Merge pull request #25 from hebron-george/dead_code_and_todos

Author: hebron-george

lib/open_fda_api/adverse_events_fields.yml

@@ -13,7 +13,7 @@ class AnimalAndVeterinary < Endpoint
     def adverse_events(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "event.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 

lib/open_fda_api/animal_and_veterinary.rb

@@ -21,7 +21,7 @@ class Device < Endpoint
     def adverse_events(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "event.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {})
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -34,7 +34,7 @@ def adverse_events(search: [], sort: [], count: [], skip: 0, limit: 1)
     def classification(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "classification.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -47,7 +47,7 @@ def classification(search: [], sort: [], count: [], skip: 0, limit: 1)
     def premarket_510ks(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "510k.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -60,7 +60,7 @@ def premarket_510ks(search: [], sort: [], count: [], skip: 0, limit: 1)
     def recall_enforcement_reports(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "enforcement.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -73,7 +73,7 @@ def recall_enforcement_reports(search: [], sort: [], count: [], skip: 0, limit:
     def premarket_approval(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "pma.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -86,7 +86,7 @@ def premarket_approval(search: [], sort: [], count: [], skip: 0, limit: 1)
     def recalls(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "recall.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -99,7 +99,7 @@ def recalls(search: [], sort: [], count: [], skip: 0, limit: 1)
     def registrations_and_listings(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "registrationlisting.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -112,7 +112,7 @@ def registrations_and_listings(search: [], sort: [], count: [], skip: 0, limit:
     def covid19_serological_tests(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "covid19serology.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -125,7 +125,7 @@ def covid19_serological_tests(search: [], sort: [], count: [], skip: 0, limit: 1
     def unique_device_identifier(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "udi.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 

lib/open_fda_api/device.rb

@@ -1,7 +1,5 @@
 # frozen_string_literal: true
 
-require "yaml"
-
 module OpenFdaApi
   # Interact with the Drugs API Endpoint:
   #  - Adverse Events
@@ -19,7 +17,7 @@ class Drugs < Endpoint
     def adverse_events(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "event.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, self.class.valid_adverse_events_fields)
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -32,7 +30,7 @@ def adverse_events(search: [], sort: [], count: [], skip: 0, limit: 1)
     def product_labeling(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "label.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -45,7 +43,7 @@ def product_labeling(search: [], sort: [], count: [], skip: 0, limit: 1)
     def ndc_directory(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "ndc.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -58,7 +56,7 @@ def ndc_directory(search: [], sort: [], count: [], skip: 0, limit: 1)
     def recall_enforcement_reports(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "enforcement.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -71,14 +69,10 @@ def recall_enforcement_reports(search: [], sort: [], count: [], skip: 0, limit:
     def drugs_at_fda(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "drugsfda.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
-    def self.valid_adverse_events_fields
-      @valid_adverse_events_fields ||= ::YAML.load_file("#{__dir__}/adverse_events_fields.yml")
-    end
-
     private
 
     def endpoint_path

lib/open_fda_api/drugs.rb

@@ -9,8 +9,8 @@ def initialize(client)
       @client = client
     end
 
-    def build_query(query_input, valid_search_fields)
-      QueryBuilder.new(query_input: query_input, valid_search_fields: valid_search_fields).build_query
+    def build_query(query_input)
+      QueryBuilder.new(query_input: query_input).build_query
     end
 
     def build_inputs(search:, sort:, count:, skip:, limit:)

lib/open_fda_api/endpoint.rb

@@ -14,7 +14,7 @@ class Food < Endpoint
     def adverse_events(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "event.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -27,7 +27,7 @@ def adverse_events(search: [], sort: [], count: [], skip: 0, limit: 1)
     def recall_enforcement_reports(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "enforcement.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 

lib/open_fda_api/food.rb

@@ -14,7 +14,7 @@ class Other < Endpoint
     def nsde(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "nsde.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 
@@ -27,7 +27,7 @@ def nsde(search: [], sort: [], count: [], skip: 0, limit: 1)
     def substance_data_reports(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "substance.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 

lib/open_fda_api/other.rb

@@ -25,12 +25,8 @@ class InvalidQueryArgument < ArgumentError; end
   #   Use in combination with limit to paginate results. Currently, the largest allowed value for the skip parameter
   #   is 25000. See Paging if you require paging through larger result sets.
   class QueryBuilder
-    # @param [Hash] valid_search_fields
     # @param [QueryInputs] query_input
-    def initialize(query_input:, valid_search_fields:)
-      # TODO: Turn validations back on once we get basic functionality working; need to flex on different field types
-      # validate_arguments!(valid_search_fields, query_input: query_input)
-      warn "You've passed in a valid_search_fields arg but it isn't being used right now..." if valid_search_fields
+    def initialize(query_input:)
       @search  = build_query_string(query_fields: query_input.search)
       @sort    = build_query_string(query_fields: query_input.sort)
       @count   = build_query_string(query_fields: query_input.count)
@@ -53,25 +49,6 @@ def build_query
 
     private
 
-    def validate_arguments!(valid_search_fields, query_input:)
-      # `search` keys must exist in adverse_events_fields.yml
-      invalid_fields = get_invalid_fields(valid_search_fields: valid_search_fields, fields: query_input.search)
-      raise InvalidQueryArgument, "'search' has invalid fields: #{invalid_fields}" if invalid_fields.any?
-
-      # `sort` keys must exist in adverse_events_fields.yml
-      invalid_fields = get_invalid_fields(valid_search_fields: valid_search_fields, fields: query_input.sort)
-      raise InvalidQueryArgument, "'sort' has invalid fields: #{invalid_fields}" if invalid_fields.any?
-
-      # `count` keys must exist in adverse_events_fields.yml
-      invalid_fields = get_invalid_fields(valid_search_fields: valid_search_fields, fields: query_input.count)
-      raise InvalidQueryArgument, "'count' has invalid fields: #{invalid_fields}" if invalid_fields.any?
-
-      # `count` and `skip` cannot be set at the same time
-      return unless count_and_skip_set?(query_input.count, query_input.skip)
-
-      raise InvalidQueryArgument, "'count' and 'skip' cannot both be set at the same time!"
-    end
-
     def build_query_string(query_fields:)
       return "" if query_fields.empty?
 
@@ -87,21 +64,5 @@ def build_groupings(fields)
         "(#{and_args.map { |k, v| "#{k}:#{v.gsub(" ", "+")}" }.join("+AND+")})"
       end.join("+")
     end
-
-    def get_invalid_fields(valid_search_fields:, fields:)
-      # TODO: valid_search_fields define types and we need to check against those
-      fields.map(&:keys).flatten.select do |field|
-        if field.include?(".") # nested field (e.g. patient.patientagegroup)
-          dig_values = field.split(".").join(",properties,").split(",")
-          valid_search_fields["properties"].dig(*dig_values).nil?
-        else
-          !valid_search_fields["properties"].keys.include?(field.to_s)
-        end
-      end
-    end
-
-    def count_and_skip_set?(count, skip)
-      skip.positive? && !count.empty?
-    end
   end
 end

lib/open_fda_api/query_builder.rb

@@ -13,7 +13,7 @@ class Tobacco < Endpoint
     def problem_reports(search: [], sort: [], count: [], skip: 0, limit: 1)
       endpoint = "problem.json"
       inputs   = build_inputs(search: search, sort: sort, count: count, skip: skip, limit: limit)
-      query    = build_query(inputs, {}) # TODO: Upload valid fields
+      query    = build_query(inputs)
       make_request(endpoint, query)
     end
 

lib/open_fda_api/tobacco.rb

@@ -3,29 +3,17 @@
 require "open_fda_api/query_builder"
 
 RSpec.describe OpenFdaApi::QueryBuilder do
-  let(:dummy_valid_data) do
-    {
-      "type" => "object",
-      "properties" => {
-        "a" => "b",
-        "c" => "d",
-        "e" => "f",
-        "foo" => "hello world"
-      }
-    }
-  end
-
   describe "#build_query" do
     context "for search" do
       subject(:build_query) do
-        described_class.new(valid_search_fields: dummy_valid_data, query_input: query_input).build_query
+        described_class.new(query_input: query_input).build_query
       end
 
       let(:query_input) { OpenFdaApi::QueryInputs.new(search: search) }
+
       context "with default" do
         subject(:build_query) do
-          described_class.new(valid_search_fields: dummy_valid_data,
-                              query_input: OpenFdaApi::QueryInputs.new).build_query
+          described_class.new(query_input: OpenFdaApi::QueryInputs.new).build_query
         end
         it { is_expected.to eq({}) }
       end
@@ -65,7 +53,7 @@
 
     context "for sort" do
       subject(:build_query) do
-        described_class.new(valid_search_fields: dummy_valid_data, query_input: query_input).build_query
+        described_class.new(query_input: query_input).build_query
       end
       let(:query_input) { OpenFdaApi::QueryInputs.new(sort: sort) }
       let(:sort) { [{ "a" => "b" }] }
@@ -76,7 +64,7 @@
 
     context "for count" do
       subject(:build_query) do
-        described_class.new(valid_search_fields: dummy_valid_data, query_input: query_input).build_query
+        described_class.new(query_input: query_input).build_query
       end
       let(:query_input) { OpenFdaApi::QueryInputs.new(count: count) }
       let(:count) { [{ "a" => "b" }] }
@@ -87,7 +75,7 @@
 
     context "for skip" do
       subject(:build_query) do
-        described_class.new(valid_search_fields: dummy_valid_data, query_input: query_input).build_query
+        described_class.new(query_input: query_input).build_query
       end
       let(:query_input) { OpenFdaApi::QueryInputs.new(skip: skip) }
       context "when positive" do