Y24 -473 generalize multiple source identifier filtering logic

app/models/concerns/source_identifier_filterable.rb

@@ -0,0 +1,73 @@
+# frozen_string_literal: true
+
+# SourceIdentifierFilterable
+#
+# This module provides functionality for filtering records based on source identifiers.
+# A source identifier can be a plate barcode, tube barcode, or a combination of plate barcode
+# and well position.
+# Models that include this module will have methods to filter records using these identifiers.
+#
+# ## Methods:
+#
+# * apply_source_identifier_filter(records, value, plate_join: :plate,
+#                                  tube_join: :tube, well_join: :well)
+#   - Filters the given records based on the provided source identifiers.
+#   - Parameters:
+#     - records: The ActiveRecord relation to filter.
+#     - value: An array of source identifiers to filter by.
+#     - plate_join: The association name for joining with the plate table (default: :plate).
+#     - tube_join: The association name for joining with the tube table (default: :tube).
+#     - well_join: The association name for joining with the well table (default: :well).
+#
+# ## Example Usage:
+#
+#   class MyModel < ApplicationRecord
+#     include SourceIdentifierFilterable
+#   end
+#
+#   records = MyModel.all
+#   source_identifiers = ['PLATE123', 'TUBE456', 'PLATE789:A1']
+#   filtered_records = MyModel.apply_source_identifier_filter(records, source_identifiers)
+#
+#   # Custom join associations
+#   filtered_records = MyModel.apply_source_identifier_filter(records, source_identifiers,
+#                                                             plate_join: :source_plate,
+#                                                             tube_join: :source_tube)
+#
+module SourceIdentifierFilterable
+  extend ActiveSupport::Concern
+
+  class_methods do # rubocop:disable Metrics/BlockLength
+    def apply_source_identifier_filter(records, value, # rubocop:disable Metrics/MethodLength,Metrics/PerceivedComplexity
+                                       plate_join: :plate, tube_join: :tube, well_join: :well)
+      rec_ids = []
+      value.each do |val|
+        # Check if the source identifier contains a colon
+        if val.include?(':')
+          # Split the source identifier into plate and well
+          plate, well = val.split(':')
+          # Filter records based on plate and well
+          if plate.present?
+            filtered_recs = records.joins(plate_join).where(plate_join => { barcode: plate })
+            if well.present?
+              filtered_recs = filtered_recs.joins(well_join).where(well_join => { position: well })
+            end
+          else
+            Rails.logger.warn("Malformed source identifier: '#{val}'. Plate part is missing.")
+            next
+          end
+        else
+          filtered_recs = records.joins(plate_join).where(plate_join => { barcode: val })
+          if filtered_recs.empty?
+            filtered_recs = records.joins(tube_join).where(tube_join => { barcode: val })
+          end
+        end
+        # Add the filtered record ids to the list
+        rec_ids.concat(filtered_recs.pluck(:id))
+      rescue StandardError => e
+        Rails.logger.warn("Invalid source identifier: #{val}, error: #{e.message}")
+      end
+      records.where(id: rec_ids)
+    end
+  end
+end

app/resources/v1/pacbio/library_resource.rb

@@ -2,19 +2,46 @@
 
 module V1
   module Pacbio
-    # @todo This documentation does not yet include a detailed description of what this resource represents.
-    # @todo This documentation does not yet include detailed descriptions for relationships, attributes and filters.
-    # @todo This documentation does not yet include any example usage of the API via cURL or similar.
-    #
-    # @note Access this resource via the `/v1/pacbio/libraries/` endpoint.
-    #
     # Provides a JSON:API representation of {Pacbio::Library}.
     #
     # For more information about JSON:API see the [JSON:API Specifications](https://jsonapi.org/format/)
     # or look at the [JSONAPI::Resources](http://jsonapi-resources.com/) package
     # for the service implementation of the JSON:API standard.
+    # This resource represents a Pacbio Library and can return all libraries, a single library or
+    # multiple libraries along with their relationships.
+    #
+    # ## Filters:
+    #
+    # * sample_name
+    # * barcode
+    # * source_identifier
+    #
+    # ## Primary relationships:
+    #
+    # * request {V1::Pacbio::RequestResource}
+    # * tube {V1::Pacbio::TubeResource}
+    # * pool {V1::Pacbio::PoolResource}
+    #
+    # ## Relationship trees:
+    #
+    # * request.sample
+    # * tube.requests
+    # * pool.libraries
+    #
+    # @example
+    #   curl -X GET http://localhost:3000/v1/pacbio/libraries/1
+    #   curl -X GET http://localhost:3000/v1/pacbio/libraries/
+    #   curl -X GET http://localhost:3000/v1/pacbio/libraries/1?include=request,tube,pool
+    #
+    #   https://localhost:3000/v1/pacbio/libraries?filter[sample_name]=sample_name
+    #   https://localhost:3000/v1/pacbio/libraries?filter[barcode]=TRAC-2-12068
+    #
+    #   https://localhost:3000/v1/pacbio/libraries?filter[barcode]=TRAC-2-12068,TRAC-2-12066,TRAC-2-12067
+    #
+    #   https://localhost:3000/v1/pacbio/libraries?filter[barcode]=TRAC-2-12068,TRAC-2-12066,TRAC-2-12067&include=request.sample,tube.requests,pool.libraries
     class LibraryResource < JSONAPI::Resource
       include Shared::RunSuitability
+      include SourceIdentifierFilterable
 
       model_name 'Pacbio::Library'
 
@@ -90,17 +117,9 @@ def self.default_sort
         records.joins(:tube).where(tubes: { barcode: value })
       }
       filter :source_identifier, apply: lambda { |records, value, _options|
-        # First we check tubes to see if there are any given the source identifier
-        recs = records.joins(:source_tube).where(source_tube: { barcode: value })
-        return recs unless recs.empty?
-
-        # If no tubes match the source identifier we check plates
-        # If source identifier specifies a well we need to match samples to well
-        # TODO: The below value[0] means we only take the first value passed in the filter
-        #       If we want to support multiple values in one filter we would need to update this
-        plate, well = value[0].split(':')
-        recs = records.joins(:source_plate).where(source_plate: { barcode: plate })
-        well ? recs.joins(:source_well).where(source_well: { position: well }) : recs
+        apply_source_identifier_filter(records, value, plate_join: :source_plate,
+                                                       tube_join: :source_tube,
+                                                       well_join: :source_well)
       }
 
       def self.records_for_populate(*_args)

app/resources/v1/pacbio/request_resource.rb

@@ -42,6 +42,8 @@ module Pacbio
     #
     #   https://localhost:3000/v1/pacbio/requests?filter[source_identifier]=TRAC-2-12068,TRAC-2-12066,TRAC-2-12067&include=well.plate,plate.wells,tube.requests
     class RequestResource < JSONAPI::Resource
+      include SourceIdentifierFilterable
+
       model_name 'Pacbio::Request', add_model_hint: false
 
       # @!attribute [rw] library_type
@@ -89,40 +91,7 @@ class RequestResource < JSONAPI::Resource
       }
 
       filter :source_identifier, apply: lambda { |records, value, _options|
-        # Initialize an empty result set
-        rec_ids = []
-
-        # Iterate over each value in the filter
-        value.each do |val|
-          if val.include?(':')
-            # If the value contains a colon, it's a plate and well identifier
-            plate, well = val.split(':')
-            if plate.present?
-              filtered_recs = records.joins(:plate).where(plate: { barcode: plate })
-              if well.present?
-                filtered_recs = filtered_recs.joins(:well).where(well: { position: well })
-              end
-            else
-              Rails.logger.warn("Malformed source identifier: '#{val}'. Plate part is missing.")
-              next
-            end
-          else
-            #  If the value does not contain a colon, it's a tube or plate identifier
-            filtered_recs = records.joins(:plate).where(plate: { barcode: val })
-            # If no records are found by plate, try to find by tube
-            if filtered_recs.empty?
-              filtered_recs = records.joins(:tube).where(tube: { barcode: val })
-            end
-          end
-          # Collect the IDs of the filtered records
-          rec_ids.concat(filtered_recs.pluck(:id))
-        rescue StandardError => e
-          # Log the error and continue with the next value
-          Rails.logger.warn("Invalid source identifier: #{val}, error: #{e.message}")
-        end
-        # Perform a final query to fetch the records by their IDs
-        combined_recs = records.where(id: rec_ids)
-        combined_recs
+        apply_source_identifier_filter(records, value)
       }
 
       def self.default_sort

spec/models/concerns/source_identifier_filterable_spec.rb

@@ -0,0 +1,138 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe SourceIdentifierFilterable do
+  let(:dummy_class) do
+    Class.new do
+      include SourceIdentifierFilterable
+
+      def apply_source_identifier_filter(records, value, plate_join: :plate, tube_join: :tube, well_join: :well)
+        self.class.apply_source_identifier_filter(records, value, plate_join: plate_join, tube_join: tube_join, well_join: well_join)
+      end
+    end
+  end
+
+  let(:dummy_instance) { dummy_class.new }
+
+  describe '#apply_source_identifier_filter' do
+    context 'when the source_identifier belongs to a plate' do
+      it 'returns the correct records' do
+        pacbio_plate = create(:plate_with_wells_and_requests, pipeline: 'pacbio')
+        pacbio_plate_requests = pacbio_plate.wells.flat_map(&:pacbio_requests)
+        records = Pacbio::Request.all
+
+        filtered_records = dummy_instance.apply_source_identifier_filter(records, [pacbio_plate.barcode])
+
+        expect(filtered_records.count).to eq(pacbio_plate_requests.count)
+        expect(filtered_records.map(&:id)).to match_array(pacbio_plate_requests.map(&:id))
+      end
+    end
+
+    context 'when the source_identifier belongs to a tube' do
+      it 'returns the correct records' do
+        pacbio_tube = create(:tube_with_pacbio_request)
+        records = Pacbio::Request.all
+
+        filtered_records = dummy_instance.apply_source_identifier_filter(records, [pacbio_tube.barcode])
+
+        expect(filtered_records.count).to eq(pacbio_tube.pacbio_requests.count)
+        expect(filtered_records.map(&:id)).to match_array(pacbio_tube.pacbio_requests.map(&:id))
+      end
+    end
+
+    context 'when the source_identifier belongs to a plate and well separated by colon' do
+      it 'returns the correct records' do
+        pacbio_plate = create(:plate_with_wells_and_requests, pipeline: 'pacbio')
+        pacbio_plate_requests = pacbio_plate.wells.first.pacbio_requests
+        records = Pacbio::Request.all
+
+        filtered_records = dummy_instance.apply_source_identifier_filter(records, ["#{pacbio_plate.barcode}:#{pacbio_plate.wells.first.position}"])
+
+        expect(filtered_records.count).to eq(pacbio_plate_requests.count)
+        expect(filtered_records.map(&:id)).to match_array(pacbio_plate_requests.map(&:id))
+      end
+    end
+
+    context 'when the source_identifier contains multiple tubes, plates and invalid values' do
+      it 'returns the correct records and logs warnings for invalid values' do
+        pacbio_tube1 = create(:tube_with_pacbio_request)
+        pacbio_tube2 = create(:tube_with_pacbio_request)
+        pacbio_plate1 = create(:plate_with_wells_and_requests, pipeline: 'pacbio')
+        pacbio_plate2 = create(:plate_with_wells_and_requests, pipeline: 'pacbio')
+        pacbio_plate1_requests = pacbio_plate1.wells.first.pacbio_requests
+        pacbio_plate2_requests = pacbio_plate2.wells.flat_map(&:pacbio_requests)
+
+        source_identifiers = [
+          pacbio_tube1.barcode,
+          pacbio_tube2.barcode,
+          "#{pacbio_plate1.barcode}:#{pacbio_plate1.wells.first.position}",
+          pacbio_plate2.barcode,
+          'INVALID_IDENTIFIER'
+        ]
+
+        records = Pacbio::Request.all
+
+        filtered_records = dummy_instance.apply_source_identifier_filter(records, source_identifiers)
+
+        total_requests = pacbio_tube1.pacbio_requests.length +
+                         pacbio_tube2.pacbio_requests.length +
+                         pacbio_plate1_requests.length +
+                         pacbio_plate2_requests.length
+
+        expect(filtered_records.count).to eq(total_requests)
+        expect(filtered_records.map(&:id)).to match_array(
+          pacbio_tube1.pacbio_requests.map(&:id) +
+          pacbio_tube2.pacbio_requests.map(&:id) +
+          pacbio_plate1_requests.map(&:id) +
+          pacbio_plate2_requests.map(&:id)
+        )
+      end
+    end
+
+    context 'when the source_identifier contains malformed strings' do
+      it 'logs warnings for malformed strings' do
+        source_identifiers = [':test']
+        records = Pacbio::Request.all
+
+        expect(Rails.logger).to receive(:warn).with("Malformed source identifier: ':test'. Plate part is missing.").at_least(:once)
+
+        filtered_records = dummy_instance.apply_source_identifier_filter(records, source_identifiers)
+
+        expect(filtered_records.count).to eq(0)
+      end
+    end
+
+    context 'when the source_identifer contains colon which includes plate barcode without well' do
+      it 'returns the correct records for plate' do
+        pacbio_plate1 = create(:plate_with_wells_and_requests, pipeline: 'pacbio')
+        pacbio_plate_requests = pacbio_plate1.wells.flat_map(&:pacbio_requests)
+        source_identifiers = ["#{pacbio_plate1.barcode}:"]
+        records = Pacbio::Request.all
+        filtered_records = dummy_instance.apply_source_identifier_filter(records, source_identifiers)
+        expect(filtered_records.count).to eq(pacbio_plate_requests.count)
+      end
+    end
+
+    context 'when using custom join conditions' do
+      it 'returns the correct records for source_plate and source_tube' do
+        pacbio_tube = create(:tube_with_pacbio_request)
+        create(:pacbio_library, request: pacbio_tube.pacbio_requests[0])
+        pacbio_plate = create(:plate_with_wells_and_requests, pipeline: 'pacbio')
+        pacbio_plate.wells.first.pacbio_requests[0]
+        create(:pacbio_library, request: pacbio_plate.wells.first.pacbio_requests[0])
+        source_identifiers = [
+          pacbio_tube.barcode,
+          "#{pacbio_plate.barcode}:#{pacbio_plate.wells.first.position}"
+        ]
+        records = Pacbio::Library.all
+        filtered_records = dummy_instance.apply_source_identifier_filter(records, source_identifiers, plate_join: :source_plate,
+                                                                                                      tube_join: :source_tube,
+                                                                                                      well_join: :source_well)
+
+        expect(filtered_records.count).to eq(records.count)
+        expect(filtered_records.map(&:id)).to match_array(records.map(&:id))
+      end
+    end
+  end
+end

spec/requests/v1/pacbio/libraries_spec.rb

@@ -230,6 +230,37 @@
             'created_at' => pacbio_library.created_at.to_fs(:us)
           )
         end
+
+        it 'when the source_identifier contains multiple values' do
+          pacbio_tube = create(:tube_with_pacbio_request)
+          pacbio_library1 = create(:pacbio_library, request: pacbio_tube.pacbio_requests[0])
+
+          pacbio_plate = create(:plate_with_wells_and_requests, pipeline: 'pacbio')
+          pacbio_requests = pacbio_plate.wells.flat_map(&:pacbio_requests)
+          pacbio_library2 = create(:pacbio_library, request: pacbio_requests[0])
+
+          source_identifiers = [
+            pacbio_tube.barcode,
+            "#{pacbio_plate.barcode}:#{pacbio_plate.wells.first.position}"
+          ]
+
+          get "#{v1_pacbio_libraries_path}?filter[source_identifier]=#{source_identifiers.join(',')}",
+              headers: json_api_headers
+
+          expect(response).to have_http_status(:success)
+          expect(json['data'].length).to eq(2)
+          [pacbio_library1, pacbio_library2].each do |library|
+            library_attributes = find_resource(type: 'libraries', id: library.id)['attributes']
+            expect(library_attributes).to include(
+              'concentration' => library.concentration,
+              'volume' => library.volume,
+              'template_prep_kit_box_barcode' => library.template_prep_kit_box_barcode,
+              'insert_size' => library.insert_size,
+              'state' => library.state,
+              'created_at' => library.created_at.to_fs(:us)
+            )
+          end
+        end
       end
 
       context 'filters - barcode' do