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CDM Platform 5.26 (scheduled for Sep 6th, 2021)

Issues: 221

Downloads:(not yet available) TaxEditor, CDM Server, Data Portal

CDM Platform 5.25 (scheduled for July 8th, 2021)

Issues: 43

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - CDM Model
    • Collector title (including protectable collector titlecache) for persons and teams
    • Explicit nomenclatural title for persons
    • New unspecific "non ..." taxon name relationship
    • New class for taxonomic operations (experimental)
    • Fix column length for author and descriptive dataset titlecache in some databases
  • - CDM Library
    • Improve field unit and specimen formatting algorithm
    • Fix titlecaches handling for some data that could not be found by search due to incorrectly stored empty titlecaches
    • Improve title generation for media title generated form underlying file name
  • - Data Portal
    • Fully refactored external links modul allows for adding removing and re-organizing external links
    • Fix formatting for references using nomenclatural code edition
    • Fix position of footnotes for notes in brackets
    • Fix a couple of errors triggered by incorrect data initialization on server side
    • Fixed bug in advanced taxon search
  • - Import / Export
    • Some improvements on CDM light export (e.g. formatting of homotypical groups)
  • - TaxEditor
    • Make all disabled fields copyable (for copy&paste)
    • Authors
      • Make new nomenclatural title and collector title (+cache) fiels editable
      • Open search dialogue immediately when adding a new team member
      • Allow search on collector titlecache
    • Bulk editor
      • Collector titlecache and protected fiels for collector and titlecache and nomenclatural titlecache available in author bulk editor
      • Set focus to remaining record after deduplication in bulk editor
    • Term tree editor
      • improved handling of newly created term trees
      • added symbols to distinguis trees and lists
      • show (disabled) details for terms
      • show supplemental data for term nodes
      • add "open in vocabulary"
      • improve drag&drop
    • Specimens
      • remove "field unit" form record basis selection combo box
      • remove title dialogue for new specimens in specimen list editor
    • Bugs:
      • incorrect filling of details view after a new misapplication has been created
      • fixed bug when editing taxon name supplemental data (e.g. name identifiers) in name editor
      • exception when deleting a synonym with no name attached
      • in specimen details view the titlecache field is not enabled if the specimen has a protected titecache
      • inform user that TaxEditor resart is required if an "OptionalDataException" is the cause of an error
  • - Web editor

# Subject Status
  cdm 6 Collapse all/Expand all
9692 Add Operation class and link from TaxonRelationship Closed
9664 Add nomenclaturalTitleCache to TeamOrPersonBase Resolved
9634 Update AgentBase and DescriptiveDataSet titleCache length where needed Closed
5655 [DISCUSS] Do we need further "non xxx" relations? Resolved
5640 [DISCUSS] Do we need a general "non" name relationship Duplicate
4311 Improve person representation in CDM Closed
  cdm-dataportal 7 Collapse all/Expand all
9685 add separator between rule applied and code edition Resolved
9674 footnote keys for annotations to multilanguageText name descriptions inside brackets Closed
9669 cdm_dataportal_search_taxon_form_advanced() fails with Allowed memory size of ... bytes exhausted Closed
9666 cdm_tokens module Closed
9659 External Links Module reimplemented for flexible configuration Closed
8364 ext-links module: problems Closed
980 Links to relevant external website(s) in taxon pages Closed
  cdmadapter 1 Collapse all/Expand all
9646 CDM Light: Add name relationship to concatenated string for homotypic group Resolved
  cdmlib 13 Collapse all/Expand all
9705 Nomenclatural references with no title and microreference are not correctly formatted Closed
9703 Improve handling of type designations with no status in TypeDesignationSetManager Resolved
9702 TypeDesignationSetManager repeats specimen string for specimens without field unit Closed
9695 Implement a preference for supportsConcepts Closed
9684 OccurrenceServiceImpl.listRootUnitDTOsByAssociatedTaxon() - [UPDATE] not permitted for 'anonymousUser' Closed
9683 Auto-initialize root bean Closed
9678 Remove Derived- and FieldUnitFacadeCacheStrategies Closed
9675 Person initials should never be empty Closed
9665 Filter out property change event for created and updated and cacheStrategy Closed
9663 Remove additional text from media title Closed
9657 OccurrenceServiceImpl.listRootUnitDTOsByAssociatedTaxon fails with HibernateException: More than one row with the given identifier was found: 51 Closed
9649 Specimens sometimes have empty titleCache instead of class<UUID> Resolved
6714 Create 001-cdm.h2.sql automatically Closed
  data 1 Collapse all/Expand all
9672 NPE when CDMPreference contains allowOverride=NULL Duplicate
  taxeditor 15 Collapse all/Expand all
9690 Exception when editing name supplemental data in taxon bulk editor Closed
9688 Make disabled fields copyable Closed
9680 Show collectorTitleCache and protectedCollectorTitleCache+ protectedNomenclaturalTitleCache in BulkEditor Closed
9655 When adding a new team member open search dialogue immediately Closed
9654 Deleting a synonym which has no name throws exception Closed
9651 After creating a new MAN the details view is filled with other MAN Closed
9647 After deduplication the remaining record should get the focus in bulk editor Closed
9629 Better handling of OptionalDataException Closed
9572 After creating a new term tree set the focus to the new tree Closed
9373 In specimen details view used within specimen tree editor titleCache field is not enabled when it is protected Closed
9337 Open issues for reimplementation of termtree editors Closed
9288 Add symbols for flags in use for term trees in term tree editor Closed
9287 Show term details in details view of term tree editor Closed
7309 Implement collectorTitle and collectorTitleCache and the same for nomenclatural title in tax editor Feedback
5244 [DISCUSS] How should specimens be created and edited? Closed

CDM Platform 5.24 (released on Jun 2nd, 2021)

Issues: 13

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - CDM Library
    • Formatting
      • remove full stop at the end of title caches for references
      • handle nomenclatural title cache similar to nomenclatural source formatting (but without detail)
  • - Data Portal
    • Search including misapplications works again
    • Image viewer displays media files much faster in specific situations.
    • Bugfix for specimen with media
  • - TaxEditor
    • Finalize "allow duplicates" handling for term trees
    • Handling of computed descriptions configurable (selectable modes: not visible, not enabled, enabled)
    • Editing field units works again
    • Fix delete synonyms that are used as "named used in source"
    • Improve handling of "OptionalDataException"
    • Fix error when deselecting a term during term selection dialogue for term tree items
  • - Web editor
    • Bugfix for name type designations in phycobank editor

CDM Platform 5.23 (released for May 19th, 2021)

Issues: 46

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - CDM Model
    • Adaptations for the upcoming taxon concept/identifier strategy for E+M
    • Rename ICNB to ICN
    • Label for nomenclatural code editions
    • Unified word seperator (underscore) for role based groups
  • - CDM Library
    • Formatting and Parsing
      • Improved formatting for teams (no et al. anymore for long citations, unified short citation handling)
      • Improved formatting for references * year behind author and followed by colon, not at the end anymore * pages for booksections * improved formatting for subsections of booksections and articles
      • Improved formatting for misapplications (when being searched via titleCache e.g. in TaxEditor)
      • Improved formatting of specimen being media
      • Improved formatting for specimen being DNA samples
      • Improved formatting for condensed distribution string for areas having subareas with various status
      • parser for original spelling
    • Media info service added for fast image metadata reading
    • role "user manager" added
  • - Imports/Exports
    • CDM Light
      • Add appended phrase to taxon table
      • move condensed distribution string to simple facts
      • fix handling of sec references of misapplied names/pro parte synonyms
  • - CDM Server
    • instances with severe problems should not start
  • - Data Portal
    • Remove duplicates from specimen trees
    • Remove redundant field unit information from derived units in specimen view
    • Bugfix for regressions in context with using extended secundum sources in 5.22
    • Some further bug fixes for specimen related data
  • - TaxEditor
    • Flag to include authors in taxon and name search in TaxEditor
    • Include misapplications and pro parte synonyms in "set secundum for subtree"
    • Improved progress monitoring and reporting for some long running tasks (like "set XXX for subtree")
    • Refresh navigator after ABCD import
    • Improved handling of specimen being media or DNA sample
    • Sorting for distribution status drop downs in distribution editor improved
    • Disable computed descriptions in factual data view
    • Bug fixes:
      • Error when swaping taxon and synonym
      • Incorrect handling of selected secundum references when moving a synonym to another accepted taxon
      • Removed warning (and data loss) before trying to open a taxon a second time in name editor
      • Problems when saving a polytoumos key (including fix for incorrect numbering after such changes)
      • Selection for team members does not filter on persons only
      • Disable details view for structure and property trees in character editor
      • Searching for not existing UUIDs in bulk editor throws exception
      • Remove duplicated terms from search in databases with >1 language (e.g. Englisch and Spanisch)

# Subject Status
  cdm 4 Collapse all/Expand all
9619 Model changes for taxon concept strategy Closed
9617 Rename ICNB to ICNP Closed
9614 Use underscore as word separator for all role based groups Closed
9536 Remove old single source citation and microCitation columns for secundum and DescriptionElementBase_OriginalSourceBase and TaxonName_NomenclaturalStatus Closed
  cdm-dataportal 2 Collapse all/Expand all
9591 Specimen Tree View: concise label for derivatives Closed
9329 Implement sec reference as original source in dataportal Closed
  cdmlib 25 Collapse all/Expand all
9624 Centralize team formatting and fix et al. position handling Closed
9623 Remove TaxonBaseShortSecCacheStrategy Closed
9618 fix historic NomenclaturalCodeEdition names ICN -> ICBN Closed
9613 Use fixed uuids for roles project manager, publish and user manager Closed
9612 ROLE_USER_MANAGER is missing as a group in FirstDataImporter Closed
9607 read image metadata from MediaInfoService if available Closed
9606 NullPointerExceptions (NPEs) in OccurrenceServiceImpl Closed
9604 Split bibliographic reference cache strategy and nomenclatural formatter + orginal source formatter Closed
9601 Set secundum for subTree does not work for misapplied names Closed
9598 Deduplicate NamedAreas with >1 representations and include label in search Closed
9597 Improve formatting of MediaSpecimen in TypeDesignationWorkingSet formatting Closed
9590 ObjectDeletedException when swap synonym and accepted taxon Closed
9588 Specimen Tree View: Duplicate derivatives Closed
9586 OccurrenceServiceImpl.pageRootUnitsByAssociatedTaxon() wrong total count in pager Closed
9583 Fix formatting of parent area in condensed distributions string if subareas have various status but at least 1 area has status native Closed
9530 Add pages to bibliographic book sections Closed
9433 Improve titleCache generation for misapplications Closed
9326 Show all authors in bibliographic references Closed
7305 [Dicuss] searching for authorteam with more than three members is incomplete Closed
6359 Remaining issues secundum for subtrees Closed
5575 DNA Sample requires CacheStrategy Closed
5573 Cache Strategy for Media Specimen required Closed
3764 Improve formatting for reference type Section Resolved
3667 Implement correct implementation of original spelling in publications Closed
3666 Implement original spelling in name parser Closed
  cdmlib-remote 1 Collapse all/Expand all
9185 DateHeaderFilter.doFilter(..) causes NPE in FrameworkServlet.processRequest(..) on 404 HTTP response Closed
  cdmserver 1 Collapse all/Expand all
9602 cdm-server must not start instances with severe db connection problems Closed
  taxeditor 13 Collapse all/Expand all
9625 Selection for team members does not filter on persons only Closed
9611 Implement setSecundumForSubtree for MAN and ppSyns in TaxEditor Closed
9605 Disable Details View for structure and property trees in character editor Closed
9603 Sorting in status drop down of distribution editor Closed
9595 Use DerivedUnit or DnaSample for DnaSampleGeneralDetailElement Closed
9594 Use MediaSpecimen as input for MediaSpecimenGeneralDetailElement Closed
9593 Changing and saving a PolytomousKey throws ConcurrentModificationException Closed
9589 Move synonym to another accepted taxon ignores the selected new sec reference Closed
9587 Unsaved changes are lost when trying to open a taxon a second time Closed
9575 Allow flag to include authors in taxon and name search in TaxEditor Closed
9469 Searching for a UUID in bulkeditor which does not belong to a record throws an exception Closed
8659 Taxon navigator: not refreshed after ABCD file import Closed
8471 Computed descriptions should be disabled in TaxEditor Closed

CDM Platform 5.22 (released Apr 16th, 2021)

Issues: 45

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - CDM Model
    • Handle taxon secundum source and classification source as "full" sources now with external links etc. (similar to nomenclatural sources) - classification sources are not yet handled as such in TaxEditor
    • Add "ratio to" for characters expressing a property ratio between 2 structures (e.g. length ration upper leave to lower leave)
  • - CDM Library
    • Improve name parser to recognize journals like PhytoKeys and PLoS ONE
    • Improve name parser to recognize and handle "ser." correctly
    • Improve formatting for bibliographic in-references
    • Improved formatting for taxa using a webpage as secundum reference (title does not include the URI anymore)
    • Improve taxon search for names with protected title cache (for these taxa the search runs on the full name and not on the name without author only now)
    • Sorting for certain invalid designations improved (e.g. for misspellings, which are set to the end now)
  • - Imports/Exports
    • Cdm light:
      • fix bug in type designation export
      • flag names in name type designations to make it possible to format them in italics
    • ABCD import:
      • mark taxon descriptions as specimens holding descriptions where suitable and use only a single description for holding specimens
  • - Data Portal
    • New implementation of the specimen tree view that shows specimen data in a collapsible derivation tree
    • Lower default zoom level for occurrence maps
    • Fix sort order in condensed distribution strings for E+M
  • - TaxEditor
    • Referencing objects
      • improve performance
      • cancelable if list is long
      • allow "open in ..." also for sources
      • improved label for some categories
      • recursive call of referencing objects view
    • Sources
      • implement advanced secundum sources
      • Reduce visible fields for nomenclatural sources
      • Remove "type" from all external links
    • Bulk editors
      • fix behavior when they are opened first time by selecting a single record (e.g. via "open in" context menu) - the bulk editor could then not be used for further search anymore
      • show and allow editing by "created by"
      • text in fields is copyable
    • Make handling of original spellings configurable when deleting a name
    • Add symbol to taxon factual datasets holding specimens
    • Add preferred stable identifier field in type designation duplicate wizard
    • Bug fixes
      • correct saving of publish flags for occurrences/specimen
      • ordering in character editor structure tree
      • multi-select handling for "open in distribution editor" in taxon navigator
      • unpersisted term tree title for newly created term trees
      • exception when reusing a name in new taxon dialogue
      • cancel behavior for "Change accepted to synonym"
  • - Web editor
    • Bug fixes
      • problems with selection of media references of type specimens (#9568)
      • Error in data transfer object needed for name part search filters (#9490)

# Subject Status
  cdm 8 Collapse all/Expand all
9507 Add ratioTo structure to Character Closed
9332 Rename TypeDesignationBase.source to .designationSource Closed
9331 Distinguish DescriptionElementSource and NamedSource Closed
9330 Remove "NomenclaturalSource" from OriginalSourceType Closed
9327 Make taxon secundum reference an original source Closed
9315 Remove old single source citation and microCitation columns Closed
9211 Handle source(s) for Classification Closed
8761 Remove TaxonName_NomenclaturalStatus MN table Closed
  cdm-dataportal 3 Collapse all/Expand all
9555 symbols for record basis (and kind of unit) in derivation tree Closed
9458 Consider lower zoom level as default Closed
7599 treeView for specimen data in dataportal Closed
  cdm-vaadin 1 Collapse all/Expand all
9568 TypeSpecimenEditor: Selection of a reference of an typified image Closed
  cdmadapter 2 Collapse all/Expand all
9574 Add html tags for names in NameTypeDesignation in CdmLightExport Closed
9515 Add DescriptionType to TaxonDescription of TaxonAssociations in ABCD import Closed
  cdmlib 15 Collapse all/Expand all
9578 Multiselect for input of distribution editor creates duplicates Closed
9571 Improve sec-formatting for taxa with webpage secundum Closed
9570 Use tagged text for NameTypeDesginations name part Closed
9567 Unify HomotypicGroupTaxonComparator and HomotypicGroupNameComparator Closed
9566 Handle nomenclatural standing correctly in cdmlight / sorting algorithms Closed
9561 In name and taxon search if titleCache is protected the search should run on titleCache also Closed
9558 General tests for cdmlight export Closed
9556 occurrence/{uuid}/fieldUnitDTOs web service adds duplicate units to response Closed
9551 Recognize "series" in article parsing Resolved
9550 Recognize PhytoKeys and PLoS ONE in name parser Closed
9529 Correct formatting for bibliographic in-reference separation Closed
9526 Sort order in E+M distribution string should be strictly alphabetic Closed
9490 avoid rank entity in TaxonNameParts Closed
9441 Move names with invalid designation name relationships to the end in taxon comparator Closed
7917 Revise ReferenceSystemTerms Feedback
  cdmlib-remote 2 Collapse all/Expand all
9557 implement occurrence/{uuid}/rootUnitDTOs Closed
9535 harmonize DefinedTermBase and KeyTerm serializations Closed
  taxeditor 14 Collapse all/Expand all
9562 Publish flag of field units and derived units are not handled correctly Closed
9549 Reduce visible fields for nomenclatural source and secundum source in TaxEditor Closed
9545 Remove "External Link type" completely Closed
9544 In bulkeditor the strings should be copyable Closed
9542 Bulk Editor search does not work after opening a name out of the bulk editor Closed
9541 Improve referencing objects handling Resolved
9538 Changing accepted to synonym closes name editor tab even if canceled Closed
9537 Implement ratioToStructure in TaxEditor Feedback
9533 NPE when reusing name for new taxon Closed
9531 Add Names in OriginalSpelling to the delete configuration Closed
9518 Add symbol to descriptions having status individual association in facts view Closed
9504 Changing term tree title is not persisted Closed
9328 Adapt Editor to switch to originalSource for taxon secundum Closed
8968 filter Bulk editor for created by Closed

CDM Platform 5.21 (released Mar 10th, 2021)

Issues: 41

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - CDM Library
    • Added distribution status "undefined" to CDM library
    • Improved formatting for classifications
  • - Data Portal
    • Correct formatting of condensed distribution string for E+M
    • Show distributions of "fallback" areas in textual representations of distributions (for E+M)
    • Remove distributions with status "undefined" from distributions in data portal (for E+M)
    • Media viewer shows source data for images
  • - TaxEditor
    • Fix problem with using TaxEditor on a system using an non-standard encoding (e.g. Turkish)
    • Fix critical bug where data changes under certain conditions can get lost if a taxon and its parent taxon is edited at the same time
    • Improve performance when saving taxa (and some other operations), mostly for database with large classification trees
    • Support workflow for taxon operations (accepted -> synonym, syn -> acc, swap acc/syn, syn->misapplication, move taxon etc) if publish flag or secundum are not equal for taxon and "parent" taxon
    • Descriptive data matrix
      • Sources for "literature" records editable
      • Specimenlist added to taxon (individual associations) are marked as such
    • Make copyright statements reusable
    • Make abbreviated title and URI editable for rights statements in supplemental data view
    • Distribution status "isAbsent" attribute editable
    • Order termlists/-trees which are marked as unordered alphabetically by default
    • Remove multi-select from default feature tree selection
    • Improved image handling for images related to taxa or specimen (media view)
    • Further bugfixes
      • exception when swapping synonym and accepted if taxon is used in a descriptive dataset
      • exception when opening default feature tree selection preference page
      • exception when trying to open orphaned taxa in name editor
      • LayoutComposite exception when working with taxon related images
  • - Web editor
    • Phycobank registration UI
      • full support for type designation references
      • UI-improvements and bugfixes

# Subject Status
  cdm 1 Collapse all/Expand all
3816 Create "Undefined" status and choose it for NULL status Closed
  cdm-dataportal 1 Collapse all/Expand all
5206 Status symbols in condensed distribution string repeated for subareas Closed
  cdm-vaadin 9 Collapse all/Expand all
9485 TaxonNamePopupEditor: StackOverflow on selecting ICN reference Closed
9483 LazyInitializationException (LIE) in TaxonNamePopupEditor when selecting trinominal rank Closed
9482 NameTypeDesignationEditor: designationReference --> new causes LIE Closed
9480 SpecimenTypeDesignationEditor: designationReference --> new should be limited to sections of the publishedUnit Closed
9479 ToOneRelatedEntityCombobox misses sending ValueChanged events to MBeanFieldGroup Closed
9478 required ToOneRelatedEntityCombobox field in SpecimenTypeDesignationDTORow fails validation Closed
9476 SpecimenTypeDesignations for existing names in other nom acts can not be created Closed
9475 NameTypeDesignations for existing names in other nom acts can not be created Closed
8981 Improve NameStatus in UI Closed
  cdmlib 9 Collapse all/Expand all
9521 Fallback areas in textual representation should always stand alone Closed
9481 ObjectDeletedException when swap syn and accepted with descriptions belonging to a descriptive dataset Closed
9470 CollectionDTO constructor prevent from circles Closed
9451 Cache strategy for classifications is missing Closed
8858 Ordering of distribution status 'undefined' is not correct in E+M Closed
8297 Fix condensed distribution string for E+M Closed
5779 Update EuroPlusMedCondensedDistributionComposer to use new symbol field Closed
5682 Implement condensed distribution string for Cuba Closed
5050 revise the subAreaPreference rule for filtering Distributions Closed
  cdmlib-remote 1 Collapse all/Expand all
9509 IIIF manifest includes media source information Closed
  taxeditor 20 Collapse all/Expand all
9525 Namerelationship source label is missing sometimes Closed
9520 Taxonnode parent merge cascade leads to non-transactional behavior Closed
9512 Descriptions being created for individual associations in matrix should have description status "Individual association" Closed
9506 Rights can not be selected for reuse Closed
9499 Make isAbsent editable in DetailsView Closed
9491 Order of terms in not order relevant trees Closed
9488 Show details of description in character matrix Closed
9472 Encoding problem with ProxyUtils.CollectionType leading to failing lazy collection loading Closed
9471 Widget is disposed exception when switching away from media before details view is completely loaded Closed
9467 AssertionFailedException when opening DefaultFeatureTreePreference and preference should not allow multi-select Closed
9466 Termselection preference pages do not check the elements Closed
9465 Open in ... NameEditor for orphan taxa results in CCE Closed
9427 Code cleaning in CdmPreferenceCache Closed
9374 ClassCastException when switching between media Closed
9340 Workflow support for secundum handling when making synonym a new accepted taxon Closed
8767 Workflow support for publish flag Closed
8198 Deleting an image gallery from image gallery view shows wrong configuration dialog Closed
7521 refresh of taxonnavigator sometimes does not work for moving taxonnodes Closed
7091 Add uri field and abbreviatedText to Righs in supplemental data Closed
5670 Refresh of Taxon Navigator Closed

CDM Platform 5.20 (released Feb 10th, 2021)

Issues: 17

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - CDM Library
    • support for pollen, leafs, and trichomes as tissue samples
    • fix formatting for taxa for taxa with secundum detail information
    • formatting for DNA Sample
    • bugfixes
    • role to allow setting the publish flag added
  • - Data Portal
    • bugfix related to missing source references of distribution data if aggregated data is involved
  • - TaxEditor
    • if a new synonym is added the publish flag now gets the same value as the accepted taxon
    • bugfix for the reference select dialog
  • - Web editor
    • Phycobank registration UI
      • designation refences for name and specimen type can now be edited
    • Distribution editor
      • fix exception when using textual taxon filter

# Subject Status
  cdm 1 Collapse all/Expand all
9434 Add pollen, leaf and trichomes to tissue sample kind-of-unit vocabulary Closed
  cdm-dataportal 1 Collapse all/Expand all
9143 Distribution data sources are missing if multiple distributions exist Closed
  cdm-vaadin 6 Collapse all/Expand all
9461 Filter in vaadin distribution editor does not work Resolved
9324 Enable designation reference editing in name type designation Closed
9301 SpecimenTypeDesignationEditor: Add fields for citation and citationDetail Closed
9290 stop setting Registration.citation as citation for TypeDesignations in all type editors by default Closed
8975 Name Status filtered in UI Closed
8522 Make type status mandatory in Name type designation editor Closed
  cdmlib 4 Collapse all/Expand all
9457 Distribution editor: Taxon filter broken due to invalid HQL in TaxonNodeServiceImpl.getUuidAndTitleCache() Closed
9429 Taxon cache strategy handles sec details 2x in some cases Closed
7529 Wrong UUID after creating a GrantedAuthority for a Role like ROLE_PUBLISH Closed
5095 Fix failing dozer related tests Closed
  cdmlib-remote 1 Collapse all/Expand all
6324 fix dozer mapping after removal of synonym relations and after using TaxonNode Closed
  taxeditor 4 Collapse all/Expand all
9443 Improve handling of TissueSamples and others in SpecimenTreeEditor Closed
9426 Set publish flag for Synonyms in accordance with accepted taxon publish flag Closed
9351 Include new locations for cdmlib-print and cdmlib-remote in jenkins release script Closed
6450 New reference with only the protected titleCache set is not found in reference select dialog Resolved

CDM Platform 5.19 (released Jan 27th, 2021)

Issues: 41

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - CDM Library
    • fix handling of 2 person teams in short citations (author + year)
  • - Data Portal
    • specimen lists further improved (work in progress)
      • Specimens without assigned field unit are now visible in the tree and "compresses" table view
    • remove disabled classifications from advanced search classification filter
  • - TaxEditor
    • show taxon name for references used as nomenclatural references in referencing objects view
    • distribution editor
    • improve sorting (now sorting is equal to sorting in taxon navigator)
    • new taxon dialogue
      • fix ignored publish flag
      • fix handling of reuse taxon in New Taxon dialogue
      • fix exception when reusing a name
    • terms
      • fix copy&paste in term tree editor
      • dirty flag not set when moving a feature in feature tree editor
      • add "open in " menu to context menu in term/term tree editor
      • main menu for term vocabularies and trees refactored and unified
    • details view
    • improve and fix handling of fields covered by (un-)protected caches
      • fix some inconsistencies
      • use light color for indirect protection
      • use various colors if >1 caches are using the field
    • media
      • changes not persisted in media bulk editor
      • missing reference detail in media specimen details view
      • update (unprotected) titlecache in media details view when underlying data is changing
      • fixing multiple bugs in media view
    • agents (person, team, instituion)
      • improve converting person to team handling (especially handling of cache fields)
      • fix duplicate entries in agent search dialogue
    • descriptive data sets navigator ordered alphabetically
    • further bug fixes:
      • fix incorrect state of taxon navigator toggle button which indicates if the taxon navigator jumps to the taxon that has the focus
      • remove area level from distribution label for distribution areas not having a level
      • alphabetic ordering of reference types in dropdown lists
      • exception when saving parsed hybrids in name editor
      • exception when adding specimen to character matrix

# Subject Status
  cdm-dataportal 5 Collapse all/Expand all
9403 cleanup function cdm_related_taxon() from used paramerters and css class attributes Closed
9397 Derivate tree view must show DerivedUnits even if the FieldUnit is missing Closed
9379 exclude disabled classifications from advanced taxon search form Closed
9213 specimen views 'compressed table' and 'derivate tree' fail when no fieldunits exists Closed
7704 Dataportal specimen table should be able to show DerivedUnits without a FieldUnit Closed
  cdmlib 8 Collapse all/Expand all
9415 DNA and other Derivatives missing in DerivedUnitDTO Closed
9395 DerivedUnit.collectFieldUnits() and findFieldUnitDTOByAssociatedTaxon() and findByAccessionNumber() in OccurrenceService to return all root units Closed
9389 further improvement and revision of derivative filtering by type and DerivedUnitDTO Closed
9384 DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams with two members Closed
9366 Specimen type designation with specimen having only collection name but not collection code does not show collection information Closed
9350 Create new taxonnode ignores the publish flag Closed
9253 revise OccurrenceServiceImpl.findFieldUnitDTO(..) Closed
7612 CacheStrategy for MediaSpecimens Duplicate
  cdmlib-remote 1 Collapse all/Expand all
9387 LazyInitializationException (LIE) in NameController.doGetTypeDesignationsInHomotypicalGroup() Closed
  taxeditor 27 Collapse all/Expand all
9422 Improve performance during Preferences startup Closed
9413 DNA details lable "Ratio of absorbance ..." corrected Closed
9412 Fix reuse existing name in NewTaxonWizard Closed
9405 Fields set to irrelevant for cache should be set by state only Closed
9391 If named area level does not exist remove the level information Closed
9382 For nomenclatural source show taxonname in referencing objects view Closed
9375 Alphabetical order for reference type drop down Closed
9372 in media details view unprotected title cache is not updated when underlying data is changed Closed
9371 Media bulk does not persist data anymore Closed
9369 Reference Detail is missing in MediaSpecimen details view Closed
9365 Reuse taxon does not work in new Taxon dialogue Closed
9360 Parsed hybrids can not be persisted Feedback
9356 Comparison method violates its general contract for SourceComparator and TypeDesignationComparator Closed
9354 Sorting in distribution editor is broken Closed
9353 Copy & Paste creates dirty data in term trees Closed
9346 Adding specimen to character matrix fails sometimes Resolved
9344 Datasets in Descriptive Dataset Navigator should be ordered Closed
9338 Restructure term menus Closed
9264 Flag for toggle button for linking taxon with navigator looses/switch value without clicking the button Closed
9208 Move cdmlib-print and cdmib-remote to taxeditor.printpublisher Closed
9142 The Agent search dialog shows duplicated entries Closed
9140 Deleting an images forgets moving operation Resolved
8874 move taxon is reverted when taxon is edited afterwards Resolved
8289 Add "Open in RefObj view" to term editor context menu Closed
7990 Moving a feature via d&d does not make the Feature Tree Editor dirty Closed
7711 Bugs in media gallery Resolved
5163 Converting persons to team members may result in "-empty team-" Closed

CDM Platform 5.18 (released Dec 3rd, 2020)

Issues: 80

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - Data Model
    • "single sources"
      • some data that refer to a single source only are now handled as full sources (before it was only a reference and a reference detail), with possibility to add further information like name used in source and external links;
      • protologues/original publications handled as external link for the nomenclatural source
      • original spelling handlied as name used in source of nomenclatural source now (before it was a name relationship)
    • added new nomenclatural status "comb. ined", protected, in sched., pro syn., orth. var. (as status)
    • labels updated for "is blocking name for" and "is isonym of", is correct spelling for, is earlier isonym of, conservation designated ; abbreviations updated for op. utique oppr., orth. cons., orth. cons. prop.
    • abbreviations added for "Flowering Period" (Fl.) and "Fruiting Period" (Fr.)
    • add [m] as predefined default measurement unit for altitude
    • improved handling of nomenclatural standing of a taxon name
  • - CDM Library
    • improve formatting with citation detail
    • improved type designation formatting
    • cloning of taxonomic subtrees (not yet available in TaxEditor)
      • more configurable
      • cloning of subtrees, not only classifications, possible
    • major upgrade of third party code
  • - Data Portal
    • specimen lists and pages fully refactored and improved (work in progress)
    • map serives improved
    • adapt sort order of taxon tree to sort order in TaxEditor
    • display of name facts improved
    • new base font size
    • improved rendering of footnotes
    • fix missing nomenclatural status on name pages and registration pages
  • - Exports
    • Several major and minor issues fixed in cdmlight export (#9262, #9256)
    • less cryptic default name for cdmlight export file
  • - TaxEditor
    • "Single Sources"
      • objects with single sources (like taxon name nomenclatural source or name relationship source, etc.) are handled as full sources now including "Name in source", "original Information", "external links" etc.
      • protologues/original publications were moved to the new nomenclatural source section as external link for the nomenclatural source
      • original spelling now available in nomenclatural source section
    • term tree (hierarchy) editors and character editors fully refactored and many bugs fixed, also preferences for term tree display added
    • reduce download size and preparation for further reducing download size
    • remove incorrect "invalid designation" handling
    • assist for secundum handling when making a synonym an accepted taxon
    • add LSIDs to persons and references
    • improve default reference type for in-reference creation dialogue (depending of the original reference type), e.g. journal for articles
    • bug fixes:
      • missing dropdown list if no rank was selected yet in name details view
      • adding derived units to derived units (e.g. DNA sample to specimen) is possile again in specimen tree editor
      • error in LSID handling
  • - Web editor (Phycobank registration UI)
    • annotations for names and field units visible
    • #8859

# Subject Status
  cdm 14 Collapse all/Expand all
9311 Update some (abbrev) labels for nomenclatural status types Closed
9282 Add nomenclatural standing Closed
9272 Add missing nomenclatural status Closed
9225 Make TaxonName.nomenclaturalSource a new DescriptionElementSource subclass Closed
9124 Altitude feature should have [m] as measurement unit by default Closed
9121 Add abbreviations to Feature Closed
9120 Update script for flowering period supports temporal data Closed
9094 Update script to update TaxonNode.source from IdentifiableSource to DescriptionElementSource Closed
9062 Remove StatisticalMeasurementValue.value_old Closed
8326 update labels for is blocking name and is isonym Closed
6591 Use name used in source for original spelling Closed
6589 Handle protologue as original source with URI link Closed
6581 Make all microreferenced references OriginalSources Closed
5795 [DISCUSS] Do we need comb. ined. as a nomenclatural status? Closed
  cdm-dataportal 18 Collapse all/Expand all
9306 Registration result list: supress "designated by" reference in portal Closed
9265 Adapt dataportal to new protologue handling Closed
9261 LazyInitializationException (LIE) in TaxonController.doGetTaxonNodes() Closed
9260 error in pages.inc calling compose_taxon_node_status() Closed
9249 compact display of collection information Closed
9240 nomenclatural status missing in name and registration page Closed
9235 Footnote key for multiple cdm entities need to be rendered together Closed
9234 Error: Object of class stdClass could not be converted to string caused by compose_cdm_specimen_or_observation_tree_entry() Closed
9224 openlayers map handles server error per layer and presents a user message Closed
9222 Adapt dataportal to switch to originalSource for remaining single sourced classes Closed
9220 adapt dataportal to /registrationDTO now using identifier as query parameter and secure against CVE-2007-0450 vulnerability Closed
9209 name page, registration page: show annotations for names and fieldunits Closed
9184 WSOD in advanced search cdm_dataportal/search Closed
8854 Choose new base font size for the portal Closed
8851 display of name facts not appropriate in all cases Closed
7685 Add Selenium tests for specimen table in data portal Closed
6356 taxontree sort order as in editor Closed
3978 Specimenview path: Compact representation of exactLocation Closed
  cdm-vaadin 6 Collapse all/Expand all
9318 TaxonNameEditor: nomenclatural reference no longer selectable Closed
9313 LazyInitializationException (LIE) in TaxonNamePopupEditor Closed
9289 LazyInitializationException (LIE) in NameTypeDesignationEditor Closed
9229 TaxonNameEditor: use NomenclaturalStatusDTO to avoid data loading probems within setters in TaxonName Closed
8859 RegistrationItemNameAndTypeButtons invalid regex pattern Closed
7936 Consider complete removal of redmine communication hub code Closed
  cdmadapter 2 Collapse all/Expand all
9262 Several open issues for cdmlight export related to Cactaceae and other Caryophallales Closed
9256 CdmLightExport: NameTypeDesignation string misses parenthesis for authors Closed
  cdmlib 19 Collapse all/Expand all
9322 Remove invalid designation taxon relationship Closed
9280 Refactor: IKeyTerm.getMessage() --> IKeyTerm.getLabel() Closed
9279 Improve type designation formatting and TypeDesignationSetManager Closed
9267 No sec reference for move change Synonym to accepted Taxon Closed
9258 Use Partial for date in FieldUnitDTO Closed
9257 revise filtering in OccurrenceServiceImpl.assembleFieldUnitDTO(FieldUnit fieldUnit) by SpecimenOrObservationType.PreservedSpecimen Closed
9252 Harmonize SpecimenOrOberservationBase related DTOs Closed
9230 Type in preparation of a published name displayed in PhycoBank Portal Name Page Closed
9223 make changes of nomenclatural references detectable again in TaxonGraphBeforeTransactionCompleteProcess Resolved
9210 invalid format string usage in MediaAutoInitializer Closed
9206 Solve cglib vs. cglib-nodep Closed
9204 Update cdmlib and taxeditor dependencies Closed
9194 Make RelationshipBase and NomenclaturalStatus reference OriginalSource Closed
9103 missing exception handling in TaxoNodeDto Closed
8458 document FieldUnitDTOOccurrenceServiceImpl.findFieldUnitDTO() Closed
7862 improve documentation on TaxonGraphHibernateListener and related classes Closed
6623 formatter for bibliografic citations with citationDetail Closed
5794 Move other invalid names to the end Closed
4866 Implement clone method for complete classifications Closed
  cdmlib-remote 6 Collapse all/Expand all
9335 termTree webservice response misses titleCache Closed
9259 reduce fields in TermBase json serializations Closed
9254 portal/occurrence/{uuid}/fieldUnitDTO.json fails with class cast exception Closed
9238 pure entities in DerivateDTO.derivates may cause LIEs Closed
9218 Change /registrationDTO/identifier/... signatures to use query parameters instead Closed
8423 OccurrenceServiceImpl.findFieldUnitDTO() fails to merge derivation paths when a FieldUnit has two derivatives Closed
  data 1 Collapse all/Expand all
9082 Update script for old empty Partials handling Closed
  devOps 1 Collapse all/Expand all
8635 install collectd + facette for server monitoring Closed
  taxeditor 13 Collapse all/Expand all
9307 Preferences for display of termtrees and entries Closed
9299 Add LSID to author and reference details Closed
9297 Improve name of zip file for cdmLightExport Closed
9286 Re-connect and change user should be disabled if no datasource is connected yet Closed
9266 Remove protologue section from TaxEditor Closed
9215 Drop down for empty rank does not work Closed
9199 Adapt TaxEditor to switch to originalSource for remaining single sourced objects Closed
9192 Layout issues for source in taxonnode details Closed
9189 Move datasource view to taxeditor.local Closed
8928 Swap menu entries for specimen bulk editors Closed
8774 Reimplement term tree editors to implement the general save strategy Closed
8547 Default type of a newly created inReference should depend on the type of the reference Closed
6947 Incorrect error for LSID field Closed

CDM Platform 5.17 (released Aug 19th, 2020)

Issues: 43

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - Data Portal
    • image viewer
      • improved thumbnail handling
      • automated creation of thumbnail URLs (avoids that always 2 or 3 versions of the image have to be stored in the database)
      • improved image meta data handling
    • possible default copyright statement below image viewer
    • improve handling of annotations and other footnotes like sources
      • some more annotations and sources are shown now
    • improved map representation for TDWG area maps
    • occurrence maps hidden if no data exists
    • fix bug that misapplied name taxa are not shown and not found in search
    • fix bug that placemark icons are not clickable in map
    • improve test system
  • - CDM Library
    • fix https handling for images
  • - Web Services
    • fix bug in taxon service that misapplied name taxa return no result
  • - TaxEditor
    • reduce download size (by >100MB)
    • make specimen media editable in specimen assistants and in specimen list editor details view (to improve workflow when editing e.g. type specimen)
    • find doubtful taxa without having "?" at beginning of search string
    • new layout for taxon node dialogue
    • additional parameters editable for taxon node placement source
    • move update site to https
    • open in browser button for ORCIDS
    • bugfixes
      • when moving synonym into homotypical group of accepted taxon
      • missing synchronization between taxon node dialogue and name editor
      • problems with name fact preferences
      • exception when editing data in bulk editor
  • - Web editor (Phycobank registration UI)
    • Collection editor extended by name filed
    • Improved authorship inferrence redarding ex-authorship
    • NameTypePopupEditor: Genus can be selectable as the name type for higher ranks
    • Registration items show type status in bold letters

# Subject Status
  cdm-dataportal 14 Collapse all/Expand all
9191 selenium test for specimen tree view (bottom up) Closed
9188 selenium web element wrapper for dynabox Closed
9186 selenium test for specimen top down view (aka devivate_path view) Closed
9181 set and get drupal variables from selenium test suite Closed
9175 hide occurrence map when no data exists Closed
9137 IPTC Keywords (and maybe other information) is not shown in Universal Viewer yet Closed
9128 Default copyright statement below image viewer Closed
9109 Search button font icon broken Closed
9099 placemark icon in kml map not clickable Closed
8850 Show annotations for DerivedUnits (Fieldunits etc) in Registration and other pages Closed
8543 overcome distinction of annotation and other foonotes Closed
8420 improve admin settings for specimens representations Closed
4372 Selenium PortalPage class also suitable for zen-basetheme Closed
2489 strategy for congruent areas in distribution maps: create merged TDWG layer with all levels Closed
  cdm-vaadin 4 Collapse all/Expand all
9182 Sub-collection and Collection vs. Collection and Super-Collection Closed
8317 Omit ex-author if ex-author=author Closed
8230 NameTypePopupEditor: genus selectable as the name type for higher ranks Closed
8156 Registration items show type status in bold letters Closed
  cdmadapter 1 Collapse all/Expand all
9110 Add additional informations to metadata table of cdmLight Feedback
  cdmlib 7 Collapse all/Expand all
9152 PreferencesService caches CdmPreferences Closed
9148 Replace sanselan library by the newer apache commons-imaging Closed
9147 Use StringBuilder in CdmUtils.concat() to avoid performance penalties Closed
9146 filter image metadata by include and exclude lists of key words Closed
9129 cdm property to store a default copyright statement for media items Closed
9105 rename NodeSortMode etc to TaxonNodeSortMode Closed
9000 UriUtils: HttpClient has ssl error connecting to pictures.bgbm.org Closed
  cdmlib-remote 4 Collapse all/Expand all
9198 option in iiif manifest creation to set canvas size to thumbnail size Closed
9193 LazyInitializationException (LIE) in portal/taxon/{uuid} web service Closed
9134 Rule based creation of additional media representations "on the fly" Feedback
9087 typedesignation/{uuid}/annotations must return pager objects Closed
  geotools - map service 1 Collapse all/Expand all
8310 Issues to solve in E+M shapefile Closed
  taxeditor 12 Collapse all/Expand all
9173 NPE when move synonym into homotypical group of accepted Closed
9172 Missing synchronisation between taxonnode wizard and name editor Closed
9171 Doubtful taxa are not found in bulkeditor Closed
9168 NameFeature selection in preferences are not shown Closed
9166 ClassCastException when editing media in taxon bulkeditor Closed
9138 Reenable BioCaseQueryServiceWrapperTest.testQueryForUnitId() Closed
9119 Remove schema create and schema update functionality from datsource view Closed
9118 Change p2 update site to https in Taxeditor Closed
9116 Adapt Editor to switch to originalSource for TaxonNode and improve layout of TaxonNode dialogue Closed
9065 Add derived unit media to DerivedUnitFacade details view Closed
9040 Implement open button for ORCIDs Closed
5752 Reduce TaxEditor size Closed

CDM Platform 5.16 (released June 30th, 2020)

Issues: 14

Downloads: TaxEditor, CDM Server, Data Portal

What is new?

  • - Data Portal
    • Fix for sortorder of taxon nodes in taxon tree
    • Fix for incorrect link for geo-coordinates in point maps
    • Fix for missing information on taxon pages (see #9095)
  • - CDM Library
    • Improved deduplication of references and authors during name parsing (the relatively empty parsed references and authors are now merged with richer references and authors, which include e.g. also URI, ISBN, lifespan, first name, etc. information)
    • Improved caching mechanism (which hopefully leads to less multiple representation exceptions in TaxEditor)
    • Improved formatting and parsing of dates and periods (now we generally use a format like "30 Jun 2020" which is more language independent)
  • - TaxEditor
    • Setting focus automatically to newly created facts in Fact View
    • Improved reference and author deduplication during creation of new taxa and synonyms
    • Improved handling of malformed URIs
    • Fix bug which threw multiple representation exceptions when editing taxa with a taxon node source (which exists very often in some databases)
    • Fix bug throwing an exception when deleting a classification
    • Fix bug throwing an exception when deleting multiple records in bulk editor

CDM Platform 5.15 (released June 23rd, 2020)

Issues: 82

Downloads: TaxEditor, CDM Server, Data Portal

What will be new?

  • - Data Model
    • TaxonNode has a "status" attribute now instead of flags "doubtful", "unplaced" and "excluded"
      • Allows to use only max. 1 of the above status for the same node
      • "Excluded Notes" changed to => "Status notes" and is valid for what ever status has been chosen
    • Measurement values handled as "BigDecimal" to avoid rounding errors related to floating point algebra and to allow to handle exactness (e.g. 1.6 differs from 1.60)
    • "Available for" attribute for features to distinguish if features are available for taxa, for names and/or for specimen
    • Temporal fact datatype for e.g. flowering periods supporting time periods like (Apr-)May-July(-Aug)
    • New feature "Flowering period"
    • New feature "Altitude" added
    • Rename "later homonym for" to "later homonym of"#
    • "Links" added to main classes like taxa, names, references, authors, ... - these allow adding an unlimited number of URL-links to these objects together with a description what this link is for
    • Key-Value structure for storing media metadata (not yet used)
  • - Data Portal
    • New implementation of the occurrence point display is maps which allows new important features:
      • Field unit information can now be shown.
      • Display of error radius
      • NOTE: More exciting features will come with the following releases.
    • The new image viewer which has been integrated into the dataportal with version 5.13 is now stable and available for all data portal installations. The new image viewer uses the iiif conform Universalviewer. The new viewer adapts to different screen sizes and supports mobile devices.
    • The beautiful Noto font family is now the default for the data portal and brings improved readability and excellent unicode support.
    • The status (unplaced, doubtful, excluded) of a taxon node is now shown on taxon pages and in the classification tree.
  • - CDM Server
    • Improved logging
    • Debian installation package improved
  • - CDM Library
    • Improved permissions for users being allowed to edit all taxonomies
  • - TaxEditor
    • Improved deduplication, especially for taxa entered via taxon node editor
    • Persons: allow editing lifespan
    • Possibility to create or update database schema via connect dialog
    • Improved layout of connect dialog
    • Taxon nodes status with status notes (see Data Model), available in taxon node wizard and in CDM light export
    • Factual Data:
      • Possibility to enter temporal data (phenology)
      • Factual dataset source is shown as (uneditable) source for each fact
      • Facts view: remember expansion state after deleting
      • Remove caching form facts view which (resulted in unexpected results)
    • Descriptive dataset editor and matrix editor:
      • Improve performance of matrix editor
      • Add context menu to matrix editor (and remove preliminary buttons)
      • Fix failing adding of specimen which are not attached to a field unit
      • Remove taxon in descriptive dataset editor only available if taxon has focus
      • Fix bug when selecting a character tree for a descriptive dataset
    • Reference bulk editor table has new included columns: year, in-reference, uri
    • Open link button for entering DOIs in reference details view
    • Features:
      • Possibility to define if a feature is available for taxa, specimen and/or taxon names
    • Improved decimal/rounding handling of quantitative data (e.g. distinguish 9.1 form 9.10)
    • Configurable if the old specimen list editor should be avialable via main menu
    • Bug fixes:
      • Broken media deatils view fixed for "MediaSpecimen"
      • Exception when creating a new taxon
      • Search does find orphaned synonyms now
      • Term search fixed
      • Exception in referencing objects view for TextualTypeDesignations
      • Exception in name details view if name relations were incomplete (no type, no from-name or no to-name)
      • Exception when deleting a descriptive dataset
      • Incorrect context menu for synonyms after moving a synonym into or out of the homotypic group
      • Opened selection dialogs lock editing in other windows
      • Remember expansions state of sections in details view and supplemental data view (this feature was lost for some time)
      • Recently used references list is not emptied anymore after using search dialog for nomenclatural reference
      • Bulk editor: multiple deduplications without saving do now remember all deduplications
      • Some widget is disposed exceptions fixed
      • fix verbatime date not persisted for books

# Subject Status
  cdm 13 Collapse all/Expand all
9064 Add ExternalLinks to IdentifiableEntities Closed
9043 Add feature "Altitude" Closed
9037 Remove old Feature.supportedXXX columns Closed
9036 Remove old TaxonNode.unplaced/doubtful/excluded columns Closed
9027 Implement Feature.availableFor Closed
9026 Implement Feature.supportedDataTypes as EnumSet Closed
9009 Add structure to store media metadata Closed
9005 Make the TaxonNode flags alternatives and change excludednotes to status notes Closed
9004 Make TaxonNode.referenceForParentChildRelation an OriginalSource and rename it to (placement)source Closed
8991 Add feature "Flowering Period" Closed
8978 Implement measurement values as BigDecimal Closed
8964 Improve label for homonym relationships Closed
8802 Implement flowering period for Flora of Cyprus Closed
  cdm-dataportal 13 Collapse all/Expand all
9076 synonymy without margin when 'Synonymy as tab' and 'Tabbed taxon page' are off Closed
9034 simple agent list page with filter function Closed
9010 Display taxon node status excluded, unplaced, placement doubtful on taxon page and taxon tree and show taxon node status note and taxon node source on taxon page Closed
8994 universal image viewer fails loading libs when clean urls is disabled Closed
8972 integrate kml layers into map viewer Closed
8900 Layout issues with new image viewer Closed
8888 responsive width for universal viewer Closed
8855 Show error radius in EDIT portal Closed
8196 display ortographic corrections in name relations as 'corrected name: <nameCache>' Closed
8134 Implement verbatim type information in dataportal Closed
6878 choose a base font for the portal and deliver it from the drupal module or theme Closed
4488 Specimen data points in map should show FieldUnit information Closed
4257 specimen map should zoom to area of distribution Closed
  cdmadapter 2 Collapse all/Expand all
9031 Adapt CdmLightExport to new TaxonNode.status Closed
8998 Terms created by abcd import should always be part of a vocabulary Resolved
  cdmlib 5 Collapse all/Expand all
9081 Handle empty Partials correctly Closed
9058 Hibernate loggs error when creating schema on MySQL due to failing index creation Closed
9047 Search does not return orphaned synonyms Closed
9020 add default role Allow_for_all_taxa (TAXONNODE.[CREATE,READ,UPDATE,DELETE]) Closed
8986 use Maven Enforcer plugin to check for dependency version conflics and to enforce the minimum maven version Closed
  cdmlib-remote 3 Collapse all/Expand all
9044 TaxonNodeDtoBeanProcessor supports new TaxonNodeStatus terms Closed
9023 option to start cdm webapp with hibernate.hbm2ddl.auto = create Closed
6113 webservice to expose FieldUnits related to a Taxon or TaxonName as KML and/or GML Closed
  cdmserver 3 Collapse all/Expand all
8682 cdm-server debian packages configured for jemalloc Closed
7085 cdmserver logfiles getting too big, use RollingFileAppender Closed
3683 add /etc/default/cdmserver to debian package Closed
  data 1 Collapse all/Expand all
9017 Update image link for FoG Willing images Resolved
  taxeditor 42 Collapse all/Expand all
9084 Make it configurable if a Description is deleted only from the Descriptive Data Set or from it's Specimen/Taxon Resolved
9070 Adapt preference page to feature.isAvailableFor... Resolved
9066 Make visiblity of Specimen List Editor menu configurable Closed
9063 Detailsview for MediaSpecimen broken Closed
9060 NPE in termsearch Closed
9059 Cancel taxon save does not clean the (factual data) cache Closed
9055 Relabel "Type Designation" to "Type Information" Feedback
9053 CCE when selecting Character Tree for descriptive dataset Closed
9052 NPE in name details view for incomplete name relationships Closed
9045 TextualTypeDesignation throws exception in referencing objects view Closed
9038 Adapt TaxEditor to use BigDecimal for StatisticalMeasurementValues Closed
9033 Adapt TaxEditor to new TaxonNode.status Closed
9032 Implement Feature.availableFor in TaxEditor Closed
9029 Adapt character matrix to using dtos instead of whole cdm entities Closed
9025 allow for creating a new schema in empty dbs via the remote login dialog Closed
9022 Implement lifespan for Person Details View Closed
9016 Adding specimen without field unit fails Closed
9013 Problems in TaxonNode Dialog Closed
8999 Verbatim date not persisted for books Closed
8990 Implement flowering periods (temporal facts) in TaxEditor Closed
8988 Add link button to DOI field for references Closed
8969 Multiple deduplications are not executed Closed
8963 Selection dialogues should be modal Closed
8962 Handle widget is disposed after closing Supplemental Data View Closed
8961 Using the selection dialogue for nomenclatural references removes the recently used list Closed
8959 Moving a synonym to the homotypical group of the accepted taxon opens the context menu of the accepted taxon Closed
8958 Add publication year, inReference (journal), and URI to reference bulk editor Closed
8957 Rename "unexpected error" to "unhandled error" Closed
8954 Details and Supplemental Data View do not save the expansion state of sections again Closed
8903 Remember expansion state in factual data view Closed
8901 Deleting an aggregated description from a descriptive matrix does not delete the aggregated description itself Resolved
8857 NonUniqueObjectException when creating new taxon Closed
8849 NPE in synonym DetailsViewer for synonyms without accepted taxon Closed
8806 Multiple representations problem on saving Desriptive Data Set Worksforme
8785 Move functionality of buttons to context menu of the character matrix Resolved
8783 Massive Heap consumption in server instance opening the Description-Matrix editor Closed
8754 DescriptionElements are not deleted with the Descriptive Data Set Resolved
8753 EagerLoadingException on opening Character Tree Editor after deleting all Desciptive Data Sets Closed
8752 Matrix Editor: Can fail showing all SpecimenDescriptions in the dataset Worksforme
8662 "Remove Taxon" in DescriptiveDataSetEditor should only be visible if taxon is selected Closed
7774 Show description source for description elements Closed
7189 Taxeditor connect dialog high-dpi suport Closed

CDM Platform 5.14 (released April 8th, 2020)

Issues: 29

Downloads: TaxEditor, CDM Server, Data Portal

What's new?

  • - Data Portal
    • Structured descriptive data is shown on specimen page as continous text
    • Bugfix for the new universal media viewer
    • Bugfix for some descriptive data pages for taxon descriptions
  • - Import/Export
    • Handling of descriptions improved for ABCD import
    • Bug fix for CDM lite export of textual type designation missing a language
  • - TaxEditor
    • Set as basionym available also for accepted taxa
    • Distribution details view: configurable to show also abbreviation for selected named areas
    • Performance improved for preference dependend descriptive data matrix editing
    • Cloned descriptions show according icon
    • User/roles/rights: * ROLE_USER_MANAGER is allowed to change passwords * unnecessary "expired" flags removed from User UI * isAdmin valid for all users having ROLE_ADMIN
    • DNA Sample view allows editing of determinations
    • Export dialogue remembers last selected folder
    • Bug fixes:
      • Handling of preferences for term lists fixed
      • ConcurrentModificationException occurring at different places fixed
      • Incorrect handling of "show descriptions only for field units" fixed
      • Missing "id in vocabulary" in term labels fixed
      • Freetext filter for name relationship type selection in name relationship dialogue fixed
      • Exception caused by missing "number of rows in status dropdown" fixed
      • Exception when opening orphaned names in name bulk editor from search result fixed

# Subject Status
  cdm-dataportal 2 Collapse all/Expand all
8914 jetty 9.4.x returns error states as json which are parsed and processes by cdm_dataportal Closed
8895 Specimen page: show specimen description as continuous text Closed
  cdm-vaadin 1 Collapse all/Expand all
8834 use TaxonNodeDto instead of UuidAndTitleCache Closed
  cdmadapter 1 Collapse all/Expand all
8905 Description Handling in ABCD import Closed
  cdmlib 4 Collapse all/Expand all
8942 Exception when try to get text of TextualTypeDesignation with language which is not available Closed
8907 replace UuidAndTitleCacheTaxonComparator by type save implementation Resolved
8815 Clean up TaxonNodeDto and UuidAndTitleCache usage in TaxonNodeService/Dao Closed
8428 NPE in ClassificationServiceImpl.loadTreeBranchToTaxon() Closed
  cdmlib-remote 2 Collapse all/Expand all
8911 LazyInitializationException (LIE) in portal/description/{uuid} Closed
8899 NullPointerException (NPE) in ManifestController Closed
  taxeditor 19 Collapse all/Expand all
8943 Term Preferences are not correctly handled in combo boxes Closed
8940 The export wizard does not remember last selected folder Closed
8939 Exception when opening Distribution Editor because of missing Preference Closed
8938 ProposalProvider in NameRelationshiptype combo does not work as expected Closed
8927 Fix isAdmin() method in LoginManager Closed
8926 Remove 'expired' flags in users details Closed
8925 Users with ROLE_USER_MANAGER must be able to change any user password Closed
8919 Shorten label for "Reference Detail" Closed
8918 Add "set as basionym" to accepted taxon Closed
8917 NPE when opening Acacia in Name bulk editor (from search) Closed
8916 ConcurrentModificationException in CdmFormFactory.destroyElement() Closed
8913 InInVoc not showing up anymore in TermEditor Closed
8910 Correct handling of preference for determinations Closed
8906 Refactor DNA Sample details view Closed
8904 Show "cloned" icon in factual data view Closed
8725 Add abbreviation to namedArea text field in distribution details view Feedback
8552 Avoid DB call for matrix state DB preferences Closed
8238 Allow interoperability between term trees Feedback
7981 Add configuration UI for matrix description aggregation Feedback

CDM Platform 5.13 (released March 23th, 2020)

Issues: 47

Downloads: TaxEditor, CDM Server, Data Portal

What's new?

  • - Data Portal
    • A new image viewer for the dataportal is now available. The new image viewer uses the iiif conform Universalviewer.
    • Several bugfixes regarding security and display of structured descriptions etc...
  • - Import/Export
    • DarwinCoreArchive: Categorical and quantitative data added to export
  • - CDM Library
    • Caching of in-references for nomenclatural references: only author's family name (without initials) is used now if available
    • Some improvements to the rights&roles management for editing of references
    • Bugfixes:
      • Names without ranks not found in taxon searches
      • Find best matching (in terms of size) image representation fixed/improved
      • some further bugfixes
  • - TaxEditor
    • Fix for failing connections (this might be the reason for many unclear errors that occurred in the past)
    • MacOS X version fixed (TaxEditor available for MacOS X again)
    • Search in bulk editors now also works on abbreviated title(caches)
    • Some improvements to the distribution editor
    • Some improvements to preference pages
    • Freetext search for all dropdown boxes available now
    • Search result view moved to the bottom of taxon navigator view (as default)
    • Taxon navigator allows open-in for multi-selection for name editor and distribution editor
    • Suggested file name for DwC-A export improved
    • Move-to functionality improved in term editor and term tree editor
    • Bugfixes:
      • Names without ranks not found in search
      • NameInSource only added after moving factual data if requested by the user
      • Measurment units added to quantitative data in descriptive data matrix editor
      • Automatically refresh available-specimen list for descriptive data matrix if descriptive dataset changes
      • Name features not visible in taxon factual data view anymore, but only in name factual data view
      • Inheriting sec-reference for root taxa from classification reference works again
      • Selection list for entering states for categorical data is sorted now
      • Deleting specimen descriptions possible now
      • Fix for deleting name types
  • - Web editor (Phycobank registration UI)
    • Bug fix in reference editor

# Subject Status
  cdm-dataportal 7 Collapse all/Expand all
8945 support statistical value type ExactValue (29736701-58c4-48b3-a9d7-41c74140cac7) Resolved
8845 external links: GGBN not shoing up in admin section Closed
8830 add missing spaces to statistical value representations Closed
8828 statistical values must not show empty brackets Closed
8328 Unpublished record visible in Portal if related name is published Closed
7766 Remaining issues for using relationship DTO webservice in portal Closed
5083 Alternative image viewer for dataportal Closed
  cdm-vaadin 1 Collapse all/Expand all
8548 ReferenceEditor: Layout problem when opening Reference editor (new journal, new book, new thesis) Closed
  cdmadapter 1 Collapse all/Expand all
8891 Add categorical and quantiative data to DwC-A Closed
  cdmlib 9 Collapse all/Expand all
8892 Taxon search does not work for names without rank Closed
8881 Use pure last names (without initials) for in-references of taxon names Closed
8868 Bump Jackson dependencies to >= 2.9.10.1 Closed
8839 Role misses toString method Closed
8836 add default role Editor-Reference (REFERENCE.[UPDATE,DELETE], TEAMORPERSONBASE.[UPDATE,DELETE]) Closed
8829 NullPointerException (NPE) in TaxonNodeService Closed
8782 Delete a description included in a CdmSource should not be possible Closed
6970 MediaUtils.filterAndOrderMediaRepresentations perfers thumbnail MediaRepresentations over full sized Closed
5022 Check for dependencies from codehaus.org Closed
  cdmlib-remote 3 Collapse all/Expand all
8867 media list services as iiif manifest service Closed
8866 LazyInitializationException (LIE) in portal/taxon/{uuid} Closed
8427 LazyInitializationException in NameController.doGetTaggedFullTitle() Closed
  taxeditor 26 Collapse all/Expand all
8897 [Mac] Jre Taxeditor fails to start in MacOS X Closed
8890 Allow multiselection for open_in menu Closed
8879 strange file name for export file Closed
8873 eu.etaxonomy.taxeditor: maven-clean runs before maven-install-plugin and deletes the eu.etaxonomy.taxeditor/target/repository/plugins/org.eclipse.*.jar files Closed
8862 move search result to the bottom of the navigator part Closed
8861 Sorted feature states Closed
8860 Sec reference not inherited from classification anymore Closed
8848 Search fails with low data rate network (64kbit/s) network connection due to lost authentication Feedback
8847 Name in Source is added always when moving description from one taxon to another Closed
8844 distinguish SocketTimeoutException from ConnectException Closed
8842 CdmServiceRequestExecutor is not stateleass and neither thread save nor access synchronized Resolved
8832 Choosing the area for distribution in details view clears the selected status Resolved
8825 Name features are shown in menu of factual data view of taxa when no preferences defined Closed
8812 Connection losses in taxeditor HTTP invoker (RemoteAccessException: Could not access HTTP invoker remote service at ...) Resolved
8791 Measurement units are not assigned to quantitative data in matrix Closed
8784 Deleting a specimen description not possible Closed
8749 Add proposalProvider to AbstractComboElement Closed
8733 Descriptive data set: Specimens of a newly added taxon are not listed in Select Specimen dialog of the matrix editor Closed
8721 Use webservice to get all biocase provider listed by gbif Closed
8688 Make OriginalSourceBase.cdmSource visible in TaxEditor Closed
8624 Add abbrev title cache to search in bulk editor Closed
8562 Remaining issues for preference pages Feedback
8531 factual data and media view always opened when opening taxon Closed
8047 Remaining issues in TaxDistributionEditor Feedback
8044 Add "Move to..." menu to term editor Closed
6036 Problems with deleting type names Closed

CDM Platform 5.12 (released Jan 20th, 2020)

Issues: 66

Downloads: TaxEditor, CDM Server, Data Portal

What's new?

  • - Data Model
    • Added "per mm²" to measurement units
    • Allow linking to CDM taxa as information source (currently only available for algorithms, not (yet) for editing in TaxEditor)
  • - Data Portal
    • Structured Descriptions
      • Show structure descriptions in general page as pseudo feature block (position configurable)
      • Implement explicit page for descriptions, using dataset character/feature tree (or general feature tree) for ordering
      • Order states by frequency
      • Improve display of average values (and other statistical vlaues) and single values
      • Support for linking to other CDM records as information source (for aggregated desciptions)
    • Show type designations for synonyms
    • Improved handling for URLs linking to not existing/deleted records (e.g. deleted polytomous keys)
  • - Import/Export
    • CDM light:
      • Typification column added to name and homotypical group files
      • Handling of name identifiers fixed
  • - CDM Library
    • Algorithms for descriptive data aggregation (distributions/structured descriptive data) fixed/improved
    • Polynomous key generation algorithm improved
    • Fix bug for deleting a taxon used in 2 different classifications
    • Fix repair term tree sortindex
    • Allow distribution aggregation to run on taxonomic subtrees
  • - Documentation
  • - TaxEditor
    • Documentation: see above
    • Editing of structured descriptive data now available as standard feature (was experimental before) * Character editor * Term search * Matrix editor * GFBio and ontology imports * Support for "allow duplicates" for term collections * Note: however there are still issues especially with the Character editor which hopefully will be fixed in the next version (we recommend to contact the EDIT team before using this feature)
    • Distribution aggregation available in taxon navigator
    • Added freetext filter to combo boxes
    • Links to other CDM records as information sources visible (but not editable)
    • "Move to ..." added to term editor
    • Improved handling for different term tree types (ordered, flat, distinct, ...)
    • Specimen import: list of existing BioCase endpoints available as dropdown
    • Fix multiple bugs related to BioCase specimen import
    • Fix collapsing tree bug when moving taxa in taxon navigator
    • Fix bug that reference search dialog does not open under certain conditions

# Subject Status
  cdm 5 Collapse all/Expand all
8803 Add "per mm²" to measurement units Closed
8738 CdmLink.startPos and .endPos should allow Null Closed
8724 Allow OriginalSource to link to Taxon Closed
8702 Remove Not null constraint for uuid in AUD tables Closed
8468 Remove old InapplicableIf tables Closed
  cdm-dataportal 19 Collapse all/Expand all
8807 description page: Adapt table header to the nature of description elements Closed
8798 description page: Show character hierarchy Resolved
8787 Improve layout for ExactValue on Description Pages Resolved
8786 Display of mean value with min max Resolved
8781 Descriptions (aggregated): futher improvements Closed
8779 Description page: use render_taxon_or_name() for creating the page and description title and taxon links Closed
8771 display of average value with precision so that it differs from min and max by one digit Resolved
8766 Aggregated Descriptions: show Sample size as [$SAMPLE_SIZE] Closed
8765 defined weight for feature and pseudo feature blocks and position "Description (aggregated)" after "Description" Resolved
8759 Description aggregation : suppress state present when more details are available Resolved
8758 Aggregated Descriptions: order states by frequency Closed
8745 Type designations of synonyms missing on specimen page Closed
8739 remaining issues for description detail page Closed
8719 installation profile 'CDM_Portal' causes Integrity constraint violation: 1048 Column 'pages' cannot be null Closed
8718 polytomousKey page: better handling of invalid uuids Closed
8714 description page: Show multiple datasets per description as list of links Resolved
8686 Support CdmLink sources in bibliography Closed
8657 Order description element in portal according to CharacterTree Closed
8595 Create description detail page Closed
  cdmadapter 3 Collapse all/Expand all
8809 CdmLight Export area without level results in NPE Closed
8808 Cdm-Light Export fix name identifier export Closed
8299 add typification column to scientific name and homotypical group in cdm light Closed
  cdmlib 13 Collapse all/Expand all
8788 Cloned descriptions do not show up in dataportal anymore Feedback
8780 Repair sortindex does not work on TermTree index Closed
8737 delete taxon included in two classifications deletes taxonname Closed
8713 Improve structured descriptive data aggregation Resolved
8684 ITaxonService.findTaxaByName misses initStrategy Parameter Closed
8683 TaxonDaoHibernateImpl.countTaxaByName rename parameter authorship authorshipCache Closed
8679 Further unify description aggregation methods Closed
8670 Unwanted distribution aggregation/display on 2 levels Closed
8472 Transmission engine for distribution aggregation needs to be adapted to new DescriptionBase.types Closed
8467 Save a "snapshot" of the SpecimenDescriptions used for aggregation Resolved
6629 TransmissionEngineDistribution misses aggregating Uzebkistan (UZB-OO) to higher rank levels Closed
5176 TransmissionEngineDistribution can run on selected taxa Closed
4134 Transmissionengine Distribution seems to miss distributions for higher Taxa Closed
  cdmlib-remote 1 Collapse all/Expand all
8770 NameControllers responds with all entities when name uuid is not found Closed
  taxeditor 25 Collapse all/Expand all
8810 In taxeditor parts without permissions should be disabled Closed
8805 In distribution editor synoms should be available as concatenated String Closed
8801 Deselected menu items are not reactivated in navigator Closed
8800 If supplemental data view shows reference it is not possible to select another reference Closed
8797 Navigator tree collapse after moving taxon node Closed
8757 ArrayIndexOutOfBoundsException in term combo Closed
8755 Show all structure/property trees in CharacterEditor Closed
8748 Supported state vocabularies should be ordered Closed
8744 LazyInitializationException (LIE) saving the Character Editor Closed
8736 LazyInitializationException (LIE) during adding Specimens to Matrix Editor Closed
8732 Descriptive Data Set Navigator: label not refreshed after change in Descriptive Dataset Editor Duplicate
8731 BioCase Specimenimport: empty result list and SWTException:Invalid thread access in search results Closed
8706 taxeditor error report with timestamps Resolved
8703 Move TermSearch and Specimen(Import)Search to editor area of taxeditor Closed
8694 Specimen online import - Specimen Search: import button layout problem on linux KDE Closed
8677 Add distribution aggregation to set subtree menu Closed
8665 Rename "New" to "New Tree" in Term Tree editors Closed
8661 "New DataSet" should ask for label and then open the dataset Closed
8656 [DISCUSS] Should only characters be allowed for DescriptiveDataSets/Character Matrix? Closed
8645 rename menu item General > Import > "OWL Import" to "Term Tree OWL Import" Closed
8511 The structure path in the character details view should have a line break Closed
8477 Implement support for TermCollection.allowDuplicates in TaxEditor Closed
8474 Make TermCollection.orderRelevant usable for TermTrees Closed
8313 Multiple categorical data get deleted when clicked on in Character Matrix Closed
8242 Implement filtered combo boxes for state selection in CharacterMatrix Closed

Previous Releases Archive

see CdmPlatformRoadmapArchive

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