Replaced Biodiversity gem with local lib calling gnparser tool

Dockerfile

@@ -29,7 +29,9 @@ RUN apt-get update && \
       nodejs \
       redis-server libhiredis-dev && \
       apt clean && \ 
-      rm -rf /var/lip/abpt/lists/* /tmp/* /var/tmp/*
+      rm -rf /var/lip/abpt/lists/* /tmp/* /var/tmp/* && \
+      wget https://gitlab.com/gogna/gnparser/uploads/643872fc2c63d9218e5612c5f545c511/gnparser-v0.13.0-linux.tar.gz && \
+      tar xf gnparser-v0.13.0-linux.tar.gz -C /usr/local/bin
 
 RUN locale-gen en_US.UTF-8
 

Dockerfile.development

@@ -26,7 +26,10 @@ RUN apt-get update && \
                        cmake \
                        nodejs && \
                        apt clean && \
-                       rm -rf /var/lip/abpt/lists/* /tmp/* /var/tmp/*
+                       rm -rf /var/lip/abpt/lists/* /tmp/* /var/tmp/* && \
+                       wget https://gitlab.com/gogna/gnparser/uploads/643872fc2c63d9218e5612c5f545c511/gnparser-v0.13.0-linux.tar.gz && \
+                       tar xf gnparser-v0.13.0-linux.tar.gz -C /usr/local/bin
+
 #
 # Install ruby
 # Source: https://github.com/drecom/docker-ubuntu-ruby/blob/2.4.4/Dockerfile

Gemfile

@@ -92,7 +92,7 @@ gem 'rgb'
 gem 'taxonifi', '0.4.0'
 gem 'sqed', '0.5.8'
 gem 'dwc-archive', '~> 1.0.1'
-gem 'biodiversity', '~> 4.0', '>= 4.0.2'
+#gem 'biodiversity', '~> 4.0', '>= 4.0.2'
 gem 'ruby-units', '~> 2.3.0', require: 'ruby_units/namespaced'
 
 # Minor Utils/helpers

Gemfile.lock

@@ -93,8 +93,6 @@ GEM
     bindex (0.8.1)
     binding_of_caller (0.8.0)
       debug_inspector (>= 0.0.1)
-    biodiversity (4.0.2)
-      ffi (~> 1.11)
     brakeman (4.7.2)
     builder (3.2.4)
     byebug (11.1.1)
@@ -538,7 +536,6 @@ DEPENDENCIES
   better_errors (~> 2.4)
   bibtex-ruby (~> 5.1.1)
   binding_of_caller
-  biodiversity (~> 4.0, >= 4.0.2)
   brakeman (~> 4.6, >= 4.6.1)
   bundler (~> 2.0)
   byebug (~> 11.1)

lib/biodiversity.rb

@@ -0,0 +1,60 @@
+module Biodiversity
+  module Parser
+
+    def self.parse(name, simple = false)
+      parsed = simple ? parse_go_simple(name) : parse_go_compact(name)
+      output(parsed, simple)
+    end
+
+    def self.output(parsed, simple)
+      if simple
+        parsed = parsed.split('|')
+        {
+          id: parsed[0],
+          verbatim: parsed[1],
+          canonicalName: {
+            full: parsed[2],
+            simple: parsed[3],
+            stem: parsed[4]
+          },
+          authorship: parsed[5],
+          year: parsed[6],
+          quality: parsed[7]
+        }
+      else
+        JSON.parse(parsed, symbolize_names: true)
+      end
+    end
+
+    private
+
+    def self.start_gnparser
+      io = {}
+
+      ['compact', 'simple'].each do |format|
+        stdin, stdout, stderr = Open3.popen3("gnparser --format #{format}")
+        io[format.to_sym] = { stdin: stdin, stdout: stdout, stderr: stderr }
+      end
+      io
+    end
+
+    @@semaphore = Mutex.new
+    @@io = start_gnparser
+
+    def self.parse_go(name, format)
+      @@semaphore.synchronize do
+        @@io[format][:stdin].puts(name)
+        @@io[format][:stdout].gets
+      end
+    end
+
+    def self.parse_go_compact(name)
+      parse_go(name, :compact)
+    end
+
+    def self.parse_go_simple(name)
+      parse_go(name, :simple)
+    end
+
+  end
+end