biodiversity 4.1.0 → 5.0.0

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@@ -1,4 +1,7 @@
1
1
  AllCops:
2
+ TargetRubyVersion: 2.6
3
+ NewCops: disable
4
+ SuggestExtensions: false
2
5
  Exclude:
3
6
  - .bundle/**/*
4
7
  - bundle_bin/**/*
@@ -1 +1 @@
1
- 2.6.6
1
+ 3.0.0
@@ -1,6 +1,7 @@
1
1
  rvm:
2
- - 2.5
3
2
  - 2.6
3
+ - 2.7
4
+ - 3.0
4
5
  before_install: "gem update bundler"
5
6
  branches:
6
7
  only:
data/CHANGELOG CHANGED
@@ -1,3 +1,5 @@
1
+ 5.0.0 -- changed GNparser to v 1.0.0
2
+
1
3
  4.0.3 -- fix memory leak in parse_ary method
2
4
 
3
5
  4.0.2 -- add MS Windows libraries
data/LICENSE CHANGED
@@ -1,6 +1,6 @@
1
1
  The MIT License (MIT)
2
2
 
3
- Copyright (c) 2008-2018 Dmitry Mozzherin
3
+ Copyright (c) 2008-2020 Dmitry Mozzherin
4
4
 
5
5
  Permission is hereby granted, free of charge, to any person obtaining
6
6
  a copy of this software and associated documentation files (the
data/README.md CHANGED
@@ -129,7 +129,7 @@ Contributors: [Patrick Leary][pleary], [Hernán Lucas Pereira][hernan]
129
129
 
130
130
 
131
131
 
132
- Copyright (c) 2008-2019 Dmitry Mozzherin. See [LICENSE][license]
132
+ Copyright (c) 2008-2020 Dmitry Mozzherin. See [LICENSE][license]
133
133
  for further details.
134
134
 
135
135
  [gem_svg]: https://badge.fury.io/rb/biodiversity.svg
@@ -5,6 +5,7 @@ $LOAD_PATH.push File.expand_path('lib', __dir__)
5
5
  require 'biodiversity/version'
6
6
 
7
7
  Gem::Specification.new do |gem|
8
+ gem.required_ruby_version = '>= 2.6'
8
9
  gem.name = 'biodiversity'
9
10
  gem.version = Biodiversity::VERSION
10
11
  gem.homepage = 'https://github.com/GlobalNamesArchitecture/biodiversity'
@@ -17,11 +18,11 @@ Gem::Specification.new do |gem|
17
18
  gem.files = `git ls-files`.split("\n")
18
19
  gem.require_paths = ['lib']
19
20
 
20
- gem.add_runtime_dependency 'ffi', '~> 1.11'
21
+ gem.add_runtime_dependency 'ffi', '~> 1.14'
21
22
 
22
- gem.add_development_dependency 'bundler', '~> 2.0'
23
- gem.add_development_dependency 'byebug', '~> 11.0'
23
+ gem.add_development_dependency 'bundler', '~> 2.2'
24
+ gem.add_development_dependency 'byebug', '~> 11.1'
24
25
  gem.add_development_dependency 'rake', '~> 13.0'
25
- gem.add_development_dependency 'rspec', '~> 3.9'
26
- gem.add_development_dependency 'rubocop', '~> 0.76'
26
+ gem.add_development_dependency 'rspec', '~> 3.10'
27
+ gem.add_development_dependency 'rubocop', '~> 1.8'
27
28
  end
@@ -1,6 +1,6 @@
1
1
  /* Code generated by cmd/cgo; DO NOT EDIT. */
2
2
 
3
- /* package gitlab.com/gogna/gnparser/binding */
3
+ /* package github.com/gnames/gnparser/binding */
4
4
 
5
5
 
6
6
  #line 1 "cgo-builtin-export-prolog"
@@ -22,7 +22,6 @@ typedef struct { const char *p; ptrdiff_t n; } _GoString_;
22
22
  #line 3 "main.go"
23
23
 
24
24
  #include "stdlib.h"
25
- #include "callback_bridge.h"
26
25
 
27
26
  #line 1 "cgo-generated-wrapper"
28
27
 
@@ -75,20 +74,23 @@ extern "C" {
75
74
  #endif
76
75
 
77
76
 
78
- // ParseToString function takes a name-string, desired format, and parses
79
- // the name-string to either JSON, or pipe-separated values, depending on
80
- // the desired format. Format can take values of 'simple', 'compact', 'pretty'.
81
- // NOTE: Read callback type as "void (*callback)(char *parsed)"
77
+ // ParseToString function takes a name-string, desired format, a withDetails
78
+ // flag as 0|1 integer. It parses the name-string to either JSON, or a CSV
79
+ // string, depending on the desired format. Format argument can take values of
80
+ // 'csv', 'compact', 'pretty'. If withDetails argument is 0, additional
81
+ // parsed details are ommited, if it is 1 -- they are included.
82
+ // true.
83
+ extern char* ParseToString(char* name, char* f, int details);
82
84
 
83
- extern void ParseToString(char* p0, char* p1, void* p2);
85
+ // FreeMemory takes a string pointer and frees its memory.
86
+ extern void FreeMemory(char* p);
84
87
 
85
- // ParseAryToStrings function takes an array of names, parsing format and a
86
- // reference to an output: an empty array of strings to return the the data
87
- // back. It populates the output array with raw strings of either JSON or
88
- // pipe-separated parsed values (depending on a given format). Format can take
89
- // values of 'simple', 'compact', or 'pretty'.
90
-
91
- extern void ParseAryToStrings(char** p0, int p1, char* p2, void* p3);
88
+ // ParseAryToString function takes an array of names, parsing format, and a
89
+ // withDetails flag as 0|1 integer. Parsed outputs are sent as a string in
90
+ // either CSV or JSON format. Format argument can take values of 'csv',
91
+ // 'compact', or 'pretty'. For withDetails argument 0 means false, 1 means
92
+ // true.
93
+ extern char* ParseAryToString(char** in, int length, char* f, int details);
92
94
 
93
95
  #ifdef __cplusplus
94
96
  }
Binary file
@@ -1,6 +1,6 @@
1
1
  /* Code generated by cmd/cgo; DO NOT EDIT. */
2
2
 
3
- /* package gitlab.com/gogna/gnparser/binding */
3
+ /* package github.com/gnames/gnparser/binding */
4
4
 
5
5
 
6
6
  #line 1 "cgo-builtin-export-prolog"
@@ -22,7 +22,6 @@ typedef struct { const char *p; ptrdiff_t n; } _GoString_;
22
22
  #line 3 "main.go"
23
23
 
24
24
  #include "stdlib.h"
25
- #include "callback_bridge.h"
26
25
 
27
26
  #line 1 "cgo-generated-wrapper"
28
27
 
@@ -75,20 +74,26 @@ extern "C" {
75
74
  #endif
76
75
 
77
76
 
78
- // ParseToString function takes a name-string, desired format, and parses
79
- // the name-string to either JSON, or pipe-separated values, depending on
80
- // the desired format. Format can take values of 'simple', 'compact', 'pretty'.
81
- // NOTE: Read callback type as "void (*callback)(char *parsed)"
77
+ // ParseToString function takes a name-string, desired format, a withDetails
78
+ // flag as 0|1 integer. It parses the name-string to either JSON, or a CSV
79
+ // string, depending on the desired format. Format argument can take values of
80
+ // 'csv', 'compact', 'pretty'. If withDetails argument is 0, additional
81
+ // parsed details are ommited, if it is 1 -- they are included.
82
+ // true.
82
83
 
83
- extern void ParseToString(char* p0, char* p1, void* p2);
84
+ extern char* ParseToString(char* p0, char* p1, int p2);
84
85
 
85
- // ParseAryToStrings function takes an array of names, parsing format and a
86
- // reference to an output: an empty array of strings to return the the data
87
- // back. It populates the output array with raw strings of either JSON or
88
- // pipe-separated parsed values (depending on a given format). Format can take
89
- // values of 'simple', 'compact', or 'pretty'.
86
+ // FreeMemory takes a string pointer and frees its memory.
90
87
 
91
- extern void ParseAryToStrings(char** p0, int p1, char* p2, void* p3);
88
+ extern void FreeMemory(char* p0);
89
+
90
+ // ParseAryToString function takes an array of names, parsing format, and a
91
+ // withDetails flag as 0|1 integer. Parsed outputs are sent as a string in
92
+ // either CSV or JSON format. Format argument can take values of 'csv',
93
+ // 'compact', or 'pretty'. For withDetails argument 0 means false, 1 means
94
+ // true.
95
+
96
+ extern char* ParseAryToString(char** p0, int p1, char* p2, int p3);
92
97
 
93
98
  #ifdef __cplusplus
94
99
  }
Binary file
@@ -1,6 +1,6 @@
1
1
  /* Code generated by cmd/cgo; DO NOT EDIT. */
2
2
 
3
- /* package gitlab.com/gogna/gnparser/binding */
3
+ /* package github.com/gnames/gnparser/binding */
4
4
 
5
5
 
6
6
  #line 1 "cgo-builtin-export-prolog"
@@ -22,7 +22,6 @@ typedef struct { const char *p; ptrdiff_t n; } _GoString_;
22
22
  #line 3 "main.go"
23
23
 
24
24
  #include "stdlib.h"
25
- #include "callback_bridge.h"
26
25
 
27
26
  #line 1 "cgo-generated-wrapper"
28
27
 
@@ -75,20 +74,23 @@ extern "C" {
75
74
  #endif
76
75
 
77
76
 
78
- // ParseToString function takes a name-string, desired format, and parses
79
- // the name-string to either JSON, or pipe-separated values, depending on
80
- // the desired format. Format can take values of 'simple', 'compact', 'pretty'.
81
- // NOTE: Read callback type as "void (*callback)(char *parsed)"
77
+ // ParseToString function takes a name-string, desired format, a withDetails
78
+ // flag as 0|1 integer. It parses the name-string to either JSON, or a CSV
79
+ // string, depending on the desired format. Format argument can take values of
80
+ // 'csv', 'compact', 'pretty'. If withDetails argument is 0, additional
81
+ // parsed details are ommited, if it is 1 -- they are included.
82
+ // true.
83
+ extern char* ParseToString(char* name, char* f, int details);
82
84
 
83
- extern void ParseToString(char* p0, char* p1, void* p2);
85
+ // FreeMemory takes a string pointer and frees its memory.
86
+ extern void FreeMemory(char* p);
84
87
 
85
- // ParseAryToStrings function takes an array of names, parsing format and a
86
- // reference to an output: an empty array of strings to return the the data
87
- // back. It populates the output array with raw strings of either JSON or
88
- // pipe-separated parsed values (depending on a given format). Format can take
89
- // values of 'simple', 'compact', or 'pretty'.
90
-
91
- extern void ParseAryToStrings(char** p0, int p1, char* p2, void* p3);
88
+ // ParseAryToString function takes an array of names, parsing format, and a
89
+ // withDetails flag as 0|1 integer. Parsed outputs are sent as a string in
90
+ // either CSV or JSON format. Format argument can take values of 'csv',
91
+ // 'compact', or 'pretty'. For withDetails argument 0 means false, 1 means
92
+ // true.
93
+ extern char* ParseAryToString(char** in, int length, char* f, int details);
92
94
 
93
95
  #ifdef __cplusplus
94
96
  }
Binary file
@@ -28,20 +28,20 @@ module Biodiversity
28
28
  callback(:parser_callback, %i[string], :void)
29
29
 
30
30
  attach_function(:parse_go, :ParseToString,
31
- %i[string string parser_callback], :void)
32
- attach_function(:parse_ary_go, :ParseAryToStrings,
33
- %i[pointer int string parser_callback], :void)
31
+ %i[string string int], :strptr)
32
+ attach_function(:parse_ary_go, :ParseAryToString,
33
+ %i[pointer int string int], :strptr)
34
+ attach_function(:free_mem, :FreeMemory, %i[pointer], :void)
34
35
 
35
- def self.parse(name, simple = false)
36
+ def self.parse(name, simple: false)
36
37
  format = simple ? 'csv' : 'compact'
37
38
 
38
- parsed = nil
39
- callback = FFI::Function.new(:void, [:string]) { |str| parsed = str }
40
- parse_go(name, format, callback)
39
+ parsed, ptr = parse_go(name, format, 0)
40
+ free_mem(ptr)
41
41
  output(parsed, simple)
42
42
  end
43
43
 
44
- def self.parse_ary(ary, simple = false)
44
+ def self.parse_ary(ary, simple: false)
45
45
  format = simple ? 'csv' : 'compact'
46
46
  in_ptr = FFI::MemoryPointer.new(:pointer, ary.length)
47
47
 
@@ -49,34 +49,41 @@ module Biodiversity
49
49
  ary.map { |s| FFI::MemoryPointer.from_string(s) }
50
50
  )
51
51
 
52
- out_ary = []
53
- callback = FFI::Function.new(:void, [:string]) do |str|
54
- out_ary << output(str, simple)
52
+ parsed, ptr = parse_ary_go(in_ptr, ary.length, format, 0)
53
+ free_mem(ptr)
54
+ if simple
55
+ CSV.new(parsed).map do |row|
56
+ csv_row(row)
57
+ end
58
+ else
59
+ JSON.parse(parsed, symbolize_names: true)
55
60
  end
56
- parse_ary_go(in_ptr, ary.length, format, callback)
57
- out_ary
58
61
  end
59
62
 
60
63
  def self.output(parsed, simple)
61
64
  if simple
62
65
  csv = CSV.new(parsed)
63
- parsed = csv.read[0]
64
- {
65
- id: parsed[0],
66
- verbatim: parsed[1],
67
- cardinality: parsed[2],
68
- canonicalName: {
69
- full: parsed[3],
70
- simple: parsed[4],
71
- stem: parsed[5]
72
- },
73
- authorship: parsed[6],
74
- year: parsed[7],
75
- quality: parsed[8]
76
- }
66
+ row = csv.readlines[0]
67
+ csv_row(row)
77
68
  else
78
69
  JSON.parse(parsed, symbolize_names: true)
79
70
  end
80
71
  end
72
+
73
+ def self.csv_row(row)
74
+ {
75
+ id: row[0],
76
+ verbatim: row[1],
77
+ cardinality: row[2],
78
+ canonical: {
79
+ stem: row[3],
80
+ simple: row[4],
81
+ full: row[5]
82
+ },
83
+ authorship: row[6],
84
+ year: row[7],
85
+ quality: row[8]
86
+ }
87
+ end
81
88
  end
82
89
  end
@@ -2,7 +2,7 @@
2
2
 
3
3
  # Biodiversity module provides a namespace for scientific name parser.
4
4
  module Biodiversity
5
- VERSION = '4.1.0'
5
+ VERSION = '5.0.0'
6
6
 
7
7
  def self.version
8
8
  VERSION
@@ -5,20 +5,20 @@
5
5
  describe Biodiversity::Parser do
6
6
  describe('parse') do
7
7
  it 'parses name in simple format' do
8
- parsed = subject.parse('Homo sapiens Linn.', true)
9
- expect(parsed[:canonicalName][:simple]).to eq 'Homo sapiens'
8
+ parsed = subject.parse('Homo sapiens Linn.', simple: true)
9
+ expect(parsed[:canonical][:simple]).to eq 'Homo sapiens'
10
10
  expect(parsed[:normalized]).to be_nil
11
11
  end
12
12
 
13
13
  it 'parsed name in full format' do
14
14
  parsed = subject.parse('Homo sapiens Linn.')
15
- expect(parsed[:canonicalName][:simple]).to eq 'Homo sapiens'
15
+ expect(parsed[:canonical][:simple]).to eq 'Homo sapiens'
16
16
  expect(parsed[:normalized]).to eq 'Homo sapiens Linn.'
17
17
  end
18
18
 
19
19
  it 'gets quality and year correctly in simple form' do
20
- parsed = subject.parse('Homo sapiens Linn. 1758', true)
21
- expect(parsed[:canonicalName][:simple]).to eq 'Homo sapiens'
20
+ parsed = subject.parse('Homo sapiens Linn. 1758', simple: true)
21
+ expect(parsed[:canonical][:simple]).to eq 'Homo sapiens'
22
22
  expect(parsed[:year]).to eq '1758'
23
23
  expect(parsed[:quality]).to eq '1'
24
24
  expect(parsed[:normalized]).to be_nil
@@ -27,9 +27,12 @@ describe Biodiversity::Parser do
27
27
 
28
28
  describe('parse_ary') do
29
29
  it 'parses names in simple format' do
30
- parsed = subject.parse_ary(['Homo sapiens Linn.', 'Pardosa moesta'], true)
31
- expect(parsed[0][:canonicalName][:simple]).to eq 'Homo sapiens'
32
- expect(parsed[1][:canonicalName][:simple]).to eq 'Pardosa moesta'
30
+ parsed = subject.parse_ary(
31
+ ['Homo sapiens Linn.', 'Pardosa moesta'],
32
+ simple: true
33
+ )
34
+ expect(parsed[0][:canonical][:simple]).to eq 'Homo sapiens'
35
+ expect(parsed[1][:canonical][:simple]).to eq 'Pardosa moesta'
33
36
  expect(parsed[0][:normalized]).to be_nil
34
37
  end
35
38
 
@@ -37,7 +40,7 @@ describe Biodiversity::Parser do
37
40
  parsed = subject.parse_ary(
38
41
  ['Homo sapiens Linn.', 'Tobacco Mosaic Virus']
39
42
  )
40
- expect(parsed[0][:canonicalName][:simple]).to eq 'Homo sapiens'
43
+ expect(parsed[0][:canonical][:simple]).to eq 'Homo sapiens'
41
44
  expect(parsed[0][:normalized]).to eq 'Homo sapiens Linn.'
42
45
  expect(parsed[1][:parsed]).to be false
43
46
  expect(parsed[1][:virus]).to be true
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: biodiversity
3
3
  version: !ruby/object:Gem::Version
4
- version: 4.1.0
4
+ version: 5.0.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Dmitry Mozzherin
8
- autorequire:
8
+ autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2020-05-13 00:00:00.000000000 Z
11
+ date: 2021-01-19 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: ffi
@@ -16,42 +16,42 @@ dependencies:
16
16
  requirements:
17
17
  - - "~>"
18
18
  - !ruby/object:Gem::Version
19
- version: '1.11'
19
+ version: '1.14'
20
20
  type: :runtime
21
21
  prerelease: false
22
22
  version_requirements: !ruby/object:Gem::Requirement
23
23
  requirements:
24
24
  - - "~>"
25
25
  - !ruby/object:Gem::Version
26
- version: '1.11'
26
+ version: '1.14'
27
27
  - !ruby/object:Gem::Dependency
28
28
  name: bundler
29
29
  requirement: !ruby/object:Gem::Requirement
30
30
  requirements:
31
31
  - - "~>"
32
32
  - !ruby/object:Gem::Version
33
- version: '2.0'
33
+ version: '2.2'
34
34
  type: :development
35
35
  prerelease: false
36
36
  version_requirements: !ruby/object:Gem::Requirement
37
37
  requirements:
38
38
  - - "~>"
39
39
  - !ruby/object:Gem::Version
40
- version: '2.0'
40
+ version: '2.2'
41
41
  - !ruby/object:Gem::Dependency
42
42
  name: byebug
43
43
  requirement: !ruby/object:Gem::Requirement
44
44
  requirements:
45
45
  - - "~>"
46
46
  - !ruby/object:Gem::Version
47
- version: '11.0'
47
+ version: '11.1'
48
48
  type: :development
49
49
  prerelease: false
50
50
  version_requirements: !ruby/object:Gem::Requirement
51
51
  requirements:
52
52
  - - "~>"
53
53
  - !ruby/object:Gem::Version
54
- version: '11.0'
54
+ version: '11.1'
55
55
  - !ruby/object:Gem::Dependency
56
56
  name: rake
57
57
  requirement: !ruby/object:Gem::Requirement
@@ -72,28 +72,28 @@ dependencies:
72
72
  requirements:
73
73
  - - "~>"
74
74
  - !ruby/object:Gem::Version
75
- version: '3.9'
75
+ version: '3.10'
76
76
  type: :development
77
77
  prerelease: false
78
78
  version_requirements: !ruby/object:Gem::Requirement
79
79
  requirements:
80
80
  - - "~>"
81
81
  - !ruby/object:Gem::Version
82
- version: '3.9'
82
+ version: '3.10'
83
83
  - !ruby/object:Gem::Dependency
84
84
  name: rubocop
85
85
  requirement: !ruby/object:Gem::Requirement
86
86
  requirements:
87
87
  - - "~>"
88
88
  - !ruby/object:Gem::Version
89
- version: '0.76'
89
+ version: '1.8'
90
90
  type: :development
91
91
  prerelease: false
92
92
  version_requirements: !ruby/object:Gem::Requirement
93
93
  requirements:
94
94
  - - "~>"
95
95
  - !ruby/object:Gem::Version
96
- version: '0.76'
96
+ version: '1.8'
97
97
  description: Parsing tool for biodiversity informatics
98
98
  email: dmozzherin@gmail.com
99
99
  executables: []
@@ -111,13 +111,10 @@ files:
111
111
  - README.md
112
112
  - Rakefile
113
113
  - biodiversity.gemspec
114
- - clib/linux/callback_bridge.h
115
114
  - clib/linux/libgnparser.h
116
115
  - clib/linux/libgnparser.so
117
- - clib/mac/callback_bridge.h
118
116
  - clib/mac/libgnparser.h
119
117
  - clib/mac/libgnparser.so
120
- - clib/win/callback_bridge.h
121
118
  - clib/win/libgnparser.h
122
119
  - clib/win/libgnparser.so
123
120
  - lib/biodiversity.rb
@@ -130,7 +127,7 @@ homepage: https://github.com/GlobalNamesArchitecture/biodiversity
130
127
  licenses:
131
128
  - MIT
132
129
  metadata: {}
133
- post_install_message:
130
+ post_install_message:
134
131
  rdoc_options: []
135
132
  require_paths:
136
133
  - lib
@@ -138,15 +135,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
138
135
  requirements:
139
136
  - - ">="
140
137
  - !ruby/object:Gem::Version
141
- version: '0'
138
+ version: '2.6'
142
139
  required_rubygems_version: !ruby/object:Gem::Requirement
143
140
  requirements:
144
141
  - - ">="
145
142
  - !ruby/object:Gem::Version
146
143
  version: '0'
147
144
  requirements: []
148
- rubygems_version: 3.0.3
149
- signing_key:
145
+ rubygems_version: 3.2.3
146
+ signing_key:
150
147
  specification_version: 4
151
148
  summary: Parser of scientific names
152
149
  test_files: []
@@ -1,3 +0,0 @@
1
- typedef void Callback(char *parsed);
2
-
3
- void callback_bridge(void *callback, char *parsed);
@@ -1,3 +0,0 @@
1
- typedef void Callback(char *parsed);
2
-
3
- void callback_bridge(void *callback, char *parsed);
@@ -1,3 +0,0 @@
1
- typedef void Callback(char *parsed);
2
-
3
- void callback_bridge(void *callback, char *parsed);