rbbt 1.1.1 → 1.1.4

data/lib/rbbt/ner/regexpNER.rb

@@ -31,18 +31,19 @@ class RegExpNER
 
 
   def initialize(lexicon, options = {})
-    options[:flatten]    = true
-    options[:ignorecase] = true if options[:ignorecase].nil?
-    options[:stopwords]  = true if options[:stopwords].nil?
+    options = {:flatten => true, :ignorecase => true, :stopwords => nil}.merge options
+
+    options[:stopwords] = $stopwords if $stopwords && (options[:stopwords].nil? || options[:stopwords] == true)
+    options[:stopwords] ||= []
 
     data = Open.to_hash(lexicon, options)
 
     @index = {}
     data.collect{|code, names|
       next if code.nil? || code == ""
-      if options[:stopwords]
+      if options[:stopwords].any?
         names = names.select{|n| 
-          ! $stopwords.include?(options[:ignorecase] ? n.downcase : n)
+          ! options[:stopwords].include?(options[:ignorecase] ? n.downcase : n)
         } 
       end
       @index[code] = RegExpNER.build_re(names, options[:ignorecase])

data/lib/rbbt/sources/biomart.rb

@@ -37,12 +37,12 @@ module BioMart
     query.sub!(/<!--MAIN-->/,"<Attribute name = \"#{main}\" />")
     query.sub!(/<!--ATTRIBUTES-->/, attrs.collect{|name| "<Attribute name = \"#{ name }\"/>"}.join("\n") )
 
-    rows = Open.read('http://www.biomart.org/biomart/martservice?query=' + query.gsub(/\n/,' '))
-    if rows =~ /Query ERROR:/
-      raise BioMart::QueryError, rows
+    response = Open.read('http://www.biomart.org/biomart/martservice?query=' + query.gsub(/\n/,' '))
+    if response =~ /Query ERROR:/
+      raise BioMart::QueryError, response
     end
 
-    rows.each{|l|
+    response.each_line{|l|
       parts = l.chomp.split(/\t/)
       main = parts.shift
       next if main.nil? || main.empty?

data/lib/rbbt/util/rake.rb

@@ -0,0 +1,18 @@
+def step(name, previous = nil, &block)
+  re = Regexp.new(/(?:^|\/)#{name}\/.*$/)
+
+  $step_descriptions ||= {}
+  if Rake.application.last_description 
+    $step_descriptions[re] = {:step => name, :message => Rake.application.last_description}
+    Rake.application.last_description = nil
+  end
+
+  if previous.nil?
+    deps = []
+  else
+    deps = lambda{|filename| filename.sub(name.to_s, previous.to_s)}
+  end
+
+  Rake.application.create_rule(re => deps, &block) 
+end
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt
 version: !ruby/object:Gem::Version 
-  version: 1.1.1
+  version: 1.1.4
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-12-02 00:00:00 +01:00
+date: 2009-12-08 00:00:00 +01:00
 default_executable: rbbt_config
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -125,6 +125,7 @@ files:
 - lib/rbbt/util/index.rb
 - lib/rbbt/util/misc.rb
 - lib/rbbt/util/open.rb
+- lib/rbbt/util/rake.rb
 - lib/rbbt/util/simpleDSL.rb
 - lib/rbbt/util/tmpfile.rb
 - tasks/install.rake