Merge branch 'development'

Dockerfile

@@ -64,9 +64,15 @@ RUN chmod +x /etc/my_init.d/init.sh && \
     chmod +x /app/public/images/tmp && \
     rm -f /etc/service/nginx/down
 
+
+
 RUN chown 9999:9999 /app/public
 RUN chown 9999:9999 /app/public/images/tmp
 RUN chown 9999:9999 /app/public/packs
+RUN chown 9999:9999 /app/log/
+
+RUN touch /app/log/production.log
+RUN chmod 0664 /app/log/production.log
 
 CMD ["/sbin/my_init"]
 

app/controllers/biological_associations_controller.rb

@@ -12,7 +12,11 @@ def index
         render '/shared/data/all/index'
       }
       format.json {
-        @biological_associations = Queries::BiologicalAssociation::Filter.new(filter_params).all.where(project_id: sessions_current_project_id).page(params[:page] || 1).per(100)
+        @biological_associations = Queries::BiologicalAssociation::Filter
+          .new(filter_params)
+          .all
+          .where(project_id: sessions_current_project_id)
+          .page(params[:page] || 1).per(500)
       }
     end
   end

app/models/image.rb

@@ -249,7 +249,7 @@ def self.scaled_to_box(params)
       if ratio > 1 # wide into tall
         c.resize(params[:box_width].to_i, (params[:box_height].to_f / ratio * box_ratio).to_i)
       else # tall into tall
-        c.resize((params[:box_width ].to_f).to_i, (params[:box_height].to_f / ratio * box_ratio).to_i)
+        c.resize((params[:box_width ].to_f * ratio * box_ratio ).to_i, (params[:box_height].to_f ).to_i)
       end
     end
   end

app/models/person.rb

@@ -169,8 +169,6 @@ def  levenshtein_similar(cutoff = 4)
     Person.where('levenshtein(last_name, ?) < ? and levenshtein(first_name, ?) < ?', last_name, cutoff, first_name, cutoff) 
   end
 
-  #  rubocop:disable Metrics/BlockNesting
-  #  rubocop:disable Metrics/MethodLength
   # @param [Integer] person_id
   # @return [Boolean]
   #   true if all records updated, false if any one failed (all or none)
@@ -184,12 +182,13 @@ def merge_with(person_id)
           # rubocop:disable Rails/SaveBang
           Role.where(person_id: r_person.id).update(person: self) # update merge person's roles to old
           # rubocop:enable Rails/SaveBang
-          l_person_hash = self.annotations_hash
+          l_person_hash = annotations_hash
+
           unless r_person.first_name.blank?
-            if self.first_name.blank?
-              self.update(first_name: r_person.first_name)
+            if first_name.blank?
+              update(first_name: r_person.first_name)
             else
-              if self.first_name != r_person.first_name
+              if first_name != r_person.first_name
                 # create a first_name alternate_value of the r_person first name
                 skip_av = false
                 av_list = l_person_hash['alternate values']
@@ -205,13 +204,15 @@ def merge_with(person_id)
                   end
                 end
 
-                AlternateValue::AlternateSpelling.create!(alternate_value_object_type:      'Person',
-                                                          value:                            r_person.first_name,
-                                                          alternate_value_object_attribute: 'first_name',
-                                                          alternate_value_object_id:        id) unless skip_av
+                AlternateValue::AlternateSpelling.create!(
+                  alternate_value_object_type:      'Person',
+                  value:                            r_person.first_name,
+                  alternate_value_object_attribute: 'first_name',
+                  alternate_value_object_id:        id) unless skip_av
               end
             end
           end
+
           unless r_person.last_name.blank?
             if self.last_name.blank?
               self.update(last_name: r_person.last_name)
@@ -240,6 +241,7 @@ def merge_with(person_id)
               end
             end
           end
+
           r_person.annotations_hash.each do |r_kee, r_objects|
             r_objects.each do |r_o|
               skip   = false
@@ -288,59 +290,65 @@ def merge_with(person_id)
                 skip
               end
               unless skip
-                # r_err                = r_o
                 r_o.annotated_object = self
                 r_o.save!
-                # r_o
               end
             end
           end
+
           # TODO: handle prefix and suffix
-          if self.prefix.blank?
-            self.prefix = r_person.prefix
+          if prefix.blank?
+            write_attribute(:prefix, r_person.prefix)
           else
             unless r_person.prefix.blank?
               # What to do when both have some content?
             end
           end
-          if self.suffix.blank?
+
+          if suffix.blank?
             self.suffix = r_person.suffix
           else
             unless r_person.suffix.blank?
               # What to do when both have some content?
             end
           end
+
           # TODO: handle years attributes
-          if self.year_born.nil?
+          if year_born.nil?
             self.year_born = r_person.year_born
           else
             unless r_person.year_born.nil?
               # What to do when both have some (different) numbers?
             end
           end
-          if self.year_died.nil?
+
+          if year_died.nil?
             self.year_died = r_person.year_died
           else
             unless r_person.year_died.nil?
               # What to do when both have some (different) numbers?
             end
           end
+
           if r_person.year_active_start # if not, r_person has nothing to contribute
             if self.year_active_start.nil? || (self.year_active_start > r_person.year_active_start)
               self.year_active_start = r_person.year_active_start
             end
           end
+
           if r_person.year_active_end # if not, r_person has nothing to contribute
             if self.year_active_end.nil? || (self.year_active_end < r_person.year_active_end)
               self.year_active_end = r_person.year_active_end
             end
           end
+
           # update type, if necesssary
           if self.type.include?('Unv')
             unless unvetted
               self.update(type: 'Person::Vetted')
             end
           end
+
           # last thing to do in the transaction...
           self.save! unless self.persisted?
         end
@@ -351,9 +359,6 @@ def merge_with(person_id)
     true
   end
 
-  #  rubocop:enable Metrics/BlockNesting
-  #  rubocop:enable Metrics/MethodLength
-
   # @return [Boolean]
   def is_determiner?
     determiner_roles.to_a.length > 0
@@ -404,8 +409,11 @@ def activity_ended_after_started
 
   # @return [Ignored]
   def not_active_after_death
-    errors.add(:year_active_start, 'is older than year of death') if year_active_start && year_died && year_active_start > year_died
-    errors.add(:year_active_end, 'is older than year of death') if year_active_end && year_died && year_active_end > year_died
+    unless is_editor? || is_author?
+      errors.add(:year_active_start, 'is older than year of death') if year_active_start && year_died && year_active_start > year_died
+      errors.add(:year_active_end, 'is older than year of death') if year_active_end && year_died && year_active_end > year_died
+    end
+    true 
   end
 
   # @return [Ignored]

app/models/role/project_role.rb

@@ -2,7 +2,6 @@
 # @todo Refactor after Housekeeping / FactoryBot issues resolved (nested set!!)
 #
 class Role::ProjectRole < Role
-
   # self.abstract_class = true
 
   include Housekeeping
@@ -13,6 +12,7 @@ class Role::ProjectRole < Role
 
   protected
 
+  # TODO: this doesn't do what we think it does
   def set_project_if_possible
     self.project = self.role_object.project if self.role_object && self.project.nil?
   end

app/models/taxon_name_author.rb

@@ -1,5 +1,4 @@
 class TaxonNameAuthor < Role::ProjectRole
-  include Housekeeping
 
   def self.human_name
     'Taxon name author'

app/models/type_designator.rb

@@ -1,5 +1,4 @@
 class TypeDesignator < Role::ProjectRole
-  include Housekeeping
 
   def self.human_name
     'Type designator'

config/routes.rb

@@ -1035,6 +1035,18 @@
       get '/character_states/:id/annotations',
         to: 'character_states#annotations'
 
+      # TODO: DRY
+      # Generate shallow routes for annotations based on model properties, like
+      # otu_citations GET /otus/:otu_id/citations(.:format) citations#index
+      ApplicationEnumeration.data_models.each do |m|
+        Shared::IsData::Annotation::ANNOTATION_TYPES.each do |t|
+          if m.send("has_#{t}?")
+            n = m.model_name
+            match "/#{n.route_key}/:#{n.param_key}_id/#{t}", to: "#{t}#index",  via: :get, constraints: {format: :json}, defaults: {format: :json}
+          end
+        end
+      end
+
     end
   end
 

lib/queries/biological_association/filter.rb

@@ -90,7 +90,7 @@ def all
         if a = and_clauses
           ::BiologicalAssociation.where(and_clauses)
         else
-          ::BiologicalAssociation.none
+          ::BiologicalAssociation.all
         end
       end
 

lib/tasks/tw.rake

@@ -72,7 +72,7 @@ namespace :tw do
     end
     @args.merge!(data_directory: (ENV['data_directory'] || default))
     # TODO: Use Dir.exists? and fix tasks that are treating data_directory as a file parameter
-    raise "path (#{default}) not found" if !File.exists?(@args[:data_directory])
+    raise Rainbow("Path to data directory (#{default}) not found").red if !File.exists?(@args[:data_directory])
     @args
   end
 

spec/models/person_spec.rb

@@ -55,6 +55,7 @@
 
   context 'years' do
     before { person.year_died = 1920 }
+
     specify 'died after birth' do
       person.year_born = 1930
       person.valid?
@@ -67,21 +68,44 @@
       expect(person.errors.include?(:year_active_start)).to be_truthy
     end
 
+    context 'as author/editor' do
+      before do 
+        person.last_name = 'Smith'
+        person.save!
+      end
+
+      specify 'active after death as editor - active start' do
+        source_bibtex.editors << person
+        person.reload
+        person.year_active_start = 1930
+        person.valid?
+        expect(person.errors.include?(:year_active_start)).to be_falsey
+      end
+
+      specify 'active after death as author - active start' do
+        source_bibtex.authors << person
+        person.reload
+        person.year_active_start = 1930
+        person.valid?
+        expect(person.errors.include?(:year_active_start)).to be_falsey
+      end
+    end
+
     specify 'not active after death - active end' do
       person.year_active_end = 1930
       person.valid?
       expect(person.errors.include?(:year_active_end)).to be_truthy
     end
 
     specify 'not active before birth - active start' do
-      person.year_born         = 1920
+      person.year_born = 1920
       person.year_active_start = 1890
       person.valid?
       expect(person.errors.include?(:year_active_start)).to be_truthy
     end
 
     specify 'not active before birth - active end' do
-      person.year_born       = 1920
+      person.year_born = 1920
       person.year_active_end = 1890
       person.valid?
       expect(person.errors.include?(:year_active_end)).to be_truthy
@@ -178,9 +202,9 @@
         p = FactoryBot.create(:person,
                               first_name: 'January', last_name: 'Smith',
                               prefix:     'Dr.', suffix: 'III')
-        gr2.georeferencers << p
-        p.data_attributes << da1
-        p
+      gr2.georeferencers << p
+      p.data_attributes << da1
+      p
       }
       let!(:person1a) {
         p = person1.dup
@@ -194,11 +218,11 @@
                               # type:              'Person::Unvetted',
                               year_born:         2000, year_died: 2015,
                               year_active_start: 2012, year_active_end: 2015)
-        tn2.taxon_name_authors << p
-        tn1.taxon_name_authors << p
-        gr1.georeferencers << p
-        p.data_attributes << da2
-        p
+      tn2.taxon_name_authors << p
+      tn1.taxon_name_authors << p
+      gr1.georeferencers << p
+      p.data_attributes << da2
+      p
       }
       let(:person1c) {
         p = FactoryBot.create(:person,
@@ -207,8 +231,8 @@
                               # type:              'Person::Unvetted',
                               year_born:         2000, year_died: 2015,
                               year_active_start: 2012, year_active_end: 2015)
-        # additional attributes not replicated yet
-        p
+      # additional attributes not replicated yet
+      p
       }
       let(:person2) { FactoryBot.create(:person, first_name: 'J.', last_name: 'McDonald') }
       let(:person3) { FactoryBot.create(:person, first_name: 'D. Keith McE.', last_name: 'Kevan') }

spec/support/features/authentication_helpers.rb

@@ -4,7 +4,7 @@ module AuthenticationHelpers
 
     def sign_in_with(email, password)
       visit signin_path
-      fill_in 'session_email', with: email, wait: 8, id: 'session_email'
+      fill_in 'session_email', with: email, wait: 9, id: 'session_email'
       fill_in 'session_password', with: password, wait: 8, id: 'session_password'
       click_button 'sign_in'
       find_link('sign_out')  # TODO: check for Capybara bug fix down the road?