flex-station-data 0.3.0 → 1.0.2

data/bin/flex-station-linear-regression

@@ -1,15 +1,13 @@
 #!/usr/bin/env ruby
+# frozen_string_literal: true
 
+require "flex_station_data/concerns/callable"
 require "flex_station_data/services/load_plates"
-require "flex_station_data/presenters/plates_csv"
-require "flex_station_data/presenters/linear_regression/plates_hash"
-require "flex_station_data/presenters/linear_regression/verbose_sample_csv"
-
-require "pry"
+require "flex_station_data/presenters/plates_hash"
 
 module FlexStationData
   class LinearRegressionApp
-    include Concerns::Service
+    include Concerns::Callable[:run]
 
     OPTION_RE = /\A--(\w+(?:-\w+)*)(?:=(.*))?\z/.freeze
 
@@ -30,15 +28,15 @@ module FlexStationData
     end
 
     def threshold
-      Float(option(:threshold)) rescue nil
-    end
-
-    def verbose?
-      option(:verbose)
+      Float(option(:threshold))
+    rescue ArgumentError, TypeError
+      nil
     end
 
     def min_r_squared
-      Float(option("min-r-squared")) rescue 0.75
+      Float(option("min-r-squared"))
+    rescue ArgumentError, TypeError
+      0.75
     end
 
     def files
@@ -51,21 +49,9 @@ module FlexStationData
       end
     end
 
-    def verbose_csv
-      plates.flat_map do |file, file_plates|
-        Presenters::PlatesCsv.present(
-          file,
-          file_plates,
-          sample_presenter: Presenters::LinearRegression::VerboseSampleCsv,
-          threshold:        threshold,
-          min_r_squared:    min_r_squared
-        )
-      end
-    end
-
-    def summary_hashes
+    def plate_hashes
       plates.flat_map do |file, file_plates|
-        Presenters::LinearRegression::PlatesHash.present(
+        Presenters::PlatesHash.present(
           file,
           file_plates,
           threshold:     threshold,
@@ -76,13 +62,13 @@ module FlexStationData
 
     def clean_values(values)
       values.each_with_object([]) do |value, memo|
-        memo << ((value != memo.compact.last) ? value : nil)
+        memo << (value != memo.compact.last ? value : nil)
       end
     end
 
-    def summary_hash
-      @summary_hash ||= begin
-        result = summary_hashes.each_with_object({}) do |hash, memo|
+    def hash
+      @hash ||= begin
+        result = plate_hashes.each_with_object({}) do |hash, memo|
           hash.each do |header, value|
             memo[header] ||= []
             memo[header] << value
@@ -94,15 +80,11 @@ module FlexStationData
       end
     end
 
-    def summary_csv
-      [ summary_hash.keys, *summary_hash.values.transpose ]
-    end
-
     def csv
-      verbose? ? verbose_csv : summary_csv
+      [ hash.keys, *hash.values.transpose ]
     end
 
-    def call
+    def run
       CSV do |out|
         csv.each do |row|
           out << row
@@ -112,4 +94,4 @@ module FlexStationData
   end
 end
 
-FlexStationData::LinearRegressionApp.call(*ARGV)
+FlexStationData::LinearRegressionApp.run(*ARGV)

data/flex-station-data.gemspec

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 lib = File.expand_path("lib", __dir__)
 $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 require "flex_station_data/version"
@@ -21,19 +23,20 @@ Gem::Specification.new do |spec|
 
   # Specify which files should be added to the gem when it is released.
   # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
-  spec.files = Dir.chdir(File.expand_path('..', __FILE__)) do
+  spec.files = Dir.chdir(File.expand_path(__dir__)) do
     `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
   end
   spec.bindir        = "bin"
   spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
 
-  spec.required_ruby_version = ">= 2.4.4"
+  spec.required_ruby_version = ">= 2.7.1"
 
   spec.add_development_dependency "bundler", "~> 2.0"
-  spec.add_development_dependency "rake", "~> 10.0"
-  spec.add_development_dependency "rspec", "~> 3.8"
   spec.add_development_dependency "pry"
+  spec.add_development_dependency "rake", "~> 13.0"
+  spec.add_development_dependency "rspec", "~> 3.8"
+  spec.add_development_dependency "rubocop-rspec"
 
   spec.add_runtime_dependency "activesupport"
   spec.add_runtime_dependency "linefit"

data/lib/flex_station_data.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "flex_station_data/version"
 
 module FlexStationData

data/lib/flex_station_data/concerns/callable.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module FlexStationData
+  module Concerns
+    module Callable
+      class << self
+        def included(base)
+          base.include with(:call)
+        end
+
+        def with(verb)
+          callable_modules[verb.to_sym] ||= Module.new do
+            define_singleton_method(:included) do |base|
+              base.define_singleton_method(verb) do |*args|
+                new(*args).public_send(verb)
+              end
+
+              base.define_singleton_method(:to_proc) do
+                method(verb).to_proc
+              end
+            end
+          end
+        end
+
+        alias [] with
+
+        def callable_modules
+          @callable_modules ||= {}
+        end
+      end
+    end
+  end
+end

data/lib/flex_station_data/concerns/presenter.rb

@@ -1,23 +1,9 @@
-require "active_support/concern"
+# frozen_string_literal: true
+
+require_relative "callable"
 
 module FlexStationData
   module Concerns
-    module Presenter
-      extend ActiveSupport::Concern
-
-      def to_proc
-        Proc.new(&method(:present))
-      end
-
-      class_methods do
-        def present(*args, &block)
-          new(*args).present(&block)
-        end
-
-        def to_proc
-          Proc.new(&method(:present))
-        end
-      end
-    end
+    Presenter = Callable[:present]
   end
 end

data/lib/flex_station_data/concerns/service.rb

@@ -1,23 +1,9 @@
-require "active_support/concern"
+# frozen_string_literal: true
+
+require_relative "callable"
 
 module FlexStationData
   module Concerns
-    module Service
-      extend ActiveSupport::Concern
-
-      def to_proc
-        Proc.new(&method(:call))
-      end
-
-      class_methods do
-        def call(*args, &block)
-          new(*args).call(&block)
-        end
-
-        def to_proc
-          Proc.new(&method(:call))
-        end
-      end
-    end
+    Service = Callable
   end
 end

data/lib/flex_station_data/default_sample_map.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module FlexStationData
+  class DefaultSampleMap
+    attr_reader :rows, :columns, :wells_per_sample
+
+    def initialize(rows, columns, wells_per_sample)
+      @rows             = rows
+      @columns          = columns
+      @wells_per_sample = wells_per_sample
+    end
+
+    def [](sample_label)
+      sample_label = Integer(sample_label)
+      map[sample_label] ||= map_sample(sample_label)
+    end
+
+    private
+
+    def map_sample(sample_label)
+      column, row = (sample_label - 1).divmod(rows)
+      row_label = ("A".ord + row).chr
+      base_column = (column * wells_per_sample) + 1
+      (0...wells_per_sample).map do |column_offset|
+        [ row_label, base_column + column_offset ].join("")
+      end
+    end
+
+    def map
+      @map ||= {}
+    end
+  end
+end

data/lib/flex_station_data/linear_regression.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "active_support/core_ext"
 require "linefit"
 

data/lib/flex_station_data/plate.rb

@@ -1,12 +1,23 @@
+# frozen_string_literal: true
+
+require "flex_station_data/sample"
+
 module FlexStationData
   class Plate
-    attr_reader :label, :times, :temperatures, :samples
+    attr_reader :label, :times, :temperatures, :wells, :sample_map
 
-    def initialize(label, times, temperatures, samples)
+    def initialize(label, times, temperatures, wells, sample_map)
       @label = label
       @times = times
       @temperatures = temperatures
-      @samples = samples
+      @wells = wells
+      @sample_map = sample_map
+    end
+
+    def samples
+      @samples ||= sample_map.map do |label, well_labels|
+        Sample.new(label, well_labels, self)
+      end
     end
   end
 end

data/lib/flex_station_data/presenters/plate_hash.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require "flex_station_data/presenters/sample_hash"
+
+module FlexStationData
+  module Presenters
+    class PlateHash
+      include Concerns::Presenter
+
+      attr_reader :plate, :options
+
+      delegate :times, :samples, to: :plate
+
+      def initialize(plate, **options)
+        @plate = plate
+        @options = options
+      end
+
+      def present
+        samples.map do |sample|
+          { "plate" => plate.label }.merge(SampleHash.present(times, sample, **options))
+        end
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/plates_hash.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require "flex_station_data/presenters/plate_hash"
+
+module FlexStationData
+  module Presenters
+    class PlatesHash
+      include Concerns::Presenter
+
+      attr_reader :file, :plates, :options
+
+      def initialize(file, plates, **options)
+        @file = file
+        @plates = plates
+        @options = options
+      end
+
+      def present
+        base = { "file" => file.basename.to_s }
+        plates.flat_map do |plate|
+          PlateHash.present(plate, **options).map(&base.method(:merge))
+        end
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/sample_hash.rb

@@ -0,0 +1,47 @@
+# frozen_string_literal: true
+
+require "flex_station_data/concerns/presenter"
+require "flex_station_data/services/sample_quality"
+require "flex_station_data/presenters/sample_regression_hash"
+
+module FlexStationData
+  module Presenters
+    class SampleHash
+      include Concerns::Presenter
+
+      attr_reader :times, :sample, :quality_control, :options
+
+      def initialize(times, sample, **options)
+        @times = times
+        @sample = sample
+        @options = options
+      end
+
+      def errors
+        @errors ||= SampleQuality.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.wells.join(", ") }
+      end
+
+      def regression_hash
+        return SampleRegressionHash.headers.zip([]).to_h if errors?
+
+        SampleRegressionHash.present(times, sample.mean, **options).transform_values(&:first)
+      end
+
+      def present
+        { "sample" => sample.label }.merge(wells_hash).merge(errors_hash).merge(regression_hash)
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/sample_regression_hash.rb

@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+require "flex_station_data/concerns/presenter"
+require "flex_station_data/linear_regression"
+
+module FlexStationData
+  module Presenters
+    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