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Release 5.5

7 days late (01/17/2019)

22%

383 issues   (48 closed — 335 open)

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Estimated time 125.10 hours
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Related issues
bug #1866: BookDefaultCacheStrategy does not show free text date published
bug #2850: Error message on empty distribution
bug #3370: ExternalLinks [ext-links]: External services: GBIF: add infraspecific taxa
bug #4348: Remove InputDialog in creating new bulk editor entities where not needed
bug #4707: LSID Authority service cannot find CoL LSIDs
bug #4847: Problem with session attributes for a UI used in different CDM Instances
bug #5095: URGENT : Fix failing dozer related tests
bug #5211: Error when creating new taxon /problem with sortindex in taxon tree
bug #5371: all name parts of taxa with flag doubtful = true are displayed in italic
bug #5440: Make maps showup with volatile areas and fix tests for EditGeoService
bug #5601: [DISCUSS] Creation of database structure via remoting
bug #5639: NPE when showing name relationships for a name originally related to a deleted name
bug #5651: Automatic deduplication of teams does sometimes duplicate team members
bug #5774: cdmserver misses to detect some errors in failed instances
bug #5823: Fehler beim parallel Editieren von Referenzen
bug #5832: It is not possible to search for hybrids in taxon search
bug #5905: remove empty homotypic-synonymy-group and clean up the synonymy page spacing and separator borders
bug #5926: Update labels in TermEditor for Vocabularies
bug #5964: It is not possible to search for hybrid formulas in taxon search
bug #6064: Edaphobase problems with webservices
bug #6192: taxon annotations only shown when 'Show accepted taxon on top of the synonymy' is enabled
bug #6250: bbox transformation for EPSG:900913 layers from the edit mapservice responses is broken
bug #6276: Nomenclatural references show parsed date string instead of publication year
bug #6287: Rolling cdmserver.log file only contains entries from startup phase
bug #6325: Handling of specimen imported via biocase with missing nomenclatural code
bug #6356: taxontree sort order as in editor
bug #6359: Remaining issues secundum for subtrees
bug #6380: typedesignations missing in homotypic group
bug #6402: palmweb: remove comment module related code and disable comments
bug #6406: Refactor MarkupTransformer class which is too large
bug #6414: use short name for excluded, unplaced taxa when the genus of the parent taxa is different
bug #6499: Remaining issues to include pages in bibliographic reference titleCaches
bug #6500: Remaining issues for volume formating in generic references
bug #6523: misspellings: display order of for- and to-taxon swapped
bug #6546: Adding identifier does not always work
bug #6609: Google Map layers are not working
bug #6627: Remaining cdm light issues
bug #6643: fix message shown in case the shown taxon is not in the chosen classification
bug #6652: [Discuss] misapplied names: hide protologue icon
bug #6814: Use CSL (Citation Style Language) for formatting citations
bug #6823: php Warning: Illegal string offset '#value' in compare_description_element_render_arrays() - line 421
bug #6951: Drag and drop does not update term hierarchy in the UI
bug #6952: Deleting terms does not get reflected in the UI and in the DB
bug #6960: Improve reference cachestrategy
bug #6963: Implement cache strategy for cultivars, bacterial names
bug #6971: Collect all remaining appearances of multiple representation exceptions since 4.10
bug #6975: improve preferred media calculation algorithm in cdmlib
bug #6976: improve preferred media calculation algorithm in dataportal
bug #6982: OriginalSource idNamespace + idInSource separator must be configurable
bug #7034: 4 busy database connections after application start
bug #7045: portal/classification/{uuid}/childNodesOf/{uuid} service slow
bug #7051: SpecimenOrObservationBase.getOriginalUnit() unimplemented but used 2x
bug #7075: Excel import for images
bug #7085: cdmserver logfiles getting too big, use DailyRollingFileAppender
bug #7087: description/accumulateDistributions webservice can not be triggered
bug #7093: choosing representation which best fits the available size for taxon profile picture not working in all cases
bug #7105: potential dangerous use of factory.openSession()
bug #7106: avoid factory.openSession() in CdmRepository and in DaoBase
bug #7113: Adapt SQL Server dialect to support all data types
bug #7145: NPE when trying to move a synonym into another homotypic group
bug #7245: validation of ToOneRelatedEntityCombobox not working
bug #7272: implement test for misapplied names in search results
bug #7278: Import in Authors correctly in Edaphobase
bug #7293: improve display of keys in tabless taxon page
bug #7321: multi-language textfields should not show empty text when there is text
bug #7342: incomplete bean initialization with specific data causes LIEs
bug #7367: Deleting a term in the term editor does not update the UI
bug #7373: TitleAndNameCacheAutoInitializer needs to be adapted to recent TaxonName model changes
bug #7426: remaining issues of change of navigator to DTOs
bug #7454: illegal argument exception for name selection in details view
bug #7465: adapt test to the change in move taxon operation
bug #7471: Invalid use of DefaultPager
bug #7480: ReferenceEditor misses institution, organization and school fields
bug #7481: ReferenceEditor: filter inReferences by applicable reference type
bug #7487: Full text misapplied name search with area filter uses fixed relation type uuid
bug #7493: Review all references to SynonymRelationshipTypes and adapt code if needed
bug #7512: Saving in Specimen Tree View creates unwanted scrolling on windows
bug #7519: Avoid static terms
bug #7521: refresh of taxonnavigator sometimes does not work for moving taxonnodes
bug #7522: Show warning if the someone has changed data in a registration graph which is not a currently authenticated curator when RegistrationState > PREPARATION
bug #7541: Insufficient rights lead to corrupted UI handling
bug #7559: possibly corrupted hiberante session after previous error on saving editor
bug #7564: remove Phycobank - Registration data - block and other outdated registration code
bug #7577: Set Publish Flag for Subtree Dialog - Further Problems with Progressmonitor
bug #7606: kompact display of CDM Point data
bug #7616: reference page: show name types
bug #7623: missing or broken import issues for ABCD import
bug #7639: SpecimenTypeDesignationEditor: Altitude not saved and displayed properly
bug #7649: Term editor loads/saves extremely slow
bug #7668: NPE when changing author
bug #7689: Mutliple representation exception when creating taxon nodes
bug #7699: NPE when searching for specimen in bulk editor
bug #7703: Multiple names cannot be shown in TypeDesignationDetailElement for specimens
bug #7709: CdmTransientEntityCacher cannot handle multiple unpersisted entities of the same type
bug #7711: Bugs in Media view
bug #7716: Apply description sources (references) for a DescriptionBase to all included description elements
bug #7732: layout issues for the media details view
bug #7733: show warning for multiple usage of media for SpecimenMedia
bug #7737: Reference Details view does NOT give a multiple usage warning
bug #7746: NPE when deleting volatile DescriptionBase
bug #7767: Incorrect handling of secundum detail reference in formatter
bug #7794: Update TaxonNodeWizard
bug #7817: Team caches should not show '& al.'
bug #7829: Improve deduplication of parsed names and references
bug #7832: rename RegistrationStatus READY to COMPLETE
bug #7833: submitters can access see any registration in any RegistrationWorkingSet
bug #7836: ClassCastException when invoking cdm light export with wrong selection
bug #7849: Improve DB Preferences handling and saving in TaxEditor
bug #7850: Further problems with term editor
bug #7856: Allow local override for distribution vocabularies
bug #7858: names used in the TaxonGraph can not be deleted if the user has no DELETE permission on Taxon
bug #7867: FieldGroup$BindException: The given field is not part of this FieldBinder in TeamOrPersonField
bug #7870: RegistrationWorkingsetEditor: Intenral error on clicking "new name"
bug #7874: TeamOrPersonBase entity can become unusable due to replacement of the title caches on using getters
bug #7877: Form elements disappear in reference dialog after changing the reference type
bug #7878: Edit CollectionCode not saved
bug #7879: Book CacheStrategy does not show 'place published', 'publisher', 'editor'
bug #7880: Implement centralized preference default loading strategy
bug #7892: RegistrationWorkingsetEditor: LIE creating new name for book section
bug #7893: RegistrationWorkingsetEditor: canceling new name editor leaves the new name button disabled
bug #7895: registrationWorkingSetDTO/{uuid} fails dur ot IndexOutOfBoundsException in RegistrationWorkingSet
bug #7896: NPE, NullPointerException in RelationshipTermBase
bug #7900: Excessive heap consuption in RegistrationWorkingsetEditor with big workingsets
bug #7904: DerivedUnitFacadeFieldUnitCacheStrategy.getCollectorAndFieldNumber() creates temporary Team objects which can not be garbage collected.
bug #7905: NPE in InstitutionEditorPresenter
bug #7907: Annotations in Reference page do not respect the annotation settings
bug #7908: Redmine communication hub slows down RegistrationWorkingSets
bug #7910: TeamOrPersonField: readonly exception on bindig data
bug #7913: Remove authorship from IJournal and IPrintSeries
bug #7915: Remove date published from journals and print series
bug #7916: SpecimenTypeDesignationEditor: Map shows error radius
bug #7924: LazyInitializationException (LIE) in taxon/{uuid}/synonymy.json when used with subtree filter
bug #7925: AbstractPopupEditor: exception handling in save method is incomplete
bug #7929: after delete of not persisted object in bulkeditor the object is still in bulkeditor list
bug #7930: Remove DOI from journals, print series and person communications
bug #7933: Adding a new Term to the "Country" vocabulary leads to corrupt data
bug #7934: sometimes the signs for deduplication are not shown
bug #7938: cdmserver sub-processes (threads) with constant high cpu
bug #7939: TaxonNodeDTO need sortIndex of Rank
bug #7940: "New" menu in navigator not available for certain users
bug #7941: Deduplication does not work in new taxon dialog
bug #7944: TaxonNamePopEditor: name part fields are required
bug #7946: RegistrationStatusFieldInstantiator must set status value internally before adding the ValueChangedListener
bug #7950: ToOneRelatedEntityCombobox: add new button "jumpes" to the right when hovering the mouse over
bug #7951: Reference Combobox option titles can be too long causing the select box to extend too much
bug #7956: RegistrationWorkingsetEditor refresh problem after saving TaxonNameEditor
bug #7969: Default Feature Tree created on serverside contains only one featureNode but this is used in a loop
bug #7974: Layout for Registration date
bug #7985: Remove Print Series from InProceedings, use "Proceedings"
bug #7994: Adding an already existing feature to a feature tree results in doubled entries
bug #7995: Registration.registrationDate not set when status is set PUBLISHED
bug #7998: Store newly created Characters in selected vocabulary
bug #7999: Allow override does not work correctly for distribution areas
feature request #2489: strategy for congruent areas in distribution maps
feature request #3747: Check if time period scope is handled correctly in data portals
feature request #3749: Check if all molecular data is shown correctly in data portal [also DISCUSS]
feature request #4227: handle generated resources in eclipse workspace
feature request #4488: Specimen data points in map should show FieldUnit information
feature request #4570: Add vocabulary for Specimen Description Features
feature request #4817: German translation for term types
feature request #4866: Implement clone method for complete classifications
feature request #5172: TaxonInteraction - add ";" and space between records and change order
feature request #5176: TransmissionEngineDistribution can run on selected taxa
feature request #5232: use TaxonBase.getTaggedTitle to get the sec reference in theme_cdm_taxonRelationships()
feature request #5334: reimplement the taxonnavigator to allow drag & drop between two nodes
feature request #5550: Add languages to the editable terms
feature request #5882: option (as new default) to show full citation of accepted name below taxon page title
feature request #5890: Implement auto-suggest for data portal
feature request #5935: use double line to separate concept relations from homotypic groups
feature request #6113: webserivce to expose FieldUnits related to a Taxon as KML and/or GML
feature request #6203: Implement unplaced and excluded in dataportal
feature request #6270: Feature Description, customized order, granular references
feature request #6305: [MASTER] Improve EDITOR import/export UI configuration panel for all imports/exports
feature request #6310: second search block
feature request #6316: display source references of media objects in media page
feature request #6394: Allow additional taxon relationships in TaxEditor to be handled similar to misapplications
feature request #6443: Feature block settings: enable sorting of TextData elements
feature request #6486: Implement handling of IntextReferences in dataportal
feature request #6516: Add instance name and instance ID to CDM meta data
feature request #6554: The details views are newly created with every change of the focus
feature request #6704: Make profile picture clickable and opening in lightbox
feature request #6732: rank selector offering 2 filtered lists of ranks (default, all) for phycobank
feature request #6772: Implement cancel for ProgressMonitorController
feature request #6774: Implement OWL export
feature request #6805: Implement drag and drop from Term Editor (Feature) to FeatureTreeEditor
feature request #6806: Add context menu to FeatureTreeEditor
feature request #6946: configurable titleCaches for specimen
feature request #7072: Nomenclatural cache for References
feature request #7163: Restructure preferences
feature request #7193: Implement area filter and rank filter in TaxEditor for exports
feature request #7217: SpecimenTypedesignationsWorkingsetEditor: Longitute Latitude fields allow values in degrees minutes seconds formats
feature request #7218: SpecimenTypedesignationsWorkingsetEditor: support for Reference system
feature request #7309: Implement collector titlecache in tax editor
feature request #7408: [E+M] Support for preferred common names in data portal
feature request #7413: Make zoological inAuthors editable in TaxEditor
feature request #7428: Open issues for updating open data while subtree is updated
feature request #7433: new service method to get specimen by genetic AccessionNumber
feature request #7434: while importing sequences it should be possible to download fasta file
feature request #7450: Allow setPublish for subtree to include misapplied names and pro parte synonyms
feature request #7457: E+M: Allow filtering for only published in search
feature request #7503: Make cells in bulk editor editable
feature request #7517: Make search parameters like wildcards configurable
feature request #7599: treeView for specimen data in dataportal
feature request #7600: public setters for entity collections
feature request #7610: Type search in PhycoBank Portal
feature request #7620: RegistrationSearch implemented with Reference filter
feature request #7637: Handle intext references in CDM light
feature request #7652: add possibility to delete only the taxon node and keep the taxon in taxon navigator
feature request #7662: Better icons for create, new, add row, remove row
feature request #7664: Use typified return types where possible
feature request #7666: Remaining issues for "Formatter and DTO for taxon relationships (e.g. misapplied names)"
feature request #7669: Greece import Willing images
feature request #7670: [DISCUSS] Do we need right click "save" menu
feature request #7680: Refactor TaxonNodeDetailElement
feature request #7685: Add Selenium tests for specimen table in data portal
feature request #7695: web service providing compact TypeDesignation representation for homotypic groups and individual taxa
feature request #7696: use compact type representations in the synonymy as provided by the typedesignations/byTaxon/{taxon_uuid} service
feature request #7718: New Registration: Exclude irrelevant reference types from list of existing publications
feature request #7747: reduce space between fields in external links section
feature request #7755: Implement detail page for field unit
feature request #7761: invalid designations should be displayed like MAN in name editor
feature request #7782: for a new synonym it should be possible to change it to missaplied name without saving
feature request #7806: GfBio Term Search issues
feature request #7820: Add cron job for deleting cdmserver log files after a specified time period
feature request #7841: identifier search: filtering by identifier types
feature request #7847: Use separate column for row state instead of symbol in titleCache column
feature request #7860: [Master] Remaining E+M editor issues
feature request #7861: TaxonGraphHibernateListener: inject the ITaxonGraphDao into TaxonGraphBeforeTransactionCompleteProcess
feature request #7864: Use short forms in cache strategy for DescriptionBase
feature request #7865: Remaining factual data view label issues
feature request #7868: Allow creating a new vocabulary in vocabulary selection dialog
feature request #7869: Run gfbio term service requests as background tasks
feature request #7871: Open character matrix as singleton
feature request #7873: Implement copy&paste for feature nodes in feature tree editor
feature request #7875: Add multiple area selection to descriptive data set editor
feature request #7887: Use DTOs in term editor
feature request #7888: TypeSpecimenEditor: Collection date should be timespan
feature request #7899: enable orthographic name correction in Vaadin
feature request #7901: Make PreferencePredicates an interface to allow multiple implementations (e.g. for client apps, for grouping, for data type specific instances, etc.)
feature request #7902: Allow default values for PreferencePredicates
feature request #7903: Add treeIndex with rank to cdm light export
feature request #7906: AbstractPopupEditor: Notify user on editor changes and provide options to choose from discard or save
feature request #7912: Enhance checkbox tree viewer
feature request #7914: Add ISBN to IProceedings
feature request #7919: GeoLocationField uses OpenTopoMap
feature request #7920: possibility to define areaspecific status selection
feature request #7922: Add possibility to save distributions created with the distribution editor in their own description
feature request #7923: Add context menu and drag'n'drop to CharacterEditor
feature request #7927: Registration not found, Portal handling registrations in preparation
feature request #7931: add symbol2 to term detailsview
feature request #7932: Implement subject resolver for CdmPreferences
feature request #7937: TaxoNamePopupEditor: Exclude current name from name relationship comboboxes
feature request #7942: SpecimenTypeDesignationEditor: Explanation on why editor can not be saved without type designation
feature request #7947: registration page shows name relations
feature request #7949: New Registration: Reference combobox to offer two search modes
feature request #7954: protected vs. unproteced caches in TaxEditor
feature request #7968: ReferenceEditor: optional validation for completenes of Partial values in datePublished
feature request #7970: Default Feature Tree Preference
feature request #7972: explicitly allow disallow access to HTTP Invoker endpoints (/remoting/**)
feature request #7975: improve display of name relations
feature request #7977: Registration page layout improved
feature request #7978: registration search result orderd by identifier descending
feature request #7993: Display "Access Denied" dialog in case the remoting service responds with status code = 4xx
task #2494: replace garland_cichorieae_cdm_taxon_list_thumbnails by settings
task #3320: Correct use of CdmApplicationDefaultConfiguration
task #4338: [MASTER] Handle abbreviated title and protected cache correctly in TaxEditor
task #4911: improve performance of distributionInfoFor service
task #5083: Alternative image viewer for dataportal [DISUSS]
task #5203: Adapt layout for login
task #5375: cdm-server without jsvc
task #6137: Urgent imports
task #6481: Sort out synonym relationships with 2 invalid taxa (Edaphobase)
task #6510: Import Rank labels in German and Latin
task #6518: Remaining minor issues for edaphobase webservices
task #6521: Check existing imports for handling new synonym structure correctly
task #6522: package cdm-server in docker container
task #6537: Import Edaphobase descriptive data
task #6590: Check if CdmVaadinAuthentication is a proper solution for handling authentications and SecurityContexts
task #6753: Edaphobase data issues before import
task #6778: remove big objects from taxeditor git repository
task #7214: discuss unexpected method behaviors in CdmTransientEntityCacher
task #7332: Registration Workingset Editor: better UI behavior with blocking Registation in same workingset
task #7515: TypeDesignationStatusComparator to sort by vocabulary first and then by term order
task #7565: cdm_taxontree remove all code for using the tree to browse drupal term taxonomies
task #7587: ToOneRelatedEntityReloader to listen and operate on PropertyDatasources directly?
task #7650: RegistrationFactory implemented
task #7651: RegistrationManager implemented
task #7811: Import higher classifications
task #7843: blocking registrations can get lost when first TaxonNamePopupEditor with new name is not saved
task #7846: PopupEditors show editor context information as 'breadcrumbs' in the header or toolbar.
task #7854: Open issues in TaxDistributionEditor
task #7866: Phycobank UI further label improvemenst
task #7890: Display of name relations in the data portal [master ticket]
task #7917: Revise ReferenceSystemTerms
task #7918: Revision of reference type specific properties
task #7961: Consider removal of the TaxonNamePopupEditorMode ORTHOGRAPHIC_CORRECTION
report #7089: Rights and Roles Workshop 2017-11
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