pubannotation_evaluator 1.1.0 → 3.0.0
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- checksums.yaml +4 -4
- data/bin/pubannotation-eval +4 -1
- data/lib/pubannotation_evaluator/pubannotation_evaluator.rb +2 -2
- metadata +3 -3
checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: a991e555a14f10b4dd49eee5d27bf53161f9819bfec2fd329f95bd943635fde9
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data.tar.gz: 3149ca24ea2bf62f6d8bfe522d4f51da44d23ac975b7ae1a01d5396296699093
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e04fc7c9f0ae7a8f4a776b2ce65824697a0036d58a36c99126fb336385c4e71f23c486495bb0319835ccd0fd2376e7311e1f0296a56c2c180133f0974086f2d4
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data.tar.gz: 9b5bddd6d398645df8e544273a2a0de80f781babcedaa9f44f1a391d858e2b61af0e731c256fe6a8bb86587e5391b39654e3546cdaf7571d0dd5eb4594699641
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data/bin/pubannotation-eval
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@@ -84,6 +84,9 @@ if verbose
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false_negatives = comparison.select{|m| m[:study].nil? && m[:reference]}
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evaluation[:false_negatives] = false_negatives unless false_negatives.empty?
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true_positives = comparison.select{|m| m[:study] && m[:reference]}
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evaluation[:true_positives] = true_positives unless true_positives.empty?
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end
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puts JSON.generate(evaluation)
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puts JSON.generate(evaluation)
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@@ -70,8 +70,8 @@ class PubannotationEvaluator
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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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study_denotations.each{|r| r.merge!(text:text[r[:span][:begin]...r[:span][:end]])}
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reference_denotations.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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@@ -1,14 +1,14 @@
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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:
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version: 3.0.0
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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: 2023-12-28 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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@@ -39,7 +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: 3.
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rubygems_version: 3.4.19
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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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