medattrib 0.0.4 → 0.0.5

checksums.yaml

@@ -1,15 +1,7 @@
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+SHA1:
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data/lib/list_taggers/#dose_amount_list_tagger.rb#

@@ -0,0 +1,24 @@
+# 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 DoseAmountListTagger < ListTagger
+    def initialize
+        @name = 'doseamount'
+        @list = [/(low|high)
+
+-? ?doses?/i]
+    end
+end

data/lib/list_taggers/DoseAmountListTagger.rb~

@@ -0,0 +1,22 @@
+# 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 = [/low-? ?doses?/i]
+    end
+end

data/lib/list_taggers/dose_amount_list_tagger.rb

@@ -0,0 +1,22 @@
+# 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 DoseAmountListTagger < ListTagger
+    def initialize
+        @name = 'doseamount'
+        @list = [/(low|high)-? ?doses?/i]
+    end
+end

data/lib/list_taggers/dose_amount_list_tagger.rb~

@@ -0,0 +1,22 @@
+# 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 DoseAmountListTagger < ListTagger
+    def initialize
+        @name = 'doseform'
+        @list = [/low-? ?doses?/i]
+    end
+end

data/lib/list_taggers/frequency_tagger.rb

@@ -21,9 +21,10 @@ class FrequencyTagger < ListTagger
         @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,
+                /(?:at\s*)?night(?:ly)?/i,
+                /(?:at\s*)bedtime/i,
+                /(?:at\s*)midday/i,
+                /in the morning/i,
                 /immediately/i,
                 /hs/i,
                 /(?x)(?:(?:every|q\.?)\s*(?:\d\-)?
@@ -34,18 +35,19 @@ class FrequencyTagger < ListTagger
                 (?: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)(?:(?:every|each)\s*\d?\s*
+                (?:day|night|week|morning|afternoon|evening))/i,
+                /(?:(?:once|twice)\s+(?:(?:a|per)\s+(?:day|week|night|month)))/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,
+                /(?x)(?:(?:\d\-?)?(?:one|two|three|four|five|\d)\s+
+                (?:times?|days?|nights?)?\s?
+                (?:a|per|\/)\s?(?:day|week|night|month))/i,
+                /(?:once|twice|(?:(?:\d+|one|two|three|four|five)\s*times))?monthly/i,
                 /(?:as|when)\s+needed/i,
                 /p\.?r\.?n\.?/i]
     end

data/lib/medattrib.rb

@@ -30,7 +30,6 @@ puts annotated_string
 #=> "take <freq>daily</freq>."
 =end
 
-gem 'standoff', '>=0.0.3' #data model
 require 'standoff'
 
 require_relative 'tagger.rb' #taggers based on regex contexts
@@ -49,16 +48,19 @@ require_relative 'taggers/timing_tagger.rb'
 
 #ListTagger child classes:
 require_relative 'list_taggers/dose_form_tagger.rb'
+require_relative 'list_taggers/dose_amount_list_tagger.rb'
 require_relative 'list_taggers/route_tagger.rb'
 require_relative 'list_taggers/frequency_tagger.rb'
 
 
 class MedAttrib
   def parse (text)
-    text = REXML::Text.new(text, false, nil, false).to_s # escape special characters
+
+#    text = REXML::Text.new(text, true, nil, false).to_s # escape special characters
     taggersExceptDoseAmount = [StrengthTagger.new,
                 StrengthUnitTagger.new,
                 DoseFormTagger.new,
+                DoseAmountListTagger.new,
                 RouteTagger.new,
                 IndicationTagger.new,
                 FrequencyTagger.new,
@@ -72,6 +74,7 @@ class MedAttrib
     taggersExceptDoseAmount.each {|tagger| tags += tagger.parse_main text}
     as = Standoff::AnnotatedString.new(:signal => text, :tags => tags)
     DoseAmountTagger.new.parse_annotated_string as
+    
     partial_xml = as.to_s
     as
 

data/lib/tagger.rb

@@ -16,11 +16,11 @@ limitations under the License.
 
 class Tagger
 
-    @@unit_search_global =
-         /(?:units?|micrograms?|milligrams?|mg|grams?|millimoles?
-           |milliequivalents?|percent|(?:au|pnu)(?:\/|per\s*)ml
-           |mg\.?(?:(?:\/|per\s*)(one|five|1|5)?\s*(?:ml|cc)\.?)?
-           |\%|gr\.?|meq\.?|mmol\.?|ugm?s?|mcg)/i
+  @@unit_search_global =
+    /(?:mg\.?(?:(?:\/|\s*per\s*)(one|five|1|5)?\s*(?:ml|cc|m2|meters? squared|m squared)\.?)?
+|units?|micrograms?|milligrams?|mg|grams?|millimoles?|milliequivalents?|percent
+|(?:au|pnu)(?:\/|per\s*)ml
+|\%|gr\.?|meq\.?|mmol\.?|ugm?s?|mcg)/ix
 
     @@number_word_search =
         /(?:one|two|three|four|five|six|seven|eight|nine|ten|fifteen|twenty|thirty|sixty)/

data/lib/taggers/duration_tagger.rb

@@ -18,7 +18,7 @@ class DurationTagger < Tagger
     def initialize
         @shared_search = /(?x)(?:\d+(?:\-\d)?|one|two|three|four|five|six|seven|
                   eight|nine|ten|fifteen|twenty|thirty|sixty)\s*
-                  (?:days?|weeks?|wks|months?|d\b)/i
+                  (?:days?|weeks?|wks|months?|cycles?|d\b)/i
         @default_precondition = /#{@shared_search}/i
         @default_search = /(?x)((?:for|x)\s?(?:a\stotal\sof\s+)?(?:up\s+to\s+)?
                        (?:the\snext\s+)?)(#{@shared_search})/i

data/lib/taggers/strength_tagger.rb

@@ -28,9 +28,9 @@ class StrengthTagger < Tagger
     def parse_text(text, precondition, search, content_group)
         tags = super text, @default_precondition, @default_search
         local_precondition = /#{@shared_search}/i
-        local_search = /(?x)\s((?:(?:\d+\/)?\d+(?:\.\d+)?|one|two)
+        local_search = /(?x)\s((?:(?:\d+\/)?(?:\d+,)?\d+(?:\.\d+)?|one|two)
                       (?:\shundred|\sthousand)?(?:(?:-|\s+to\s+)
-                      (?:\d+(?:\.\d+)?|one|two)
+                      (?:(?:\d+,)?\d+(?:\.\d+)?|one|two)
                       (?:\shundred|\sthousand)?)?)\s*(#{@shared_search})/i
         tags += super text, local_precondition, local_search
         return tags

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: medattrib
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors:
 - Cheryl Clark
@@ -18,14 +18,14 @@ dependencies:
   name: standoff
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.0.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.0.5
 description: A text tagger that annotates prescription concepts
@@ -39,12 +39,15 @@ files:
 - README.md
 - bin/medattrib
 - lib/list_tagger.rb
+- lib/list_taggers/#dose_amount_list_tagger.rb#
+- lib/list_taggers/DoseAmountListTagger.rb~
+- lib/list_taggers/dose_amount_list_tagger.rb
+- lib/list_taggers/dose_amount_list_tagger.rb~
 - lib/list_taggers/dose_form_tagger.rb
 - lib/list_taggers/frequency_tagger.rb
 - lib/list_taggers/route_tagger.rb
 - lib/medattrib.rb
 - lib/run_medattrib.rb
-- lib/run_medattrib.rb~
 - lib/tagger.rb
 - lib/taggers/dispense_quantity_tagger.rb
 - lib/taggers/dose_amount_tagger.rb
@@ -65,17 +68,17 @@ 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: 2.4.3
+rubygems_version: 2.5.2.1
 signing_key: 
 specification_version: 4
 summary: MedAttrib!

data/lib/run_medattrib.rb~

@@ -1,9 +0,0 @@
-#!/usr/bin/ruby
-
-require "medattrib"
-
-tagger = MedAttrib.new
-
-while line = gets do
-  puts tagger.parse(line).to_s
-end