bio-plates 0.2.0

data/spec/fixtures/emptyrowcol.csv

@@ -0,0 +1,3 @@
+Plate,Well,Row,Column,Drug,Conc,Junk,siRNA
+1,A01,,,si1,,si1,si1
+1,A02,,,,si1,si1,si1

data/spec/fixtures/rowname-error.csv

@@ -0,0 +1 @@
+Plate,Badnamel,Badname,Column,Drug,Conc

data/spec/plate_spec.rb

@@ -0,0 +1,66 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'fakefs/spec_helpers'
+
+describe BioPlates::Plate do
+
+
+  context "accessing wells by row and column" do
+    before(:all) do
+      p96 = BioPlates.read(File.join(File.dirname(__FILE__),"fixtures","4x96.csv"))
+      @plate = p96["Plate1"]
+    end
+
+    it "returns a hash of arrays of well object, by column" do
+      expect(@plate.columns.class).to be Hash
+      expect(@plate.columns.first[1][0].class).to be BioPlates::Plate::Well
+    end
+
+    it "returns an array of rows" do
+      expect(@plate.rows.class).to be Hash
+      expect(@plate.rows.first[1][0].class).to be BioPlates::Plate::Well
+    end
+  end
+
+  context "adding leading zeroes to wells" do
+    before(:all) do
+      p96 = BioPlates.read("spec/fixtures/4x96.csv")
+      @plate = p96["Plate1"]
+    end
+
+    it "adds a zero if the column has only one digit" do
+      @plate.wells[1].column = 1
+      @plate.add_leading_zeroes!
+      expect(@plate.wells[1].column).to eq "01"
+    end
+
+    it "doesn't add a zero to two digit numbers" do
+      @plate.wells[10].column = 10
+      @plate.add_leading_zeroes!
+      expect(@plate.wells[10].column).to eq "10"
+    end
+  end
+
+  context "output" do
+    before(:all) do
+      p96 = BioPlates.read("spec/fixtures/4x96.csv")
+      @plate = p96["Plate1"]
+    end
+
+    it "outputs a CSV file" do
+      expect(CSV).to receive(:open)
+      @plate.dump
+    end
+
+    it "is of the correct length" do
+      expect_any_instance_of(CSV).to receive(:<<).exactly(97).times
+      @plate.dump
+    end
+
+    it "includes arbitrary well annotations" do
+      include FakeFS::SpecHelpers
+      @plate.dump("spec/tmp/output.txt")
+      output = File.open("spec/tmp/output.txt", &:readline)
+      expect(output.chomp).to eq "Plate,Row,Column,drug,conc"
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,32 @@
+require 'simplecov'
+
+module SimpleCov::Configuration
+  def clean_filters
+    @filters = []
+  end
+end
+
+SimpleCov.configure do
+  clean_filters
+  load_adapter 'test_frameworks'
+end
+
+ENV["COVERAGE"] && SimpleCov.start do
+  add_filter "/.rvm/"
+end
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+require 'rspec'
+require 'bio-plates'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  config.before(:suite) do 
+    fixtures_dir = File.join(File.dirname(__FILE__),'fixtures')
+  end
+end
+

data/spec/tmp/output.txt

@@ -0,0 +1,97 @@
+Plate,Row,Column,drug,conc
+Plate1,A,01,si1,5
+Plate1,A,02,si2,5
+Plate1,A,03,si3,5
+Plate1,A,04,si4,5
+Plate1,A,05,si5,5
+Plate1,A,06,si6,5
+Plate1,A,07,si7,5
+Plate1,A,08,si8,5
+Plate1,A,09,si9,5
+Plate1,A,10,si10,5
+Plate1,A,11,si11,5
+Plate1,A,12,si12,5
+Plate1,B,01,si1,5
+Plate1,B,02,si2,5
+Plate1,B,03,si3,5
+Plate1,B,04,si4,5
+Plate1,B,05,si5,5
+Plate1,B,06,si6,5
+Plate1,B,07,si7,5
+Plate1,B,08,si8,5
+Plate1,B,09,si9,5
+Plate1,B,10,si10,5
+Plate1,B,11,si11,5
+Plate1,B,12,si12,5
+Plate1,C,01,si1,5
+Plate1,C,02,si2,5
+Plate1,C,03,si3,5
+Plate1,C,04,si4,5
+Plate1,C,05,si5,5
+Plate1,C,06,si6,5
+Plate1,C,07,si7,5
+Plate1,C,08,si8,5
+Plate1,C,09,si9,5
+Plate1,C,10,si10,5
+Plate1,C,11,si11,5
+Plate1,C,12,si12,5
+Plate1,D,01,si1,5
+Plate1,D,02,si2,5
+Plate1,D,03,si3,5
+Plate1,D,04,si4,5
+Plate1,D,05,si5,5
+Plate1,D,06,si6,5
+Plate1,D,07,si7,5
+Plate1,D,08,si8,5
+Plate1,D,09,si9,5
+Plate1,D,10,si10,5
+Plate1,D,11,si11,5
+Plate1,D,12,si12,5
+Plate1,E,01,si1,5
+Plate1,E,02,si2,5
+Plate1,E,03,si3,5
+Plate1,E,04,si4,5
+Plate1,E,05,si5,5
+Plate1,E,06,si6,5
+Plate1,E,07,si7,5
+Plate1,E,08,si8,5
+Plate1,E,09,si9,5
+Plate1,E,10,si10,5
+Plate1,E,11,si11,5
+Plate1,E,12,si12,5
+Plate1,F,01,si1,5
+Plate1,F,02,si2,5
+Plate1,F,03,si3,5
+Plate1,F,04,si4,5
+Plate1,F,05,si5,5
+Plate1,F,06,si6,5
+Plate1,F,07,si7,5
+Plate1,F,08,si8,5
+Plate1,F,09,si9,5
+Plate1,F,10,si10,5
+Plate1,F,11,si11,5
+Plate1,F,12,si12,5
+Plate1,G,01,si1,5
+Plate1,G,02,si2,5
+Plate1,G,03,si3,5
+Plate1,G,04,si4,5
+Plate1,G,05,si5,5
+Plate1,G,06,si6,5
+Plate1,G,07,si7,5
+Plate1,G,08,si8,5
+Plate1,G,09,si9,5
+Plate1,G,10,si10,5
+Plate1,G,11,si11,5
+Plate1,G,12,si12,5
+Plate1,H,01,si1,5
+Plate1,H,02,si2,5
+Plate1,H,03,si3,5
+Plate1,H,04,si4,5
+Plate1,H,05,si5,5
+Plate1,H,06,si6,5
+Plate1,H,07,si7,5
+Plate1,H,08,si8,5
+Plate1,H,09,si9,5
+Plate1,H,10,si10,5
+Plate1,H,11,si11,5
+Plate1,H,12,si12,5

metadata

@@ -0,0 +1,180 @@
+--- !ruby/object:Gem::Specification
+name: bio-plates
+version: !ruby/object:Gem::Version
+  version: 0.2.0
+platform: ruby
+authors:
+- Steve Pettitt
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2016-01-29 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.3'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  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: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: fakefs
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.10'
+description: Methods for handling multiwell plate annotations, includes ranges and
+  quadrants
+email: spettitt@gmail.com
+executables:
+- bioplates
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- ".document"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- bin/bioplates
+- lib/bio-plates.rb
+- lib/bio-plates/plates.rb
+- spec/bio-plates_spec.rb
+- spec/fixtures/384.csv
+- spec/fixtures/4x96.csv
+- spec/fixtures/anno96.csv
+- spec/fixtures/emptyrowcol.csv
+- spec/fixtures/rowname-error.csv
+- spec/plate_spec.rb
+- spec/spec_helper.rb
+- spec/tmp/output.txt
+homepage: http://github.com/stveep/bioruby-plates
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.1.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.5
+signing_key: 
+specification_version: 4
+summary: Methods for handling multiwell plate annotations
+test_files: []