name-spotter 0.0.5 → 0.0.6

data/README.rdoc

@@ -2,6 +2,10 @@
 
 Finds biodiversity scientific names in texts using TaxonFinder (by Patrick Leary) or NetiNeti (by Lakshmi Manohar Akella) libraries. This gem works with ruby >= 1.9.2
 
+== Requirements
+
+* Python 2.6/2.7 with NLTK module, http://www.nltk.org/
+
 == Installation
 
 * Install the gem
@@ -28,8 +32,8 @@ Finds biodiversity scientific names in texts using TaxonFinder (by Patrick Leary
 
     #then
     
-    easy_install virtualenv
-    easy_install tornado
+    sudo easy_install virtualenv
+    sudo easy_install tornado
     python neti_env.py virtualenvs/neti
     cp config/neti_http_config.cfg.example config/neti_http_config.cfg
     python neti_tornado_server.py 

data/VERSION

@@ -1 +1 @@
-0.0.5
+0.0.6

data/lib/name-spotter/taxon_finder_client.rb

@@ -13,6 +13,7 @@ class NameSpotter
     end
 
     def find(str, from_web_form=false)
+      @names = []
       return [] if str.nil? || str.empty?
 
       # These are for the data-send-back that happens in TaxonFinder

data/name-spotter.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "name-spotter"
-  s.version = "0.0.5"
+  s.version = "0.0.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Anthony Goddard", "Chuck Ha", "Dmitry Mozzherin"]
-  s.date = "2012-01-12"
+  s.date = "2012-05-04"
   s.description = "The gem searches for scientific names in texts using socket servers running TaxonFinder (by Patrick Leary) and NetiNeti (by Lakshmi Manohar Akella)"
   s.email = "dmozzherin@gmail.com"
   s.extra_rdoc_files = [

data/spec/name-spotter_spec.rb

@@ -45,6 +45,19 @@ describe "NameSpotter" do
     res = @tf.find(text)[:names].map { |n| n[:scientificName] } 
     res.should == ["Betula alba", "Mus musculus", "B[etula] alba", "Varanus"]
   end
+  
+  it "should not remember previous search results" do
+    text = "Some text that has Betula\n alba and Mus musculus and \neven B. alba and even M. mus-\nculus. Also it has name unknown before: Varanus bitatawa species"
+    res = @neti.find(text)[:names].map { |n| n[:scientificName] } 
+    res.should == ["Betula alba", "Mus musculus", "B. alba", "Varanus bitatawa"]
+    res = @tf.find(text)[:names].map { |n| n[:scientificName] } 
+    res.should == ["Betula alba", "Mus musculus", "B[etula] alba", "Varanus"]
+    text = "Some another text that has Xysticus \ncanadensis and Pardosa moesta and \neven X. canadensis and even P. mo-\nesta."
+    res = @neti.find(text)[:names].map { |n| n[:scientificName] } 
+    res.should == ['Xysticus canadensis', 'Pardosa moesta', 'X. canadensis']
+    res = @tf.find(text)[:names].map { |n| n[:scientificName] } 
+    res.should == ['Xysticus canadensis', 'Pardosa moesta', 'X[ysticus] canadensis']
+  end
 
   it "should get back correct names using offsets in utf-8 based text" do
     text = "A text with multibyte characters नेति नेति:  Some text that has Betula\n alba and Mus musculus and \neven B. alba and even M. mus-\nculus. Also it has name unknown before: Varanus bitatawa species"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: name-spotter
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
   prerelease: 
 platform: ruby
 authors:
@@ -11,11 +11,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-12 00:00:00.000000000Z
+date: 2012-05-04 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &70195014203460 !ruby/object:Gem::Requirement
+  requirement: &70270525418200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -23,10 +23,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70195014203460
+  version_requirements: *70270525418200
 - !ruby/object:Gem::Dependency
   name: rest-client
-  requirement: &70195014202720 !ruby/object:Gem::Requirement
+  requirement: &70270525417200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -34,10 +34,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70195014202720
+  version_requirements: *70270525417200
 - !ruby/object:Gem::Dependency
   name: builder
-  requirement: &70195014201980 !ruby/object:Gem::Requirement
+  requirement: &70270525416360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -45,10 +45,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70195014201980
+  version_requirements: *70270525416360
 - !ruby/object:Gem::Dependency
   name: json
-  requirement: &70195014201240 !ruby/object:Gem::Requirement
+  requirement: &70270525415220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -56,10 +56,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70195014201240
+  version_requirements: *70270525415220
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70195014200520 !ruby/object:Gem::Requirement
+  requirement: &70270525413940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -67,10 +67,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *70195014200520
+  version_requirements: *70270525413940
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &70195014192980 !ruby/object:Gem::Requirement
+  requirement: &70270525413200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -78,10 +78,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70195014192980
+  version_requirements: *70270525413200
 - !ruby/object:Gem::Dependency
   name: capybara
-  requirement: &70195014192200 !ruby/object:Gem::Requirement
+  requirement: &70270525412520 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -89,10 +89,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70195014192200
+  version_requirements: *70270525412520
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70195014191560 !ruby/object:Gem::Requirement
+  requirement: &70270525411840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -100,10 +100,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *70195014191560
+  version_requirements: *70270525411840
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70195014190980 !ruby/object:Gem::Requirement
+  requirement: &70270525411180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -111,10 +111,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *70195014190980
+  version_requirements: *70270525411180
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &70195014190320 !ruby/object:Gem::Requirement
+  requirement: &70270525410600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -122,10 +122,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70195014190320
+  version_requirements: *70270525410600
 - !ruby/object:Gem::Dependency
   name: ruby-debug19
-  requirement: &70195014189720 !ruby/object:Gem::Requirement
+  requirement: &70270525409760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -133,7 +133,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70195014189720
+  version_requirements: *70270525409760
 description: The gem searches for scientific names in texts using socket servers running
   TaxonFinder (by Patrick Leary) and NetiNeti (by Lakshmi Manohar Akella)
 email: dmozzherin@gmail.com
@@ -180,7 +180,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 3702065529209434709
+      hash: -1996477105956361084
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: