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 



147
148
149
150
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 147

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

#datacite_funder_contributor(meta) ⇒ Object 



170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 170

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 



152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 152

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 



207
208
209
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 207

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

#datacite_is_identical_to(meta) ⇒ Object 



199
200
201
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 199

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

#datacite_is_new_version_of(meta) ⇒ Object 



215
216
217
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 215

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

#datacite_is_original_form_of(meta) ⇒ Object 



223
224
225
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 223

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

#datacite_is_part_of(meta) ⇒ Object 



203
204
205
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 203

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

#datacite_is_previous_version_of(meta) ⇒ Object 



211
212
213
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 211

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

#datacite_is_referenced_by(meta) ⇒ Object 



231
232
233
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 231

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

#datacite_is_reviewed_by(meta) ⇒ Object 



247
248
249
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 247

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

#datacite_is_supplement_to(meta) ⇒ Object 



235
236
237
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 235

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

#datacite_is_supplemented_by(meta) ⇒ Object 



239
240
241
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 239

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

#datacite_is_variant_form_of(meta) ⇒ Object 



219
220
221
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 219

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

#datacite_references(meta) ⇒ Object 



227
228
229
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 227

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

#datacite_related_identifier(meta, relation_type: nil) ⇒ Object 



192
193
194
195
196
197
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 192

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 



243
244
245
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 243

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

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



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
44
45
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 6

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 



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
144
145
 
# File 'lib/bolognese/readers/datacite_reader.rb', line 47

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