Merge branch 'development'

CHANGELOG.md

@@ -9,6 +9,45 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.35.0] - 2023-10-19
+
+### 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+- Outdated names task for CollectionObjects (compare to COL) [#2585]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]
+
+
+[#2585]: https://github.com/SpeciesFileGroup/taxonworks/issues/2585
+[#1009]: https://github.com/SpeciesFileGroup/taxonworks/issues/1009
+[#3593]: https://github.com/SpeciesFileGroup/taxonworks/issues/3593
+[#3594]: https://github.com/SpeciesFileGroup/taxonworks/issues/3594
+[#3590]: https://github.com/SpeciesFileGroup/taxonworks/issues/3590
+[#3434]: https://github.com/SpeciesFileGroup/taxonworks/issues/3434
+[#3591]: https://github.com/SpeciesFileGroup/taxonworks/issues/3591
+
 ## [0.34.6] - 2023-10-06
 
 ### Added
@@ -42,7 +81,6 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - GeographicAreas not registering for some DWCA imports [#3575]
 - New collecting event: georeference from verbatim button creates two identical georeferences [#3573]
 
-
 [#3035]: https://github.com/SpeciesFileGroup/taxonworks/issues/3035
 [#1355]: https://github.com/SpeciesFileGroup/taxonworks/issues/1355
 [#3562]: https://github.com/SpeciesFileGroup/taxonworks/issues/3562
@@ -3941,7 +3979,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Loosing input page numbers when switching tabs on New Taxon Name task
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.6...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.35.0...development
+[0.35.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.6...v0.35.0
 [0.34.6]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.5...v0.34.6
 [0.34.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.4...v0.34.5
 [0.34.4]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.3...v0.34.4

Gemfile

@@ -28,7 +28,7 @@ gem 'roo', '~> 2.8', '>= 2.8.3'
 gem 'roo-xls', '~> 1.2'
 gem 'net-smtp', '~> 0.3.1'
 gem 'mail', '~> 2.8', '>= 2.8.1'
-gem "matrix", "~> 0.4.2"
+gem 'matrix', '~> 0.4.2'
 
 # Geo
 
@@ -104,7 +104,7 @@ gem 'chartkick', '~> 4.0'
 gem 'groupdate', '~> 5.2'
 gem 'dropzonejs-rails', '~> 0.8.1'
 gem 'kaminari', '~> 1.2.0'
-gem "best_in_place", git: "https://github.com/mmotherwell/best_in_place"
+gem 'best_in_place', git: 'https://github.com/mmotherwell/best_in_place'
 gem 'redcarpet', '~> 3.4'
 gem 'sassc-rails', '~> 2.1.0'
 gem 'waxy', '~> 0.1.1'
@@ -123,6 +123,8 @@ gem 'dwc-archive', github: 'LocoDelAssembly/dwc-archive', branch: 'overhaul' # '
 gem 'biodiversity', github: 'GlobalNamesArchitecture/biodiversity', branch: 'pipe_approach' # '~> 5.1', '>= 5.1.1'
 gem 'ruby-units', '~> 2.3.0', require: 'ruby_units/namespaced'
 
+gem 'colrapi', '~>0.1.1'
+
 # Global Names
 gem 'gnfinder', '~> 1.0'
 
@@ -189,7 +191,7 @@ end
 group :test do
   gem 'rspec', '~> 3.6'
   gem 'codecov', '~> 0.6.0'
-  gem 'simplecov', :require => false
+  gem 'simplecov', require: false
   gem 'capybara', '~> 3.18'
   gem 'timecop', '~> 0.9.1'
   gem 'webmock', '~> 3.8' # , '>= 3.6.2'

Gemfile.lock

@@ -197,6 +197,10 @@ GEM
     codecov (0.6.0)
       simplecov (>= 0.15, < 0.22)
     coderay (1.1.3)
+    colrapi (0.1.1)
+      faraday (~> 2.2)
+      faraday-follow_redirects (>= 0.1, < 0.4)
+      multi_json (~> 1.15)
     concurrent-ruby (1.2.2)
     crack (0.4.5)
       rexml
@@ -217,7 +221,7 @@ GEM
     debug_inspector (1.1.0)
     delayed_job (4.1.11)
       activesupport (>= 3.0, < 8.0)
-    delayed_job_active_record (4.1.7)
+    delayed_job_active_record (4.1.8)
       activerecord (>= 3.0, < 8.0)
       delayed_job (>= 3.0, < 5)
     diff-lcs (1.5.0)
@@ -226,7 +230,7 @@ GEM
       unf (>= 0.0.5, < 1.0.0)
     dropzonejs-rails (0.8.5)
       rails (> 3.1)
-    dwc_agent (3.0.13.0)
+    dwc_agent (3.0.15.0)
       namae (~> 1)
       namecase (~> 2)
     erubi (1.12.0)
@@ -320,7 +324,7 @@ GEM
       parslet
     logical_query_parser (0.3.2)
       treetop (~> 1.6.8)
-    loofah (2.21.3)
+    loofah (2.21.4)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     lumberjack (1.2.9)
@@ -345,7 +349,7 @@ GEM
     namae (1.1.1)
     namecase (2.0.0)
     nenv (0.3.0)
-    net-imap (0.4.0)
+    net-imap (0.4.1)
       date
       net-protocol
     net-pop (0.1.2)
@@ -370,7 +374,7 @@ GEM
     paperclip-meta (3.1.0)
       paperclip (>= 5.0)
     parallel (1.23.0)
-    parallel_tests (4.2.2)
+    parallel_tests (4.3.0)
       parallel
     parser (3.2.2.4)
       ast (~> 2.4.1)
@@ -456,11 +460,11 @@ GEM
     rdoc (6.3.3)
     redcarpet (3.6.0)
     redis (4.8.1)
-    regexp_parser (2.8.1)
+    regexp_parser (2.8.2)
     request_store (1.5.1)
       rack (>= 1.4)
     require_all (3.0.0)
-    responders (3.1.0)
+    responders (3.1.1)
       actionpack (>= 5.2)
       railties (>= 5.2)
     rest-client (2.1.0)
@@ -515,12 +519,12 @@ GEM
       rspec-support (~> 3.10)
     rspec-support (3.12.1)
     rtesseract (3.1.3)
-    rubocop (1.56.4)
+    rubocop (1.57.1)
       base64 (~> 0.1.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.3)
+      parser (>= 3.2.2.4)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
@@ -568,7 +572,7 @@ GEM
       rdoc (>= 5.0)
     seedbank (0.5.0)
       rake (>= 10.0)
-    selenium-webdriver (4.13.1)
+    selenium-webdriver (4.14.0)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)
@@ -655,7 +659,7 @@ GEM
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
-    wikidata-client (0.1.0.pre.rc1)
+    wikidata-client (0.1.0)
       excon (~> 0.92)
       faraday (~> 2.2)
       faraday-excon (~> 2.1)
@@ -695,6 +699,7 @@ DEPENDENCIES
   citeproc-ruby (~> 1.1.10)
   closure_tree (~> 7.0)
   codecov (~> 0.6.0)
+  colrapi (~> 0.1.1)
   csl (~> 1.6.0)
   csl-styles (~> 1.0.1.8)
   daemons (~> 1.4.1)

app/controllers/alternate_values_controller.rb

@@ -12,15 +12,15 @@ def index
         # !! This is project-only, it will be tricky to find all created at this point. We would have
         # to reference all project members and link through created/modified on all community opbjects.
         # These would show up throughout the Users project as well, confusing things across project.
-        @recent_objects = Queries::AlternateValue::Filter.new(params.merge(project_id: sessions_current_project_id))
+        @recent_objects = ::Queries::AlternateValue::Filter.new(params.merge(project_id: sessions_current_project_id))
           .all
           .order(updated_at: :desc).limit(10)
           render '/shared/data/all/index'
       }
       format.json {
         # !! You must merge project_id to handle community data exceptions.  This is a contrast to other filter patterns
         # where the project_id is scoped here.
-        @alternate_values = Queries::AlternateValue::Filter.new(
+        @alternate_values = ::Queries::AlternateValue::Filter.new(
           params.merge(project_id: sessions_current_project_id)
         )
         .all.page(params[:page])
@@ -106,7 +106,7 @@ def autocomplete
 
   # GET /alternate_values/download
   def download
-    send_data Export::Download.generate_csv(AlternateValue.where(project_id: sessions_current_project_id)), type: 'text', filename: "alternate_values_#{DateTime.now}.csv"
+    send_data Export::Download.generate_csv(AlternateValue.where(project_id: sessions_current_project_id)), type: 'text', filename: "alternate_values_#{DateTime.now}.tsv"
   end
 
   # GET /alternate_values/:global_id/metadata

app/controllers/asserted_distributions_controller.rb

@@ -15,7 +15,7 @@ def index
         render '/shared/data/all/index'
       }
       format.json {
-        @asserted_distributions = Queries::AssertedDistribution::Filter.new(params)
+        @asserted_distributions = ::Queries::AssertedDistribution::Filter.new(params)
           .all
           .where(project_id: sessions_current_project_id)
           .page(params[:page])
@@ -27,7 +27,6 @@ def index
   # GET /asserted_distributions/1
   # GET /asserted_distributions/1.json
   def show
-    # @asserted_distribution = AssertedDistribution.find(params[:id])
   end
 
   # GET /asserted_distributions/new
@@ -90,7 +89,7 @@ def list
   end
 
   def autocomplete
-    @asserted_distributions = Queries::AssertedDistribution::Autocomplete.new(params.require(:term), project_id: sessions_current_project_id).autocomplete
+    @asserted_distributions = ::Queries::AssertedDistribution::Autocomplete.new(params.require(:term), project_id: sessions_current_project_id).autocomplete
   end
 
   # TODO: deprecate
@@ -107,7 +106,7 @@ def download
     send_data(
       Export::Download.generate_csv(AssertedDistribution.where(project_id: sessions_current_project_id)),
       type: 'text',
-      filename: "asserted_distributions_#{DateTime.now}.csv")
+      filename: "asserted_distributions_#{DateTime.now}.tsv")
   end
 
   # GET /asserted_distributions/batch_load
@@ -149,7 +148,7 @@ def create_simple_batch_load
   end
 
   def api_index
-    @asserted_distributions = Queries::AssertedDistribution::Filter.new(params.merge!(api: true))
+    @asserted_distributions = ::Queries::AssertedDistribution::Filter.new(params.merge!(api: true))
       .all
       .where(project_id: sessions_current_project_id)
       .includes(:citations, :otu, geographic_area: [:parent, :geographic_area_type], origin_citation: [:source])

app/controllers/attributions_controller.rb

@@ -1,6 +1,6 @@
 class AttributionsController < ApplicationController
   include DataControllerConfiguration::ProjectDataControllerConfiguration
-  
+
   before_action :set_attribution, only: [:show, :edit, :update, :destroy]
   after_action -> { set_pagination_headers(:attributions) }, only: [:index, :api_index ], if: :json_request?
 
@@ -13,7 +13,7 @@ def index
         render '/shared/data/all/index'
       end
       format.json {
-        @attributions = Queries::Attribution::Filter.new(params).all.where(project_id: sessions_current_project_id).
+        @attributions = ::Queries::Attribution::Filter.new(params).all.where(project_id: sessions_current_project_id).
         page(params[:page]).per(params[:per] || 500)
       }
     end

app/controllers/citations_controller.rb

@@ -126,7 +126,7 @@ def autocomplete
 
   # GET /citations/download
   def download
-    send_data Export::Download.generate_csv(Citation.where(project_id: sessions_current_project_id)), type: 'text', filename: "citations_#{DateTime.now}.csv"
+    send_data Export::Download.generate_csv(Citation.where(project_id: sessions_current_project_id)), type: 'text', filename: "citations_#{DateTime.now}.tsv"
   end
 
   def api_index

app/controllers/collecting_events_controller.rb

@@ -148,7 +148,7 @@ def autocomplete_collecting_event_verbatim_locality
   def download
     send_data(Export::Download.generate_csv(CollectingEvent.where(project_id: sessions_current_project_id)),
               type: 'text',
-              filename: "collecting_events_#{DateTime.now}.csv")
+              filename: "collecting_events_#{DateTime.now}.tsv")
   end
 
   # parse verbatim label, return date and coordinates

app/controllers/collection_object_observations_controller.rb

@@ -101,17 +101,17 @@ def search
   def download
     send_data(Export::Download.generate_csv(CollectionObjectObservation.where(project_id: sessions_current_project_id)),
               type: 'text',
-              filename: "collection_object_observations_#{DateTime.now}.csv")
+              filename: "collection_object_observations_#{DateTime.now}.tsv")
   end
 
   private
     # Use callbacks to share common setup or constraints between actions.
-    def set_collection_object_observation
-      @collection_object_observation = CollectionObjectObservation.where(project_id: sessions_current_project_id).find(params[:id])
-    end
+  def set_collection_object_observation
+    @collection_object_observation = CollectionObjectObservation.where(project_id: sessions_current_project_id).find(params[:id])
+  end
 
     # Never trust parameters from the scary internet, only allow the white list through.
-    def collection_object_observation_params
-      params.require(:collection_object_observation).permit(:data)
-    end
+  def collection_object_observation_params
+    params.require(:collection_object_observation).permit(:data)
+  end
 end

app/controllers/collection_objects_controller.rb

@@ -258,7 +258,7 @@ def search
 
   # GET /collection_objects/download
   def download
-    send_data Export::Download.generate_csv(CollectionObject.where(project_id: sessions_current_project_id), header_converters: []), type: 'text', filename: "collection_objects_#{DateTime.now}.csv"
+    send_data Export::Download.generate_csv(CollectionObject.where(project_id: sessions_current_project_id), header_converters: []), type: 'text', filename: "collection_objects_#{DateTime.now}.tsv"
   end
 
   # GET collection_objects/batch_load

app/controllers/concerns/whitelist.rb

@@ -6,7 +6,7 @@ def whitelist_constantize(klass_name)
     # if Rails.env.development?
     #   ApplicationEnumeration.data_models.inject({}){|hsh, k| hsh.merge!(k.name => k)}.fetch(klass_name)
     # elsif Rails.env.production?
-      ::DATA_MODELS.fetch(klass_name)
+    ::DATA_MODELS.fetch(klass_name)
     # else
     #   raise TaxonWorks::Error, 'whitelist attempted in unknown environment'
     # end

app/controllers/confidences_controller.rb

@@ -64,7 +64,7 @@ def update
     end
   end
 
-  def confidence_object_update 
+  def confidence_object_update
     @confidence_object = confidence_object
     if @confidence_object.update(confidences_params)
       flash[:notice] = 'Successfully updated record.'
@@ -94,7 +94,7 @@ def search
 
   # GET /confidences/download
   def download
-    send_data Export::Download.generate_csv(Confidence.where(project_id: sessions_current_project_id)), type: 'text', filename: "confidences_#{DateTime.now}.csv"
+    send_data Export::Download.generate_csv(Confidence.where(project_id: sessions_current_project_id)), type: 'text', filename: "confidences_#{DateTime.now}.tsv"
   end
 
   def exists

app/controllers/contents_controller.rb

@@ -114,7 +114,7 @@ def download
     send_data(
       Export::Download.generate_csv(::Content.where(project_id: sessions_current_project_id)),
       type: 'text',
-      filename: "contents_#{DateTime.now}.csv")
+      filename: "contents_#{DateTime.now}.tsv")
   end
 
   # GET /api/v1/content

app/controllers/controlled_vocabulary_terms_controller.rb

@@ -121,7 +121,7 @@ def download
     send_data(
       Export::Download.generate_csv(ControlledVocabularyTerm.where(project_id: sessions_current_project_id)),
       type: 'text',
-      filename: "controlled_vocabulary_terms_#{DateTime.now}.csv")
+      filename: "controlled_vocabulary_terms_#{DateTime.now}.tsv")
   end
 
   # GET /controlled_vocabulary_terms/1/tagged_objects