medattrib 0.0.5 → 0.0.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 5714a6d8bd82639ca8f9a7f60eff1a59d14f27af
+  metadata.gz: 227bec7d4279a4fd39a16399199ff8799b736b12
+  data.tar.gz: 34c4d46a42970f5e5f8130d1e22677bb740cd006
 SHA512:
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+  metadata.gz: e38309aa298ba3e1a9e4340d8b9e78f3c6ec99b546859fdd49b791ee2f9300f4f7e17a7949488cc3ab8d0a42511e621a16bde6f5ed75e0ae32678f3764efbab8
+  data.tar.gz: 5b8cfb0ac7781d96d5449a68c3f11c44f84548b6dacf3debe6c0a3d327b6b8a0088c98961c2b2fa4f749b04a5ff3c8cab315e705d935834e596b456c86b5affa

data/lib/tagger.rb

@@ -17,7 +17,7 @@ limitations under the License.
 class Tagger
 
   @@unit_search_global =
-    /(?:mg\.?(?:(?:\/|\s*per\s*)(one|five|1|5)?\s*(?:ml|cc|m2|meters? squared|m squared)\.?)?
+    /(?: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

data/lib/taggers/#duration_tagger.rb#

@@ -0,0 +1,31 @@
+=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
+
+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?|cycles?|courses?|d\b)/i
+        @cycles_courses_only_search = /(?x)(?:\d+(?:\-\d)?|one|two|three|four|five|six|seven|
+                  eight|nine|ten|fifteen|twenty|thirty|sixty)\s*
+                  (?:|cycles?|courses?|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})|(?:@cycles_courses_only_search)i/
+        @content_group = 2
+        @name = 'duration'
+    end
+end

data/lib/taggers/dose_amount_tagger.rb

@@ -37,12 +37,44 @@ class DoseAmountTagger < Tagger
         local_search = /(?x)((?:(?:\d\s+)?(?:\d(?:\/|-))?(?:\d+(?:\.\d+)?
                        (?:\s?(?:-|\/)\s?\d+)?)|one|two))(\s+
                        (?:(?:#{@shared_search})|<route))/i
-        
+
+        # AnnotatedString::to_s interpolates standoff tags into inline XML.
+        # This is necessary because the regexes rely on other tag adjacency for search context.
+        # This is kludgy, and should at some point be replaced by using the standoff annotation directly so we can leave the signal text alone.
         new_tags += parse_text as.to_s, local_precondition, local_search
-        as.tags += new_tags
+
+        # Because of the conversion from standoff to inline tags (above), match positions will be wrong.
+        # The following line is a necessary workaround to map the start and end positions from the xml-augmented strings back to the signal text.
+        new_tags2 = map_annotation_from_inline_to_clean as.to_s, as.tags, new_tags
+
+        as.tags += new_tags2
         return as
     end
 
+  def map_annotation_from_inline_to_clean(string_with_annots, existing_annotations, new_annotations)
+    clean_string = ""
+    annots_re = /<[^>]+>/
+    first_original = 0
+    last_original = string_with_annots.length
+
+    #re_result = str.scan(annots_re)
+    re_results = string_with_annots.to_enum(:scan, annots_re).map { Regexp.last_match }
+
+    map_dirty_to_clean_annot = lambda do |dirty_annot,re_results|
+      clean_annot = dirty_annot.dup
+      #correction = re_results.map{ |item| item.offset(0)[1] <= dirty_annot.start ? item.offset(0)[1] - item.offset(0)[0] : 0}.reduce(0, :+)
+      prior_lengths = re_results.map{ |item| item.offset(0)[1] <= dirty_annot.start ? item.offset(0)[1] - item.offset(0)[0] : 0}
+      correction = prior_lengths.reduce(0, :+)
+      clean_annot.start = clean_annot.start - correction
+      clean_annot.end = clean_annot.end - correction
+      clean_annot
+    end
+
+    clean_annots = new_annotations.map{|old_entry| map_dirty_to_clean_annot[old_entry, re_results] }
+
+    clean_annots
+  end
+
   def normalize(dose)
     re = {:int =>  /^\d+$/,
         :decimal => /^(\d+)?\.\d+$/,

data/lib/taggers/duration_tagger.rb

@@ -18,10 +18,13 @@ 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?|cycles?|d\b)/i
+                  (?:days?|weeks?|wks|months?|cycles?|courses?|d\b)/i
+        @cycles_courses_only_search = /(?x)(?:\d+(?:\-\d)?|one|two|three|four|five|six|seven|
+                  eight|nine|ten|fifteen|twenty|thirty|sixty)\s*
+                  (?:|cycles?|courses?|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
+                       (?:the\snext\s+)?)(#{@shared_search})|(?:@cycles_courses_only_search)/i
         @content_group = 2
         @name = 'duration'
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: medattrib
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
 platform: ruby
 authors:
 - Cheryl Clark
@@ -49,6 +49,7 @@ files:
 - lib/medattrib.rb
 - lib/run_medattrib.rb
 - lib/tagger.rb
+- lib/taggers/#duration_tagger.rb#
 - lib/taggers/dispense_quantity_tagger.rb
 - lib/taggers/dose_amount_tagger.rb
 - lib/taggers/duration_tagger.rb