biodiversity 1.0.10 → 3.0.0

data/spec/parser/todo.txt

@@ -26,3 +26,30 @@ Polypodium lineare C.Chr. f. caudatoattenuatum Takeda   Polypodium
 
 Rosa gallica × tomentosa var. eglandulosa R.Keller      Rosa gallica
 Rosa gallica × afzeliana subsp. vosagiaca forma subcomplicata R.Keller        Rosa gallica
+
+Salmonella sp. (ser.) brancaster Macdonald, Sivell, Emms and Taylor 1948
+
+Stanhopea tigrina Bateman ex Lindl. x S. ecornuta Lem.
+
+
+Junellia o'donelli Moldenke, 1946
+
+119052670 | Human rhinovirus A11 |
+
+Rubus idaeus monst. obtusifolius (Willd.) Focke | Rubus idaeus
+
+Kerana var. cameroni |Kerana var
+
+A. alba
+A.alba
+
+Bangalaia viridis sbsp. distinctemaculata Lepesme & Breuning, 1956
+
+Clostridium sp. enrichment culture clone M4C16
+
+
+000913765 Rubus x gracilidens Sudre
+          Rubus gracilidens | 1
+
+
+Salix myrtilloides x starkeana ssp. starkeana 

metadata

@@ -1,137 +1,178 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: biodiversity
-version: !ruby/object:Gem::Version 
-  hash: 3
+version: !ruby/object:Gem::Version
+  version: 3.0.0
   prerelease: 
-  segments: 
-  - 1
-  - 0
-  - 10
-  version: 1.0.10
 platform: ruby
-authors: 
+authors:
 - Dmitry Mozzherin
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-01-25 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  version_requirements: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id001
+date: 2013-05-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :runtime
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
   name: treetop
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.4'
   type: :runtime
-- !ruby/object:Gem::Dependency 
-  version_requirements: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id002
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
   name: parallel
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.6'
+- !ruby/object:Gem::Dependency
+  name: unicode_utils
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.4'
   type: :runtime
-- !ruby/object:Gem::Dependency 
-  version_requirements: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id003
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: debugger
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.5'
+- !ruby/object:Gem::Dependency
   name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.8'
   type: :development
-- !ruby/object:Gem::Dependency 
-  version_requirements: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id004
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.8'
+- !ruby/object:Gem::Dependency
   name: treetop
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-- !ruby/object:Gem::Dependency 
-  version_requirements: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id005
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: parallel
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-- !ruby/object:Gem::Dependency 
-  version_requirements: &id006 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id006
-  prerelease: false
-  name: json
-  type: :runtime
-- !ruby/object:Gem::Dependency 
-  version_requirements: &id007 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id007
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Tools for biodiversity informatics
 email: dmozzherin@gmail.com
-executables: 
+executables:
 - nnparse
 - parserver
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE
-- README.rdoc
-files: 
+- README.md
+files:
 - .document
 - .rvmrc
+- .travis.yml
+- CHANGELOG
 - Gemfile
 - Gemfile.lock
 - LICENSE
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - bin/nnparse
@@ -158,36 +199,29 @@ files:
 - spec/spec_helper.rb
 homepage: http://github.com/GlobalNamesArchitecture/biodiversity
 licenses: []
-
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: -3993295929745438801
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: Parser of scientific names
 test_files: []
-

data/README.rdoc

@@ -1,99 +0,0 @@
-= Biodiversity
-
-Parses taxonomic scientific name and breaks it into semantic elements.
-
-== Installation
-
-To install gem you need RubyGems >= 1.3.6
-
-  $ sudo gem install biodiversity #for ruby 1.8.x
-  $ sudo gem install biodiversity19 #for ruby 1.9.x
-
-== Example usage
-
-=== As a command line script
-
-You can parse file with taxonomic names from command line. File should contain one scientific name per line
-
-  nnparser file_with_names
-
-=== As a socket server
-
-If you do not use ruby and need a fast access to the parser functionality  you can use a socket server
-
-  parserver
-
-options:
-
-  parserver --output=canonical
-
-to return a canonical form of the name string
-
-  parserver --output=canonical_with_rank
-
-the same as above, but infraspecies' rank is shown if available
-
-  parserver --port 5555
-
-run socket server on a different port
-
-Then you can access it via 4334 port using a socket client library of your programming language.  You can find socket client script example in the examples directory of the gem.
-
-If you want to check if socket server works for you:
-
-  #run server in one terminal
-  parserver
-
-  #in another terminal window type
-  telnet localhost 4334
-
-If you enter a line with a scientific name server will send you back parsed information in json format.
-
-To stop telnet client type any of 'end','exit','q', '.' (without quotes) instead of scientific name
-
-  $ telnet localhost 4334
-  Trying ::1...
-  Connected to localhost.
-  Escape character is '^]'.
-  Acacia abyssinica Hochst. ex Benth. ssp. calophylla Brenan
-  {"scientificName":{"canonical":"Acacia abyssinica calophylla","parsed":true,"parser_run":1,"verbatim":"Acacia abyssinica Hochst. ex Benth. ssp. calophylla Brenan\r\n","positions":{"0":["genus",6],"18":["author_word",25],"29":["author_word",35],"7":["species",17],"41":["infraspecies",51],"52":["author_word",58]},"hybrid":false,"normalized":"Acacia abyssinica Hochst. ex Benth. ssp. calophylla Brenan","details":[{"species":{"basionymAuthorTeam":{"exAuthorTeam":{"author":["Benth."],"authorTeam":"Benth."},"author":["Hochst."],"authorTeam":"Hochst."},"string":"abyssinica","authorship":"Hochst. ex Benth."},"infraspecies":[{"basionymAuthorTeam":{"author":["Brenan"],"authorTeam":"Brenan"},"string":"calophylla","rank":"ssp.","authorship":"Brenan"}],"genus":{"string":"Acacia"}}]}}
-
-
-=== As a library
-
-You can use it as a library
-
-  require 'biodiversity'
-
-  parser = ScientificNameParser.new
-
-  # to parse a scientific name into a ruby hash
-  parser.parse("Plantago major")
-
-  #to get json representation
-  parser.parse("Plantago").to_json
-  #or
-  parser.parse("Plantago")
-  parser.all_json
-
-  # to clean name up
-  parser.parse("             Plantago       major    ")[:scientificName][:normalized]
-
-  # to get only cleaned up latin part of the name
-  parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003")[:scientificName][:canonical]
-
-  # to get detailed information about elements of the name
-  parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003")[:scientificName][:details]
-
-  # to parse using several CPUs (4 seem to be optimal)
-  parser = ParallelParser.new # ParallelParser.new(4) will try to run 4 processes if hardware allows
-  array_of_names = ["Betula alba", "Homo sapiens"....]
-  parser.parse(array_of_names) # -> {"Betula alba" => {:scientificName...}, "Homo sapiens" => {:scientificName...}, ...}
-
-  parallel parser takes list of names and returns back a hash with names as keys and parsed data as values
-
-  # to resolve lsid and get back RDF file
-  LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")
-
-Copyright (c) 2009-2011 Marine Biological Laboratory. See LICENSE.txt for
-further details.