Add search service and normalizer for list

app/services/protocol_importers/search_protocols_service.rb

@@ -0,0 +1,70 @@
+# frozen_string_literal: true
+
+module ProtocolImporters
+  class SearchProtocolsService
+    extend Service
+
+    attr_reader :errors, :protocols_list
+
+    CONSTANTS = Constants::PROTOCOLS_IO_V3_API
+
+    def initialize(protocol_source:, query_params: {})
+      @protocol_source = protocol_source
+      @query_params = query_params
+      @errors = Hash.new { |h, k| h[k] = {} }
+    end
+
+    def call
+      return self unless valid?
+
+      api_response = api_client.protocol_list(@query_params)
+
+      @protocols_list = normalizer.normalize_list(api_response)
+
+      self
+    end
+
+    def succeed?
+      @errors.none?
+    end
+
+    private
+
+    def valid?
+      # try if key is not empty
+      @errors[:invalid_params][:key] = 'Key cannot be empty' if @query_params[:key].blank?
+
+      # try if page id is ok
+      if @query_params[:page_id] && !@query_params[:page_id].positive?
+        @errors[:invalid_params][:page_id] = 'Page needs to be positive'
+      end
+
+      # try if order_field is ok
+      if CONSTANTS[:available_order_fields]&.exclude? @query_params[:order_field].to_sym
+        @errors[:invalid_params][:order_field] = 'Order field is not ok'
+      end
+
+      # try if order dir is ok
+      if CONSTANTS[:available_order_dirs]&.exclude? @query_params[:order_dir].to_sym
+        @errors[:invalid_params][:order_dir] = 'Order dir is not ok'
+      end
+
+      # try if endpints exists
+      @errors[:invalid_params][:source_endpoint] = 'Wrong source endpoint' unless endpoint_name&.is_a?(String)
+
+      succeed?
+    end
+
+    def endpoint_name
+      Constants::PROTOCOLS_ENDPOINTS.dig(*@protocol_source.split('/').map(&:to_sym))
+    end
+
+    def api_client
+      "ProtocolImporters::#{endpoint_name}::ApiClient".constantize.new
+    end
+
+    def normalizer
+      "ProtocolImporters::#{endpoint_name}::ProtocolNormalizer".constantize.new
+    end
+  end
+end

app/utilities/protocol_importers/protocol_normalizer.rb

@@ -2,7 +2,7 @@
 
 module ProtocolImporters
   class ProtocolNormalizer
-    def normalize_all_protocols(_client_data)
+    def normalize_list(_client_data)
       raise NotImplementedError
     end
 

app/utilities/protocol_importers/protocols_io/v3/protocol_normalizer.rb

@@ -50,6 +50,24 @@ module ProtocolImporters
 
           { protocol: normalized_data }
         end
+
+        def normalize_list(client_data)
+          # client_data is HttpParty ApiReponse object
+          protocols_hash = client_data.parsed_response.with_indifferent_access[:items]
+          normalized_data = {}
+          normalized_data[:protocols] = protocols_hash.map do |e|
+            {
+              "id": e[:id],
+              "title": e[:title],
+              "created_on": e[:created_on],
+              "authors": e[:authors].map { |a| a[:name] }.join(', '),
+              "nr_of_steps": e[:stats][:number_of_steps],
+              "nr_of_views": e[:stats][:number_of_views],
+              "uri": e[:uri]
+            }
+          end
+          normalized_data
+        end
       end
     end
   end

config/initializers/constants.rb

@@ -203,6 +203,8 @@ class Constants
     base_uri: 'https://www.protocols.io/api/v3/',
     default_timeout: 10,
     debug_level: :debug,
+    available_order_fields: %i(title created_on),
+    available_order_dirs: %i(asc desc),
     endpoints: {
       protocols: {
         default_query_params: {

spec/fixtures/files/protocol_importers/normalized_list.json

@@ -0,0 +1,94 @@
+{
+  "protocols": [
+    {
+      "id": 22532,
+      "title": "Producing rooted cassava plantlets for use in pot experiments",
+      "created_on": 1556012701,
+      "authors": "Matema Imakumbili",
+      "nr_of_steps": 13,
+      "nr_of_views": 37,
+      "uri": "producing-rooted-cassava-plantlets-for-use-in-pot-z9cf92w"
+    },
+    {
+      "id": 832,
+      "title": "Preparation of Virus DNA from Seawater for Metagenomics",
+      "created_on": 1434495014,
+      "authors": "Matthew Sullivan Lab",
+      "nr_of_steps": 11,
+      "nr_of_views": 457,
+      "uri": "Preparation-of-Virus-DNA-from-Seawater-for-Metagen-c28yhv"
+    },
+    {
+      "id": 14506,
+      "title": "MALE CIRCUMCISION FOR PREVENTION OF HETEROSEXUAL TRANSMISSION OF HIV IN ADULT MALES IN SOWETO, what do indicators and incidence rates show?untitled protocol",
+      "created_on": 1533553359,
+      "authors": "Hillary Mukudu, Neil Martinson, Benn Sartorius",
+      "nr_of_steps": 0,
+      "nr_of_views": 5,
+      "uri": "male-circumcision-for-prevention-of-heterosexual-t-seiebce"
+    },
+    {
+      "id": 10927,
+      "title": "physiological and biochemical parameters",
+      "created_on": 1521454618,
+      "authors": "Amor Slama, Elhem Mallek-Maalej, Hatem Ben Mohamed, Thouraya Rhim, Leila Radhouane, Amor SLAMA",
+      "nr_of_steps": 0,
+      "nr_of_views": 34,
+      "uri": "physiological-and-biochemical-parameters-nwpdfdn"
+    },
+    {
+      "id": 822,
+      "title": "Iron Chloride Precipitation of Viruses from Seawater",
+      "created_on": 1434402745,
+      "authors": "Seth John,  Bonnie Poulos,  Christine Schirmer",
+      "nr_of_steps": 17,
+      "nr_of_views": 1805,
+      "uri": "Iron-Chloride-Precipitation-of-Viruses-from-Seawat-c2wyfd"
+    },
+    {
+      "id": 12115,
+      "title": "Measuring specific leaf area and water content",
+      "created_on": 1526074093,
+      "authors": "Etienne Laliberté",
+      "nr_of_steps": 33,
+      "nr_of_views": 259,
+      "uri": "measuring-specific-leaf-area-and-water-content-p3tdqnn"
+    },
+    {
+      "id": 1842,
+      "title": "Purification of viral assemblages from seawater in CsCl gradients",
+      "created_on": 1445287995,
+      "authors": "Janice E. Lawrence and Grieg F. Steward",
+      "nr_of_steps": 23,
+      "nr_of_views": 116,
+      "uri": "Purification-of-viral-assemblages-from-seawater-in-d2s8ed"
+    },
+    {
+      "id": 12540,
+      "title": "An improved primer set and PCR amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region using the SymVar primer pair",
+      "created_on": 1527418313,
+      "authors": "Benjamin Hume, Maren Ziegler, Christian Voolstra, Julie Poulain, Xavier Pochon, Sarah Romac, Emilie Boissin, Colomban de Vargas, Serge Planes, Patrick Wincker",
+      "nr_of_steps": 1,
+      "nr_of_views": 234,
+      "uri": "an-improved-primer-set-and-pcr-amplification-proto-qg4dtyw"
+    },
+    {
+      "id": 985,
+      "title": "NATURAL SEAWATER-BASED PRO99 MEDIUM",
+      "created_on": 1435347035,
+      "authors": "Chisholm Lab",
+      "nr_of_steps": 10,
+      "nr_of_views": 85,
+      "uri": "NATURAL-SEAWATER-BASED-PRO99-MEDIUM-c7zzp5"
+    },
+    {
+      "id": 1033,
+      "title": "SN Maintenance Medium for Synechococcus",
+      "created_on": 1435778857,
+      "authors": "JB Waterbury \u0026 JM Willey",
+      "nr_of_steps": 6,
+      "nr_of_views": 33,
+      "uri": "SN-Maintenance-Medium-for-Synechococcus-c9hz35"
+    }
+  ]
+}

spec/services/protocol_importers/search_protocols_service_spec.rb

@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+describe ProtocolImporters::SearchProtocolsService do
+  let(:service_call) do
+    ProtocolImporters::SearchProtocolsService.call(protocol_source: 'protocolsio/v3',
+                                                   query_params: {
+                                                     key: 'someting',
+                                                     page_id: 5,
+                                                     order_field: 'title',
+                                                     order_dir: 'asc'
+                                                   })
+  end
+
+  let(:service_call_with_wrong_params) do
+    ProtocolImporters::SearchProtocolsService.call(protocol_source: 'protocolsio3',
+                                                   query_params: {
+                                                     key: '',
+                                                     page_id: -1,
+                                                     order_field: 'gender',
+                                                     order_dir: 'descc'
+                                                   })
+  end
+  let(:normalized_list) do
+    JSON.parse(file_fixture('protocol_importers/normalized_list.json').read).to_h.with_indifferent_access
+  end
+
+  context 'when have invalid attributes' do
+    it 'returns an error when params are invalid' do
+      expect(service_call_with_wrong_params.errors).to have_key(:invalid_params)
+    end
+  end
+
+  context 'when have valid attributes' do
+    before do
+      client_data = double('api_response')
+
+      allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
+        .to(receive(:protocol_list)
+              .and_return(client_data))
+
+      allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer)
+        .to(receive(:normalize_list).with(client_data)
+              .and_return(normalized_list))
+    end
+
+    it 'returns an error when params are invalid' do
+      expect(service_call.protocols_list).to be == normalized_list
+    end
+  end
+end

spec/utilities/protocol_importers/protocol_normalizer_spec.rb

@@ -3,11 +3,11 @@
 require 'rails_helper'
 
 describe ProtocolImporters::ProtocolNormalizer do
-  describe '.normalize_all_protocols' do
-    it { expect { subject.normalize_all_protocols({}) }.to raise_error(NotImplementedError) }
+  describe '.normalize_list' do
+    it { expect { subject.normalize_list({}) }.to raise_error(NotImplementedError) }
   end
 
-  describe '.normalize_protocols' do
+  describe '.normalize_protocol' do
     it { expect { subject.normalize_protocol({}) }.to raise_error(NotImplementedError) }
   end
 end

spec/utilities/protocol_importers/protocols_io/v3/protocol_normalizer_spec.rb

@@ -5,20 +5,27 @@ require 'rails_helper'
 describe ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer do
   let(:client_data) { double('api_response') }
 
-  let(:response) do
+  let(:protocols_io_single_protocol) do
     JSON.parse(file_fixture('protocol_importers/protocols_io/v3/single_protocol.json').read)
         .to_h.with_indifferent_access
   end
 
   let(:response_without_title) do
-    res_without_title = response
+    res_without_title = protocols_io_single_protocol
     res_without_title[:protocol].reject! { |a| a == 'title' }
     res_without_title
   end
 
-  let(:normalized_result) do
-    JSON.parse(file_fixture('protocol_importers/normalized_single_protocol.json').read)
-        .to_h.with_indifferent_access
+  let(:protocols_io_list) do
+    JSON.parse(file_fixture('protocol_importers/protocols_io/v3/protocols.json').read).to_h.with_indifferent_access
+  end
+
+  let(:normalized_protocol) do
+    JSON.parse(file_fixture('protocol_importers/normalized_single_protocol.json').read).to_h.with_indifferent_access
+  end
+
+  let(:normalized_list) do
+    JSON.parse(file_fixture('protocol_importers/normalized_list.json').read).to_h.with_indifferent_access
   end
 
   describe '#normalize_protocol' do
@@ -30,9 +37,9 @@ describe ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer do
     context 'when have all data' do
       it 'should normalize data correctly' do
         allow(client_data).to receive_message_chain(:parsed_response)
-          .and_return(response)
+          .and_return(protocols_io_single_protocol)
 
-        expect(subject.normalize_protocol(client_data).deep_stringify_keys).to be == normalized_result
+        expect(subject.normalize_protocol(client_data).deep_stringify_keys).to be == normalized_protocol
       end
     end
 
@@ -45,4 +52,12 @@ describe ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer do
       end
     end
   end
+
+  describe '#normalize_list' do
+    it 'should normalize data correctly' do
+      allow(client_data).to receive_message_chain(:parsed_response).and_return(protocols_io_list)
+
+      expect(subject.normalize_list(client_data).deep_stringify_keys).to be == normalized_list
+    end
+  end
 end