copath_parser 0.0.1

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in copath_parser.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2012 Utkarsh Kukreti
+
+MIT License
+
+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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+# CopathParser
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'copath_parser'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install copath_parser
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+
+require 'rspec/core/rake_task'
+
+RSpec::Core::RakeTask.new('spec')
+
+# If you want to make this the default task
+task :default => :spec
+
+task :pry do
+  system "pry -Ilib -r./lib/copath_parser -e 'include CopathParser'"
+end

data/bin/copath-parser

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+#!/usr/bin/env ruby
+
+$:.unshift(File.expand_path('../lib', __FILE__))
+
+require 'copath_parser'
+
+CopathParser::CLI.new(ARGV)

data/copath_parser.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'copath_parser/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "copath_parser"
+  gem.version       = CopathParser::VERSION
+  gem.authors       = ["Utkarsh Kukreti"]
+  gem.email         = ["utkarshkukreti@gmail.com"]
+  gem.description   = %q{Copath Parser}
+  gem.summary       = %q{Copath Parser}
+  gem.homepage      = "https://github.com/utkarshkukreti/copath_parser"
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+
+  gem.add_dependency 'parslet'
+  gem.add_dependency 'docopt'
+  gem.add_development_dependency 'rspec'
+  gem.add_development_dependency 'pry'
+end

data/lib/copath_parser.rb

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+require "pry" rescue nil
+
+require "csv"
+require "docopt"
+require "parslet"
+
+require "copath_parser/cli"
+require "copath_parser/parsers/prostrate"
+require "copath_parser/version"

data/lib/copath_parser/cli.rb

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+module CopathParser
+  class CLI
+    Doc = <<DOC
+Copath Parser
+
+Usage:
+  copath_parser <type> <input-file> <output-file>
+  copath_parser -v | --version
+
+Options:
+  <type>  Type of data, e.g. "prostrate"
+DOC
+
+    def initialize(argv)
+      require "pp"
+      begin
+        options = Docopt::docopt(Doc)
+        puts "You passed in:"; pp options
+        if options["-v"] || options["--version"]
+          puts "Copath Parser #{CopathParser::VERSION}"
+          exit 0
+        end
+
+        type = options["<type>"]
+        case type
+        when /prostrate/i
+          parser = Parsers::Prostrate
+        else
+          raise "Invalid type."
+        end
+
+        puts "Parsing..."
+        csv = parser.parse_to_csv(File.read(options["<input-file>"]))
+        puts "Parsed!"
+        puts "Writing csv to #{options["<output-file>"]}..."
+        File.write(options["<output-file>"], csv)
+        puts "Done!"
+      end
+    end
+  end
+end

data/lib/copath_parser/parsers/prostrate.rb

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+module CopathParser
+  module Parsers
+    class Prostrate < Parslet::Parser
+      def self.parse_records(records)
+        ret = []
+        records.split(/\n\s*\n/).each do |record|
+          parsed = new.parse record
+          date = parsed[0][:date]
+          case_number = parsed[0][:case_number]
+          fmp = parsed[0][:fmp]
+          i = 1
+          parsed[1..-1].each do |addition|
+            addition = addition[:addition]
+            primary = addition[:first_number]
+            secondary = addition[:second_number]
+            sum = addition[:sum]
+            block = i
+            ret << [date, case_number, block, fmp, primary, secondary, sum].map(&:to_s).map(&:strip)
+            i += 1
+          end
+        end
+        ret
+      end
+
+      def self.parse_to_csv(records)
+        CSV.generate do |csv|
+          parse_records(records).each do |record|
+            csv << record
+          end
+        end
+      end
+
+      root(:record)
+
+      # Helpers
+      rule(:sp) { match('\s') }
+      rule(:sp?) { sp.repeat }
+      rule(:word) { (sp.absent? >> any).repeat(1) >> sp? }
+      rule(:number) { match['0-9'].repeat(1) >> sp? }
+      rule(:eq) { str('=') >> sp? }
+      rule(:plus) { str('+') >> sp? }
+      rule(:f) { number.as(:first_number) }
+      rule(:s) { number.as(:second_number) }
+      rule(:sum) { number.as(:sum) }
+      rule(:minus) { str('-') >> sp? }
+      rule(:ob) { str('[') >> sp? }
+      rule(:cb) { str(']') >> sp? }
+      rule(:op) { str('(') >> sp? }
+      rule(:cp) { str(')') >> sp? }
+
+      rule(:addition) do
+        f >> plus >> s >> eq >> sum |
+        sum >> eq >> f >> plus >> s |
+        f >> plus >> s >> minus >> sum |
+        sum >> ob >> f >> plus >> s >> cb |
+        f >> plus >> s >> (sum.absent? >> any).repeat >> sum |
+        sum >> op >> f >> plus >> s >> cp
+      end
+
+      rule(:record) do
+        word.as(:date) >>
+        word.as(:case_number) >>
+        word.as(:fmp) >>
+        ((addition.absent? >> any).repeat >> addition.as(:addition)).repeat >>
+        any.repeat
+      end
+    end
+  end
+end

data/lib/copath_parser/version.rb

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+module CopathParser
+  VERSION = "0.0.1"
+end

data/spec/data/prostrate-input-1.txt

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+01/01/01  S01-12345 20/111-22-1001 A.  PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:                           
+                                   TOTAL GLEASON SCORE:  GLEASON 5+4=9                                     
+                   
+01/02/02  S02-1234 20/111-22-1002 PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:      
+                                    GLEASON SCORE:  3 + 3 = 6 WITH TERTIARY PATTERN OF 5.                   
+                                   
+05/02/03  S03-1234  31/111-22-1003 PROSTATECTOMY:  ADENOCARCINOMA, GLEASON GRADE 4+3=7.             
+                                   GLEASON SCORE:  7=4+3.                                                      
+
+07/17/04  S04-123  30/111-22-1004  C)  RADICAL PROSTATECTOMY: ADENOCARCINOMA.                                    
+                                       GLEASON SCORE:  3+4-7.                                                  
+
+01/28/05  S05-1234  20/111-22-1005 PROSTATECTOMY:                                                              
+                                        PROSTATIC ADENOCARCINOMA, GLEASON SCORE 7 [3+4].                       
+                                                  
+07/18/06  S06-10686 20/111-22-1006 A.  PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:
+                                       TOTAL GLEASON SCORE:  GLEASON 4+3 WITH TERTIARY GLEASON PATTERN 5       
+
+02/22/07  S07-2749  20/111-22-1007 A.  PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:
+                                       HISTOLOGIC PATTERN:  GLEASON SCORE 6 (3+3)        
+

data/spec/data/prostrate-output-1.csv

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+01/01/01,S01-12345,1,20/111-22-1001,5,4,9
+01/02/02,S02-1234,1,20/111-22-1002,3,3,6
+05/02/03,S03-1234,1,31/111-22-1003,4,3,7
+05/02/03,S03-1234,2,31/111-22-1003,4,3,7
+07/17/04,S04-123,1,30/111-22-1004,3,4,7
+01/28/05,S05-1234,1,20/111-22-1005,3,4,7
+07/18/06,S06-10686,1,20/111-22-1006,4,3,5
+02/22/07,S07-2749,1,20/111-22-1007,3,3,6

data/spec/parsers/prostrate_spec.rb

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+require 'spec_helper'
+
+describe CopathParser::Parsers::Prostrate do
+  it "should parse input-1.txt" do
+    input = File.read("spec/data/prostrate-input-1.txt")
+    output = File.read("spec/data/prostrate-output-1.csv")
+
+    csv = CopathParser::Parsers::Prostrate.parse_to_csv(input)
+    csv.should eq(output)
+  end
+end

data/spec/spec_helper.rb

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+require 'bundler/setup'
+require 'copath_parser'
+
+RSpec.configure do |config|
+
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: copath_parser
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Utkarsh Kukreti
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-11-12 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: parslet
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: docopt
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Copath Parser
+email:
+- utkarshkukreti@gmail.com
+executables:
+- copath-parser
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/copath-parser
+- copath_parser.gemspec
+- lib/copath_parser.rb
+- lib/copath_parser/cli.rb
+- lib/copath_parser/parsers/prostrate.rb
+- lib/copath_parser/version.rb
+- spec/data/prostrate-input-1.txt
+- spec/data/prostrate-output-1.csv
+- spec/parsers/prostrate_spec.rb
+- spec/spec_helper.rb
+homepage: https://github.com/utkarshkukreti/copath_parser
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Copath Parser
+test_files:
+- spec/data/prostrate-input-1.txt
+- spec/data/prostrate-output-1.csv
+- spec/parsers/prostrate_spec.rb
+- spec/spec_helper.rb
+has_rdoc: