flex-station-data 0.3.2 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -9,3 +9,4 @@
 
 # rspec failure tracking
 .rspec_status
+.idea/

data/.ruby-version

@@ -0,0 +1 @@
+2.5.6

data/CHANGELOG.md

@@ -1,3 +1,15 @@
+# 1.0.0
+
+* Removed option for sample data report and verbose linear regression report.
+
+# 0.3.2
+
+* Internal refactoring
+
+# 0.3.1
+
+* Fixed bug
+
 # 0.3.0
 
 * The linear regression analysis report now produces a summary report of the

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    flex-station-data (0.3.2)
+    flex-station-data (1.0.0)
       activesupport
       linefit
 

data/README.md

@@ -2,8 +2,6 @@
 
 Tools for reading and analyzing data from the FlexStation microplate reader.
 
-Currently this is somewhere between alpha and beta.
-
 ## Installation
 
 Add this line to your application's Gemfile:
@@ -28,51 +26,40 @@ To update your installation, use:
 
 ## Usage
 
-### Viewing the sample data
-
-To view the sample results from a set of plate readings, use the following
+To perform a linear regression analysis on the sample data, use the following
 command:
 
-    $ flex-station sample-data <source file> [--threshold=<threshold>]
+    $ flex-station linear-regression <source file> [--threshold=<threshold>] [--min-r-squared=<minimum R²>]
 
 Where `source file` is the file that you got from the reader. You can specify
 multiple source files. The `threshold` setting is optional. If provided,
 samples with values that are below the `threshold` value will be skipped.
 `threshold` must be a number.
 
+If a `--min-r-squared` value is given, samples with a R² value that falls
+below the threshold will be flagged as "poor fits." If no `--min-r-squared` is
+specified, a default of 0.75 will be used.
+
 The output is in CSV format. You'll probably want to save it to a file. You
 can do that by piping the output to a file:
 
-    $ flex-station sample-data source-data.csv --threshold=300 > sample-data.csv
-
-### Performing linear regression analysis on the sample data
-
-To perform a linear regression analysis on the sample data, use the following
-command:
-
-    $ flex-station-data linear-regression <source file> [--threshold=<threshold>] [--verbose] [--min-r-squared=<mininmum R²>]
-
-Note that the `source file` and `threshold` options are the same as for the
-`sample-data` command above. If a `--min-r-squared` value is given, samples
-with a R² value that falls below the threshold will be flagged as "poor fits."
-If no `--min-r-squared` is specified, a default of 0.75 will be used.
-
-By default the linear regression tool will produce a summary report giving the
-slope, intercept, and R² values for each sample. However if `--verbose` is
-specified, it will also include the sample data and regressions for each well.
-
-As with the sample data tool, you will probably want to pipe the output to a file:
-
     $ flex-station linear-regression source-data.csv --threshold=300 > linear-regression.csv
 
 ## Contributing
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/johncarney/flex-station-data. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+Bug reports and pull requests are welcome on GitHub at
+https://github.com/johncarney/flex-station-data. This project is intended to
+be a safe, welcoming space for collaboration, and contributors are expected to
+adhere to the [Contributor Covenant](http://contributor-covenant.org) code of
+conduct.
 
 ## License
 
-The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+The gem is available as open source under the terms of the
+[MIT License](https://opensource.org/licenses/MIT).
 
 ## Code of Conduct
 
-Everyone interacting in the FlexStationData project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/johncarney/flex-station-data/blob/master/CODE_OF_CONDUCT.md).
+Everyone interacting in the FlexStationData project’s codebases, issue
+trackers, chat rooms and mailing lists is expected to follow the
+[code of conduct](https://github.com/johncarney/flex-station-data/blob/master/CODE_OF_CONDUCT.md).

data/bin/flex-station-linear-regression

@@ -1,9 +1,7 @@
 #!/usr/bin/env ruby
 
 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 "flex_station_data/presenters/plates_hash"
 
 module FlexStationData
   class LinearRegressionApp
@@ -31,10 +29,6 @@ module FlexStationData
       Float(option(:threshold)) rescue nil
     end
 
-    def verbose?
-      option(:verbose)
-    end
-
     def min_r_squared
       Float(option("min-r-squared")) rescue 0.75
     end
@@ -49,21 +43,9 @@ module FlexStationData
       end
     end
 
-    def verbose_csv
+    def plate_hashes
       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
-      plates.flat_map do |file, file_plates|
-        Presenters::LinearRegression::PlatesHash.present(
+        Presenters::PlatesHash.present(
           file,
           file_plates,
           threshold:     threshold,
@@ -78,9 +60,9 @@ module FlexStationData
       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
@@ -92,12 +74,8 @@ 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

data/flex-station-data.gemspec

@@ -28,7 +28,7 @@ Gem::Specification.new do |spec|
   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 = ">= 2.5.6"
 
   spec.add_development_dependency "bundler", "~> 2.0"
   spec.add_development_dependency "rake", "~> 10.0"

data/lib/flex_station_data/default_sample_map.rb

@@ -0,0 +1,31 @@
+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/presenters/plate_hash.rb

@@ -0,0 +1,24 @@
+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 +1,24 @@
+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 +1,45 @@
+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 +1,42 @@
+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

data/lib/flex_station_data/services/load_plates.rb

@@ -18,7 +18,10 @@ 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 +29,11 @@ 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_readings.rb

@@ -10,18 +10,20 @@ 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 headers
-      @headers ||= plate_readings_block.first.reverse.drop_while(&:blank?).reverse
+    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 matrix
-      @matrix ||= Matrix[
-        *plate_readings_block.drop(1).map { |row| parse_row(row[0...headers.size]) }.select { |row| row.any?(&:present?) }
-      ]
+    def headers
+      @headers ||= plate_data.detect(&method(:header_row?)).reverse.drop_while(&:blank?).reverse
     end
 
     def times
@@ -32,11 +34,6 @@ module FlexStationData
       @temperatures ||= matrix.column(1).to_a.compact
     end
 
-    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
-
     def wells
       Wells.new(wells_matrix)
     end
@@ -65,10 +62,33 @@ module FlexStationData
 
     private
 
+    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
 
-    attr_reader :plate_readings_block
+    def matrix
+      @matrix ||= Matrix[
+        *readings_block.map { |row| parse_row(row[0...headers.size]) }
+      ]
+    end
+
+    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_data
   end
 end

data/lib/flex_station_data/services/parse_sample_map.rb

@@ -7,14 +7,25 @@ module FlexStationData
   class ParseSampleMap
     include Concerns::Service
 
-    attr_reader :sample_map_block
+    attr_reader :plate_data
 
-    def initialize(sample_map_block)
-      @sample_map_block = sample_map_block
+    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
-      labels.zip(matrix.column(1).to_a.each_slice(wells_per_sample).to_a).to_h
+      sample_map_rows.each_with_object([]) do |(label, well), memo|
+        memo << [ label, [] ] if label.present?
+        memo.last.last << well
+      end.to_h
     end
 
     private
@@ -28,23 +39,7 @@ module FlexStationData
     end
 
     def sample_map_header?(row)
-      row[0] == "Sample"
-    end
-
-    def sample_map_rows
-      sample_map_block.map(&method(:parse_row)).split(&method(:sample_map_header?)).drop(1).first.split(&method(:empty_row?)).first
-    end
-
-    def matrix
-      @matrix ||= Matrix[*sample_map_rows]
-    end
-
-    def labels
-      @labels ||= matrix.column(0).to_a.compact
-    end
-
-    def wells_per_sample
-      matrix.row_count / labels.size
+      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

@@ -4,16 +4,15 @@ 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

data/lib/flex_station_data/services/value_quality.rb

@@ -23,7 +23,7 @@ module FlexStationData
       attr_reader :description
 
       def initialize(description)
-        @description ||= description
+        @description = description
       end
 
       def good?

data/lib/flex_station_data/version.rb

@@ -1,3 +1,3 @@
 module FlexStationData
-  VERSION = "0.3.2"
+  VERSION = "1.0.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: flex-station-data
 version: !ruby/object:Gem::Version
-  version: 0.3.2
+  version: 1.0.0
 platform: ruby
 authors:
 - John Carney
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-08-28 00:00:00.000000000 Z
+date: 2019-09-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -100,12 +100,12 @@ email:
 executables:
 - flex-station
 - flex-station-linear-regression
-- flex-station-sample-data
 extensions: []
 extra_rdoc_files: []
 files:
 - ".gitignore"
 - ".rspec"
+- ".ruby-version"
 - CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
@@ -115,21 +115,17 @@ 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/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/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
@@ -154,14 +150,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.4.4
+      version: 2.5.6
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubyforge_project: 
+rubygems_version: 2.7.6.2
 signing_key: 
 specification_version: 4
 summary: Data analysis tool for FlexStation microplate reader

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.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
-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.values, sample.mean ]
-        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

@@ -1,34 +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 present
-        [
-          [ "Plate #{plate.label}" ],
-          *samples_csv
-        ]
-      end
-
-      private
-
-      def samples_csv
-        samples.flat_map do |sample|
-          sample_presenter.present(times, sample, **options)
-        end
-      end
-    end
-  end
-end

data/lib/flex_station_data/presenters/plates_csv.rb

@@ -1,33 +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 present
-        [
-          [ "File: #{file.basename.to_path}" ],
-          *plates_csv
-        ]
-      end
-
-      private
-
-      def plates_csv
-        plates.flat_map do |plate|
-          plate_presenter.present(plate, **options)
-        end
-      end
-    end
-  end
-end

data/lib/flex_station_data/presenters/sample_csv.rb

@@ -1,61 +0,0 @@
-require "flex_station_data/concerns/presenter"
-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 errors
-        @errors ||= quality_control.call(sample, **options).reject(&:good?)
-      end
-
-      def present
-        [
-          [ label ],
-          *body_csv,
-          [ ]
-        ]
-      end
-
-      private
-
-      def label
-        "Sample #{sample.label}"
-      end
-
-      def errors?
-        errors.present?
-      end
-
-      def errors_csv
-        errors.map(&:to_s).map(&method(:Array))
-      end
-
-      def headers
-        [ "time", *sample.wells, "mean" ]
-      end
-
-      def values
-        [ times, *sample.values, sample.mean ]
-      end
-
-      def values_csv
-        [ headers, *values.transpose ]
-      end
-
-      def body_csv
-        errors? ? errors_csv : values_csv
-      end
-    end
-  end
-end