research_metadata 0.1.0
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +7 -0
- data/.gitignore +18 -0
- data/CHANGELOG.md +10 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +51 -0
- data/Rakefile +1 -0
- data/lib/research_metadata/transformer/dataset.rb +233 -0
- data/lib/research_metadata/version.rb +5 -0
- data/lib/research_metadata.rb +4 -0
- data/research_metadata.gemspec +23 -0
- data/spec/spec_helper.rb +4 -0
- data/spec/transformer/dataset_spec.rb +39 -0
- metadata +87 -0
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
|
|
1
|
+
---
|
2
|
+
SHA1:
|
3
|
+
metadata.gz: 44b8ec73389b2fb8f75aa96fca6213b0fbe7fb1e
|
4
|
+
data.tar.gz: 5dcdf92b3c6437da322181ae345b418e37e0312c
|
5
|
+
SHA512:
|
6
|
+
metadata.gz: 95c845a1a08d31f1d63085382598be3011230a400bfd76ce31c5604c0e03bc1678b425974a996e0b014e319d4ec10f42c7895738b406c8ab0e9158b42832a58f
|
7
|
+
data.tar.gz: def6a7e3e6078b1974ed06f8156908316acfdb6a58bdc9164bf49c42bcc8c5598c46bfe335a28652a611f60d23b5e3e12210c4704de126cb8675eab248c7d24b
|
data/.gitignore
ADDED
data/CHANGELOG.md
ADDED
@@ -0,0 +1,10 @@
|
|
1
|
+
# Change Log
|
2
|
+
All notable changes to this project will be documented in this file.
|
3
|
+
This project adheres to [Semantic Versioning](http://semver.org/).
|
4
|
+
|
5
|
+
## Unreleased
|
6
|
+
|
7
|
+
## 0.1.0 - 2017-02-03
|
8
|
+
### Added
|
9
|
+
- Working product supports datasets.
|
10
|
+
- RSpec tests for datasets.
|
data/Gemfile
ADDED
data/LICENSE.txt
ADDED
@@ -0,0 +1,22 @@
|
|
1
|
+
Copyright (c) 2017 Adrian Albin-Clark
|
2
|
+
|
3
|
+
MIT License
|
4
|
+
|
5
|
+
Permission is hereby granted, free of charge, to any person obtaining
|
6
|
+
a copy of this software and associated documentation files (the
|
7
|
+
"Software"), to deal in the Software without restriction, including
|
8
|
+
without limitation the rights to use, copy, modify, merge, publish,
|
9
|
+
distribute, sublicense, and/or sell copies of the Software, and to
|
10
|
+
permit persons to whom the Software is furnished to do so, subject to
|
11
|
+
the following conditions:
|
12
|
+
|
13
|
+
The above copyright notice and this permission notice shall be
|
14
|
+
included in all copies or substantial portions of the Software.
|
15
|
+
|
16
|
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
17
|
+
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
|
18
|
+
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
19
|
+
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
|
20
|
+
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
|
21
|
+
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
|
22
|
+
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
data/README.md
ADDED
@@ -0,0 +1,51 @@
|
|
1
|
+
# ResearchMetadata [![Gem Version](https://badge.fury.io/rb/research_metadata.svg)](https://badge.fury.io/rb/research_metadata)
|
2
|
+
|
3
|
+
Extraction and Transformation for Loading by DataCite's API.
|
4
|
+
|
5
|
+
## Installation
|
6
|
+
|
7
|
+
Add this line to your application's Gemfile:
|
8
|
+
|
9
|
+
gem 'research_metadata'
|
10
|
+
|
11
|
+
And then execute:
|
12
|
+
|
13
|
+
$ bundle
|
14
|
+
|
15
|
+
Or install it yourself as:
|
16
|
+
|
17
|
+
$ gem install research_metadata
|
18
|
+
|
19
|
+
## Usage
|
20
|
+
|
21
|
+
### Configuration
|
22
|
+
Configure Purée.
|
23
|
+
|
24
|
+
```ruby
|
25
|
+
Puree.base_url = ENV['PURE_BASE_URL']
|
26
|
+
Puree.username = ENV['PURE_USERNAME']
|
27
|
+
Puree.password = ENV['PURE_PASSWORD']
|
28
|
+
Puree.basic_auth = true
|
29
|
+
```
|
30
|
+
|
31
|
+
### Transformation
|
32
|
+
|
33
|
+
Create a metadata transformer for a Pure dataset...
|
34
|
+
|
35
|
+
```ruby
|
36
|
+
transformer = ResearchMetadata::Transformer::Dataset.new
|
37
|
+
```
|
38
|
+
|
39
|
+
...and give it a Pure identifier and a DOI...
|
40
|
+
|
41
|
+
```ruby
|
42
|
+
metadata = transformer.transform uuid: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx',
|
43
|
+
doi: '10.1234/foo/bar/1'
|
44
|
+
```
|
45
|
+
|
46
|
+
...to get DataCite-ready metadata.
|
47
|
+
|
48
|
+
## Documentation
|
49
|
+
[API in YARD](http://www.rubydoc.info/gems/research_metadata)
|
50
|
+
|
51
|
+
[Detailed usage in GitBook](https://aalbinclark.gitbooks.io/research_metadata)
|
data/Rakefile
ADDED
@@ -0,0 +1 @@
|
|
1
|
+
require "bundler/gem_tasks"
|
@@ -0,0 +1,233 @@
|
|
1
|
+
# Extraction (from Pure) and Transformation for Loading by DataCite's API
|
2
|
+
#
|
3
|
+
module ResearchMetadata
|
4
|
+
|
5
|
+
# Transformer
|
6
|
+
#
|
7
|
+
module Transformer
|
8
|
+
|
9
|
+
# Dataset
|
10
|
+
#
|
11
|
+
class Dataset
|
12
|
+
|
13
|
+
# Dataset transformation
|
14
|
+
#
|
15
|
+
# @param id [String]
|
16
|
+
# @param uuid [String]
|
17
|
+
# @param doi [String]
|
18
|
+
# @return [String]
|
19
|
+
def transform(id: nil, uuid: nil, doi: nil)
|
20
|
+
@dataset = extract uuid: uuid, id: id
|
21
|
+
raise 'No metadata to transform' if @dataset.metadata.empty?
|
22
|
+
person_o = person
|
23
|
+
file_o = file
|
24
|
+
resource = ::Datacite::Mapping::Resource.new(
|
25
|
+
identifier: identifier(doi),
|
26
|
+
creators: person_o['creator'],
|
27
|
+
titles: [ title ],
|
28
|
+
publisher: publisher,
|
29
|
+
publication_year: publication_year,
|
30
|
+
subjects: subjects,
|
31
|
+
contributors: person_o['contributor'],
|
32
|
+
dates: dates,
|
33
|
+
language: language,
|
34
|
+
resource_type: resource_type,
|
35
|
+
related_identifiers: related_identifiers,
|
36
|
+
sizes: file_o.map { |i| i['size'] },
|
37
|
+
formats: file_o.map { |i| i['mime'] },
|
38
|
+
rights_list: file_o.map { |i| i['license']['name'] },
|
39
|
+
descriptions: description,
|
40
|
+
geo_locations: spatial
|
41
|
+
)
|
42
|
+
resource.write_xml
|
43
|
+
end
|
44
|
+
|
45
|
+
private
|
46
|
+
|
47
|
+
def affiliations(person)
|
48
|
+
person.affiliation.map { |i| i['name'] }
|
49
|
+
end
|
50
|
+
|
51
|
+
def dates
|
52
|
+
a = []
|
53
|
+
available = ::Datacite::Mapping::Date.new value: Puree::Date.iso(@dataset.available),
|
54
|
+
type: ::Datacite::Mapping::DateType::AVAILABLE
|
55
|
+
a << available
|
56
|
+
|
57
|
+
temporal = @dataset.temporal
|
58
|
+
temporal_range = ''
|
59
|
+
if !temporal['start']['year'].empty?
|
60
|
+
temporal_range << Puree::Date.iso(temporal['start'])
|
61
|
+
if !temporal['end']['year'].empty?
|
62
|
+
temporal_range << '/'
|
63
|
+
temporal_range << Puree::Date.iso(temporal['end'])
|
64
|
+
end
|
65
|
+
if !temporal_range.empty?
|
66
|
+
collected = ::Datacite::Mapping::Date.new value: temporal_range,
|
67
|
+
type: ::Datacite::Mapping::DateType::COLLECTED
|
68
|
+
a << collected
|
69
|
+
end
|
70
|
+
end
|
71
|
+
|
72
|
+
a
|
73
|
+
end
|
74
|
+
|
75
|
+
def description
|
76
|
+
desc = @dataset.description
|
77
|
+
if !desc.empty?
|
78
|
+
d = ::Datacite::Mapping::Description.new value: desc,
|
79
|
+
type: ::Datacite::Mapping::DescriptionType::ABSTRACT
|
80
|
+
[d]
|
81
|
+
else
|
82
|
+
[]
|
83
|
+
end
|
84
|
+
end
|
85
|
+
|
86
|
+
def extract(uuid: nil, id: nil)
|
87
|
+
d = Puree::Dataset.new
|
88
|
+
if !uuid.nil?
|
89
|
+
d.find uuid: uuid
|
90
|
+
else
|
91
|
+
d.find id: id
|
92
|
+
end
|
93
|
+
d
|
94
|
+
end
|
95
|
+
|
96
|
+
def file
|
97
|
+
@dataset.file
|
98
|
+
end
|
99
|
+
|
100
|
+
def identifier(doi)
|
101
|
+
::Datacite::Mapping::Identifier.new(value: doi)
|
102
|
+
end
|
103
|
+
|
104
|
+
def language
|
105
|
+
@dataset.locale
|
106
|
+
end
|
107
|
+
|
108
|
+
def name_identifier_orcid(person)
|
109
|
+
name_identifier = nil
|
110
|
+
if !person.orcid.empty?
|
111
|
+
name_identifier = ::Datacite::Mapping::NameIdentifier.new scheme: 'ORCID',
|
112
|
+
scheme_uri: URI('http://orcid.org/'),
|
113
|
+
value: person.orcid
|
114
|
+
end
|
115
|
+
name_identifier
|
116
|
+
end
|
117
|
+
|
118
|
+
def person
|
119
|
+
o = {}
|
120
|
+
o['creator'] = []
|
121
|
+
o['contributor'] = []
|
122
|
+
person_types = %w(internal external other)
|
123
|
+
person_types.each do |person_type|
|
124
|
+
@dataset.person[person_type].each do |dataset_person|
|
125
|
+
pure_role = dataset_person['role'].gsub(/\s+/, '')
|
126
|
+
name = "#{dataset_person['name']['last']}, #{dataset_person['name']['first']}"
|
127
|
+
if pure_role == 'Creator'
|
128
|
+
human = ::Datacite::Mapping::Creator.new name: name
|
129
|
+
else
|
130
|
+
pure_role = 'Other' if pure_role === 'Contributor'
|
131
|
+
contributor_type = ::Datacite::Mapping::ContributorType.find_by_value pure_role
|
132
|
+
if contributor_type
|
133
|
+
human = ::Datacite::Mapping::Contributor.new name: name,
|
134
|
+
type: contributor_type
|
135
|
+
end
|
136
|
+
end
|
137
|
+
if human
|
138
|
+
if !dataset_person['uuid'].empty?
|
139
|
+
person = Puree::Person.new
|
140
|
+
person.find uuid: dataset_person['uuid']
|
141
|
+
if !person.metadata.empty?
|
142
|
+
identifier = name_identifier_orcid(person)
|
143
|
+
human.identifier = identifier if !identifier.nil?
|
144
|
+
|
145
|
+
affiliation = affiliations(person)
|
146
|
+
human.affiliations = affiliation if !affiliation.empty?
|
147
|
+
end
|
148
|
+
end
|
149
|
+
if dataset_person['role'] == 'Creator'
|
150
|
+
o['creator'] << human
|
151
|
+
else
|
152
|
+
o['contributor'] << human
|
153
|
+
end
|
154
|
+
end
|
155
|
+
end
|
156
|
+
end
|
157
|
+
o
|
158
|
+
end
|
159
|
+
|
160
|
+
def publication_year
|
161
|
+
@dataset.available['year']
|
162
|
+
end
|
163
|
+
|
164
|
+
def publisher
|
165
|
+
@dataset.publisher
|
166
|
+
end
|
167
|
+
|
168
|
+
def related_identifiers
|
169
|
+
publications = @dataset.publication
|
170
|
+
data = []
|
171
|
+
publications.each do |i|
|
172
|
+
if i['type'] === 'Dataset'
|
173
|
+
# Do nothing as the relationship cannot currently be determined
|
174
|
+
# pub = Puree::Dataset.new
|
175
|
+
next
|
176
|
+
else
|
177
|
+
pub = Puree::Publication.new
|
178
|
+
end
|
179
|
+
pub.find uuid: i['uuid']
|
180
|
+
doi = pub.doi
|
181
|
+
if doi && !doi.empty?
|
182
|
+
doi_part_to_remove = 'http://dx.doi.org/'
|
183
|
+
doi_short = doi.gsub(doi_part_to_remove, '')
|
184
|
+
doi_short.gsub!('/', '-')
|
185
|
+
related_identifier =
|
186
|
+
::Datacite::Mapping::RelatedIdentifier.new(
|
187
|
+
value: doi_short,
|
188
|
+
identifier_type: ::Datacite::Mapping::RelatedIdentifierType::DOI,
|
189
|
+
relation_type: ::Datacite::Mapping::RelationType::IS_REFERENCED_BY)
|
190
|
+
data << related_identifier
|
191
|
+
end
|
192
|
+
end
|
193
|
+
data
|
194
|
+
end
|
195
|
+
|
196
|
+
def resource_type
|
197
|
+
::Datacite::Mapping::ResourceType.new(
|
198
|
+
resource_type_general: ::Datacite::Mapping::ResourceTypeGeneral::DATASET,
|
199
|
+
value: 'Dataset'
|
200
|
+
)
|
201
|
+
end
|
202
|
+
|
203
|
+
def spatial
|
204
|
+
# Pure has free text to list place names and does not allow a point to
|
205
|
+
# be associated with a specific place
|
206
|
+
|
207
|
+
# Place names
|
208
|
+
arr = @dataset.spatial.map { |i| ::Datacite::Mapping::GeoLocation.new place: i }
|
209
|
+
|
210
|
+
# Lat Long point
|
211
|
+
spatial_point = @dataset.spatial_point
|
212
|
+
if !spatial_point.empty?
|
213
|
+
point = ::Datacite::Mapping::GeoLocationPoint.new latitude: spatial_point['latitude'],
|
214
|
+
longitude: spatial_point['longitude']
|
215
|
+
geolocation = ::Datacite::Mapping::GeoLocation.new point: point
|
216
|
+
arr << geolocation
|
217
|
+
end
|
218
|
+
arr
|
219
|
+
end
|
220
|
+
|
221
|
+
def subjects
|
222
|
+
@dataset.keyword.map { |i| ::Datacite::Mapping::Subject.new value: i }
|
223
|
+
end
|
224
|
+
|
225
|
+
def title
|
226
|
+
::Datacite::Mapping::Title.new value: @dataset.title
|
227
|
+
end
|
228
|
+
|
229
|
+
end
|
230
|
+
|
231
|
+
end
|
232
|
+
|
233
|
+
end
|
@@ -0,0 +1,23 @@
|
|
1
|
+
# coding: utf-8
|
2
|
+
lib = File.expand_path('../lib', __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require 'research_metadata/version'
|
5
|
+
|
6
|
+
Gem::Specification.new do |spec|
|
7
|
+
spec.name = "research_metadata"
|
8
|
+
spec.version = ResearchMetadata::VERSION
|
9
|
+
spec.authors = ["Adrian Albin-Clark"]
|
10
|
+
spec.email = ["a.albin-clark@lancaster.ac.uk"]
|
11
|
+
spec.summary = %q{Extraction and Transformation for Loading by the DataCite API.}
|
12
|
+
spec.description = %q{Extraction and Transformation for Loading by the DataCite API.}
|
13
|
+
spec.homepage = "https://aalbinclark.gitbooks.io/research_metadata"
|
14
|
+
spec.license = "MIT"
|
15
|
+
|
16
|
+
spec.files = `git ls-files -z`.split("\x0")
|
17
|
+
spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
|
18
|
+
spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
|
19
|
+
spec.require_paths = ["lib"]
|
20
|
+
|
21
|
+
spec.add_runtime_dependency "puree", "~> 0.20"
|
22
|
+
spec.add_runtime_dependency "datacite-mapping", "~> 0.2"
|
23
|
+
end
|
data/spec/spec_helper.rb
ADDED
@@ -0,0 +1,39 @@
|
|
1
|
+
require 'spec_helper'
|
2
|
+
|
3
|
+
describe 'Dataset' do
|
4
|
+
|
5
|
+
def setup
|
6
|
+
Puree.base_url = ENV['PURE_BASE_URL']
|
7
|
+
Puree.username = ENV['PURE_USERNAME']
|
8
|
+
Puree.password = ENV['PURE_PASSWORD']
|
9
|
+
Puree.basic_auth = true
|
10
|
+
@t = ResearchMetadata::Transformer::Dataset.new
|
11
|
+
end
|
12
|
+
|
13
|
+
it '#new' do
|
14
|
+
t = ResearchMetadata::Transformer::Dataset.new
|
15
|
+
expect(t).to be_an_instance_of ResearchMetadata::Transformer::Dataset
|
16
|
+
end
|
17
|
+
|
18
|
+
describe 'data transformation' do
|
19
|
+
before(:all) do
|
20
|
+
setup
|
21
|
+
end
|
22
|
+
|
23
|
+
it '#transform with valid UUID' do
|
24
|
+
metadata = @t.transform uuid: ENV['PURE_DATASET_UUID'],
|
25
|
+
doi: '10.1234/foo/bar/1'
|
26
|
+
is_xml = metadata.downcase.start_with?('<resource')
|
27
|
+
expect(is_xml).to match(true)
|
28
|
+
end
|
29
|
+
|
30
|
+
it '#transform with valid ID' do
|
31
|
+
metadata = @t.transform id: ENV['PURE_DATASET_ID'],
|
32
|
+
doi: '10.1234/foo/bar/1'
|
33
|
+
is_xml = metadata.downcase.start_with?('<resource')
|
34
|
+
expect(is_xml).to match(true)
|
35
|
+
end
|
36
|
+
|
37
|
+
end
|
38
|
+
|
39
|
+
end
|
metadata
ADDED
@@ -0,0 +1,87 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: research_metadata
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.1.0
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Adrian Albin-Clark
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2017-02-06 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: puree
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - "~>"
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '0.20'
|
20
|
+
type: :runtime
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - "~>"
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '0.20'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: datacite-mapping
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - "~>"
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '0.2'
|
34
|
+
type: :runtime
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - "~>"
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '0.2'
|
41
|
+
description: Extraction and Transformation for Loading by the DataCite API.
|
42
|
+
email:
|
43
|
+
- a.albin-clark@lancaster.ac.uk
|
44
|
+
executables: []
|
45
|
+
extensions: []
|
46
|
+
extra_rdoc_files: []
|
47
|
+
files:
|
48
|
+
- ".gitignore"
|
49
|
+
- CHANGELOG.md
|
50
|
+
- Gemfile
|
51
|
+
- LICENSE.txt
|
52
|
+
- README.md
|
53
|
+
- Rakefile
|
54
|
+
- lib/research_metadata.rb
|
55
|
+
- lib/research_metadata/transformer/dataset.rb
|
56
|
+
- lib/research_metadata/version.rb
|
57
|
+
- research_metadata.gemspec
|
58
|
+
- spec/spec_helper.rb
|
59
|
+
- spec/transformer/dataset_spec.rb
|
60
|
+
homepage: https://aalbinclark.gitbooks.io/research_metadata
|
61
|
+
licenses:
|
62
|
+
- MIT
|
63
|
+
metadata: {}
|
64
|
+
post_install_message:
|
65
|
+
rdoc_options: []
|
66
|
+
require_paths:
|
67
|
+
- lib
|
68
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
69
|
+
requirements:
|
70
|
+
- - ">="
|
71
|
+
- !ruby/object:Gem::Version
|
72
|
+
version: '0'
|
73
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
74
|
+
requirements:
|
75
|
+
- - ">="
|
76
|
+
- !ruby/object:Gem::Version
|
77
|
+
version: '0'
|
78
|
+
requirements: []
|
79
|
+
rubyforge_project:
|
80
|
+
rubygems_version: 2.2.2
|
81
|
+
signing_key:
|
82
|
+
specification_version: 4
|
83
|
+
summary: Extraction and Transformation for Loading by the DataCite API.
|
84
|
+
test_files:
|
85
|
+
- spec/spec_helper.rb
|
86
|
+
- spec/transformer/dataset_spec.rb
|
87
|
+
has_rdoc:
|