gn_crossmap 3.0.3 → 3.1.0
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- checksums.yaml +4 -4
- data/.rubocop.yml +1 -0
- data/.ruby-version +1 -0
- data/.travis.yml +1 -2
- data/CHANGELOG.md +6 -0
- data/Gemfile +2 -0
- data/README.md +6 -0
- data/Rakefile +2 -0
- data/exe/crossmap +6 -2
- data/gn_crossmap.gemspec +8 -8
- data/lib/gn_crossmap.rb +8 -4
- data/lib/gn_crossmap/collector.rb +2 -0
- data/lib/gn_crossmap/column_collector.rb +2 -0
- data/lib/gn_crossmap/errors.rb +2 -0
- data/lib/gn_crossmap/reader.rb +3 -1
- data/lib/gn_crossmap/resolver.rb +9 -5
- data/lib/gn_crossmap/result_processor.rb +41 -8
- data/lib/gn_crossmap/sci_name_collector.rb +2 -0
- data/lib/gn_crossmap/version.rb +3 -1
- data/lib/gn_crossmap/writer.rb +6 -2
- metadata +33 -32
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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|
1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
|
4
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-
data.tar.gz:
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3
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+
metadata.gz: 540a1ea4dd47918c8d98c6de7e38f0f6cc116798
|
4
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+
data.tar.gz: eca75610cb8974aced0dbed71a51c38c865c4a27
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5
5
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SHA512:
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6
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-
metadata.gz:
|
7
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-
data.tar.gz:
|
6
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+
metadata.gz: 4f008fac59680bac5c8160f8a5e3f8caf22b801b67be088145b0ef1d8ed3657fa50f72d36960efac54410f11f2853cdd6354a1bd2bc7535d87e30d84558ad45e
|
7
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+
data.tar.gz: ba229e5d5f0d954e9884a7bb31ace418eeb3c5131e77ebc70df945706d66990a042a8e73865ca925da5c16eb4dfd1ca021aba82a9e2ebed35447ce159990ff00
|
data/.rubocop.yml
CHANGED
data/.ruby-version
ADDED
@@ -0,0 +1 @@
|
|
1
|
+
2.4.1
|
data/.travis.yml
CHANGED
data/CHANGELOG.md
CHANGED
data/Gemfile
CHANGED
data/README.md
CHANGED
@@ -59,6 +59,9 @@ cat my_list.csv | crossmap -i - -o - > output
|
|
59
59
|
# to keep only taxonID (if given) from original input
|
60
60
|
# no original fields will be kept without taxonID
|
61
61
|
cat my_list.csv | crossmap -i my_list.csv -s
|
62
|
+
|
63
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+
# to show classification from the source
|
64
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+
cat my_list.csv | crossmap -i my_list.csv -w
|
62
65
|
```
|
63
66
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|
64
67
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### Usage as Ruby Library (API description)
|
@@ -97,6 +100,9 @@ instead of the headers supplied with the file
|
|
97
100
|
``resolver_url``
|
98
101
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: URL to globalnames' resolver. Default is ``http://resolver.globalnames.org``
|
99
102
|
|
103
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+
``with_classification``
|
104
|
+
: (boolean) if true, adds classification path to the output
|
105
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+
|
100
106
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#### `GnCrossmap.logger=`
|
101
107
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|
102
108
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Allows to set logger to a custom logger (default is `STDERR`)
|
data/Rakefile
CHANGED
data/exe/crossmap
CHANGED
@@ -1,11 +1,13 @@
|
|
1
1
|
#!/usr/bin/env ruby
|
2
|
+
# frozen_string_literal: true
|
3
|
+
|
2
4
|
require "trollop"
|
3
5
|
require "gn_crossmap"
|
4
6
|
|
5
|
-
puts "This program requires Ruby >= v. 2.1
|
7
|
+
puts "This program requires Ruby >= v. 2.4.1" if RUBY_VERSION < "2.4.1"
|
6
8
|
|
7
9
|
CATALOGUE_OF_LIFE = 1
|
8
|
-
OUTPUT = "output.csv"
|
10
|
+
OUTPUT = "output.csv"
|
9
11
|
opts = Trollop.options do
|
10
12
|
banner "Compares a list of scientific names to scientific names from a " \
|
11
13
|
"data source from Global Names Resolver\n\n " \
|
@@ -18,6 +20,8 @@ opts = Trollop.options do
|
|
18
20
|
default: CATALOGUE_OF_LIFE)
|
19
21
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opt(:skip_original, "If given, only 'taxonID' is shown " \
|
20
22
|
"from the original input", type: :boolean)
|
23
|
+
opt(:with_classification, "If given, returns classification path of " \
|
24
|
+
"matched names", type: :boolean)
|
21
25
|
end
|
22
26
|
|
23
27
|
Trollop.die :input, "must be set" if opts[:input].nil?
|
data/gn_crossmap.gemspec
CHANGED
@@ -1,4 +1,4 @@
|
|
1
|
-
#
|
1
|
+
# frozen_string_literal: true
|
2
2
|
|
3
3
|
lib = File.expand_path("../lib", __FILE__)
|
4
4
|
|
@@ -30,18 +30,18 @@ Gem::Specification.new do |gem|
|
|
30
30
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gem.executables = gem.files.grep(%r{^exe/}) { |f| File.basename(f) }
|
31
31
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gem.require_paths = ["lib"]
|
32
32
|
|
33
|
-
gem.add_dependency "trollop", "~> 2.1"
|
34
33
|
gem.add_dependency "biodiversity", "~> 3.1"
|
35
|
-
gem.add_dependency "rest-client", "~> 2.0"
|
36
|
-
gem.add_dependency "logger-colors", "~> 1.0"
|
37
34
|
gem.add_dependency "gn_uuid", "~> 0.5"
|
35
|
+
gem.add_dependency "logger-colors", "~> 1.0"
|
36
|
+
gem.add_dependency "rest-client", "~> 2.0"
|
37
|
+
gem.add_dependency "trollop", "~> 2.1"
|
38
38
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|
39
39
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gem.add_development_dependency "bundler", "~> 1.7"
|
40
|
-
gem.add_development_dependency "rake", "~> 11.0"
|
41
|
-
gem.add_development_dependency "rspec", "~> 3.2"
|
42
|
-
gem.add_development_dependency "rubocop", "~> 0.31"
|
43
|
-
gem.add_development_dependency "coveralls", "~> 0.8"
|
44
40
|
gem.add_development_dependency "byebug", "~> 9.0"
|
41
|
+
gem.add_development_dependency "coveralls", "~> 0.8"
|
42
|
+
gem.add_development_dependency "rake", "~> 12.0"
|
43
|
+
gem.add_development_dependency "rspec", "~> 3.2"
|
44
|
+
gem.add_development_dependency "rubocop", "~> 0.49"
|
45
45
|
end
|
46
46
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|
47
47
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# rubocop:enable Metrics/BlockLength:
|
data/lib/gn_crossmap.rb
CHANGED
@@ -1,3 +1,5 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
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+
|
1
3
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require "csv"
|
2
4
|
require "ostruct"
|
3
5
|
require "rest_client"
|
@@ -19,8 +21,8 @@ require "gn_crossmap/stats"
|
|
19
21
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|
20
22
|
# Namespace module for crossmapping checklists wth GN sources
|
21
23
|
module GnCrossmap
|
22
|
-
INPUT_MODE = "r:utf-8"
|
23
|
-
OUTPUT_MODE = "w:utf-8"
|
24
|
+
INPUT_MODE = "r:utf-8"
|
25
|
+
OUTPUT_MODE = "w:utf-8"
|
24
26
|
MATCH_TYPES = {
|
25
27
|
0 => "No match",
|
26
28
|
1 => "Exact string match",
|
@@ -65,11 +67,13 @@ module GnCrossmap
|
|
65
67
|
private
|
66
68
|
|
67
69
|
def create_resolver(writer, opts)
|
68
|
-
Resolver.new(writer, opts.data_source_id, opts.resolver_url,
|
70
|
+
Resolver.new(writer, opts.data_source_id, opts.resolver_url,
|
71
|
+
opts.stats, opts.with_classification)
|
69
72
|
end
|
70
73
|
|
71
74
|
def create_writer(reader, output_io, opts)
|
72
|
-
Writer.new(output_io, reader.original_fields,
|
75
|
+
Writer.new(output_io, reader.original_fields,
|
76
|
+
output_name(opts.output), opts.with_classification)
|
73
77
|
end
|
74
78
|
|
75
79
|
def create_reader(input_io, opts)
|
data/lib/gn_crossmap/errors.rb
CHANGED
data/lib/gn_crossmap/reader.rb
CHANGED
@@ -1,3 +1,5 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
1
3
|
module GnCrossmap
|
2
4
|
# Reads supplied csv file and creates ruby structure to compare
|
3
5
|
# with a Global Names Resolver source
|
@@ -99,7 +101,7 @@ module GnCrossmap
|
|
99
101
|
|
100
102
|
def taxon_id_header(hdrs)
|
101
103
|
hdrs.each do |h|
|
102
|
-
return [h] if h
|
104
|
+
return [h] if h && h.match?(/taxonid\s*$/i)
|
103
105
|
end
|
104
106
|
[]
|
105
107
|
end
|
data/lib/gn_crossmap/resolver.rb
CHANGED
@@ -1,12 +1,16 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
1
3
|
module GnCrossmap
|
2
4
|
# Sends data to GN Resolver and collects results
|
3
5
|
class Resolver
|
4
6
|
attr_reader :stats
|
5
7
|
|
6
|
-
def initialize(writer, data_source_id,
|
8
|
+
def initialize(writer, data_source_id,
|
9
|
+
resolver_url, stats, with_classification = false)
|
7
10
|
@stats = stats
|
8
11
|
@resolver_url = resolver_url
|
9
|
-
@processor = GnCrossmap::ResultProcessor.
|
12
|
+
@processor = GnCrossmap::ResultProcessor.
|
13
|
+
new(writer, @stats, with_classification)
|
10
14
|
@ds_id = data_source_id
|
11
15
|
@count = 0
|
12
16
|
@current_data = {}
|
@@ -57,12 +61,12 @@ module GnCrossmap
|
|
57
61
|
|
58
62
|
def collect_names(slice)
|
59
63
|
@current_data = {}
|
60
|
-
slice.each_with_object(
|
64
|
+
slice.each_with_object([]) do |row, str|
|
61
65
|
id = row[:id].strip
|
62
66
|
@current_data[id] = row[:original]
|
63
67
|
@processor.input[id] = { rank: row[:rank] }
|
64
|
-
str << "#{id}|#{row[:name]}
|
65
|
-
end
|
68
|
+
str << "#{id}|#{row[:name]}"
|
69
|
+
end.join("\n")
|
66
70
|
end
|
67
71
|
|
68
72
|
def remote_resolve(names)
|
@@ -1,9 +1,13 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
1
3
|
module GnCrossmap
|
2
4
|
# Processes data received from the GN Resolver
|
3
5
|
class ResultProcessor
|
4
6
|
attr_reader :input, :writer
|
5
7
|
|
6
|
-
def initialize(writer, stats)
|
8
|
+
def initialize(writer, stats, with_classification = false)
|
9
|
+
@with_classification = with_classification
|
10
|
+
@parser = ScientificNameParser.new
|
7
11
|
@stats = stats
|
8
12
|
@writer = writer
|
9
13
|
@input = {}
|
@@ -28,8 +32,8 @@ module GnCrossmap
|
|
28
32
|
@stats.stats[:resolved_records] += 1
|
29
33
|
res = @original_data[datum[:supplied_id]]
|
30
34
|
res += [GnCrossmap::MATCH_TYPES[0], datum[:supplied_name_string], nil,
|
31
|
-
|
32
|
-
nil, nil, nil]
|
35
|
+
datum[:supplied_canonical_form], nil,
|
36
|
+
@input[datum[:supplied_id]][:rank], nil, nil, nil, nil]
|
33
37
|
@writer.write(res)
|
34
38
|
end
|
35
39
|
|
@@ -50,13 +54,28 @@ module GnCrossmap
|
|
50
54
|
@original_data[datum[:supplied_id]] + new_data(datum, result)
|
51
55
|
end
|
52
56
|
|
57
|
+
# rubocop:disable Metrics/AbcSize
|
58
|
+
|
53
59
|
def new_data(datum, result)
|
54
60
|
synonym = result[:current_name_string] ? "synonym" : nil
|
55
|
-
[matched_type(result), datum[:supplied_name_string],
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
|
61
|
+
res = [matched_type(result), datum[:supplied_name_string],
|
62
|
+
result[:name_string], canonical(datum[:supplied_name_string]),
|
63
|
+
result[:canonical_form], @input[datum[:supplied_id]][:rank],
|
64
|
+
matched_rank(result), synonym,
|
65
|
+
result[:current_name_string] || result[:name_string],
|
66
|
+
result[:edit_distance], result[:score], result[:taxon_id]]
|
67
|
+
res << classification(result) if @with_classification
|
68
|
+
res
|
69
|
+
end
|
70
|
+
|
71
|
+
# rubocop:enable all
|
72
|
+
|
73
|
+
def canonical(name_string)
|
74
|
+
parsed = @parser.parse(name_string)[:scientificName]
|
75
|
+
parsed[:canonical].nil? || parsed[:hybrid] ? nil : parsed[:canonical]
|
76
|
+
rescue StandardError
|
77
|
+
@parser = ScientificNameParser.new
|
78
|
+
nil
|
60
79
|
end
|
61
80
|
|
62
81
|
def matched_rank(record)
|
@@ -66,5 +85,19 @@ module GnCrossmap
|
|
66
85
|
def matched_type(record)
|
67
86
|
GnCrossmap::MATCH_TYPES[record[:match_type]]
|
68
87
|
end
|
88
|
+
|
89
|
+
# rubocop:disable Metrics/AbcSize
|
90
|
+
|
91
|
+
def classification(result)
|
92
|
+
return nil if result[:classification_path].to_s.strip == ""
|
93
|
+
path = result[:classification_path].split("|")
|
94
|
+
ranks = result[:classification_path_ranks].split("|")
|
95
|
+
if path.size == ranks.size
|
96
|
+
path = path.zip(ranks).map { |e| "#{e[0]}(#{e[1]})" }
|
97
|
+
end
|
98
|
+
path.join(", ")
|
99
|
+
end
|
100
|
+
|
101
|
+
# rubocop:enable all
|
69
102
|
end
|
70
103
|
end
|
data/lib/gn_crossmap/version.rb
CHANGED
data/lib/gn_crossmap/writer.rb
CHANGED
@@ -1,9 +1,13 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
1
3
|
module GnCrossmap
|
2
4
|
# Saves output from GN Resolver to disk
|
3
5
|
class Writer
|
4
|
-
def initialize(output_io, original_fields, output_name
|
6
|
+
def initialize(output_io, original_fields, output_name,
|
7
|
+
with_classification = false)
|
5
8
|
@output_io = output_io
|
6
9
|
@output_fields = output_fields(original_fields)
|
10
|
+
@output_fields << :classification if with_classification
|
7
11
|
@output = CSV.new(@output_io, col_sep: "\t")
|
8
12
|
@output << @output_fields
|
9
13
|
@output_name = output_name
|
@@ -22,7 +26,7 @@ module GnCrossmap
|
|
22
26
|
private
|
23
27
|
|
24
28
|
def output_fields(original_fields)
|
25
|
-
original_fields + %i[matchedType inputName matchedName
|
29
|
+
original_fields + %i[matchedType inputName matchedName inputCanonicalForm
|
26
30
|
matchedCanonicalForm inputRank matchedRank
|
27
31
|
synonymStatus acceptedName matchedEditDistance
|
28
32
|
matchedScore matchTaxonID]
|
metadata
CHANGED
@@ -1,85 +1,85 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: gn_crossmap
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 3.0
|
4
|
+
version: 3.1.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Dmitry Mozzherin
|
8
8
|
autorequire:
|
9
9
|
bindir: exe
|
10
10
|
cert_chain: []
|
11
|
-
date: 2017-
|
11
|
+
date: 2017-08-08 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
|
-
name:
|
14
|
+
name: biodiversity
|
15
15
|
requirement: !ruby/object:Gem::Requirement
|
16
16
|
requirements:
|
17
17
|
- - "~>"
|
18
18
|
- !ruby/object:Gem::Version
|
19
|
-
version: '
|
19
|
+
version: '3.1'
|
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: '
|
26
|
+
version: '3.1'
|
27
27
|
- !ruby/object:Gem::Dependency
|
28
|
-
name:
|
28
|
+
name: gn_uuid
|
29
29
|
requirement: !ruby/object:Gem::Requirement
|
30
30
|
requirements:
|
31
31
|
- - "~>"
|
32
32
|
- !ruby/object:Gem::Version
|
33
|
-
version: '
|
33
|
+
version: '0.5'
|
34
34
|
type: :runtime
|
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: '
|
40
|
+
version: '0.5'
|
41
41
|
- !ruby/object:Gem::Dependency
|
42
|
-
name:
|
42
|
+
name: logger-colors
|
43
43
|
requirement: !ruby/object:Gem::Requirement
|
44
44
|
requirements:
|
45
45
|
- - "~>"
|
46
46
|
- !ruby/object:Gem::Version
|
47
|
-
version: '
|
47
|
+
version: '1.0'
|
48
48
|
type: :runtime
|
49
49
|
prerelease: false
|
50
50
|
version_requirements: !ruby/object:Gem::Requirement
|
51
51
|
requirements:
|
52
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- - "~>"
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- !ruby/object:Gem::Version
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version: '
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+
version: '1.0'
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- !ruby/object:Gem::Dependency
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name:
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+
name: rest-client
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '
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+
version: '2.0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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-
version: '
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+
version: '2.0'
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- !ruby/object:Gem::Dependency
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-
name:
|
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+
name: trollop
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
|
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- !ruby/object:Gem::Version
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-
version: '
|
75
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+
version: '2.1'
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type: :runtime
|
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prerelease: false
|
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
|
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- - "~>"
|
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- !ruby/object:Gem::Version
|
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-
version: '
|
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+
version: '2.1'
|
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- !ruby/object:Gem::Dependency
|
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name: bundler
|
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requirement: !ruby/object:Gem::Requirement
|
@@ -95,75 +95,75 @@ dependencies:
|
|
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- !ruby/object:Gem::Version
|
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version: '1.7'
|
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- !ruby/object:Gem::Dependency
|
98
|
-
name:
|
98
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+
name: byebug
|
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99
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requirement: !ruby/object:Gem::Requirement
|
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requirements:
|
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101
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- - "~>"
|
102
102
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- !ruby/object:Gem::Version
|
103
|
-
version: '
|
103
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+
version: '9.0'
|
104
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type: :development
|
105
105
|
prerelease: false
|
106
106
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version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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- - "~>"
|
109
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- !ruby/object:Gem::Version
|
110
|
-
version: '
|
110
|
+
version: '9.0'
|
111
111
|
- !ruby/object:Gem::Dependency
|
112
|
-
name:
|
112
|
+
name: coveralls
|
113
113
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requirement: !ruby/object:Gem::Requirement
|
114
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|
requirements:
|
115
115
|
- - "~>"
|
116
116
|
- !ruby/object:Gem::Version
|
117
|
-
version: '
|
117
|
+
version: '0.8'
|
118
118
|
type: :development
|
119
119
|
prerelease: false
|
120
120
|
version_requirements: !ruby/object:Gem::Requirement
|
121
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requirements:
|
122
122
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- - "~>"
|
123
123
|
- !ruby/object:Gem::Version
|
124
|
-
version: '
|
124
|
+
version: '0.8'
|
125
125
|
- !ruby/object:Gem::Dependency
|
126
|
-
name:
|
126
|
+
name: rake
|
127
127
|
requirement: !ruby/object:Gem::Requirement
|
128
128
|
requirements:
|
129
129
|
- - "~>"
|
130
130
|
- !ruby/object:Gem::Version
|
131
|
-
version: '0
|
131
|
+
version: '12.0'
|
132
132
|
type: :development
|
133
133
|
prerelease: false
|
134
134
|
version_requirements: !ruby/object:Gem::Requirement
|
135
135
|
requirements:
|
136
136
|
- - "~>"
|
137
137
|
- !ruby/object:Gem::Version
|
138
|
-
version: '0
|
138
|
+
version: '12.0'
|
139
139
|
- !ruby/object:Gem::Dependency
|
140
|
-
name:
|
140
|
+
name: rspec
|
141
141
|
requirement: !ruby/object:Gem::Requirement
|
142
142
|
requirements:
|
143
143
|
- - "~>"
|
144
144
|
- !ruby/object:Gem::Version
|
145
|
-
version: '
|
145
|
+
version: '3.2'
|
146
146
|
type: :development
|
147
147
|
prerelease: false
|
148
148
|
version_requirements: !ruby/object:Gem::Requirement
|
149
149
|
requirements:
|
150
150
|
- - "~>"
|
151
151
|
- !ruby/object:Gem::Version
|
152
|
-
version: '
|
152
|
+
version: '3.2'
|
153
153
|
- !ruby/object:Gem::Dependency
|
154
|
-
name:
|
154
|
+
name: rubocop
|
155
155
|
requirement: !ruby/object:Gem::Requirement
|
156
156
|
requirements:
|
157
157
|
- - "~>"
|
158
158
|
- !ruby/object:Gem::Version
|
159
|
-
version: '
|
159
|
+
version: '0.49'
|
160
160
|
type: :development
|
161
161
|
prerelease: false
|
162
162
|
version_requirements: !ruby/object:Gem::Requirement
|
163
163
|
requirements:
|
164
164
|
- - "~>"
|
165
165
|
- !ruby/object:Gem::Version
|
166
|
-
version: '
|
166
|
+
version: '0.49'
|
167
167
|
description: Gem uses a checklist in a comma-separated format as an input, and returns
|
168
168
|
back a new comma-separated list crossmapping the scientific names to one of the
|
169
169
|
data sources from http://resolver.globalnames.org
|
@@ -177,6 +177,7 @@ files:
|
|
177
177
|
- ".gitignore"
|
178
178
|
- ".rspec"
|
179
179
|
- ".rubocop.yml"
|
180
|
+
- ".ruby-version"
|
180
181
|
- ".travis.yml"
|
181
182
|
- CHANGELOG.md
|
182
183
|
- Gemfile
|