biodiversity 4.1.0 → 5.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: f6b81ed3f5b9a62fa8e4a084b21672ad86718424a4db5435269cbc4563e04d83
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+  data.tar.gz: 29106bdb8e3f74060c4e891779484bb76759b1d81a66a8676e5fef043e324df8
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+  metadata.gz: 4e4c8d955e6ac7219f5c11f9d26c51600f3c6609496390a3fbee03654704ef68376a0a297e9d5d49ea2c2df03a3b68b8b954b51942e22f38eb8243b676696c0e
+  data.tar.gz: 3bf85048cbe1a8e7fc79a6614dab6812818665a3bb998dbe78010b51adf5d2582df2dee884e79555339a3a9c8219ddf33a98deb2a877ca195baf7031909b3015

data/.rubocop.yml

@@ -1,4 +1,7 @@
 AllCops:
+  TargetRubyVersion: 2.6
+  NewCops: disable
+  SuggestExtensions: false
   Exclude:
     - .bundle/**/*
     - bundle_bin/**/*

data/.ruby-version

@@ -1 +1 @@
-2.6.6
+3.0.0

data/.travis.yml

@@ -1,6 +1,7 @@
 rvm:
-  - 2.5
   - 2.6
+  - 2.7
+  - 3.0
 before_install: "gem update bundler"
 branches:
   only:

data/CHANGELOG

@@ -1,3 +1,11 @@
+5.1.2 -- upgrade to gnparser v1.0.2
+
+5.1.1 -- simplified signature of methods
+
+5.1.0 -- changed sinature of methods
+
+5.0.0 -- changed GNparser to v 1.0.0
+
 4.0.3 -- fix memory leak in parse_ary method
 
 4.0.2 -- add MS Windows libraries

data/LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2008-2018 Dmitry Mozzherin
+Copyright (c) 2008-2020 Dmitry Mozzherin
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.md

@@ -129,7 +129,7 @@ Contributors: [Patrick Leary][pleary], [Hernán Lucas Pereira][hernan]
 
 
 
-Copyright (c) 2008-2019 Dmitry Mozzherin. See [LICENSE][license]
+Copyright (c) 2008-2020 Dmitry Mozzherin. See [LICENSE][license]
 for further details.
 
 [gem_svg]: https://badge.fury.io/rb/biodiversity.svg

data/biodiversity.gemspec

@@ -5,6 +5,7 @@ $LOAD_PATH.push File.expand_path('lib', __dir__)
 require 'biodiversity/version'
 
 Gem::Specification.new do |gem|
+  gem.required_ruby_version = '>= 2.6'
   gem.name          = 'biodiversity'
   gem.version       = Biodiversity::VERSION
   gem.homepage      = 'https://github.com/GlobalNamesArchitecture/biodiversity'
@@ -17,11 +18,11 @@ Gem::Specification.new do |gem|
   gem.files         = `git ls-files`.split("\n")
   gem.require_paths = ['lib']
 
-  gem.add_runtime_dependency 'ffi', '~> 1.11'
+  gem.add_runtime_dependency 'ffi', '~> 1.14'
 
-  gem.add_development_dependency 'bundler', '~> 2.0'
-  gem.add_development_dependency 'byebug', '~> 11.0'
+  gem.add_development_dependency 'bundler', '~> 2.2'
+  gem.add_development_dependency 'byebug', '~> 11.1'
   gem.add_development_dependency 'rake', '~> 13.0'
-  gem.add_development_dependency 'rspec', '~> 3.9'
-  gem.add_development_dependency 'rubocop', '~> 0.76'
+  gem.add_development_dependency 'rspec', '~> 3.10'
+  gem.add_development_dependency 'rubocop', '~> 1.8'
 end

data/clib/linux/libgnparser.h

@@ -1,6 +1,6 @@
 /* Code generated by cmd/cgo; DO NOT EDIT. */
 
-/* package gitlab.com/gogna/gnparser/binding */
+/* package github.com/gnames/gnparser/binding */
 
 
 #line 1 "cgo-builtin-export-prolog"
@@ -22,7 +22,6 @@ typedef struct { const char *p; ptrdiff_t n; } _GoString_;
 #line 3 "main.go"
 
 	#include "stdlib.h"
-	#include "callback_bridge.h"
 
 #line 1 "cgo-generated-wrapper"
 
@@ -75,20 +74,23 @@ extern "C" {
 #endif
 
 
-// ParseToString function takes a name-string, desired format, and parses
-// the name-string to either JSON, or pipe-separated values, depending on
-// the desired format. Format can take values of 'simple', 'compact', 'pretty'.
-// NOTE: Read callback type as "void (*callback)(char *parsed)"
+// ParseToString function takes a name-string, desired format, a withDetails
+// flag as 0|1 integer. It parses the name-string to either JSON, or a CSV
+// string, depending on the desired format. Format argument can take values of
+// 'csv', 'compact', 'pretty'. If withDetails argument is 0, additional
+// parsed details are ommited, if it is 1 -- they are included.
+// true.
+extern char* ParseToString(char* name, char* f, int details);
 
-extern void ParseToString(char* p0, char* p1, void* p2);
+// FreeMemory takes a string pointer and frees its memory.
+extern void FreeMemory(char* p);
 
-// ParseAryToStrings function takes an array of names, parsing format and a
-// reference to an output: an empty array of strings to return the the data
-// back. It populates the output array with raw strings of either JSON or
-// pipe-separated parsed values (depending on a given format). Format can take
-// values of 'simple', 'compact', or 'pretty'.
-
-extern void ParseAryToStrings(char** p0, int p1, char* p2, void* p3);
+// ParseAryToString function takes an array of names, parsing format, and a
+// withDetails flag as 0|1 integer.  Parsed outputs are sent as a string in
+// either CSV or JSON format.  Format argument can take values of 'csv',
+// 'compact', or 'pretty'. For withDetails argument 0 means false, 1 means
+// true.
+extern char* ParseAryToString(char** in, int length, char* f, int details);
 
 #ifdef __cplusplus
 }

data/clib/mac/libgnparser.h

@@ -1,6 +1,6 @@
 /* Code generated by cmd/cgo; DO NOT EDIT. */
 
-/* package gitlab.com/gogna/gnparser/binding */
+/* package github.com/gnames/gnparser/binding */
 
 
 #line 1 "cgo-builtin-export-prolog"
@@ -22,7 +22,6 @@ typedef struct { const char *p; ptrdiff_t n; } _GoString_;
 #line 3 "main.go"
 
 	#include "stdlib.h"
-	#include "callback_bridge.h"
 
 #line 1 "cgo-generated-wrapper"
 
@@ -75,20 +74,23 @@ extern "C" {
 #endif
 
 
-// ParseToString function takes a name-string, desired format, and parses
-// the name-string to either JSON, or pipe-separated values, depending on
-// the desired format. Format can take values of 'simple', 'compact', 'pretty'.
-// NOTE: Read callback type as "void (*callback)(char *parsed)"
+// ParseToString function takes a name-string, desired format, a withDetails
+// flag as 0|1 integer. It parses the name-string to either JSON, or a CSV
+// string, depending on the desired format. Format argument can take values of
+// 'csv', 'compact', 'pretty'. If withDetails argument is 0, additional
+// parsed details are ommited, if it is 1 -- they are included.
+// true.
+extern char* ParseToString(char* name, char* f, int details);
 
-extern void ParseToString(char* p0, char* p1, void* p2);
+// FreeMemory takes a string pointer and frees its memory.
+extern void FreeMemory(char* p);
 
-// ParseAryToStrings function takes an array of names, parsing format and a
-// reference to an output: an empty array of strings to return the the data
-// back. It populates the output array with raw strings of either JSON or
-// pipe-separated parsed values (depending on a given format). Format can take
-// values of 'simple', 'compact', or 'pretty'.
-
-extern void ParseAryToStrings(char** p0, int p1, char* p2, void* p3);
+// ParseAryToString function takes an array of names, parsing format, and a
+// withDetails flag as 0|1 integer.  Parsed outputs are sent as a string in
+// either CSV or JSON format.  Format argument can take values of 'csv',
+// 'compact', or 'pretty'. For withDetails argument 0 means false, 1 means
+// true.
+extern char* ParseAryToString(char** in, int length, char* f, int details);
 
 #ifdef __cplusplus
 }

data/clib/win/libgnparser.h

@@ -1,6 +1,6 @@
 /* Code generated by cmd/cgo; DO NOT EDIT. */
 
-/* package gitlab.com/gogna/gnparser/binding */
+/* package github.com/gnames/gnparser/binding */
 
 
 #line 1 "cgo-builtin-export-prolog"
@@ -22,7 +22,6 @@ typedef struct { const char *p; ptrdiff_t n; } _GoString_;
 #line 3 "main.go"
 
 	#include "stdlib.h"
-	#include "callback_bridge.h"
 
 #line 1 "cgo-generated-wrapper"
 
@@ -75,20 +74,23 @@ extern "C" {
 #endif
 
 
-// ParseToString function takes a name-string, desired format, and parses
-// the name-string to either JSON, or pipe-separated values, depending on
-// the desired format. Format can take values of 'simple', 'compact', 'pretty'.
-// NOTE: Read callback type as "void (*callback)(char *parsed)"
+// ParseToString function takes a name-string, desired format, a withDetails
+// flag as 0|1 integer. It parses the name-string to either JSON, or a CSV
+// string, depending on the desired format. Format argument can take values of
+// 'csv', 'compact', 'pretty'. If withDetails argument is 0, additional
+// parsed details are ommited, if it is 1 -- they are included.
+// true.
+extern char* ParseToString(char* name, char* f, int details);
 
-extern void ParseToString(char* p0, char* p1, void* p2);
+// FreeMemory takes a string pointer and frees its memory.
+extern void FreeMemory(char* p);
 
-// ParseAryToStrings function takes an array of names, parsing format and a
-// reference to an output: an empty array of strings to return the the data
-// back. It populates the output array with raw strings of either JSON or
-// pipe-separated parsed values (depending on a given format). Format can take
-// values of 'simple', 'compact', or 'pretty'.
-
-extern void ParseAryToStrings(char** p0, int p1, char* p2, void* p3);
+// ParseAryToString function takes an array of names, parsing format, and a
+// withDetails flag as 0|1 integer.  Parsed outputs are sent as a string in
+// either CSV or JSON format.  Format argument can take values of 'csv',
+// 'compact', or 'pretty'. For withDetails argument 0 means false, 1 means
+// true.
+extern char* ParseAryToString(char** in, int length, char* f, int details);
 
 #ifdef __cplusplus
 }

data/lib/biodiversity/parser.rb

@@ -28,55 +28,64 @@ module Biodiversity
     callback(:parser_callback, %i[string], :void)
 
     attach_function(:parse_go, :ParseToString,
-                    %i[string string parser_callback], :void)
-    attach_function(:parse_ary_go, :ParseAryToStrings,
-                    %i[pointer int string parser_callback], :void)
+                    %i[string string int], :strptr)
+    attach_function(:parse_ary_go, :ParseAryToString,
+                    %i[pointer int string int], :strptr)
+    attach_function(:free_mem, :FreeMemory, %i[pointer], :void)
 
-    def self.parse(name, simple = false)
+    def self.parse(name, simple: false)
       format = simple ? 'csv' : 'compact'
+      with_details = simple ? 0 : 1
 
-      parsed = nil
-      callback = FFI::Function.new(:void, [:string]) { |str| parsed = str }
-      parse_go(name, format, callback)
+      parsed, ptr = parse_go(name, format, with_details)
+      free_mem(ptr)
       output(parsed, simple)
     end
 
-    def self.parse_ary(ary, simple = false)
+    def self.parse_ary(ary, simple: false)
       format = simple ? 'csv' : 'compact'
-      in_ptr = FFI::MemoryPointer.new(:pointer, ary.length)
+      with_details = simple ? 0 : 1
 
+      in_ptr = FFI::MemoryPointer.new(:pointer, ary.length)
       in_ptr.write_array_of_pointer(
         ary.map { |s| FFI::MemoryPointer.from_string(s) }
       )
 
-      out_ary = []
-      callback = FFI::Function.new(:void, [:string]) do |str|
-        out_ary << output(str, simple)
+      parsed, ptr = parse_ary_go(in_ptr, ary.length, format, with_details)
+      free_mem(ptr)
+      if simple
+        CSV.new(parsed).map do |row|
+          csv_row(row)
+        end
+      else
+        JSON.parse(parsed, symbolize_names: true)
       end
-      parse_ary_go(in_ptr, ary.length, format, callback)
-      out_ary
     end
 
     def self.output(parsed, simple)
       if simple
         csv = CSV.new(parsed)
-        parsed = csv.read[0]
-        {
-          id: parsed[0],
-          verbatim: parsed[1],
-          cardinality: parsed[2],
-          canonicalName: {
-            full: parsed[3],
-            simple: parsed[4],
-            stem: parsed[5]
-          },
-          authorship: parsed[6],
-          year: parsed[7],
-          quality: parsed[8]
-        }
+        row = csv.readlines[0]
+        csv_row(row)
       else
         JSON.parse(parsed, symbolize_names: true)
       end
     end
+
+    def self.csv_row(row)
+      {
+        id: row[0],
+        verbatim: row[1],
+        cardinality: row[2],
+        canonical: {
+          stem: row[3],
+          simple: row[4],
+          full: row[5]
+        },
+        authorship: row[6],
+        year: row[7],
+        quality: row[8]
+      }
+    end
   end
 end

data/lib/biodiversity/version.rb

@@ -2,7 +2,7 @@
 
 # Biodiversity module provides a namespace for scientific name parser.
 module Biodiversity
-  VERSION = '4.1.0'
+  VERSION = '5.1.2'
 
   def self.version
     VERSION

data/spec/lib/parser_spec.rb

@@ -5,20 +5,21 @@
 describe Biodiversity::Parser do
   describe('parse') do
     it 'parses name in simple format' do
-      parsed = subject.parse('Homo sapiens Linn.', true)
-      expect(parsed[:canonicalName][:simple]).to eq 'Homo sapiens'
+      parsed = subject.parse('Homo sapiens Linn.', simple: true)
+      expect(parsed[:canonical][:simple]).to eq 'Homo sapiens'
       expect(parsed[:normalized]).to be_nil
     end
 
     it 'parsed name in full format' do
       parsed = subject.parse('Homo sapiens  Linn.')
-      expect(parsed[:canonicalName][:simple]).to eq 'Homo sapiens'
+      expect(parsed[:canonical][:simple]).to eq 'Homo sapiens'
       expect(parsed[:normalized]).to eq 'Homo sapiens Linn.'
+      expect(parsed[:words].size).to eq 3
     end
 
     it 'gets quality and year correctly in simple form' do
-      parsed = subject.parse('Homo sapiens Linn. 1758', true)
-      expect(parsed[:canonicalName][:simple]).to eq 'Homo sapiens'
+      parsed = subject.parse('Homo sapiens Linn. 1758', simple: true)
+      expect(parsed[:canonical][:simple]).to eq 'Homo sapiens'
       expect(parsed[:year]).to eq '1758'
       expect(parsed[:quality]).to eq '1'
       expect(parsed[:normalized]).to be_nil
@@ -27,20 +28,26 @@ describe Biodiversity::Parser do
 
   describe('parse_ary') do
     it 'parses names in simple format' do
-      parsed = subject.parse_ary(['Homo sapiens Linn.', 'Pardosa moesta'], true)
-      expect(parsed[0][:canonicalName][:simple]).to eq 'Homo sapiens'
-      expect(parsed[1][:canonicalName][:simple]).to eq 'Pardosa moesta'
+      parsed = subject.parse_ary(
+        ['Homo sapiens Linn.', 'Pardosa moesta'],
+        simple: true
+      )
+      expect(parsed[0][:canonical][:simple]).to eq 'Homo sapiens'
       expect(parsed[0][:normalized]).to be_nil
+
+      expect(parsed[1][:canonical][:simple]).to eq 'Pardosa moesta'
     end
 
     it 'parsed name in full format' do
       parsed = subject.parse_ary(
         ['Homo sapiens  Linn.', 'Tobacco Mosaic Virus']
       )
-      expect(parsed[0][:canonicalName][:simple]).to eq 'Homo sapiens'
+      expect(parsed[0][:canonical][:simple]).to eq 'Homo sapiens'
       expect(parsed[0][:normalized]).to eq 'Homo sapiens Linn.'
+      expect(parsed[0][:words].size).to eq 3
       expect(parsed[1][:parsed]).to be false
       expect(parsed[1][:virus]).to be true
+      expect(parsed[1][:words]).to be_nil
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: biodiversity
 version: !ruby/object:Gem::Version
-  version: 4.1.0
+  version: 5.1.2
 platform: ruby
 authors:
 - Dmitry Mozzherin
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-05-13 00:00:00.000000000 Z
+date: 2021-01-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -16,42 +16,42 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.11'
+        version: '1.14'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.11'
+        version: '1.14'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: '2.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: '2.2'
 - !ruby/object:Gem::Dependency
   name: byebug
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '11.0'
+        version: '11.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '11.0'
+        version: '11.1'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -72,28 +72,28 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.9'
+        version: '3.10'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.9'
+        version: '3.10'
 - !ruby/object:Gem::Dependency
   name: rubocop
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.76'
+        version: '1.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.76'
+        version: '1.8'
 description: Parsing tool for biodiversity informatics
 email: dmozzherin@gmail.com
 executables: []
@@ -111,13 +111,10 @@ files:
 - README.md
 - Rakefile
 - biodiversity.gemspec
-- clib/linux/callback_bridge.h
 - clib/linux/libgnparser.h
 - clib/linux/libgnparser.so
-- clib/mac/callback_bridge.h
 - clib/mac/libgnparser.h
 - clib/mac/libgnparser.so
-- clib/win/callback_bridge.h
 - clib/win/libgnparser.h
 - clib/win/libgnparser.so
 - lib/biodiversity.rb
@@ -130,7 +127,7 @@ homepage: https://github.com/GlobalNamesArchitecture/biodiversity
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -138,15 +135,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: '2.6'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
-signing_key: 
+rubygems_version: 3.2.6
+signing_key:
 specification_version: 4
 summary: Parser of scientific names
 test_files: []

data/clib/linux/callback_bridge.h

@@ -1,3 +0,0 @@
-typedef void Callback(char *parsed);
-
-void callback_bridge(void *callback, char *parsed);

data/clib/mac/callback_bridge.h

@@ -1,3 +0,0 @@
-typedef void Callback(char *parsed);
-
-void callback_bridge(void *callback, char *parsed);

data/clib/win/callback_bridge.h

@@ -1,3 +0,0 @@
-typedef void Callback(char *parsed);
-
-void callback_bridge(void *callback, char *parsed);