areas below country (customizable in preferences)
    • taxon filter for derivate search view
    • split amplification in amplification (more general) and amplification results (more specific)
    • enhanced usability of Derivate Editor
    • multiple FieldUnits can be opened in one editor
    • option to create FieldUnits
    • option to delete specimens
    • filter for IndividualsAssociations in Factual Data View

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.4.0 |cdm-server RELEASE 3.4.0 |cdmlib RELEASE 3.4.0 |TaxEditor RELEASE 3.4.0 |CDM UML 3.4 ,group=milestone)]]]

CDM Platform 3.3.7 (released on Sept. 4th, 2014)

What's new?

  • EDIT DataPortal

    • references are no longer mixed up with annotation footnotes, they are now shown per default in a separate bibliography block on the general page
    • custom presence and absence term colors can be configured for distribution maps

  • Taxonomic Editor:

    • several important bug fixes
    • new simple media interface allowing to add media only by specifying the media URI

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.3.7|cdm-server RELEASE 3.3.7|cdmlib RELEASE 3.3.7|TaxEditor RELEASE 3.3.7,group=milestone)]]]

CDM Platform 3.3.6 (released on Jul. 8th, 2014)

What's new?

  • ...

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.3.6|cdm-server RELEASE 3.3.6|cdmlib RELEASE 3.3.6|TaxEditor RELEASE 3.3.6|Remoting 2.0,group=milestone)]]]

CDM Platform 3.3.5 (released on May. 30th, 2014)

What's new?

  • Occurrence search web service

  • Specimen features for Editor

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.3.5|cdm-server RELEASE 3.3.5|cdmlib RELEASE 3.3.5|TaxEditor RELEASE 3.3.5,group=milestone)]]]

CDM Platform 3.3.4 (released on May. 13th, 2014)

What's new?

  • Urgent fixes for data portal .

  • Country list updates.

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.3.4|cdm-server RELEASE 3.3.4|cdmlib RELEASE 3.3.4,group=milestone)]]]

CDM Platform 3.3.3 (released on Apr. 16th, 2014)

What's new?

  • Urgent Bug Fixes for the CDM Library and Data Portal

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.3.3|cdm-server RELEASE 3.3.3|cdmlib RELEASE 3.3.3|TaxEditor RELEASE 3.3.3,group=milestone)]]]

CDM Platform 3.3.2 (released on Apr. 10th, 2014)

What's new?

  • ...

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.3.2|cdm-server RELEASE 3.3.2|cdmlib RELEASE 3.3.2|TaxEditor RELEASE 3.3.2,group=milestone)]]]

CDM Platform 3.3.1 (released on Mar. 28th, 2014)

What's new?

  • several bug fixes and performance improvements

  • Data Portal

    • It is possible to exclude classification from the classification switch in the taxon tree browser
    • The Maps have a more modern an pleasant user interface

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.3.1|cdm-server RELEASE 3.3.1|cdmlib RELEASE 3.3.1|TaxEditor RELEASE 3.3.1,group=milestone)]]]

No TaxEditor 3.3.1 release

CDM Platform 3.3.0 (released on January 15, 2014)

What's new?

  • Major improvements to the cdm data model:

    • Improved handling of terms
    • Improved and extended model for molecular data
    • Improved handling of SpecimenOrObservation types including new types like Media Specimen
    • Unified handling of min, max and freetext for altitude and distance to ground
    • Abbreviated titles for references
    • DOIs for references (not yet implemented in Dataportal and Taxonomic Editor)
    • Better handling of long title caches (up to 800 characters now) and long URIs
    • Ordering of taxa in classifications (not yet implemented in Dataportal and Taxonomic Editor)
    • Treeindex implemantation for improved search performance in trees (classifications, feature trees, identification trees)
    • publish flags on taxa and specimen

  • ...

Milestones and tickets

[[[TicketQuery(milestone=CDM|UML 3.3|cdm_dataportal RELEASE 3.3.0|cdm-server RELEASE 3.3.0|cdmlib RELEASE 3.3.0|TaxEditor RELEASE 3.3.0,group=milestone)]]]

CDM Platform 3.2.3 (released on August. 26th, 2013)

What's new?

  • More taxon profile image settings, e.g. max entend, user defined placeholder (no image available) image

  • Improvements to the new DataPortal base theme.

  • The web service debug box has completely been replaced by the CDM web service debug block. It is usually only visible for administrative roles like administrator and CDM admin

  • ...

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.2.3|cdm-server RELEASE 3.2.3|cdmlib RELEASE 3.2.3|TaxEditor RELEASE 3.2.3,group=milestone)]]]

CDM Platform 3.2.2 (released on July. 1st, 2013)

What's new?

  • Improved Accepted Taxon to Synonym (and vice-versa) functionality in the Editor .

  • Implemented Hibernate 4 compatibility (including fixes for long-running sessions) for the Editor.

  • ...

Milestones and tickets

RELEASE 3.2.2,group=milestone)]

CDM Platform 3.2.1 (released on June. 6th, 2013)

What's new?

  • The new DataPortal base theme supports legacy browsers as IE8, IE7 and IE6

  • Bugs in the taxon tree browser widget have been fixed

  • Improved installation profile

  • The sdm server allows stopping and restarting of cdm instances. This reduces maintenance downtimes.

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.2.1|cdm-server RELEASE 3.2.1|cdmlib RELEASE 3.2.1,group=milestone)]]]

No TaxEditor 3.2.1 release

CDM Platform 3.2 (released on for May. 2nd, 2013)

What's new?

  • Hibernate migrated to version 4

  • Distribution transmission engine now allows aggregation of distribution information by rank and by area see #2625

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.2|cdm-server RELEASE 3.2|cdmlib RELEASE 3.2|TaxEditor RELEASE 3.2,group=milestone)]]]

No TaxEditor 3.2.0 release

CDM Platform 3.1.4 (released on March 18th, 2013)

What's new?

  • The simple search, which can be executed via the search block, will by default search on all classifications. Remove the tick from the according check-box in the settings (CDM DataPortal -> Settings -> Layout -> Search) if you want your portal to still search on the classification selected in the classification browser selector.

  • ...

No TaxEditor 3.1.4 release

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.1.4|cdm-server RELEASE 3.1.4|cdmlib RELEASE 3.1.4,group=milestone)]]]

CDM Platform 3.1.3 (released on 14th, 2013)

What's new?

  • ABCD import improved and bugs fixed

  • A lot of improvements in the display of specimens and observations:

    • Chain of derivatives is now shown
    • Display of associated data like specimen descriptions
    • (for more in depth information please refer to the below listed tickets)

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.1.3|cdm-server RELEASE 3.1.3|cdmlib RELEASE 3.1.3|TaxEditor RELEASE 3.1.3,group=milestone)]]]

CDM Platform 3.1.2 (released on Dez. 3rd, 2012)

What's new?

  • A new base theme for the Drupal 7 DataPortals:

    • adaptive and thus suitable for desktop computers, smart phones and tablets
    • banner and background images configurable
    • colors configurable
    • faster page loading

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.1.2|cdm-server RELEASE 3.1.2|cdmlib RELEASE 3.1.2|TaxEditor RELEASE 3.1.2,group=milestone)]]]

CDM Platform 3.1.1 (released on Nov. 21th, 2012)

What's new?

  • EDIT DataPortal now upgraded to Drupal 7

No TaxEditor 3.1.1 release

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.1.1|cdm_dataportal - upgrade to Drupal 7|cdm-server RELEASE 3.1.1|cdmlib RELEASE 3.1.1,group=milestone)]]]

CDM Platform 3.1 (released on 06.11.2012)

What's new?

  • Security, roles and users are implemented in to the cdmlib and into the Taxonomic Editor. It is now possible to define roles for users and to restrict write and delete permissions to Taxa, Descriptions in general or specifically. Most importantly this is also possible for sub trees of the classification. So the permission to edit a taxonomic subgroup of a whole classification can be restricted to a defined group of users.

  • Prototype of the polytomous key editor (use with caution)

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.1|cdm-server RELEASE 3.1|cdmlib RELEASE 3.1|TaxEditor RELEASE 3.1,group=milestone)]]]

CDM Platform 3.0.13 (released on 17.10.2012)

What's new?

  • Full text search on taxon descriptions (available in the DataPortal under Advanced search), on taxa and names and on both simultaneously (not yet in the DataPortal).

  • Despite of the above this release is mainly a bug fix release

  • Polytomous Key functionality added to the Taxonomic Editor

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.0.13|cdm-server RELEASE 3.0.13|cdmlib RELEASE 3.0.13,group=milestone)]]]

!TaxEditor 3.0.13 (released on 25.10.2012):

RELEASE 3.0.13,group=milestone)]

CDM Platform 3.0.12 (released on June 19th, 2012)

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.0.12|cdm-server RELEASE 3.0.12|cdmlib RELEASE 3.0.12|TaxEditor RELEASE 3.0.12,group=milestone)]]]

CDM Platform 3.0.11 (released on June 27th, 2012)

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.0.11|cdm-server RELEASE 3.0.11|cdmlib RELEASE 3.0.11|TaxEditor RELEASE 3.0.11,group=milestone)]]]

CDM Platform 3.0.10 (released on Mai 8th, 2012)

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.0.10|cdm-server RELEASE 3.0.10|cdmlib RELEASE 3.0.10,group=milestone)]]]

TaxEditor 3.0.10 (released on May 25th, 2012):

RELEASE 3.0.10,group=milestone)]

CDM Platform 3.0.9 (released on Feb. 7th, 2012)

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.0.9|cdm-server RELEASE 3.0.9|cdmlib RELEASE 3.0.9|TaxEditor RELEASE 3.0.9,group=milestone)]]]

CDM Platform 3.0.8 (released on Sept. 19th, 2011)

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.0.8|cdm-server RELEASE 3.0.8|cdmlib RELEASE 3.0.8|TaxEditor RELEASE 3.0.8,group=milestone)]]]

CDM Platform 3.0.7 (planned for Aug. 15th, 2011)

Milestones and tickets

[[[TicketQuery(milestone=cdm_dataportal|RELEASE 3.0.7|cdm-server RELEASE 3.0.7|cdmlib RELEASE 3.0.7|TaxEditor RELEASE 3.0.7,group=milestone)]]]

CDM Platform 3.0.6 (July 2011)

Milestones and tickets

RELEASE 3.0.6)]

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