strain-code 0.1.0

checksums.yaml

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data/Gemfile

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+source 'https://rubygems.org'
+gemspec
+
+group :test do
+  gem 'simplecov'
+end
+
+gem 'rake', '~> 13.0'

data/LICENSE

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+MIT License
+
+Copyright (c) 2025 The SeqCode Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

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+# StrainCode
+
+A gem for parsing and formatting strain numbers
+from microbiological culture collections
+
+## Installation
+
+```bash
+gem install strain-code
+```
+
+## Usage
+
+```ruby
+require 'strain_code'
+
+# Parse one or more numbers in a variety of formats
+str_no = StrainCode.parse <<STR_NO
+  ATCC 33152  = CCUG 9568  = CIP 103854  ;
+  DSM 25069  = DSM_7513  = JCM:7571;
+  NBIMCC:8848 = NCTC 11192, Strain Philadelphia 1
+STR_NO
+
+# Get the URLs to the entry in the corresponding catalogues
+str_no.map(&:url)
+
+# Get the name and country of each catalogue (if available)
+str_no.map(&:catalogue).map { |i| [i.name, i.country_code] if i }
+```
+

data/Rakefile

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+require 'bundler/gem_tasks'
+require 'rake/testtask'
+
+$:.unshift File.join(File.dirname(__FILE__), 'lib')
+
+require 'strain_code/version'
+
+SOURCES = FileList['lib/**/*.rb']
+
+desc 'Default Task'
+task :default => :test
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+  t.pattern = 'test/*_test.rb'
+  t.verbose = true
+end

data/lib/strain_code/catalogue.rb

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+
+class StrainCode::Catalogue
+  class << self
+    def catalogues_path
+      File.join(StrainCode.data_path, 'catalogues.yaml')
+    end
+
+    def catalogues_source
+      @catalogues_source ||= YAML.load_file(
+        catalogues_path,
+        permitted_classes: [OpenStruct, Symbol, Date]
+      )
+    end
+
+    def catalogue_hash(code)
+      hsh = catalogues_source['catalogues'].find do |i|
+        i['codes'].include? code.to_s.upcase
+      end
+    end
+
+    def catalogue(code)
+      hsh = catalogue_hash(code)
+      new(hsh) if hsh
+    end
+  end
+
+  attr_accessor :codes, :country_code, :name, :name_en, :organization
+  attr_accessor :url, :url_pattern
+
+  def initialize(code)
+    code = self.class.catalogue_hash(code) unless code.is_a?(Hash)
+    code.each { |k, v| self.send("#{k}=", v) unless k =~ /^_/ } if code
+  end
+end

data/lib/strain_code/common.rb

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+require 'yaml'
+require 'ostruct'
+require 'strain_code/version'
+require 'strain_code/catalogue'
+
+class StrainCode
+  class << self
+    def root_path
+      File.expand_path('../../..', __FILE__)
+    end
+
+    def data_path
+      File.join(root_path, 'data')
+    end
+  end
+end

data/lib/strain_code/parser.rb

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+require 'strain_code/strain_number'
+
+class StrainCode::Parser
+  class << self
+    def clean(numbers)
+      numbers.to_s.strip.gsub(/\s+/, ' ').gsub(/ *[=;,] */, ' = ')
+    end
+
+    def parse(numbers)
+      clean(numbers).split(' = ').map do |number|
+        StrainCode::StrainNumber.new(number)
+      end
+    end
+  end
+end
+
+class StrainCode
+  class << self
+    def parse(numbers)
+      StrainCode::Parser.parse(numbers)
+    end
+
+    def number(number)
+      StrainCode::StrainNumber.new(StrainCode::Parser.clean(number))
+    end
+
+    def catalogue(code)
+      c = StrainCode::Catalogue.new(code)
+      c.codes ? c : nil
+    end
+  end
+end

data/lib/strain_code/strain_number.rb

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+class StrainCode::StrainNumber
+  attr_accessor :ori_number, :code, :accession
+
+  def initialize(number)
+    @ori_number = number.to_s.strip
+    @code, @accession = ori_number.split(/[ :_]+/, 2)
+    @code, @accession = @accession, @code if @accession.nil?
+  end
+
+  def number
+    catalogue ? [code, accession].compact.join(' ') : ori_number
+  end
+
+  def url
+    catalogue.url_pattern % accession if catalogue&.url_pattern
+  end
+
+  def catalogue
+    @catalogue ||= StrainCode.catalogue(code)
+  end
+
+  def to_s
+    number
+  end
+end

data/lib/strain_code/version.rb

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+class StrainCode
+  VERSION       = '0.1.0'
+  VERSION_ARRAY = VERSION.split(/\./).map { |x| x.to_i } # :nodoc:
+  VERSION_MAJOR = VERSION_ARRAY[0] # :nodoc:
+  VERSION_MINOR = VERSION_ARRAY[1] # :nodoc:
+  VERSION_BUILD = VERSION_ARRAY[2] # :nodoc:
+end

data/lib/strain_code.rb

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+require 'strain_code/common'
+require 'strain_code/parser'
+#require 'strain_code/styler'

metadata

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+--- !ruby/object:Gem::Specification
+name: strain-code
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Luis M. Rodriguez-R
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2025-03-19 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  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: test-unit
+  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'
+description: Strain numbers are microbiological culture collection identifiers
+email: lmrodriguezr@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- README.md
+files:
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- lib/strain_code.rb
+- lib/strain_code/catalogue.rb
+- lib/strain_code/common.rb
+- lib/strain_code/parser.rb
+- lib/strain_code/strain_number.rb
+- lib/strain_code/version.rb
+homepage: https://github.com/seq-code/strain-code
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options:
+- lib
+- README.md
+- "--main"
+- README.md
+- "--title"
+- Parsing and formatting of strain numbers
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.6
+signing_key: 
+specification_version: 4
+summary: Parsing and formatting of strain numbers
+test_files: []