medattrib 0.0.4

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data/LICENSE

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data/README.md

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+# License
+
+Copyright 2015 The MITRE Corporation.
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+zlimitations under the License.”
+
+# medattrib
+
+## Description
+
+A replacement for MedAttrib.pl. 
+
+The MedAttrib class method parse(text) returns an
+AnnotatedString which contains the original text and a list of the tags
+found. Because "doseamount" depends on the presence of other tags,
+the taggers have been split into pre- and post-doseamount taggers.
+
+
+## Example usage
+
+MedAttrib can be accessed either directly by Ruby code or as a command line executable.
+
+To use the library in Ruby:
+
+```require "medattrib"
+tagger = MedAttrib.new
+annotated_string = tagger.parse("take daily.")
+# annotated_string is now "take daily." with a "freq" tag labeling "daily" in standoff annotation (class AnnotatedString). This can be printed as inline xml using AnnotatedString#to_s:
+```
+
+Then inspect the output of "annotated_string":
+
+```ruby
+puts annotated_string
+```
+
+And you should get output similar to this:
+
+```
+#=> "take <freq normalized='qd'>daily</freq>."
+```
+
+Alternatively, the command line executable tags text line by line, and reads from standard in and writes to standard out.
+
+``` $ medattrib
+take daily.
+take <freq normalized='qd'>daily</freq>.
+```
+
+## Running tests
+
+To run all the tests:
+
+```bash
+rake test
+```
+
+To run a specific test:
+
+```bash
+ruby -I'lib:test' test/test_medattrib.rb -n test_no_sub_tag
+```
+
+## Building and install gem
+
+Build your gem:
+
+```bash
+gem build medattrib.gemspec
+```
+
+Install your gem:
+
+```bash
+gem install medattrib-0.0.3.gem
+```

data/bin/medattrib

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+#!/usr/bin/env ruby
+
+=begin
+Copyright 2015 The MITRE Corporation
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+   http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+=end
+
+require "medattrib"
+
+tagger = MedAttrib.new
+
+while line = gets do
+  puts tagger.parse(line).to_s
+end

data/lib/list_tagger.rb

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+=begin
+Copyright 2015 The MITRE Corporation
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+   http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+=end
+
+require_relative "tagger.rb"
+
+class ListTagger < Tagger
+    def parse_text(text, precondition, search, content_group = @content_group)
+        tags = []
+        content_group = 1
+        @list.each do |form|
+            if text =~ form
+                precondition = form
+                search = /(\b#{form})/i
+                tags += super text, precondition, search, content_group
+            end
+        end
+        return tags
+    end
+
+    def parse_main(text)
+        return parse_text(text, @default_precondition, @default_search, @content_group)
+    end
+end

data/lib/list_taggers/dose_form_tagger.rb

@@ -0,0 +1,93 @@
+# coding: utf-8
+=begin
+Copyright 2015 The MITRE Corporation.
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+zlimitations under the License.”
+=end
+
+class DoseFormTagger < ListTagger
+    def initialize
+        @name = 'doseform'
+        @list = [/(?:micro )?neb(?:ulizer)?s?/i,
+                /(?:(?:powdered|metered)(?:\s+|\-)dose\s+)?inhalers?/i,
+                /bar\b/i,
+                /beads/i,
+                /cake/i,
+                /caplets?/i,
+                /capsules?/i,
+                /cement/i,
+                /chewable bars?/i,
+                /(?:(?:chewable|disintegrating)\s+)?tab(?:let)?s?/i,
+                /chewing gum/i,
+                /cream/i,
+                /crystals/i,
+                /disk(?:us)?\b/i,
+                /douche/i,
+                /drops?/i,
+                /drug implant/i,
+                /dry powder inhaler/i,
+                /enema/i,
+                /enteric coated capsule/i,
+                /enteric coated tablet/i,
+                /extended release capsules?/i,
+                /extended release enteric coated capsules?/i,
+                /extended release enteric coated tablets?/i,
+                /extended release suspension/i,
+                /extended release tablets?/i,
+                /flakes/i,
+                /foam/i,
+                /gas for inhalation/i,
+                /gel/i,
+                /granules/i,
+                /gtts?/i,
+                /inhalant(?:\s+powder|solution)?/i,
+                /injectable solution/i,
+                /injectable suspension/i,
+                /intraperitoneal solution/i,
+                /irrigation solution/i,
+                /jelly/i,
+                /liniment/i,
+                /liquid/i,
+                /liquid cleanser/i,
+                /lotion/i,
+                /lozenges?/i,
+                /(?:medicated\s+)?(?:bar|liquid)\s+soap/i,
+                /medicated pad/i,
+                /medicated shampoo/i,
+                /medicated swab/i,
+                /medicated tape/i,
+                /mouthwash/i,
+                /oil/i,
+                /ointment/i,
+                /paste/i,
+                /patch/i,
+                /pellets?/i,
+                /pills?/i,
+                /powder/i,
+                /prefilled applicator/i,
+                /prefilled syringe/i,
+                /pudding/i,
+                /rinse/i,
+                /solid/i,
+                /solution/i,
+                /sprays?/i,
+                /strip/i,
+                /suppository/i,
+                /suspension/i,
+                /sustained release buccal tablets?/i,
+                /syrup/i,
+                /tincture/i,
+                /toothpaste/i,
+                /troche/i,
+                /wafers?/i]
+    end
+end

data/lib/list_taggers/frequency_tagger.rb

@@ -0,0 +1,91 @@
+=begin
+Copyright 2015 The MITRE Corporation.
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+zlimitations under the License."
+=end
+
+require_relative '../list_tagger.rb'
+
+class FrequencyTagger < ListTagger
+    def initialize
+        @name = 'freq'
+        @list = [/q\.?\s?(?:a\.?m\.?|morning)/i,
+                /q\.?\s?(?:p\.?m\.?|afternoon)/i,
+                /q\.?\s?h\.?(?:s\.?)?/i,
+                /nightly/i,
+                /bedtime/i,
+                /stat\b/i,
+                /immediately/i,
+                /hs/i,
+                /(?x)(?:(?:every|q\.?)\s*(?:\d\-)?
+                (?:2|3|4|5|6|7|8|9|10|11|12|24|36|48|72|
+                two|four|six|eight|twelve)(?:(?:-|\s+to\s+)
+                (?:2|3|4|5|6|7|8|9|10|11|12|24|36|48|72|
+                two|four|six|eight|twelve))?\s*
+                (?:h(?:rs?|(?:ours?))?\.?))/i,
+                /q\.?\s?d(?:\.|ay)?/i,
+                /q-day/i,
+                /(?x)(?:(?:every|each)\s*
+                (?:day|hour|night|week|morning|afternoon|evening))/i,
+                /(?:(?:once|twice)\s+(?:(?:a|per)\s+(?:day|week|night)))/i,
+                /(?x)(?:(?:(?:(?:\d\-)?(?:two|three|four|five|\d)
+                \s+times?\s+)|(once|twice)\s+)?(?:daily|weekly|hourly))/i,
+                /qod/i,
+                /every other day/i,
+                /[bqt]\.i\.d\./i,
+                /[bqt]idh?\b/i,
+                /(?x)(?:(?:\d\-)?(?:two|three|four|five|\d)\s+
+                (?:times?|days?|nights?)\s?
+                (?:a|per|\/)\s?(?:day|week|night))/i,
+                /(?:as|when)\s+needed/i,
+                /p\.?r\.?n\.?/i]
+    end
+    
+  def normalize(freq)
+    numwords = {"one"=>"1","two"=>"2","three"=>"3","four"=>"4","five"=>"5","six"=>"6","seven"=>"7","eight"=>"8"}
+    case freq
+      when /prn.?/i, /as needed/i
+        return :prn
+      when /qod/i
+        return :qod
+      when /(\d+(-\d+)?|[a-z]+) times? ((a|per) )?(day|week|daily|weekly)/i
+        return :range if $2
+        num, unit = $1, $5.downcase
+        subs = {"1" => "q", "2" => "bi", "3" => "ti", "4" => "qi"}
+        num = numwords[num] || num
+        num = subs[num] || num+"i"
+        return (num + unit[0]).to_sym
+      when /(once |twice )(a )?(day|week|daily|weekly)/i
+        num, unit = $1, ($3).downcase
+        return ("bi"+unit[0]).to_sym if ($1).downcase == "twice "
+        return ("q"+unit[0]).to_sym
+      when /daily/i #we've checked other contexts for daily already
+        return :qd
+      when /(q|every|each) ?(\d+(-\d+)?|[a-z]+)? ?(days?|ho?u?rs?|morning|night)/i
+        return :qod if $2 && ["other","two","2"].include?(($2).downcase) && $4 == "day"
+        return :range if $3
+        subs = {"morning" => "am", "afternoon" => "pm", "night" => "hs"}
+        num, unit = $2, $4
+        num = numwords[num] || num
+        unit = subs[unit.downcase] || unit[0].downcase
+        return ("q" + num.to_s + unit).to_sym
+      when /q(\d+(-\d+)?)?(am|d|hs|pm|w|h)/i
+        return :range if $2
+        return $&.downcase.to_sym
+      when /(b|t|q|(\d+(-\d+)?))i(w|h|d)/i
+        return :range if $3
+        return $&.downcase.to_sym
+      end
+          
+  end
+
+end