Sequence params into obs

app/classes/query/image_with_observations.rb

@@ -28,7 +28,7 @@ def initialize_flavor
       initialize_association_parameters
       add_where_conditions
       initialize_boolean_parameters
-      initialize_search_parameters
+      initialize_obs_search_parameters
       add_bounding_box_conditions_for_observations
       initialize_content_filters(Observation)
       super
@@ -51,7 +51,7 @@ def initialize_boolean_parameters
       initialize_is_collection_location_parameter
       initialize_with_public_lat_lng_parameter
       initialize_with_name_parameter
-      initialize_with_notes_parameter
+      initialize_with_obs_notes_parameter
       add_join(:observations, :comments) if params[:with_comments]
       add_join(:observations, :sequences) if params[:with_sequences]
       add_with_notes_fields_condition(params[:with_notes_fields])

app/classes/query/initializers/observations.rb

@@ -48,19 +48,19 @@ def add_ids_condition(table = model.table_name, ids = :ids)
         add_is_collection_location_condition_for_locations
       end
 
-      def initialize_herbaria_parameter
-        add_id_condition(
-          "herbarium_records.herbarium_id",
-          lookup_herbaria_by_name(params[:herbaria]),
-          :observations, :observation_herbarium_records, :herbarium_records
+      def initialize_obs_date_parameter(param_name = :date)
+        add_date_condition(
+          "observations.when",
+          params[param_name],
+          :observations
         )
       end
 
-      def initialize_herbarium_records_parameter
-        add_id_condition(
-          "observation_herbarium_records.herbarium_record_id",
-          lookup_herbarium_records_by_name(params[:herbarium_records]),
-          :observations, :observation_herbarium_records
+      def initialize_confidence_parameter
+        add_range_condition(
+          "observations.vote_cache",
+          params[:confidence],
+          :observations
         )
       end
 
@@ -76,15 +76,35 @@ def initialize_is_collection_location_parameter
         add_boolean_condition(
           "observations.is_collection_location IS TRUE",
           "observations.is_collection_location IS FALSE",
-          params[:is_collection_location]
+          params[:is_collection_location],
+          :observations
         )
       end
 
       def initialize_with_public_lat_lng_parameter
         add_boolean_condition(
           "observations.lat IS NOT NULL AND observations.gps_hidden IS FALSE",
           "observations.lat IS NULL OR observations.gps_hidden IS TRUE",
-          params[:with_public_lat_lng]
+          params[:with_public_lat_lng],
+          :observations
+        )
+      end
+
+      def initialize_with_images_parameter
+        add_boolean_condition(
+          "observations.thumb_image_id IS NOT NULL",
+          "observations.thumb_image_id IS NULL",
+          params[:with_images],
+          :observations
+        )
+      end
+
+      def initialize_with_specimen_parameter
+        add_boolean_condition(
+          "observations.specimen IS TRUE",
+          "observations.specimen IS FALSE",
+          params[:with_specimen],
+          :observations
         )
       end
 
@@ -99,15 +119,16 @@ def initialize_with_name_parameter
         )
       end
 
-      def initialize_with_notes_parameter
+      def initialize_with_obs_notes_parameter(param_name = :with_notes)
         add_boolean_condition(
           "observations.notes != #{escape(Observation.no_notes_persisted)}",
           "observations.notes  = #{escape(Observation.no_notes_persisted)}",
-          params[:with_notes]
+          params[param_name],
+          :observations
         )
       end
 
-      def initialize_search_parameters
+      def initialize_obs_search_parameters
         add_search_condition(
           "observations.notes",
           params[:notes_has]

app/classes/query/location_with_observations.rb

@@ -29,7 +29,7 @@ def initialize_flavor
       initialize_association_parameters
       add_range_condition("observations.vote_cache", params[:confidence])
       initialize_boolean_parameters
-      initialize_search_parameters
+      initialize_obs_search_parameters
       initialize_content_filters(Observation)
       super
     end
@@ -53,7 +53,7 @@ def initialize_boolean_parameters
       initialize_is_collection_location_parameter
       initialize_with_public_lat_lng_parameter
       initialize_with_name_parameter
-      initialize_with_notes_parameter
+      initialize_with_obs_notes_parameter
       add_with_notes_fields_condition(params[:with_notes_fields])
       add_join(:observations, :comments) if params[:with_comments]
       add_join(:observations, :sequences) if params[:with_sequences]

app/classes/query/modules/associations.rb

@@ -4,6 +4,22 @@ module Query
   module Modules
     # Helper methods for turning Query parameters into SQL conditions.
     module Associations
+      def initialize_herbaria_parameter
+        add_id_condition(
+          "herbarium_records.herbarium_id",
+          lookup_herbaria_by_name(params[:herbaria]),
+          :observations, :observation_herbarium_records, :herbarium_records
+        )
+      end
+
+      def initialize_herbarium_records_parameter
+        add_id_condition(
+          "observation_herbarium_records.herbarium_record_id",
+          lookup_herbarium_records_by_name(params[:herbarium_records]),
+          :observations, :observation_herbarium_records
+        )
+      end
+
       def add_where_condition(table, vals, *)
         return if vals.empty?
 

app/classes/query/name_with_observations.rb

@@ -28,7 +28,7 @@ def initialize_flavor
       add_where_conditions
       initialize_association_parameters
       initialize_boolean_parameters
-      initialize_search_parameters
+      initialize_obs_search_parameters
       initialize_name_parameters(:observations)
       add_range_condition("observations.vote_cache", params[:confidence])
       add_bounding_box_conditions_for_observations
@@ -53,7 +53,7 @@ def initialize_boolean_parameters
       initialize_is_collection_location_parameter
       initialize_with_public_lat_lng_parameter
       initialize_with_name_parameter
-      initialize_with_notes_parameter
+      initialize_with_obs_notes_parameter
       add_with_notes_fields_condition(params[:with_notes_fields])
       add_join(:observations, :comments) if params[:with_comments]
       add_join(:observations, :sequences) if params[:with_sequences]

app/classes/query/observation_base.rb

@@ -45,25 +45,23 @@ def local_parameter_declarations
       }
     end
 
-    # rubocop:disable Metrics/AbcSize
     def initialize_flavor
       add_ids_condition
       add_owner_and_time_stamp_conditions("observations")
       add_by_user_condition("observations")
-      add_date_condition("observations.when", params[:date])
+      initialize_obs_date_parameter(:date)
       add_pattern_condition
       add_advanced_search_conditions
       add_needs_naming_condition
       initialize_name_parameters
       initialize_association_parameters
       initialize_boolean_parameters
-      initialize_search_parameters
-      add_range_condition("observations.vote_cache", params[:confidence])
+      initialize_obs_search_parameters
+      initialize_confidence_parameter
       add_bounding_box_conditions_for_observations
       initialize_content_filters(Observation)
       super
     end
-    # rubocop:enable Metrics/AbcSize
 
     def add_pattern_condition
       return if params[:pattern].blank?
@@ -160,24 +158,11 @@ def add_location_in_region_condition
       where << conds
     end
 
-    # The tricky thing here is, without the user.id being the value passed in
-    # params[:filter][:term], we're hunting for a user from a string like
-    # "Name <name>". Better to have the id as the value!
-    # Below uses the method in query/initializers/advanced_search to get a
-    # string but is expensive. Something like
-    # joins(:users).where((User[:login] + User[:name]).matches(str))
-    # def add_by_user_condition
-    #   return unless params[:by_user]
-    #
-    #   user = find_cached_parameter_instance(User, :by_user)
-    #   user = params[:by_user].to_s.gsub(/ *<[^<>]*>/, "")
-    # end
-
     def initialize_boolean_parameters
       initialize_is_collection_location_parameter
       initialize_with_public_lat_lng_parameter
       initialize_with_name_parameter
-      initialize_with_notes_parameter
+      initialize_with_obs_notes_parameter
       add_with_notes_fields_condition(params[:with_notes_fields])
       add_join(:comments) if params[:with_comments]
       add_join(:sequences) if params[:with_sequences]

app/classes/query/sequence_base.rb

@@ -4,6 +4,7 @@ module Query
   # Methods to validate parameters and initialize Query's which return Sequences
   class SequenceBase < Query::Base
     include Query::Initializers::Names
+    include Query::Initializers::Observations
 
     def model
       Sequence
@@ -89,13 +90,14 @@ def search_fields
     def initialize_association_parameters
       add_id_condition("sequences.observation_id", params[:observations])
       initialize_observers_parameter
-      initialize_locations_parameter
+      add_where_condition("observations", params[:locations], :observations)
       initialize_herbaria_parameter
       initialize_herbarium_records_parameter
       initialize_projects_parameter
       initialize_species_lists_parameter
     end
 
+    # Different because it can take multiple users
     def initialize_observers_parameter
       add_id_condition(
         "observations.user_id",
@@ -104,47 +106,10 @@ def initialize_observers_parameter
       )
     end
 
-    def initialize_locations_parameter
-      add_id_condition(
-        "observations.location_id",
-        lookup_locations_by_name(params[:locations]),
-        :observations
-      )
-    end
-
-    def initialize_herbaria_parameter
-      add_id_condition(
-        "herbarium_records.herbarium_id",
-        lookup_herbaria_by_name(params[:herbaria]),
-        :observations, :observation_herbarium_records, :herbarium_records
-      )
-    end
-
-    def initialize_herbarium_records_parameter
-      add_id_condition(
-        "observation_herbarium_records.herbarium_record_id",
-        lookup_herbarium_records_by_name(params[:herbarium_records]),
-        :observations, :observation_herbarium_records
-      )
-    end
-
     def initialize_observation_parameters
-      add_date_condition(
-        "observations.when",
-        params[:obs_date],
-        :observations
-      )
-      add_boolean_condition(
-        "observations.is_collection_location IS TRUE",
-        "observations.is_collection_location IS FALSE",
-        params[:is_collection_location],
-        :observations
-      )
-      add_range_condition(
-        "observations.vote_cache",
-        params[:confidence],
-        :observations
-      )
+      initialize_obs_date_parameter(:obs_date)
+      initialize_is_collection_location_parameter
+      initialize_confidence_parameter
     end
 
     def initialize_exact_match_parameters
@@ -157,48 +122,10 @@ def initialize_boolean_parameters
       initialize_with_images_parameter
       initialize_with_specimen_parameter
       initialize_with_name_parameter
-      initialize_with_obs_notes_parameter
+      initialize_with_obs_notes_parameter(:with_obs_notes)
       add_with_notes_fields_condition(params[:with_notes_fields], :observations)
     end
 
-    def initialize_with_images_parameter
-      add_boolean_condition(
-        "observations.thumb_image_id IS NOT NULL",
-        "observations.thumb_image_id IS NULL",
-        params[:with_images],
-        :observations
-      )
-    end
-
-    def initialize_with_specimen_parameter
-      add_boolean_condition(
-        "observations.specimen IS TRUE",
-        "observations.specimen IS FALSE",
-        params[:with_specimen],
-        :observations
-      )
-    end
-
-    def initialize_with_name_parameter
-      genus = Name.ranks[:Genus]
-      group = Name.ranks[:Group]
-      add_boolean_condition(
-        "names.`rank` <= #{genus} or names.`rank` = #{group}",
-        "names.`rank` > #{genus} and names.`rank` < #{group}",
-        params[:with_name],
-        :observations, :names
-      )
-    end
-
-    def initialize_with_obs_notes_parameter
-      add_boolean_condition(
-        "observations.notes != #{escape(Observation.no_notes_persisted)}",
-        "observations.notes  = #{escape(Observation.no_notes_persisted)}",
-        params[:with_obs_notes],
-        :observations
-      )
-    end
-
     def initialize_search_parameters
       add_search_condition("sequences.locus", params[:locus_has])
       add_search_condition("sequences.accession", params[:accession_has])