class DoseAmountTagger
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.
Public Class Methods
new()
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TODO replace the use of regular expressions searching for “<doseform” with checking for presence of the standoff annotations
# File lib/taggers/dose_amount_tagger.rb, line 19 def initialize @name = 'doseamount' @content_group = 1 @shared_search = /(?x)(?:puffs?|tablespoons?|teaspoons?|bolus(?:es)?| scoops?|caps?fuls?|ampules?|tubes?|drops?|gtts?| milliliters?|ml|c\.c\.|cc\b|\bL\b|tsp|tbsp)/i @default_precondition = /(<doseform)/i @default_search = /(?x)((?:\d\s+)?(?:\d(?:\/|-))?\d+(?:\.\d+)? (?:\s?(?:-|\/)\s+\d+)?|one|two)(\s+<strength> (?:[^<])+<\/strength>\s+<strength_unit>(?:[^<])+ <\/strength_unit>)?(\s+<doseform)/i end
Public Instance Methods
map_annotation_from_inline_to_clean(string_with_annots, existing_annotations, new_annotations)
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# File lib/taggers/dose_amount_tagger.rb, line 54 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
normalize(dose)
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# File lib/taggers/dose_amount_tagger.rb, line 78 def normalize(dose) re = {:int => /^\d+$/, :decimal => /^(\d+)?\.\d+$/, :fraction => /^(\d+) ?\/ ?(\d+)$/, :compound => /^(\d+) (\d+) ?\/ ?(\d+)$/, :range => /^([0-9\/\.]+) ?- ?([0-9\/\.]+)$/} x = case dose when re[:int] Integer dose when re[:decimal] Float dose when re[:fraction] # simple fraction num, denom = dose.split '/' Float(num) / Float(denom) when re[:compound] # compound fraction Integer(dose[re[:compound], 1]) + Float(dose[re[:compound], 2] )/Float(dose[re[:compound], 3]) when re[:range] normalize(dose[re[:range], 1]) .. normalize(dose[re[:range], 2]) else [nil,"one","two","three","four","five","six","seven","eight","nine","ten"].index dose.downcase end end
parse_annotated_string(as)
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# File lib/taggers/dose_amount_tagger.rb, line 34 def parse_annotated_string(as) new_tags = parse_text as.to_s, @default_precondition, @default_search local_precondition = /((#{@shared_search})|<route)/i 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 # 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