flex-station-data 0.3.0 → 1.0.2

data/lib/flex_station_data/sample.rb

@@ -1,16 +1,31 @@
-require "flex_station_data/readings"
+# frozen_string_literal: true
+
+require "matrix"
+
+require "flex_station_data/services/compute_mean"
 
 module FlexStationData
   class Sample
-    attr_reader :label, :readings
+    attr_reader :label, :wells, :plate
 
-    def initialize(label, readings)
+    delegate :wells, to: :plate, prefix: true
+
+    def initialize(label, wells, plate)
       @label = label
-      @readings = readings
+      @wells = wells
+      @plate = plate
+    end
+
+    def values
+      wells.map(&plate_wells.method(:values))
+    end
+
+    def readings
+      @readings ||= wells.zip(values).map { |well, v| Readings.new(well, v) }
     end
 
     def mean
-      @mean ||= Readings.mean(*readings)
+      @mean ||= values.transpose.map(&ComputeMean)
     end
   end
 end

data/lib/flex_station_data/services/compute_mean.rb

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

data/lib/flex_station_data/services/load_plates.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "csv"
 require "active_support/core_ext"
 
@@ -18,7 +20,10 @@ module FlexStationData
     end
 
     def data_blocks
-      @data_blocks ||= data.split { |row| row[0] == "Plate:" }.drop(1)
+      @data_blocks ||= data.each_with_object([]) do |row, blocks|
+        blocks << [] if plate_row?(row)
+        blocks.last&.push(row)
+      end
     end
 
     def call
@@ -26,5 +31,11 @@ module FlexStationData
         FlexStationData::ParsePlate.call(index + 1, data_block)
       end
     end
+
+    private
+
+    def plate_row?(row)
+      row[0].to_s =~ /\A\s*Plate:\s*/i
+    end
   end
 end

data/lib/flex_station_data/services/parse_plate.rb

@@ -1,7 +1,9 @@
+# frozen_string_literal: true
+
 require "active_support/core_ext"
 
 require "flex_station_data/services/parse_plate_readings"
-require "flex_station_data/services/parse_plate_samples"
+require "flex_station_data/services/parse_sample_map"
 require "flex_station_data/plate"
 
 module FlexStationData
@@ -16,13 +18,13 @@ module FlexStationData
     end
 
     def data_blocks
-      plate_data.split { |row| row[0] == "~End" }
+      plate_data.split { |row| row[0] =~ /\A~End\s*\z/ }
     end
 
     def call
       times, temperatures, wells = ParsePlateReadings.call(data_blocks[0])
-      samples = ParsePlateSamples.call(data_blocks[1], wells)
-      Plate.new(label, times, temperatures, samples)
+      sample_map = ParseSampleMap.call(data_blocks[1])
+      Plate.new(label, times, temperatures, wells, sample_map)
     end
   end
 end

data/lib/flex_station_data/services/parse_plate_readings.rb

@@ -1,4 +1,7 @@
+# frozen_string_literal: true
+
 require "active_support/core_ext"
+require "matrix"
 
 require "flex_station_data/wells"
 require "flex_station_data/concerns/service"
@@ -9,49 +12,32 @@ module FlexStationData
 
     delegate :parse_time, :parse_value, :parse_row, to: :class
 
-    def initialize(plate_readings_block)
-      @plate_readings_block = plate_readings_block
+    def initialize(plate_data)
+      @plate_data = plate_data
     end
 
-    def column_count
-      @column_count ||= headers.reverse.drop_while(&:blank?).size
+    def readings_block
+      @readings_block ||= plate_data
+        .drop_while { |row| !header_row?(row) }
+        .drop_while { |row| !sample_row?(row) }
+        .take_while { |row| !end_row?(row) }
+        .select     { |row| row.any?(&:present?) }
     end
 
-    def parsed_rows
-      @parsed_rows ||= begin
-        rows = plate_readings_data.map { |row| parse_row(row[0...column_count]) }
-        rows.select { |row| row.any?(&:present?) }
-      end
-    end
-
-    def parsed_columns
-      @parsed_columns ||= parsed_rows.transpose
+    def headers
+      @headers ||= plate_data.detect(&method(:header_row?)).reverse.drop_while(&:blank?).reverse
     end
 
     def times
-      @times ||= parsed_columns[0].compact
+      @times ||= matrix.column(0).to_a.compact
     end
 
     def temperatures
-      @temperatures ||= parsed_columns[1].compact
-    end
-
-    def values
-      @values ||= parsed_columns.drop(2)
-    end
-
-    def wells_row_count
-      parsed_rows.size / times.size
-    end
-
-    def plate_readings_matrix
-      values.map do |values_column|
-        values_column.each_slice(wells_row_count).to_a.transpose
-      end.transpose
+      @temperatures ||= matrix.column(1).to_a.compact
     end
 
     def wells
-      Wells.new(plate_readings_matrix)
+      Wells.new(wells_matrix)
     end
 
     def call
@@ -67,7 +53,9 @@ module FlexStationData
       end
 
       def parse_value(v)
-        return Float(v) rescue v.presence
+        Float(v)
+      rescue ArgumentError, TypeError
+        v.presence
       end
 
       def parse_row(row)
@@ -78,14 +66,33 @@ module FlexStationData
 
     private
 
-    def headers
-      plate_readings_block.first
+    def header_row?(row)
+      row[1].to_s =~ /\A\s*Temperature\b/i
+    end
+
+    def sample_row?(row)
+      row[0].to_s =~ /\A\s*\d+:\d+:\d+\s*\z/
+    end
+
+    def end_row?(row)
+      row[0].to_s =~ /\A\s*~End\s*\z/i
+    end
+
+    def well_values
+      matrix.minor(0..-1, 2..-1)
+    end
+
+    def matrix
+      @matrix ||= Matrix[
+        *readings_block.map { |row| parse_row(row[0...headers.size]) }
+      ]
     end
 
-    def plate_readings_data
-      @plate_readings_data ||= plate_readings_block.drop(1)
+    def wells_matrix
+      well_row_count = matrix.row_count / times.size
+      Matrix[*well_values.column_vectors.map { |col| col.to_a.each_slice(well_row_count).to_a.transpose }.transpose]
     end
 
-    attr_reader :plate_readings_block
+    attr_reader :plate_data
   end
 end

data/lib/flex_station_data/services/parse_sample_map.rb

@@ -0,0 +1,47 @@
+# frozen_string_literal: true
+
+require "matrix"
+require "active_support/core_ext"
+
+require "flex_station_data/concerns/service"
+
+module FlexStationData
+  class ParseSampleMap
+    include Concerns::Service
+
+    attr_reader :plate_data
+
+    def initialize(plate_data)
+      @plate_data = plate_data
+    end
+
+    def sample_map_rows
+      plate_data
+        .drop_while { |row| !sample_map_header?(row) }
+        .drop(1)
+        .take_while { |row| !empty_row?(row) }
+        .map(&method(:parse_row))
+    end
+
+    def call
+      sample_map_rows.each_with_object([]) do |(label, well), memo|
+        memo << [ label, [] ] if label.present?
+        memo.last.last << well
+      end.to_h
+    end
+
+    private
+
+    def parse_row(row)
+      row.take(2).map(&:presence)
+    end
+
+    def empty_row?(row)
+      row.all?(&:blank?)
+    end
+
+    def sample_map_header?(row)
+      row[0].to_s =~ /\A\s*Sample\s*\z/i && row[1].to_s =~ /\A\s*Wells\s*\z/i
+    end
+  end
+end

data/lib/flex_station_data/services/sample_quality.rb

@@ -1,23 +1,24 @@
+# frozen_string_literal: true
+
 require "flex_station_data/services/value_quality"
 
 module FlexStationData
   class SampleQuality
     include Concerns::Service
 
-    attr_reader :sample, :value_quality_control, :options
+    attr_reader :sample, :options
 
-    def initialize(sample, value_quality_control: ValueQuality, **options)
+    def initialize(sample, **options)
       @sample = sample
-      @value_quality_control = value_quality_control
       @options = options
     end
 
     def value_quality(value)
-      value_quality_control.call(value, **options)
+      ValueQuality.call(value, **options)
     end
 
     def call
-      sample.readings.flat_map(&:values).map(&method(:value_quality)).uniq(&:to_s)
+      sample.values.flatten.map(&method(:value_quality)).uniq(&:to_s)
     end
   end
 end

data/lib/flex_station_data/services/value_quality.rb

@@ -1,6 +1,10 @@
+# frozen_string_literal: true
+
 require "singleton"
 require "active_support/core_ext"
 
+require "flex_station_data/concerns/service"
+
 module FlexStationData
   class ValueQuality
     include Concerns::Service
@@ -21,7 +25,7 @@ module FlexStationData
       attr_reader :description
 
       def initialize(description)
-        @description ||= description
+        @description = description
       end
 
       def good?

data/lib/flex_station_data/version.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module FlexStationData
-  VERSION = "0.3.0"
+  VERSION = "1.0.2"
 end

data/lib/flex_station_data/wells.rb

@@ -1,29 +1,30 @@
-require "flex_station_data/readings"
+# frozen_string_literal: true
+
+require "matrix"
 
 module FlexStationData
   class Wells
-    def initialize(plate_readings_matrix)
-      @plate_readings_matrix = plate_readings_matrix
+    attr_reader :matrix
+
+    def initialize(matrix)
+      @matrix = matrix
     end
 
-    def readings(well_label)
-      well_index[well_label] ||= begin
-        row, column = parse_well_label(well_label)
-        Readings.new(well_label, plate_readings_matrix[row][column])
-      end
+    def values(well_label)
+      matrix[*coordinates(well_label)]
     end
 
-    def parse_well_label(well_label)
-      row, column = well_label.scan(/\A([A-Z])(\d+)\z/).first
-      [ row.ord - "A".ord, column.to_i - 1 ]
+    def coordinates(well_label)
+      coordinates_index[well_label] ||= begin
+        row, column = well_label.scan(/\A([A-Z])(\d+)\z/).first
+        [ row.ord - "A".ord, column.to_i - 1 ]
+      end
     end
 
     private
 
-    def well_index
-      @well_index ||= {}
+    def coordinates_index
+      @coordinates_index ||= {}
     end
-
-    attr_reader :plate_readings_matrix
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: flex-station-data
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 1.0.2
 platform: ruby
 authors:
 - John Carney
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-08-24 00:00:00.000000000 Z
+date: 2020-07-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -24,20 +24,34 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -53,7 +67,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '3.8'
 - !ruby/object:Gem::Dependency
-  name: pry
+  name: rubocop-rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -100,12 +114,14 @@ email:
 executables:
 - flex-station
 - flex-station-linear-regression
-- flex-station-sample-data
 extensions: []
 extra_rdoc_files: []
 files:
+- ".github/workflows/ruby.yml"
 - ".gitignore"
 - ".rspec"
+- ".rubocop.yml"
+- ".ruby-version"
 - CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
@@ -115,28 +131,24 @@ files:
 - Rakefile
 - bin/flex-station
 - bin/flex-station-linear-regression
-- bin/flex-station-sample-data
 - flex-station-data.gemspec
 - lib/flex_station_data.rb
+- lib/flex_station_data/concerns/callable.rb
 - lib/flex_station_data/concerns/presenter.rb
 - lib/flex_station_data/concerns/service.rb
+- lib/flex_station_data/default_sample_map.rb
 - lib/flex_station_data/linear_regression.rb
 - lib/flex_station_data/plate.rb
-- lib/flex_station_data/presenters/linear_regression/plate_hash.rb
-- lib/flex_station_data/presenters/linear_regression/plates_hash.rb
-- lib/flex_station_data/presenters/linear_regression/sample_hash.rb
-- lib/flex_station_data/presenters/linear_regression/sample_regression_hash.rb
-- lib/flex_station_data/presenters/linear_regression/verbose_sample_csv.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/readings.rb
+- lib/flex_station_data/presenters/plate_hash.rb
+- lib/flex_station_data/presenters/plates_hash.rb
+- lib/flex_station_data/presenters/sample_hash.rb
+- lib/flex_station_data/presenters/sample_regression_hash.rb
 - lib/flex_station_data/sample.rb
 - lib/flex_station_data/services/compute_mean.rb
 - lib/flex_station_data/services/load_plates.rb
 - 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/parse_sample_map.rb
 - lib/flex_station_data/services/sample_quality.rb
 - lib/flex_station_data/services/value_quality.rb
 - lib/flex_station_data/version.rb
@@ -155,14 +167,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.4.4
+      version: 2.7.1
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.1.2
 signing_key: 
 specification_version: 4
 summary: Data analysis tool for FlexStation microplate reader