pubannotation_evaluator 1.0.5 → 1.1.0
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checksums.yaml
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metadata.gz: 806a1cccb5be0bc733f7deb05fe647d03816235a28bffec791aeb450a33cca46
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data.tar.gz: a10d449746dd75e7923a4c08e82e1c6e8ac7310ddf9524b876c61327d88e8936
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metadata.gz: 27486eff982a8a8972a03aa42d9eeca6f7598d9bf76631ba2881251be786bde75254b02b9502701e5601a81e7b6edb052d852ef3d1f006477a213bde602b3631
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data.tar.gz: 6ea8c8f982c327a86c5cfa61a51a8f5bc4d3d03edd75d407ca720bf3494ab572d4d78f86c114d87211d533cb8172984d467f9267ef75b137168510207b35e623
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@@ -3,17 +3,17 @@ class PubannotationEvaluator
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SOFT_MATCH_WORDS = 2
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EXACT_TYPE_MATCH = 'study_type == reference_type ? 1 : 0'
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def initialize(soft_match_chatacters
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@soft_match_chatacters = soft_match_chatacters
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@soft_match_words = soft_match_words
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def initialize(soft_match_chatacters, soft_match_words, denotation_type_match, relation_type_match)
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@soft_match_chatacters = soft_match_chatacters || SOFT_MATCH_CHARACTERS
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@soft_match_words = soft_match_words || SOFT_MATCH_WORDS
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@denotation_type_match = eval <<-HEREDOC
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Proc.new do |study_type, reference_type|
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#{denotation_type_match}
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#{denotation_type_match || EXACT_TYPE_MATCH}
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end
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HEREDOC
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@relation_type_match = eval <<-HEREDOC
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Proc.new do |study_type, reference_type|
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#{relation_type_match}
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#{relation_type_match || EXACT_TYPE_MATCH}
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end
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HEREDOC
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end
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@@ -41,7 +41,6 @@ class PubannotationEvaluator
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comparison_modifications.collect{|a| a.merge(type: :modification)}
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docspec = {sourcedb:study_annotations[:sourcedb], sourceid:study_annotations[:sourceid]}
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docspec[:divid] = study_annotations[:divid] if study_annotations.has_key?(:divid)
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comparison.collect{|d| d.merge(docspec)}
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end
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matches = find_denotation_matches(mmatches)
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false_positives = study_denotations - matches.collect{|r| r[:study]}
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false_negatives = reference_denotations - matches.collect{|r| r[:reference]}
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false_positives.each{|r| r.merge!(text:text[r[:span][:begin]...r[:span][:end]])}
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false_negatives.each{|r| r.merge!(text:text[r[:span][:begin]...r[:span][:end]])}
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comparison = matches + false_positives.collect{|s| {study:s}} + false_negatives.collect{|r| {reference:r}}
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[comparison, mmatches]
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end
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metadata
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--- !ruby/object:Gem::Specification
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name: pubannotation_evaluator
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version: !ruby/object:Gem::Version
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version: 1.0
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version: 1.1.0
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platform: ruby
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authors:
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- Jin-Dong Kim
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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2021-12-19 00:00:00.000000000 Z
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dependencies: []
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description: A tool to evaluate the accuracy of a set of annotations.
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email: jdkim@dbcls.rois.ac.jp
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@@ -39,8 +39,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubygems_version: 2.7.9
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rubygems_version: 3.0.9
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signing_key:
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specification_version: 4
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summary: It compares a set of annotations (study annotations) against another set
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