rbbt-sources 3.2.3 → 3.2.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 34440772758a57a082f3bb856579b1932be5814fa4e48b5794850529b19c0e66
+  metadata.gz: fc74a3b7d26cc888bbd71f7aaa41918c2abb97e7a99abd027b9ea9086ee909e2
+  data.tar.gz: 4ed848475f09c4fcfb0c3c21cba8a515ee4005b475883ec148bb9b27808e24af
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+  data.tar.gz: 11f70fd175e9c1cca781103da79f443558a5078ea2827bc2302e3a4e178f561bdc69bb7385c00e999a8067f938479d6f64baba418799e9bc32fd57bba6086566

data/lib/rbbt/sources/entrez.rb

@@ -2,7 +2,6 @@ require 'rbbt-util'
 require 'rbbt/tsv'
 require 'rbbt/resource'
 require 'rbbt/util/filecache'
-require 'rbbt/bow/bow'
 require 'set'
 
 module Entrez
@@ -15,7 +14,7 @@ module Entrez
 
     taxs = [taxs] unless Array === taxs
     options.merge! :grep => taxs.collect{|t| "^" + t.to_s}, :fixed_grep => false
-    
+
     tsv = Rbbt.share.databases.entrez.gene_info.tsv :flat, options
     tsv.key_field = "Entrez Gene ID"
     tsv.fields    = ["Native ID"]
@@ -27,7 +26,7 @@ module Entrez
 
     taxs = [taxs] unless Array === taxs
     options.merge! :grep => taxs.collect{|t| "^" + t.to_s}, :fixed_grep => false
-    
+
     tsv = Rbbt.share.databases.entrez.gene_info.tsv :flat, options
     tsv.key_field = "Entrez Gene ID"
     tsv.fields    = ["Associated Gene Name"]
@@ -43,7 +42,7 @@ module Entrez
 
     Rbbt.share.databases.entrez.gene2pubmed.tsv :flat, options
   end
-  
+
   class Gene
     attr_reader :organism, :symbol, :description, :aka, :protnames, :summary, :comentaries
 
@@ -97,7 +96,7 @@ module Entrez
 
       values.each do |xml|
         geneid = xml.match(/<Gene-track_geneid>(\d+)/)[1]
-        
+
         result[geneid] = xml
       end
 
@@ -114,30 +113,31 @@ module Entrez
     end
   end
 
-# Counts the words in common between a chunk of text and the text
-# found in Entrez Gene for that particular gene. The +gene+ may be a
-# gene identifier or a Gene class instance.
-def self.gene_text_similarity(gene, text)
-
-  case
-  when Entrez::Gene === gene
-    gene_text = gene.text
-  when String === gene || Fixnum === gene
-    begin
-      gene_text =  get_gene(gene).text
-    rescue NoMethodError, CMD::CMDError
+  # Counts the words in common between a chunk of text and the text
+  # found in Entrez Gene for that particular gene. The +gene+ may be a
+  # gene identifier or a Gene class instance.
+  def self.gene_text_similarity(gene, text)
+    require 'rbbt/bow/bow'
+
+    case
+    when Entrez::Gene === gene
+      gene_text = gene.text
+    when String === gene || Fixnum === gene
+      begin
+        gene_text =  get_gene(gene).text
+      rescue NoMethodError, CMD::CMDError
+        return 0
+      end
+    else
       return 0
     end
-  else
-    return 0
-  end
 
-  gene_words = gene_text.words.to_set
-  text_words = text.words.to_set
+    gene_words = gene_text.words.to_set
+    text_words = text.words.to_set
 
-  return 0 if gene_words.empty? || text_words.empty?
+    return 0 if gene_words.empty? || text_words.empty?
 
-  common = gene_words.intersection(text_words)
-  common.length / (gene_words.length + text_words.length).to_f
-end
+    common = gene_words.intersection(text_words)
+    common.length / (gene_words.length + text_words.length).to_f
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.2.3
+  version: 3.2.4
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-02-27 00:00:00.000000000 Z
+date: 2023-03-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -24,20 +24,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 4.0.0
-- !ruby/object:Gem::Dependency
-  name: mechanize
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement