Class: Toccatore::Base

Inherits:
Object
  • Object
show all
Defined in:
lib/toccatore/base.rb

Direct Known Subclasses

OrcidUpdate

Instance Method Summary collapse

Instance Method Details

#clean_doi(doi) ⇒ Object

remove non-printing whitespace



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# File 'lib/toccatore/base.rb', line 275

def clean_doi(doi)
  doi.gsub(/\u200B/, '')
end

#cleanup_author(author) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 322

def cleanup_author(author)
  # detect pattern "Smith J.", but not "Smith, John K."
  author = author.gsub(/[[:space:]]([A-Z]\.)?(-?[A-Z]\.)$/, ', \1\2') unless author.include?(",")

  # titleize strings
  # remove non-standard space characters
  author.my_titleize
        .gsub(/[[:space:]]/, ' ')
end

#config_fields ⇒ Object 



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# File 'lib/toccatore/base.rb', line 258

def config_fields
  [:url, :push_url, :access_token]
end

#doi_as_url(doi) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 288

def doi_as_url(doi)
  Addressable::URI.encode("https://doi.org/#{clean_doi(doi)}") if doi.present?
end

#doi_from_url(url) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 279

def doi_from_url(url)
  if /(http|https):\/\/(dx\.)?doi\.org\/(\w+)/.match(url)
    uri = Addressable::URI.parse(url)
    uri.path[1..-1].upcase
  elsif url.starts_with?("doi:")
    url[4..-1].upcase
  end
end

#get_authors(authors, options = {}) ⇒ Object

parse array of author strings into CSL format



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# File 'lib/toccatore/base.rb', line 340

def get_authors(authors, options={})
  Array(authors).map { |author| get_one_author(author, options) }
end

#get_contributions(obj, items) ⇒ Object

we are flipping subj and obj for contributions



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# File 'lib/toccatore/base.rb', line 236

def get_contributions(obj, items)
  prefix = obj["DOI"][/^10\.\d{4,5}/]

  Array(items).reduce([]) do |sum, item|
    orcid = item.split(':', 2).last
    orcid = validate_orcid(orcid)

    return sum if orcid.nil?

    sum << { prefix: prefix,
             message_type: "contribution",
             relation: { "subj_id" => orcid_as_url(orcid),
                         "obj_id" => obj["pid"],
                         "relation_type_id" => nil,
                         "source_id" => source_id,
                         "publisher_id" => obj["publisher_id"],
                         "registration_agency_id" => "datacite",
                         "occurred_at" => obj["issued"] },
             obj: obj }
  end
end

#get_data(options = {}) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 85

def get_data(options={})
  query_url = get_query_url(options)
  Maremma.get(query_url, options)
end

#get_doi_relations(subj, items) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 208

def get_doi_relations(subj, items)
  prefix = subj["DOI"][/^10\.\d{4,5}/]

  Array(items).reduce([]) do |sum, item|
    raw_relation_type, _related_identifier_type, related_identifier = item.split(':', 3)
    doi = related_identifier.strip.upcase
    registration_agency = get_doi_ra(doi)

    if source_id == "datacite_crossref" && registration_agency == "datacite"
      sum
    else
      _source_id = registration_agency == "crossref" ? "datacite_crossref" : "datacite_related"
      pid = doi_as_url(doi)

      sum << { prefix: prefix,
               relation: { "subj_id" => subj["pid"],
                           "obj_id" => pid,
                           "relation_type_id" => raw_relation_type.underscore,
                           "source_id" => _source_id,
                           "publisher_id" => subj["publisher_id"],
                           "registration_agency_id" => registration_agency,
                           "occurred_at" => subj["issued"] },
               subj: subj }
    end
  end
end

#get_github_relations(subj, items) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 167

def get_github_relations(subj, items)
  prefix = subj["DOI"][/^10\.\d{4,5}/]

  Array(items).reduce([]) do |sum, item|
    raw_relation_type, _related_identifier_type, related_identifier = item.split(':', 3)

    # get parent repo
    # code from https://github.com/octokit/octokit.rb/blob/master/lib/octokit/repository.rb
    related_identifier = PostRank::URI.clean(related_identifier)
    github_hash = github_from_url(related_identifier)
    owner_url = github_as_owner_url(github_hash)
    repo_url = github_as_repo_url(github_hash)

    sum << { prefix: prefix,
             relation: { "subj_id" => subj["pid"],
                         "obj_id" => related_identifier,
                         "relation_type_id" => raw_relation_type.underscore,
                         "source_id" => source_id,
                         "publisher_id" => subj["publisher_id"],
                         "registration_agency_id" => "github",
                         "occurred_at" => subj["issued"] },
             subj: subj }

    # if relatedIdentifier is release URL rather than repo URL
    if related_identifier != repo_url
      sum << { relation: { "subj_id" => related_identifier,
                           "obj_id" => repo_url,
                           "relation_type_id" => "is_part_of",
                           "source_id" => source_id,
                           "publisher_id" => "github",
                           "registration_agency_id" => "github" } }
    end

    sum << {  message_type: "contribution",
              relation: { "subj_id" => owner_url,
                          "obj_id" => repo_url,
                          "source_id" => "github_contributor",
                          "registration_agency_id" => "github" }}
  end
end

#get_hashed_authors(authors) ⇒ Object

parse array of author hashes into CSL format



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# File 'lib/toccatore/base.rb', line 345

def get_hashed_authors(authors)
  Array(authors).map { |author| get_one_hashed_author(author) }
end

#get_name_identifier(author) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 357

def get_name_identifier(author)
  name_identifier = author.fetch("nameIdentifier", nil)
  name_identifier_scheme = author.fetch("nameIdentifierScheme", "orcid").downcase
  if name_identifier_scheme == "orcid" && name_identifier = validate_orcid(name_identifier)
    "http://orcid.org/#{name_identifier}"
  else
    nil
  end
end

#get_one_author(author, options = {}) ⇒ Object

parse author string into CSL format only assume personal name when using sort-order: “Turing, Alan”



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# File 'lib/toccatore/base.rb', line 306

def get_one_author(author, options = {})
  return { "literal" => "" } if author.strip.blank?

  author = cleanup_author(author)
  names = Namae.parse(author)

  if names.blank? || is_personal_name?(author).blank?
    { "literal" => author }
  else
    name = names.first

    { "family" => name.family,
      "given" => name.given }.compact
  end
end

#get_one_hashed_author(author) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 349

def get_one_hashed_author(author)
  raw_name = author.fetch("creatorName", nil)

  author_hsh = get_one_author(raw_name)
  author_hsh["ORCID"] = get_name_identifier(author)
  author_hsh.compact
end

#get_query_url(options = {}) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 23

def get_query_url(options={})
  updated = "updated:[#{options[:from_date]}T00:00:00Z TO #{options[:until_date]}T23:59:59Z]"
  fq = "#{updated} AND has_metadata:true AND is_active:true"

  if options[:doi].present?
    q = "doi:#{options[:doi]}"
  elsif options[:orcid].present?
    q = "nameIdentifier:ORCID\\:#{options[:orcid]}"
  elsif options[:query].present?
    q = options[:query]
  else
    q = query
  end

  params = { q: q,
             start: options[:offset],
             rows: options[:rows],
             fl: "doi,creator,title,publisher,publicationYear,resourceTypeGeneral,datacentre_symbol,relatedIdentifier,nameIdentifier,xml,minted,updated",
             fq: fq,
             wt: "json" }
  url +  URI.encode_www_form(params)
end

#get_relations_with_related_works(items) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 120

def get_relations_with_related_works(items)
  Array(items).reduce([]) do |sum, item|
    doi = item.fetch("doi", nil)
    prefix = doi[/^10\.\d{4,5}/]
    pid = doi_as_url(doi)
    type = item.fetch("resourceTypeGeneral", nil)
    publisher_id = item.fetch("datacentre_symbol", nil)

    xml = Base64.decode64(item.fetch('xml', "PGhzaD48L2hzaD4=\n"))
    xml = Hash.from_xml(xml).fetch("resource", {})
    authors = xml.fetch("creators", {}).fetch("creator", [])
    authors = [authors] if authors.is_a?(Hash)

    subj = { "pid" => pid,
             "DOI" => doi,
             "author" => get_hashed_authors(authors),
             "title" => item.fetch("title", []).first,
             "container-title" => item.fetch("publisher", nil),
             "published" => item.fetch("publicationYear", nil),
             "issued" => item.fetch("minted", nil),
             "publisher_id" => publisher_id,
             "registration_agency_id" => "datacite",
             "tracked" => true,
             "type" => type }

    related_doi_identifiers = item.fetch('relatedIdentifier', []).select { |id| id =~ /:DOI:.+/ }
    sum += get_doi_relations(subj, related_doi_identifiers)

    related_github_identifiers = item.fetch('relatedIdentifier', []).select { |id| id =~ /:URL:https:\/\/github.com.+/ }
    sum += get_github_relations(subj, related_github_identifiers)

    name_identifiers = item.fetch('nameIdentifier', []).select { |id| id =~ /^ORCID:.+/ }
    sum += get_contributions(subj, name_identifiers)

    if source_id == "datacite_import"
      sum += [{ prefix: prefix,
                relation: { "subj_id" => subj["pid"],
                            "source_id" => source_id,
                            "publisher_id" => subj["publisher_id"],
                            "occurred_at" => subj["issued"] },
                subj: subj }]
    end

    sum
  end
end

#get_total(options = {}) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 46

def get_total(options={})
  query_url = get_query_url(options.merge(rows: 0))
  result = Maremma.get(query_url, options)
  result.body.fetch("data", {}).fetch("response", {}).fetch("numFound", 0)
end

#is_personal_name?(author) ⇒ Boolean 



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# File 'lib/toccatore/base.rb', line 332

def is_personal_name?(author)
  return true if author.include?(",")

  # lookup given name
  name_detector.name_exists?(author.split.first)
end

#job_batch_size ⇒ Object 



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# File 'lib/toccatore/base.rb', line 270

def job_batch_size
  1000
end

#name_detector ⇒ Object 



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# File 'lib/toccatore/base.rb', line 367

def name_detector
  GenderDetector.new
end

#orcid_as_url(orcid) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 296

def orcid_as_url(orcid)
  "http://orcid.org/#{orcid}" if orcid.present?
end

#orcid_from_url(url) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 292

def orcid_from_url(url)
  Array(/\Ahttp:\/\/orcid\.org\/(.+)/.match(url)).last
end

#parse_data(result, options = {}) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 90

def parse_data(result, options={})
  return result.body.fetch("errors") if result.body.fetch("errors", nil).present?

  items = result.fetch("data", {}).fetch('response', {}).fetch('docs', nil)
  get_relations_with_related_works(items)
end

#process_data(options = {}) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 76

def process_data(options = {})
  data = get_data(options.merge(timeout: timeout, source_id: source_id))
  data = parse_data(data, options.merge(source_id: source_id))

  return [OpenStruct.new(body: { "data" => [] })] if data.empty?

  push_data(data, options)
end

#push_data(items, options = {}) ⇒ Object

push to Lagotto deposit API if no error and we have collected works



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# File 'lib/toccatore/base.rb', line 98

def push_data(items, options={})
  if items.empty?
    puts "No works found for date range #{options[:from_date]} - #{options[:until_date]}."
  else
    Array(items).map do |item|
      relation = item.fetch(:relation, {})
      deposit = { "deposit" => { "subj_id" => relation.fetch("subj_id", nil),
                                 "obj_id" => relation.fetch("obj_id", nil),
                                 "relation_type_id" => relation.fetch("relation_type_id", nil),
                                 "source_id" => relation.fetch("source_id", nil),
                                 "publisher_id" => relation.fetch("publisher_id", nil),
                                 "subj" => item.fetch(:subj, {}),
                                 "obj" => item.fetch(:obj, {}),
                                 "message_type" => item.fetch(:message_type, "relation"),
                                 "prefix" => item.fetch(:prefix, nil),
                                 "source_token" => uuid } }

      Maremma.post push_url, data: deposit.to_json, content_type: 'json', token: access_token
    end
  end
end

#queue_jobs(options = {}) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 52

def queue_jobs(options={})
  options[:offset] = options[:offset].to_i || 0
  options[:rows] = options[:rows].presence || job_batch_size
  options[:from_date] = options[:from_date].presence || (Time.now.to_date - 1.day).iso8601
  options[:until_date] = options[:until_date].presence || Time.now.to_date.iso8601

  total = get_total(options)

  if total > 0
    # walk through paginated results
    total_pages = (total.to_f / job_batch_size).ceil

    (0...total_pages).each do |page|
      options[:offset] = page * job_batch_size
      process_data(options)
    end
  else
    puts "No works found for date range #{options[:from_date]} - #{options[:until_date]}."
  end

  # return number of works queued
  total
end

#timeout ⇒ Object 



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# File 'lib/toccatore/base.rb', line 266

def timeout
  120
end

#unfreeze(hsh) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 371

def unfreeze(hsh)
  new_hash = {}
  hsh.each_pair { |k,v| new_hash.merge!({k.downcase.to_sym => v})  }
  new_hash
end

#url ⇒ Object 



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# File 'lib/toccatore/base.rb', line 262

def url
  "https://search.datacite.org/api?"
end

#validate_orcid(orcid) ⇒ Object 



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# File 'lib/toccatore/base.rb', line 300

def validate_orcid(orcid)
  Array(/\A(?:http:\/\/orcid\.org\/)?(\d{4}-\d{4}-\d{4}-\d{3}[0-9X]+)\z/.match(orcid)).last
end