biodiversity 1.0.0 → 1.0.1

data/README.rdoc

@@ -23,11 +23,31 @@ If you do not use ruby and need a fast access to the parser functionality  you c
 
   parserver
 
-Then you can access it via 4334 port using a socket client library of your programming language. If you want to check if socket server works for you try:
-  
+options:
+
+  parserver --output=canonical
+
+to return a canonical form of the name string
+
+  parserver --output=canonical_with_rank
+
+the same as above, but infracpecies' rank is shown if available
+
+  praserver --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. 
+
+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
 
@@ -37,33 +57,34 @@ To stop telnet client type any of 'end','exit','q', '.' (without quotes) instead
   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] 
-  
+  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 resolve lsid and get back RDF file
   LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")
 

data/VERSION

@@ -1 +1 @@
-1.0.0
+1.0.1

data/bin/parserver

@@ -11,6 +11,7 @@ OPTIONS = {
   :port => DEFAULT_PORT
 }
 
+options = {}
 ARGV.options do |opts|
   script_name = File.basename($0)
   opts.banner = "Usage: ruby #{script_name} [options]"
@@ -22,13 +23,13 @@ ARGV.options do |opts|
     json - parsed results in json
     canonical - canonical version
     canonical_with_rank - canonical with rank",
-          "Default: json") { |OPTIONS[:output]| }
+          "Default: json") { |output| options[:output] = output }
 
   opts.separator ""
 
   opts.on("-p", "--port=port", String,
           "Specifies the port number",
-          "Default: #{DEFAULT_PORT}") { |OPTIONS[:port]| }
+          "Default: #{DEFAULT_PORT}") { |port| options[:port] = port }
 
   opts.separator ""
 
@@ -38,8 +39,8 @@ ARGV.options do |opts|
   opts.parse!
 end
 
-OPTIONS[:output] = "json" unless ['canonical', 'canonical_with_rank'].include?(OPTIONS[:output])
-OPTIONS[:port] = (OPTIONS[:port].to_i > 0 ? OPTIONS[:port].to_i : DEFAULT_PORT)
+OPTIONS[:output] = options[:output] if ['canonical', 'canonical_with_rank'].include?(options[:output])
+OPTIONS[:port] = options[:port].to_i if options[:port].to_i > 0
 
 def parser_error(name_string)
   {:scientificName => {:parsed => false, :verbatim => name_string,  :error => 'Parser error'}}

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: biodiversity
 version: !ruby/object:Gem::Version 
-  hash: 23
+  hash: 21
   prerelease: false
   segments: 
   - 1
   - 0
-  - 0
-  version: 1.0.0
+  - 1
+  version: 1.0.1
 platform: ruby
 authors: 
 - Dmitry Mozzherin