dwc-archive 0.7.6 → 0.7.7
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- data/Gemfile +5 -5
- data/Gemfile.lock +21 -17
- data/Rakefile +9 -9
- data/VERSION +1 -1
- data/lib/dwc-archive.rb +2 -12
- data/lib/dwc-archive/classification_normalizer.rb +3 -4
- data/lib/dwc-archive/generator.rb +1 -1
- data/lib/dwc-archive/generator_eml_xml.rb +1 -1
- data/lib/dwc-archive/generator_meta_xml.rb +1 -1
- data/lib/dwc-archive/ingester.rb +2 -7
- metadata +30 -30
data/Gemfile
CHANGED
@@ -9,10 +9,10 @@ source "http://rubygems.org"
|
|
9
9
|
gem "parsley-store", "~> 0.3.0"
|
10
10
|
|
11
11
|
group :development do
|
12
|
-
gem "rspec", "~> 2.
|
13
|
-
gem "nokogiri"
|
14
|
-
gem "cucumber", "
|
15
|
-
gem "bundler", "~> 1.0
|
12
|
+
gem "rspec", "~> 2.7.0"
|
13
|
+
gem "nokogiri", "~> 1.5.0"
|
14
|
+
gem "cucumber", "~> 1.1.3"
|
15
|
+
gem "bundler", "~> 1.0"
|
16
16
|
gem "jeweler", "~> 1.6.4"
|
17
|
-
gem "ruby-debug19"
|
17
|
+
gem "ruby-debug19", "~> 0.11.6"
|
18
18
|
end
|
data/Gemfile.lock
CHANGED
@@ -2,42 +2,46 @@ GEM
|
|
2
2
|
remote: http://rubygems.org/
|
3
3
|
specs:
|
4
4
|
archive-tar-minitar (0.5.2)
|
5
|
-
biodiversity19 (1.0.
|
5
|
+
biodiversity19 (1.0.9)
|
6
|
+
parallel
|
7
|
+
parallel
|
8
|
+
treetop
|
6
9
|
treetop
|
7
10
|
builder (3.0.0)
|
8
|
-
columnize (0.3.
|
9
|
-
cucumber (1.1.
|
11
|
+
columnize (0.3.5)
|
12
|
+
cucumber (1.1.3)
|
10
13
|
builder (>= 2.1.2)
|
11
14
|
diff-lcs (>= 1.1.2)
|
12
|
-
gherkin (~> 2.
|
15
|
+
gherkin (~> 2.6.7)
|
13
16
|
json (>= 1.4.6)
|
14
17
|
term-ansicolor (>= 1.0.6)
|
15
18
|
diff-lcs (1.1.3)
|
16
|
-
gherkin (2.
|
19
|
+
gherkin (2.6.8)
|
17
20
|
json (>= 1.4.6)
|
18
21
|
git (1.2.5)
|
19
22
|
jeweler (1.6.4)
|
20
23
|
bundler (~> 1.0)
|
21
24
|
git (>= 1.2.5)
|
22
25
|
rake
|
23
|
-
json (1.6.
|
26
|
+
json (1.6.3)
|
24
27
|
linecache19 (0.5.12)
|
25
28
|
ruby_core_source (>= 0.1.4)
|
26
29
|
nokogiri (1.5.0)
|
30
|
+
parallel (0.5.9)
|
27
31
|
parsley-store (0.3.0)
|
28
32
|
biodiversity19
|
29
33
|
redis
|
30
34
|
polyglot (0.3.3)
|
31
|
-
rake (0.9.2)
|
35
|
+
rake (0.9.2.2)
|
32
36
|
redis (2.2.2)
|
33
|
-
rspec (2.
|
34
|
-
rspec-core (~> 2.
|
35
|
-
rspec-expectations (~> 2.
|
36
|
-
rspec-mocks (~> 2.
|
37
|
-
rspec-core (2.
|
38
|
-
rspec-expectations (2.
|
37
|
+
rspec (2.7.0)
|
38
|
+
rspec-core (~> 2.7.0)
|
39
|
+
rspec-expectations (~> 2.7.0)
|
40
|
+
rspec-mocks (~> 2.7.0)
|
41
|
+
rspec-core (2.7.1)
|
42
|
+
rspec-expectations (2.7.0)
|
39
43
|
diff-lcs (~> 1.1.2)
|
40
|
-
rspec-mocks (2.
|
44
|
+
rspec-mocks (2.7.0)
|
41
45
|
ruby-debug-base19 (0.11.25)
|
42
46
|
columnize (>= 0.3.1)
|
43
47
|
linecache19 (>= 0.5.11)
|
@@ -57,10 +61,10 @@ PLATFORMS
|
|
57
61
|
ruby
|
58
62
|
|
59
63
|
DEPENDENCIES
|
60
|
-
bundler
|
64
|
+
bundler
|
61
65
|
cucumber
|
62
|
-
jeweler
|
66
|
+
jeweler
|
63
67
|
nokogiri
|
64
68
|
parsley-store (~> 0.3.0)
|
65
|
-
rspec
|
69
|
+
rspec
|
66
70
|
ruby-debug19
|
data/Rakefile
CHANGED
@@ -46,12 +46,12 @@ end
|
|
46
46
|
|
47
47
|
task :default => :spec
|
48
48
|
|
49
|
-
require 'rdoc/task'
|
50
|
-
Rake::RDocTask.new do |rdoc|
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
end
|
49
|
+
# require 'rdoc/task'
|
50
|
+
# Rake::RDocTask.new do |rdoc|
|
51
|
+
# version = File.exist?('VERSION') ? File.read('VERSION') : ""
|
52
|
+
#
|
53
|
+
# rdoc.rdoc_dir = 'rdoc'
|
54
|
+
# rdoc.title = "dwc-archive #{version}"
|
55
|
+
# rdoc.rdoc_files.include('README*')
|
56
|
+
# rdoc.rdoc_files.include('lib/**/*.rb')
|
57
|
+
# end
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.7.
|
1
|
+
0.7.7
|
data/lib/dwc-archive.rb
CHANGED
@@ -2,20 +2,10 @@
|
|
2
2
|
$:.unshift(File.dirname(__FILE__)) unless
|
3
3
|
$:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
|
4
4
|
R19 = RUBY_VERSION.split('.')[0..1].join('').to_i > 18
|
5
|
+
raise "IMPORTANT: dwc-archive gem requires ruby >= 1.9.1" unless R19
|
5
6
|
require 'fileutils'
|
6
7
|
require 'ostruct'
|
7
|
-
|
8
|
-
if R19
|
9
|
-
require 'csv'
|
10
|
-
else
|
11
|
-
raise "IMPORTANT: dwc-archive gem requires ruby >= 1.9.1"
|
12
|
-
require 'fastercsv'
|
13
|
-
CSV = FasterCSV
|
14
|
-
if (defined?(Rails) && Rails::VERSION::MAJOR >= 3 && Rails.env.test?)
|
15
|
-
$" << 'csv.rb'
|
16
|
-
end
|
17
|
-
end
|
18
|
-
|
8
|
+
require 'csv'
|
19
9
|
require 'logger'
|
20
10
|
require 'dwc-archive/xml_reader'
|
21
11
|
require 'dwc-archive/ingester'
|
@@ -67,7 +67,6 @@ class DarwinCore
|
|
67
67
|
private
|
68
68
|
|
69
69
|
def get_canonical_name(a_scientific_name)
|
70
|
-
a_scientific_name.force_encoding('utf-8')
|
71
70
|
if @with_canonical_names
|
72
71
|
canonical_name = @parser.parse(a_scientific_name, :canonical_only => true)
|
73
72
|
canonical_name.to_s.empty? ? a_scientific_name : canonical_name
|
@@ -102,10 +101,10 @@ class DarwinCore
|
|
102
101
|
def set_scientific_name(row, fields)
|
103
102
|
row[fields[:scientificname]] = 'N/A' unless row[fields[:scientificname]]
|
104
103
|
canonical_name = nil
|
105
|
-
scientific_name = row[fields[:scientificname]].strip
|
104
|
+
scientific_name = row[fields[:scientificname]].strip
|
106
105
|
if separate_canonical_and_authorship?(row, fields)
|
107
|
-
canonical_name = row[fields[:scientificname]].strip
|
108
|
-
scientific_name += " #{row[fields[:scientificnameauthorship]].strip
|
106
|
+
canonical_name = row[fields[:scientificname]].strip if @with_canonical_names
|
107
|
+
scientific_name += " #{row[fields[:scientificnameauthorship]].strip}"
|
109
108
|
else
|
110
109
|
canonical_name = get_canonical_name(row[fields[:scientificname]]) if @with_canonical_names
|
111
110
|
end
|
@@ -9,7 +9,7 @@ class DarwinCore
|
|
9
9
|
FileUtils.mkdir(@path)
|
10
10
|
@meta_xml_data = {:extensions => []}
|
11
11
|
@eml_xml_data = {:id => nil, :title => nil, :authors => [], :abstract => nil, :citation => nil, :url => nil}
|
12
|
-
@write =
|
12
|
+
@write = 'w:utf-8'
|
13
13
|
end
|
14
14
|
|
15
15
|
#TODO refactor!
|
data/lib/dwc-archive/ingester.rb
CHANGED
@@ -40,13 +40,8 @@ class DarwinCore
|
|
40
40
|
|
41
41
|
def process_csv_row(result, errors, row)
|
42
42
|
str = row.join('')
|
43
|
-
|
44
|
-
|
45
|
-
str.encoding.name == "UTF-8" && str.valid_encoding? ? result << row : errors << row
|
46
|
-
else
|
47
|
-
require File.join(File.dirname(__FILE__), 'utf_regex_ruby18')
|
48
|
-
UTF8RGX === str ? result << row : errors << row
|
49
|
-
end
|
43
|
+
str = str.force_encoding('utf-8')
|
44
|
+
str.encoding.name == "UTF-8" && str.valid_encoding? ? result << row.map { |f| f.nil? ? nil : f.force_encoding('utf-8') } : errors << row
|
50
45
|
end
|
51
46
|
|
52
47
|
def get_attributes(exception)
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: dwc-archive
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.7.
|
4
|
+
version: 0.7.7
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
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authors:
|
@@ -9,11 +9,11 @@ authors:
|
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2011-
|
12
|
+
date: 2011-12-02 00:00:00.000000000Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: parsley-store
|
16
|
-
requirement: &
|
16
|
+
requirement: &70157662627320 !ruby/object:Gem::Requirement
|
17
17
|
none: false
|
18
18
|
requirements:
|
19
19
|
- - ~>
|
@@ -21,54 +21,54 @@ dependencies:
|
|
21
21
|
version: 0.3.0
|
22
22
|
type: :runtime
|
23
23
|
prerelease: false
|
24
|
-
version_requirements: *
|
24
|
+
version_requirements: *70157662627320
|
25
25
|
- !ruby/object:Gem::Dependency
|
26
26
|
name: rspec
|
27
|
-
requirement: &
|
27
|
+
requirement: &70157662625740 !ruby/object:Gem::Requirement
|
28
28
|
none: false
|
29
29
|
requirements:
|
30
30
|
- - ~>
|
31
31
|
- !ruby/object:Gem::Version
|
32
|
-
version: 2.
|
32
|
+
version: 2.7.0
|
33
33
|
type: :development
|
34
34
|
prerelease: false
|
35
|
-
version_requirements: *
|
35
|
+
version_requirements: *70157662625740
|
36
36
|
- !ruby/object:Gem::Dependency
|
37
37
|
name: nokogiri
|
38
|
-
requirement: &
|
38
|
+
requirement: &70157662614720 !ruby/object:Gem::Requirement
|
39
39
|
none: false
|
40
40
|
requirements:
|
41
|
-
- -
|
41
|
+
- - ~>
|
42
42
|
- !ruby/object:Gem::Version
|
43
|
-
version:
|
43
|
+
version: 1.5.0
|
44
44
|
type: :development
|
45
45
|
prerelease: false
|
46
|
-
version_requirements: *
|
46
|
+
version_requirements: *70157662614720
|
47
47
|
- !ruby/object:Gem::Dependency
|
48
48
|
name: cucumber
|
49
|
-
requirement: &
|
49
|
+
requirement: &70157662612960 !ruby/object:Gem::Requirement
|
50
50
|
none: false
|
51
51
|
requirements:
|
52
|
-
- -
|
52
|
+
- - ~>
|
53
53
|
- !ruby/object:Gem::Version
|
54
|
-
version:
|
54
|
+
version: 1.1.3
|
55
55
|
type: :development
|
56
56
|
prerelease: false
|
57
|
-
version_requirements: *
|
57
|
+
version_requirements: *70157662612960
|
58
58
|
- !ruby/object:Gem::Dependency
|
59
59
|
name: bundler
|
60
|
-
requirement: &
|
60
|
+
requirement: &70157662610660 !ruby/object:Gem::Requirement
|
61
61
|
none: false
|
62
62
|
requirements:
|
63
63
|
- - ~>
|
64
64
|
- !ruby/object:Gem::Version
|
65
|
-
version: 1.0
|
65
|
+
version: '1.0'
|
66
66
|
type: :development
|
67
67
|
prerelease: false
|
68
|
-
version_requirements: *
|
68
|
+
version_requirements: *70157662610660
|
69
69
|
- !ruby/object:Gem::Dependency
|
70
70
|
name: jeweler
|
71
|
-
requirement: &
|
71
|
+
requirement: &70157662608200 !ruby/object:Gem::Requirement
|
72
72
|
none: false
|
73
73
|
requirements:
|
74
74
|
- - ~>
|
@@ -76,21 +76,21 @@ dependencies:
|
|
76
76
|
version: 1.6.4
|
77
77
|
type: :development
|
78
78
|
prerelease: false
|
79
|
-
version_requirements: *
|
79
|
+
version_requirements: *70157662608200
|
80
80
|
- !ruby/object:Gem::Dependency
|
81
81
|
name: ruby-debug19
|
82
|
-
requirement: &
|
82
|
+
requirement: &70157662604880 !ruby/object:Gem::Requirement
|
83
83
|
none: false
|
84
84
|
requirements:
|
85
|
-
- -
|
85
|
+
- - ~>
|
86
86
|
- !ruby/object:Gem::Version
|
87
|
-
version:
|
87
|
+
version: 0.11.6
|
88
88
|
type: :development
|
89
89
|
prerelease: false
|
90
|
-
version_requirements: *
|
90
|
+
version_requirements: *70157662604880
|
91
91
|
- !ruby/object:Gem::Dependency
|
92
92
|
name: parsley-store
|
93
|
-
requirement: &
|
93
|
+
requirement: &70157662602720 !ruby/object:Gem::Requirement
|
94
94
|
none: false
|
95
95
|
requirements:
|
96
96
|
- - ! '>='
|
@@ -98,10 +98,10 @@ dependencies:
|
|
98
98
|
version: 0.3.0
|
99
99
|
type: :runtime
|
100
100
|
prerelease: false
|
101
|
-
version_requirements: *
|
101
|
+
version_requirements: *70157662602720
|
102
102
|
- !ruby/object:Gem::Dependency
|
103
103
|
name: rspec
|
104
|
-
requirement: &
|
104
|
+
requirement: &70157662577620 !ruby/object:Gem::Requirement
|
105
105
|
none: false
|
106
106
|
requirements:
|
107
107
|
- - ! '>='
|
@@ -109,10 +109,10 @@ dependencies:
|
|
109
109
|
version: 1.2.9
|
110
110
|
type: :development
|
111
111
|
prerelease: false
|
112
|
-
version_requirements: *
|
112
|
+
version_requirements: *70157662577620
|
113
113
|
- !ruby/object:Gem::Dependency
|
114
114
|
name: cucumber
|
115
|
-
requirement: &
|
115
|
+
requirement: &70157662576480 !ruby/object:Gem::Requirement
|
116
116
|
none: false
|
117
117
|
requirements:
|
118
118
|
- - ! '>='
|
@@ -120,7 +120,7 @@ dependencies:
|
|
120
120
|
version: '0'
|
121
121
|
type: :development
|
122
122
|
prerelease: false
|
123
|
-
version_requirements: *
|
123
|
+
version_requirements: *70157662576480
|
124
124
|
description: Darwin Core Archive is the current standard exchange format for GLobal
|
125
125
|
Names Architecture modules. This gem makes it easy to incorporate files in Darwin
|
126
126
|
Core Archive format into a ruby project.
|