Merge branch 'development'

CHANGELOG.md

@@ -9,6 +9,46 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.37.0] - 2023-12-14
+
+### 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
+
+[#187]: https://github.com/SpeciesFileGroup/taxonpages/issues/187
+[#2749]: https://github.com/SpeciesFileGroup/taxonworks/issues/2749
+[#3113]: https://github.com/SpeciesFileGroup/taxonworks/issues/3113
+[#3645]: https://github.com/SpeciesFileGroup/taxonworks/issues/3645
+[#3680]: https://github.com/SpeciesFileGroup/taxonworks/issues/3680 
+[#3690]: https://github.com/SpeciesFileGroup/taxonworks/issues/3690
+[#3696]: https://github.com/SpeciesFileGroup/taxonworks/issues/3696
+
 ## [0.36.0] - 2023-11-30
 
 ### Added
@@ -4138,7 +4178,8 @@ 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/v0.36.0...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.37.0...development
+[0.37.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.36.0...v0.37.0
 [0.36.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.35.3...v0.36.0
 [0.35.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.35.2...v0.35.3
 [0.35.2]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.35.1...v0.35.2

Gemfile.lock

@@ -147,7 +147,7 @@ GEM
       zeitwerk (~> 2.3)
     acts_as_list (1.1.0)
       activerecord (>= 4.2)
-    addressable (2.8.5)
+    addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
     afm (0.2.2)
     amazing_print (1.4.0)
@@ -157,7 +157,7 @@ GEM
     babel-transpiler (0.7.0)
       babel-source (>= 4.0, < 6)
       execjs (~> 2.0)
-    barby (0.6.8)
+    barby (0.6.9)
     base64 (0.2.0)
     bcp47_spec (0.2.1)
     bcrypt (3.1.20)
@@ -218,7 +218,7 @@ GEM
       database_cleaner-core (~> 2.0.0)
     database_cleaner-core (2.0.1)
     date (3.3.4)
-    debug_inspector (1.1.0)
+    debug_inspector (1.2.0)
     delayed_job (4.1.11)
       activesupport (>= 3.0, < 8.0)
     delayed_job_active_record (4.1.8)
@@ -236,7 +236,7 @@ GEM
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
-    excon (0.105.0)
+    excon (0.106.0)
     execjs (2.8.1)
     factory_bot (6.4.2)
       activesupport (>= 5.0.0)
@@ -300,7 +300,7 @@ GEM
     jquery-turbolinks (2.1.0)
       railties (>= 3.1.0)
       turbolinks
-    json (2.6.3)
+    json (2.7.1)
     kaminari (1.2.2)
       activesupport (>= 4.1.0)
       kaminari-actionview (= 1.2.2)
@@ -337,7 +337,7 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1003)
+    mime-types-data (3.2023.1205)
     mimemagic (0.3.10)
       nokogiri (~> 1)
       rake
@@ -348,7 +348,7 @@ GEM
     namae (1.1.1)
     namecase (2.0.0)
     nenv (0.3.0)
-    net-imap (0.4.7)
+    net-imap (0.4.8)
       date
       net-protocol
     net-pop (0.1.2)
@@ -358,7 +358,7 @@ GEM
     net-smtp (0.3.3)
       net-protocol
     netrc (0.11.0)
-    nio4r (2.6.1)
+    nio4r (2.7.0)
     nokogiri (1.15.5-x86_64-darwin)
       racc (~> 1.4)
     nokogiri (1.15.5-x86_64-linux)
@@ -459,7 +459,7 @@ GEM
     rdoc (6.3.3)
     redcarpet (3.6.0)
     redis (4.8.1)
-    regexp_parser (2.8.2)
+    regexp_parser (2.8.3)
     request_store (1.5.1)
       rack (>= 1.4)
     require_all (3.0.0)
@@ -518,15 +518,15 @@ GEM
       rspec-support (~> 3.10)
     rspec-support (3.12.1)
     rtesseract (3.1.3)
-    rubocop (1.57.2)
+    rubocop (1.59.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.2.2.4)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.28.1, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.30.0)
@@ -571,7 +571,7 @@ GEM
       rdoc (>= 5.0)
     seedbank (0.5.0)
       rake (>= 10.0)
-    selenium-webdriver (4.15.0)
+    selenium-webdriver (4.16.0)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)

app/assets/stylesheets/base/dimensions.scss

@@ -1,4 +1,3 @@
-
 $viewport_height: 768px;
 $viewport_width: 1024px;
 
@@ -22,6 +21,10 @@ $viewport_width: 1024px;
   width: 100%;
 }
 
+.full_height {
+  height: 100%;
+}
+
 .width-auto {
   width: auto !important;
 }
@@ -38,15 +41,16 @@ $viewport_width: 1024px;
   width: 20%;
 }
 
-.one_third_width, .width-30 {
+.one_third_width,
+.width-30 {
   width: 30%;
 }
 
-.half_width { 
+.half_width {
   width: 50%;
 }
 
-.three_quarter_width { 
+.three_quarter_width {
   width: 75%;
 }
 
@@ -58,13 +62,11 @@ $viewport_width: 1024px;
   width: 40%;
 }
 
-
-
 // this might belong elsewhere
-.attributes  {
+.attributes {
   p {
-    width:100%;
-    word-wrap:break-word;
+    width: 100%;
+    word-wrap: break-word;
   }
 }
 
@@ -76,9 +78,10 @@ $viewport_width: 1024px;
   display: block;
 }
 
-p.list { margin-top: 0em;
-         margin-bottom: 0em;
-         margin-left: 1em;
+p.list {
+  margin-top: 0em;
+  margin-bottom: 0em;
+  margin-left: 1em;
 }
 
 .overflow-x-scroll {
@@ -87,4 +90,4 @@ p.list { margin-top: 0em;
 
 .overflow-y-scroll {
   overflow-y: scroll;
-}
+}

app/assets/stylesheets/views/loans/loans.scss

@@ -16,7 +16,7 @@
   margin: 0 auto;
   max-width: 1020px;
 
-  .loan_address { 
+  .address {
     display:inline-block;
     max-width: 5cm;
   }
@@ -58,6 +58,16 @@
     margin-bottom: 1em;
   }
 
+  pre {
+    padding-top: 4px;
+    background-color: transparent;
+    padding: 4px 0px 0px 0px;
+    margin: 0px;
+    color: $default_text;
+    font-family: IBM Plex Sans,Helvetica,Arial,Verdana,Tahoma;
+    font-size: 13px !important;
+  }
+
   #lender_details {
     text-align: right;
     li {
@@ -68,6 +78,10 @@
   #recipient_details {
     margin-bottom: 1em;
     max-width: 40%;
+    text-align: left;
+     li {
+      list-style: none;
+    }
   }
 
   #loan_items {

app/controllers/asserted_distributions_controller.rb

@@ -113,11 +113,16 @@ def download
   def batch_load
   end
 
-  # PATCH /asserted_distributions/batch_move.json?asserted_distribution_query=<>&geographic_area_id
-  def batch_move
-    if @result = AssertedDistribution.batch_move(params)
+  # PATCH /asserted_distributions/batch_update.json?asserted_distributions_query=<>&asserted_distribution={taxon_name_id=123}}
+  def batch_update
+    if r = AssertedDistribution.batch_update(
+        preview: params[:preview], 
+        asserted_distribution: asserted_distribution_params.merge(by: sessions_current_user_id),
+        asserted_distribution_query: params[:asserted_distribution_query],
+    )
+      render json: r.to_json, status: :ok
     else
-      render json: {success: false}
+      render json: {}, status: :unprocessable_entity
     end
   end
 

app/controllers/biological_associations_controller.rb

@@ -131,26 +131,12 @@ def api_index
     end
   end
 
-  # POST /biological_associations/batch_update.json?biological_association_query=<>&biological_association={}
+  # PATCH /biological_associations/batch_update.json?biological_association_query=<>&biological_association={}
   def batch_update
     if r = BiologicalAssociation.batch_update(
-        {
-          preview: params[:preview],
-          biological_association: biological_association_params.merge(by: sessions_current_user_id) ,
-          biological_association_query: params[:biological_association_query]
-        }
-    )
-      render json: r.to_json, status: :ok
-    else
-      render json: {}, status: :unprocessable_entity
-    end
-  end
-
-  # POST /biological_associations/batch_rotate.json?biological_association_query=<>&biological_association={}
-  def batch_rotate
-    if r = BiologicalAssociation.batch_rotate(
-        params.merge(by: sessions_current_user_id)
-    )
+        preview: params[:preview],
+        biological_association: biological_association_params.merge(by: sessions_current_user_id),
+        biological_association_query: params[:biological_association_query] )
       render json: r.to_json, status: :ok
     else
       render json: {}, status: :unprocessable_entity
@@ -169,6 +155,7 @@ def biological_association_params
       :biological_association_object_id, :biological_association_object_type,
       :subject_global_id,
       :object_global_id,
+      :rotate,
       origin_citation_attributes: [:id, :_destroy, :source_id, :pages],
       citations_attributes: [:id, :is_original, :_destroy, :source_id, :pages, :citation_object_id, :citation_object_type],
     )

app/controllers/collecting_events_controller.rb

@@ -124,13 +124,13 @@ def autocomplete
     @collecting_events = Queries::CollectingEvent::Autocomplete.new(params[:term], project_id: sessions_current_project_id).autocomplete
   end
 
-  # POST /collecting_events/batch_update.json?collecting_event_query=<>&collecting_event={}
+  # PATCH /collecting_events/batch_update.json?collecting_event_query=<>&collecting_event={}
   def batch_update
-    if c = CollectingEvent.batch_update(
-        collecting_event: collecting_event_params.merge(by: sessions_current_user_id) ,
-        collecting_event_query: params[:collecting_event_query]
-     )
-      render json: {}, status: :ok
+    if r = CollectingEvent.batch_update(
+        preview: params[:preview],
+        collecting_event: collecting_event_params.merge(by: sessions_current_user_id),
+        collecting_event_query: params[:collecting_event_query])
+      render json: r.to_json, status: :ok
     else
       render json: {}, status: :unprocessable_entity
     end

app/controllers/collection_objects_controller.rb

@@ -398,13 +398,16 @@ def batch_update_dwc_occurrence
     end
   end
 
-  # POST /collection_object/batch_update.json?collection_object_query=<>&collection_object={}
+  # PATCH /collection_object/batch_update.json?collection_object_query=<>&collection_object={}
   def batch_update
-    c = CollectionObject.query_batch_update({
-      collection_object: collection_object_params.merge(by: sessions_current_user_id),
-      collection_object_query: params[:collection_object_query]
-    })
-    render json: c[:result], status: c[:status]
+    if c = CollectionObject.batch_update(
+        preview: params[:preview],
+        collection_object: collection_object_params.merge(by: sessions_current_user_id),
+        collection_object_query: params[:collection_object_query])
+      render json: c.to_json, status: :ok
+    else
+      render json: {}, status: :unprocessable_entity
+    end
   end
 
   private
@@ -437,6 +440,7 @@ def collection_object_params
       collecting_event_attributes: [],  # needs to be filled out!
       data_attributes_attributes: [ :id, :_destroy, :controlled_vocabulary_term_id, :type, :value ],
       tags_attributes: [:id, :_destroy, :keyword_id],
+      depictions_attributes: [:id, :_destroy, :svg_clip, :svg_view_box, :position, :caption, :figure_label, :image_id],
       identifiers_attributes: [
         :id,
         :_destroy,

app/controllers/downloads_controller.rb

@@ -70,6 +70,7 @@ def list
   def file
     if @download.ready?
       @download.increment!(:times_downloaded)
+      response.headers["Content-Length"] = File.size(@download.file_path).to_s
       send_file @download.file_path
     else
       redirect_to download_url