Renamed Herbarium model to Collection

Gemfile.lock

@@ -473,6 +473,7 @@ GEM
       webrick (~> 1.7.0)
 
 PLATFORMS
+  ruby
   x86_64-linux
 
 DEPENDENCIES

app/assets/javascripts/datatable_initialisation.js

@@ -32,11 +32,11 @@ jQuery(function() {
         "order": [ 2, 'desc' ]
     } );
 
-    //HERBARIA
-    $('#herbaria').DataTable( {
+    //COLLECTIONS
+    $('#collections').DataTable( {
         bProcessing: true,
         bServerSide: true,
-        sAjaxSource: $('#herbaria').data('source'),
+        sAjaxSource: $('#collections').data('source'),
         "columnDefs": [
             { "orderable": false, "targets": 3 }
         ],

app/assets/javascripts/selects_with_select2.js

@@ -46,13 +46,13 @@ jQuery(function() {
 
     // INDIVIDUALS
     $('#individual_taxon_id').select2((select2AutocompleteOptions("/taxa/filter", "a taxon")));
-    $('#individual_herbarium_id').select2(select2SingleSelectOptions('an herbarium'));
+    $('#individual_collection_id').select2(select2SingleSelectOptions('a collection'));
     $('#individual_tissue_id').select2(select2SingleSelectOptions('a tissue type'));
     $('#individual_project_ids').select2(select2MultiselectOptions);
 
     // INDIVIDUAL SEARCHES
     $('#individual_search_specimen_id').select2((select2AutocompleteOptions("/individuals/filter?name_only=1", "a specimen")));
-    $('#individual_search_herbarium').select2(select2SingleSelectOptions('an herbarium'));
+    $('#individual_search_collection').select2(select2SingleSelectOptions('a collection'));
     $('#individual_search_taxon').select2((select2AutocompleteOptions("/taxa/filter?name_only=1", "a taxon")));
 
     // ISOLATES

app/controllers/herbaria_controller.rb → app/controllers/collections_controller.rb

@@ -20,80 +20,80 @@
 # along with BarKeeper.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-class HerbariaController < ApplicationController
+class CollectionsController < ApplicationController
   load_and_authorize_resource
 
-  before_action :set_herbarium, only: [:show, :edit, :update, :destroy]
+  before_action :set_collection, only: [:show, :edit, :update, :destroy]
 
-  # GET /herbaria
-  # GET /herbaria.json
+  # GET /collections
+  # GET /collections.json
   def index
     respond_to do |format|
       format.html
-      format.json { render json: HerbariumDatatable.new(view_context) }
+      format.json { render json: CollectionDatatable.new(view_context) }
     end
   end
 
-  # GET /herbaria/1
-  # GET /herbaria/1.json
+  # GET /collections/1
+  # GET /collections/1.json
   def show;end
 
-  # GET /herbaria/new
+  # GET /collections/new
   def new
-    @herbarium = Herbarium.new
+    @collection = Collection.new
   end
 
-  # GET /herbaria/1/edit
+  # GET /collections/1/edit
   def edit;end
 
-  # POST /herbaria
-  # POST /herbaria.json
+  # POST /collections
+  # POST /collections.json
   def create
-    @herbarium = Herbarium.new(herbarium_params)
+    @collection = Collection.new(collection_params)
 
     respond_to do |format|
-      if @herbarium.save
-        format.html { redirect_to @herbarium, notice: 'Herbarium was successfully created.' }
-        format.json { render :show, status: :created, location: @herbarium }
+      if @collection.save
+        format.html { redirect_to @collection, notice: 'Collection was successfully created.' }
+        format.json { render :show, status: :created, location: @collection }
       else
         format.html { render :new }
-        format.json { render json: @herbarium.errors, status: :unprocessable_entity }
+        format.json { render json: @collection.errors, status: :unprocessable_entity }
       end
     end
   end
 
-  # PATCH/PUT /herbaria/1
-  # PATCH/PUT /herbaria/1.json
+  # PATCH/PUT /collections/1
+  # PATCH/PUT /collections/1.json
   def update
     respond_to do |format|
-      if @herbarium.update(herbarium_params)
-        format.html { redirect_to @herbarium, notice: 'Herbarium was successfully updated.' }
-        format.json { render :show, status: :ok, location: @herbarium }
+      if @collection.update(collection_params)
+        format.html { redirect_to @collection, notice: 'Collection was successfully updated.' }
+        format.json { render :show, status: :ok, location: @collection }
       else
         format.html { render :edit }
-        format.json { render json: @herbarium.errors, status: :unprocessable_entity }
+        format.json { render json: @collection.errors, status: :unprocessable_entity }
       end
     end
   end
 
-  # DELETE /herbaria/1
-  # DELETE /herbaria/1.json
+  # DELETE /collections/1
+  # DELETE /collections/1.json
   def destroy
-    @herbarium.destroy
+    @collection.destroy
     respond_to do |format|
-      format.html { redirect_to herbaria_url, notice: 'Herbarium was successfully destroyed.' }
+      format.html { redirect_to collections_url, notice: 'Collection was successfully destroyed.' }
       format.json { head :no_content }
     end
   end
 
   private
     # Use callbacks to share common setup or constraints between actions.
-    def set_herbarium
-      @herbarium = Herbarium.find(params[:id])
+    def set_collection
+      @collection = Collection.find(params[:id])
     end
 
     # Never trust parameters from the scary internet, only allow the white list through.
-    def herbarium_params
-      params.require(:herbarium).permit(:name, :acronym)
+    def collection_params
+      params.require(:collection).permit(:name, :acronym)
     end
 end

app/controllers/individual_searches_controller.rb

@@ -102,6 +102,6 @@ def set_individual_search
   # Never trust parameters from the scary internet, only allow the white list through.
   def individual_search_params
     params.require(:individual_search).permit(:title, :DNA_bank_id, :has_issue, :has_problematic_location,
-                                              :has_taxon, :taxon, :specimen_id, :herbarium)
+                                              :has_taxon, :taxon, :specimen_id, :collection)
   end
 end

app/controllers/individuals_controller.rb

@@ -131,7 +131,7 @@ def set_individual
   # Never trust parameters from the scary internet, only allow the white list through.
   def individual_params
     params.require(:individual).permit(:specimen_id, :DNA_bank_id, :collector, :specimen_id, :herbarium_code,
-                                       :herbarium_id, :country, :state_province, :locality, :latitude, :longitude,
+                                       :collection_id, :country, :state_province, :locality, :latitude, :longitude,
                                        :latitude_original, :longitude_original, :elevation, :exposition, :habitat,
                                        :substrate, :life_form, :collectors_field_number, :collected, :determination,
                                        :revision, :confirmation, :comments, :taxon_id, :taxon_name, :tissue_id,

app/datatables/herbarium_datatable.rb → app/datatables/collection_datatable.rb

@@ -22,7 +22,7 @@
 
 # frozen_string_literal: true
 
-class HerbariumDatatable
+class CollectionDatatable
   include Rails.application.routes.url_helpers
   delegate :url_helpers, to: 'Rails.application.routes'
 
@@ -35,43 +35,43 @@ def initialize(view)
   def as_json(_options = {})
     {
         sEcho: params[:sEcho].to_i,
-        iTotalRecords: Herbarium.count,
-        iTotalDisplayRecords: herbaria.total_entries,
+        iTotalRecords: Collection.count,
+        iTotalDisplayRecords: collections.total_entries,
         aaData: data
     }
   end
 
   private
 
   def data
-    herbaria.map do |herbarium|
+    collections.map do |collection|
       name = ''
 
-      name = link_to herbarium.name, edit_herbarium_path(herbarium) if herbarium.name
+      name = link_to collection.name, edit_collection_path(collection) if collection.name
 
       [
           name,
-          herbarium.acronym,
-          herbarium.updated_at.in_time_zone('CET').strftime('%Y-%m-%d %H:%M:%S'),
-          link_to('Delete', herbarium, method: :delete, data: { confirm: 'Are you sure?' })
+          collection.acronym,
+          collection.updated_at.in_time_zone('CET').strftime('%Y-%m-%d %H:%M:%S'),
+          link_to('Delete', collection, method: :delete, data: { confirm: 'Are you sure?' })
       ]
     end
   end
 
-  def herbaria
-    @herbaria ||= fetch_herbaria
+  def collections
+    @collections ||= fetch_collections
   end
 
-  def fetch_herbaria
-    herbaria = Herbarium.all.order("#{sort_column} #{sort_direction}")
+  def fetch_collections
+    collections = Collection.all.order("#{sort_column} #{sort_direction}")
 
-    herbaria = herbaria.page(page).per_page(per_page)
+    collections = collections.page(page).per_page(per_page)
 
     if params[:sSearch].present?
-      herbaria = herbaria.where('herbaria.name ILIKE :search OR herbaria.acronym ILIKE :search', search: "%#{params[:sSearch]}%")
+      collections = collections.where('collections.name ILIKE :search OR collections.acronym ILIKE :search', search: "%#{params[:sSearch]}%")
     end
 
-    herbaria
+    collections
   end
 
   def page
@@ -83,7 +83,7 @@ def per_page
   end
 
   def sort_column
-    columns = %w[herbaria.name herbaria.acronym herbaria.updated_at]
+    columns = %w[collections.name collections.acronym collections.updated_at]
     columns[params[:iSortCol_0].to_i]
   end
 

app/datatables/individual_datatable.rb

@@ -52,12 +52,12 @@ def data
       taxon = ''
 
       taxon = link_to individual.taxon.scientific_name, edit_taxon_path(individual.taxon) if individual.taxon
-      herbarium = link_to individual.herbarium.acronym, edit_herbarium_path(individual.herbarium) if individual.herbarium
+      collection = link_to individual.collection.acronym, edit_collection_path(individual.collection) if individual.collection
 
       [
         link_to(individual.specimen_id, edit_individual_path(individual)),
         taxon,
-        herbarium,
+        collection,
         individual.collector,
         individual.collectors_field_number,
         individual.updated_at.in_time_zone('CET').strftime('%Y-%m-%d %H:%M:%S'),
@@ -72,17 +72,17 @@ def individuals
 
   def fetch_individuals
     if @taxon_id
-      individuals = Individual.includes(:taxon, :herbarium).where(taxon_id: @taxon_id).in_project(@current_default_project).order("#{sort_column} #{sort_direction}")
+      individuals = Individual.includes(:taxon, :collection).where(taxon_id: @taxon_id).in_project(@current_default_project).order("#{sort_column} #{sort_direction}")
     else
-      individuals = Individual.includes(:taxon, :herbarium).in_project(@current_default_project).order("#{sort_column} #{sort_direction}")
+      individuals = Individual.includes(:taxon, :collection).in_project(@current_default_project).order("#{sort_column} #{sort_direction}")
     end
 
     individuals = individuals.page(page).per_page(per_page)
 
     if params[:sSearch].present?
       individuals = individuals.where('individuals.specimen_id ILIKE :search
 OR taxa.scientific_name ILIKE :search
-OR herbaria.acronym ILIKE :search
+OR collections.acronym ILIKE :search
 OR individuals.collector ILIKE :search
 OR individuals.collectors_field_number ILIKE :search', search: "%#{params[:sSearch]}%")
       .references(:taxon)
@@ -100,7 +100,7 @@ def per_page
   end
 
   def sort_column
-    columns = %w[individuals.specimen_id taxa.scientific_name herbaria.acronym individuals.collector individuals.collectors_field_number individuals.updated_at]
+    columns = %w[individuals.specimen_id taxa.scientific_name collections.acronym individuals.collector individuals.collectors_field_number individuals.updated_at]
     columns[params[:iSortCol_0].to_i]
   end
 

app/datatables/individual_search_result_datatable.rb

@@ -54,12 +54,12 @@ def data
         taxon_id = individual.taxon.id
       end
 
-      herbarium = link_to individual.herbarium.acronym, edit_herbarium_path(individual.herbarium) if individual.herbarium
+      collection = link_to individual.collection.acronym, edit_collection_path(individual.collection) if individual.collection
 
       [
         link_to(individual.specimen_id, edit_individual_path(individual)),
         link_to(taxon_name, edit_taxon_path(taxon_id)),
-        herbarium,
+        collection,
         individual.latitude_original,
         individual.longitude_original,
         individual.updated_at.in_time_zone('CET').strftime('%Y-%m-%d %H:%M:%S'),
@@ -69,14 +69,14 @@ def data
   end
 
   def individuals_data
-    @search_result ||= IndividualSearch.find_by_id(@search_id).individuals.includes(:taxon, :herbarium).reorder("#{sort_column} #{sort_direction}")
+    @search_result ||= IndividualSearch.find_by_id(@search_id).individuals.includes(:taxon, :collection).reorder("#{sort_column} #{sort_direction}")
 
     @search_result = @search_result.page(page).per_page(per_page)
 
     if params[:sSearch].present?
       @search_result = @search_result.where('individuals.specimen_id ILIKE :search
 OR taxa.scientific_name ILIKE :search
-OR herbaria.acronym ILIKE :search', search: "%#{params[:sSearch]}%")
+OR collections.acronym ILIKE :search', search: "%#{params[:sSearch]}%")
                                      .references(:taxon)
     end
 
@@ -92,7 +92,7 @@ def per_page
   end
 
   def sort_column
-    columns = %w[individuals.specimen_id taxa.scientific_name herbaria.acronym individuals.latitude_original individuals.longitude_original individuals.updated_at]
+    columns = %w[individuals.specimen_id taxa.scientific_name collections.acronym individuals.latitude_original individuals.longitude_original individuals.updated_at]
     columns[params[:iSortCol_0].to_i]
   end
 

app/models/ability.rb

@@ -36,7 +36,7 @@ def initialize(user)
 
     can %i[edit index filter taxonomy_tree associated_specimen find_ancestry show_individuals show_children], Taxon
     can %i[edit index filter locality], Individual
-    can %i[edit index], Herbarium
+    can %i[edit index], Collection
 
     can %i[edit index filter change_via_script as_fasq], Contig
     can %i[edit index filter show_clusters], Isolate

app/models/herbarium.rb → app/models/collection.rb

@@ -20,7 +20,7 @@
 # along with BarKeeper.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-class Herbarium < ApplicationRecord
+class Collection < ApplicationRecord
   include PgSearch::Model
 
   validates_presence_of :acronym

app/models/concerns/import.rb

@@ -66,7 +66,7 @@ def query_dna_bank(id, data_source = 'dna_bank')
       results[:genus] = unit.at_xpath('//abcd21:GenusOrMonomial')&.content&.strip
       results[:species_epithet] = unit.at_xpath('//abcd21:FirstEpithet')&.content&.strip
       results[:infraspecific] = unit.at_xpath('//abcd21:InfraspecificEpithet')&.content&.strip
-      results[:herbarium] = unit.at_xpath('//abcd21:SourceInstitutionCode')&.content&.strip
+      results[:collection] = unit.at_xpath('//abcd21:SourceInstitutionCode')&.content&.strip
       results[:collector] = unit.at_xpath('//abcd21:GatheringAgent')&.content&.strip
       results[:locality] = unit.at_xpath('//abcd21:LocalityText')&.content&.strip
       results[:longitude] = unit.at_xpath('//abcd21:LongitudeDecimal')&.content&.strip

app/models/individual.rb

@@ -29,7 +29,7 @@ class Individual < ApplicationRecord
 
   has_many :isolates
   belongs_to :taxon
-  belongs_to :herbarium
+  belongs_to :collection
   belongs_to :tissue
 
   has_many_attached :voucher_images
@@ -53,7 +53,7 @@ class Individual < ApplicationRecord
   scope :bad_location, -> { bad_latitude.or(Individual.bad_longitude) }
 
   def self.to_csv(project_id)
-    header = %w{ Database_ID specimen_id taxon_name determination herbarium collectors_field_number collector collection_date
+    header = %w{ Database_ID specimen_id taxon_name determination collection collectors_field_number collector collection_date
 state_province country latitude longitude elevation exposition locality habitat comments }
 
     attributes = %w{ id specimen_id taxon_name determination herbarium_code collectors_field_number collector collected
@@ -111,9 +111,9 @@ def read_abcd_results(abcd_results)
     self.latitude_original = abcd_results[:latitude] if abcd_results[:latitude]
     self.longitude_original = abcd_results[:longitude] if abcd_results[:longitude]
 
-    if abcd_results[:herbarium]
-      herbarium = Herbarium.find_or_create_by(acronym: abcd_results[:herbarium])
-      self.herbarium = herbarium
+    if abcd_results[:collection]
+      collection = Collection.find_or_create_by(acronym: abcd_results[:collection])
+      self.collection = collection
     end
 
     if abcd_results[:higher_taxon_name] && abcd_results[:higher_taxon_rank]