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Recent Releases of TaxonWorks

TaxonWorks - Version 0.49.0 release

Added

  • Cross link DwcOccurrence to Otu in filters (with fixes on others)
  • /api/v1/field_occurrences/:id/dwc
  • /api/v1/otus/:id/inventory/determined_to_rank
  • Append mode to multi update data attributes task #4204
  • <in progress Batch add/remove Protocols>
  • Protocol is_machine_output attribute to facilitate MachineObservation types
  • Batch change Protocol references
  • Sticky navbar on browse nomenclature and collecting event
  • Move button to citations and depiction slices in radial annotator
  • Freeze column checkbox to filter tasks #4220
  • Sort layout columns on filter tasks #4219
  • Field occurrence panel to Browse OTU
  • Field occurrence attributes to DwcOccurrence
  • Browse field occurrence
  • Filter field occurrences
  • Field occurrences appear in OTU inventory endpoints
  • Taxon names with gender filter facet
  • Subject/object restrictions in filter nomenclature #3094

Changed

  • Filter attribute facet now more precise
  • DwcOccurrence by otu_id now checks FieldOccurrence as well
  • Updating a Person updates DwcOccurrence across projects
  • All updates to DwcOccurrence are via delayed jobs
  • Add total to unmatched panel on Nomenclature match task
  • Prevent user destroy last saved TD on New FO task #4225
  • Updated Ruby gems and Node packages
  • Navigation bar layout

Fixed

  • SimpleMappr output for large results
  • Synonymy section of Edit Nomenclature alphabetically sorted
  • Duplicate CollectingEvents filtered when Collectors facet used
  • FieldOccurrences not destroyable
  • DwcOccurrences being updated out of scope
  • Unescaped search strings on Project vocabulary
  • &sort=alphabetical|classification param to /taxon_names/
  • AssertedDistributions duplicating because of is_absent state #4226
  • verbatim_label not batch loading to "Castor" form #4230
  • Otu content export rendering exceptions
  • ObservationMatrixColumItem show rendering
  • Rendering of Identifier::Local::RecordNumber
  • Reset button is not working on Unify people
  • Import dataset description uniqueness validation failing to detect duplicate
  • CSD: It is not possible to add new taxon determinations to an existing CO #4227
  • New FO, CE Panel: Saved identifiers aren't loaded in the UI on page reload #4241
  • Unify object task: reset button doesn't clear autocompletes #4242
  • Capybara/Chrome testing
  • Venn queries with nested elements (candidate fix) #4224, #3983

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 month ago

TaxonWorks - Version 0.48.0 release

Added

  • Browse Field Occurrence task #4200
  • Help for Project Vocabulary task UI fields #4192

Changed

  • Sort asserted distributions alphabetically in Quick Forms
  • Update taxon nomenclatural date after source update
  • Updated Ruby Gems

Fixed

  • Failure to set dwc_occurrences for rebuild for background processing
  • New collecting event task: Identifier panel sets and displays an incorrect identifier number #4208
  • Comprehensive digitization sometimes failing to save identifiers #4206
  • Bad link when creating a synonym where the old name has children and then clicking the green edit button in Edit Taxon Name #4196
  • Taxon names not being displayed in relationships facet of Filter Nomenclature task. #4193

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 3 months ago

TaxonWorks - Version 0.47.0 release

Added

  • Use Rails 7.2 and Ruby 3.3.6
  • New image task: Add field occurrence to depict some list #4135
  • Grab cursor to make sorting feature visible #4153
  • API endpoint for image matrix
  • Order of depictions coming from the image matrix
  • Hub tasks: Add visual effect for fav icons and tooltip for categories #4177
  • Distribution to COLDP exports #3148
  • Taxon links to COLDP exports
  • SpeciesInteraction to COLDP exports #3158
  • Specs and optimizations to COLDP
  • Pull metadata from ChecklistBank in order to merge updated metadata into COLDP exports
  • Filter's match identifiers facet can now be quickly accessed with shift-ctrl-m in a modal form
  • gift facet to Filter loans.
  • Multi data attribute update task #4142
  • Keys are now multifurcatable #4148
  • Identical Document validation
  • Some inline help and visual improvements #4177
  • Keys can be cloned, merged, and inserted to #4056
  • API endpoint for serving Image matrices

Changed

  • Match identifiers defaults to match Identifier, not internal, \n, and caseless match #4176
  • Added Gift status notices to loans form #4174
  • Improved and clarified DwcOccurrence indexing concepts and application
  • Improved writing to cached* fields for TaxonName

Fixed

  • Fixes to TaxonWorks CSL style
  • Bug in Image autocomplete
  • CatalogNumbers attached to Containers not appearing in CollectionObject tag #4163
  • OriginRelationship creation for Sequences #4180
  • CSD: change of namespace not updating #4147
  • TaxonWorks bibliography style for book chapter.
  • Removed obsolete Description table from COLDP exports
  • Remove [sic] from COLDP name fields #3833
  • Autonym synonyms bug in COLDP exporter #4175
  • New taxon name: Show only subject relationships on Relationships section
  • Images added before saving field occurrence are not saved #4134
  • Rendering Family group names from invalid names #4187
  • Verbatim latitude not displaying #4178

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 3 months ago

TaxonWorks - Version 0.46.1 release

Fixed

  • Add citation back to gallery endpoint #4136

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 5 months ago

TaxonWorks - Version 0.46.0 release

Added

  • Topics can be unified #4106
  • Task - Controlled vocabulary terms across projects #4112
  • Source filter can operate on cached_* fields enabling link to project vocabulary #4123
  • /api/v1/otus/:id/inventory/images?sort_order= param to sort by class of Depiction object type
  • Task - Simplemappr (https://www.simplemappr.net) export support from Filter collection objects
  • Print key task #4071 #4117
  • /api/v1/leads/key/:id endpoint serving pinpoint key app
  • Filter loans: Identifiers, created by and updated by columns #4098
  • Edit/New loan task: Add none status option
  • Edit/New Field occurence task: biological associations panel #4103
  • Edit/New Field occurence task: depictions panel #4108
  • Matrix row coder task: Now and Today lock buttons #4110
  • More TaxonName soft validations

Fixed

  • /api/v1/otus/:id/inventory/images out of context depictions #4129
  • Unifying related BiologicalAssociations #4099
  • Async DwcOccurrence refreshes that referenced destroyed objects
  • FieldOccurrence Radial Navigator
  • Unify objects: Same object can be selected on both sides #4100
  • New taxon name: Cannot create new combination (under ICN) #4127
  • Syncronize misspellings #4109
  • Blank terms to /autocomplete endpoints raising
  • Rendering subspecies names in botany
  • TypeMaterial autocomplete
  • Some async DwcOccurrence updating callbacks

Changed

  • /api/v1/otus/:id/inventory/images response structure
  • Update Gemfiles

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 5 months ago

TaxonWorks - Version 0.45.0 release

Added

  • Created/updated overviews for user data
  • Unify objects task #970
  • Attribution to ObservationMatrix
  • New biological association task #4026
  • Duplicate OTU predictor task #4083
  • DwcOccurrenceHooks for BiocurationGroups, OTUs
  • New image task: is original checkbox to source panel #4090
  • Confidence facets and batch operations to all Filters #4043
  • Browse nomenclature task: Radial annotator for OTUs

Changed

  • RecordNumber identifiers can be duplicated (namespace + identifier combinations) across CollectionObjects #4096
  • Local identifier display in CollectionObject tag now prefers position to break tie with RecordNumber and CatalogNumber #4074
  • Filter CO: Show only current taxon determination #4092

Fixed

  • Loan OTU facet #4087
  • With/out facets failing in combination with other facets #4089
  • Simple TaxonName batch load failing with invalid children
  • api/v1/images/:id broken for non-integer ids
  • Containerizing objects prevented identific increments
  • New dichotomous key: Radial annotator is not loading the correct data #4076

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 6 months ago

TaxonWorks - Version 0.44.3 release

Added

  • dwc_occurrence_id[] param to dwc_gallery endpoint
  • Image matrix link to radial linker and radial matrix

Fixed

  • Date received facet on loans #4067
  • api/v1/images/975145cf4d25d7ed35893170abc2e852 style calls finding images by id, not fingerprint #3918

Changed

  • Updated Ruby gems
  • In DwC Import Otu name is now only set via use of identificationQualifier

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 7 months ago

TaxonWorks - Version 0.44.2 release

Added

  • Sort by identifier match option #4065
  • /collection_objects/123/dwc_compact - DwC fields for those populated #3994
  • Pagination to /api/v1/otus/:otu_id/inventory/dwc_gallery

Fixed

  • Display of missing DwC fields #4051
  • verbatim_field_number updates ignored #4066
  • DwC importer verbatim_field_number collision with Identifier validation
  • Shortcuts: Keys pressed are not removed after user switches windows/tab

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 7 months ago

TaxonWorks - Version 0.44.1 release

Added

  • /api/v1/otus/:id/inventory/keys a list of keys scoped to or containing the Otu
  • otu_id to ObservationMatrix, to facilitate setting scope and indexing of multi-entry keys
  • is_public flag to ObservationMatrix

Changed

  • Revert strict verbatim_field_number validation #4061
  • Renamed CollectingEvent verbatim_trip_code to verbatim_field_number #4058

Fixed

  • DwC eventDate should not be populated without an explict year reference #4053
  • DwC month should not be populated when range-provided #4055

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 7 months ago

TaxonWorks - Version 0.44.0 release

Added

  • Create container task #3038
  • Endpoint crossreferencing dwc_occurrences and images api/v1/otus/:otu_id/inventory/dwc_gallery.json?per=1&page=2
  • Creating depictions of CollectionObjects now updates their DwcOccurrence automatically
  • Filters: Custom button to records per page selector #4032
  • New asserted distribution: Confidence panel #4044

Changed

  • Updated Ruby gems

Fixed

  • DwcOccurrence now actually selects the valid name on export
  • OTU taxonomy inventory API endpoint crashing on protonyms with no cached year and author.
  • DwC importer column indexing confusion when there are blank headers
  • Filter collecting event: Remove duplicate radial linker #4050

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 8 months ago

TaxonWorks - Version 0.43.3 release

Added

  • With/out facets for Loan dates #3729
  • FieldNumber local identifier sensu DwC
  • RecordNumber local identifier sensu DwC #4016
  • DwC importer support for FieldNumber and RecordNumber #4016 #3800
  • DwC export support for FieldNumber, RecordNumber
  • New RecordNumber panel for Comprehensive Digization
  • Filter Otu: With/without common names
  • Radial annotator: Add sort to identifiers slice #4021
  • extend[]=valid_name to /taxon_names
  • Valid name column in filter nomenclature

Changed

  • DwC export will now use a valid taxon name if linked first to an invalid, and it is available
  • EventID and verbatim_trip_code are disentangled in DwC Importer, they do not map to one-another now #3800 #2852
  • TripCode is now FieldNumber (all data migrated)
  • DwcOccurrence rebuilds triggered for changes to TaxonNameRelationship #4019, TypeMaterial, TaxonDetermination, Identifier::Global
  • Wikidata IDs are now also loaded into recordedByID and identifiedByID #3989
  • Sort order of descendant inventory
  • Removed net-pop gem workaround for Ruby 3.3.3
  • Facet geographic area: Spatial mode by default
  • Facet nomenclature rank: Remove selected ranks from select input
  • Updated Ruby gems
  • New taxon name task: Add manual mode for subsequent combinations section when taxon rank is not in the list #4009
  • Optimized performance of Combination name rendering and use
  • Filters with Geographic area facet default to 'Spatial'

Fixed

  • Header labels print without higher taxonomy #4030
  • Staged images tab on collection object report
  • Non-integer identifier start/end ranges raising
  • Various facets in Filter OTUs not being scoped to unique records
  • Saving a bad identifier from annotator fails to show message why
  • Download formatted references as PDF
  • Quickly clicking save before load-in on Comprehensive can detach CollectingEvent from CollectionObject
  • Filter collecting events: data attribute table view is empty #4013
  • Field synchronize: URI Too Large error when user pass a long query #4017
  • DwC importer crashing on record with blank basisOfRecord #4024

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 8 months ago

TaxonWorks - Version 0.43.2 release

Added

  • all button to predicate selector in Field Synchronize #4005
  • recent_target parameter to filters, one of updated_at (default) or created_at #4004
  • verbatim_name facet to Filter Nomenclature
  • Soft validation (and fix) identifying redudant use of verbatim_name in Combinations

Changed

  • Comprehensive Specimen Digitization: Prevent user add duplicate types for type materials #4002
  • Improved visual differentiation of Sandboxes

Fixed

  • Fixed Loan rendering when date_sent is blank #4001
  • New combination: Links in Other matchespanel didn't work

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 9 months ago

TaxonWorks - Version 0.43.1 release

Changed

  • Updated gems

Fixed

  • Integer type checking impacting AssertedDistribution filter
  • Editing DataAttributes trigger complete re-index of the DwcOccurences #4000
  • Misspelled DwcOccurrence attribute

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 9 months ago

TaxonWorks - Version 0.43.0 release

Added

  • Task to add image and as depictions to the objects identified in their filename #3986
  • PDF version of styled/formatted source download #3996
  • Type checking pattern for integers sent to *_id params in the API
  • Radial annotator: Pagination to depictions slice
  • Comprehensive: Pagination to depictions panel
  • Browse collection objects Pagination to depictions panel
  • Filter source: add ID to list #3984
  • TW_DISABLE_DEPLOY_UPDATE_DATABASE env var to disable DB backup and migration at deploy time.

Changed

  • repositories/autocomplete label #3981
  • Updated Ruby gems

Fixed

  • TaxonName filter Original combination with/out facet (both with and without)
  • Removed deprecated GoogleMap georeference form #3991
  • Print label generation #3992
  • Generating a TaxonWorks Download for a bibtex result failing #3997
  • Removed bad foreign-key constraint on BiocurationClassifications, TaxonDeterminations
  • Content autocomplete not scoped to projects
  • Some hotkeys don't work on Firefox on Linux #3988
  • Cancel previous autocomplete requests #3982

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 9 months ago

TaxonWorks - Version 0.42.0 release

Added

  • Nexus file import #2029
  • POST /annotations/move?from_global_id=<>&to_global_id=<>&only[]=&except[]=
  • Clone CollectingEvent can include annotations, incremented identifiers
  • Model Identifier::Local::Event in part: #3800
  • Task - DwcOccurrence status
  • /api/v1/taxon_names/origin_citation.csv, taxon names plus their origin citation
  • Reasonable min/max elevations hard validations
  • Increased scope of string cleaning #3947
  • DwcOccurrence filter on all attributes
  • DwcOccurrence visible in Project vocabulary
  • Confirmation modal on mass annotator #3969
  • TW_ACTION_MAILER_SMTP_SETTINGS_USER_NAME, TW_ACTION_MAILER_SMTP_SETTINGS_PASSWORD and TW_ACTION_MAILER_SMTP_SETTINGS_AUTHENTICATION_TYPE env vars for container deployments

Fixed

  • CE batch update collectors #3936
  • Broken BiologicalAssociation scope for DwC download #3949
  • NeXML render to screen #3961
  • People queries referencing use_min and use_max in combination with other facets
  • /observation_matrix_column/list
  • Queries referencing emtpy identifier_start or end failing
  • Moving depiciton from an Otu could fail in some cases
  • OTU inventory endpoint failing when synonyms are empty
  • CachedMap metadata raises when out-of-date
  • Encoding unencodable text as Code128 breaks label preview
  • Identifier between range breaks filter when blank params passed
  • DwcIndex failing to update on Georeference, Role, BiocurationClassification, TaxonName, InternalAttribute changes
  • Sometimes URL parameters are set incorrectly in facets.
  • A COLDP export name and taxon remarks bug #3837
  • Project dump not working when all params were supplied #3967
  • Radial annotator: Selected object in "Move to" section is not displayed in Depictions slice
  • Project SQL export failed to export tables with NULL project_id.
  • Spatial Summary of the results in Filter Collecting Event "URI too large error" #3937

Changed

  • Upgraded to Rails 7. #3819
  • Changed default URL protocol to HTTPS for TaxonWorks-generated e-mails in production environments
  • Added bootsnap gem to speed up boot times. tmp/cache dir is used as cache by this gem
  • Removed versions_associations and shortened_urls tables from Project SQL export
  • Replace validations modal in Browse nomenclature task #3974
  • Updated Ruby gems
  • Georeference error_radius rounded to nearest meter before save #3946

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 10 months ago

TaxonWorks - Version 0.41.1 release

Added

  • An extended biological associations API endpoint #3944

Fixed

  • Empty higherClassification included ""
  • Resaving Image resets height/width and original filename
  • New image from Data raising from path error
  • Filters: JSON request URL overflows container when too long
  • PDF Button is missing in Filter Sources
  • DwC Import task: Replace dialog shows undefined instead the current value
  • Radial annotator: Data attributes can't be deleted from the list
  • Radial quick forms: Collecting event slice doesn't render correctly
  • CSD: In some cases, the locking mechanism does not work correctly #3941

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 12 months ago

TaxonWorks - Version 0.41.0 release

Added

  • Field synchronizer task- batch edit (regex too), update and syncronize columns and between columns
  • misspelling option to API taxon_name_relationship_set[]

Changed

  • Gemfile update
  • Improvements(?) to Collecting Event level classifier #3821

Fixed

  • Asynchronous batch updates on individual objects
  • Invisible edges in biological associations graph viz
  • PDF button is available for all document types #3933

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly 12 months ago

TaxonWorks - Version 0.40.6 release

Changed

  • Updated Ruby gems

Fixed

  • Notes params not applied in Source filters (anywhere) #3927
  • OTU autocomplete raises when no taxon names match
  • CSD: Catalog number panel displays warning messages when the namespace is set

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.40.5 release

Added

  • /api/v1/taxon_name_relationships.csv endpoint

Changed

  • Dwca otu_name only includes Otu#name, never anything else.
  • api/v1/otus/autocomplete now more acurately returns the label of the matching term, i.e. Combinations are supported in rendering [https://github.com/SpeciesFileGroup/taxonpages/issues/193]
  • Update Ruby gems

Fixed

  • Quick forms: Lock buttons don't work on Biological associations.
  • Week in review task #3926
  • Missing Image metadata breaks radial
  • Basic endemism task had a broken link out
  • Prevent raise on bad polygon (LinearRing) Georeferences

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.40.4 release

Added

  • User estimated time tracking at the per-project level
  • Orphaned DwcOccurrence and DelayedJob job metadata to admin Health report

Changed

  • Unified some methods on dwca export, refactored for speedups and memory
  • Updated Ruby gems

Fixed

  • Dwca error from missmatched ids leading to bad sorts
  • Manage controlled vocabulary task: New button resets type #3923
  • Resource is spelled recource #3922

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.40.3 release

Changed

  • Browse OTU: Replace descendants endpoint for the same used on TaxonPages. Now this panel is available for all ranks

Fixed

  • 2 issues with taxon names autocomplete (internal and api/v1)

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.40.2 release

Added

  • "Venn" factets to filter- logical operations on filter results #3908
  • Sort column on project vocabulary task #3915

Fixed

  • New collecting event: It tries to save the label even if it is empty
  • Spatial summary return to filter with empty cached level fields #3907
  • Comprehensive form: Sometimes Attributes are not cleaned when new collection object is created #3910
  • DwC importer crashing when uploading files with CSV extension.
  • DwC importer not honouring field and string delimiters when processing headers
  • DwC importing wrongly allowing unreadable files to be staged

Changed

  • Updated Ruby gems.

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.40.1 release

Added

  • Some more quality-of-life changes to Leads/keys
  • Spatial summary report for CollectingEvent filter
  • Geographic Area radial navigator links to associated filters
  • Radial nomenclature: verbatim_author slice #3896

Changed

  • Gems updated

Fixed

  • Async batch update calls on individual objects failing #3905
  • DwC export without CollectingEvents failing #3897
  • Cloning CollectingEvents sets creator to the person who cloned the record
  • Filter Staged Images missing filter button #3901

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.40.0 release

Added

  • Model FieldOccurrence (observations sensu iNaturalist), with corresponding "new" task #1643
  • Model "Lead" (dichotomous key support), with corresponding "new" task" #1691
  • Key hub task #3881
  • New OTU task
  • "Week in review" task, visualize records added and navigate to them in filter context
  • OTU name to Filter CO result #3861
  • Batch add/remove sources to project from Source filter #3888
  • Add taxon name autocomplete to Type specimen facet
  • DwC Dashboard: Use the same DwC download of collection object filter task
  • DwC-A Workbench: Add pagination for created imports
  • Clone mode on image matrix
  • Radial CO: Add preparation type slice #3889
  • Radial mass navigation #3672
  • Batch update or add data attributes #3748
  • !! TODO: Include OTU name in filter collection objects result [#XXXX]
  • Text file delimiter options to DwC import #3894
  • CSV format for DwC importer

Changed

  • Images can no longer be duplicated attempting and are seemlessly normalized at creation #2909
  • Filter images: Remove quick forms for Depictions #3869
  • New image task: Add alert when trying to restart the interface without applying changes
  • New CE: Destroy label when print label input is empty #3878
  • Updated Ruby gems
  • DwC importer now defaults to use " as string delimiter when importing and downloading tables.

Fixed

  • Project vocabulary handling of numeric fields
  • Rediculous number of identifiers preventing collecting event editing #3715
  • Community-based models not showing AlternateValues #3883
  • Browse OTUs: headers do not link to correct panel #3868
  • DwC-A importer crashing on hybrid formula scientific names
  • Crash when georeferencing with zero meters of uncertainty
  • New CE: Custom attributes don't refresh on new/edit CE [#3874]
  • Radial quick forms: Asserted distribution screen partially blocked by a white rectangle #3891
  • Print label task doesn't apply styles to labels #3776
  • Missing collection object links on map markers
  • Handling of [sic] in Protonym#original_combination_infraspecific_element [#3867]

Special thanks to Tom Klein for his amazing open-source contributions on this release!.

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.39.0 release

Added

  • Project vocabulary task #864
  • Global identifier classes for Web of Science and Zoological Record #3853
  • /api/v1/biological_associations/simple.csv endpoint
  • Return a png of any image via /api/v1/images/:id/scale_to_box(/:x/:y/:width/:height/:box_width/:box_height) #3852
  • content_type and original_png attributes to /api/v1//images/123 #3852
  • Ability to extend housekeeping on some filters to check changes on related models #3851
  • Some new soft validations on Misspellings

Fixed

  • Handle bad BibTeX coming back from CrossRef.
  • Quick Forms: Observation matrices slice doesn't work
  • Quick Forms: Content slice doesn't display contents #3850
  • Browse OTU: Load preferences
  • New loan task: reset button doesn't work #3856
  • New image task doesn't create citations without attributions
  • Missing pagination headers for 4 endpoints #3859

Changed

  • Allow omitting seconds in non-interval ISO-8601 date times in DwC importer.

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.38.3 release

Added

  • /api/v1/common_names #3794
  • /api/v1/biological_associations/simple A simple table format for BiologicalAssociations
  • Housekeeping facet in filters has "Recent" button with options to populate past date ranges
  • Radials to New image task

Fixed

  • DwC download not scoping DataAttributes correctly when records are a subset of objecs from a CollectingEvent
  • DwC Dashboard buttons scoped to recent timeframes #3774
  • A couple .csv endpoints for /api/v1
  • Radial annotator: Filter tab doesn't work in depictions slice #3824
  • Filters: Geographic area facet doesn't clear geographic area after reset #3840
  • Radial collection object: Taxon determination list is not visible
  • Align metadata in GeographicItem debug view
  • Biological associations filter bugs
  • Several radial annotator and batch annotator slice fixes
  • DwC checklist importer fails quietly when taxonomicStatus is empty #3783

Changed

  • Documents are no longer destroyed when the last documentation referencing them are deleted.
  • Use Ruby 3.3
  • CI build/test with PostgreSQL 15
  • CI base image uses Node 20

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.38.2 release

Added

  • Highlight row on click in DwC Importer #3795
  • Batch update CollectingEvent from CollectionObject filter radial
  • Batch update meta_prioritize_geographic_area from CollectingEvent filter radial #3498

Fixed

  • CollectionObject summary nomenclature tag failing when no names are present
  • Papertrail views for most models were failing
  • Syncronized winding of polygons and multipolygons #3712, and others
  • DataAttribute alignment in DwC, take 3 #3802
  • Radial Annotator: Citation count no longer updates #3806
  • Radial Annotator: Depiction count no longer updates #3813
  • Radial annotator: Attribution slice loads incorrect records
  • Image matrix: OTU depictions cells are not displaying the correct images when otu_filter parameter is set
  • New combination task freezes in some cases
  • SQL project dump duplicating hierarchies tables rows causing index creation to fail on restore
  • OtuPicker doesn't display OTU label when a new OTU is created in New loan task [#3809]

Changed

  • All polygons and multi_polygons in GeographicItems are wound to CCW after save
  • Updated Ruby gems

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.38.1 release

Fixed

  • DwC dumps cross-mapping attributes between CollectingEvent and CollectionObject (for real?) #3802
  • Favorite cards section layout
  • Radial batch triggers "re-search" when nothing is changed
  • Custom attributes component loads auto filled with incorrect values #3805
  • DwC importer crashing on real DwC-A zip archives when first table rows are not headers.

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.38.0 release

Added

  • GeographicItem debug task
  • documentation_object_type and documentation_object_id to documentation filter

Changed

  • Use zeitwerk loading framework #2718

Fixed

  • DwC dumps cross-mapping attributes between CollectingEvent and CollectionObject #3802
  • Staged Image filter failing on some identifier queries
  • TaxonName batch update
  • Contributing link #3752
  • Uncaught promise errors #3767
  • Custom attributes triggers isUpdated ce state #3764
  • Custom attributes panels don't check if data attributes already exist #3762
  • Gender agreement of misspellings [#3782]
  • Loan item list doesn't update when adding a loan item from Tag or Pinboard #3784
  • Unable to add a CO loan item to a loan that already has an OTU loan item with the same id #3785
  • CO Loan gifts have tag "On Loan until false" #3731
  • Figure panel in New content task
  • DwC Occurrence Importer using out of project scope http://rs.tdwg.org/dwc/terms/FossilSpecimen biocuration class.
  • Hub: Status filter doesn't work correctly #3791
  • Hub: Left and right arrow keys on task hub don't work as expected. #3792

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 1 year ago

TaxonWorks - Version 0.37.1 release

Added

  • Emendavit status for ICN names #3716
  • "CONFIRM" screen when editing a collecting event with > 100 attached COs #3727
  • epithet_only parameter and facet to taxon name filter #3589
  • Links for users profiles on project members list (only for administrators)
  • Cursor and text to reveal project preference predicates can be reordered #3736
  • Batch append collectors to Collecting Events within CE filter
  • Batch set Collecting Event date and time within CE filter
  • Darwin Core superfamily, subfamily, tribe, subtribe export support
  • Darwin Core exporter: include Notes from most recent TaxonDetermination as identificationRemarks
  • Save user's custom layout tables #3756 #3307 #3568

Changed

  • DwC Occurrence Importer: Parse authorship information in typeStatus field
  • DwC Exporter: recordedBy and identifiedBy fields use First Prefix Last Suffix order
  • Project member list now has links for users profiles (only for administrators)

Fixed

  • dwc_occurrence_id param to /api/v1/dwc_occurrences
  • Another project_id scope issue in Otu Filter
  • Update DwcOccurence index endpoint
  • Uniquify people: Always show radials for selected person
  • Remove property doesn't work on Biological relationship composer
  • Feet to meter conversion does not work as expected #2110
  • OTUs autocomplete API endpoint ignoring having_taxon_name_only param
  • DwC importer creating multiple namespaces instead of just one for occurrenceID and eventID
  • Combination always visible #3366
  • Copy text from PDF

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.37.0 release

Added

  • DwC verbatimLabel support #2749
  • Preview option and results reports for filter based batch updates #3690
  • Freeform digtization, draw shapes to stub CollectionObjects #3113
  • superfamily, tribe and subtribe DwC terms now supported in occurrences importer [#3705]

Changed

  • Improved simplified taxonomy rendering
  • Unifies all filter-originating batch updates to a common look and feel #3690
  • Report file size to browser for downloads
  • DwC Checklist Importer: blank originalNameUsageID skip original combination creation instead of erroring #3680

Fixed

  • Ordering of descriptors in TNT format [#3711]
  • Some ObservationMatrix views/formats were broken or unavailable for preview
  • DwC-A checklist importer: fix importer crash caused by nil parent
  • Address rendering on loan form #3645
  • Citation topic whitespace for paper catalog #187
  • Source filter with duplicate results when coming from another filter #3696
  • ancestrify parameter for Otu queries not scoping to TaxonNames correctly
  • Filter source: BibTeX type facet
  • Project data SQL export obfuscating all users instead of just non-members
  • Project data SQL export outputting only two rows per hierarchy-related tables
  • AssertedDistributions API index call failed when OTU not linked to taxon name
  • Missing valid names in nomenclature match task
  • DwC Occurrence Importer: prefer correct protonym spelling when misspelling matches current conjugation

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.36.0 release

Added

  • Staged image CollectionObjects are destroy if a) stubs and b) depictions are removed from them to another CollectionObject #3172
  • /api/v1/biological_associations/123/globi (preview experiment)
  • /api/v1/biological_associations/123/resource_relationship (preview experiment)
  • BiologicalAssociations as raw TaxonWorks data/api/v1/biological_associations.csv
  • BiologicalRelationships as raw TaxonWorks data/api/v1/biological_relationships.csv
  • DwC ResourceRelationship extension (preview) #2554
  • Taxonomy summary to CollectionObject summary report
  • Metadata summary report from Filter BiologicalAssociations
  • Biological associations simple table preview, sortable columns #1946
  • GLOBI format table from Filter BiologicalAssociations (preliminary)
  • Family by genera report from Filter BiologicalAssociations
  • DwC ResourceRelationship extension preview from Filter BiologicalAssociations
  • Visualize network from Filter BiologicalAssociations
  • BiologicalRelationship can have Identifiers
  • "ancestrify" option to TaxonName and Otu filters (adds ancestors of filter result)
  • Auto UUIDs as new Identifier::Global::Uuid::Auto for models
  • Auto UUIDs are created for BiologicalAssociations and OTUs
  • Maintenance Task to add UUIDs to objects that can have them but don't
  • TaxonName model to customize attributes
  • TaxonNameRelationship model, added validation for the rank of type species and type genus.
  • New source task: Person source
  • Index view to API for /depictions
  • Added extend[]=role_counts to /person/123.json
  • Batch update OTU taxon_name within OTU filter #3656
  • DwC Checklist importer: support "invalid", "incorrectOriginalSpelling" taxonomic Status
  • DwC Checklist importer: option to match and update existing names rather than create new hierarchy from Root
  • DwC Occurrence importer: search for repository URL

Changed

  • CachedMaps of ancestors are set for rebuild when a descendant Georeference or AssertedDistribution is created
  • Radial annotator: Move selected source to the bottom in citation form #3652
  • DwC Occurrence importer: more helpful protonym, institution error messages
  • Filter interfaces: remove items from list instead redirect to data view #3659
  • New BiologicalAssociation defaults to task, not old form
  • Extracted CSV generating code to lib/export/csv

Fixed

  • Buttons to remove BiologicalProperties in composer failing #3673
  • Could not destroy BiologicalRelationship if properties attached
  • Some CollectionObject summary values were not scoped to filter query
  • Filtering People returned duplicate values one name string searches
  • BiologicalAssociations passed to TaxonNames missed object names
  • Nulified cached values in Collecting Event, if Geographic area deleted #3668
  • Match TaxonName based on original combination #3365
  • Radial AD: Quick/recent selector broken on "Move". #3640
  • New taxon name: Author panel overflow when source has a long link
  • Edit Loan: Loans created without recipient or supervisor cannot be updated
  • Fixed bug in DwC importer background processor that was not dealing with errored records.
  • Browse OTU: autocomplete overflow #3667
  • Comprehensive: Relationship doesn't show up on biological associations list #3671
  • DwC Occurrence importer: protonyms could not be found if authorship information didn't match
  • DwC Occurrence importer: protonyms could not be found if author was Person #3677
  • DwC Checklist importer: empty scientificNameAuthorship field would cause row to error #3660
  • DwC Checklist importer: subsequent combinations with synonym status whose parents are synonyms would cause row to error
  • Could not set Repository Index Herbariorum flag in interface
  • Uniquify People: autocomplete would not select people for merging if already present in Match people table

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.35.3 release

Added

  • Radial collection object: Add repository #3637

Changed

  • CachedMaps (WebLevel1) is now based on "State" shapes only, improving resolution
  • CachedMap build process adds pre-build step to greatly minimize overall number of spatial calculations
  • CachedMap spatial calculations use a intersection + "smoothing" approach
  • Also use year of publication to determine correct protonyn having homonyms #3630
  • Improved error message when typeStatus name is a homonym in DwC occurrences importer #3632

Fixed

  • Duplicate loans appearing Loan filter [#3636]
  • New source when cloned and saved is not added to the project sources #3629
  • Sequence display when not a Primer
  • CachedMap indexing speedups failed to properly utilize prior work
  • Duplicate CachedMapRegister rows being created per object
  • New Image task, second "Apply" button is not working #3628
  • ' [sic]' not removed when searching for synonyms in database to compare with typeStatus in DwC occurrence importer #3633

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.35.2 release

Changed

  • Update Gemfiles
  • CachedMap algorithm, now far more precise.
  • Browse OTU: Image gallery section is now available for all ranks #3612
  • Map saves tile preferences #3619

Fixed

  • Anyone can destroy a Community (Global) identifier on a Community object #3601
  • Newfoundland/CAR mapping issue #3588
  • Role callbacks interfered with creation of nested objects #3622 !! Potentially breaking fix !!
  • Queries to /api/v1/sources not scoping to project when project_token used #3623
  • CollectionObject summary report tab clicks
  • Cached map preview incorrect/default GeographicItem id for GeographicAreas
  • Collection object summary report bad link
  • Task Biological associations graph: Save fails when trying to update a graph
  • Role picker doesn't show organization name when created #3611
  • Spinner hangs when apply fails in New Images task #3620

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.35.1 release

Changed

  • Doubled the number of favoritable tasks to 40 #3600

Fixed

  • TaxonPage stats, maybe, who knows at this point.
  • Images for OTU type material expanded to all protonyms
  • Reset project preferences #3599
  • Project TSV dump permissions on server side
  • Clone moved CVT, not cloned project

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.35.0 release

Added

  • Outdated names task for CollectionObjects (compare to COL) #2585
  • Unified project data download task #1009, in part
  • Download project as zipped TSV tables in Download #1009
  • CSV generating endpoints /api/v1/taxon_names.csv and /api/v1/otus.csv
  • Filter CollectionObject links to "Collection Summary" task #3434
  • CollectionObject type facet
  • Coordinate and collecting event sections in Browse OTUs

Changed

  • Download routes now name files as .tsv
  • CollectingEvent allowable max records made smart #3590
  • Added extend[]=attribution to /images/123.json

Fixed

  • TaxonNameClassification download
  • TaxonName descendants facet always included self, it shouldn't have
  • Without document facet
  • Object cloning in OriginRelationship caused infinite loops #3594
  • Quote handling in API autocomplete calls
  • Organization name not displaying in attribution copyright label
  • Manage Controlled vocabulary term: CVT list is not reloading after clone them from other project
  • Not possible to delete asserted distribution once added in radial object #3591
  • Manage controlled vocabulary: Delete button doesn't work #3593

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.34.6 release

Added

  • WKT and GeoJSON endpoints for /geographic_items/123.wkt
  • Clone ControlledVocabularies across projects #3562
  • Batch move taxon names to a new parent within TaxonName filter #3584
  • Batch update Source with a Serial within Source filter #3561
  • Browse nomenclature hierachy nav counts of invalid/valid link to filter
  • Reset forms for user preferences and project card favorites #3545
  • Otu RCC5 relationships to the COLDP exporter [#3569]
  • Filter images slice in radial linker #3574
  • Name relations to Catalogue of Life data package exports [#1211]
  • Type Materials to Catalogue of Life data package exports [#3213]
  • Filter list: Add border to highlight the last row where a radial was opened #3583

Changed

  • Update Gemfile
  • TaxonName stats metadata includes coordinate OTUs and synonyms of self
  • Change map position in Filter collecting events #3571
  • Add type material button is now blue #3579
  • Radial navigator: close radial menu when slices are opened in a new tab/window clicking and pressing ctrl/shift/meta keys #3582

Fixed

  • Loans referencing containers have 'Total' properly calculated #3035
  • TaxonDetermination sort order on CollectionObject comprehensive/browse... again #1355
  • OTU API autocomplete not resolving to valid OTU
  • Attribution rendering had cryptic license value #3577
  • GeographicAreas not registering for some DWCA imports [#3575]
  • New collecting event: georeference from verbatim button creates two identical georeferences #3573

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.34.5 release

Added

  • Cached map item report (linked from Filter OTUs)
  • Depictions list on Filter image

Changed

  • Calls to /api/v1 have a new key/value signature
  • Staged image metadata field format from JSON to JSONB [#3446]
  • Updated Ruby gems

Fixed

  • Batch import BibTeX failing on empty entries
  • Chronology stats report
  • ImportAttribute facet not working on any predicate searches
  • Taxon name/otus filter order bug
  • Staged image queries failing when multiple facets used #3556
  • Citations list is truncated in Radial Annotator #3560
  • DwC attributes are now showing in Stepwise determinations task
  • Quick taxon name only works for species #3554
  • Filter Images: Change per doesn't update the table #3566

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.34.4 release

Added

  • ImportAttribute facets to various filters
  • Project data curation issue tracking URL field (and to base API response) #3550
  • Manual option to regenerate derivative images on Show Image
  • API gallery endpoint /depictions/gallery
  • Image quick forms, add depictions in the context of an image #3540
  • Tables of data to nomenclature stats plots, with option to copy to clipboard
  • With/out nomenclature date facet on filter nomenclature
  • Determiners can be re-ordered (topmost, regardless of year, is preferred) #1355

Changed

  • Updated Gemfile
  • Updated JS packages
  • Derivative images strip EXIF and auto orient
  • TaxonName autocomplete change to a strict match mode.
  • Bold geographic levels in Type specimen panel in Browse OTU #3544

Fixed

  • Subqueries in unified filters were silently ignoring components of the query, e.g. fix spatial + subquery requests #3552
  • Geographic level names not displaying on Browse OTU #3553
  • Sqed images that fail processing will try again with slower method automatically #3070 #3443
  • TaxonName dynamic observation matrix row not properly scoped #3454
  • OTU API autocomplete fails to sort results
  • Duplicate type status per CollectionObject are not allowed #3535
  • Edit/New taxon name: Author order for taxon name does not match author order of source #3551
  • Some issues with order of roles (e.g. Determinations) in display #1355

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.34.3 release

Added

  • Task - Nomenclature by year plots #2472
  • API for BiologicalRelationships -api/v1/biological_relationships?extend[]=biological_property #3525
  • Organization to Attribution slice in Radial annotator #3529
  • Delayed job queue cached, currently used in Role-related updates #3437
  • Allow organization determiners in DwC occurrences importer

Changed

  • Error radius also captured as literal value in addition to conversion to error polygon #3471
  • Batch update of collecting event geographic areas is now run in the background, limited to 250 record #3527
  • Reverted index-based TaxonName autocomplete to comprehensive version
  • Upgraded docker env to Postgis 3.4

Fixed

  • Missing synonym record for basionym in COLDP export [#3482]
  • Fixed loan related links in several places #3463
  • Common name language ISO when no language #3530
  • Attribution displays owner/copyright holder Organization names #3515
  • CollectingEvent filter fails on cachedgeo* fields #3526
  • Reviewing and Organization's related data
  • CollectionObject timeline didn't show loans when object containerized #3528
  • Browse Annotations "On" filter doesn't work #3505
  • Georeferences are not cleaned after unset current collecting event in comprehensive specimen digitization task #3533
  • Fix collection object pagination in Browse OTU

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.34.2 release

Added

  • Subsequent Name Form section in New taxon name #3460
  • Original form section in New taxon name

Changed

  • New species name button is now always visible in Type section on New taxon name task
  • Improve COLDP export delimiter usability [#3522]
  • Updated Node packages and Ruby gems

Fixed

  • Role scoping broken, affecting things like Verifiers list #3514
  • api/v1/citation failing on last page of results #3524
  • Fix generation of Unit tray labels from Filter nomenclature
  • Object graph view failing to render (controller object no longer available!?)
  • People as sources missing missing relationship (broke object graph)
  • Combinations in COLDP exports lack rank #3516
  • Fix coldp.rb undefined method iso8601 for nil:NilClass #3512
  • Improve TaxonName autocomplete result prioritization #3509
  • Clone button is not clearing input after cloning

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.34.1 release

Fixed

  • Missing organization tab in Owner panel on New image task
  • BibTeX download shows incorrect results on New source task #3510
  • Asserted distribution API endpoint crashing when count is above 50

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.34.0 release

Added

  • api/v1/data_attributes/brief endpoint
  • api/v1/controlled_vocabulary_terms endpoint
  • Extracts are citable
  • modified and modifiedBy fields to the COL data package exporter #3464
  • Pagination to Labels and TypeMaterial .json endpoints #3472
  • DataAttribute columns for CollectingEvent and TaxonName filters
  • Added ranks for viruses
  • CachedMap framework - compute low-resolution maps quickly #3010
  • .json and .geojson endpoints implement CachedMaps at /api/v1/otus/:id/inventory/distribution
  • Administrator dashboard for CachedMap status
  • New indices for some name/cached related fields (Otu, TaxonName, Source)
  • Batch update Geographic area radial to filter collecting events
  • Customized API version of OTU autocomplete
  • GBIF map tiles as an option on maps
  • Add related option to nodes in Biological associations graph task
  • Layout settings for New image task

Changed

  • Predicted adjectives for the epithets ending with -ger and -fer
  • Optimized Gnfinder playground new-name detection
  • Optimized /api/v1/asserted_distribution, also now uses extend[]=geo_json (disabled if > 50 records requested)
  • Updated /api/v1/biological_associations to report full taxonomy #3438
  • Updated Ruby gems
  • Added date format recognition ####-##-## [#3453]
  • Add hyperlinks to OTU labels in Filter biological associations table #3444
  • Updated many relationships to validate based on presence of objects, rather than parameters
  • Simplified behavior of Otu and TaxonName autocomplete to use new fuzzier indicies
  • Clone loan button redirects to new loan task #3462
  • Multiple improvements in DwC importers

Fixed

  • Georeference parsing didn't handle new Z
  • Clearing PinboardItems by class
  • Rendering TNT matrix labels
  • Initializing new Extract when no Extracts present
  • DataAttribute filter facet not working for non-exact matches
  • Speed response for Filter's returning DataAttributes #3452
  • Going from Image filter to others could result in duplicated rows
  • DWCA Importer: Geographic Areas not imported #1852
  • Error on catalog_helper: history_other_name
  • Error on taxon_name_relationship on rank_name.
  • Create new asserted distribution when is_absent is checked in New asserted distribution task
  • Repository selection does not appear in Filter Collection Objects #3430
  • Docker pointing to outdated base image.
  • Global identifiers resolve check not honouring HTTPS
  • Interactive keys were not properly scoping to projects in some cases
  • Annotations were sometimes added to objects that no longer existed #3445
  • Disable editing of imported rows in DwC importer task #3469
  • Fixed URL hostname string matching in some places.
  • Matrix Column Coder throws an error after autosave ends and observation to be saved no longer exists
  • New line delimiter doesn't work in Filter collection object #3480

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 1 year ago

TaxonWorks - Version 0.33.1 release

Added

  • NOMEN batch importer error handling/reporting improvements #3427
  • More annotation-related facets to Observations filter

Changed

  • Autocomplete requests optimized by speed
  • NOMEN batch importer treats authors only as verbvatim, Roles are no longer created.

Fixed

  • Without depictions filter facets
  • Descriptors facets referencing observation/matrix presence/absence
  • Errors on taxon_name.rank_name and paper_catalogue.combination
  • Documents facet in Source filter
  • Documents from other projects appearing in count on radial annotator #3348
  • Verbatim name contained 'Suffix' #3425
  • Observation matrix facet doesn't work in Filter descriptors
  • Lock Is original and Is absent checkboxes in citation form
  • Pagination doesn't work correctly in Filter biological associations #3426
  • Records per page doesn't work on page change in Citations by source task

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 2 years ago

TaxonWorks - Version 0.33.0 release

Added

  • Basic RCC5 support (= OtuRelationship) #257
  • Unified filter to observation matrix integration #3415
  • Biological associations can now be depicted
  • Data depiction facets
  • Biological associations filter annotation-based facets
  • New stage-only staged image type #3400
  • New left-t stage layout #3367
  • Add button to add biological associations from Related modal in new biological associations task
  • ImportDataset facet in Filter collection objects #3419

Changed

  • Updated author and year string for family-group names
  • Recent predicate list
  • Recent languages list
  • People autocomplete
  • GeographicArea autocomplete (exact match on alternate value)

Fixed

  • Nomen (was "castor") batch load was not assigning parent correctly #3409
  • Source and People API endpoints don't try to authenticate #3407
  • Date range in filter Collection Object not being applied #3418
  • Year import in NOMEN (was "castor") import #3411
  • PublicContent missing is_community? method preventing reporting.
  • Loans dashboard fails to render when no loans are present
  • Staged image processing when boundaries fail to be calculated and calculate incorrectly
  • Bug with engine in interactive keys #3416
  • Collection object classification summary #3412
  • BibTeX typo #3408
  • Includes type material and type material observations don't work in Filter images
  • Changing the number of items per page or the page shows loan items that are not from the current loan in New/edit loan task #3413
  • Sort by name gives an wrong order in filter nomenclature task

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 2 years ago

TaxonWorks - Version 0.32.3 release

Added

  • Add/move/return collection objects from collection object filter #3387
  • Interpretation help for full name facet in people filter #3394
  • Total individuals to loan show/recipient form #3398
  • Download SVG button in Biological associations graph task
  • Related modal in Biological associations graph task
  • Return BibTeX with extend[]=bibtex on calls to /api/v1/sources
  • Related button to biological associations in Browse OTU
  • Pagination for loan items in Edit/new loan task #3391
  • Caption and figure label editable in Depictions list in Radial annotator #3396

Changed

  • Pagination headers are exposed via CORS #3380
  • Updated bundle gems
  • Ruby 3.2 is now required as minimum
  • API /people and /sources resources no longer require authentication #3385
  • The genus rank is allowed as incertae sedis
  • Trigger filter after change records per page selector
  • Always show pin button
  • Browse OTU biological association table contains related modal

Fixed

  • Global identifiers not appearing on community data #3393
  • Lag in selecting loan items on edit loan #3399
  • Collection object was loanable 2x in some cases
  • An issue when geo-json related facets were not being applied in Otu filter
  • Image filter with otu_id only returns as expected
  • Depictions/Images facet not consistent and broken #3395
  • Missing pagination for asserted_distributions API endpoint #3377
  • Delete wrong node in Biological associations graph #3383
  • Cannot clear Returned on date input for loan items in Edit/new loan task #3390

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 2 years ago

TaxonWorks - Version 0.32.2 release

Added

  • Geographic area smart-selector has click-to-select map option #3293
  • Add collection object quick forms in New type specimen task
  • New layout for collection objects filter - Data attributes
  • DarwinCoreasscociatedTaxa indexing via data attributes #3371

Fixed

  • Paper catalog raised when rendering some type material records #3364
  • Lock buttons are not working on New source task
  • Some rows don't show name string in Citations by source task #3370
  • Updating a data attributes updates related DwcOccurrences
  • API catalog method call #3368
  • Alternate values appear on community data #3363

Changed

  • Updated bundle gems
  • New D3 engine for object graph greatly improves performance, new rendering options
  • New DwC occurrence version reflecting #3371

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 2 years ago

TaxonWorks - Version 0.32.1 release

Fixed

  • Date related rendering error in Catalog

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 2 years ago

TaxonWorks - Version 0.32.0 release

Added

  • New biological association task #1638, in part #2143
  • New options to extend results in Nomenclature filter #3361
  • New panels for Adminstrators User activity dashboard
  • Deaccessioned layout for filter collection objects

Changed

  • Replace GeoJSON long/lat format to lat/long on interfaces #3359
  • Returned ability to show TaxonNameClassifications (from /taxon_name_classifications/list)

Fixed

  • Deaccessioned facet in Filter collection objects #3352
  • Reversed OTU taxon name facet #3360
  • Relationships are not listed in biological associations form in Quick forms
  • Topics are not listed after create them on Citation form in Quick forms
  • Combination names are missing in Citations by source
  • Handle another class of SQED raises
  • TaxonNameClassification API call raises
  • Raises related to cached_nomenclature_date
  • PublicContent causing OTU destruction to raise
  • Several paper-catalog rendering issues
  • Geographic area smart selector is not rendering correctly on Common names slice in Quick Forms

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 2 years ago

TaxonWorks - Version 0.31.3 release

Added

  • JSON nomenclature inventory endpoint /api/v1/taxon_names/:id/inventory/catalog

Fixed

  • Serial name filter query doesn't work
  • Serial facet
  • Authors facet doesn't work on Filter nomenclature
  • Fixed bug preventing combination update
  • Loan facet doesn't work on Filter collection objects #3345
  • Valid name is not provided for all matches on Match nomenclature task #3343
  • Object links don't work on Interactive key

Changed

  • Updated Ruby gems
  • nomenclature related validation changed from nomenclature_date to cached_nomenclature_date, which should speadup the process

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 2 years ago

TaxonWorks - Version 0.31.2 release

Added

  • Link from AssertedDistribution filter to BiologicalAssociations filter
  • All tab to biological relationships facet #3334
  • Biological Property to Manage controlled vocabulary terms

Changed

  • Add nomenclature code to relationships and statuses labels in Filter nomenclature #3333
  • All Loan edit requests resolve to the edit task #3330

Fixed

  • Biological association filter raises #3335
  • Mass annotator for Sources showed no options
  • People filtering doesn't work on Filter nomenclature #3332
  • Biological associations section shows incorrect results in Browse Otu #3336
  • Error message on Combination [#3340]
  • Clone last citation button doesn't work
  • Missing asserted distributions in Browse OTU and Quick forms radial #3337

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 2 years ago

TaxonWorks - Version 0.31.1 release

Fixed

  • Radial annotator documentation shows too much #3326
  • Cached values not updated #3324
  • Roles not displaying while edint loan #3327
  • Loan autocomplete #3329
  • Set as current button doesn't work on Original combination section in New taxon name task #3325
  • Repository autocomplete #3331
  • Some staged filter results failing to set size of window #3328
  • Fixed repository, source, serial, people autocomplete with new project_id param. New specs added
  • Short URLs not working due to Ruby 3.2 incompatibility.

Changed

  • /combinations/<id> redirects to /taxon_names/<id>

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 2 years ago

TaxonWorks - Version 0.31.0 release

Added

  • Filter asserted distributions task #1035
  • Filter biological associations task #1156
  • Filter content task
  • Filter descriptors task #2802
  • Filter loans task #2124
  • Filter observations task #3291 #3062
  • Filters can mass-annotate select rows (e.g. Notes, Citations) #2257 #2340
  • Filter collection objects with/out preparations #2937
  • Filter collecting events with/out any date value, verbaitm or parsed #2940
  • Filter collecting events with any/no value in field (covers, in part #2756)
  • Collection object filter - add with/out local identifiers facet #2699
  • Collection object filter - de-accession facet #3195
  • Data attributes facet returns results matching/without any predicate value
  • Integrated filters (pass results from one to another) #2652 Also in full/part #1649 #1744 #2178 #2147 #2770
  • Match identifiers facet added across filters/API #3151 #3058
  • Nomenclature filter - facets for names with/out citations and with/out documentation #2865
  • Nomenclature filter - facet for by year described #2059
  • Nomenclature filter - facet to return names with/out (subsequent) combinations #3051
  • Nomenclature filter - facet to for with/out original combination #2496
  • Protocol facet to collection object, collecting event filters #2803
  • Task - Loans dashboard #2116 (in part)
  • Task - Source citation totals (linked from Source filter) #2305
  • Ability to "coordinatify" an OTU filter result #3317
  • Figure label in label on image API response
  • Input to create N records in Simple new specimen #3269
  • Soft_validation for seniority of synonyms
  • Added cached_author to TaxonName

Fixed

  • Local identifier facet in filter CollectionObject #3275
  • Identifier within range includes +1,-1 results #2179
  • Data attribute facets #3075
  • Collection object filter finds objects by container identifiers #1240
  • Clarified collection object loan facet #3005
  • Radius based map searchers returned intersections, not covering results #2552
  • Data attributes not appending to DwC export #3280
  • DwC download from CollectionObject "not downloading"/closing #3313
  • Filter nomenclature returns original combination when there is none #3024
  • Staged image visualization incorrectly cropped #3260
  • Staged images incorrectly returning records with local-identified containers #3258
  • PK sequences was not setup in the correct dump stage in Export project task occasionally causing PK constraints errors on usage.
  • Radial object redirects to Data page after destroy a collection object in Simple new specimen task #3284
  • Wrong label for display unscored columns in Matrix column coder #3292
  • Duplicate records in nomenclature match task #3300
  • NeXML rendering bug
  • Breaking CoL export bug #3310

Changed

  • Unified look and feel of all filters #445 [#1677]
  • Filter OTUs completely rebuilt, numerous new facets #1633
  • Filter collection objects displays (customizable) columns of many types, not just DwC #3197 #2931
  • Unified form of filter/API *_ids and *_id parameters to always use singular #2188
  • Merged 'Task - Overdue loans' with Loans dashboard #2116
  • Export project task now removes hierarchies rows that don't belong to selected project #3271
  • Export project task no longer includes delayed_jobs and imports tables.
  • Clipboard hotkey combination #3273
  • Recently used confidence levels improvements
  • Multiple nomenclatural soft validation improvements
  • Improvements to intelligence of various autocompletes
  • Improved cursor focus on new source task
  • Update Ruby to 3.2.1
  • Updated Ruby gems
  • Updated Docker container (including psql client version to 15)

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 2 years ago

TaxonWorks - Version 0.30.3 release

Added

  • Search panel in New source task

Fixed

  • Programming error breaking loop with exit instead of break when calculating previous OTU.
  • Crash when attempting to view a Verbatim source because BibTeX panel cannot work with that type of sources.

Changed

  • Updated Ruby gems.

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.30.2 release

Fixed

  • Asserted distribution citation label in Browse OTU
  • Records per page selector doesn't work in Filter Stage Images #3259
  • In NeXML output, TIFF images were not converted to JPG
  • Error when calculating previous OTU for navigation

Changed

  • Updated Ruby gems.

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.30.1 release

Added

  • BibTeX type facet for Filter sources task #3218
  • With/without Source::Bibtex title in Filter source task #3219
  • Hyperling names in Nomenclature match

Fixed

  • "Remarks" column displays in Browse collection object DwC/gbifference panel
  • Browse OTU navigation dead ends #3056
  • Setting a Namespace to virtual updates cache properly #3256
  • Virtual namespaces identifier tags don't include duplicated Namespace #3256
  • Virtual namespace identifier preview does not render namespace
  • Incorrect valid name in Nomenclature match task

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.30.0 release

Added

  • CoL data package improvements for Remarks, metadata,
  • Integrated GBIF remarks flags into Browse collection object #3136
  • Next/previous navigation arrows to Browse collection object #3229
  • More details to steps in stepwise determinations task
  • Added soft validation for duplicate family group name forms and misspellings [#3185]
  • With/out local identifier facet for collection objects and stagd images #3173
  • Filter by housekeeping and staged-image data attributes #3171
  • Delete selected collection objects (and their related data) from filter #3174
  • Collection object Autocomplete has loan and deaccession banners #3192
  • Autocomplete on Browse collection object #3189
  • Task - Collection object chronology, a plot of object by year collected, that's all
  • Endpoint to return related data preventing or included in destroy, e.g. /metadata/related_summary?klass=CollectionObject&id[]=16701&id[]...
  • Filter by gender and form classifications in filter nomenclature #3212
  • Serial facet to Filter sources #3211
  • tooltips and actions configuration properties to Map component #3234

Fixed

  • White-space around unit-tray headers #3191
  • Stepwise determinations confounded by invisible white-space #3009
  • OTU smart selector did not include items from the pinboard #3139
  • Source in n project autocomplete response [#3142]
  • 'Also create OTU' on batch taxon name upload causing raise
  • Media observations removed if they have no more depictions via updates
  • Citation link in biological association panel on Browse OTU
  • Type relationship text/rendering is inverted in New taxon name task #3182
  • Sqed processing failing to encode HEIC images #3188
  • Common list component doesn't filter created status on New taxon name task #3205
  • Collectors facet doesn't work on Filter collecting event #3216
  • original combination label disappears when relationship doesn't include the current taxon name [#3067]
  • Sometimes keyboard table is duplicating shortcuts
  • Export Project Database task not exporting rows whose project_id is NULL #3203
  • Close icon is difficult to distinguish when modal background is transparent #3245
  • Missing identifiers and determinations on collection object table in New collecting event task #3246
  • Click "Manage Synonymy" in Edit Taxon Name task does not redirect #3250

Changed

  • Behaviour of recent records (smart selectors) updated to reference updates, not just created timestamps
  • Lock, navigation, UI, and code refreshments to Simple new specimen #3190
  • "TODO list" now a faceted search named 'Filter staged images' #3171
  • Refactored observation cell component for Image matrix
  • Updated Ruby gems
  • Webpack binaries: Replaced npm bin for npm root to allow compatibility with recent NPM versions
  • Nomenclature match updates #2176
  • Navigation key combination for radial annotator #3233
  • Truncate smart selector lists
  • Allow compare n objects in collection object match #3238
  • Include total of match/unmatched in Collection object match [#3237]

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.29.6 release

Added

  • Print unit-tray headers from TaxonNames via Filter nomenclature #3160
  • New radial "Filter" navigators facilitating cross-linking to filters #2297
  • Option to force DwC indexing to prioritize names from Geographic Area #3143
  • Functionality to update CollectingEvents in the context of Browse collection object
  • Character state filter in Matrix Column Coder #3141
  • Better error handling and reporting when parsing BibTeX
  • Index for caching the numeric component of Identifiers

Changed

  • Updated Browse collection object interface #2297
  • Reload New source task by pressing New and loading source
  • Updated Ruby gems
  • Updated node packages

Fixed

  • Browse nomenclature crashing when taxon name descendants have no cached author year
  • Soft validation crashing when cached nomenclature date is absent
  • Role picker is missing after create a source from BibTeX #3180

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.29.5 release

Changed

  • Changed author labels on Filter source #3134
  • Minor changes to plots on administration activity dashboard
  • Parallelize some indexing rake tasks

Fixed

  • Recent and Quick list are empty on Citation annotator #3133

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.29.4 release

Added

  • Distribution, Material Examined sections, and zip download for paper catalog [#3098]
  • Code full columns, destroy all observations in a column #3117
  • "Display only unscored rows" on Matrix column coder #3103
  • Previous and next links in Matrix row coder #3107
  • Match identifiers facet to Filter extract task #3089
  • Clone previous citation to citation panels #3097
  • Populate column button for Matrix Column Coder #3117
  • scientificName is now implied in typeStatus when only the type of type is specified in DwC occurrences importer
  • Additional DwC classification terms #3118

Fixed

  • Broken URL for images in NeXML #2811
  • Improved Confidence annotation speed #3126
  • Destroying a Georefernce re-indexes related CollectingEvent #3114
  • Numerous issues in "Castor" TaxonName batch load
  • CollectingEvent cached geo-names (e.g. used in DwC export) missclassified #2614
  • Order of descriptors in nexus and tnt output is updated to reflect the column ordering
  • Homonyms without replacement name are now marked as invalid
  • Visible identifiers raising (e.g. broken object graph)
  • Presence Descriptor is not saving in Matrix row coder #3099
  • Missing number of objects for presence/absence descriptors on Interactive keys #3102
  • New column button doesn't add the new column to the interface #3109
  • Taxonomy inventory API failing with common names when language is not set
  • Missing taxon_name_relationships parameters #3096
  • Create matrix row button redirects to wrong OTU in OTU radial
  • Determinations not added to containers in "Edit Loan"task #1935
  • OTU images disappear when moving other images to observation cells #3111
  • Basic nomenclature failing to redirect when no name was selected
  • List of All Topics is not displayed #3125
  • Refactor confidence form #3129
  • Destroy selected Labels does not work #3127
  • Creating multiple type materials in comprehensive task #3131
  • DwC occurrences importer not reporting error when typeStatus is non-empty and yet it doesn't have correct format
  • Interactive key - Presence / absence descriptors are placed in non relevant list #3100

Changed

  • Removed New OTU link from New observation matrix task #3101
  • Disabled horizontal resizing for textarea inputs on comprehensive

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.29.3 release

Fixed

  • View image matrix button doesn't work in Interactive key task
  • Missing collectors parameters in Filter collecting events.
  • Pagination on Image Matrix task
  • Project Preferences task causing internal server errors
  • Boolean params not handled correctly on specific conditions in some filters

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.29.2 release

Added

  • Administration level project classification visualization #3092
  • Recent paramter to asserted distribution filter #3086

Changed

  • Updated Gemfile
  • Handle long queries to match facets in filters #3088

Fixed

  • Collecting event filter matching user creator/updator broken #3008
  • Rendering type material label with document label failed
  • Failed attempts at destroying a Predicate no longer raise
  • Prevent some breaking raises for Georeferences with invalid shapes
  • Select all button doesn't work in Print labels task #3093

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.29.1 release

[0.29.1] - 2022-08-31

Fixed

  • Radial navigator for TaxonName broken [#3087]
  • OTU link in New asserted distribution

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.29.0 release

Added

  • A simple paper catalog generator (preview!) #1473
  • Functions to summarize distributions for catalogs
  • GeographicAreas autocomplete references alternate values
  • People filter, with many facets #2876
  • Matches identifiers (results by delimited list of some identifier type) facet, to most filters #3080
  • Crosslink by ID between CollectionObject and CollectingEvent filters
  • Open in filter collection object button in Filter collecting event task
  • Added verbatim_label support for Collecting Event Castor batch load. #3059
  • Lock is_original and is_absent for Asserted distribution form in OTU quick forms #3085

Fixed

  • Local identifiers on community objects were displayed across projects
  • Object type is missing when otu filter param is passed instead observation matrix id in Image matrix task

Changed

  • Alternate values can be used on GeographicAreas #2506
  • Alternate values on community objects are shared by all projects
  • Global identifiers on community objects are shared across all projects
  • Optimized identifier next/previous, not fully resolved #3078
  • Updated Ruby gems.
  • Upgraded to newer Gnfinder service.
  • Enabled 10km tolerance to geographic area validation for verbatim georeferences.

Data

  • Migrates annotations on Community objects to be accessilbe across projects

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.28.1 release

Fixed

  • Settings modal is scrolled to the bottom when the modal is open.
  • Edit in image matrix and Open in matrix buttons don't open image matrix task on edit mode.
  • Create verbatim coordinates button dissapears after create request fails in New collecting event task
  • Depictions are not displayed correctly in Browse collecting event #3012
  • Cloned georeference are not loaded after cloning a collecting event #3076

Changed

  • Updated Ruby gems.
  • Updated Node packages.
  • Expanded drag and drop section in observation cell in Image matrix

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.28.0 release

Added

  • Adds data_attributes, data_attribute_value, data_attribute_predicate_id, data_attribute_exact in filter concern #2922
  • /api/v1/tags endpoint with tag_object_type[],tag_object_id[], tag_object_type, object_global_id, keyword_id[] #3061
  • Added pagination in the image_matrix
  • Matrix Column Coder - coding by descriptor #1385
  • Soft validation and fix for adding subsequen combination when original combination is different #3051
  • Added 'electronic only' field for the source to flag sources published in electronic only format
  • Default collectionCode namespace mappings as falback when institutionCode:collectionCode mappings do not contain a match in DwC occurrences importer.

Changed

  • Remove search box in observation matrix hub #3032
  • Type material form allows multiple type species in comprehensive task. #2584
  • Updated Ruby gems.
  • wikidata-client dependency is now fetching from RubyGems rather than custom fork.
  • serrano has been changed to a new custom branch which is identical to official gem except thor dependency has been downgraded for TW compatibility.
  • DwC occurrences importer mappings are not sorted by institutionCode:collectionCode

Fixed

  • Object global id param in identifiers API/filter
  • Bad logic check on adding new user to project
  • Dependency loop problem in DwC checklist importer

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 2 years ago

TaxonWorks - Version 0.27.3 release

Added

  • Soft_validation for the year of taxon description compared to person years of life #2595
  • Pagination to Image matrix task

Fixed

  • Fixes rendering the author string in the catalogue #2825
  • Include facet is not working properly in Filter nomenclature #3023
  • Role picker changes order of roles after removing one #3003
  • Observation matrix TNT export failed due to undefined method error #3034
  • Date start and Date end display flipped in "Filter Collecting Events" #3039
  • Role picker list doesn't display suffix and preffix
  • By user facet is passing member id
  • Project user last seen at correctly reported

Changed

  • ElectronicPulbications moved from NomenNudum to Unavailable.
  • Updated Ruby gems and Node packages
  • OTU name string into link in Observation matrices dashboard task

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.27.2 release

Fixed

  • Content panel in browse OTU not working properly
  • Darwin Core Export failing on specific combinations of data attributes selection.

Changed

  • Updated Ruby gems and Node packages

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.27.1 release

Changed

  • People/Name toggle remove historical option for name #3028

Fixed

  • Content attributes response

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.27.0 release

Added

  • Task to manage pubilcation of Content to PublicContent #3004 in part
  • Task to merge taxon name relationships from one taxon to another #3022
  • Add determiner_name_regex to collection object filter #3026
  • API interactive key engine endpoint /api/v1/observation_matrices/123/key.json
  • API depictions endpoint api/v1/depictions/123.json?extend[]=image&extend[]=sqed_depiction&extend[]=figures
  • Taxon determinations stats in stats API
  • Setting tags for collecting events and collection objects in DwC occurrences importer #3019, #2855

Changed

  • Column order in Observation matrices dashboard task
  • Size of description input in Protocol form
  • Error code for merge people response

Fixed

  • Annotations panel doesn't display notes in Browse nomenclature
  • Wildcard matches on collecting event attributes failing
  • Select row in Observation matrices dashboard assigns incorrect ID
  • Last week citations stats in API showing values for images. #3020
  • Annotations panel doesn't display notes in Browse nomenclature
  • Geographic areas download failing to generate CSV
  • Flip is not working propertly in Uniquify people task

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.26.2 release

Changed

  • Updated Ruby gems

Fixed

  • Filter collection object not working when attempting to show the record

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.26.1 release

Changed

  • Upgraded to Ruby 3.1 #3011
  • Updated Ruby gems

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.26.0 release

Added

  • Task - Stepwise determinations, facilitate verbatim to parsed determinations en masse #2911
  • Two more digitization stage types, "T" and "Inverted T" #2863
  • Added soft_validation fix to missing collection_object determination, when the type is designated [#2907]
  • Confirmation button for tags, preparation type and repository panels in CO Match #2995

Changed

  • Upgraded Node to version 16
  • Replaced Webpacker for Shakapacker gem
  • Upgrade PDF viewer library

Fixed

  • Nomenclature and observation matrix stats #1124 #1356
  • Cannot add a determination after editing one in comprehensive task #2996
  • "In project" button is not updated after select a different source in Edit source task #3000

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.25.0 release

Added

  • Link to Download project in show project #2775
  • OTU geo-json inventory API endpoint, /api/v1/otus/123/inventory/distribution.
  • Collection object classification summary task #1864
  • Notes facet to Collection Objects filter #2966
  • Confirmation modal for clone button on New collecting event task #2978
  • Minutes/record estimate in project activity task #2979
  • Pagination in Citations by source task
  • Current repository facet in collection object filter #2975

Changed

  • Identifiers added to print labels [2959]
  • Improved Extract tables #2884 #2881
  • Improved Repository autocomplete #2993
  • Refactor citations by source task
  • Person autocomplete optimization
  • Cleaned up Label UI text
  • Removed some jQuery
  • Updated Ruby gems via bundle update
  • Use Catalog for API source of OTU nomenclature citations

Fixed

  • Extract/protocol UI issues #2990
  • Source year_suffix preventing cloning #2992
  • Dwca eml.xml file validates locally #2986
  • Missing params for api_nomenclature_citations added
  • Converted wkt parsing errors from exceptions to validation
  • DwcOccurrence version scope to project in Hub
  • Fixed soft validation on Collection Object related to determination date #2949
  • Original combination soft validations are not loaded when New taxon name task is opened
  • ObservationMatrixRow|ColumnItem index view failing because new links are not available
  • Author roles are no visible in Citations by source task
  • Increasing number of labels to print while label is selected adds that many to preview #2973
  • Geographic areas are not suggested based on verbatim coordinates in comprehensive and new collecting event task #2982
  • Cannot sort by column in filter collecting event task #2970
  • "Recent" determiners not working in Comprehensive #2985
  • Determiners locked are missing after press "Save and new" in comprehensive task #2943
  • Crashing when creating georeferences with invalid WKT input
  • ObservationMatrixRow|Column index and autocomplete calls
  • Lock source button is not working in OTU radial - biological associations form [#2989]
  • New type specimen duplicates specimen when updated after creating #2994
  • Sort column option is not working on Filter collection objects
  • Toggle members buttons is not working on Browse annotator

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.24.5 release

Fixed

  • Previously loaned and returned CollectionObjects are unloanable #2964
  • People smart selector doesn't work to add new roles #2963
  • Type species section is empty in Browse OTU
  • Missing depictions caption and figure label in Image matrix task #2965

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.24.4 release

Added

  • Organization roles to taxon determinations model

Fixed

  • Repository autocomplete raises #2960
  • Duplicated text in TaxonDetermination link #2947
  • Housekeeping facet in CollectingEvent filter broken #2957
  • Cannot set Determiner of CO to department/organization #2915
  • Combination view is broken on Browse nomenclature #2952
  • Matrix row coder button in Observation matrix dashboard task redirect to a wrong OTU in Image Matrix task [#2956]
  • Depiction radials are not working in Image matrix task #2954

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly almost 3 years ago

TaxonWorks - Version 0.24.3 release

Added

  • DwC export includes occurrenceStatus #2935
  • Tag panel for images in New images task #2919
  • Repository section for Collection object match task #2918
  • Preparations section for CO Match task #2930
  • Match collection object button in Filter collection object #2917
  • Lock button for By section in New extract task #2926
  • With preparation facet in Filter collection objects #2937

Changed

  • Improved(?) behaviour of Extract autocomplete #2923
  • New BiBTeX based Sources match and/or create Serials for some types #2719
  • Improvements for taxon determinations in comprehensive task
  • Observation Matrix CSV dump uses full object labels #2912
  • Allow multiple origin relationships in New extract task #2928
  • Enable biocuration buttons only for the current collection object in comprehensive task [#2946]
  • Updated ruby gems

Fixed

  • Display full citation in image viewer #2857
  • Extract filter OTU id match not matching determinations #2925
  • Improve observation matrix row label handling #2902
  • Showing related data for Descriptor broken #2934
  • Collection object label is not updated after saving determinations in comprehensive task #2899
  • Label form is not updated after loading a collecting event in Comprehensive task #2898
  • Preferred catalog number for collection objects using first created rather than top of the list (also fixes wrong otherCatalogNumbers in DwC export) #2904
  • Missing not fixable error message for automatically soft validations #2877
  • Recent lists on Data have broken flex CSS #2920
  • Generating label from collecting event with verbatim trip identifier duplicates tripcode #2921
  • Leaflet map does not center the view on shapes
  • Programming typos affecting error handling in some batch loaders
  • PDF reading causing software crash with some PDF documents (e.g. encrypted and/or having unsupported features)
  • "virtual" spelled "virutal" #2938
  • Protocols should not display origin #2927
  • Determination lock not working for "Add to container" in Comprehensive task #2943
  • Role types table in uniquify people renders poorly when "show found people" or "show match people" enabled #2894
  • Syntax error during code generating synonyms and descendants for catalogs

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 3 years ago

TaxonWorks - Version 0.24.2 release

Added

  • New units mg, µg, ng, ml, µl, nl, ng/µl, Ratio (for Descriptor, etc.) #2887
  • Project activity report includes community data (but not scoped to project) #2893
  • Protocols for Observations #2889
  • Increment tripcode in New collecting event task #2441
  • Now and today buttons for time/date made #2888
  • Radial navigator to New extract task #2885

Changed

  • Refactor Uniquify People task. Added improvements #2858
  • Removed PDF viewer broad channel event
  • Updated Ruby gems

Fixed

  • Extract -> show rendering raising #2886
  • People being set as invalid during automatic activity updates
  • Project activity session report shows hours properly #2878
  • xAxis category ordering of Project activity #2891
  • Sometimes it's not possible move images from one cell to another in Image matrix task [#2874]
  • Uniquify people task are not merging all selected match people #2892
  • Media observations are not displayed after creating them using drag and drop box in Matrix row coder task. [#2880]
  • New extract task loads incorrect repository for existing extracts #2883
  • Extract edit link in New observation matrix task #2896
  • Incorrect matrix list is displayed on Observation matrix slice in Radial object #2901
  • Pages label is not displayed in citation form in comprehensive task #2903

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 3 years ago

TaxonWorks - Version 0.24.1 release

Changed

  • Time ranges for eventTime in DwC occurrences importer are now supported
  • Updated Ruby gems

Fixed

  • Observation matrix row filter generalized to work for all observation object types #2873

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 3 years ago

TaxonWorks - Version 0.24.0 release

Added

  • Collection object current_repository_id and interface toggle #2866
  • Use Namespace as DwC collectionCode #2726
  • Notes on CollectionObject export to DwC occurrenceRemarks #2850
  • Link to comprehensive digitization collection object via ?dwc_occurrence_object_id=123 #2851
  • Project user activity report task #50 #1062
  • 'Inferred combination' to Browse taxon name header, when required #2836
  • Extract autocomplete
  • Matrix row coder supports mutiple Quantitative and Sample observations per "cell"
  • Extracts are observable #2037
  • Download observation matrix descriptors as text
  • Download observation matrix observations in .tab format
  • Observations have made_year|month|day|time attributes
  • Qualitative descriptor batch loader (Data->Descriptors->Batch load) #1831 (in part)
  • Modal depictions for all descriptors in Matrix row coder #2847
  • New georeference type for user-supplied points #2843
  • Extract rows in New observation matrix
  • Depiction modal for all descriptors in Interactive key
  • Link CollectionObject batch load to DwCA importer #2868

Changed

  • Administration activity report
  • DwC export uses a "sorted" column order #2844
  • Observations now are polymorphic #2037
  • Replace autocompletes by smart selectors in Common Name form on OTU radial #2840
  • Updated Ruby gems
  • DwC importer sex mapped changed to prioritize http://rs.tdwg.org/dwc/terms/sex DwC URI and also create sex biocuration group with such URI if none exist.
  • Taxon name label for original combination label in Citations by source task.
  • Add separate scrollbars to row and column tables in New observation matrix task #2799
  • Change form fields order in OTU radial - Biological associations
  • Updated ruby gems
  • Close modal after select a status in New taxon name
  • Escape new additional pseudo-LaTeX encodings from BibTex data

Fixed

  • DwC georeferencedProtocol references Protocols properly #2842
  • DwC georeferencedBy references Georeferencers properly #2846
  • Administration activity report raising #2864
  • OTUs and collection objects batch-loaders failing to initialize due to Ruby syntax error
  • Sqed depictions crash on cache update when no processing results are available
  • Asserted distributions on OTU radial is_absent no longer locks #2848
  • After saving an area with 'is absent' flag, the form stays locked in OTU radial Asserted distribution
  • Uniquify people roles list is missing role_object_tag #2853
  • Large list of taxon names are not loaded in Citations by source
  • Missing source_id parameter in Citation by source link on New asserted distribution and Browse OTU
  • New CO assigns a wrong Identifier type in New collecting event task #2862

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 3 years ago

TaxonWorks - Version 0.23.1 release

Added

  • Qualitative descriptor modal in matrix row coder #2763
  • Pin button for organization in attribution annotator #2551
  • Image inventory/filter endpoint for OTUs /api/v1/otus/123/inventory/images #2656
  • Option to error records if typeStatus is unprocessable in DwC occurrences importer #2829
  • Several taxon name classifications in DwC checklist importer #2732

Changed

  • Allow matching protonyms in DwC occurrences importer even on cases where the imported classification is a subset of the existing one #2740
  • Updated Ruby gems
  • Copying observations from object to object also copies their depictions #2823

Fixed

  • DwC importer looking up collecting events outside the scope of the current project
  • Missing names in hierarchy tree on Browse nomenclature task #2827
  • DwC importer finding names by original combination without project scope #2828
  • DwC export month field exporting day value rather than month #2835
  • Use unofficial serrano repo to fix problems with citeproc-json responses
  • DwC Occurrence Importer settings modal lags on open when many namespaces set #2834
  • Destroying last Depiction for Observation::Media destroys Observations #2269
  • Allowing to use same Namespace short name with different casing (e.g. 'alpha', 'Alpha')

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 3 years ago

TaxonWorks - Version 0.23.0 release

Added

  • Extract Filter #2270
  • Protocol facets for filters, currently on Extract filter
  • OTU descendants API endpoint .../otus/123/inventory/descendants #2791
  • Download SVG button in object graph task #2804
  • Rake task to generate docs.taxonworks.org Data documentation #2352
  • Confirmation window for delete documentation in radial annotator #2820
  • Drag and drop to sort predicates in project preferences #2821
  • Endpoints for observation matrix row and column labels #2800
  • Matrix row navigation in Matrix row coder #2800
  • Download enabled for controlled vocabulary terms #2809
  • Type materials metadata extension for /api/v1/otus

Changed

  • Tweaked how Extracts are displayed in various views
  • Browse nomenclature task was renamed to Browse nomenclature and classifications #2638
  • Add origin citations for taxon name relationships/classifications, renames route #2790
  • Add Download customization #2748
  • Show Images section in Browse OTU for GenusGroup #2786
  • User facet: Now button sets end date in Filter interfaces #2788
  • Changes content and layout ouf hierarchy navigator in Browse nomenclature task #2797
  • Scroll tables in New observation matrix task #2799
  • Updated Ruby gems
  • Replace autocomplete with OTU picker in biological associations form in radial object

Fixed

  • Author string for incorrect original spelling #2743
  • Type species section doesn't work in new taxon name #2785
  • Missing Variety and Form ranks in original combination section for ICZN in New taxon name task #2795
  • Check if current identifier is the same as current in comprehensive task #2550
  • Comprehensive digitization - entering '0' in total breaks the interface #2807
  • Download link doesn't work in data list view
  • Edit in Browse collecting event #2814
  • DwC importer is more robust to invalid taxon names

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly about 3 years ago

TaxonWorks - Version 0.22.7 release

Added

  • Add more date (redundant) fields to DwC export #2780
  • Import and export custom label style in print label task
  • Attributions in Filter images #2639
  • People, role, images stats to /api/v1/stats
  • basisOfRecord in DwC exports can be FossilSpecimen via biocuration
  • Classification section for Combination in New taxon name (botanical nomenclature support) #2681
  • API /api/v1/otus/:id includes &extend[] for parents

Changed

  • New interface for biocuration groups and classes
  • DwCA export is much faster
  • CSV export optimized
  • basisOfRecord now maps as http://rs.tdwg.org/dwc/terms/FossilSpecimen biocuration classification in DwC occurrences importer.
  • Updated ruby gems
  • Updated js packages
  • cached_is_valid is now used in interfaces to show if a taxon is valid or invalid
  • Refactor Manage biocuration classes and groups task #83

Fixed

  • occurrenceID missing from DwC exports. #2766
  • Cloning columns from matrices sometimes partially failed #2772
  • Missing Custom style button in Print label task #2764
  • Missing valid/invalid/combination mark in citation by source task #2760
  • Missing observation matrices in copy columns/rows from another matrix in New observation matrix task #2753
  • Handing of family names starting with O' being recognized as given names #2747
  • Error 500 deleting a biocuration term #2181
  • Uniquify people task shows "0" in used column and no roles #2769

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.22.6 release

Added

  • Option to select all and quick tag in Filter image task #2744

Changed

  • Perform georeferences caching in background for faster DwC occurrences import #2741
  • Permit use of Ruby 3.1
  • Updated Ruby gems.
  • DwC occurrences importer: When matching protonyms also consider their alternate gender names if there are no matches by exact name. #2738
  • Allow import of specimens with empty catalogNumber even when institutionCode and/or collectionCode are set.

Fixed

  • Several batch loaders not working due to syntax incompatibility with currently used Ruby version. #2739

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.22.5 release

Fixed

  • Fixed "eye" validation crash when activated in Browse Nomenclature task #2736

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.22.4 release

Added

  • Add reset filters button in DwC import task #2730

Changed

  • Add space on navbar in New taxon name #2701
  • Updated ruby gems and node packages.
  • Tabindex in model view

Fixed

  • Overdue loan date time ago #2712
  • Descriptor character state destroy raising #2713
  • Loan items status not updatable (also new specs) #2714
  • Collecting event filter depictions facet #2720
  • Taxonifi wrapper init was broken
  • Character order selector sends null value on blank selection #2707
  • Interactive keys is loading two matrices on autocomplete search #2706
  • Select observation matrix is not displaying all observation matrices #2708
  • Crashing when attempting to download DwC results from Filter Collection Objects task with 'Treat geographic areas as spatial' set.
  • Stats response contains projects count when project token is set.
  • Menu options broken when right-click on matrices in Observation matrix hub #2716
  • Copy rows from matrix in New observation matrix
  • GnFinder playground incompatibility with current GnFinder API
  • DwC checklist importer issue with synonyms have wrong rank #2715
  • Scientific name not cached properly when the taxon name is classified as part of speech #2721
  • Depictions dropzone tries to create Depictions before saving collecting event
  • Clipboard is not releasing key combination when the user clicks outside the window and release keys #2724
  • Removed destroy! pattern from various controllers
  • Unable to create loan items in Collection object match task #2731
  • DwC import search criteria is missing when search box is reopen #2729
  • Unable to download CoLDP exports
  • Otu facet in Filter image task

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.22.3 release

Added

  • Ability to inject links into Content via hot-key searching #1674

Changed

  • Upgraded to Postgres 12 in Docker Compose development environment. Postgres 10 container and volume are still present to allow for automatic data migration.

Fixed

  • Identifier form elements on SQED breakdown #2700

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.22.2 release

Changed

  • Upped from 40 to 500 the cutoff point at which updating a collecing event will trigger a DwcOccurrence rebuild
  • Added a url_base option when rendering metadata partial

Fixed

  • Author by first letter (/people.json) [2697]
  • Loan recipient helper methods were confused with loan helper methods
  • Subsequent combination link in new taxon name task #2695
  • Unable to create tags in batches due to Ruby 3 syntax changes.
  • Observation matrices crashing due to response pagination bug.
  • Unable to create namespaces due to debug code accidentally added.

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.22.1 release

Added

  • Georeferences can link to Protocols

Changed

  • API -added extend character_state option to /observations

Fixed

  • Custom attributes are not cleared on new record #2692
  • API - /api/v1/observation_matrices with no params failed
  • Asserted distribution link wasn't HTML safe

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.22.0 release

Add

  • Indecies on taxon name hierarchies table
  • Batch create user admin task #2680
  • Radial navigation in loan task
  • is_gift boolean to Loan
  • Loan item notes, type status, and recipient form layout improvements #2657
  • Recipient form link in Edit loan task
  • Gift checkbox in Loan task
  • API routes for data attributes via /api/v1/data_attributes #2366
  • API routes for observation matrices via /api/v1/observation_matrices
  • API route "status" for taxon names /taxon_names/api/v1/123/status #2243
  • API route "activity" for recent records/project /api/v1/activity?project_token=123&past_days=9 #2207
  • Indecies for updated_at on some large models
  • Observation matrix query filter (minimal)
  • Add download table button in DwC Importer
  • Confidence button on subsequent combination in New taxon name task
  • Create and new button in New descriptor task #2594
  • Content text is cropped on edit in OTU radial #2676
  • Diagnosis status in matrix row coder #2674
  • Layout preferences in comprehensive task #2673
  • API /api/v1/collection_objects includes &extend[] for dwc_fields and type_material
  • API /api/v1/taxon_names/123/status endpoint for human readable taxon name data and metadata (in part #2665)
  • is_virtual option to Namespace

Changed

  • Upgraded to Ruby 3.0.2
  • OTUs can be loaned 2x #2648
  • Upgraded gems
  • /collection_objects.json response uses &extend[]=dwc_fields to return DwC fields; includes metadata
  • Removed a loan item status 'Loaned on' (it's inferrred)
  • Replaced Webrick with Puma (developers-only change)
  • Improved loan autocomplete metadata #2485
  • API observation responses are now isolated from internal
  • DwC occurrences importer now accepts |, :, ; and , as separators for higherClassification.
  • Restrict subsequent combination fields for genus and subgenus. #2677
  • Moved matrix autocomplete into Include in matrix section in New descriptor task #2685

Fixed

  • Containerized specimens export their identifier to DwC
  • Biological association objects could be destroyed when referenced in biological association
  • Reordering matrices by nomenclature when some rows have none
  • Tag facet bug affecting all filters but Source #2678
  • View errors on rows with no metadata in DwC importer
  • Scrollbar in alternate values annotator #2651
  • Missing data on response in citations annotator #2653
  • Missing author and year in taxon name on Citation by source #2650
  • Duplicate combinations in subsequent combination on New taxon name #2654
  • Missing documents in source filter #2661
  • Clonning source does not clean the doccumentation section #2663
  • Extra scrollbar in asserted distributions annotator #2662
  • The citations annotator sometimes displays a created citations that are not part of the object
  • Move synonyms section not visible #2670
  • Collecting Event collectors are not loaded when CE is selected using smart selector in Comprehensive task #2669
  • Genus descriptor interface
  • Free text character not saved if pasted from clipboard in Matrix Row Coder #2672
  • DwC importer crashing on invalid nomenclatural code
  • DwC exporter swapped decimalLatitude/decimalLongitude
  • Error in Filter Collecting Event task when filtering by attributes that are stored as numbers in database
  • Set as current button it isn't working when taxon parent is root on Subsequent combination #2688
  • DwC checklist importing: original combination having wrong genus in some cases #2684

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.21.3 release

Changed

  • Loan addresses don't strip line-endings, and display in form #2641
  • Replace radial navigator icon [#2645]
  • Update smart selector tab selected on refresh

Fixed

  • Loan id facet #2632
  • Roles in Image viewer
  • Missing roles after trigger page autosave in new taxon name #2631
  • Tag smart selector in new image task

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.21.2 release

Added

  • Support for DwC terms on body of water depth #2628
  • Filter Collection Objects by a specific Loan [#2632]

Changed

  • Updated ruby gems.

Fixed

  • Containerized specimens display catalog number in tag correctly #2623
  • Improved CrossRef parsing for a new source [#997] [#2620]
  • Container label shows catalog number for loan items #1275
  • Determiners are not saved after lock the list in comprehensive form #2626
  • Wrong rank for original combinations in DwC checklist importer #2621
  • No longer exposing exception data for failed records (not to be confused with errored) in DwC importer.
  • Smart selector is not working in Browse Annotations
  • Biological associations in OTU radial #2630
  • Fix citations on asserted distribution list in OTU radial #2629
  • Subsequent combinations are not scoped #2634
  • Missing scroll in alternate value annotator #2635
  • Smart selectors are not refreshing in New source #2636
  • Radial navigation doesn't work on source in New taxon name task #2633
  • Determiner is not selectable on Grid Digitizer after "Create and new" #2637
  • DwC Dashboard data version counts correct now #2627
  • Common statuses are not displayed in New taxon name task #2642
  • Nomenclature and OTU (biology) display the same thing on Browse OTU page #2644
  • New combination task hangs editing a combination #2646

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.21.1 release

Fixed

  • Citations in image viewer

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.21.0 release

Added

  • Add new task 'Object graph', visualize and navigate your Things via a force-directed-graph (network) #2587
  • New combination editing, including support for multiple authors in plant names #666 #2407
  • Add new global identifier class for glbio repositories
  • New parameters for fine-tuning the API responses, &extend[]= and &embed[] #2531
  • Parameter value origin_citation via &extend[]= to all basic GET /object(/:id) requests #2531
  • Parameter value pinboard_item via &extend[]= to all basic GET /object(/:id) requests #2531
  • Parameter value citations via &extend[]= to all basic GET /object/:id requests #2531
  • Parameter values roles and documents via &extend[]= to /sources(/:id).json #2531
  • Parameter values protonyms and placement via &extend[]= to `/combinations(/:id).json #2531
  • Parameter values parent, otus, roles, ancestor_ids, children, type_taxon_name_relationship via &extend[]= to /taxon_names(/:id).json #2531
  • Parameter values level_names, geographic_area_type, parent via &extend[]= and shape via &embed[]= to /geographic_areas(/:id).json #2531
  • Parameter value subject, object, biological_relationship, family_names via &extend[]= to /biological_associations(/:id).json #2531
  • Parameter value citation_object, citation_topics, source, target_document via &extend[]= to /citations(/:id).json #2531
  • API route /taxon_names/parse?query_string=Aus bus for resolving names to Protonyms
  • Parameter value roles via &extend[]= to /collecting_events(/:id).json #2531
  • Param to isolate TaxonName smart select to Protonym if optional
  • Resize column in Filter tasks #2606
  • Confirmation banner in 'Collection Object Match'

Changed

  • Added new DwcOccurrence date-version
  • dwcSex and dwcStage are now referenced by BiocurationGroup #2615
  • Improved autocomplete search for Serials, Sources and Repositories #2612
  • Ordering of GeorgaphicArea autocomplete results. Used areas and areas with shapes are prioritized
  • Basic (REST) endpoints send less information, use &extend[] and &embed[] to return more #2531
  • Numerous tasks updated to use the new REST pattern
  • Objects in basic show/index JSON endpoints are represented by their metadata, rather than all their attributes in many cases now #2531
  • Metadata in extensions does not cascade and return metadata of metadata #2531
  • JSON smart-selector data (/sources/select_options) includes base attributes, not metadata #2531
  • Updated corresponding ap1/v1 endpoints to use the &extend[] pattern for /otus, /taxon_names, /combinations, /sources, /citations (in part) and biological_associations to match the new parameter values above
  • API /api/v1/biological_associations uses metadata for related objects
  • Optimized Source smart selection queries
  • Added option in DwC importer to specific the dataset type (defaults to auto-detection).
  • Replace autocomplete for smart selector in alternate values annotator #2610

Fixed

  • DwC recordedBy not referencing verbatim_collectors, only collectors #2617
  • DwC recordedByID returning delimiter only records
  • DwC decimalLatitude/Longitude incorrectly mapped #2616
  • Citation style taxonworks.csl is updated [#2600]
  • collector_id broken in CollecitonObject filter
  • Failure when setting up namespaces in DwC importer with datasets having unnamed columns
  • Namespace settings are not cleared when unmatched and re-opened in DwC Import #2586
  • ScientificNameAuthorship parsing issues in DwC importer #2589
  • Author and editor roles are missing after save or create a source in New source task [#2607]
  • Rank genus not being auto-detected when uninomial name in scientificName matches genus term value exactly
  • Soft validation block is displayed when is empty in New source task #2611
  • Clipboard shortcut hot-keys were broken
  • Serial raises on failed destroy gracefully handled
  • CrossRef assigns the wrong serial when journal is not present (partial) #2620

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.20.1 release

Added

  • Added Attribution attributes to /images API show responses
  • API /images can return images by image_file_fingerprint (MD5), in addition to id

Changed

  • Removed footprintWKT from DwcOccurrence. It will be re-instated as optional in the future.
  • Removed GeographicArea from consideration as a georeference in DwcOccurrence
  • Changed associatedMedia format, pointed it to
  • Removed redundant 'Rebuild' button from Browse collection objects

Fixed

  • DwC Dashboard past links are properly scoped
  • DwC Dashboard graphs show proper count ranges
  • DwC archive no longer truncated at 10k records
  • OccurrenceID was not being added to DwcOccurrence attributes in all cases #2573
  • Observation matrix show expand was referencing the wrong id #2540
  • Copy pasting into verbatim year with alphanumeric gives error even though numeric are all that are visible in New taxon name #2577
  • Record doesn't sync/update the list in OTU quick forms #2576
  • TIFF images are not visible in filter image task #2575
  • Repository input shows value, when not set #2574
  • Images don't load after expand depictions sections in comprehensive task
  • DwC occurrences importer being too strict when checking against existing nomenclature #2581

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.20.0 release

Added

  • Task DwC Import for importing DwC Archive files
  • Task DwC Dashboard facilitating DwCA download, metadata reporting, and "health" checks #1467
  • Updated framework for producing and downloading DwC Archives (DwCA) #1775 #1303
  • Increased from 21 to 53 the number of fields referenced in the (DwCA) dump, including identifiedByID and recordedByID #1269 #1230
  • Auto-generation of UUIDs for instances that don't have global identifiers during DwcOccurrence record building #2186
  • Wikidata (Q) and ORCiD support for people references in DwCA dumps
  • Georeferences can have Confidences assigned to them #1772
  • CSL style 'taxonworks.csl' used as the default style for displaying sources #2517
  • Custom CSL citation support for reference formating (see styles at bottom of select format list). New .cls submitted via issue tracker and integrated to source.
  • New .csl style 'world_chalcidoidea_book.csl"
  • BibTeX fields support verbatim values using "{}" for fields otherwise processed in BibTeX sources (e.g. author)
  • New specs for rendering Source citations
  • &extend[] and &embed[] helper methods for REST responses #2532
  • A new soft validation option to auto fix for objective synonym that must share the same type
  • Add Download, Full size and Radial navigation buttons in Image viewer #2423
  • Endpoint /tasks/dwc/dashboard/index_versions returns the dates at which DwcOccurrence indexing was modified. !! TODO: update date of merge.
  • Endpoint /dwc_occurrences/metadata, for stats on the state of DwcOccurrence index
  • Endpoint /dwc_occurrencs/predicates to return a list of Predicates used on CollectionObjects and CollectingEvents
  • Endpoint /dwc_occurrences/status to check whether DwcOccurrence records are up-to-date
  • Endpoint /dwc_occurrences/collector_id_metadata to check whether People referenced in DwcOccurences have GUIDs
  • Task on Administration panel, "Reindex", with (temporary) options to re-index small blocks of DwcOccurrence records
  • Button on CollectionObject filter to download filter result as DwC Archive #1303
  • User can select a corresponding Person as their data representation (facilitates Identifiers for Users) #1486
  • Centroid index on GeographicItem
  • Field total_records on Download
  • Index on polymorphic fields of DwcIndex (e.g. faster queries to CollectionObject)
  • Index on data_origin for GeographicAreasGeographicItem
  • Identifiers for AssertedDistributions
  • Various relationships enabling the joining of DwcOccurrence directly to other classes of data (e.g. Georeferences)
  • Isolated Georeference related utilities into their own module CollectingEvent::Georeference
  • A Taxonomy module that caches classification values, used in CollectionObject, and Otu
  • Methods to return when a record attribute was updated (e.g. verbatim_locality changed), and who did it for Papertrail including classes of data
  • Methods to handle multiple classes of globally unique identifiers on DwcOccurrence records
  • Pattern for isolating modules that aid DwC serialization per class of data
  • Optimized to_wkt to quickly return well-known-text for geo-shapes (in part, #2526)
  • New subclass of UUID Identifier::Global::Uuid::TaxonworksDwcOccurrence
  • Clarified, viageoreferenceSources and georeferenceProtocol why there are many decimal points in DwC latitude/longitude referencing fields #915 #1175
  • Option to rebuild single DwcOccurrence record for CollectionObject #2563
  • Ability to show observation matrices > 10k cells in size [#1790]
  • Rake task to rebuild source cached
  • Add download and radial buttons for image viewer in filter image

Fixed

  • Downloading formatted sources with mixed types (BibTeX/Verbatim) failed #2512
  • Collection object filter type material param
  • Taxon name filter type metadata param fails #2511
  • Cloning a collecting event fails #2533
  • Modified recordedBy fields to only reference collector #2567 #2558
  • Many TDWG gazeteer references will now be properly categorized into state and country labels #2542
  • In Browse Nomenclature removed link to self for invalid taxon names with no synonymy #2327
  • Add missing original citation to synonym names in CoLDP export #2543
  • Uniquify people slow when many roles present #2528
  • Match combination when protonym has synonym relationships [#2525]
  • TaxonNameRelationsip type_method returns nil properly on unmatched types [#2504]
  • Taxon determinations list in comprehensive task
  • The clone button doesn't trigger update taxon name after authors were cloned [#2513]
  • Georeference count in new collecting event task #2519
  • Autofocus in New taxon name task #2523
  • Geographic area counts as georeference. Soft validations are sometimes loaded before saving georeferences #2519
  • import_dataset_id parameter persist on after resetState in DwC Importer #2529
  • Updated Ruby gems and Node packages
  • In project button #2530
  • View image matrix is passing wrong ids [#2537]
  • Observations with depictions sometimes are removed after move a depiction #2549
  • Relationship facet in Filter nomenclature
  • Determiner facet (param) in Filter collection objects
  • Verbatim year input allows alphanumeric numbers in New taxon name
  • Labels list renders for those linked to objects, or not

Changed

  • Radial annotator Tag form uses a Keyword smart selector #2564
  • DwcOccurrence is rebuilt/refreshed each time Browse Collection Object is hit
  • footprintWKT is hidden in Browse CollectionOjbect #2559
  • Tweak geo coordinate matching on verbatim labels
  • Year suffix, stated year, language, translated title and notes added to bibliography rendering via to_citeproc
  • Removed label_html from /people responses
  • /people JSON param from &include_roles=true to &extend[]=roles
  • Prefer project sources in source autocomplete
  • Status name 'not for nomenclature' changed to 'not in published work'
  • Year letter is no longer appended to year in BibTeX exports
  • Include project's name in CoLDP exports filename #2509
  • Implemented STI for downloads #2498\
  • Upgraded gnfinder gem that makes use of new REST API
  • Refactor help code
  • Unified various DwC value returning methods in their own explicitly named extensions
  • Isolated CollectionObject filter and API param handling to their own module for reference in multiple controllers
  • DwcOccurrence individualCount is now Integer
  • Database ConnectionTimeoutErrors now result in a 503 response rather than a raise/email-warning
  • Added various :inverse_of across collection objects related models
  • DwcOccurrence#individualCount is integer now
  • Simplified SQL for ordering GeographicArea shapes
  • Tweak validation of ORCIDid format
  • Move autocomplete and lookup keyword to CVT controller #2571
  • Task Content by nomenclature can be customized by selecting a Topic
  • Remove identifier section in New type specimen
  • Nill strings ("\u0000") are stripped from fields before writing

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.19.7 release

Add

  • Export Observation::Media depictions as proxies for Otu depictions in NeXML #2142
  • Protonym verbatim_author parens should be properly closed when present #2453
  • Protonym verbatim_author can not contain digits (like years) #2452
  • Generic date field component #2451
  • New taxon determination component
  • Smart selectors in asserted distribution and biological association quick forms.

Changed

  • Cleaned up taxon name navigator appearance
  • Destroying a loanable object destroys corresponding LoanItems automatically #2319
  • NeXML image URLs use shortened URLs
  • Reorder date fields in comprehensive, extract and new collecting event tasks #2450
  • Set Vue 3 reactive vuex state in comprehensive store, removed unnecesary mutations and getters
  • Updated Ruby gems and Node packages
  • Bumped database_cleaner
  • Upgraded to ruby 6.1 #2474
  • Remove Taxon determination slice from OTU quick forms(Radial object)
  • Set active author tab in New taxon name #2461
  • Moved data-project-id to project name
  • Moved collection object soft validations in comprehensive task #2491
  • Remove reactivity in map component. Maps should render much faster now

Fixed

  • Tazon name hierarchical navigation broken #2487
  • CollectionObject filter type material facet bug
  • Trim buttons in comprehensive task
  • Trip code fields are empty after save.
  • Confidence button
  • spring not working on MacOS. Now RGeo/Proj is warmed up at initialization time
  • Combination preview label in New combination task
  • Smart selector is not refreshing after save #2468
  • Group and formation fields in comprehensive task
  • Changed date label #2473
  • Warning message persists when date exists in User facet #2480
  • Collection Object TODO List Task does not append right identifier number #2486
  • Loan item checkboxes reset when loan items "Updated" #2492
  • Loan item "select/deselect all" buttons missing after vue 3 migration #2493
  • Checkbox unbinding is not synced with update in Loan task #2495
  • Filter collection objects shortcuts
  • Fix identifier update in new type specimen task
  • Radial menus are inheriting CSS properties in some cases #2505

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.19.6 release

Added

  • New namespace task #1891
  • Taxon determination list lock button in comprehensive task #2088 #2443
  • Add elevation accuracy parsing for verbatim labels #2448

Changed

  • Date fields order in comprehensive task
  • Auto advance date fields in comprehensive task
  • Changed checkbox label sortable fields to reorder fields #2442
  • Modified behaviour of Source autocomplete and pattern for limiting results
  • Removed deprecated Travis CI files.

Fixed

  • Source autocomplete exact ID was not prioritized and/or skipped
  • Keyboard shortcuts modal reopens when closing help #2436
  • Title attribute contains html tags on citations in browse OTU
  • Increment identifier in CO editor keeps number of leading zeros, changing length of number #2435
  • Collecting event lock in comprehensive task
  • Georeferences are not locked with collecting event #2449
  • Elevation not being parsed from labels properly #2447

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.19.5 release

Added

  • Content smart selector
  • Biological association list lock button in comprehensive task
  • Dynamic shortcuts for radial annotator and radial object. Shortcut is the first letter of the slice

Changed

  • Replaced panels with modals in Content editor task
  • Soft validation panel in new type specimen task
  • Replaced create predicate with link to project attributes customization page in custom attributes section #2426
  • Editing from Browse Collecting Event now redirects to Collecting Event task.

Fixed

  • Create georeference from verbatim does not take uncertainty into account #2421
  • Cannot edit Georeference uncertainty in New collecting event task #2420
  • Georeference edit/delete button does not show up immediately on creation #2422
  • Unable to create a type specimen with an existing collection object
  • Catalog number is not updating after selecting another type specimen
  • Duplicate verbatim georeference on generate label in New collecting event and comprehensive tasks [#2427]
  • Biological association list persist after save and create a new collection object in comprehensive task
  • Comprehensive specimen task reset button adds false history entry in browser #2432
  • Whitespace chars in label preventing georefs to be properly parsed #2415
  • Rubocop broken settings
  • Extra semicolon in collecting event label when verbatim locality is blank

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago

TaxonWorks - Version 0.19.4 release

Fixed

  • Geographic areas not scoped in Georeferences pane until georeference added #2408
  • Georeference from previous collecting event shows up on new collecting event #2411
  • Fix biological associations in comprehensive form
  • Removed events for links in radial navigation #2412

Added

  • Storage for PDF viewer

Biosphere - Biodiversity Data Access and Management - Ruby
Published by LocoDelAssembly over 3 years ago