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CDM Platform 5.22 (scheduled for Apr 10th, 2021)

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

What will be new?

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

CDM Platform 5.20 (released Feb 10th, 2021)

Issues: 18

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
9324 Enable designation reference editing in name type designation Closed
9461 Filter in vaadin distribution editor does not work Resolved
8522 Make type status mandatory in Name type designation editor Closed
8975 Name Status filtered in UI 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
  cdmlib 5 Collapse all/Expand all
9457 Distribution editor: Taxon filter broken due to invalid HQL in TaxonNodeServiceImpl.getUuidAndTitleCache() Closed
5575 DNA Sample requires CacheStrategy Resolved
5095 Fix failing dozer related tests 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
  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
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
9426 Set publish flag for Synonyms in accordance with accepted taxon publish flag Closed

CDM Platform 5.19 (released Jan 27th, 2021)

Issues: 47

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
7704 Dataportal specimen table should be able to show DerivedUnits without a FieldUnit 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
  cdmlib 8 Collapse all/Expand all
7612 CacheStrategy for MediaSpecimens In Progress
9350 Create new taxonnode ignores the publish flag Closed
9384 DefaultReferenceCacheStrategy.createShortCitation() working not correctly for Teams with two members Closed
9395 DerivedUnit.collectFieldUnits() and findFieldUnitDTOByAssociatedTaxon() and findByAccessionNumber() in OccurrenceService to return all root units Closed
9415 DNA and other Derivatives missing in DerivedUnitDTO Closed
9389 further improvement and revision of derivative filtering by type and DerivedUnitDTO Closed
9253 revise OccurrenceServiceImpl.findFieldUnitDTO(..) Closed
9366 Specimen type designation with specimen having only collection name but not collection code does not show collection information Resolved
  cdmlib-remote 1 Collapse all/Expand all
9387 LazyInitializationException (LIE) in NameController.doGetTypeDesignationsInHomotypicalGroup() Closed
  taxeditor 33 Collapse all/Expand all
8289 Add "Open in RefObj view" to term editor context menu Closed
9346 Adding specimen to character matrix fails sometimes Resolved
9375 Alphabetical order for reference type drop down Closed
7711 Bugs in media gallery Resolved
9356 Comparison method violates its general contract for SourceComparator and TypeDesignationComparator Closed
5163 Converting persons to team members may result in "-empty team-" Closed
9353 Copy & Paste creates dirty data in term trees Closed
9344 Datasets in Descriptive Dataset Navigator should be ordered Closed
9140 Deleting an images forgets moving operation Resolved
9413 DNA details lable "Ratio of absorbance ..." corrected Closed
9405 Fields set to irrelevant for cache should be set by state only Closed
9412 Fix reuse existing name in NewTaxonWizard Closed
9264 Flag for toggle button for linking taxon with navigator looses/switch value without clicking the button Closed
9382 For nomenclatural source show taxonname in referencing objects view Closed
9391 If named area level does not exist remove the level information Closed
8476 Implement support for TermCollection.isFlat in TaxEditor In Progress
9422 Improve performance during Preferences startup Closed
9372 in media details view unprotected title cache is not updated when underlying data is changed Closed
8474 Make TermCollection.orderRelevant usable for TermTrees In Progress
9371 Media bulk does not persist data anymore Closed
9208 Move cdmlib-print and cdmib-remote to taxeditor.printpublisher Closed
8874 move taxon is reverted when taxon is edited afterwards Resolved
7990 Moving a feature via d&d does not make the Feature Tree Editor dirty Closed
9398 ObjectNotFoundException when removing a synonym that is used as NameInSource In Progress
8776 Open issues for TermCollection.allowDuplicates handling in TaxEditor In Progress
9360 Parsed hybrids can not be persisted Resolved
9369 Reference Detail is missing in MediaSpecimen details view Closed
8889 Remaining issues for distribution editor - continue In Progress
9338 Restructure term menus Closed
9365 Reuse taxon does not work in new Taxon dialogue Closed
9354 Sorting in distribution editor is broken Closed
9142 The Agent search dialog shows duplicated entries Closed
8529 [DISCUSS]Display of aggregated descriptions New

CDM Platform 5.18 (released Dec 3rd, 2020)

Issues: 82

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
9121 Add abbreviations to Feature Closed
9272 Add missing nomenclatural status Closed
9282 Add nomenclatural standing Closed
9124 Altitude feature should have [m] as measurement unit by default Closed
6589 Handle protologue as original source with URI link Closed
6581 Make all microreferenced references OriginalSources Closed
9225 Make TaxonName.nomenclaturalSource a new DescriptionElementSource subclass Closed
9062 Remove StatisticalMeasurementValue.value_old Closed
8326 update labels for is blocking name and is isonym Closed
9120 Update script for flowering period supports temporal data Closed
9094 Update script to update TaxonNode.source from IdentifiableSource to DescriptionElementSource Closed
9311 Update some (abbrev) labels for nomenclatural status types Closed
6591 Use name used in source for original spelling Closed
5795 [DISCUSS] Do we need comb. ined. as a nomenclatural status? Closed
  cdm-dataportal 18 Collapse all/Expand all
9220 adapt dataportal to /registrationDTO now using identifier as query parameter and secure against CVE-2007-0450 vulnerability Closed
9265 Adapt dataportal to new protologue handling Closed
9222 Adapt dataportal to switch to originalSource for remaining single sourced classes Closed
7685 Add Selenium tests for specimen table in data portal Closed
8854 Choose new base font size for the portal Closed
9249 compact display of collection information Closed
8851 display of name facts not appropriate in all cases Closed
9260 error in pages.inc calling compose_taxon_node_status() Closed
9234 Error: Object of class stdClass could not be converted to string caused by compose_cdm_specimen_or_observation_tree_entry() Closed
9235 Footnote key for multiple cdm entities need to be rendered together Closed
9261 LazyInitializationException (LIE) in TaxonController.doGetTaxonNodes() Closed
9209 name page, registration page: show annotations for names and fieldunits Closed
9240 nomenclatural status missing in name and registration page Closed
9224 openlayers map handles server error per layer and presents a user message Closed
9306 Registration result list: supress "designated by" reference in portal Closed
3978 Specimenview path: Compact representation of exactLocation Closed
6356 taxontree sort order as in editor Closed
9184 WSOD in advanced search cdm_dataportal/search Closed
  cdm-vaadin 6 Collapse all/Expand all
7936 Consider complete removal of redmine communication hub code Closed
9289 LazyInitializationException (LIE) in NameTypeDesignationEditor Closed
9313 LazyInitializationException (LIE) in TaxonNamePopupEditor Closed
8859 RegistrationItemNameAndTypeButtons invalid regex pattern Closed
9318 TaxonNameEditor: nomenclatural reference no longer selectable Closed
9229 TaxonNameEditor: use NomenclaturalStatusDTO to avoid data loading probems within setters in TaxonName Closed
  cdmadapter 2 Collapse all/Expand all
9256 CdmLightExport: NameTypeDesignation string misses parenthesis for authors Closed
9262 Several open issues for cdmlight export related to Cactaceae and other Caryophallales Closed
  cdmlib 20 Collapse all/Expand all
8458 document FieldUnitDTOOccurrenceServiceImpl.findFieldUnitDTO() Closed
6623 formatter for bibliografic citations with citationDetail Closed
9252 Harmonize SpecimenOrOberservationBase related DTOs Closed
4866 Implement clone method for complete classifications Closed
7862 improve documentation on TaxonGraphHibernateListener and related classes Closed
9279 Improve type designation formatting and TypeDesignationSetManager In Progress
9210 invalid format string usage in MediaAutoInitializer Closed
9223 make changes of nomenclatural references detectable again in TaxonGraphBeforeTransactionCompleteProcess Resolved
9194 Make RelationshipBase and NomenclaturalStatus reference OriginalSource Closed
9103 missing exception handling in TaxoNodeDto Closed
5794 Move other invalid names to the end Closed
9267 No sec reference for move change Synonym to accepted Taxon Closed
9302 Phycobank related issues for TypeDesignation formatting In Progress
9280 Refactor: IKeyTerm.getMessage() --> IKeyTerm.getLabel() Closed
9322 Remove invalid designation taxon relationship Closed
9257 revise filtering in OccurrenceServiceImpl.assembleFieldUnitDTO(FieldUnit fieldUnit) by SpecimenOrObservationType.PreservedSpecimen Closed
9206 Solve cglib vs. cglib-nodep Closed
9230 Type in preparation of a published name displayed in PhycoBank Portal Name Page Closed
9204 Update cdmlib and taxeditor dependencies Closed
9258 Use Partial for date in FieldUnitDTO Closed
  cdmlib-remote 6 Collapse all/Expand all
9335 termTree webservice response misses titleCache 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
9254 portal/occurrence/{uuid}/fieldUnitDTO.json fails with class cast exception Closed
9238 pure entities in DerivateDTO.derivates may cause LIEs Closed
9259 reduce fields in TermBase json serializations 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 14 Collapse all/Expand all
9199 Adapt TaxEditor to switch to originalSource for remaining single sourced objects Closed
9299 Add LSID to author and reference details Closed
9245 Creating derived units from existing derived unit is not possible in specimen tree editor Feedback
8547 Default type of a newly created inReference should depend on the type of the reference Closed
9215 Drop down for empty rank does not work Closed
9297 Improve name of zip file for cdmLightExport Closed
6947 Incorrect error for LSID field Closed
9192 Layout issues for source in taxonnode details Closed
9189 Move datasource view to taxeditor.local Closed
9307 Preferences for display of termtrees and entries Closed
9286 Re-connect and change user should be disabled if no datasource is connected yet Closed
8774 Reimplement term tree editors to implement the general save strategy Closed
9266 Remove protologue section from TaxEditor Closed
8928 Swap menu entries for specimen bulk editors 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
9128 Default copyright statement below image viewer Closed
9175 hide occurrence map when no data exists Closed
8420 improve admin settings for specimens representations Closed
9137 IPTC Keywords (and maybe other information) is not shown in Universal Viewer yet Closed
8543 overcome distinction of annotation and other foonotes Closed
9099 placemark icon in kml map not clickable Closed
9109 Search button font icon broken Closed
4372 Selenium PortalPage class also suitable for zen-basetheme Closed
9186 selenium test for specimen top down view (aka devivate_path view) Closed
9191 selenium test for specimen tree view (bottom up) Closed
9188 selenium web element wrapper for dynabox Closed
9181 set and get drupal variables from selenium test suite Closed
8850 Show annotations for DerivedUnits (Fieldunits etc) in Registration and other pages Closed
2489 strategy for congruent areas in distribution maps: create merged TDWG layer with all levels Closed
  cdm-vaadin 4 Collapse all/Expand all
8230 NameTypePopupEditor: genus selectable as the name type for higher ranks Closed
8317 Omit ex-author if ex-author=author Closed
8156 Registration items show type status in bold letters Closed
9182 Sub-collection and Collection vs. Collection and Super-Collection Closed
  cdmadapter 1 Collapse all/Expand all
9110 Add additional informations to metadata table of cdmLight Feedback
  cdmlib 7 Collapse all/Expand all
9129 cdm property to store a default copyright statement for media items Closed
9146 filter image metadata by include and exclude lists of key words Closed
9152 PreferencesService caches CdmPreferences Closed
9105 rename NodeSortMode etc to TaxonNodeSortMode Closed
9148 Replace sanselan library by the newer apache commons-imaging Closed
9000 UriUtils: HttpClient has ssl error connecting to pictures.bgbm.org Closed
9147 Use StringBuilder in CdmUtils.concat() to avoid performance penalties Closed
  cdmlib-remote 4 Collapse all/Expand all
9193 LazyInitializationException (LIE) in portal/taxon/{uuid} web service Closed
9198 option in iiif manifest creation to set canvas size to thumbnail size 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
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
9118 Change p2 update site to https in Taxeditor Closed
9166 ClassCastException when editing media in taxon bulkeditor Closed
9171 Doubtful taxa are not found in bulkeditor Closed
9040 Implement open button for ORCIDs Closed
9172 Missing synchronisation between taxonnode wizard and name editor Closed
9168 NameFeature selection in preferences are not shown Closed
9173 NPE when move synonym into homotypical group of accepted Closed
5752 Reduce TaxEditor size Closed
9138 Reenable BioCaseQueryServiceWrapperTest.testQueryForUnitId() Closed
9119 Remove schema create and schema update functionality from datsource view Closed

CDM Platform 5.16 (released June 30th, 2020)

Issues: 15

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
8991 Add feature "Flowering Period" Closed
9009 Add structure to store media metadata Closed
9027 Implement Feature.availableFor Closed
9026 Implement Feature.supportedDataTypes as EnumSet Closed
8802 Implement flowering period for Flora of Cyprus Closed
8978 Implement measurement values as BigDecimal Closed
8964 Improve label for homonym relationships Closed
9004 Make TaxonNode.referenceForParentChildRelation an OriginalSource and rename it to (placement)source Closed
9005 Make the TaxonNode flags alternatives and change excludednotes to status notes Closed
9037 Remove old Feature.supportedXXX columns Closed
9036 Remove old TaxonNode.unplaced/doubtful/excluded columns Closed
  cdm-dataportal 13 Collapse all/Expand all
6878 choose a base font for the portal and deliver it from the drupal module or theme Closed
8196 display ortographic corrections in name relations as 'corrected name: <nameCache>' 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
8134 Implement verbatim type information in dataportal 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
9034 simple agent list page with filter function Closed
4488 Specimen data points in map should show FieldUnit information Closed
4257 specimen map should zoom to area of distribution Closed
9076 synonymy without margin when 'Synonymy as tab' and 'Tabbed taxon page' are off Closed
8994 universal image viewer fails loading libs when clean urls is disabled 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
9020 add default role Allow_for_all_taxa (TAXONNODE.[CREATE,READ,UPDATE,DELETE]) Closed
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
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
9023 option to start cdm webapp with hibernate.hbm2ddl.auto = create Closed
9044 TaxonNodeDtoBeanProcessor supports new TaxonNodeStatus terms Closed
6113 webservice to expose FieldUnits related to a Taxon or TaxonName as KML and/or GML Closed
  cdmserver 3 Collapse all/Expand all
3683 add /etc/default/cdmserver to debian package Closed
8682 cdm-server debian packages configured for jemalloc Closed
7085 cdmserver logfiles getting too big, use RollingFileAppender Closed
  data 1 Collapse all/Expand all
9017 Update image link for FoG Willing images Resolved
  taxeditor 42 Collapse all/Expand all
8662 "Remove Taxon" in DescriptiveDataSetEditor should only be visible if taxon is selected Closed
9029 Adapt character matrix to using dtos instead of whole cdm entities Closed
9070 Adapt preference page to feature.isAvailableFor... Resolved
9033 Adapt TaxEditor to new TaxonNode.status Closed
9038 Adapt TaxEditor to use BigDecimal for StatisticalMeasurementValues Closed
8988 Add link button to DOI field for references Closed
8958 Add publication year, inReference (journal), and URI to reference bulk editor Closed
9016 Adding specimen without field unit fails Closed
9025 allow for creating a new schema in empty dbs via the remote login dialog Closed
9059 Cancel taxon save does not clean the (factual data) cache Closed
9053 CCE when selecting Character Tree for descriptive dataset Closed
8901 Deleting an aggregated description from a descriptive matrix does not delete the aggregated description itself Resolved
8754 DescriptionElements are not deleted with the Descriptive Data Set Resolved
8954 Details and Supplemental Data View do not save the expansion state of sections again Closed
9063 Detailsview for MediaSpecimen broken Closed
8753 EagerLoadingException on opening Character Tree Editor after deleting all Desciptive Data Sets Closed
8962 Handle widget is disposed after closing Supplemental Data View Closed
9032 Implement Feature.availableFor in TaxEditor Closed
8990 Implement flowering periods (temporal facts) in TaxEditor Closed
9022 Implement lifespan for Person Details View Closed
9084 Make it configurable if a Description is deleted only from the Descriptive Data Set or from it's Specimen/Taxon Resolved
9066 Make visiblity of Specimen List Editor menu configurable Closed
8783 Massive Heap consumption in server instance opening the Description-Matrix editor Closed
8752 Matrix Editor: Can fail showing all SpecimenDescriptions in the dataset Worksforme
8785 Move functionality of buttons to context menu of the character matrix Resolved
8959 Moving a synonym to the homotypical group of the accepted taxon opens the context menu of the accepted taxon Closed
8969 Multiple deduplications are not executed Closed
8806 Multiple representations problem on saving Desriptive Data Set Worksforme
8857 NonUniqueObjectException when creating new taxon Closed
9052 NPE in name details view for incomplete name relationships Closed
8849 NPE in synonym DetailsViewer for synonyms without accepted taxon Closed
9060 NPE in termsearch Closed
9013 Problems in TaxonNode Dialog Closed
9055 Relabel "Type Designation" to "Type Information" Feedback
8903 Remember expansion state in factual data view Closed
8957 Rename "unexpected error" to "unhandled error" Closed
8963 Selection dialogues should be modal Closed
7774 Show description source for description elements Closed
7189 Taxeditor connect dialog high-dpi suport Closed
9045 TextualTypeDesignation throws exception in referencing objects view Closed
8961 Using the selection dialogue for nomenclatural references removes the recently used list Closed
8999 Verbatim date not persisted for books 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
8815 Clean up TaxonNodeDto and UuidAndTitleCache usage in TaxonNodeService/Dao Closed
8942 Exception when try to get text of TextualTypeDesignation with language which is not available Closed
8428 NPE in ClassificationServiceImpl.loadTreeBranchToTaxon() Closed
8907 replace UuidAndTitleCacheTaxonComparator by type save implementation Resolved
  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
8918 Add "set as basionym" to accepted taxon Closed
8725 Add abbreviation to namedArea text field in distribution details view Feedback
7981 Add configuration UI for matrix description aggregation Feedback
8238 Allow interoperability between term trees Feedback
8552 Avoid DB call for matrix state DB preferences Closed
8916 ConcurrentModificationException in CdmFormFactory.destroyElement() Closed
8910 Correct handling of preference for determinations Closed
8939 Exception when opening Distribution Editor because of missing Preference Closed
8927 Fix isAdmin() method in LoginManager Closed
8913 InInVoc not showing up anymore in TermEditor Closed
8917 NPE when opening Acacia in Name bulk editor (from search) Closed
8938 ProposalProvider in NameRelationshiptype combo does not work as expected Closed
8906 Refactor DNA Sample details view Closed
8926 Remove 'expired' flags in users details Closed
8919 Shorten label for "Reference Detail" Closed
8904 Show "cloned" icon in factual data view Closed
8943 Term Preferences are not correctly handled in combo boxes Closed
8940 The export wizard does not remember last selected folder Closed
8925 Users with ROLE_USER_MANAGER must be able to change any user password Closed

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
8830 add missing spaces to statistical value representations Closed
5083 Alternative image viewer for dataportal Closed
8845 external links: GGBN not shoing up in admin section Closed
7766 Remaining issues for using relationship DTO webservice in portal Closed
8828 statistical values must not show empty brackets Closed
8945 support statistical value type ExactValue (29736701-58c4-48b3-a9d7-41c74140cac7) Resolved
8328 Unpublished record visible in Portal if related name is published 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
6970 MediaUtils.filterAndOrderMediaRepresentations perfers thumbnail MediaRepresentations over full sized Closed
8836 add default role Editor-Reference (REFERENCE.[UPDATE,DELETE], TEAMORPERSONBASE.[UPDATE,DELETE]) Closed
8868 Bump Jackson dependencies to >= 2.9.10.1 Closed
5022 Check for dependencies from codehaus.org Closed
8782 Delete a description included in a CdmSource should not be possible Closed
8829 NullPointerException (NPE) in TaxonNodeService Closed
8839 Role misses toString method Closed
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
  cdmlib-remote 3 Collapse all/Expand all
8866 LazyInitializationException (LIE) in portal/taxon/{uuid} Closed
8427 LazyInitializationException in NameController.doGetTaggedFullTitle() Closed
8867 media list services as iiif manifest service Closed
  taxeditor 26 Collapse all/Expand all
8044 Add "Move to..." menu to term editor Closed
8624 Add abbrev title cache to search in bulk editor Closed
8749 Add proposalProvider to AbstractComboElement Closed
8890 Allow multiselection for open_in menu 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
8812 Connection losses in taxeditor HTTP invoker (RemoteAccessException: Could not access HTTP invoker remote service at ...) Resolved
8784 Deleting a specimen description not possible Closed
8733 Descriptive data set: Specimens of a newly added taxon are not listed in Select Specimen dialog of the matrix editor Closed
8844 distinguish SocketTimeoutException from ConnectException 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
8531 factual data and media view always opened when opening taxon Closed
8688 Make OriginalSourceBase.cdmSource visible in TaxEditor Closed
8791 Measurement units are not assigned to quantitative data in matrix Closed
8862 move search result to the bottom of the navigator part Closed
8825 Name features are shown in menu of factual data view of taxa when no preferences defined Closed
8847 Name in Source is added always when moving description from one taxon to another Closed
6036 Problems with deleting type names Closed
8562 Remaining issues for preference pages Feedback
8047 Remaining issues in TaxDistributionEditor Feedback
8848 Search fails with low data rate network (64kbit/s) network connection due to lost authentication Feedback
8860 Sec reference not inherited from classification anymore Closed
8861 Sorted feature states Closed
8879 strange file name for export file Closed
8721 Use webservice to get all biocase provider listed by gbif Closed
8897 [Mac] Jre Taxeditor fails to start in MacOS X Closed

CDM Platform 5.12 (released Jan 20th, 2020)

Issues: 65

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
8724 Allow OriginalSource to link to Taxon Closed
8738 CdmLink.startPos and .endPos should allow Null 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
8758 Aggregated Descriptions: order states by frequency Closed
8766 Aggregated Descriptions: show Sample size as [$SAMPLE_SIZE] Closed
8595 Create description detail page Closed
8765 defined weight for feature and pseudo feature blocks and position "Description (aggregated)" after "Description" Resolved
8807 description page: Adapt table header to the nature of description elements Closed
8798 description page: Show character hierarchy Resolved
8714 description page: Show multiple datasets per description as list of links Resolved
8759 Description aggregation : suppress state present when more details are available Resolved
8779 Description page: use render_taxon_or_name() for creating the page and description title and taxon links Closed
8781 Descriptions (aggregated): futher improvements Closed
8786 Display of mean value with min max Resolved
8771 display of average value with precision so that it differs from min and max by one digit Resolved
8787 Improve layout for ExactValue on Description Pages Resolved
8719 installation profile 'CDM_Portal' causes Integrity constraint violation: 1048 Column 'pages' cannot be null Closed
8657 Order description element in portal according to CharacterTree Closed
8718 polytomousKey page: better handling of invalid uuids Closed
8739 remaining issues for description detail page Closed
8686 Support CdmLink sources in bibliography Closed
8745 Type designations of synonyms missing on specimen page Closed
  cdmadapter 3 Collapse all/Expand all
8299 add typification column to scientific name and homotypical group in cdm light Closed
8808 Cdm-Light Export fix name identifier export Closed
8809 CdmLight Export area without level results in NPE Closed
  cdmlib 13 Collapse all/Expand all
8788 Cloned descriptions do not show up in dataportal anymore Feedback
8737 delete taxon included in two classifications deletes taxonname Closed
8679 Further unify description aggregation methods Closed
8713 Improve structured descriptive data aggregation Resolved
8684 ITaxonService.findTaxaByName misses initStrategy Parameter Closed
8780 Repair sortindex does not work on TermTree index Closed
8467 Save a "snapshot" of the SpecimenDescriptions used for aggregation Resolved
8683 TaxonDaoHibernateImpl.countTaxaByName rename parameter authorship authorshipCache Closed
8472 Transmission engine for distribution aggregation needs to be adapted to new DescriptionBase.types Closed
4134 Transmissionengine Distribution seems to miss distributions for higher Taxa Closed
5176 TransmissionEngineDistribution can run on selected taxa Closed
6629 TransmissionEngineDistribution misses aggregating Uzebkistan (UZB-OO) to higher rank levels Closed
8670 Unwanted distribution aggregation/display on 2 levels Closed
  cdmlib-remote 1 Collapse all/Expand all
8770 NameControllers responds with all entities when name uuid is not found Closed
  taxeditor 24 Collapse all/Expand all
8661 "New DataSet" should ask for label and then open the dataset Closed
8677 Add distribution aggregation to set subtree menu Closed
8757 ArrayIndexOutOfBoundsException in term combo Closed
8731 BioCase Specimenimport: empty result list and SWTException:Invalid thread access in search results Closed
8732 Descriptive Data Set Navigator: label not refreshed after change in Descriptive Dataset Editor Duplicate
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
8242 Implement filtered combo boxes for state selection in CharacterMatrix Closed
8477 Implement support for TermCollection.allowDuplicates in TaxEditor Closed
8805 In distribution editor synoms should be available as concatenated String Closed
8810 In taxeditor parts without permissions should be disabled Closed
8736 LazyInitializationException (LIE) during adding Specimens to Matrix Editor Closed
8744 LazyInitializationException (LIE) saving the Character Editor Closed
8703 Move TermSearch and Specimen(Import)Search to editor area of taxeditor Closed
8313 Multiple categorical data get deleted when clicked on in Character Matrix Closed
8797 Navigator tree collapse after moving taxon node Closed
8665 Rename "New" to "New Tree" in Term Tree editors Closed
8645 rename menu item General > Import > "OWL Import" to "Term Tree OWL Import" Closed
8755 Show all structure/property trees in CharacterEditor Closed
8694 Specimen online import - Specimen Search: import button layout problem on linux KDE Closed
8748 Supported state vocabularies should be ordered Closed
8706 taxeditor error report with timestamps Resolved
8511 The structure path in the character details view should have a line break Closed
8656 [DISCUSS] Should only characters be allowed for DescriptiveDataSets/Character Matrix? Closed

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
8625 Add count parameter to StateData Closed
8628 Add ORCID as person identifier Closed
8673 Allow OriginalSource to link to other CDM objects Closed
8466 Delete FeatureTree tables Closed
  cdm-dataportal 3 Collapse all/Expand all
8596 Add a list of descriptions to the taxon page Closed
8622 Missing specimen Identifier leads to empty brackets in portal Closed
8610 tagged_text_extract_nomstatus() fails handling more than one status Closed
  cdmadapter 2 Collapse all/Expand all
8632 ABCD retrieves DNA Sample from Biocase Provider even if it is not selected in the import configuration Closed
8533 missing collector and fieldnumber in abcd import Closed
  cdmlib 3 Collapse all/Expand all
8253 Authors for genus autonyms Closed
8676 TaxonDaoHibernateImpl.countTaxaByName misses parameter authorship Closed
8651 Unify description aggregation methods (distribution and structured descriptive data) Closed
  cdmlib-remote 1 Collapse all/Expand all
8570 PolytomousKeyNode.otherNode missing in REST service response Closed
  cdmserver 2 Collapse all/Expand all
5048 cdm-server causes unusual high native memory consumption for jvm Closed
8674 configure cdm-server docker image to run with jemalloc Closed
  taxeditor 24 Collapse all/Expand all
8631 ABCD import fails to put new taxa into the classification, create mediaspecimens, etc Closed
8410 Add nomenclatural code edition to ruleConsidered in TaxEditor Closed
8642 Add tree editor for rank, NamedArea and PresenceAbsence Closed
8584 Appended phrase should be shown on top level for misapplied names Closed
8630 ClassCastException when ABCD import has finished Closed
8652 disentangle confusion when connecting to development cdm instance fails Closed
7457 E+M: Allow filtering for only published in search Closed
8685 Exception when calling DwC-A Export Closed
7143 Finish not enabled when unprotecting titleCache in new Person dialog Closed
8613 For distribution editor default reference should be used also when new source is created Closed
8470 Handle username constraints in user and group editing Closed
8568 improve performance for term and vocabulary preference pages Closed
8486 Indicating doubtful state in navigator and add set-doubtful to Set-Flags menu Closed
8226 make modifiers for description elements configurable Closed
8667 Make Person.orcid editable in TaxEditor Closed
8581 Naming inconsitency: Taxon Navigator or Taxonomic Tree? Closed
8634 NullPointerException (NPE) in PreferencesUtil.getLocalAbcdImportConfigurator() on starting ABCD import Closed
8653 NullPointerException (NPE) when focusing Taxion Name Editor Resolved
8609 Rename Taxon Node context menu entry Open in .. -> Taxon Node Wizard Closed
8572 Rule considered configurable Closed
8648 Simplify name details view configuration Closed
7019 sort import menu Closed
8664 SQLGrammarException when opening Specimen selection Closed
8582 Taxon Navigator: Classification label not refreshed & new taxa not visible 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
8565 external links and dois no longer showing up Closed
8504 Name page: allow hiding the Taxon section via settings Closed
8594 registration search results page showing: cdm_compose_url(): missing pathParameter 0 for !uri_pattern Closed
  cdm-vaadin 8 Collapse all/Expand all
8409 add nomenclatural code select to NameRelationField Closed
8408 add nomenclatural code select to NomenclaturalStatusRow Closed
8014 Label wording im UI Name Editor Closed
8462 NoSuchElementException accessing Optional<RegistrationDTO> in RegistrationWorkingsetPresenter.findRegistrationInContext() Closed
8376 RegistrationWorkingsetEditor: prevent clicking any futher buttons after the openting of a popup editor has been triggered Closed
8342 shift field Field number Closed
8527 TaxonNameEdior: 'Validations' and 'Orthographocal corrections' are lost when editor is saved a second time Closed
8377 TypeDesignationsEditors: Delete must not be allowe before the workingset is saved Closed
  cdmlib 6 Collapse all/Expand all
8513 CdmUtils: remove MUST_EXIST_FILE and getResourceFolderSeperator() Closed
8505 ConfigFileUtil: turn all spring bean methods into not statical methods. Closed
8456 FieldUnitDTO: remove newInstanceMethod Closed
8425 FieldUnitDTO: remove taxonRelatedDerivedUnits Closed
8519 ROLE_USER_MANAGER missing in FirstDataInserter Closed
8517 SpecimenOrObservation: data from protected titleCache missig in portal pages Resolved
  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
8539 Add IndividualsAssociation when adding specimens to the character matrix Closed
8488 Characters can not be added to feature trees Closed
8386 Disable admin menu when not logged into a DB Closed
8489 Further issues for DB preferences Resolved
8564 Link to PlatformDocumentation wiki page Closed
8382 Local Supplemental Data Source Preferences should reflect the state of admin preferences Closed
8123 Make available features a DB preference Closed
7321 multi-language textfields should not show empty text when there is text Closed
8034 Recently used references shows all references Closed
8350 Search dialog for named areas should work with abbreviations Closed
8092 set default for term and vocabulary selection preferences in selection wizard Closed
8335 Store character matrix table state as DB preference 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
8441 Add FeatureState class Closed
8442 Add fields to handle external terms to DefinedTermBase or TermBase Closed
8398 Add nomenclatural code edition to ruleConsidered Closed
8180 Add property term "Presence/Absence" to CDM default terms Closed
7957 Add types for taxon description (as EnumSet) Closed
8281 Doubtful flag for TaxonNode Closed
7099 Make CdmAuthority a persistable class Resolved
8454 Only allow certain patterns as username and groupname Closed
8429 Rename DeterminationEvent_Reference.setOfReferences_id Resolved
3972 Strictly validate username to not null and not empty Closed
4884 Update Reference_AUD.refType to allow NULL Closed
7470 Verbatim type designation information Closed
  cdm-dataportal 11 Collapse all/Expand all
8166 Adapt dataportal to term structure changes Closed
8495 classification tree horizontally scrolls to active entrty Closed
8449 improve layout of registration page to clearly show the nomencaltural act Closed
8448 Maps settings > Bounding box inconsistent Closed
8430 maps zoom to wrong bbox with some layers Closed
8402 ordering typedesignations in name and taxon page Closed
8440 specimen accession numbers link to specimen page Closed
8406 specimens and occurrence code cleaning and harmonization Closed
8418 specimens and occurrence links must not have a target=_blank attribute Closed
8502 taxa with doubtful flag lack proper formatting Resolved
8415 use /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup to speed up type designation retrieval Closed
  cdmlib 8 Collapse all/Expand all
8437 ITermTreeService provides a list method which supports filtering by TermTree.termType, Resolved
8404 Add update step list within updaters Closed
8446 Allow setPublish for subtree to filter for hybrids Closed
7450 Allow setPublish for subtree to include misapplied names and pro parte synonyms Closed
8426 IndexOutOfBoundsException during serialization of RegistrationWorkingSet Closed
8482 java.lang.IllegalArgumentException: Collection is empty in DescriptionType.includesType(DescriptionType.java:151) Closed
8422 Make PolytomousKeyGenerator work (correctly) Closed
3472 Update name in source data when changing an accepted taxon into a synonym Closed
  cdmlib-remote 5 Collapse all/Expand all
8434 Change FeatureTree contollers to TermTree controllers Closed
8436 featureTree/* services should filter the termTrees by the TermType Feature Closed
8390 implement /portal/name/{uuuid}/typeDesignationsInHomotypicalGroup Closed
8395 NullPointerException (NPE) in NameCatalogueController Closed
8414 occurrence controller code cleaning and harmonization Closed
  taxeditor 15 Collapse all/Expand all
8475 Adapt applicable state detail view elements to FeatureState Closed
8447 Adapt setPublishForSubtree to new parameters for pro parte, misapplications and hybrids Closed
8485 Add column groups to character matrix Closed
7597 Aggregate and persist descriptions on taxon level Closed
8532 common name language selection is not selected Resolved
8389 Correct handling of default values with allowOverride=false Resolved
8235 Create separate menu for term tree editors for each term tree type Closed
8282 Implement placementDoubtful in TaxEditor Closed
8135 Implement verbatim type information in TaxEditor Closed
8334 Move sources for type designations to details view Closed
8385 Open issues in DB preferences Closed
8444 Show warning if misapplied names / pro parte synonyms are used more then once Closed
8526 Swap synonym with accepted taxon does not work Resolved
8465 Term nodes order in term trees is ignored in term tree editor Closed
8480 Use DescriptionTypes for matrix descriptions 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
4177 display of name relationships in synonymy broken Closed
6316 display source references of media objects in media page Closed
6709 Do not show UUID on media page Closed
8370 feature blocks created by compose_description_element_individuals_association() are broken Closed
7975 Implement a block to display name relations Closed
8245 Improve representation of DescriptionElementBase.timeperiod Closed
8320 Links to reference page as appendend icon instead of having the whole citation as link Closed
8304 Name page redirects to according taxon depending on query parameter Feedback
8108 Name page shows complete name information (I) Closed
8352 name page: show nomenclatorical acts Closed
8351 name page: show type designations with map Closed
8321 Namepage shows wrong taxa as related to the name Closed
8347 point map zooms to wrong area when using sphericalMercator maps like OpenTopo OSM etc. Closed
8280 polyfills folder check in zen_dataportal/theme-settings.php fails when portal is installed in subfolder Closed
5855 potential improvements in settings for name relationship types Closed
8368 problems in compose_cdm_specimen_or_observation_tree_entry() Closed
8306 Registration page links to registered taxon name Closed
8016 Registration page: subheadline with event type Closed
7966 Registration search simplify type select options Closed
7620 RegistrationSearch implemented with Reference filter Closed
8366 Same typedesignation display for registration page as in name page Closed
8182 show blast search result In Progress
5857 show nomenclatural status for for representations of TaxonName Closed
8318 TaxonName processing for taggedFullTitle Closed
6380 typedesignations missing in homotypic group Closed
8388 UTIS search block Closed
  cdm-vaadin 6 Collapse all/Expand all
8279 ClassCastException in CdmUserHelper.user() Closed
8346 Curators and admins can edit arbitrary Annotations (Notes) Closed
8278 LazyInitializationException (LIE) in ReferenceEllypsisCaptionGenerator Closed
8167 Permission denied for Submitter when adding section to newly created journal Resolved
8345 RegistrationListView: filter option for publication Closed
8284 starting a registration for an existing name causes the name editor to pop up in read only mode Closed
  cdmadapter 5 Collapse all/Expand all
8273 abcd import: check for all specimen for DNA in DNABank Feedback
8322 add sortindex to cdm light export Resolved
8344 cdm light export: add dummy line in simpla facts table Feedback
8264 excluded and excluded notes in cdmlight export Closed
6627 Remaining cdm light issues Resolved
  cdmlib 14 Collapse all/Expand all
7902 Allow default values for PreferencePredicates Closed
8365 DerivedUnitFacadeCacheStrategy should remove collection codes from accession numbers Closed
7904 DerivedUnitFacadeFieldUnitCacheStrategy.getCollectorAndFieldNumber() creates temporary Team objects which can not be garbage collected. Feedback
7296 externalize redmine api key Closed
7932 Implement subject resolver for CdmPreferences In Progress
7829 Improve deduplication of parsed names and references Closed
8062 Make default preferences deletable serverside In Progress
7433 new service method to get specimen by genetic AccessionNumber Resolved
8330 RegistrationDao search method Closed
8287 RegistrationServiceImpl.page( .... Collection<UUID> typeDesignationStatusUuids ... ) fails when NULL and UUIDs are passed Closed
8257 Remove factory methods for term node creation Closed
8369 SpecimenTypeDesignationDTO can not be serialized to JSON Closed
8314 TaxonName provides the FullTitleCache as TaggedText Closed
8354 taxonomic registration search by name finds also typifications for this name Closed
  cdmlib-remote 2 Collapse all/Expand all
8319 NomenclaturalStatus webservice implemented Closed
7621 registration search also covers typified names Closed
  cdmserver 1 Collapse all/Expand all
5774 cdmserver misses to detect some errors in failed instances Closed
  taxeditor 13 Collapse all/Expand all
8283 Allow adding media to terms in taxeditor Closed
8260 Details and Supplemental Data View do not save the expansion state of sections Closed
8293 Distribution preferences for details view should be serverside preferences Feedback
8332 Excel matrix exports only the visible rows Closed
8058 Further issues for (local) preferences Feedback
8045 Improve handling of default values and override in local preferences Feedback
8129 Load images asynchronously in media details view Closed
8294 Make display of ID in source and ID Namespace configurable Closed
8323 Make nom.status and rank lists a CdmPreference Feedback
8088 Open taxon node wizard issues Feedback
7920 Possibility to define area specific status selection Feedback
8256 Show all status preferences as table Feedback
8333 Show modifiers for states in Character Matrix Closed

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
8220 incomplete creation of blocking registration in case of registering existing name which misses the nomenclatural reference Closed
8252 reference ellypsis must not be applied to all reference types Closed
8250 ReferenceEditor: inReference must not be required for type book Closed
7965 Registration search simplify type select options Closed
8246 TaxonNamePopupEditor can not be canceled Closed
8193 TaxonNamePopupEditor: add select form element for Nomenclatural status Closed
8209 use ellypsed references for all reference comboboxes Resolved
8215 User demand: sorting order in reference editor 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
8267 common name preference saving does not work correctly Closed
8258 Default Feature Tree contains name features and features Closed
8316 Endless loop when editing name in source of distribution Feedback
8263 Improve performance of term editor Resolved
8266 local preference is not evaluated for distribution editor status Closed
8349 NPE in ParseHandler when parsing name without nomencl reference Closed
8315 Parsing existing references with inReferences changes the inReference Closed
8265 Referencing objects view does not work for term editor Closed
8229 reload of the bulkeditor does not work correctly Closed
8241 Rename FeatureTreeEditor to TermTreeEditor 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
3747 Check if time period is handled correctly for description elements in data portals Closed
8093 harmonize registrationId links and make tesing easier Closed
8106 improve image gallery settings labeling Closed
3616 Show DescriptionElementBase.timeperiod in Dataportals Closed
5699 user profile settigs in cdm_dataportal module done wrong Closed
  cdm-vaadin 23 Collapse all/Expand all
8188 Allow configuring hibernate properties via properties file Closed
8158 cascade="all-delete-orphan" problem when .... Closed
8160 CdmBeanItemContainerFactory as readonly service bean Closed
8050 Create blocking registrations for un-registered names which are to be used in nomenclatural acts Closed
8099 Error saving name type designation editor due to problem in poupeditor context Closed
8065 HibernateException: corrupt session problem breaks SpecimenTypeDesignationworkingsetEditor type designation table Closed
8194 LazyInitializationException (LIE) on deleting the nomenclatural referenz (Section) of a Name Closed
8075 multiple cascade all-delete-orphan exceptions related to DefinedTermBase.representations Closed
8213 MySQLSyntaxErrorException with 'Submitter' user acessing view registration#!regStart Closed
8107 NPE when throwing PopupEditorException in AbstractPopupEditor Closed
7962 PopupEditors: *DTO in context 'breadcrumbs' to be transformed into more humane labels Closed
8097 Problem with inserting a section - inReference is "lost" Closed
7881 reference selection combobox broken after error in ... Closed
8149 ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic and NULL Closed
7968 ReferenceEditor: optional validation for completenes of Partial values in datePublished Closed
8191 ReferencePopupEditor: When coming from NameEdior editing of the inreference should not be blocked Closed
8218 Show appropriate error message when accessing RegistrationWorkingsetEditor without sufficient permissions Closed
8184 SpecimenTypedesignationEditor: add new specimen broken Chrome browser Closed
7963 TaxonNamePopEditor: name part field visibility not correct for all ranks Closed
8192 The curator must be able to unlock a published registration for edition Closed
8217 ToManyRelatedEntitiesComboboxSelect edit button not enabled Closed
8214 WeaklyRelatedEntityCombobox is not validated Closed
8176 WeaklyRelatedEntityCombobox is slow 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
7106 avoid factory.openSession() in CdmRepository Closed
7896 NPE, NullPointerException in RelationshipTermBase Closed
615 remove suns repository Closed
8104 TaxonName.getLastNamePart erroneously renamed .getFamiliyNamePart Closed
  cdmlib-remote 2 Collapse all/Expand all
8096 Implement CacheUpdater as long running task with correct progress monitoring Closed
8173 spring profile remoting enabled by default Closed
  taxeditor 28 Collapse all/Expand all
8124 Activate Name Facts in Taxeditor Closed
8146 Adapt taxeditor UI to structure and property term type Closed
8147 Add "plural" to representation detail element Closed
7923 Add context menu and drag'n'drop to CharacterEditor 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
8121 Allow selecting structural/property modifiers when creating a character Closed
8200 Changing title(cache) for factual data set not possible Closed
8222 Deleting a type designation from a name is directly persisted Closed
8197 Deleting Media from Image Gallery View does not make view dirty Closed
8225 Deleting one of two type designations removes both Closed
3836 Implement modifiers and modifying text for Description Elements in TaxEditor Closed
8136 Implement sources for type designations in TaxEditor Closed
4545 Implement TeamOrPersonBaseSelectionDialog Closed
8011 Implement term search view Closed
7541 Insufficient rights lead to missing focus in name editor Closed
8143 It is possible to open multiple instances of the login dialog Closed
8148 Login Dialog cuts off information Closed
8234 Move description elements issues Closed
8115 NPE when moving factual data Closed
7428 Open issues for updating open data while subtree is updated Closed
8228 refresh of details for same object in different bulk editors does not work Closed
7865 Remaining factual data view label issues Resolved
8211 Trigger new search when clicking on identifier search Closed
7515 TypeDesignationStatusComparator to sort by vocabulary first and then by term order Resolved
8223 Urgent TaxonNode wizard issues Resolved
8111 User selection dialog for groups does not filter out existing users Closed
6413 [DISCUSS] How to create type duplicates (e.g. isotypes) for a taxon name 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
7914 Add ISBN to IProceedings Closed
8030 Cache updater service methods externalized and base class specific Closed
7913 Remove authorship from IJournal and IPrintSeries Closed
7915 Remove date published from journals and print series Closed
7930 Remove DOI from journals, print series and person communications Closed
7918 Revision of reference type specific properties Closed
  cdm-dataportal 13 Collapse all/Expand all
7907 Annotations in Reference page do not respect the annotation settings Closed
8076 implement test for typified name for registration page Closed
8051 improve display of registration items lists Closed
7974 Layout for Registration date Closed
7616 reference page: show name types Closed
7927 Registration not found, Portal handling registrations in preparation Closed
8074 Registration page has fatal error when registration identifier in url path is ivalid Closed
7977 Registration page layout improved Closed
7947 registration page shows name relations Closed
8073 Registration page: show typified name for registrations covering typifications only Closed
7564 remove Phycobank - Registration data - block and other outdated registration code Closed
8048 Selenium test for Registration page Closed
8056 WSOD in cdm_dataportal/search/results/taxon Closed
  cdm-vaadin 45 Collapse all/Expand all
7925 AbstractPopupEditor: exception handling in save method is incomplete Closed
7906 AbstractPopupEditor: Notify user on editor changes and provide options to choose from discard or save Closed
8031 Cannot add existing name to blank workingset Closed
7878 Edit CollectionCode not saved Closed
7899 enable orthographic name correction in Vaadin Closed
7900 Excessive heap consuption in RegistrationWorkingsetEditor with big workingsets Closed
7867 FieldGroup$BindException: The given field is not part of this FieldBinder in TeamOrPersonField Closed
7919 GeoLocationField uses OpenTopoMap Closed
8013 LazyInitializationException (LIE) in RegistrationDTO.makeBibliographicCitationStrings Closed
8063 multiple representations problem wirth collector being author of the registration citation Closed
7718 New Registration: Exclude irrelevant reference types from list of existing publications Closed
7949 New Registration: Reference combobox to offer two search modes Closed
8064 NPE in AbstractHibernateTaxonGraphProcessor.assureSingleTaxon() on saving new name for new registration with new genus Closed
7905 NPE in InstitutionEditorPresenter 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
7866 Phycobank UI further label improvements Closed
7846 PopupEditors show editor context information as 'breadcrumbs' in the header or toolbar. Closed
7559 possibly corrupted hiberante session after previous error on saving editor Closed
7908 Redmine communication hub slows down RegistrationWorkingSets Closed
7951 Reference Combobox option titles can be too long causing the select box to extend too much Closed
8090 Reference editor: Label In proceedings in InProceedings missing Closed
7480 ReferenceEditor misses institution, organization and school fields Closed
7481 ReferenceEditor: filter inReferences by applicable reference type Closed
8070 ReferencePopupEditor: apply sensible reference type pre-set for in references Closed
8071 ReferencePopupEditor: saving a newly created inreference is not refreshing the inrefernce field with the new entity Closed
8072 Registration items in list view is using the wrong button icons for blocking regs and validation errors Closed
7995 Registration.registrationDate not set when status is set PUBLISHED Closed
7946 RegistrationStatusFieldInstantiator must set status value internally before adding the ValueChangedListener Closed
8069 RegistrationUI: remove all messaging related code and message indicators from all views Closed
7956 RegistrationWorkingsetEditor refresh problem after saving TaxonNameEditor Closed
7893 RegistrationWorkingsetEditor: canceling new name editor leaves the new name button disabled Closed
7870 RegistrationWorkingsetEditor: Internal error on clicking "new name" Closed
7892 RegistrationWorkingsetEditor: LIE creating new name for book section Closed
7639 SpecimenTypeDesignationEditor: Altitude not saved and displayed properly Closed
7942 SpecimenTypeDesignationEditor: Explanation on why editor can not be saved without type designation Closed
7916 SpecimenTypeDesignationEditor: Map shows error radius Closed
7218 SpecimenTypedesignationsWorkingsetEditor: support for Reference system Closed
7833 submitters can access see any registration in any RegistrationWorkingSet Rejected
7937 TaxoNamePopupEditor: Exclude current name from name relationship comboboxes Closed
7944 TaxonNamePopEditor: name part fields are required Closed
7910 TeamOrPersonField: readonly exception on bindig data Closed
7950 ToOneRelatedEntityCombobox: add new button "jumpes" to the right when hovering the mouse over Closed
7888 TypeSpecimenEditor: Collection date should be timespan Closed
7245 validation of ToOneRelatedEntityCombobox not working 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
7901 Make PreferencePredicates an interface to allow multiple implementations (e.g. for client apps, for grouping, for data type specific instances, etc.) Closed
7600 public setters for entity collections Closed
7217 SpecimenTypedesignationsWorkingsetEditor: Longitute Latitude fields allow values in degrees minutes seconds formats Closed
7939 TaxonNodeDTO need sortIndex of Rank Closed
7874 TeamOrPersonBase entity can become unusable due to replacement of the title caches on using getters Closed
  cdmlib-remote 4 Collapse all/Expand all
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
7978 registration search result ordered by identifier descending Closed
8042 UI is too restricted for users with right Project Manager 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
8037 "Detail" is not saved in taxon node wizard Closed
7940 "New" menu in navigator not available for certain users Feedback
6806 Add context menu to FeatureTreeEditor Closed
7875 Add multiple area selection to descriptive data set editor Closed
7931 add symbol2 to term detailsview Closed
7933 Adding a new Term to the "Country" vocabulary leads to corrupt data Closed
7929 after delete of not persisted object in bulkeditor the object is still in bulkeditor list Closed
7868 Allow creating a new vocabulary in vocabulary selection dialog Closed
7856 Allow local override for distribution vocabularies Closed
7999 Allow override does not work correctly for distribution areas Closed
7836 ClassCastException when invoking cdm light export with wrong selection Closed
7941 Deduplication does not work in new taxon dialog Closed
7367 Deleting a term in the term editor does not update the UI Closed
8026 details view is empty for some references in bulk editor Closed
7993 Display "Access Denied" dialog in case the remoting service responds with status code = 4xx Closed
6951 Drag and drop does not update term hierarchy in the UI Closed
7912 Enhance checkbox tree viewer Closed
7877 Form elements disappear in reference dialog after changing the reference type Closed
7850 Further problems with term editor Duplicate
7806 GfBio Term Search issues Closed
4227 handle generated resources in eclipse workspace Feedback
7880 Implement centralized preference default loading strategy Closed
7873 Implement copy&paste for feature nodes in feature tree editor Closed
6805 Implement drag and drop from Term Editor (Feature) to FeatureTreeEditor Closed
7849 Improve DB Preferences handling and saving in TaxEditor Closed
7761 Invalid designations should be displayed like misapplied names in name editor Closed
7668 NPE when changing author Closed
7746 NPE when deleting volatile DescriptionBase Closed
8032 NPE when editing Local Prefs -> Factual Data Closed
7871 Open character matrix as singleton Closed
7854 Open issues in TaxDistributionEditor Closed
8041 PatternSyntaxException in FeatureTreeSelectionDialog Closed
7954 protected vs. unproteced caches in TaxEditor Closed
7680 Refactor TaxonNodeDetailElement Closed
7737 Reference Details view does NOT give a multiple usage warning Closed
7985 Remove Print Series from InProceedings, use "Proceedings" Closed
7163 Restructure preferences Closed
7869 Run gfbio term service requests as background tasks Closed
7934 sometimes the signs for deduplication are not shown Closed
7998 Store newly created Characters in selected vocabulary Closed
7649 Term editor loads/saves extremely slow Closed
5926 Update labels in TermEditor for Vocabularies Closed
7794 Update TaxonNodeWizard Closed
7887 Use DTOs in term editor Closed
7847 Use separate column for row state instead of symbol in titleCache column Closed

Previous Releases Archive

see CdmPlatformRoadmapArchive

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