rbbt-text 1.1.2 → 1.1.3

checksums.yaml

@@ -1,15 +1,7 @@
 ---
-!binary "U0hBMQ==":
-  metadata.gz: !binary |-
-    YmM3MTY4MmVhNDM3NmFlMTFhNTEwZGNkYWQyMGIzZjZhZWU0ZjA4YQ==
-  data.tar.gz: !binary |-
-    YTVkYWFlMmQzOTA3M2M2YjZlZjIxNzNjOTE3MTA3NzNlZDc1OGY0Zg==
+SHA1:
+  metadata.gz: 8e24d9496396b5679cdea2d9e4659fdc86bf9baf
+  data.tar.gz: 97b1cafa958ee4e60bd66e64fc3803d2fa2bf972
 SHA512:
-  metadata.gz: !binary |-
-    NWFhODc1YTMzOTA0MTIxNDU4NzJjZjJiOGFjMzcxNmY5OTcwMTE3ZWYzZjcw
-    ODVhNjM4ZWQ5ZjBkODQ2YjFmOGJmNDU2YmVmYzg0N2M5Yzk4N2YyNmNiMjQ0
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-  data.tar.gz: !binary |-
-    MTQ1NjgzYjBkYjhiNzgyNjc0ZmU4MmQ2MzZiZDkyZjQyN2YyM2MzNDBiNDA4
-    ZjQ4M2ZmYzhlNTJmNjhmZGZjZTNkMGI2MmJiYzgyYjM4ZjIwOThlMmI4NWZh
-    ODE3YzZjYzU0ODhlZjFiMjc2ZmZhZjU5NDhlNDc1MTExM2RkZGM=
+  metadata.gz: 21c91bf76cfb78e0c2a674a62c5c8e7971e981c631e74091524610f37351992d3b9ca5b197fcfccfe7d5315df5125cd1d6b5dfbc3b70566d9df7f9afe90d0a32
+  data.tar.gz: dbfd6442800434cf7073591f27007392e003d9511f2e00d0bd6c12c6ad5fd22bdde4b9e4b729334ddf6957f64aba360a0b407f926fa0e8c7bbe84e2bb9318bcf

data/lib/rbbt/ner/chemical_tagger.rb

@@ -21,8 +21,7 @@ class ChemicalTagger < NER
     begin
       matches = @@RbbtChemicalTagger.match(text)
     rescue
-      Log.debug "ChemicalTagger Error: #{$!.message}"
-      ddd $!.backtrace
+      Log.exception $!
       return []
     end
 

data/test/rbbt/ner/test_finder.rb

@@ -9,13 +9,13 @@ require 'rbbt/sources/NCI'
 class TestFinder < Test::Unit::TestCase
 
   def test_namespace_and_format
-    f = Finder.new(CMD.cmd("head -n 1000", :in => Open.open(Organism.identifiers("Hsa/jun2011").produce.find)))
+    f = Finder.new(CMD.cmd("head -n 1000", :in => Open.open(Organism.identifiers(Organism.default_code("Hsa")).produce.find)))
     assert_equal "Hsa", f.instances.first.namespace
     assert_equal "Ensembl Gene ID", f.instances.first.format
   end
 
   def test_find
-    f = Finder.new(Organism.lexicon("Hsa/jun2011"), :grep => ["SF3B1"])
+    f = Finder.new(Organism.lexicon(Organism.default_code("Hsa")), :grep => ["SF3B1"])
 
     assert_equal "ENSG00000115524", f.find("SF3B1").first
     if defined? Entity
@@ -25,7 +25,7 @@ class TestFinder < Test::Unit::TestCase
   end
 
   def test_find
-    f = Finder.new(Organism.lexicon("Hsa/jun2011"), :grep => ["RASGRF2"])
+    f = Finder.new(Organism.lexicon(Organism.default_code("Hsa")), :grep => ["RASGRF2"])
 
     assert f.find("RAS").include? "ENSG00000113319"
   end

metadata

@@ -1,86 +1,86 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-text
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.1.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-19 00:00:00.000000000 Z
+date: 2014-08-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 4.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 4.0.0
 - !ruby/object:Gem::Dependency
   name: stemmer
   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: libxml-ruby
   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: json
   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: rjb
   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'
-description: ! 'Text mining tools: named entity recognition and normalization, document
+description: 'Text mining tools: named entity recognition and normalization, document
   classification, bag-of-words, dictionaries, etc'
 email: miguel.vazquez@fdi.ucm.es
 executables:
@@ -168,41 +168,41 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.0
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Text mining tools for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/bow/test_misc.rb
-- test/rbbt/bow/test_bow.rb
-- test/rbbt/bow/test_dictionary.rb
-- test/rbbt/ner/test_ngram_prefix_dictionary.rb
-- test/rbbt/ner/test_NER.rb
-- test/rbbt/ner/segment/test_named_entity.rb
+- test/rbbt/nlp/open_nlp/test_sentence_splitter.rb
+- test/rbbt/nlp/test_nlp.rb
+- test/rbbt/ner/test_regexpNER.rb
+- test/rbbt/ner/test_banner.rb
 - test/rbbt/ner/segment/test_transformed.rb
 - test/rbbt/ner/segment/test_segmented.rb
+- test/rbbt/ner/segment/test_named_entity.rb
+- test/rbbt/ner/test_abner.rb
+- test/rbbt/ner/test_oscar4.rb
+- test/rbbt/ner/test_finder.rb
 - test/rbbt/ner/test_patterns.rb
+- test/rbbt/ner/test_rnorm.rb
 - test/rbbt/ner/test_segment.rb
-- test/rbbt/ner/test_finder.rb
-- test/rbbt/ner/test_chemical_tagger.rb
+- test/rbbt/ner/test_ngram_prefix_dictionary.rb
 - test/rbbt/ner/test_token_trieNER.rb
-- test/rbbt/ner/test_oscar4.rb
-- test/rbbt/ner/test_abner.rb
-- test/rbbt/ner/test_regexpNER.rb
-- test/rbbt/ner/test_rnorm.rb
-- test/rbbt/ner/test_banner.rb
+- test/rbbt/ner/test_NER.rb
 - test/rbbt/ner/test_linnaeus.rb
-- test/rbbt/nlp/test_nlp.rb
-- test/rbbt/nlp/open_nlp/test_sentence_splitter.rb
+- test/rbbt/ner/test_chemical_tagger.rb
 - test/rbbt/entity/test_document.rb
+- test/rbbt/bow/test_bow.rb
+- test/rbbt/bow/test_dictionary.rb
+- test/rbbt/bow/test_misc.rb
 - test/test_helper.rb