pubannotation_evaluator 1.0.3 → 1.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1ba6d5024226dba72a62356ced9473f6d9c3d0761bf2591240a9463d539b9d47
-  data.tar.gz: 5fc854a7de2767f26b57d02e7bbf5b371613a08f49a10c3fed9aa2a9e055b2b7
+  metadata.gz: 221340084b2e71edebc25671fe196d05f0e17ebeb3b2b9e8bca72c0fd6c42266
+  data.tar.gz: 2c88f506c78a19a43d72c5c009cc40d0c586146b9e13d02bb5075a9460162596
 SHA512:
-  metadata.gz: 57c31f7d5c7d4a9400ceed1f582c92c093bf2ea5d47960d57a24b9c1d99cf6e5d9c94e6f138a298f6b0213b01d6bf562d44147ce964a94285aa8182a45ce74e5
-  data.tar.gz: 9e6bb76a8db19410bd4a66c8442b0cc19a5b50397c63d134bf9128b13963071cd015604588a073ad2c1b3ee91bba76f10ffca2c75ff8a9f8774026b13e26fca2
+  metadata.gz: 6ab795d95e7a6e44406932e132c65f0a5391f4a2623bba8d35126cdec68e7ae9c097d2dc2bb7da7e8f9db121d147a9dbf18a52e3b9f9f040bf272efbe468e1f1
+  data.tar.gz: 40efce24c19bfe9b2d4b62065a553a1b218a36703c6e1e2b074462788afabb68fbe3b4fce9ab666fc74e2fe0147bc7405206d02b784db5fcfe5fb6878c7961ac

data/bin/pubannotation-eval

@@ -84,6 +84,11 @@ if verbose
 
 	false_negatives = comparison.select{|m| m[:study].nil? && m[:reference]}
 	evaluation[:false_negatives] = false_negatives unless false_negatives.empty?
+
+	true_positives = comparison.select{|m| m[:study] && m[:reference]}
+	evaluation[:true_positives] = true_positives unless true_positives.empty?
 end
 
-puts JSON.generate(evaluation)
+puts JSON.generate(evaluation)
+
+# puts JSON.generate(comparison)

data/lib/pubannotation_evaluator/pubannotation_evaluator.rb

@@ -3,17 +3,17 @@ class PubannotationEvaluator
 	SOFT_MATCH_WORDS = 2
 	EXACT_TYPE_MATCH = 'study_type == reference_type ? 1 : 0'
 
-	def initialize(soft_match_chatacters = SOFT_MATCH_CHARACTERS, soft_match_words = SOFT_MATCH_WORDS, denotation_type_match = EXACT_TYPE_MATCH, relation_type_match = EXACT_TYPE_MATCH)
-		@soft_match_chatacters = soft_match_chatacters
-		@soft_match_words = soft_match_words
+	def initialize(soft_match_chatacters, soft_match_words, denotation_type_match, relation_type_match)
+		@soft_match_chatacters = soft_match_chatacters || SOFT_MATCH_CHARACTERS
+		@soft_match_words = soft_match_words || SOFT_MATCH_WORDS
 		@denotation_type_match = eval <<-HEREDOC
 			Proc.new do |study_type, reference_type|
-				#{denotation_type_match}
+				#{denotation_type_match || EXACT_TYPE_MATCH}
 			end
 		HEREDOC
 		@relation_type_match = eval <<-HEREDOC
 			Proc.new do |study_type, reference_type|
-				#{relation_type_match}
+				#{relation_type_match || EXACT_TYPE_MATCH}
 			end
 		HEREDOC
 	end
@@ -41,7 +41,6 @@ class PubannotationEvaluator
 								 comparison_modifications.collect{|a| a.merge(type: :modification)}
 
 		docspec = {sourcedb:study_annotations[:sourcedb], sourceid:study_annotations[:sourceid]}
-		docspec[:divid] = study_annotations[:divid] if study_annotations.has_key?(:divid)
 		comparison.collect{|d| d.merge(docspec)}
 	end
 
@@ -71,6 +70,8 @@ class PubannotationEvaluator
 		matches  = find_denotation_matches(mmatches)
 		false_positives = study_denotations - matches.collect{|r| r[:study]}
 		false_negatives = reference_denotations - matches.collect{|r| r[:reference]}
+		study_denotations.each{|r| r.merge!(text:text[r[:span][:begin]...r[:span][:end]])}
+		reference_denotations.each{|r| r.merge!(text:text[r[:span][:begin]...r[:span][:end]])}
 		comparison = matches + false_positives.collect{|s| {study:s}} + false_negatives.collect{|r| {reference:r}}
 		[comparison, mmatches]
 	end
@@ -168,8 +169,7 @@ class PubannotationEvaluator
 
 		# predicate match
 		match_pred_weight = @relation_type_match.call(s[:pred], r[:pred])
-
-		return (match_subj[:weight] + match_obj[:weight] + match_pred_weight).to_f / 3
+		# return (match_subj[:weight] + match_obj[:weight] + match_pred_weight).to_f / 3
 	end
 
 	def find_relation_matches(matches)
@@ -195,11 +195,11 @@ class PubannotationEvaluator
 		r_matched = []
 		matches_group_by_s = matches.group_by{|m| m[:study]}
 		matches_group_by_s.each_value do |m|
+			m.delete_if{|i| r_matched.include?(i[:reference])}
 			if m.length == 1
 				s_matched << m[0][:study]
 				r_matched << m[0][:reference]
-			else
-				m.delete_if{|i| r_matched.include?(i[:reference])}
+			elsif m.length > 1
 				m_sel = m.max{|a, b| comp.call(a, b)}
 				m.replace([m_sel])
 				s_matched << m_sel[:study]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: pubannotation_evaluator
 version: !ruby/object:Gem::Version
-  version: 1.0.3
+  version: 1.2.0
 platform: ruby
 authors:
 - Jin-Dong Kim
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-30 00:00:00.000000000 Z
+date: 2021-12-22 00:00:00.000000000 Z
 dependencies: []
 description: A tool to evaluate the accuracy of a set of annotations.
 email: jdkim@dbcls.rois.ac.jp
@@ -39,8 +39,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.9
+rubygems_version: 3.0.9
 signing_key: 
 specification_version: 4
 summary: It compares a set of annotations (study annotations) against another set