Merge branch 'development'

CHANGELOG.md

@@ -9,6 +9,41 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.32.0] - 2023-03-22
+
+### 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
+
+[#1638]: https://github.com/SpeciesFileGroup/taxonworks/issues/1638
+[#2143]: https://github.com/SpeciesFileGroup/taxonworks/issues/2143
+[#3352]: https://github.com/SpeciesFileGroup/taxonworks/issues/3352
+[#3359]: https://github.com/SpeciesFileGroup/taxonworks/issues/3359
+[#3360]: https://github.com/SpeciesFileGroup/taxonworks/issues/3360
+[#3361]: https://github.com/SpeciesFileGroup/taxonworks/issues/3361
+
 ## [0.31.3] - 2023-03-17
 
 ### Added
@@ -18,12 +53,14 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ### Fixed
 
 - Serial name filter query doesn't work
-- Serial facet
+- Serial facet <IN WHERE>
 - 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
+- Alternate values on ObservationMatrix name failing
+- Start and End date in Collecting Event related facets
 
 ### Changed
 
@@ -3451,7 +3488,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
 
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.31.3...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.32.0...development
+[0.32.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.31.3...v0.32.0
 [0.31.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.31.2...v0.31.3
 [0.31.2]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.31.1...v0.31.2
 [0.31.1]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.31.0...v0.31.1

app/assets/stylesheets/base/help.scss

@@ -8,19 +8,16 @@
   height: 55px;
   opacity: 0.4;
   border-radius: 50%;
-  background-color: #FF8F00;
-  background-image: image-url("help.svg");
+  background-color: #ff8f00;
+  background-image: image-url('help.svg');
   background-repeat: no-repeat;
   background-position: center;
   background-size: 35px;
   box-shadow: 0px 1px 2px 0px #444;
   transition: background-size 0.5s ease, opacity 0.3s ease;
-  transition: right 0.5s ease, left 0.5s ease,
-  background-position 0.5s ease,
-  background-size 0.5s ease,
-  width 0.5s ease,
-  height 0.5s ease,
-  opacity 0.5s ease;
+  transition: right 0.5s ease, left 0.5s ease, background-position 0.5s ease,
+    background-size 0.5s ease, width 0.5s ease, height 0.5s ease,
+    opacity 0.5s ease;
 }
 
 .help-button:hover {
@@ -43,15 +40,14 @@
   right: -10px;
   background-size: 35px;
   background-position: center;
-  transition: opacity 0.5s ease,
-  right 0.5s ease,
-  background-size 0.5s ease;
+  transition: opacity 0.5s ease, right 0.5s ease, background-size 0.5s ease;
 }
 
 .help-button-active:hover {
   background-size: 40px;
   background-position: center;
-  transition: opacity 0.5s ease, bottom 0.5s ease, right 0.5s ease, background-position 0.5s ease, background-size 0.5s ease;
+  transition: opacity 0.5s ease, bottom 0.5s ease, right 0.5s ease,
+    background-position 0.5s ease, background-size 0.5s ease;
 
   .help-button-description {
     display: none;
@@ -82,7 +78,7 @@
 .help-legend {
   display: none;
   border-radius: 2px;
-  padding: $standard_padding*0.5;
+  padding: $standard_padding * 0.5;
   padding-left: $standard_padding;
   padding-right: $standard_padding;
   box-shadow: 0px 1px 1px 0px rgba(0, 0, 0, 0.2);
@@ -113,7 +109,7 @@
   font-weight: 300;
   position: absolute;
   white-space: nowrap;
-  padding: $standard_padding*0.5;
+  padding: $standard_padding * 0.5;
   background-color: $color-help-description;
   color: $color-help-text;
   box-shadow: 0px 1px 1px 0px rgba(0, 0, 0, 0.2);
@@ -138,10 +134,10 @@
   height: 30px;
   position: absolute;
   left: -15px;
-  bottom: -15px;
+  top: -15px;
   border-radius: 50%;
   background-color: $color-help-bubbles;
-  color: #FFF;
+  color: #fff;
   font-weight: 300;
   box-shadow: 0px 1px 1px 0px rgba(0, 0, 0, 0.2);
   opacity: 0.8;

app/assets/stylesheets/helpers/list/tables.scss

@@ -1,4 +1,8 @@
 .table-striped {
+  tr {
+    border-bottom: 1px solid $navigation_border;
+  }
+
   tr:nth-of-type(even) {
     @extend .list_line_even;
   }
@@ -17,31 +21,31 @@ table {
   width: auto;
   border-spacing: 0;
   background-color: $panel_background;
-  border-collapse: collapse;  
+  border-collapse: collapse;
 
   .underlined_elements {
-      border-spacing: 0; 
+    border-spacing: 0;
   }
 
   .top_align_text {
     td {
-      vertical-align: top; 
+      vertical-align: top;
     }
   }
 
-  th.headerSortUp { 
+  th.headerSortUp {
     background-image: image-url('arrow-up.svg');
     background-position: right $standard_padding center;
     padding-right: $standard_padding;
     background-repeat: no-repeat;
-  } 
+  }
 
-  th.headerSortDown { 
+  th.headerSortDown {
     background-image: image-url('arrow-down.svg');
     background-position: right $standard_padding center;
     padding-right: $standard_padding;
-    background-repeat: no-repeat;  
-  } 
+    background-repeat: no-repeat;
+  }
 
   .table-options {
     display: none;
@@ -55,7 +59,7 @@ table {
 
   td {
     padding-left: $standard_padding;
-    padding-right: $standard_padding; 
+    padding-right: $standard_padding;
   }
 
   th:hover {
@@ -84,7 +88,7 @@ table {
     }
   }
 
-  .contextMenuCells { 
+  .contextMenuCells {
     td {
       border-bottom: 1px solid $navigation_border;
       border-left: 1px solid $navigation_border;
@@ -94,11 +98,11 @@ table {
     background-color: $color-complement-2;
     color: $default_text;
     td {
-      border-left:1px solid transparent;
+      border-left: 1px solid transparent;
     }
   }
 
   .highlight {
-    background-color: #E3E8E3 !important;
+    background-color: #e3e8e3 !important;
   }
 }

app/controllers/biological_associations_graphs_controller.rb

@@ -2,12 +2,22 @@ class BiologicalAssociationsGraphsController < ApplicationController
   include DataControllerConfiguration::ProjectDataControllerConfiguration
 
   before_action :set_biological_associations_graph, only: [:show, :edit, :update, :destroy]
+  after_action -> { set_pagination_headers(:biological_associations_graphs) }, only: [:index], if: :json_request?
 
   # GET /biological_associations_graphs
   # GET /biological_associations_graphs.json
   def index
-    @recent_objects = BiologicalAssociationsGraph.recent_from_project_id(sessions_current_project_id).order(updated_at: :desc).limit(10)
-    render '/shared/data/all/index'
+    respond_to do |format|
+      format.html do
+        @recent_objects = BiologicalAssociationsGraph.recent_from_project_id(sessions_current_project_id).order(updated_at: :desc).limit(10)
+        render '/shared/data/all/index'
+      end
+      format.json {
+        @biological_associations_graphs = ::Queries::BiologicalAssociationsGraph::Filter.new(params).all
+          .page(params[:page])
+          .per(params[:per])
+      }
+    end
   end
 
   # GET /biological_associations_graphs/1
@@ -69,24 +79,34 @@ def destroy
     end
   end
 
+  def autocomplete
+    @biological_associations_graphs = Queries::BiologicalAssociationsGraph::Autocomplete.new(
+      params.require(:term),
+      project_id: sessions_current_project_id
+    ).autocomplete
+  end
+
+  # TODO: remove!
   def search
     if params[:id].blank?
       redirect_to biological_associations_graphs_path, alert: 'You must select an item from the list with a click or tab press before clicking show.'
     else
-      redirect_to biological_association_graph_path(params[:id])
+      redirect_to biological_associations_graph_path(params[:id])
     end
   end
-  
+
   private
-  
+
   def set_biological_associations_graph
     @biological_associations_graph = BiologicalAssociationsGraph.where(project_id: sessions_current_project_id).find(params[:id])
   end
 
   def biological_associations_graph_params
     params.require(:biological_associations_graph).permit(
       :name,
-      origin_citation_attributes: [:id, :_destroy, :source_id, :pages] 
+      :layout,
+      origin_citation_attributes: [:id, :_destroy, :source_id, :pages] ,
+      biological_associations_biological_associations_graphs_attributes: [:id, :_destroy, :biological_association_id]
     )
   end
 end

app/controllers/tasks/biological_associations/biological_associations_graph_controller.rb

@@ -0,0 +1,4 @@
+class Tasks::BiologicalAssociations::BiologicalAssociationsGraphController < ApplicationController
+  include TaskControllerConfiguration
+
+end

app/controllers/tasks/nomenclature/paper_catalog_controller.rb

@@ -11,10 +11,12 @@ def index
   end
 
   def preview
+    redirect_to action: :index, warning: 'You must (re)select a TaxonName for each of Preview/Download' and return if params[:taxon_name_id].blank?
+
     @taxon_name = TaxonName.where(project_id: sessions_current_project_id).find(params[:taxon_name_id])
 
     c = @taxon_name.descendants.that_is_valid.count
-    if c > 5000
+    if c > 10000
       redirect_to :index, message: "Export of #{c} is too presently too large." and return
     end