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CDM Platform 5.18 (scheduled for Sep 30th, 2020)

Issues: 319

What will be new?

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

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
  • Vaadin / Registration

    • 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
8420 improve admin settings for specimens representations Closed
8850 Show annotations for DerivedUnits (Fieldunits etc) in Registration and other pages Closed
9099 placemark icon in kml map not clickable Closed
9109 Search button font icon broken Closed
9128 Default copyright statement below image viewer Closed
9137 IPTC Keywords (and maybe other information) is not shown in Universal Viewer yet Closed
9175 hide occurrence map when no data exists Closed
9188 selenium web element wrapper for dynabox Closed
9181 set and get drupal variables from selenium test suite Closed
8543 overcome distinction of annotation and other foonotes Closed
9186 selenium test for specimen top down view (aka devivate_path view) Closed
9191 selenium test for specimen tree view (bottom up) Closed
2489 strategy for congruent areas in distribution maps: create merged TDWG layer with all levels Closed
4372 Selenium PortalPage class also suitable for zen-basetheme Closed
  cdm-vaadin 4 Collapse all/Expand all
8156 Registration items show type status in bold letters Closed
8230 NameTypePopupEditor: genus selectable as the name type for higher ranks Closed
9182 Sub-collection and Collection vs. Collection and Super-Collection Closed
8317 Omit ex-author if ex-author=author Closed
  cdmadapter 1 Collapse all/Expand all
9110 Add additional informations to metadata table of cdmLight Feedback
  cdmlib 7 Collapse all/Expand all
9105 rename NodeSortMode etc to TaxonNodeSortMode Closed
9000 UriUtils: HttpClient has ssl error connecting to pictures.bgbm.org Closed
9152 PreferencesService caches CdmPreferences Closed
9146 filter image metadata by include and exclude lists of key words Closed
9129 cdm property to store a default copyright statement for media items Closed
9148 Replace sanselan library by the newer apache commons-imaging Closed
9147 Use StringBuilder in CdmUtils.concat() to avoid performance penalties Closed
  cdmlib-remote 4 Collapse all/Expand all
9134 Rule based creation of additional media representations "on the fly" Feedback
9087 typedesignation/{uuid}/annotations must return pager objects Closed
9193 LazyInitializationException (LIE) in portal/taxon/{uuid} web service Closed
9198 option in iiif manifest creation to set canvas size to thumbnail size Closed
  geotools - map service 1 Collapse all/Expand all
8310 Issues to solve in E+M shapefile Resolved
  taxeditor 12 Collapse all/Expand all
5752 Reduce TaxEditor size Closed
9040 Implement open button for ORCIDs Closed
9065 Add derived unit media to DerivedUnitFacade details view Closed
9138 Reenable BioCaseQueryServiceWrapperTest.testQueryForUnitId() Closed
9172 Missing synchronisation between taxonnode wizard and name editor Closed
9168 NameFeature selection in preferences are not shown Closed
9171 Doubtful taxa are not found in bulkeditor Closed
9166 ClassCastException when editing media in taxon bulkeditor Closed
9118 Change p2 update site to https in Taxeditor Closed
9119 Remove schema create and schema update functionality from datsource view Closed
9116 Adapt Editor to switch to originalSource for TaxonNode and improve layout of TaxonNode dialogue Closed
9173 NPE when move synonym into homotypical group of accepted 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
8802 Implement flowering period for Flora of Cyprus Closed
8964 Improve label for homonym relationships Closed
8991 Add feature "Flowering Period" 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
9009 Add structure to store media metadata Closed
9036 Remove old TaxonNode.unplaced/doubtful/excluded columns Closed
9037 Remove old Feature.supportedXXX columns Closed
9043 Add feature "Altitude" Closed
8978 Implement measurement values as BigDecimal Closed
9026 Implement Feature.supportedDataTypes as EnumSet Closed
9027 Implement Feature.availableFor Closed
9064 Add ExternalLinks to IdentifiableEntities Closed
  cdm-dataportal 13 Collapse all/Expand all
4257 specimen map should zoom to area of distribution Closed
4488 Specimen data points in map should show FieldUnit information Closed
6878 choose a base font for the portal and deliver it from the drupal module or theme Closed
8134 Implement verbatim type information in dataportal Closed
8855 Show error radius in EDIT portal Closed
8888 responsive width for universal viewer Closed
8900 Layout issues with new image viewer Closed
8994 universal image viewer fails loading libs when clean urls is disabled Closed
8972 integrate kml layers into map viewer 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
9034 simple agent list page with filter function Closed
8196 display ortographic corrections in name relations as 'corrected name: <nameCache>' Closed
9076 synonymy without margin when 'Synonymy as tab' and 'Tabbed taxon page' are off Closed
  cdmadapter 2 Collapse all/Expand all
8998 Terms created by abcd import should always be part of a vocabulary Resolved
9031 Adapt CdmLightExport to new TaxonNode.status Closed
  cdmlib 5 Collapse all/Expand all
9020 add default role Allow_for_all_taxa (TAXONNODE.[CREATE,READ,UPDATE,DELETE]) Closed
9047 Search does not return orphaned synonyms Closed
9058 Hibernate loggs error when creating schema on MySQL due to failing index creation Closed
8986 use Maven Enforcer plugin to check for dependency version conflics and to enforce the minimum maven version Closed
9081 Handle empty Partials correctly Closed
  cdmlib-remote 3 Collapse all/Expand all
6113 webservice to expose FieldUnits related to a Taxon or TaxonName as KML and/or GML Closed
9023 option to start cdm webapp with hibernate.hbm2ddl.auto = create Closed
9044 TaxonNodeDtoBeanProcessor supports new TaxonNodeStatus terms Closed
  cdmserver 3 Collapse all/Expand all
7085 cdmserver logfiles getting too big, use RollingFileAppender Closed
3683 add /etc/default/cdmserver to debian package Closed
8682 cdm-server debian packages configured for jemalloc Closed
  data 1 Collapse all/Expand all
9017 Update image link for FoG Willing images Resolved
  taxeditor 42 Collapse all/Expand all
8785 Move functionality of buttons to context menu of the character matrix Resolved
8754 DescriptionElements are not deleted with the Descriptive Data Set Resolved
8901 Deleting an aggregated description from a descriptive matrix does not delete the aggregated description itself Resolved
9070 Adapt preference page to feature.isAvailableFor... Resolved
9084 Make it configurable if a Description is deleted only from the Descriptive Data Set or from it's Specimen/Taxon Resolved
9055 Relabel "Type Designation" to "Type Information" Feedback
7774 Show description source for description elements Closed
7189 Taxeditor connect dialog high-dpi suport Closed
8662 "Remove Taxon" in DescriptiveDataSetEditor should only be visible if taxon is selected Closed
8857 NonUniqueObjectException when creating new taxon Closed
8903 Remember expansion state in factual data view Closed
8958 Add publication year, inReference (journal), and URI to reference bulk editor Closed
8959 Moving a synonym to the homotypical group of the accepted taxon opens the context menu of the accepted taxon Closed
8849 NPE in synonym DetailsViewer for synonyms without accepted taxon Closed
8963 Selection dialogues should be modal Closed
8988 Add link button to DOI field for references Closed
8990 Implement flowering periods (temporal facts) in TaxEditor Closed
8961 Using the selection dialogue for nomenclatural references removes the recently used list Closed
8969 Multiple deduplications are not executed Closed
9022 Implement lifespan for Person Details View Closed
8999 Verbatim date not persisted for books Closed
9025 allow for creating a new schema in empty dbs via the remote login dialog Closed
9029 Adapt character matrix to using dtos instead of whole cdm entities Closed
9033 Adapt TaxEditor to new TaxonNode.status Closed
9063 Detailsview for MediaSpecimen broken Closed
9045 TextualTypeDesignation throws exception in referencing objects view Closed
9053 CCE when selecting Character Tree for descriptive dataset Closed
8753 EagerLoadingException on opening Character Tree Editor after deleting all Desciptive Data Sets Closed
8783 Massive Heap consumption in server instance opening the Description-Matrix editor Closed
8957 Rename "unexpected error" to "unhandled error" Closed
8954 Details and Supplemental Data View do not save the expansion state of sections again Closed
8962 Handle widget is disposed after closing Supplemental Data View Closed
9013 Problems in TaxonNode Dialog Closed
9016 Adding specimen without field unit fails Closed
9032 Implement Feature.availableFor in TaxEditor Closed
9038 Adapt TaxEditor to use BigDecimal for StatisticalMeasurementValues Closed
9066 Make visiblity of Specimen List Editor menu configurable Closed
9052 NPE in name details view for incomplete name relationships Closed
9059 Cancel taxon save does not clean the (factual data) cache Closed
9060 NPE in termsearch Closed
8806 Multiple representations problem on saving Desriptive Data Set Worksforme
8752 Matrix Editor: Can fail showing all SpecimenDescriptions in the dataset Worksforme

CDM Platform 5.14 (released April 8th, 2020)

Issues: 30

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
8895 Specimen page: show specimen description as continuous text Closed
8914 jetty 9.4.x returns error states as json which are parsed and processes by cdm_dataportal 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
8907 replace UuidAndTitleCacheTaxonComparator by type save implementation Resolved
8428 NPE in ClassificationServiceImpl.loadTreeBranchToTaxon() Closed
8942 Exception when try to get text of TextualTypeDesignation with language which is not available Closed
8815 Clean up TaxonNodeDto and UuidAndTitleCache usage in TaxonNodeService/Dao Closed
  cdmlib-remote 2 Collapse all/Expand all
8899 NullPointerException (NPE) in ManifestController Closed
8911 LazyInitializationException (LIE) in portal/description/{uuid} Closed
  taxeditor 20 Collapse all/Expand all
8756 Refresh button for structure tree and property tree in Character Editor Resolved
7981 Add configuration UI for matrix description aggregation Feedback
8238 Allow interoperability between term trees Feedback
8725 Add abbreviation to namedArea text field in distribution details view Feedback
8906 Refactor DNA Sample details view Closed
8916 ConcurrentModificationException in CdmFormFactory.destroyElement() Closed
8927 Fix isAdmin() method in LoginManager Closed
8917 NPE when opening Acacia in Name bulk editor (from search) Closed
8943 Term Preferences are not correctly handled in combo boxes Closed
8552 Avoid DB call for matrix state DB preferences Closed
8910 Correct handling of preference for determinations Closed
8913 InInVoc not showing up anymore in TermEditor Closed
8919 Shorten label for "Reference Detail" Closed
8925 Users with ROLE_USER_MANAGER must be able to change any user password Closed
8904 Show "cloned" icon in factual data view Closed
8926 Remove 'expired' flags in users details Closed
8938 ProposalProvider in NameRelationshiptype combo does not work as expected Closed
8940 The export wizard does not remember last selected folder Closed
8918 Add "set as basionym" to accepted taxon Closed
8939 Exception when opening Distribution Editor because of missing Preference 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
8945 support statistical value type ExactValue (29736701-58c4-48b3-a9d7-41c74140cac7) Resolved
7766 Remaining issues for using relationship DTO webservice in portal Closed
5083 Alternative image viewer for dataportal Closed
8328 Unpublished record visible in Portal if related name is published Closed
8830 add missing spaces to statistical value representations Closed
8845 external links: GGBN not shoing up in admin section Closed
8828 statistical values must not show empty brackets 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
8782 Delete a description included in a CdmSource should not be possible Closed
8881 Use pure last names (without initials) for in-references of taxon names Closed
8892 Taxon search does not work for names without rank Closed
8829 NullPointerException (NPE) in TaxonNodeService 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
8839 Role misses toString method Closed
  cdmlib-remote 3 Collapse all/Expand all
8427 LazyInitializationException in NameController.doGetTaggedFullTitle() Closed
8866 LazyInitializationException (LIE) in portal/taxon/{uuid} Closed
8867 media list services as iiif manifest service Closed
  taxeditor 26 Collapse all/Expand all
8812 Connection losses in taxeditor HTTP invoker (RemoteAccessException: Could not access HTTP invoker remote service at ...) Resolved
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
8047 Remaining issues in TaxDistributionEditor Feedback
8848 Search fails with low data rate network (64kbit/s) network connection due to lost authentication Feedback
8562 Remaining issues for preference pages Feedback
6036 Problems with deleting type names Closed
8624 Add abbrev title cache to search in bulk editor Closed
8847 Name in Source is added always when moving description from one taxon to another Closed
8897 [Mac] Jre Taxeditor fails to start in MacOS X Closed
8791 Measurement units are not assigned to quantitative data in matrix 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
8890 Allow multiselection for open_in menu Closed
8825 Name features are shown in menu of factual data view of taxa when no preferences defined Closed
8688 Make OriginalSourceBase.cdmSource visible in TaxEditor Closed
8862 move search result to the bottom of the navigator part Closed
8879 strange file name for export file Closed
8721 Use webservice to get all biocase provider listed by gbif 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
8860 Sec reference not inherited from classification anymore Closed
8861 Sorted feature states Closed
8531 factual data and media view always opened when opening taxon Closed
8749 Add proposalProvider to AbstractComboElement Closed
8044 Add "Move to..." menu to term editor Closed
8784 Deleting a specimen description not possible 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
8468 Remove old InapplicableIf tables Closed
8803 Add "per mm²" to measurement units Closed
8702 Remove Not null constraint for uuid in AUD tables Closed
8738 CdmLink.startPos and .endPos should allow Null Closed
8724 Allow OriginalSource to link to Taxon Closed
  cdm-dataportal 19 Collapse all/Expand all
8765 defined weight for feature and pseudo feature blocks and position "Description (aggregated)" after "Description" Resolved
8771 display of average value with precision so that it differs from min and max by one digit Resolved
8786 Display of mean value with min max 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
8798 description page: Show character hierarchy Resolved
8787 Improve layout for ExactValue on Description Pages Resolved
8686 Support CdmLink sources in bibliography Closed
8718 polytomousKey page: better handling of invalid uuids Closed
8719 installation profile 'CDM_Portal' causes Integrity constraint violation: 1048 Column 'pages' cannot be null Closed
8745 Type designations of synonyms missing on specimen page Closed
8779 Description page: use render_taxon_or_name() for creating the page and description title and taxon links Closed
8739 remaining issues for description detail page Closed
8758 Aggregated Descriptions: order states by frequency Closed
8781 Descriptions (aggregated): futher improvements Closed
8595 Create description detail page Closed
8657 Order description element in portal according to CharacterTree Closed
8766 Aggregated Descriptions: show Sample size as [$SAMPLE_SIZE] Closed
8807 description page: Adapt table header to the nature of description elements 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
8670 Unwanted distribution aggregation/display on 2 levels Resolved
8467 Save a "snapshot" of the SpecimenDescriptions used for aggregation Resolved
8713 Improve structured descriptive data aggregation Resolved
8788 Cloned descriptions do not show up in dataportal anymore Feedback
4134 Transmissionengine Distribution seems to miss distributions for higher Taxa Closed
6629 TransmissionEngineDistribution misses aggregating Uzebkistan (UZB-OO) to higher rank levels Closed
8472 Transmission engine for distribution aggregation needs to be adapted to new DescriptionBase.types Closed
8683 TaxonDaoHibernateImpl.countTaxaByName rename parameter authorship authorshipCache Closed
8684 ITaxonService.findTaxaByName misses initStrategy Parameter Closed
8737 delete taxon included in two classifications deletes taxonname Closed
8679 Further unify description aggregation methods Closed
8780 Repair sortindex does not work on TermTree index Closed
5176 TransmissionEngineDistribution can run on selected taxa 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
8706 taxeditor error report with timestamps Resolved
8677 Add distribution aggregation to set subtree menu Closed
8731 BioCase Specimenimport: empty result list and SWTException:Invalid thread access in search results Closed
8805 In distribution editor synoms should be available as concatenated String Closed
8797 Navigator tree collapse after moving taxon node Closed
8810 In taxeditor parts without permissions should be disabled Closed
8242 Implement filtered combo boxes for state selection in CharacterMatrix Closed
8313 Multiple categorical data get deleted when clicked on in Character Matrix Closed
8477 Implement support for TermCollection.allowDuplicates in TaxEditor Closed
8511 The structure path in the character details view should have a line break Closed
8645 rename menu item General > Import > "OWL Import" to "Term Tree OWL Import" Closed
8665 Rename "New" to "New Tree" in Term Tree editors Closed
8661 "New DataSet" should ask for label and then open the dataset Closed
8694 Specimen online import - Specimen Search: import button layout problem on linux KDE Closed
8703 Move TermSearch and Specimen(Import)Search to editor area of taxeditor Closed
8736 LazyInitializationException (LIE) during adding Specimens to Matrix Editor Closed
8744 LazyInitializationException (LIE) saving the Character Editor Closed
8748 Supported state vocabularies should be ordered Closed
8755 Show all structure/property trees in CharacterEditor Closed
8757 ArrayIndexOutOfBoundsException in term combo Closed
8800 If supplemental data view shows reference it is not possible to select another reference Closed
8801 Deselected menu items are not reactivated in navigator Closed
8656 [DISCUSS] Should only characters be allowed for DescriptiveDataSets/Character Matrix? Closed
8732 Descriptive Data Set Navigator: label not refreshed after change in Descriptive Dataset Editor Duplicate

CDM Platform 5.11 (released Nov 15th, 2019)

Issues: 38

Downloads: Ask the edit team for backups of this version

What's new?

  • Data Model

    • Added count parameter for statics during data aggregation of categorical (structured descriptive) data
    • Added ORCID identifier to persons
    • Added CDM source links (sources may link to other information in the same CDM instance)
  • Data Portal

    • Fixed polytomous key display for key parts linked from multiple places
    • Fix label formatting for specimen with missing collection identifier in specimen tables
    • Fixing problem with names having multiple nomenclatural status
  • Import/Export

    • ABCD:
      • Fix collector and field number handling for derived units missing this data (but available in field unit record)
  • CDM Library

    • Better parsing for infrageneric autonyms with authors
    • Imporved distribution and descriptive data aggregation
  • CDM Server

    • Fix memory leaks
  • TaxEditor

    • Taxon search: new filter to search only for published taxa
    • Terms:
      • Tree editor for Named Areas, Ranks and Distribution Status available (to define user defined term collections and orders, including cross-vocabulary collections) - usage of such collections will be implemented in future releases
    • Taxon/Name details view
      • Nomenclatural code edition editable for rule considered (nomenclatural status and name relationships)
      • Rule considered and nomenclatural code editon visibility configurable (serverside and local)
      • Minor changes in ordering of misapplied name details view
    • Person details view
      • ORCID editable
    • Taxon navigator:
      • Taxon node doubtful flag editable via context menu
      • Rename view to "Taxon Navigator" (regression in one of the last releases)
      • Refresh problem after editing classfication label or adding child taxon to classification
      • Rename open-in for Taxon Node (Wizard) to ... Dialogue
      • Reorder and rename import menu (items)
    • Import/Export:
      • Multiple fixes for file based ABCD import
      • Fix for DwC-A export
    • Factual Data View
      • Visibility of "modifier" and "modifying text" is configurable now
    • Distribution Editor
      • Default source also used when creating an additional source for an existing source
    • User administration
      • Better error handling for user and group names with not allowed characters

# Subject Status
  cdm 4 Collapse all/Expand all
8466 Delete FeatureTree tables Closed
8625 Add count parameter to StateData Closed
8628 Add ORCID as person identifier Closed
8673 Allow OriginalSource to link to other CDM objects Closed
  cdm-dataportal 3 Collapse all/Expand all
8610 tagged_text_extract_nomstatus() fails handling more than one status Closed
8596 Add a list of descriptions to the taxon page Closed
8622 Missing specimen Identifier leads to empty brackets in portal Closed
  cdmadapter 2 Collapse all/Expand all
8533 missing collector and fieldnumber in abcd import Closed
8632 ABCD retrieves DNA Sample from Biocase Provider even if it is not selected in the import configuration Closed
  cdmlib 3 Collapse all/Expand all
8253 Authors for genus autonyms Closed
8651 Unify description aggregation methods (distribution and structured descriptive data) Closed
8676 TaxonDaoHibernateImpl.countTaxaByName misses parameter authorship Closed
  cdmlib-remote 1 Collapse all/Expand all
8570 PolytomousKeyNode.otherNode missing in REST service response Closed
  cdmserver 2 Collapse all/Expand all
8674 configure cdm-server docker image to run with jemalloc Closed
5048 cdm-server causes unusual high native memory consumption for jvm Closed
  taxeditor 23 Collapse all/Expand all
7143 Finish not enabled when unprotecting titleCache in new Person dialog Closed
7457 E+M: Allow filtering for only published in search Closed
8685 Exception when calling DwC-A Export Closed
8410 Add nomenclatural code edition to ruleConsidered in TaxEditor Closed
8470 Handle username constraints in user and group editing Closed
8568 improve performance for term and vocabulary preference pages Closed
8572 Rule considered configurable Closed
8581 Naming inconsitency: Taxon Navigator or Taxonomic Tree? Closed
8582 Taxon Navigator: Classification label not refreshed & new taxa not visible Closed
8613 For distribution editor default reference should be used also when new source is created Closed
8584 Appended phrase should be shown on top level for misapplied names Closed
8609 Rename Taxon Node context menu entry Open in .. -> Taxon Node Wizard Closed
8642 Add tree editor for rank, NamedArea and PresenceAbsence Closed
8664 SQLGrammarException when opening Specimen selection Closed
8667 Make Person.orcid editable in TaxEditor Closed
8630 ClassCastException when ABCD import has finished Closed
8631 ABCD import fails to put new taxa into the classification, create mediaspecimens, etc Closed
8648 Simplify name details view configuration Closed
8634 NullPointerException (NPE) in PreferencesUtil.getLocalAbcdImportConfigurator() on starting ABCD import Closed
7019 sort import menu Closed
8226 make modifiers for description elements configurable Closed
8486 Indicating doubtful state in navigator and add set-doubtful to Set-Flags menu Closed
8652 disentangle confusion when connecting to development cdm instance fails Closed

CDM Platform 5.10 (released Sep 23rd, 2019)

Issues: 30

Downloads: Ask the edit team for backups of this version

What's new?

  • Data Portal

    • Taxon section in name page can be suppressed via settings.
    • Bug fix of a regression related to the display of DOIs and publication reference links.
  • Import/Export

    • CDM light export:
      • type designation export differs between textual and specimen type designation
    • Biocase search:
      • add possibility to search for Higher Taxon
  • CDM Library

    • Bugfixes and code maintenance
      • Providing the default user role USER_MANAGER to all databases.
  • TaxEditor

    • Bugfix for swap taxon and synonym
    • Further improvements to preference handling
    • Search dialogue for distribution areas works with abbreviations
    • Old taxeditor documentation made available.
  • Web editor (Phycobank registration UI)

    • Name relations and nomencaltural status now offering fields to mention the nomenclatural code edition.
    • Layout and user experience (UX) issues in the UI have been solved (#8014, #8342, #8377).
    • Fixing important bug to prevent data loss and corruption (#8462, #8527)

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

CDM Platform 5.9 (released Aug 29th, 2019)

Issues: 51

Downloads: TaxEditor, CDM Server, Data Portal

What's new?

  • Data Model

    • Term structure improved to allow all types of relations between terms and to allow vocabulary independent term collections/graphs (partly implemented in TaxEditor)
    • Add state vocabulary for presence/absence of a biological structure
    • Improve structure for inapplicableIf handling in character trees used for descriptive data matrices/datasets and for indentification keys
    • Improve authority handling in data model (preparation only)
    • Allow certain patterns only as usernames (Latin letters, numbers, '_', '.' are allowed)
    • Doubtful (placement) flag for taxon nodes
    • List of nomenclatural code editions (e.g. Melbourne Code) additional to rule considered in nomenclatural status, name relationship and hybrid relationship
    • Fields added to allow externally managed terms and vocabularies (not yet in TaxEditor)
    • Fields for textual/verbatim type designation information
    • Possibility to add fixed markers/types to a description (e.g. to mark a description as a computed/aggregated description which should not be editable)
  • Data Portal

    • Adapted to term structure changes in the data model.
    • Improved ordering of type designations in the name and taxon pages.
    • Harmonization and improvement of the specimen display in various parts of the portal, including better intra portal linking.
    • Performance improvement regarding to type designations.
    • Auto-zooming of maps has been fixed for different map projections.
    • Improved layout of the registration page to clearly show the nomenclatural act.
    • Classification tree horizontally automatically scrolls to active entry.
  • Import/Export

    • CDM light export:
      • add textual/verbatim type designations
      • some minor adaptations
  • CDM Library

    • Fix and improve polytomous key generation (to be used from descriptive data set, experimental feature)
    • Multiple improvements and bug fixes to web services
  • TaxEditor

    • Add textual/verbatim type designations to details view
    • Use feature states for applicability of term nodes
    • Improvement and harmonization of serverside and local preferences
    • Update name in source data when changing an accepted taxon into a synonym (configurable)
    • Allow setPublish for subtree to include misapplied names, pro parte synonyms and exclude hybrids
    • Seperate term tree editor for each term type available
    • Warning if misapplied names or pro parte synonyms are used/linked from more then 1 other taxon.
    • Bugs.
      • fixed term order of term trees

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

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

Issues: 68

Downloads: Ask the edit team for backups of this version

What's new?

  • Data Portal

    • cm added as measurment unit
  • Data Portal

    • Improvements to the media page related to source references and the media title
    • Name page shows more information: name relations, type designation with specimen map, related taxa, nomenclatural acts (registrations)
      • The automatic redirect behavior to the taxon page is now configurable
    • Registration search:
      • Support for filtering by references
      • Improved search by type designation status and name
    • Registration page:
      • Subheadline to show the type of the nomenclatural event
    • General layout improvements
      • Links to reference pages as unobtrusive icon link
    • Maps:
    • User interface to search the Unified Taxonomic Information Service (UTIS)
    • Bugfixes related to
      • Name relations
      • Nomenclatural status
      • Type designations
  • CDM Server

    • improved error detection when failing to start
  • TaxEditor

    • improved deduplication for references in name editor (hotfix 5.7.3)
    • handling of preferences improved
      • consistent model to always allow default and specific values and to handle override more intuitive
      • area specific status list preferences for distribution data
      • status list serverside preferences for distribution data handled in details view
      • ranks as serverside preferences
      • nomenclatural status as serverside preferences
      • visibility of fields Source.idInSource and Source.IdNamespace as preferences
    • CDMlight export
      • includes excluded flag and excluded notes
      • sortindex for taxa added
      • improvements in ABCD import
    • Terms allow adding media in term editor
    • Media:

      • media loaded asynchronously to improve performance (has open issues)
    • Bugs

      • exception/freezing when opening name in source search dialogue (hotfix 5.7.3)
      • recognize again the previous state (opened sections) of details view and supplemental data view (hotfix 5.7.3)
      • refresh in name bulk editor after search (hotfix 5.7.3)
  • Web editor (Phycobank registration UI)

    • Registration list view with reference filter
    • Curators and admins can edit arbitrary Annotations (Notes)
    • Bugfixes related to
      • user permissions
      • ...

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

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
8209 use ellypsed references for all reference comboboxes Resolved
7965 Registration search simplify type select options Closed
8193 TaxonNamePopupEditor: add select form element for Nomenclatural status Closed
8215 User demand: sorting order in reference editor Closed
8220 incomplete creation of blocking registration in case of registering existing name which misses the nomenclatural reference Closed
8246 TaxonNamePopupEditor can not be canceled Closed
8250 ReferenceEditor: inReference must not be required for type book Closed
8252 reference ellypsis must not be applied to all reference types Closed
  cdmlib 2 Collapse all/Expand all
7953 Book in BookSeries: incomplete titleCache misses series title Feedback
8189 Allow configuration of 'user.home' via the spring environment Closed
  cdmlib-remote 1 Collapse all/Expand all
8251 LazyInitializationException (LIE) in featureTree webservice Closed
  taxeditor 10 Collapse all/Expand all
8263 Improve performance of term editor Resolved
8316 Endless loop when editing name in source of distribution Feedback
8229 reload of the bulkeditor does not work correctly Closed
8241 Rename FeatureTreeEditor to TermTreeEditor Closed
8258 Default Feature Tree contains name features and features Closed
8265 Referencing objects view does not work for term editor Closed
8267 common name preference saving does not work correctly Closed
8315 Parsing existing references with inReferences changes the inReference Closed
8266 local preference is not evaluated for distribution editor status Closed
8349 NPE in ParseHandler when parsing name without nomencl reference 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
8162 Move term related classes from model.common to model.term Closed
8190 Default FeatureTree throws exception Closed
  cdm-dataportal 5 Collapse all/Expand all
3616 Show DescriptionElementBase.timeperiod in Dataportals Closed
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
5699 user profile settigs in cdm_dataportal module done wrong Closed
  cdm-vaadin 23 Collapse all/Expand all
7962 PopupEditors: *DTO in context 'breadcrumbs' to be transformed into more humane labels Closed
7963 TaxonNamePopEditor: name part field visibility not correct for all ranks Closed
7881 reference selection combobox broken after error in ... Closed
7968 ReferenceEditor: optional validation for completenes of Partial values in datePublished Closed
8050 Create blocking registrations for un-registered names which are to be used in nomenclatural acts Closed
8097 Problem with inserting a section - inReference is "lost" Closed
8149 ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic and NULL Closed
8160 CdmBeanItemContainerFactory as readonly service bean Closed
8214 WeaklyRelatedEntityCombobox is not validated Closed
8176 WeaklyRelatedEntityCombobox is slow Closed
8184 SpecimenTypedesignationEditor: add new specimen broken Chrome browser Closed
8217 ToManyRelatedEntitiesComboboxSelect edit button not enabled Closed
8191 ReferencePopupEditor: When coming from NameEdior editing of the inreference should not be blocked Closed
8192 The curator must be able to unlock a published registration for edition Closed
8194 LazyInitializationException (LIE) on deleting the nomenclatural referenz (Section) of a Name Closed
8213 MySQLSyntaxErrorException with 'Submitter' user acessing view registration#!regStart Closed
8075 multiple cascade all-delete-orphan exceptions related to DefinedTermBase.representations Closed
8107 NPE when throwing PopupEditorException in AbstractPopupEditor Closed
8188 Allow configuring hibernate properties via properties file Closed
8099 Error saving name type designation editor due to problem in poupeditor context Closed
8218 Show appropriate error message when accessing RegistrationWorkingsetEditor without sufficient permissions Closed
8065 HibernateException: corrupt session problem breaks SpecimenTypeDesignationworkingsetEditor type designation table Closed
8158 cascade="all-delete-orphan" problem when .... Closed
  cdmadapter 1 Collapse all/Expand all
8175 add name facts to cdm light export Closed
  cdmlib 6 Collapse all/Expand all
7106 avoid factory.openSession() in CdmRepository Closed
7896 NPE, NullPointerException in RelationshipTermBase Closed
8104 TaxonName.getLastNamePart erroneously renamed .getFamiliyNamePart Closed
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
615 remove suns repository Closed
  cdmlib-remote 2 Collapse all/Expand all
8173 spring profile remoting enabled by default Closed
8096 Implement CacheUpdater as long running task with correct progress monitoring Closed
  taxeditor 28 Collapse all/Expand all
7865 Remaining factual data view label issues Resolved
7515 TypeDesignationStatusComparator to sort by vocabulary first and then by term order Resolved
8223 Urgent TaxonNode wizard issues Resolved
7428 Open issues for updating open data while subtree is updated Closed
7923 Add context menu and drag'n'drop to CharacterEditor Closed
7541 Insufficient rights lead to missing focus in name editor Closed
8115 NPE when moving factual data Closed
8147 Add "plural" to representation detail element Closed
8121 Allow selecting structural/property modifiers when creating a character Closed
8124 Activate Name Facts in Taxeditor Closed
8136 Implement sources for type designations in TaxEditor Closed
8143 It is possible to open multiple instances of the login dialog Closed
8146 Adapt taxeditor UI to structure and property term type Closed
8150 Allow editing the representation label of characters in details view Closed
8151 after creating a new synonym and pasting a name string the default string is not removed Closed
8197 Deleting Media from Image Gallery View does not make view dirty Closed
8211 Trigger new search when clicking on identifier search Closed
8228 refresh of details for same object in different bulk editors does not work Closed
8200 Changing title(cache) for factual data set not possible Closed
8225 Deleting one of two type designations removes both Closed
8234 Move description elements issues Closed
8222 Deleting a type designation from a name is directly persisted Closed
3836 Implement modifiers and modifying text for Description Elements in TaxEditor Closed
4545 Implement TeamOrPersonBaseSelectionDialog Closed
6413 [DISCUSS] How to create type duplicates (e.g. isotypes) for a taxon name Closed
8011 Implement term search view Closed
8111 User selection dialog for groups does not filter out existing users Closed
8148 Login Dialog cuts off information 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
7930 Remove DOI from journals, print series and person communications Closed
7918 Revision of reference type specific properties Closed
8030 Cache updater service methods externalized and base class specific Closed
7914 Add ISBN to IProceedings Closed
7915 Remove date published from journals and print series Closed
7913 Remove authorship from IJournal and IPrintSeries Closed
  cdm-dataportal 13 Collapse all/Expand all
7616 reference page: show name types Closed
7907 Annotations in Reference page do not respect the annotation settings Closed
7927 Registration not found, Portal handling registrations in preparation Closed
7947 registration page shows name relations Closed
7977 Registration page layout improved Closed
8056 WSOD in cdm_dataportal/search/results/taxon Closed
8048 Selenium test for Registration page Closed
8074 Registration page has fatal error when registration identifier in url path is ivalid Closed
7564 remove Phycobank - Registration data - block and other outdated registration code Closed
7974 Layout for Registration date Closed
8051 improve display of registration items lists Closed
8073 Registration page: show typified name for registrations covering typifications only Closed
8076 implement test for typified name for registration page Closed
  cdm-vaadin 45 Collapse all/Expand all
7559 possibly corrupted hiberante session after previous error on saving editor Closed
7245 validation of ToOneRelatedEntityCombobox not working Closed
7481 ReferenceEditor: filter inReferences by applicable reference type Closed
7846 PopupEditors show editor context information as 'breadcrumbs' in the header or toolbar. Closed
7870 RegistrationWorkingsetEditor: Internal error on clicking "new name" Closed
7888 TypeSpecimenEditor: Collection date should be timespan Closed
7878 Edit CollectionCode not saved Closed
7892 RegistrationWorkingsetEditor: LIE creating new name for book section Closed
7906 AbstractPopupEditor: Notify user on editor changes and provide options to choose from discard or save Closed
7900 Excessive heap consuption in RegistrationWorkingsetEditor with big workingsets Closed
7916 SpecimenTypeDesignationEditor: Map shows error radius Closed
7925 AbstractPopupEditor: exception handling in save method is incomplete Closed
7910 TeamOrPersonField: readonly exception on bindig data Closed
7937 TaxoNamePopupEditor: Exclude current name from name relationship comboboxes Closed
7944 TaxonNamePopEditor: name part fields are required Closed
7946 RegistrationStatusFieldInstantiator must set status value internally before adding the ValueChangedListener Closed
7949 New Registration: Reference combobox to offer two search modes Closed
7950 ToOneRelatedEntityCombobox: add new button "jumpes" to the right when hovering the mouse over Closed
7951 Reference Combobox option titles can be too long causing the select box to extend too much Closed
7956 RegistrationWorkingsetEditor refresh problem after saving TaxonNameEditor Closed
7995 Registration.registrationDate not set when status is set PUBLISHED Closed
8013 LazyInitializationException (LIE) in RegistrationDTO.makeBibliographicCitationStrings Closed
8031 Cannot add existing name to blank workingset Closed
8059 NPE when adding existing but un-registered name to workingset Closed
8063 multiple representations problem wirth collector being author of the registration citation Closed
8064 NPE in AbstractHibernateTaxonGraphProcessor.assureSingleTaxon() on saving new name for new registration with new genus Closed
7480 ReferenceEditor misses institution, organization and school fields Closed
7639 SpecimenTypeDesignationEditor: Altitude not saved and displayed properly Closed
7718 New Registration: Exclude irrelevant reference types from list of existing publications Closed
7866 Phycobank UI further label improvements Closed
7867 FieldGroup$BindException: The given field is not part of this FieldBinder in TeamOrPersonField Closed
7893 RegistrationWorkingsetEditor: canceling new name editor leaves the new name button disabled Closed
7899 enable orthographic name correction in Vaadin Closed
7905 NPE in InstitutionEditorPresenter Closed
7908 Redmine communication hub slows down RegistrationWorkingSets Closed
7942 SpecimenTypeDesignationEditor: Explanation on why editor can not be saved without type designation Closed
8039 NPE when creating new name in unsaved NameTypeDesignation for exising name in workingset which has no registration yet 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
8090 Reference editor: Label In proceedings in InProceedings missing Closed
7218 SpecimenTypedesignationsWorkingsetEditor: support for Reference system Closed
7919 GeoLocationField uses OpenTopoMap Closed
8072 Registration items in list view is using the wrong button icons for blocking regs and validation errors Closed
8069 RegistrationUI: remove all messaging related code and message indicators from all views Closed
7833 submitters can access see any registration in any RegistrationWorkingSet Rejected
  cdmadapter 1 Collapse all/Expand all
7903 Add treeIndex with rank to cdm light export Resolved
  cdmlib 6 Collapse all/Expand all
7874 TeamOrPersonBase entity can become unusable due to replacement of the title caches on using getters Closed
7939 TaxonNodeDTO need sortIndex of Rank Closed
8066 CdmUserHelper.createAuthorityFor() causes flush of pending transactions Closed
7600 public setters for entity collections Closed
7901 Make PreferencePredicates an interface to allow multiple implementations (e.g. for client apps, for grouping, for data type specific instances, etc.) Closed
7217 SpecimenTypedesignationsWorkingsetEditor: Longitute Latitude fields allow values in degrees minutes seconds formats 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
7849 Improve DB Preferences handling and saving in TaxEditor Feedback
7940 "New" menu in navigator not available for certain users Feedback
4227 handle generated resources in eclipse workspace Feedback
6805 Implement drag and drop from Term Editor (Feature) to FeatureTreeEditor Closed
6806 Add context menu to FeatureTreeEditor Closed
7163 Restructure preferences Closed
7668 NPE when changing author Closed
7680 Refactor TaxonNodeDetailElement Closed
7746 NPE when deleting volatile DescriptionBase Closed
7761 Invalid designations should be displayed like misapplied names in name editor Closed
7794 Update TaxonNodeWizard Closed
7737 Reference Details view does NOT give a multiple usage warning Closed
7854 Open issues in TaxDistributionEditor Closed
7856 Allow local override for distribution vocabularies Closed
7931 add symbol2 to term detailsview Closed
7934 sometimes the signs for deduplication are not shown Closed
7929 after delete of not persisted object in bulkeditor the object is still in bulkeditor list Closed
7985 Remove Print Series from InProceedings, use "Proceedings" Closed
7993 Display "Access Denied" dialog in case the remoting service responds with status code = 4xx Closed
7998 Store newly created Characters in selected vocabulary Closed
8026 details view is empty for some references in bulk editor Closed
7999 Allow override does not work correctly for distribution areas Closed
8041 PatternSyntaxException in FeatureTreeSelectionDialog Closed
5926 Update labels in TermEditor for Vocabularies Closed
6951 Drag and drop does not update term hierarchy in the UI Closed
7367 Deleting a term in the term editor does not update the UI Closed
7649 Term editor loads/saves extremely slow Closed
7806 GfBio Term Search issues Closed
7868 Allow creating a new vocabulary in vocabulary selection dialog Closed
7869 Run gfbio term service requests as background tasks Closed
7836 ClassCastException when invoking cdm light export with wrong selection Closed
7847 Use separate column for row state instead of symbol in titleCache column Closed
7871 Open character matrix as singleton Closed
7873 Implement copy&paste for feature nodes in feature tree editor Closed
7875 Add multiple area selection to descriptive data set editor Closed
7877 Form elements disappear in reference dialog after changing the reference type Closed
7887 Use DTOs in term editor Closed
7880 Implement centralized preference default loading strategy Closed
7933 Adding a new Term to the "Country" vocabulary leads to corrupt data Closed
7912 Enhance checkbox tree viewer Closed
7941 Deduplication does not work in new taxon dialog Closed
7954 protected vs. unproteced caches in TaxEditor Closed
8032 NPE when editing Local Prefs -> Factual Data Closed
8037 "Detail" is not saved in taxon node wizard Closed
7850 Further problems with term editor Duplicate

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

Issues: 54

Downloads: Ask the edit team for backups of this version

What's new?

  • Documentation

    • online webservice documentation was broken since 5.3. Fixed.
  • Dataportal

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

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

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

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

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

Downloads: Ask the edit team for backups of this version

Issues: 51

What's new?

  • General

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

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

    • Improved handling for types in CDM light export
  • TaxEditor

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

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

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

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

Downloads: Ask the edit team for backups of this version

Issues: 76

What's new?

  • General

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

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

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

    • TBC: name registration issues

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

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

Downloads: TaxEditor, CDM Server, Data Portal

Issues: 42

What's new?

  • General

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

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

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

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

# Subject Status
  cdm 2 Collapse all/Expand all
7468 Updated script for mediaCreated does not work for PostGreSQL Closed
7469 Updated script for individualCount column type in Postgres Closed
  cdm-dataportal 3 Collapse all/Expand all
7417 Make pro parte and partial synonym relationships always visible in data portals Resolved
6659 Show mediaCreated in dataportal Closed
7451 ExternalLinks [ext-links]: update search urls Closed
  cdm-vaadin 14 Collapse all/Expand all
7386 TaxonNamePopEditor: com.vaadin.data.Property$ReadOnlyException on saving a basionym Resolved
7223 ReferenceEditor: disable fields depending on the Reference type Feedback
7313 eu.etaxonomy.cdm.dataInserter.RegistrationRequiredDataInserter add all terms to vocabulary Closed
7338 Validate taxon name against the higher taxon name Closed
7364 TaxonNameEditor supports editing of a validated name Closed
7461 Add oder by ISSN an ISBN to the PagingProvider for all Reference comboboxes Closed
7453 Registration Workingsets inconsistent for registrations for sections of publications Closed
7458 Note field for TaxonName , NameType and SpecimenType editors Closed
7477 TeamOrPersonField: ToManyRelatedEntitiesListSelect blocks removing new entries Closed
7476 RegistrationWorkingSetEditor: existing name combobox broken after saving a popup editor Closed
7482 TaxonNameEditor relpacedSynonym not set after adding or editing the related name Closed
7475 error when saving Reference editor with new empty Person in Team when OK or NEW was not pressed Closed
7498 ClassCastException on saving popup editor for validated name Closed
7257 Activate Enter key to send login in vaadin login Closed
  cdmlib 7 Collapse all/Expand all
7478 Fix pro parte synonym search Resolved
4101 Default value for publish bit of new taxa must be configurable via DB preferences Closed
5477 lucene index not updated in all cases after Taxon.addMisappliedName Closed
7467 taxon name parts lookup method with support for wildcard searches Closed
7486 Fulltext taxon and name search not correct for Synonym based queries Closed
7340 OderedVocabularies are initialised with DefinedTerms Closed
7445 Empty term uri and isoXXX fields should be null Closed
  cdmlib-remote 2 Collapse all/Expand all
3560 Withheld unpublished taxa from webservice used in E+M dataportal Resolved
7508 Add language information to term representations Closed
  data 1 Collapse all/Expand all
7092 Adapt dates in Nicks images after mediaCreated became TimePeriod Resolved
  taxeditor 13 Collapse all/Expand all
4362 Some File->New dialogs do not work Feedback
4363 Show more informative message for unsupported specimen structures in specimen bulk editor Feedback
3984 Easier reference selection - recently used references Closed
7010 Adapt handlers for multiple selection in e4 views Closed
7422 Set nom. illeg as default in NomenclaturalStatusType ComboBox Closed
7472 lazy loading exception for MAN with type specimen Closed
7463 Move taxonnodes should be available for multiple selection Closed
7430 New team members should be added at the end of the member list Closed
7439 Use NatTable for BulkEditor Closed
7452 TitleCache is not correctly set for new Person Closed
7499 NPE when trying to open a taxon which belongs to 2 taxon nodes and cancel Closed
7464 make move Taxonnodes a longrunning task Closed
7227 New name bulk editor shows all menu entries Worksforme

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

Issues: 124

What's new?

  • General

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

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

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

# Subject Status
  cdm 17 Collapse all/Expand all
7096 Add second symbol attribute to DefinedTermBase Resolved
7334 Make pro parte and partial synonyms real concept relationships Resolved
2335 Make WorkingSet IdentifiableEntity Closed
6588 Add URL and URL comment to OriginalSource / ExternalLink Closed
6699 Delete term version from CdmMetaData Closed
6720 Make individualCount a string Closed
6752 Add verbatimDate Closed
6879 Update uuid and name for admin user group Closed
7144 Add country as level to all areas of type Country. Closed
6943 Allow zoological in-Authors in taxon names Closed
7074 Use TimePeriod for Media.mediaCreated Closed
7384 Order SpecimenTypeDesignationStatus according to new order in vocabulary Closed
7405 Rename WorkingSet to DescriptiveDataSet Closed
7285 Edaphobase import: implement ranks Cohort, Hyporder Closed
7109 Rename nom. valid to nom. val. Closed
7238 Rename lastName and firstName Closed
7277 Add micrometer to MeasurmentUnit Closed
  cdm-vaadin 24 Collapse all/Expand all
7244 DistributionStatus editor help Resolved
7249 NameTypeDesignationEditor delete not working Closed
7322 registration workingset editor handles multiple different submitters correctly Closed
7343 PersonField allows editing the nomenclaturalTitle Closed
7350 Collection date is not being saved Closed
7337 creating of new NameTypeDesignation for empty registration ends up without typified name Closed
7366 TeamOrPersonField readonly if users lacks edit permissions Closed
7382 SpecimenTypedesignationsWorkingsetEditor blocks saving as long as typeDesignations are missing Closed
7385 TaxonNameEditor adapt field visibility to rank Closed
7333 LIE when creating registration for existing name Closed
7425 Implement VerbatimTimeField for cdm-vaadin and use this in the ReferencePopupEditor Closed
7344 TaxonNamesEditor to fill authorship fields automatically if nomref and basionym are set? Closed
7353 SpecimenTypedesignationsWorkingsetEditor: error on saving after changing kindOfUnit Closed
7381 LIE (LazyInitializationException) when saving SpecimenTypeDesignationWorkingsetEditor for Registration with existing name Closed
7387 TaxonNamePopEditor: ConstraintViolationException on saving a basionym Closed
7241 Missing rights are not correctly indicated in Vaadin distribution editor - flexible vaadin errorhandler is needed Closed
7269 Use redmine as message hub for submitter curator communication Closed
7355 TaxonNamePopupEditor: newly created nomenclatural reference should be selected immediately Closed
7349 RegistrationPopupEditor fails saving new References with new Team with 2 new memers Closed
7359 cdm popuop editors in readonly mode if the user is not permitted to edit Closed
7365 enable CdmPopupEditors to operate on CdmDecoratorDTOs Closed
7314 support for dot and comma in Georeferenz, Error radius, Altitude, Distance to ... Closed
6707 transient properties managed by ToManyRelatedEntitiesListSelect are not updated on save Duplicate
7363 TaxonNameEditor supports replaced synonyms Duplicate
  cdmlib 11 Collapse all/Expand all
8183 Make Feature IndividualAssociation a generalization of Specimen and Observation In Progress
7323 RegistrationVoter ignores uuid if propery given Closed
7354 DerivedUnitConverter handles associated SpecimenTypeDesignation correctly Closed
7360 users NOT having DELETE are permitted to delete References Closed
7392 Remove Cascade from relations Closed
7209 use git repos instead of svn in all pom.xml Closed
7287 Unit tests using the DefaultTermInitializer break subsequent integration tests in the suite Closed
7289 hibernate warning HHH90000003 pollutes log files Closed
7308 Add nomen oblitum to zoological taxon name status Closed
7368 cdm entities report persistence state Closed
7390 possible permission clash when adding basionym Duplicate
  data 1 Collapse all/Expand all
7374 Set titleCache of feature trees to protected as long as i18n support does not yet exist. Closed
  documentation 3 Collapse all/Expand all
6572 Adapt/Add Wiki pages for e4 development Closed
7001 Show date and/or version-number on taxeditor download site Closed
6158 Update EDIT documentation from svn to git Closed
  taxeditor 68 Collapse all/Expand all
6804 Order areas in Distribution Selection Editor Resolved
7284 Multiple taxeditor jars created in p2 update for a single jenkins build Resolved
3746 Implement time period scope for description elements in TaxEditor Closed
5783 Rename demo instances back to demo I and demo II Closed
6219 Deleting synonym is persisted immediately, but the editor is set dirty Closed
5687 search for alternative identifiers Closed
5696 When selecting a new name for a given taxon the name relationships are not updated Closed
6533 New taxon wizard does not refresh is excluded and excluded note information Closed
6389 Returning a Map in cdmlib leads to data loss Closed
6568 Migrate perspectives Closed
6668 NPE in DetailsView when deleting a type specimen Closed
7239 Rename last name by family name and first name by "Other/given names" Closed
7282 Still remaining feature tree editor issues Closed
7292 TaxonSelectionDialog throws error when searching for '?' Closed
7279 p2 sites are extremely huge Closed
7295 When creating homotypic synonym the accepted taxon and new synonym are not shown anymore Closed
7307 Synonyms should not be shown when creating a new concept relation Closed
7320 dirty flag is not set when clicking "Erneuere Knoten" in Polytomous Keynode editor Closed
7325 Taxeditor uses CdmTransientEntityCacher from cdmlib-cache Closed
7291 PolytomousKey Node should not allow to search for synonym Closed
7300 NPE when selecting team member after merge in bulkeditor Closed
7326 NPE when setting focus on specimen in Specimen Editor (hierarchy) Closed
7378 doubtful in misapplied names incorrect Closed
7379 right click menu of accepted taxa should not show "change to" Closed
7393 Fix regressions resulting from cascade removal from relationships in TaxEditor Closed
2450 DateTime field - Old values do not get deleted if you enter a new value to the parse field Closed
6455 Remove not possible for country in field/derived unit details view Closed
6526 Show types in correct order Closed
6437 Always update titleCache for nomenclatural reference Closed
6565 [MASTER] Eclipse 4 Migration Closed
6779 Allow drag&drop for features in GrantedAuthority editor Closed
6909 Migrate taxon navigator Closed
6913 Remove e3 parts and dependencies Closed
6925 Migrate general framework Closed
6746 Implement DetailsView and show SupplementalDataView for Feature Tree and FeatureNode Closed
6769 Usages can not be created anymore in usage perspective Closed
6838 Implement i18n for FeatureTreeEditor Closed
6931 Migrate uses view Closed
6973 Refreshing details and supplemental view Closed
7009 Replace part descriptor IDs in open handler with AppModel constants Closed
7102 Enable EDIT and DELETE for specimen determinations Closed
7226 Name relationship Dialog shows same name Closed
7031 Open in referencing objects view must not show "Open in referencing Objects" Closed
7079 P2 updates not found Closed
7215 Implement pro parte misapplied names in TaxEditor Closed
7230 Refresh in name editor does not work if using "reuse taxon" in Misapplied Name View (e4) Closed
7268 Re-implement own preference dialog Closed
7324 Add "Open in.." for GatheringEvents in ReferencingObjectsView Closed
7290 Creating the first node in a new polytomous key throws NPE Closed
7328 Add label provider for GatheringEvent in referencing objects view Closed
7329 Unify naming for both specimen editors (bulk and hierarchy) Closed
7336 Implement partial misapplied names in TaxEditor Closed
7335 Allow editing of pro parte and partial synonyms in the same way as misapplied names in the NameEditor Closed
7399 Adding taxon nodes to working sets leads to MultipleRepresentationException Closed
7421 Implement verbatim date for references in TaxEditor Closed
7395 Selection of nomenclatural code does not work in new taxon dialog Closed
2380 TaxonNavigator should work with DTO objects instead of full blown cdm instances Closed
5637 Selecting a new name for a taxon does not update the details view Closed
6330 Defined sort order for Mediarepresentations Closed
7065 When updating a subtree the affected and opened taxa are not updated in name editor this needs to be handled Closed
7312 some preferences are saved immediately, cancel has no effect Closed
7411 adapt mediaCreated in taxeditor to timePeriod Closed
3161 Term Editors are no singletons Closed
6318 Truncate TextData in FactualData View Closed
4136 authorship part of names not being refreshed in taxon navigator Closed
5193 Changing the name of a taxon does not refresh the taxon navigator Worksforme
7301 Refresh open name editors when deleting specimen used in type designation Worksforme
4048 Changing the name in free text editor does not refresh the taxon navigator view Worksforme

  • Browser Editor (Vaadin)

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

# Subject Status
  cdm 17 Collapse all/Expand all
7096 Add second symbol attribute to DefinedTermBase Resolved
7334 Make pro parte and partial synonyms real concept relationships Resolved
2335 Make WorkingSet IdentifiableEntity Closed
6588 Add URL and URL comment to OriginalSource / ExternalLink Closed
6699 Delete term version from CdmMetaData Closed
6720 Make individualCount a string Closed
6752 Add verbatimDate Closed
6879 Update uuid and name for admin user group Closed
7144 Add country as level to all areas of type Country. Closed
6943 Allow zoological in-Authors in taxon names Closed
7074 Use TimePeriod for Media.mediaCreated Closed
7384 Order SpecimenTypeDesignationStatus according to new order in vocabulary Closed
7405 Rename WorkingSet to DescriptiveDataSet Closed
7285 Edaphobase import: implement ranks Cohort, Hyporder Closed
7109 Rename nom. valid to nom. val. Closed
7238 Rename lastName and firstName Closed
7277 Add micrometer to MeasurmentUnit Closed
  cdm-vaadin 24 Collapse all/Expand all
7244 DistributionStatus editor help Resolved
7249 NameTypeDesignationEditor delete not working Closed
7322 registration workingset editor handles multiple different submitters correctly Closed
7343 PersonField allows editing the nomenclaturalTitle Closed
7350 Collection date is not being saved Closed
7337 creating of new NameTypeDesignation for empty registration ends up without typified name Closed
7366 TeamOrPersonField readonly if users lacks edit permissions Closed
7382 SpecimenTypedesignationsWorkingsetEditor blocks saving as long as typeDesignations are missing Closed
7385 TaxonNameEditor adapt field visibility to rank Closed
7333 LIE when creating registration for existing name Closed
7425 Implement VerbatimTimeField for cdm-vaadin and use this in the ReferencePopupEditor Closed
7344 TaxonNamesEditor to fill authorship fields automatically if nomref and basionym are set? Closed
7353 SpecimenTypedesignationsWorkingsetEditor: error on saving after changing kindOfUnit Closed
7381 LIE (LazyInitializationException) when saving SpecimenTypeDesignationWorkingsetEditor for Registration with existing name Closed
7387 TaxonNamePopEditor: ConstraintViolationException on saving a basionym Closed
7241 Missing rights are not correctly indicated in Vaadin distribution editor - flexible vaadin errorhandler is needed Closed
7269 Use redmine as message hub for submitter curator communication Closed
7355 TaxonNamePopupEditor: newly created nomenclatural reference should be selected immediately Closed
7349 RegistrationPopupEditor fails saving new References with new Team with 2 new memers Closed
7359 cdm popuop editors in readonly mode if the user is not permitted to edit Closed
7365 enable CdmPopupEditors to operate on CdmDecoratorDTOs Closed
7314 support for dot and comma in Georeferenz, Error radius, Altitude, Distance to ... Closed
6707 transient properties managed by ToManyRelatedEntitiesListSelect are not updated on save Duplicate
7363 TaxonNameEditor supports replaced synonyms Duplicate
  cdmlib 11 Collapse all/Expand all
8183 Make Feature IndividualAssociation a generalization of Specimen and Observation In Progress
7323 RegistrationVoter ignores uuid if propery given Closed
7354 DerivedUnitConverter handles associated SpecimenTypeDesignation correctly Closed
7360 users NOT having DELETE are permitted to delete References Closed
7392 Remove Cascade from relations Closed
7209 use git repos instead of svn in all pom.xml Closed
7287 Unit tests using the DefaultTermInitializer break subsequent integration tests in the suite Closed
7289 hibernate warning HHH90000003 pollutes log files Closed
7308 Add nomen oblitum to zoological taxon name status Closed
7368 cdm entities report persistence state Closed
7390 possible permission clash when adding basionym Duplicate
  data 1 Collapse all/Expand all
7374 Set titleCache of feature trees to protected as long as i18n support does not yet exist. Closed
  documentation 3 Collapse all/Expand all
6572 Adapt/Add Wiki pages for e4 development Closed
7001 Show date and/or version-number on taxeditor download site Closed
6158 Update EDIT documentation from svn to git Closed
  taxeditor 68 Collapse all/Expand all
6804 Order areas in Distribution Selection Editor Resolved
7284 Multiple taxeditor jars created in p2 update for a single jenkins build Resolved
3746 Implement time period scope for description elements in TaxEditor Closed
5783 Rename demo instances back to demo I and demo II Closed
6219 Deleting synonym is persisted immediately, but the editor is set dirty Closed
5687 search for alternative identifiers Closed
5696 When selecting a new name for a given taxon the name relationships are not updated Closed
6533 New taxon wizard does not refresh is excluded and excluded note information Closed
6389 Returning a Map in cdmlib leads to data loss Closed
6568 Migrate perspectives Closed
6668 NPE in DetailsView when deleting a type specimen Closed
7239 Rename last name by family name and first name by "Other/given names" Closed
7282 Still remaining feature tree editor issues Closed
7292 TaxonSelectionDialog throws error when searching for '?' Closed
7279 p2 sites are extremely huge Closed
7295 When creating homotypic synonym the accepted taxon and new synonym are not shown anymore Closed
7307 Synonyms should not be shown when creating a new concept relation Closed
7320 dirty flag is not set when clicking "Erneuere Knoten" in Polytomous Keynode editor Closed
7325 Taxeditor uses CdmTransientEntityCacher from cdmlib-cache Closed
7291 PolytomousKey Node should not allow to search for synonym Closed
7300 NPE when selecting team member after merge in bulkeditor Closed
7326 NPE when setting focus on specimen in Specimen Editor (hierarchy) Closed
7378 doubtful in misapplied names incorrect Closed
7379 right click menu of accepted taxa should not show "change to" Closed
7393 Fix regressions resulting from cascade removal from relationships in TaxEditor Closed
2450 DateTime field - Old values do not get deleted if you enter a new value to the parse field Closed
6455 Remove not possible for country in field/derived unit details view Closed
6526 Show types in correct order Closed
6437 Always update titleCache for nomenclatural reference Closed
6565 [MASTER] Eclipse 4 Migration Closed
6779 Allow drag&drop for features in GrantedAuthority editor Closed
6909 Migrate taxon navigator Closed
6913 Remove e3 parts and dependencies Closed
6925 Migrate general framework Closed
6746 Implement DetailsView and show SupplementalDataView for Feature Tree and FeatureNode Closed
6769 Usages can not be created anymore in usage perspective Closed
6838 Implement i18n for FeatureTreeEditor Closed
6931 Migrate uses view Closed
6973 Refreshing details and supplemental view Closed
7009 Replace part descriptor IDs in open handler with AppModel constants Closed
7102 Enable EDIT and DELETE for specimen determinations Closed
7226 Name relationship Dialog shows same name Closed
7031 Open in referencing objects view must not show "Open in referencing Objects" Closed
7079 P2 updates not found Closed
7215 Implement pro parte misapplied names in TaxEditor Closed
7230 Refresh in name editor does not work if using "reuse taxon" in Misapplied Name View (e4) Closed
7268 Re-implement own preference dialog Closed
7324 Add "Open in.." for GatheringEvents in ReferencingObjectsView Closed
7290 Creating the first node in a new polytomous key throws NPE Closed
7328 Add label provider for GatheringEvent in referencing objects view Closed
7329 Unify naming for both specimen editors (bulk and hierarchy) Closed
7336 Implement partial misapplied names in TaxEditor Closed
7335 Allow editing of pro parte and partial synonyms in the same way as misapplied names in the NameEditor Closed
7399 Adding taxon nodes to working sets leads to MultipleRepresentationException Closed
7421 Implement verbatim date for references in TaxEditor Closed
7395 Selection of nomenclatural code does not work in new taxon dialog Closed
2380 TaxonNavigator should work with DTO objects instead of full blown cdm instances Closed
5637 Selecting a new name for a taxon does not update the details view Closed
6330 Defined sort order for Mediarepresentations Closed
7065 When updating a subtree the affected and opened taxa are not updated in name editor this needs to be handled Closed
7312 some preferences are saved immediately, cancel has no effect Closed
7411 adapt mediaCreated in taxeditor to timePeriod Closed
3161 Term Editors are no singletons Closed
6318 Truncate TextData in FactualData View Closed
4136 authorship part of names not being refreshed in taxon navigator Closed
5193 Changing the name of a taxon does not refresh the taxon navigator Worksforme
7301 Refresh open name editors when deleting specimen used in type designation Worksforme
4048 Changing the name in free text editor does not refresh the taxon navigator view Worksforme

Previous Releases Archive

see CdmPlatformRoadmapArchive

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