flex-station-data 0.1.1 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    flex-station-data (0.1.1)
+    flex-station-data (0.2.0)
       activesupport
       linefit
 

data/bin/flex-station-linear-regression

@@ -3,16 +3,41 @@
 #!/usr/bin/env ruby
 
 require "flex_station_data/services/load_plates"
-require "flex_station_data/linear_regression"
+require "flex_station_data/presenters/plates_csv"
+require "flex_station_data/presenters/plate_csv"
+require "flex_station_data/presenters/sample_linear_regression_csv"
 
 module FlexStationData
   class LinearRegressionApp
     include Concerns::Service
 
-    attr_reader :args
+    OPTION_RE = /\A--(\w+(?:-\w+)*)(?:=(.*))?\z/.freeze
+
+    attr_reader :args, :options
 
     def initialize(*args)
-      @args = 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 value_quality_control
+      @value_quality_control ||= begin
+        value_threshold = threshold
+        ->(value) { ValueQuality.call(value, threshold: value_threshold) }
+      end
+    end
+
+    def sample_quality_control
+      ->(sample) { SampleQuality.call(sample, value_quality_control: value_quality_control) }
     end
 
     def files
@@ -25,32 +50,23 @@ module FlexStationData
       end
     end
 
-    def call
-      plates.each do |file, file_plates|
-        puts "File: #{file.to_path}"
-        file_plates.each_with_index.map do |plate, plate_index|
-          puts "Plate: #{plate_index + 1}"
-          plate.samples.each do |sample|
-            readings_labels = sample.readings.map(&:label)
-            puts "Sample #{sample.label}"
-            CSV do |out|
-              readings = [*sample.readings, sample.mean]
-              out << ["time", *readings.map(&:label)]
-              plate.times.zip(*readings.map(&:values)).each do |row|
-                out << row
-              end
-
-              regression_factory = LinearRegression.method(:new).curry(2)[plate.times]
-              regressions = readings.map(&:values).map(&regression_factory)
-              out << ["slope", *regressions.map(&:slope)]
-              out << ["R²", *regressions.map(&:r_squared)]
-
-              out << []
-            end
+    def csv
+      plates.flat_map do |file, file_plates|
+        Presenters::PlatesCsv.present(file, file_plates) do |plate|
+          Presenters::PlateCsv.present(plate) do |times, sample|
+            Presenters::SampleLinearRegressionCsv.present(times, sample, quality_control: sample_quality_control)
           end
         end
       end
     end
+
+    def call
+      CSV do |out|
+        csv.each do |row|
+          out << row
+        end
+      end
+    end
   end
 end
 

data/bin/flex-station-sample-data

@@ -1,15 +1,39 @@
 #!/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
 
-    attr_reader :args
+    OPTION_RE = /\A--(\w+(?:-\w+)*)(?:=(.*))?\z/.freeze
+
+    attr_reader :args, :options
 
     def initialize(*args)
-      @args = 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 value_quality_control
+      @value_quality_control ||= begin
+        value_threshold = threshold
+        ->(value) { ValueQuality.call(value, threshold: value_threshold) }
+      end
+    end
+
+    def sample_quality_control
+      ->(sample) { SampleQuality.call(sample, value_quality_control: value_quality_control) }
     end
 
     def files
@@ -22,26 +46,23 @@ module FlexStationData
       end
     end
 
-    def call
-      plates.each do |file, file_plates|
-        puts "File: #{file.to_path}"
-        file_plates.each_with_index.map do |plate, plate_index|
-          puts "Plate: #{plate_index + 1}"
-          plate.samples.each do |sample|
-            readings_labels = sample.readings.map(&:label)
-            puts "Sample #{sample.label}"
-            CSV do |out|
-              mean = sample.mean
-              out << ["time", *sample.readings.map(&:label), mean.label]
-              plate.times.zip(*sample.readings.map(&:values), mean.values).each do |row|
-                out << row
-              end
-              out << []
-            end
+    def csv
+      plates.flat_map do |file, file_plates|
+        Presenters::PlatesCsv.present(file, file_plates) do |plate|
+          Presenters::PlateCsv.present(plate) do |times, sample|
+            Presenters::SampleCsv.present(times, sample, quality_control: sample_quality_control)
           end
         end
       end
     end
+
+    def call
+      CSV do |out|
+        csv.each do |row|
+          out << row
+        end
+      end
+    end
   end
 end
 

data/lib/flex_station_data/concerns/presenter.rb

@@ -0,0 +1,23 @@
+require "active_support/concern"
+
+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
+  end
+end

data/lib/flex_station_data/concerns/service.rb

@@ -5,6 +5,10 @@ module FlexStationData
     module Service
       extend ActiveSupport::Concern
 
+      def to_proc
+        Proc.new(&method(:call))
+      end
+
       class_methods do
         def call(*args, &block)
           new(*args).call(&block)

data/lib/flex_station_data/plate.rb

@@ -1,8 +1,9 @@
 module FlexStationData
   class Plate
-    attr_reader :times, :temperatures, :samples
+    attr_reader :label, :times, :temperatures, :samples
 
-    def initialize(times, temperatures, samples)
+    def initialize(label, times, temperatures, samples)
+      @label = label
       @times = times
       @temperatures = temperatures
       @samples = samples

data/lib/flex_station_data/presenters/plate_csv.rb

@@ -0,0 +1,23 @@
+require "flex_station_data/presenters/sample_csv"
+
+module FlexStationData
+  module Presenters
+    class PlateCsv
+      include Concerns::Presenter
+
+      attr_reader :plate
+
+      delegate :times, :samples, to: :plate
+
+      def initialize(plate)
+        @plate = plate
+      end
+
+      def present(&sample_presenter)
+        sample_presenter ||= SampleCsv
+        sample_presenter = sample_presenter.curry(2)[times]
+        [ ["Plate #{plate.label}"], *samples.flat_map(&sample_presenter) ]
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/plates_csv.rb

@@ -0,0 +1,21 @@
+require "flex_station_data/presenters/plate_csv"
+
+module FlexStationData
+  module Presenters
+    class PlatesCsv
+      include Concerns::Presenter
+
+      attr_reader :file, :plates
+
+      def initialize(file, plates)
+        @file = file
+        @plates = plates
+      end
+
+      def present(&plate_presenter)
+        plate_presenter ||= PlateCsv
+        [ ["File: #{file.to_path}"], *plates.flat_map(&plate_presenter) ]
+      end
+    end
+  end
+end

data/lib/flex_station_data/presenters/sample_csv.rb

@@ -0,0 +1,55 @@
+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
+
+      def initialize(times, sample, quality_control: SampleQuality)
+        @times = times
+        @sample = sample
+        @quality_control = quality_control
+      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).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/presenters/sample_linear_regression_csv.rb

@@ -0,0 +1,29 @@
+require "flex_station_data/presenters/sample_csv"
+require "flex_station_data/linear_regression"
+
+module FlexStationData
+  module Presenters
+    class SampleLinearRegressionCsv < SampleCsv
+      include Concerns::Presenter
+
+      def regression_factory
+        LinearRegression.method(:new).curry(2)[times]
+      end
+
+      def regressions
+        [ *sample.readings, sample.mean ].map(&:values).map(&regression_factory)
+      end
+
+      def regressions_csv
+        [
+          [ "slope", *regressions.map(&:slope) ],
+          [ "R²",    *regressions.map(&:r_squared) ]
+        ]
+      end
+
+      def values_csv
+        super + regressions_csv
+      end
+    end
+  end
+end

data/lib/flex_station_data/services/load_plates.rb

@@ -22,7 +22,9 @@ module FlexStationData
     end
 
     def call
-      data_blocks.map(&FlexStationData::ParsePlate)
+      data_blocks.each_with_index.map do |data_block, index|
+        FlexStationData::ParsePlate.call(index + 1, data_block)
+      end
     end
   end
 end

data/lib/flex_station_data/services/parse_plate.rb

@@ -8,9 +8,10 @@ module FlexStationData
   class ParsePlate
     include Concerns::Service
 
-    attr_reader :plate_data
+    attr_reader :label, :plate_data
 
-    def initialize(plate_data)
+    def initialize(label, plate_data)
+      @label = label
       @plate_data = plate_data
     end
 
@@ -21,7 +22,7 @@ module FlexStationData
     def call
       times, temperatures, wells = ParsePlateReadings.call(data_blocks[0])
       samples = ParsePlateSamples.call(data_blocks[1], wells)
-      Plate.new(times, temperatures, samples)
+      Plate.new(label, times, temperatures, samples)
     end
   end
 end

data/lib/flex_station_data/services/sample_quality.rb

@@ -0,0 +1,18 @@
+require "flex_station_data/services/value_quality"
+
+module FlexStationData
+  class SampleQuality
+    include Concerns::Service
+
+    attr_reader :sample, :value_quality_control
+
+    def initialize(sample, value_quality_control: ValueQuality)
+      @sample = sample
+      @value_quality_control = value_quality_control
+    end
+
+    def call
+      sample.readings.flat_map(&:values).map(&value_quality_control).uniq(&:to_s)
+    end
+  end
+end

data/lib/flex_station_data/services/value_quality.rb

@@ -0,0 +1,73 @@
+require "singleton"
+require "active_support/core_ext"
+
+module FlexStationData
+  class ValueQuality
+    include Concerns::Service
+
+    class Good
+      include Singleton
+
+      def good?
+        true
+      end
+
+      def to_s
+        "good"
+      end
+    end
+
+    class Bad
+      attr_reader :description
+
+      def initialize(description)
+        @description ||= description
+      end
+
+      def good?
+        false
+      end
+
+      def to_s
+        description
+      end
+    end
+
+    attr_reader :value, :threshold
+
+    def initialize(value, threshold: nil)
+      @value = value
+      @threshold = threshold
+    end
+
+    def no_data?
+      value.blank?
+    end
+
+    def saturated?
+      value == "#SAT"
+    end
+
+    def invalid?
+      !(no_data? || saturated? || value.is_a?(Numeric))
+    end
+
+    def below_threshold?
+      threshold.present? && value.is_a?(Numeric) && value < threshold
+    end
+
+    def call
+      if no_data?
+        Bad.new("No data")
+      elsif saturated?
+        Bad.new("Saturated")
+      elsif invalid?
+        Bad.new("Invalid data")
+      elsif below_threshold?
+        Bad.new("Below threshold")
+      else
+        Good.instance
+      end
+    end
+  end
+end

data/lib/flex_station_data/version.rb

@@ -1,3 +1,3 @@
 module FlexStationData
-  VERSION = "0.1.1"
+  VERSION = "0.2.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: flex-station-data
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.2.0
 platform: ruby
 authors:
 - John Carney
@@ -117,9 +117,14 @@ files:
 - bin/flex-station-sample-data
 - flex-station-data.gemspec
 - lib/flex_station_data.rb
+- lib/flex_station_data/concerns/presenter.rb
 - lib/flex_station_data/concerns/service.rb
 - lib/flex_station_data/linear_regression.rb
 - lib/flex_station_data/plate.rb
+- lib/flex_station_data/presenters/plate_csv.rb
+- lib/flex_station_data/presenters/plates_csv.rb
+- lib/flex_station_data/presenters/sample_csv.rb
+- lib/flex_station_data/presenters/sample_linear_regression_csv.rb
 - lib/flex_station_data/readings.rb
 - lib/flex_station_data/sample.rb
 - lib/flex_station_data/services/compute_mean.rb
@@ -127,6 +132,8 @@ files:
 - lib/flex_station_data/services/parse_plate.rb
 - lib/flex_station_data/services/parse_plate_readings.rb
 - lib/flex_station_data/services/parse_plate_samples.rb
+- lib/flex_station_data/services/sample_quality.rb
+- lib/flex_station_data/services/value_quality.rb
 - lib/flex_station_data/version.rb
 - lib/flex_station_data/wells.rb
 homepage: https://github.com/johncarney/flex-station-data
@@ -150,8 +157,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.6
+rubygems_version: 3.0.3
 signing_key: 
 specification_version: 4
 summary: Data analysis tool for FlexStation microplate reader