biodiversity19 1.0.5 → 1.0.6

data/.rvmrc

@@ -0,0 +1 @@
+rvm use ruby-1.9.2-p290@biodiversity--create

data/Gemfile

@@ -0,0 +1,11 @@
+source "http://rubygems.org"
+
+gem "jeweler"
+gem "treetop"
+gem "facter"
+gem "parallel"
+
+group :test do
+  gem "ruby-debug19", :require => "ruby-debug"
+  gem "rspec"
+end

data/Gemfile.lock

@@ -0,0 +1,49 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    archive-tar-minitar (0.5.2)
+    columnize (0.3.4)
+    diff-lcs (1.1.3)
+    facter (1.6.3)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    linecache19 (0.5.12)
+      ruby_core_source (>= 0.1.4)
+    parallel (0.5.9)
+    polyglot (0.3.3)
+    rake (0.9.2.2)
+    rspec (2.7.0)
+      rspec-core (~> 2.7.0)
+      rspec-expectations (~> 2.7.0)
+      rspec-mocks (~> 2.7.0)
+    rspec-core (2.7.1)
+    rspec-expectations (2.7.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.7.0)
+    ruby-debug-base19 (0.11.25)
+      columnize (>= 0.3.1)
+      linecache19 (>= 0.5.11)
+      ruby_core_source (>= 0.1.4)
+    ruby-debug19 (0.11.6)
+      columnize (>= 0.3.1)
+      linecache19 (>= 0.5.11)
+      ruby-debug-base19 (>= 0.11.19)
+    ruby_core_source (0.1.5)
+      archive-tar-minitar (>= 0.5.2)
+    treetop (1.4.10)
+      polyglot
+      polyglot (>= 0.3.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  facter
+  jeweler
+  parallel
+  rspec
+  ruby-debug19
+  treetop

data/VERSION

@@ -1 +1 @@
-1.0.5
+1.0.6

data/lib/biodiversity/parser.rb

@@ -23,6 +23,31 @@ module PreProcessor
   end   
 end
 
+class ParallelParser
+
+  def initialize
+    require 'facter'
+    require 'parallel'
+    cpu_num
+    @processes_num = cpu_num > 1 ? cpu_num - 1 : 1
+  end
+
+  def parse(names_list)
+    parsed = Parallel.map(names_list.uniq, :in_processes => @processes_num) { |n| [n, parse_process(n)] }
+    parsed.inject({}) { |res, x| res[x[0]] = x[1]; res }
+  end
+
+  def cpu_num
+    @cpu_num ||= Facter.processorcount.to_i
+  end
+
+  private
+  def parse_process(name)
+    p = ScientificNameParser.new
+    p.parse(name).to_json rescue {'scientificName' => {'parsed' => false, 'verbatim' => name,  'error' => 'Parser error'}}.to_json
+  end
+end
+
 # we can use these expressions when we are ready to parse virus names
 # class VirusParser
 #   def initialize

data/spec/parser/scientific_name.spec.rb

@@ -43,3 +43,22 @@ describe ScientificNameParser do
     parse('Nile virus')[:scientificName][:parser_version].should_not be_nil
   end
 end
+
+
+describe ParallelParser do
+  it "should find number of cpus" do
+    pparser = ParallelParser.new
+    pparser.cpu_num.should > 0
+  end
+
+  it "should parse several names in parallel" do
+    names = []
+    read_test_file { |n| names << (n[:name]) if n[:name] }
+    names.uniq!
+    pparser = ParallelParser.new
+    res = pparser.parse(names)
+    names.size.should > 100
+    res.keys.size.should == names.size
+  end
+
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity19
 version: !ruby/object:Gem::Version
-  version: 1.0.5
+  version: 1.0.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,55 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-08-09 00:00:00.000000000Z
+date: 2011-11-17 00:00:00.000000000Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &70228377889480 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *70228377889480
+- !ruby/object:Gem::Dependency
+  name: treetop
+  requirement: &70228377827560 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *70228377827560
+- !ruby/object:Gem::Dependency
+  name: facter
+  requirement: &70228377827080 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *70228377827080
+- !ruby/object:Gem::Dependency
+  name: parallel
+  requirement: &70228377826600 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *70228377826600
 - !ruby/object:Gem::Dependency
   name: treetop
-  requirement: &70129715072740 !ruby/object:Gem::Requirement
+  requirement: &70228377826120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +65,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70129715072740
+  version_requirements: *70228377826120
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70129715071500 !ruby/object:Gem::Requirement
+  requirement: &70228377825640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,7 +76,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70129715071500
+  version_requirements: *70228377825640
 description: Tools for biodiversity informatics
 email: dmozzherin@gmail.com
 executables:
@@ -44,6 +88,9 @@ extra_rdoc_files:
 - README.rdoc
 files:
 - .document
+- .rvmrc
+- Gemfile
+- Gemfile.lock
 - LICENSE
 - README.rdoc
 - Rakefile
@@ -89,7 +136,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.6
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: Parser of scientific names