Merge branch 'development'

SpeciesFileGroup · Oct 6, 2023 · e3d7168 · e3d7168
2 parents 7464d16 + ce005c2
commit e3d7168
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,54 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.34.6] - 2023-10-06
+
+### 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]
+
+
+[#3035]: https://github.com/SpeciesFileGroup/taxonworks/issues/3035
+[#1355]: https://github.com/SpeciesFileGroup/taxonworks/issues/1355
+[#3562]: https://github.com/SpeciesFileGroup/taxonworks/issues/3562
+[#3584]: https://github.com/SpeciesFileGroup/taxonworks/issues/3584
+[#3561]: https://github.com/SpeciesFileGroup/taxonworks/issues/3561
+[#3545]: https://github.com/SpeciesFileGroup/taxonworks/issues/3545
+[#3571]: https://github.com/SpeciesFileGroup/taxonworks/issues/3571
+[#3573]: https://github.com/SpeciesFileGroup/taxonworks/issues/3573
+[#3574]: https://github.com/SpeciesFileGroup/taxonworks/issues/3574
+[#3577]: https://github.com/SpeciesFileGroup/taxonworks/issues/3577
+[#3579]: https://github.com/SpeciesFileGroup/taxonworks/issues/3579
+[#3582]: https://github.com/SpeciesFileGroup/taxonworks/issues/3582
+[#3583]: https://github.com/SpeciesFileGroup/taxonworks/issues/3583
+
 ## [0.34.5] - 2023-09-26
 
 ### Added
@@ -3893,7 +3941,8 @@ 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/v0.34.5...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.6...development
+[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
 [0.34.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.2...v0.34.3

diff --git a/Gemfile b/Gemfile
@@ -82,7 +82,8 @@ gem 'sprockets-es6', '~> 0.9.2', require: 'sprockets/es6'
 gem 'uglifier', '~> 4.2'
 
 gem 'jquery-rails', '~> 4.4'
-gem 'jquery-ui-rails', '~> 6.0.1'
+# gem 'jquery-ui-rails', '~> 6.0.1'
+gem "jquery-ui-rails", :git => 'https://github.com/jquery-ui-rails/jquery-ui-rails.git'
 gem 'rails-jquery-autocomplete', '~> 1.0.3'
 
 gem 'turbolinks', '~> 5.2.0'

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -55,6 +55,13 @@ GIT
       rexml (~> 3.2, >= 3.2.5)
       thor (~> 1.2.0, >= 1.2.0)
 
+GIT
+  remote: https://github.com/jquery-ui-rails/jquery-ui-rails.git
+  revision: c7460b447589eb04aa948ecaf0d1245c88f6ff45
+  specs:
+    jquery-ui-rails (7.0.0)
+      railties (>= 3.2.16)
+
 GIT
   remote: https://github.com/mjy/rqrcode.git
   revision: 7dfe8f371ca74099148cb58d3c9054c7e39eb038
@@ -226,7 +233,7 @@ GEM
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
-    excon (0.103.0)
+    excon (0.104.0)
     execjs (2.8.1)
     factory_bot (6.2.1)
       activesupport (>= 5.0.0)
@@ -245,7 +252,7 @@ GEM
     faraday-follow_redirects (0.3.0)
       faraday (>= 1, < 3)
     faraday-net_http (3.0.2)
-    ffi (1.16.2)
+    ffi (1.16.3)
     ffi-geos (2.4.0)
       ffi (>= 1.0.0)
     formatador (1.1.0)
@@ -290,8 +297,6 @@ GEM
     jquery-turbolinks (2.1.0)
       railties (>= 3.1.0)
       turbolinks
-    jquery-ui-rails (6.0.1)
-      railties (>= 3.2.16)
     json (2.6.3)
     kaminari (1.2.2)
       activesupport (>= 4.1.0)
@@ -329,7 +334,7 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.0808)
+    mime-types-data (3.2023.1003)
     mimemagic (0.3.10)
       nokogiri (~> 1)
       rake
@@ -340,7 +345,7 @@ GEM
     namae (1.1.1)
     namecase (2.0.0)
     nenv (0.3.0)
-    net-imap (0.3.7)
+    net-imap (0.4.0)
       date
       net-protocol
     net-pop (0.1.2)
@@ -367,7 +372,7 @@ GEM
     parallel (1.23.0)
     parallel_tests (4.2.2)
       parallel
-    parser (3.2.2.3)
+    parser (3.2.2.4)
       ast (~> 2.4.1)
       racc
     parslet (2.0.0)
@@ -509,8 +514,8 @@ GEM
       rspec-mocks (~> 3.10)
       rspec-support (~> 3.10)
     rspec-support (3.12.1)
-    rtesseract (3.1.2)
-    rubocop (1.56.3)
+    rtesseract (3.1.3)
+    rubocop (1.56.4)
       base64 (~> 0.1.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
@@ -534,7 +539,7 @@ GEM
     rubocop-performance (1.19.1)
       rubocop (>= 1.7.0, < 2.0)
       rubocop-ast (>= 0.4.0)
-    rubocop-rails (2.21.1)
+    rubocop-rails (2.21.2)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
@@ -631,7 +636,7 @@ GEM
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.8.2)
-    unicode-display_width (2.4.2)
+    unicode-display_width (2.5.0)
     validates_timeliness (4.1.1)
       timeliness (>= 0.3.10, < 1)
     vcr (6.2.0)
@@ -712,7 +717,7 @@ DEPENDENCIES
   jbuilder (~> 2.7)
   jquery-rails (~> 4.4)
   jquery-turbolinks (~> 2.1)
-  jquery-ui-rails (~> 6.0.1)
+  jquery-ui-rails!
   kaminari (~> 1.2.0)
   logic_tools
   logical_query_parser

diff --git a/app/assets/stylesheets/helpers/list/lists.scss b/app/assets/stylesheets/helpers/list/lists.scss
@@ -3,43 +3,42 @@
   position: absolute;
   top: 45%;
   left: 50%;
-
   transform: translateX(-50%);
+
   ul {
     list-style: none;
     margin: 0;
     padding: 0;
-    display: flex;
-    flex-direction: column;
+    width: 1080px;
 
     li {
-      width: 1040px;
+      display: flex;
+      justify-content: space-between;
+      width: 100%;
       padding: 5px;
-      border-bottom:1px solid $navigation_border;
-      text-align: right;
       align-items: center;
+      border-bottom:1px solid $navigation_border;
       font-size: 12px;
       cursor: pointer;
-      display: flex;
-      flex-direction: row;
-      justify-content: space-between;
     }
 
     li:hover {
       background-color: $navigation_background;
       opacity: 1 !important;
     }
+    .navigation-item {
+      display: none;
+    }
     a {
       text-align: left;
       text-decoration: none;
     }
-    a:nth-child(2) {
-      align-items: center;
-      text-align: left;
-      text-decoration: none;
-      display: none;
+  }
+
+  em {
+    display: flex;
+    justify-content: center;
 
-    }
   }
 }
 

diff --git a/app/assets/stylesheets/helpers/list/tables.scss b/app/assets/stylesheets/helpers/list/tables.scss
@@ -97,9 +97,6 @@ table {
   .contextMenuCells:hover {
     background-color: $color-complement-2;
     color: $default_text;
-    td {
-      border-left: 1px solid transparent;
-    }
   }
 
   .highlight {

diff --git a/app/assets/stylesheets/helpers/pinboard/pinboard_items.scss b/app/assets/stylesheets/helpers/pinboard/pinboard_items.scss
@@ -2,6 +2,7 @@
   .slide-panel-category-item {
     position: relative;
     min-height: 28px;
+    word-break: break-all;
   }
 
   .pinboard-default-item {
@@ -22,15 +23,10 @@
     border-radius: 50%;
     width: 60px;
     height: 60px;
-    transition: border-radius 0.3s ease,
-    height 0.3s ease,
-    width 0.3s ease;
+    transition: border-radius 0.3s ease, height 0.3s ease, width 0.3s ease;
   }
   img:hover {
-
-    transition: border-radius 0.3s ease,
-    height 0.3s ease,
-    width 0.3s ease;
+    transition: border-radius 0.3s ease, height 0.3s ease, width 0.3s ease;
   }
 
   ul {
@@ -83,7 +79,7 @@
     align-items: center;
     padding-left: $standard_padding * 0.5;
     padding-right: $standard_padding * 0.5;
-    background-color: #FFF;
+    background-color: #fff;
   }
   .pinboard-menu-bar {
     width: 14px;
@@ -108,13 +104,13 @@
 
   li {
     position: relative;
-    border-bottom: 1px solid #FAFAFA;
+    border-bottom: 1px solid #fafafa;
     border-left: 5px solid transparent;
     display: flex;
     align-items: center;
     justify-content: space-between;
-    padding: $standard_padding*0.5;
-    padding-left: $standard_padding*2;
+    padding: $standard_padding * 0.5;
+    padding-left: $standard_padding * 2;
   }
   li:hover {
     opacity: 1;

diff --git a/app/assets/stylesheets/views/tasks/nomenclature/browse.scss b/app/assets/stylesheets/views/tasks/nomenclature/browse.scss
@@ -3,6 +3,11 @@
     transform: rotate(180deg);
   }
 
+  .switch-radio label {
+    width: 100%;
+    min-width: auto;
+  }
+
   #vue-browse-validation-panel {
     .soft-validation-box {
       height: 100%;

diff --git a/app/controllers/asserted_distributions_controller.rb b/app/controllers/asserted_distributions_controller.rb
@@ -37,7 +37,6 @@ def new
 
   # GET /asserted_distributions/1/edit
   def edit
-    @asserted_distribution.source = Source.new if !@asserted_distribution.source
   end
 
   # POST /asserted_distributions
@@ -115,7 +114,7 @@ def download
   def batch_load
   end
 
-  # POST /asserted_distributions/batch_move.json?asserted_distribution_query=<>&geographic_area_id
+  # PATCH /asserted_distributions/batch_move.json?asserted_distribution_query=<>&geographic_area_id
   def batch_move
     if @result = AssertedDistribution.batch_move(params)
     else

diff --git a/app/controllers/contents_controller.rb b/app/controllers/contents_controller.rb
@@ -9,7 +9,7 @@ class ContentsController < ApplicationController
   def index
     respond_to do |format|
       format.html do
-        @recent_objects = Content.where(project_id: sessions_current_project_id).recently_updated.limit(10)
+        @recent_objects = ::Content.where(project_id: sessions_current_project_id).recently_updated.limit(10)
         render '/shared/data/all/index'
       end
       format.json {
@@ -25,7 +25,7 @@ def show
 
   # GET /contents/new
   def new
-    @content = Content.new
+    @content = ::Content.new
   end
 
   # GET /contents/1/edit
@@ -35,7 +35,7 @@ def edit
   # POST /contents
   # POST /contents.json
   def create
-    @content = Content.new(content_params)
+    @content = ::Content.new(content_params)
 
     respond_to do |format|
       if @content.save
@@ -78,7 +78,7 @@ def destroy
   end
 
   def list
-    @contents = Content.with_project_id(sessions_current_project_id).order(:id).page(params[:page])
+    @contents = ::Content.with_project_id(sessions_current_project_id).order(:id).page(params[:page])
   end
 
   def search
@@ -91,11 +91,11 @@ def search
   end
 
   def select_options
-    @contents = Content.select_optimized(sessions_current_user_id, sessions_current_project_id)
+    @contents = ::Content.select_optimized(sessions_current_user_id, sessions_current_project_id)
   end
 
   def autocomplete
-    @contents = Content.find_for_autocomplete(params.merge(project_id: sessions_current_project_id))
+    @contents = ::Content.find_for_autocomplete(params.merge(project_id: sessions_current_project_id))
     data = @contents.collect do |t|
       {id: t.id,
        label: ApplicationController.helpers.taxon_works_content_tag(t),
@@ -112,7 +112,7 @@ def autocomplete
   # GET /contents/download
   def download
     send_data(
-      Export::Download.generate_csv(Content.where(project_id: sessions_current_project_id)),
+      Export::Download.generate_csv(::Content.where(project_id: sessions_current_project_id)),
       type: 'text',
       filename: "contents_#{DateTime.now}.csv")
   end
@@ -134,7 +134,7 @@ def api_show
   private
 
   def set_content
-    @content = Content.with_project_id(sessions_current_project_id).find(params[:id])
+    @content = ::Content.with_project_id(sessions_current_project_id).find(params[:id])
     @recent_object = @content
   end