Module: Bolognese::Readers::DataciteReader

Included in:
MetadataUtils
Defined in:
lib/bolognese/readers/datacite_reader.rb

Instance Method Summary collapse

Instance Method Details

#datacite_date(dates, date_type) ⇒ Object 



145
146
147
148
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 145

def datacite_date(dates, date_type)
  dd = dates.find { |d| d["dateType"] == date_type } || {}
  dd.fetch("__content__", nil)
end

#datacite_funder_contributor(meta) ⇒ Object 



168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 168

def datacite_funder_contributor(meta)
  Array.wrap(meta.dig("contributors", "contributor")).reduce([]) do |sum, f|
    if f["contributorType"] == "Funder"
      # handle special case of OpenAIRE metadata
      id = f.dig("nameIdentifier", "__content__").to_s.start_with?("info:eu-repo/grantAgreement/EC") ? "https://doi.org/10.13039/501100000780" : nil

      funder = { "type" => "Organization",
                 "id" => id,
                 "name" => f["contributorName"] }.compact
      if f.dig("nameIdentifier", "nameIdentifierScheme") == "info"
        sum << { "type" => "Award",
                 "identifier" => f.dig("nameIdentifier", "__content__").split("/").last,
                 "funder" => funder }
      else
        sum << funder
      end
    else
      sum
    end
  end
end

#datacite_funding_reference(meta) ⇒ Object 



150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 150

def datacite_funding_reference(meta)
  Array.wrap(meta.dig("fundingReferences", "fundingReference")).map do |f|
    funder_id = parse_attributes(f["funderIdentifier"])
    funder = { "type" => "Organization",
               "id" => normalize_id(funder_id),
               "name" => f["funderName"] }.compact
    if f["awardNumber"].present? || f["awardTitle"].present?
      { "type" => "Award",
        "name" => f.fetch("awardTitle", nil),
        "identifier" => f["awardNumber"].is_a?(Hash) ? f.dig("awardNumber", "__content__") : f["awardNumber"],
        "url" => f["awardNumber"].is_a?(Hash) ? f.dig("awardNumber", "awardURI") : nil,
        "funder" => funder }.compact
    else
      funder
    end
  end.uniq
end

#datacite_has_part(meta) ⇒ Object 



205
206
207
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 205

def datacite_has_part(meta)
  datacite_related_identifier(meta, relation_type: "HasPart")
end

#datacite_is_identical_to(meta) ⇒ Object 



197
198
199
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 197

def datacite_is_identical_to(meta)
  datacite_related_identifier(meta, relation_type: "IsIdenticalTo")
end

#datacite_is_new_version_of(meta) ⇒ Object 



213
214
215
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 213

def datacite_is_new_version_of(meta)
  datacite_related_identifier(meta, relation_type: "IsNewVersionOf")
end

#datacite_is_original_form_of(meta) ⇒ Object 



221
222
223
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 221

def datacite_is_original_form_of(meta)
  datacite_related_identifier(meta, relation_type: "IsOriginalFormOf")
end

#datacite_is_part_of(meta) ⇒ Object 



201
202
203
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 201

def datacite_is_part_of(meta)
  datacite_related_identifier(meta, relation_type: "IsPartOf")
end

#datacite_is_previous_version_of(meta) ⇒ Object 



209
210
211
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 209

def datacite_is_previous_version_of(meta)
  datacite_related_identifier(meta, relation_type: "IsPreviousVersionOf")
end

#datacite_is_referenced_by(meta) ⇒ Object 



229
230
231
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 229

def datacite_is_referenced_by(meta)
  datacite_related_identifier(meta, relation_type: "IsCitedBy IsReferencedBy").presence
end

#datacite_is_reviewed_by(meta) ⇒ Object 



245
246
247
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 245

def datacite_is_reviewed_by(meta)
  datacite_related_identifier(meta, relation_type: "IsReviewedBy").presence
end

#datacite_is_supplement_to(meta) ⇒ Object 



233
234
235
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 233

def datacite_is_supplement_to(meta)
  datacite_related_identifier(meta, relation_type: "IsSupplementTo")
end

#datacite_is_supplemented_by(meta) ⇒ Object 



237
238
239
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 237

def datacite_is_supplemented_by(meta)
  datacite_related_identifier(meta, relation_type: "isSupplementedBy")
end

#datacite_is_variant_form_of(meta) ⇒ Object 



217
218
219
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 217

def datacite_is_variant_form_of(meta)
  datacite_related_identifier(meta, relation_type: "IsVariantFormOf")
end

#datacite_references(meta) ⇒ Object 



225
226
227
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 225

def datacite_references(meta)
  datacite_related_identifier(meta, relation_type: "References Cites").presence
end

#datacite_related_identifier(meta, relation_type: nil) ⇒ Object 



190
191
192
193
194
195
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 190

def datacite_related_identifier(meta, relation_type: nil)
  arr = Array.wrap(meta.dig("relatedIdentifiers", "relatedIdentifier")).select { |r| %w(DOI URL).include?(r["relatedIdentifierType"]) }
  arr = arr.select { |r| relation_type.split(" ").include?(r["relationType"]) } if relation_type.present?

  arr.map { |work| { "type" => "CreativeWork", "id" => normalize_id(work["__content__"]) } }.unwrap
end

#datacite_reviews(meta) ⇒ Object 



241
242
243
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 241

def datacite_reviews(meta)
  datacite_related_identifier(meta, relation_type: "Reviews").presence
end

#get_datacite(id: nil, **options) ⇒ Object 



4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 4

def get_datacite(id: nil, **options)
  return { "string" => nil, "state" => "not_found" } unless id.present?

  search_url = doi_search(id, options)
  doi = doi_from_url(id)
  params = { q: doi,
             fl: "doi,url,xml,state,allocator_symbol,datacentre_symbol,media,minted,updated",
             defType: "edismax",
             wt: "json" }
  search_url += "?" + URI.encode_www_form(params)

  response = Maremma.get search_url
  attributes = response.body.dig("data", "response", "docs").first
  return { "string" => nil, "state" => "not_found" } unless attributes.present?

  string = attributes.fetch('xml', nil)
  string = Base64.decode64(string) if string.present?

  if string.present?
    doc = Nokogiri::XML(string, nil, 'UTF-8', &:noblanks)

    # remove leading and trailing whitespace in text nodes
    doc.xpath("//text()").each do |node|
      if node.content =~ /\S/
        node.content = node.content.strip
      else
        node.remove
      end
    end
    string = doc.to_xml(:indent => 2)
  end

  { "string" => string,
    "b_url" => attributes.fetch("url", nil),
    "state" => attributes.fetch("state", nil),
    "date_registered" => attributes.fetch("minted", nil),
    "date_updated" => attributes.fetch("updated", nil),
    "provider_id" => attributes.fetch("allocator_symbol", nil),
    "client_id" => attributes.fetch("datacentre_symbol", nil) }
end

#read_datacite(string: nil, **options) ⇒ Object 



45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 45

def read_datacite(string: nil, **options)
  meta = Maremma.from_xml(string).to_h.fetch("resource", {})
  schema_version = meta.fetch("xmlns", nil)

  # validate only when option is set, as this step is expensive and
  # not needed if XML comes from DataCite MDS
  if options[:validate]
    errors = datacite_errors(xml: string, schema_version: schema_version)
    return { "errors" => errors } if errors.present?
  end

  if options[:doi]
    id = normalize_doi(options[:doi], sandbox: options[:sandbox])
  else
    id = normalize_doi(meta.dig("identifier", "__content__") || options[:id], sandbox: options[:sandbox])
  end

  doi = doi_from_url(id)
  resource_type_general = meta.dig("resourceType", "resourceTypeGeneral")
  additional_type = meta.fetch("resourceType", {}).fetch("__content__", nil)
  type = Bolognese::Utils::CR_TO_SO_TRANSLATIONS[additional_type.to_s.underscore.camelcase] || Bolognese::Utils::DC_TO_SO_TRANSLATIONS[resource_type_general.to_s.dasherize] || "CreativeWork"
  title = Array.wrap(meta.dig("titles", "title")).map do |r|
    if r.is_a?(String)
      sanitize(r)
    else
      { "title_type" => r["titleType"], "lang" => r["xml:lang"], "text" => sanitize(r["__content__"]) }.compact
    end
  end.unwrap

  container_title = Array.wrap(meta.dig("descriptions", "description")).find { |r| r["descriptionType"] == "SeriesInformation" }.to_h.fetch("__content__", nil)

  alternate_name = Array.wrap(meta.dig("alternateIdentifiers", "alternateIdentifier")).map do |r|
    { "type" => r["alternateIdentifierType"], "name" => r["__content__"] }.compact
  end.unwrap
  description = Array.wrap(meta.dig("descriptions", "description")).select { |r| r["descriptionType"] != "SeriesInformation" }.map do |r|
    { "type" => r["descriptionType"], "text" => sanitize(r["__content__"]) }.compact
  end.unwrap
  license = Array.wrap(meta.dig("rightsList", "rights")).map do |r|
    { "id" => normalize_url(r["rightsURI"]), "name" => r["__content__"] }.compact
  end.unwrap
  keywords = Array.wrap(meta.dig("subjects", "subject")).map do |k|
    if k.nil?
      nil
    elsif k.is_a?(String)
      sanitize(k)
    else
      { "subject_scheme" => k["subjectScheme"], "scheme_uri" => k["schemeURI"], "text" => sanitize(k["__content__"]) }.compact
    end
  end.compact
  dates = Array.wrap(meta.dig("dates", "date"))
  funding = begin
    f = datacite_funder_contributor(meta) + datacite_funding_reference(meta)
    f.length > 1 ? f : f.first
  end
  state = doi.present? ? "findable" : "not_found"

  { "id" => id,
    "type" => type,
    "additional_type" => additional_type,
    "citeproc_type" => Bolognese::Utils::CR_TO_CP_TRANSLATIONS[additional_type.to_s.underscore.camelcase] || Bolognese::Utils::SO_TO_CP_TRANSLATIONS[type] || "article",
    "bibtex_type" => Bolognese::Utils::CR_TO_BIB_TRANSLATIONS[additional_type.to_s.underscore.camelcase] || Bolognese::Utils::SO_TO_BIB_TRANSLATIONS[type] || "misc",
    "ris_type" => Bolognese::Utils::CR_TO_RIS_TRANSLATIONS[additional_type.to_s.underscore.camelcase] || Bolognese::Utils::DC_TO_RIS_TRANSLATIONS[resource_type_general.to_s.dasherize] || "GEN",
    "resource_type_general" => resource_type_general,
    "doi" => doi,
    "url" => options.fetch(:url, nil),
    "title" => title,
    "alternate_name" => alternate_name,
    "author" => get_authors(Array.wrap(meta.dig("creators", "creator"))),
    "editor" => get_authors(Array.wrap(meta.dig("contributors", "contributor")).select { |r| r["contributorType"] == "Editor" }),
    "container_title" => container_title,
    "publisher" => meta.fetch("publisher", nil),
    "service_provider" => "DataCite",
    "funding" => funding,
    "is_identical_to" => datacite_is_identical_to(meta),
    "is_part_of" => datacite_is_part_of(meta),
    "has_part" => datacite_has_part(meta),
    "references" => datacite_references(meta),
    "is_referenced_by" => datacite_is_referenced_by(meta),
    "is_supplement_to" => datacite_is_supplement_to(meta),
    "is_supplemented_by" => datacite_is_supplemented_by(meta),
    "date_created" => datacite_date(dates, "Created"),
    "date_accepted" => datacite_date(dates, "Accepted"),
    "date_available" => datacite_date(dates, "Available"),
    "date_copyrighted" => datacite_date(dates, "Copyrightes"),
    "date_collected" => datacite_date(dates, "Collected"),
    "date_submitted" => datacite_date(dates, "Submitted"),
    "date_valid" => datacite_date(dates, "Valid"),
    "date_published" => datacite_date(dates, "Issued") || meta.fetch("publicationYear", nil),
    "date_modified" => datacite_date(dates, "Updated"),
    "description" => description,
    "license" => license,
    "b_version" => meta.fetch("version", nil),
    "keywords" => keywords,
    "language" => meta.fetch("language", nil),
    "content_size" => meta.fetch("size", nil),
    "schema_version" => schema_version,
    "state" => state
  }
end