copath_parser 0.0.1
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- data/.gitignore +17 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +29 -0
- data/Rakefile +12 -0
- data/bin/copath-parser +7 -0
- data/copath_parser.gemspec +24 -0
- data/lib/copath_parser.rb +9 -0
- data/lib/copath_parser/cli.rb +41 -0
- data/lib/copath_parser/parsers/prostrate.rb +69 -0
- data/lib/copath_parser/version.rb +3 -0
- data/spec/data/prostrate-input-1.txt +21 -0
- data/spec/data/prostrate-output-1.csv +8 -0
- data/spec/parsers/prostrate_spec.rb +11 -0
- data/spec/spec_helper.rb +6 -0
- metadata +130 -0
data/.gitignore
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2012 Utkarsh Kukreti
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# CopathParser
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TODO: Write a gem description
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## Installation
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Add this line to your application's Gemfile:
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gem 'copath_parser'
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install copath_parser
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## Usage
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TODO: Write usage instructions here
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## Contributing
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1. Fork it
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create new Pull Request
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data/Rakefile
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require "bundler/gem_tasks"
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require 'rspec/core/rake_task'
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RSpec::Core::RakeTask.new('spec')
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# If you want to make this the default task
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task :default => :spec
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task :pry do
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system "pry -Ilib -r./lib/copath_parser -e 'include CopathParser'"
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end
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data/bin/copath-parser
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# -*- encoding: utf-8 -*-
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'copath_parser/version'
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Gem::Specification.new do |gem|
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gem.name = "copath_parser"
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gem.version = CopathParser::VERSION
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gem.authors = ["Utkarsh Kukreti"]
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gem.email = ["utkarshkukreti@gmail.com"]
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gem.description = %q{Copath Parser}
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gem.summary = %q{Copath Parser}
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gem.homepage = "https://github.com/utkarshkukreti/copath_parser"
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gem.files = `git ls-files`.split($/)
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gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
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gem.test_files = gem.files.grep(%r{^(test|spec|features)/})
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gem.require_paths = ["lib"]
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gem.add_dependency 'parslet'
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gem.add_dependency 'docopt'
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gem.add_development_dependency 'rspec'
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gem.add_development_dependency 'pry'
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end
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module CopathParser
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class CLI
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Doc = <<DOC
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Copath Parser
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Usage:
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copath_parser <type> <input-file> <output-file>
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copath_parser -v | --version
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Options:
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<type> Type of data, e.g. "prostrate"
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DOC
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def initialize(argv)
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require "pp"
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begin
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options = Docopt::docopt(Doc)
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puts "You passed in:"; pp options
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if options["-v"] || options["--version"]
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puts "Copath Parser #{CopathParser::VERSION}"
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exit 0
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end
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type = options["<type>"]
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case type
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when /prostrate/i
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parser = Parsers::Prostrate
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else
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raise "Invalid type."
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end
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puts "Parsing..."
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csv = parser.parse_to_csv(File.read(options["<input-file>"]))
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puts "Parsed!"
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puts "Writing csv to #{options["<output-file>"]}..."
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File.write(options["<output-file>"], csv)
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puts "Done!"
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end
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end
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end
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end
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module CopathParser
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module Parsers
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class Prostrate < Parslet::Parser
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def self.parse_records(records)
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ret = []
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records.split(/\n\s*\n/).each do |record|
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parsed = new.parse record
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date = parsed[0][:date]
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case_number = parsed[0][:case_number]
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fmp = parsed[0][:fmp]
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i = 1
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parsed[1..-1].each do |addition|
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addition = addition[:addition]
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primary = addition[:first_number]
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secondary = addition[:second_number]
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sum = addition[:sum]
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block = i
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ret << [date, case_number, block, fmp, primary, secondary, sum].map(&:to_s).map(&:strip)
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i += 1
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end
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end
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ret
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end
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def self.parse_to_csv(records)
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CSV.generate do |csv|
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parse_records(records).each do |record|
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csv << record
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end
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end
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end
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root(:record)
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# Helpers
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rule(:sp) { match('\s') }
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rule(:sp?) { sp.repeat }
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rule(:word) { (sp.absent? >> any).repeat(1) >> sp? }
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rule(:number) { match['0-9'].repeat(1) >> sp? }
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rule(:eq) { str('=') >> sp? }
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rule(:plus) { str('+') >> sp? }
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rule(:f) { number.as(:first_number) }
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rule(:s) { number.as(:second_number) }
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rule(:sum) { number.as(:sum) }
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rule(:minus) { str('-') >> sp? }
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rule(:ob) { str('[') >> sp? }
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rule(:cb) { str(']') >> sp? }
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rule(:op) { str('(') >> sp? }
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rule(:cp) { str(')') >> sp? }
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rule(:addition) do
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f >> plus >> s >> eq >> sum |
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sum >> eq >> f >> plus >> s |
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f >> plus >> s >> minus >> sum |
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sum >> ob >> f >> plus >> s >> cb |
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f >> plus >> s >> (sum.absent? >> any).repeat >> sum |
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sum >> op >> f >> plus >> s >> cp
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end
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rule(:record) do
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word.as(:date) >>
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word.as(:case_number) >>
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word.as(:fmp) >>
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((addition.absent? >> any).repeat >> addition.as(:addition)).repeat >>
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any.repeat
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end
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end
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end
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end
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01/01/01 S01-12345 20/111-22-1001 A. PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:
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TOTAL GLEASON SCORE: GLEASON 5+4=9
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01/02/02 S02-1234 20/111-22-1002 PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:
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GLEASON SCORE: 3 + 3 = 6 WITH TERTIARY PATTERN OF 5.
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05/02/03 S03-1234 31/111-22-1003 PROSTATECTOMY: ADENOCARCINOMA, GLEASON GRADE 4+3=7.
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GLEASON SCORE: 7=4+3.
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07/17/04 S04-123 30/111-22-1004 C) RADICAL PROSTATECTOMY: ADENOCARCINOMA.
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GLEASON SCORE: 3+4-7.
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01/28/05 S05-1234 20/111-22-1005 PROSTATECTOMY:
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PROSTATIC ADENOCARCINOMA, GLEASON SCORE 7 [3+4].
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07/18/06 S06-10686 20/111-22-1006 A. PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:
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TOTAL GLEASON SCORE: GLEASON 4+3 WITH TERTIARY GLEASON PATTERN 5
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02/22/07 S07-2749 20/111-22-1007 A. PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:
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HISTOLOGIC PATTERN: GLEASON SCORE 6 (3+3)
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01/01/01,S01-12345,1,20/111-22-1001,5,4,9
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01/02/02,S02-1234,1,20/111-22-1002,3,3,6
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05/02/03,S03-1234,1,31/111-22-1003,4,3,7
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05/02/03,S03-1234,2,31/111-22-1003,4,3,7
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07/17/04,S04-123,1,30/111-22-1004,3,4,7
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01/28/05,S05-1234,1,20/111-22-1005,3,4,7
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07/18/06,S06-10686,1,20/111-22-1006,4,3,5
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02/22/07,S07-2749,1,20/111-22-1007,3,3,6
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require 'spec_helper'
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describe CopathParser::Parsers::Prostrate do
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it "should parse input-1.txt" do
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input = File.read("spec/data/prostrate-input-1.txt")
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output = File.read("spec/data/prostrate-output-1.csv")
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csv = CopathParser::Parsers::Prostrate.parse_to_csv(input)
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csv.should eq(output)
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end
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end
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data/spec/spec_helper.rb
ADDED
metadata
ADDED
@@ -0,0 +1,130 @@
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--- !ruby/object:Gem::Specification
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name: copath_parser
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version: !ruby/object:Gem::Version
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version: 0.0.1
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prerelease:
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platform: ruby
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authors:
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- Utkarsh Kukreti
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2012-11-12 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: parslet
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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27
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- - ! '>='
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28
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: docopt
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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35
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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41
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none: false
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requirements:
|
43
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+
- - ! '>='
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44
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+
- !ruby/object:Gem::Version
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version: '0'
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46
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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51
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+
- - ! '>='
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52
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- !ruby/object:Gem::Version
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version: '0'
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type: :development
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55
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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59
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+
- - ! '>='
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60
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+
- !ruby/object:Gem::Version
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61
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version: '0'
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62
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+
- !ruby/object:Gem::Dependency
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63
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name: pry
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64
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requirement: !ruby/object:Gem::Requirement
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65
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none: false
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66
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requirements:
|
67
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+
- - ! '>='
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68
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+
- !ruby/object:Gem::Version
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69
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version: '0'
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70
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type: :development
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71
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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73
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none: false
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requirements:
|
75
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- - ! '>='
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76
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- !ruby/object:Gem::Version
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77
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version: '0'
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78
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description: Copath Parser
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79
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email:
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- utkarshkukreti@gmail.com
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executables:
|
82
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- copath-parser
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83
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extensions: []
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84
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extra_rdoc_files: []
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85
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files:
|
86
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- .gitignore
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87
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- Gemfile
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88
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+
- LICENSE.txt
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89
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- README.md
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90
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+
- Rakefile
|
91
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+
- bin/copath-parser
|
92
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+
- copath_parser.gemspec
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93
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+
- lib/copath_parser.rb
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94
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+
- lib/copath_parser/cli.rb
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95
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- lib/copath_parser/parsers/prostrate.rb
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96
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+
- lib/copath_parser/version.rb
|
97
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- spec/data/prostrate-input-1.txt
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98
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- spec/data/prostrate-output-1.csv
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99
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- spec/parsers/prostrate_spec.rb
|
100
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+
- spec/spec_helper.rb
|
101
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+
homepage: https://github.com/utkarshkukreti/copath_parser
|
102
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licenses: []
|
103
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+
post_install_message:
|
104
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+
rdoc_options: []
|
105
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+
require_paths:
|
106
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- lib
|
107
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+
required_ruby_version: !ruby/object:Gem::Requirement
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108
|
+
none: false
|
109
|
+
requirements:
|
110
|
+
- - ! '>='
|
111
|
+
- !ruby/object:Gem::Version
|
112
|
+
version: '0'
|
113
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
114
|
+
none: false
|
115
|
+
requirements:
|
116
|
+
- - ! '>='
|
117
|
+
- !ruby/object:Gem::Version
|
118
|
+
version: '0'
|
119
|
+
requirements: []
|
120
|
+
rubyforge_project:
|
121
|
+
rubygems_version: 1.8.23
|
122
|
+
signing_key:
|
123
|
+
specification_version: 3
|
124
|
+
summary: Copath Parser
|
125
|
+
test_files:
|
126
|
+
- spec/data/prostrate-input-1.txt
|
127
|
+
- spec/data/prostrate-output-1.csv
|
128
|
+
- spec/parsers/prostrate_spec.rb
|
129
|
+
- spec/spec_helper.rb
|
130
|
+
has_rdoc:
|