flex-station-data 0.3.0 → 1.0.2

data/bin/flex-station-sample-data

@@ -1,54 +0,0 @@
-#!/usr/bin/env ruby
-
-require "flex_station_data/services/load_plates"
-require "flex_station_data/presenters/plates_csv"
-
-module FlexStationData
-  class SampleDataApp
-    include Concerns::Service
-
-    OPTION_RE = /\A--(\w+(?:-\w+)*)(?:=(.*))?\z/.freeze
-
-    attr_reader :args, :options
-
-    def initialize(*args)
-      @options, @args = args.partition { |arg| arg =~ OPTION_RE }
-      @options.map! do |option|
-        option.scan(OPTION_RE).first
-      end
-    end
-
-    def threshold
-      name, value = options.reverse.detect { |name, value| name == "threshold" }
-      return nil if name.blank?
-
-      Float(value)
-    end
-
-    def files
-      @files ||= args.map { |arg| Pathname(arg) }
-    end
-
-    def plates
-      @plates ||= files.map do |file|
-        [ file, LoadPlates.call(file) ]
-      end
-    end
-
-    def csv
-      plates.flat_map do |file, file_plates|
-        Presenters::PlatesCsv.present(file, file_plates, threshold: threshold)
-      end
-    end
-
-    def call
-      CSV do |out|
-        csv.each do |row|
-          out << row
-        end
-      end
-    end
-  end
-end
-
-FlexStationData::SampleDataApp.call(*ARGV)

data/lib/flex_station_data/presenters/linear_regression/plate_hash.rb

@@ -1,27 +0,0 @@
-require "flex_station_data/presenters/linear_regression/sample_hash"
-
-module FlexStationData
-  module Presenters
-    module LinearRegression
-      class PlateHash
-        include Concerns::Presenter
-
-        attr_reader :plate, :sample_presenter, :options
-
-        delegate :times, :samples, to: :plate
-
-        def initialize(plate, sample_presenter: SampleHash, **options)
-          @plate = plate
-          @sample_presenter = sample_presenter
-          @options = options
-        end
-
-        def present
-          samples.map do |sample|
-            { "plate" => plate.label }.merge(sample_presenter.present(times, sample, **options))
-          end
-        end
-      end
-    end
-  end
-end

data/lib/flex_station_data/presenters/linear_regression/plates_hash.rb

@@ -1,28 +0,0 @@
-require "flex_station_data/presenters/linear_regression/plate_hash"
-
-module FlexStationData
-  module Presenters
-    module LinearRegression
-      class PlatesHash
-        include Concerns::Presenter
-
-        attr_reader :file, :plates, :plate_presenter, :options
-
-        def initialize(file, plates, plate_presenter: PlateHash, **options)
-          @file = file
-          @plates = plates
-          @plate_presenter = plate_presenter
-          @options = options
-        end
-
-        def present
-          plates.flat_map do |plate|
-            plate_presenter.present(plate, **options).map do |plate_hash|
-              { "file" => file.basename.to_s }.merge(plate_hash)
-            end
-          end
-        end
-      end
-    end
-  end
-end

data/lib/flex_station_data/presenters/linear_regression/sample_hash.rb

@@ -1,47 +0,0 @@
-require "flex_station_data/presenters/sample_csv"
-require "flex_station_data/presenters/linear_regression/sample_regression_hash"
-
-module FlexStationData
-  module Presenters
-    module LinearRegression
-      class SampleHash
-        include Concerns::Presenter
-
-        attr_reader :times, :sample, :quality_control, :options
-
-        def initialize(times, sample, quality_control: SampleQuality, **options)
-          @times = times
-          @sample = sample
-          @quality_control = quality_control
-          @options = options
-        end
-
-        def errors
-          @errors ||= quality_control.call(sample, **options).reject(&:good?)
-        end
-
-        def errors?
-          errors.present?
-        end
-
-        def errors_hash
-          { "error" => errors.first&.to_s }
-        end
-
-        def wells_hash
-          { "wells" => sample.readings.map(&:label).join(", ") }
-        end
-
-        def regression_hash
-          return SampleRegressionHash.headers.zip([]).to_h if errors?
-
-          SampleRegressionHash.present(times, sample.mean.values, **options).transform_values(&:first)
-        end
-
-        def present
-          { "sample" => sample.label }.merge(wells_hash).merge(errors_hash).merge(regression_hash)
-        end
-      end
-    end
-  end
-end

data/lib/flex_station_data/presenters/linear_regression/sample_regression_hash.rb

@@ -1,43 +0,0 @@
-require "flex_station_data/linear_regression"
-
-module FlexStationData
-  module Presenters
-    module LinearRegression
-      class SampleRegressionHash
-        include Concerns::Presenter
-
-        PRODUCTS = {
-          slope:     "slope",
-          intercept: "intercept",
-          r_squared: "R²",
-          quality:   "quality"
-        }.freeze
-
-        attr_reader :times, :sample_values, :min_r_squared, :options
-
-        def initialize(times, *sample_values, min_r_squared: nil, **options)
-          @times = times
-          @sample_values = sample_values
-          @min_r_squared = min_r_squared
-          @options = options
-        end
-
-        def sample_regressions
-          @sample_regressions ||= sample_values.map do |values|
-            FlexStationData::LinearRegression.new(times, values, min_r_squared: min_r_squared)
-          end
-        end
-
-        def present
-          PRODUCTS.each_with_object({}) do |(method, label), memo|
-            memo[label] = sample_regressions.map(&method)
-          end
-        end
-
-        def self.headers
-          PRODUCTS.values
-        end
-      end
-    end
-  end
-end

data/lib/flex_station_data/presenters/linear_regression/verbose_sample_csv.rb

@@ -1,28 +0,0 @@
-require "flex_station_data/presenters/sample_csv"
-require "flex_station_data/presenters/linear_regression/sample_regression_hash"
-
-module FlexStationData
-  module Presenters
-    module LinearRegression
-      class VerboseSampleCsv < Presenters::SampleCsv
-        include Concerns::Presenter
-
-        def sample_values
-          [ *sample.readings, sample.mean ].map(&:values)
-        end
-
-        def regressions_hash
-          SampleRegressionHash.present(times, *sample_values, **options)
-        end
-
-        def regressions_csv
-          regressions_hash.to_a.map(&:flatten)
-        end
-
-        def values_csv
-          super + regressions_csv
-        end
-      end
-    end
-  end
-end

data/lib/flex_station_data/presenters/plate_csv.rb

@@ -1,29 +0,0 @@
-require "flex_station_data/presenters/sample_csv"
-
-module FlexStationData
-  module Presenters
-    class PlateCsv
-      include Concerns::Presenter
-
-      attr_reader :plate, :sample_presenter, :options
-
-      delegate :times, :samples, to: :plate
-
-      def initialize(plate, sample_presenter: SampleCsv, **options)
-        @plate = plate
-        @sample_presenter = sample_presenter
-        @options = options
-      end
-
-      def samples_csv
-        samples.flat_map do |sample|
-          sample_presenter.present(times, sample, **options)
-        end
-      end
-
-      def present
-        [ ["Plate #{plate.label}"], *samples_csv ]
-      end
-    end
-  end
-end

data/lib/flex_station_data/presenters/plates_csv.rb

@@ -1,28 +0,0 @@
-require "flex_station_data/presenters/plate_csv"
-
-module FlexStationData
-  module Presenters
-    class PlatesCsv
-      include Concerns::Presenter
-
-      attr_reader :file, :plates, :plate_presenter, :options
-
-      def initialize(file, plates, plate_presenter: PlateCsv, **options)
-        @file = file
-        @plates = plates
-        @plate_presenter = plate_presenter
-        @options = options
-      end
-
-      def plates_csv
-        plates.flat_map do |plate|
-          plate_presenter.present(plate, **options)
-        end
-      end
-
-      def present
-        [ ["File: #{file.to_path}"], *plates_csv ]
-      end
-    end
-  end
-end

data/lib/flex_station_data/presenters/sample_csv.rb

@@ -1,56 +0,0 @@
-require "flex_station_data/concerns/presenter"
-require "flex_station_data/readings"
-require "flex_station_data/services/sample_quality"
-
-module FlexStationData
-  module Presenters
-    class SampleCsv
-      include Concerns::Presenter
-
-      attr_reader :times, :sample, :quality_control, :options
-
-      def initialize(times, sample, quality_control: SampleQuality, **options)
-        @times = times
-        @sample = sample
-        @quality_control = quality_control
-        @options = options
-      end
-
-      def readings
-        @readings ||= [ Readings.new("time", times), *sample.readings, sample.mean ]
-      end
-
-      def headers
-        readings.map(&:label)
-      end
-
-      def rows
-        readings.map(&:values).transpose
-      end
-
-      def label
-        "Sample #{sample.label}"
-      end
-
-      def errors
-        @errors ||= quality_control.call(sample, **options).reject(&:good?)
-      end
-
-      def errors?
-        errors.present?
-      end
-
-      def errors_csv
-        errors.map(&:to_s).map(&method(:Array))
-      end
-
-      def values_csv
-        [ headers, *rows ]
-      end
-
-      def present
-        [ [label] ] + (errors? ? errors_csv : values_csv) + [ [] ]
-      end
-    end
-  end
-end

data/lib/flex_station_data/readings.rb

@@ -1,16 +0,0 @@
-require "flex_station_data/services/compute_mean"
-
-module FlexStationData
-  class Readings
-    attr_reader :label, :values
-
-    def initialize(label, values)
-      @label = label
-      @values = values
-    end
-
-    def self.mean(*readings, label: "mean")
-      new(label, readings.map(&:values).transpose.map(&ComputeMean))
-    end
-  end
-end

data/lib/flex_station_data/services/parse_plate_samples.rb

@@ -1,49 +0,0 @@
-require "flex_station_data/readings"
-require "flex_station_data/concerns/service"
-
-require "flex_station_data/sample"
-
-module FlexStationData
-  class ParsePlateSamples
-    include Concerns::Service
-
-    def initialize(sample_map_block, wells)
-      @sample_map_block = sample_map_block
-      @wells = wells
-    end
-
-    def map_rows
-      @map_rows ||= begin
-        rows = sample_map_block.drop_while { |row| row[0] != "Sample" }.drop(1)
-        rows = rows.map { |row| row.map(&:presence) }
-        rows.take_while { |row| row.any?(&:present?) }.to_a
-      end
-    end
-
-    def map_columns
-      @map_columns ||= map_rows.transpose
-    end
-
-    def labels
-      @labels ||= map_columns[0].compact
-    end
-
-    def wells_per_sample
-      map_rows.size / labels.size
-    end
-
-    def sample_map
-      @sample_map ||= map_columns[1].each_slice(wells_per_sample).to_a
-    end
-
-    def call
-      labels.zip(sample_map).map do |label, well_labels|
-        Sample.new(label, well_labels.map(&wells.method(:readings)))
-      end
-    end
-
-    private
-
-    attr_reader :sample_map_block, :wells
-  end
-end