sas2yaml 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: cdbfd522aa2b75913e825ff59ea05de81e35ce2d
+  data.tar.gz: bcb279dd496c036991a20d7aa1c22c359faab60e
+SHA512:
+  metadata.gz: 38e7dc54d3467f37b1b7284539d2aa74ee3e3567f05cec458fed07aee69e0b2ecd7ea69d44d450f7859dad6fdda7c0602bde2f5fdb1e128c1016f955d8d1ba47
+  data.tar.gz: e40c5d66386bdedd659a6392e7ba40f6686675aa0723eb6c2264df041dda0f468e531a239243700c78334759c792808873cc0323fe1700796cd4a49c71710442

data/.gitignore

@@ -0,0 +1,9 @@
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/.travis.yml

@@ -0,0 +1,4 @@
+language: ruby
+rvm:
+  - 2.2.3
+before_install: gem install bundler -v 1.10.5

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in sas2yaml.gemspec
+gemspec

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2015 Outcomes Insights, Inc.
+
+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

@@ -0,0 +1,47 @@
+# Sas2Yaml
+
+This gem installs a CLI program, `sas2yaml` which will (attempt) to read in a SAS input statement and turn it into a [YAML](http://yaml.org/) file with the name of each variable along with its position in a fixed-width file, length, and type (assuming that information is available).
+
+This gem was developed in order to decipher the fixed-width file structure of SEER Medicare SAS input statement files and works (fairly) well in processing those files.  Your mileage almost certainly will vary.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'sas2yaml'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install sas2yaml
+
+## Usage
+
+```
+sas2yaml file1.sas file2.sas ...
+```
+
+For each file listed, a lot of output will hit your screen, the program will hopefully not bomb out, and you'll end up with files named "file1.yml" and "file2.yml" (from the example above).
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake false` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Thanks
+- [Outcomes Insights, Inc.](http://outins.com/)
+  - Many thanks for allowing me to release a portion of my work as Open Source Software!
+- [Ruby](https://www.ruby-lang.org/en/)
+  - For being such an awesome language that it can pretend to be another (and much more awful) language **cough** *SAS* **cough**.
+
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/sas2yaml.
+

data/Rakefile

@@ -0,0 +1 @@
+require "bundler/gem_tasks"

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "sas2yaml"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

@@ -0,0 +1,7 @@
+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/exe/sas2yaml

@@ -0,0 +1,21 @@
+#!/usr/bin/env ruby
+
+require "escort"
+require "bundler/setup"
+require "sas2yaml"
+
+Escort::App.create do |app|
+  app.version Sas2Yaml::VERSION
+  app.summary Sas2Yaml::SUMMARY
+  app.description Sas2Yaml::DESCRIPTION
+
+  app.action do |options, arguments|
+    begin
+      Sas2Yaml::AssembleCommand.new(options, arguments).execute
+    rescue
+      puts $!.message
+      puts $!.backtrace.join("\n")
+      raise
+    end
+  end
+end

data/lib/sas2yaml.rb

@@ -0,0 +1,6 @@
+require "sas2yaml/metadata"
+require "sas2yaml/assemble_command"
+
+module Sas2Yaml
+  # Your code goes here...
+end

data/lib/sas2yaml/assemble_command.rb

@@ -0,0 +1,21 @@
+require_relative 'sas_processor'
+require_relative 'sassifier'
+require 'psych'
+
+module Sas2Yaml
+  class AssembleCommand < ::Escort::ActionCommand::Base
+    def execute
+      arguments.each do |sas_file|
+        puts "Processing #{sas_file}"
+        processed_sas = SasProcessor.new(sas_file).lines.join("\n")
+        sassy_file = File.join(Dir.tmpdir, File.basename(sas_file, '.*') + '.sassy')
+        File.write(sassy_file, processed_sas)
+        puts "Temp at  #{sassy_file}"
+        sassy = Sassifier.new(processed_sas)
+        puts "NUM COLUMNS: #{sassy.hash.keys.length}"
+        file = sas_file.gsub(/\..+$/, '.yml')
+        File.write(file, sassy.hash.to_yaml)
+      end
+    end
+  end
+end

data/lib/sas2yaml/metadata.rb

@@ -0,0 +1,6 @@
+module Sas2Yaml
+  VERSION = "0.0.1"
+  SUMMARY = "Convert SAS Input files into YAML describing layout of the data"
+  DESCRIPTION = "Converts a SAS Input file into a YAML file which details each column along with its type, length, and start column."
+end
+

data/lib/sas2yaml/process_sas.rb

@@ -0,0 +1,34 @@
+# Script that drives processing each SAS file to glean the field type
+# information e.g.
+# Column position
+# Length
+# Format
+# Data type
+
+require 'psych'
+require 'fileutils'
+require 'tmpdir'
+
+require_relative '../parsers/sas/sas_processor'
+require_relative '../parsers/sas/sassifier'
+
+module ProcessSas
+  extend self
+
+  def run
+    dir = 'ddls'
+    FileUtils.mkdir(dir) unless File.exist?(dir)
+    Dir.glob("sas/*").each do |sas_file|
+      puts "=" * 90
+      puts sas_file
+      puts "=" * 90
+      processed_sas = SasProcessor.new(sas_file).lines.join("\n")
+      sassy = Sassifier.new(processed_sas)
+      puts "NUM COLUMNS: #{sassy.hash.keys.length}"
+      file = File.join(dir, sas_file.gsub(/.+\//, '').gsub(/\..+$/, '.yml'))
+      File.open(file, 'w') { |f| f.puts sassy.hash.to_yaml }
+
+      File.write(File.join(Dir.tmpdir, File.basename(file, '.*') + '.sassy'), processed_sas)
+    end
+  end
+end

data/lib/sas2yaml/rangifier.rb

@@ -0,0 +1,24 @@
+# Given an input of something like mon1-mon288
+# will return %w(mon1 mon2 ... mon288) when #values is called
+class Rangifier
+  TRAILING_DIGITS_REGEXP = /(\d+)$/
+  def initialize(input)
+    @input = input
+  end
+
+  def values
+    @values ||= get_values
+  end
+
+private
+  def get_values
+    parts = @input.sub(/;/, '').strip.split('-').map(&:strip)
+    return [@input] unless parts.first =~ TRAILING_DIGITS_REGEXP
+    puts "Rangifying #@input => #{parts}"
+    first = parts.first.match(TRAILING_DIGITS_REGEXP)[1].to_i
+    last = parts.last.match(TRAILING_DIGITS_REGEXP)[1].to_i
+    prefix = parts.first.sub(TRAILING_DIGITS_REGEXP, '')
+    puts "Ranging #{prefix} from #{first} - #{last}"
+    (first..last).map { |i| "#{prefix}#{i}"}
+  end
+end

data/lib/sas2yaml/sas_processor.rb

@@ -0,0 +1,221 @@
+require_relative 'rangifier'
+
+# Translates SAS code into executable Ruby code
+#
+# This is a very gross translation and most code is skipped completely
+# When I was looking at the SAS code to read in the ALL dataset, I noticed
+# that I couldn't simply parse out each line and read the field information
+# directly from the SAS file because sometimes the SAS file used loops
+# to define the columns for some of the fields
+#
+# Also, some of the data type information was assigned to arrays in those
+# loops.
+#
+# BUT I did notice that SAS looks a bit like Ruby and, with a little
+# pruning and translating, the SAS code could be converted to Ruby
+#
+# So this class will parse a SAS file looking for the first line that
+# starts with INPUT and will parse the file until it hits a line that
+# says LABELs
+#
+# The resulting Ruby code uses instance variables to store all
+# the information during processing.  This is to avoid problems where the
+# SAS code is using reserved words or method names in Ruby.
+# The SAS code frequently uses variable names like "begin" and "end" which are
+# reserved words in Ruby and "inc" and "pos" which are common method names
+#
+# See below for information about how certain lines are handled
+class SasProcessor
+  @@def_regexp = /@[^;]/
+  @@array_regexp = /array/
+  @@label_start_regexp = /^label/i
+  @@comment_regexp =%r{/\*.*?\*/}m
+  @@blank_line_regexp = /^$/
+  @@mode = :skip
+  @@do_regexp = /^do /
+  @@equals_regexp = /=/
+  @@infile_regexp = /^infile\s+/i
+  @@op_regexp = %r{([+-/=*]+)}
+
+  def initialize(file_path)
+    @file_path = file_path
+  end
+
+  # Given blah01-blah02 or (blah01-blah02)
+  # Return ('blah01'..'blah02')
+  def rangify(range)
+    '%w(' + Rangifier.new(strip_parens(range)).values.join(' ') + ')'
+  end
+
+  # Given "(something)"
+  # Return "something"
+  def strip_parens(text)
+    text.gsub(/[()]/, '')
+  end
+
+  # Given what could either be a variable name or a number literal, returns
+  # either an instance variable with the same name, or the number literal
+  # "001" => "1"
+  # "var" => "@var"
+  # "12var34" => "@12var34"
+  def var_or_num(v_or_n)
+    return v_or_n.gsub(/^0+(\d)/,'\1') if /^\d+$/.match(v_or_n)
+    ivarify(v_or_n)
+  end
+
+  # Expect inputs like
+  # cred10 which we just return
+  # or (plan1-plan2) which we return as the range ('plan1'..'plan2')
+  # or some_arr(2) which we return as @some_arr[2]
+  def fix_name(text)
+    return "'#{text}'" unless /\(/.match(text)
+    return rangify(text) if /^\(/.match(text)
+    ivarify(text.gsub(/\(([^)]+)\)/) do |match|
+      '[' + var_or_num($1) + ']'
+    end)
+  end
+
+  # Prepends "@" to the string
+  def ivarify(var_name)
+    '@' + var_name
+  end
+
+  # Definition lines start with "@111" or "input @pos + 2"
+  # But either way, we're interested in everything after the @ sign
+  # for these lines
+  # Examples
+  # @012  bic        $char2.
+  # input @inc2 dgn(j)  $char5.
+  def translate_def(line)
+    # Strip up through the @
+    line.gsub!(/^.*@/, '')
+    parts = line.split(/\s+/)
+    # Type information is always the last word on the line
+    type = parts.pop
+    # The name is always the second to the last word on the line
+    name = fix_name(parts.pop)
+
+    # The rest of the line could be as simple as a number literal or something like
+    # (pos + 1)
+    # So we put spaces between all the operators and then translate each part
+    rest = blow_out_ops(strip_parens(parts.join(' '))).split(/\s+/).map { |w| var_or_num_or_op(w) }.join(' ')
+
+    # Spit out Ruby code that will tranlate the contents of this definition line
+    "at(#{rest}, #{name}, '#{type}')"
+  end
+
+  # SAS seems to be able to store input definitions into arrays
+  # I don't know the mechanism, but I know how to translate it
+  # We'll take a line like
+  # array dgn(10) $ dgn_cd1-dgn_cd10;
+  def translate_array(line)
+    parts = line.split('$')
+    # Last word has a ';' and then then a range that defines the field names
+    # assigned to this array
+    range = rangify(parts.pop.chop.sub(/^[\s\d]*/, ''))
+    parts = parts.first.split(/\s+/)
+    # We'll use the array's name as it appears in SAS to store the array
+    # of field names
+    # The array name starts as arr(10) so we'll chop off the part in parens
+    puts parts[1]
+    array_name = ivarify(parts[1].gsub(/\(.*/, ''))
+    puts array_name
+    # Spit out Ruby that assigns the array of field names to the array instance variable
+    "#{array_name} = #{range}"
+  end
+
+  # Given do i = 1 to 24;
+  # Return:
+  #   (1..24).each do |i|
+  #     @i = i
+  def translate_do(line)
+    parts = line.chop.split(/\s+/)
+    lines = []
+    finish = var_or_num(parts.pop)
+    parts.pop # skip to
+    start = var_or_num(parts.pop)
+    parts.pop # skip equals
+    var = parts.pop
+
+    lines << "(#{start} - 1..#{finish} - 1).each do |#{var}|"
+    lines << "\t#{ivarify(var)} = #{var}"
+    lines.join("\n")
+  end
+
+  # Given a variable, number literal, or operator
+  # return the appropriate translation
+  # See var_or_num for variables and numbers
+  # Operators are returned the same as they came in e.g.
+  # "+" => "+"
+  def var_or_num_or_op(vno)
+    return vno if @@op_regexp.match(vno)
+    var_or_num(vno)
+  end
+
+  # Places spaces around all operators so that
+  # we can split on white space and pick up the operators as tokens
+  def blow_out_ops(text)
+    text.gsub(@@op_regexp, ' \1 ')
+  end
+
+  # Given a line that assigns a value to something on the left hand side
+  # We need to do some basic translation of the line e.g.
+  # "inc2=inc2+5;" => "@inc2 = @inc2 + 5"
+  def translate_equals(line)
+    blow_out_ops(line.chop).split(/\s+/).map { |w| var_or_num_or_op(w) }.join(' ')
+  end
+
+  def translate_infile(line)
+    md = /lrecl\s*=\s*(\d+)/.match(line)
+    puts md
+    return "" if md.nil?
+    return "record_len(#{md[1]})"
+  end
+
+  # This method processes the SAS file and translates all relevant lines
+  def lines
+    if @lines.nil?
+      @lines = []
+      @@mode = :skip
+      File.open(@file_path).each_line do |l|
+        # Strip out all comments from each line
+        line = l.chomp.strip.gsub(@@comment_regexp, '')
+
+        # Once we hit a line with "input", start processing
+        @@mode = :process if line.match(/^input/i) || line.match(@@infile_regexp)
+        next if @@mode == :skip
+
+        # @; is ignorable, so make it a blank line
+        line.gsub!(/@;/, '')
+
+        # Skip blank lines
+        next if line.match(@@blank_line_regexp)
+
+        case line
+        when @@def_regexp
+          @lines << translate_def(line.downcase)
+        when @@array_regexp
+          @lines << translate_array(line.downcase)
+        when @@do_regexp
+          @lines << translate_do(line.downcase)
+        when @@infile_regexp
+          @lines << translate_infile(line.downcase)
+        when @@equals_regexp
+          @lines << translate_equals(line.downcase)
+        when @@label_start_regexp
+          # We hit the start of the labels, we can quit processing the file
+          break
+        when /^end;/
+          @lines << line.chop.downcase
+        end
+      end
+    end
+    @lines
+  end
+
+  def save(file_path)
+    File.open(file_path, 'w') do |f|
+      f.puts lines.join("\n")
+    end
+  end
+end

data/lib/sas2yaml/sassifier.rb

@@ -0,0 +1,82 @@
+# Runs the code that we generate by translating a SAS file into Ruby
+#
+# This class uses "eval" to get it's job done, so be wary about what code
+# you feed it
+class Sassifier
+  def initialize(code)
+    @_code = code
+  end
+
+  def run
+    puts @_code
+    # eval the code, using the current class's context
+    # so that the code has access to the class's supporting methods
+    eval @_code, binding()
+    check_record_length
+    nil
+  end
+
+  def check_record_length
+    return if @record_length.nil?
+    last_column = @_hash.values.last
+    last_position = last_column[:column] + last_column[:length]
+    return if last_position >= @record_length
+    at(last_position, '_fill', (@record_length - last_position).to_s)
+    @_hash.values.last[:droppable] = true
+  end
+
+  # Hash where we store the field information
+  # Memoized so that we run the code to populate the hash on the
+  # first attempt to access the hash
+  def hash
+    if @_hash.nil?
+      @_hash = {}
+      run
+    end
+    @_hash
+  end
+
+  # Given a SAS-orient type string, return the data type
+  # '10.' => :integer
+  # '15.2' => :decimal
+  # All else seems to be string (so far)
+  def get_type(type_str)
+    return :integer if /^\d+\.$/.match(type_str)
+    return :decimal if /^\d+\.\d+$/.match(type_str)
+    return :string
+  end
+
+  # Given the same type string as described in get_type
+  # Return the length
+  # '10.' => 10
+  # '15.2' => 15
+  # '$char2' => 2
+  def get_length(type_str)
+    type_str.gsub(/^\D+/, '').to_i
+  end
+
+  # Given a column position, a set of names, and a type_str
+  # store information about the field for each name
+  def at(column, names, type_str)
+    length = get_length(type_str)
+    type = get_type(type_str)
+
+    # If we receive a set of names, then we assume that the names represent
+    # individual slices of a contiguous set of columns, all the same length
+    #
+    # So if we have column position of 1 and names %w(name1 name2) and a length of 2
+    # then name1 is column 1, length 2 and name2 is column3 length 2
+    if names.is_a?(Array)
+      names.each do |name|
+        at(column, name, type_str)
+        column += length
+      end
+    else
+      @_hash[names.to_sym] = {column: column, name: names, type: type, length: length, format: type_str}
+    end
+  end
+
+  def record_len(length)
+    @record_length = length
+  end
+end

data/sas2yaml.gemspec

@@ -0,0 +1,34 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'sas2yaml/metadata'
+
+Gem::Specification.new do |spec|
+  spec.name          = "sas2yaml"
+  spec.version       = Sas2Yaml::VERSION
+  spec.authors       = ["Ryan Duryea"]
+  spec.email         = ["aguynamedryan@gmail.com"]
+
+  spec.summary       = Sas2Yaml::SUMMARY
+  spec.description   = Sas2Yaml::DESCRIPTION
+  spec.homepage      = "https://github.com/outcomesinsights/sas2yaml"
+
+  spec.licenses      = ["MIT"]
+
+  # Prevent pushing this gem to RubyGems.org by setting 'allowed_push_host', or
+  # delete this section to allow pushing this gem to any host.
+  if spec.respond_to?(:metadata)
+    spec.metadata['allowed_push_host'] = "https://rubygems.org"
+  else
+    raise "RubyGems 2.0 or newer is required to protect against public gem pushes."
+  end
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.10"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_dependency "escort", "~> 0.4.0"
+end

metadata

@@ -0,0 +1,107 @@
+--- !ruby/object:Gem::Specification
+name: sas2yaml
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Ryan Duryea
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2015-09-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: escort
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+description: Converts a SAS Input file into a YAML file which details each column
+  along with its type, length, and start column.
+email:
+- aguynamedryan@gmail.com
+executables:
+- sas2yaml
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- exe/sas2yaml
+- lib/sas2yaml.rb
+- lib/sas2yaml/assemble_command.rb
+- lib/sas2yaml/metadata.rb
+- lib/sas2yaml/process_sas.rb
+- lib/sas2yaml/rangifier.rb
+- lib/sas2yaml/sas_processor.rb
+- lib/sas2yaml/sassifier.rb
+- sas2yaml.gemspec
+homepage: https://github.com/outcomesinsights/sas2yaml
+licenses:
+- MIT
+metadata:
+  allowed_push_host: https://rubygems.org
+post_install_message: 
+rdoc_options: []
+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: []
+rubyforge_project: 
+rubygems_version: 2.4.6
+signing_key: 
+specification_version: 4
+summary: Convert SAS Input files into YAML describing layout of the data
+test_files: []
+has_rdoc: