Class: Uc3DmpId::Helper

Inherits:
Object
  • Object
show all
Defined in:
lib/uc3-dmp-id/helper.rb

Overview

Helper functions for working with DMP IDs

Constant Summary collapse

PK_DMP_PREFIX = 
'DMP#'
PK_DMP_REGEX = 
%r{DMP#[a-zA-Z0-9\-_.]+/[a-zA-Z0-9]{2}\.[a-zA-Z0-9./:]+}
SK_DMP_PREFIX = 
'VERSION#'
SK_DMP_REGEX = 
/VERSION#\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}\+\d{2}:\d{2}/
SK_HARVESTER_MODS = 
"HARVESTER_MODS"
DOI_REGEX =

TODO: Verify the assumed structure of the DOI is valid

%r{[0-9]{2}\.[0-9]{4,}/[a-zA-Z0-9/_.-]+}
URL_REGEX = 
%r{(https?://)?([a-zA-Z0-9\-_]\.)+[a-zA-Z0-9\-_]{2,3}(:[0-9]+)?/?}
DMP_LATEST_VERSION = 
"#{SK_DMP_PREFIX}latest".freeze
DMP_TOMBSTONE_VERSION = 
"#{SK_DMP_PREFIX}tombstone".freeze
DEFAULT_API_URL = 
'https://api.dmphub.uc3dev.cdlib.net/dmps/'
DEFAULT_LANDING_PAGE_URL = 
'https://dmphub.uc3dev.cdlib.net/dmps/'
MSG_DMP_EXISTS = 
'DMP already exists. Try :update instead.'
MSG_DMP_FORBIDDEN = 
'You do not have permission.'
MSG_DMP_INVALID_DMP_ID = 
'Invalid DMP ID format.'
MSG_DMP_NO_DMP_ID = 
'A DMP ID could not be registered at this time.'
MSG_DMP_NO_HISTORICALS = 
'You cannot modify a historical version of the DMP.'
MSG_DMP_NO_TOMBSTONE = 
'Unable to tombstone the DMP ID at this time.'
MSG_DMP_NO_UPDATE = 
'Unable to update the DMP ID at this time.'
MSG_DMP_NOT_FOUND = 
'DMP does not exist.'
MSG_DMP_UNABLE_TO_VERSION = 
'Unable to version this DMP.'
MSG_DMP_UNKNOWN = 
'DMP does not exist. Try :create instead.'
MSG_NO_CHANGE = 
'The updated record has no changes.'
MSG_NO_OWNER_ORG = 
'Could not determine ownership of the DMP ID.'
MSG_NO_PROVENANCE_OWNER = 
'Unable to determine the provenance of the DMP ID.'
MSG_SERVER_ERROR = 
'Something went wrong.'

Class Method Summary collapse

Class Method Details

.annotate_dmp_json(provenance:, p_key:, json:) ⇒ Object

Add DMPHub specific fields to the DMP ID JSON rubocop:disable Metrics/AbcSize, Metrics/MethodLength



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# File 'lib/uc3-dmp-id/helper.rb', line 184

def annotate_dmp_json(provenance:, p_key:, json:)
  json = parse_json(json:)
  bool_vals = [1, '1', true, 'true', 'yes']
  return json if provenance.nil? || p_key.nil? || !json.is_a?(Hash)

  # Fail the json as is if the :PK does not match the :dmp_id if the json has a :PK
  id = dmp_id_to_pk(json: json.fetch('dmp_id', {}))
  return json if id != p_key && !json['PK'].nil?

  annotated = deep_copy_dmp(obj: json)
  annotated['PK'] = json['PK'] || append_pk_prefix(p_key:)
  annotated['SK'] = DMP_LATEST_VERSION

  # Ensure that the :dmp_id matches the :PK
  annotated['dmp_id'] = JSON.parse(pk_to_dmp_id(p_key: remove_pk_prefix(p_key: annotated['PK'])).to_json)

  owner_id = extract_owner_id(json:)
  owner_org = extract_owner_org(json:)

  # Set the :dmproadmap_featured flag appropriately
  featured = annotated.fetch('dmproadmap_featured', 'no')
  annotated['dmproadmap_featured'] = bool_vals.include?(featured.to_s.downcase) ? '1' : '0'

  # Update the modification timestamps
  annotated['dmphub_modification_day'] = Time.now.utc.strftime('%Y-%m-%d')
  annotated['dmphub_owner_id'] = owner_id unless owner_id.nil?
  annotated['dmphub_owner_org'] = owner_org unless owner_org.nil?
  annotated['registered'] = annotated['modified'] if annotated['registered'].nil?
  return annotated unless json['dmphub_provenance_id'].nil?

  annotated['dmphub_provenance_id'] = provenance.fetch('PK', '')
  return annotated if !annotated['dmphub_provenance_identifier'].nil? ||
                      json.fetch('dmp_id', {})['identifier'].nil?

  # Record the original Provenance system's identifier
  # If we are currently seeding records for existing DMP IDs, then use the :dmproadmap_links
  if provenance.fetch('seedingWithLiveDmpIds', false).to_s.downcase == 'true' &&
     !annotated.fetch('dmproadmap_links', {})['get'].nil?
    annotated['dmphub_provenance_identifier'] = annotated.fetch('dmproadmap_links', {})['get']
  else
    annotated['dmphub_provenance_identifier'] = format_provenance_id(
      provenance:, value: json.fetch('dmp_id', {})['identifier']
    )
  end
  annotated
end

.append_pk_prefix(p_key:) ⇒ Object

Append the PK prefix for the object



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# File 'lib/uc3-dmp-id/helper.rb', line 45

def append_pk_prefix(p_key:)
  p_key.is_a?(String) ? "#{PK_DMP_PREFIX}#{remove_pk_prefix(p_key:)}" : nil
end

.append_sk_prefix(s_key:) ⇒ Object

Append the SK prefix for the object



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# File 'lib/uc3-dmp-id/helper.rb', line 57

def append_sk_prefix(s_key:)
  s_key.is_a?(String) ? "#{SK_DMP_PREFIX}#{remove_sk_prefix(s_key:)}" : nil
end

.citable_related_identifiers(dmp:) ⇒ Object

Extracts the related identifiers that we can fetch a citation for



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# File 'lib/uc3-dmp-id/helper.rb', line 255

def citable_related_identifiers(dmp:)
  return [] unless dmp.is_a?(Hash)

  related_identifiers = dmp.fetch('dmproadmap_related_identifiers', [])
  # Ignore the identifier that points to the narrative PDF document and any identifiers that
  # we have already fetched the citation for
  related_identifiers.reject do |id|
    (id['work_type'] == 'output_management_plan' && id['descriptor'] == 'is_metadata_for') ||
      (id['type'] == 'doi' && !id['citation'].nil?)
  end
end

.cleanse_dmp_json(json:) ⇒ Object

Recursive method that strips out any DMPHub related metadata from a DMP record before sending it to the caller rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity, Metrics/PerceivedComplexity



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# File 'lib/uc3-dmp-id/helper.rb', line 236

def cleanse_dmp_json(json:)
  return json unless json.is_a?(Hash) || json.is_a?(Array)
  # If it's an array clean each of the objects individually
  return json.map { |obj| cleanse_dmp_json(json: obj) }.compact if json.is_a?(Array)

  cleansed = {}
  allowable = %w[dmphub_modifications dmphub_versions]
  json.each_key do |key|
    next if (key.to_s.start_with?('dmphub') && !allowable.include?(key)) || %w[PK SK].include?(key.to_s)

    obj = json[key]
    # If this object is a Hash or Array then recursively cleanse it
    cleansed[key] = obj.is_a?(Hash) || obj.is_a?(Array) ? cleanse_dmp_json(json: obj) : obj
  end
  cleansed.keys.any? ? cleansed : nil
end

.deep_copy_dmp(obj:) ⇒ Object

Ruby’s clone/dup methods do not clone/dup the children, so we need to do it here

rubocop:disable Metrics/AbcSize



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# File 'lib/uc3-dmp-id/helper.rb', line 270

def deep_copy_dmp(obj:)
  case obj.class.name
  when 'Array'
    obj.map { |item| deep_copy_dmp(obj: item) }
  when 'Hash'
    hash = obj.dup
    hash.each_pair do |key, value|
      if key.is_a?(::String) || key.is_a?(::Symbol)
        hash[key] = deep_copy_dmp(obj: value)
      else
        hash.delete(key)
        hash[deep_copy_dmp(obj: key)] = deep_copy_dmp(obj: value)
      end
    end
    hash
  else
    obj.dup
  end
end

.dmp_id_base_url ⇒ Object

Return the base URL for a DMP ID



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# File 'lib/uc3-dmp-id/helper.rb', line 68

def dmp_id_base_url
  url = ENV.fetch('DMP_ID_BASE_URL', DEFAULT_LANDING_PAGE_URL)
  url&.end_with?('/') ? url : "#{url}/"
end

.dmp_id_to_pk(json:) ⇒ Object

Append the :PK prefix to the :dmp_id



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# File 'lib/uc3-dmp-id/helper.rb', line 104

def dmp_id_to_pk(json:)
  return nil if !json.is_a?(Hash) || json['identifier'].nil?

  # If it's a DOI format it correctly
  dmp_id = format_dmp_id(value: json['identifier'].to_s)
  return nil if dmp_id.nil? || dmp_id == ''

  append_pk_prefix(p_key: dmp_id.gsub(%r{https?://}, ''))
end

.eql?(dmp_a:, dmp_b:) ⇒ Boolean

Compare the DMP IDs to see if they are the same rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity, Metrics/PerceivedComplexity

Returns:

  • (Boolean) 


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# File 'lib/uc3-dmp-id/helper.rb', line 133

def eql?(dmp_a:, dmp_b:)
  return dmp_a == dmp_b unless dmp_a.is_a?(Hash) && !dmp_a['dmp'].nil? && dmp_b.is_a?(Hash) && !dmp_b['dmp'].nil?

  # return true if they're identical
  return true if dmp_a == dmp_b

  # If the PK do not match, then they are not equivalent!
  return false unless dmp_a.is_a?(Hash) && dmp_a['dmp'].fetch('PK', '').start_with?(Helper::PK_DMP_PREFIX) &&
                      dmp_b.is_a?(Hash) && dmp_b['dmp'].fetch('PK', '').start_with?(Helper::PK_DMP_PREFIX) &&
                      dmp_a['dmp']['PK'] == dmp_b['dmp']['PK']

  a = deep_copy_dmp(obj: dmp_a)
  b = deep_copy_dmp(obj: dmp_b)

  # ignore some of the attributes before comparing
  %w[SK dmphub_modification_day modified created dmphub_versions].each do |key|
    a['dmp'].delete(key) unless a['dmp'][key].nil?
    b['dmp'].delete(key) unless b['dmp'][key].nil?
  end
  a == b
end

.extract_owner_id(json: {}) ⇒ Object

Extract the Contact’s ORCID id



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# File 'lib/uc3-dmp-id/helper.rb', line 156

def extract_owner_id(json: {})
  return nil unless json.is_a?(Hash)

  dmp = json['dmp'].nil? ? json : json['dmp']
  id = dmp.fetch('contact', {}).fetch('contact_id', {})['identifier']
  return id unless id.nil?

  dmp.fetch('contributor', []).map { |contributor| contributor.fetch('contributor_id', {})['identifier'] }.first
end

.extract_owner_org(json: {}) ⇒ Object

Extract the Contact’s affiliaiton ROR ID



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# File 'lib/uc3-dmp-id/helper.rb', line 167

def extract_owner_org(json: {})
  return nil unless json.is_a?(Hash)

  dmp = json['dmp'].nil? ? json : json['dmp']
  owner_org = dmp.fetch('contact', {}).fetch('dmproadmap_affiliation', {}).fetch('affiliation_id',
                                                                                 {})['identifier']
  return owner_org unless owner_org.nil?

  orgs = dmp.fetch('contributor', []).map do |contributor|
    contributor.fetch('dmproadmap_affiliation', {}).fetch('affiliation_id', {})['identifier']
  end
  orgs.compact.max_by { |i| orgs.count(i) }
end

.format_dmp_id(value:, with_protocol: false) ⇒ Object

Format the DMP ID in the way we want it



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# File 'lib/uc3-dmp-id/helper.rb', line 80

def format_dmp_id(value:, with_protocol: false)
  dmp_id = value.match(DOI_REGEX).to_s
  return nil if dmp_id.nil? || dmp_id == ''
  # If it's already a URL, return it as is
  return with_protocol ? value : value.gsub(%r{https?://}, '') if value.start_with?('http')

  dmp_id = dmp_id.gsub('doi:', '')
  dmp_id = dmp_id[1..dmp_id.length] if dmp_id.start_with?('/')
  base_domain = with_protocol ? dmp_id_base_url : dmp_id_base_url.gsub(%r{https?://}, '')
  "#{base_domain}#{dmp_id}"
end

.format_provenance_id(provenance:, value:) ⇒ Object

Appends the Provenance system’s identifier to the value

For a DOI, it will return the DOI as-is

For a :provenance whose PK is 'PROVENANCE#example' and homepage is 'https://example.com' and
callbackUri is 'https://example.com/callback':
  when the :value is '12345', it will return 'example#12345'
  when the :value is 'https://example.com/dmps/12345', it will return 'example#dmp/12345'
  when the :value is 'https://example.com/callback/12345' it will return 'example#12345'

rubocop:disable Metrics/AbcSize



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# File 'lib/uc3-dmp-id/helper.rb', line 301

def format_provenance_id(provenance:, value:)
  # return it as-is if there is no provenance or it's already a URL
  return value if provenance.nil?

  # return it as-is if it's a DOI
  doi = value.match(DOI_REGEX).to_s
  return value unless doi.nil? || doi == '' || !value.start_with?('http')

  # Remove the homepage or callbackUri because we will add this when needed. we just want the id
  val = value.downcase
             .gsub(provenance.fetch('callbackUri', '').downcase, '')
             .gsub(provenance.fetch('homepage', '').downcase, '')
  val = val.gsub(%r{https?://}, '')
  val = val[1..val.length] if val.start_with?('/')
  id = provenance['PK']&.gsub('PROVENANCE#', '')
  "#{id}##{val}"
end

.landing_page_url ⇒ Object

The landing page URL (NOT the DOI URL)



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# File 'lib/uc3-dmp-id/helper.rb', line 74

def landing_page_url
  url = ENV.fetch('DMP_ID_LANDING_URL', DEFAULT_LANDING_PAGE_URL)
  url&.end_with?('/') ? url : "#{url}/"
end

.parse_json(json:) ⇒ Object

Parse the incoming JSON if necessary or return as is if it’s already a Hash



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# File 'lib/uc3-dmp-id/helper.rb', line 125

def parse_json(json:)
  return json if json.is_a?(Hash)

  json.is_a?(String) ? JSON.parse(json) : nil
end

.path_parameter_to_pk(param:) ⇒ Object

Convert an API PathParameter (DMP ID) into a PK



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# File 'lib/uc3-dmp-id/helper.rb', line 93

def path_parameter_to_pk(param:)
  return nil unless param.is_a?(String) && !param.strip.empty?

  base_domain = dmp_id_base_url.gsub(%r{https?://}, '')
  p_key = param if param.start_with?(dmp_id_base_url) || param.start_with?(base_domain)
  p_key = CGI.unescape(p_key.nil? ? param : p_key)
  p_key = format_dmp_id(value: p_key)
  append_pk_prefix(p_key:)
end

.pk_to_dmp_id(p_key:) ⇒ Object

Derive the DMP ID by removing the :PK prefix



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# File 'lib/uc3-dmp-id/helper.rb', line 115

def pk_to_dmp_id(p_key:)
  return nil if p_key.nil?

  {
    type: 'doi',
    identifier: format_dmp_id(value: remove_pk_prefix(p_key:), with_protocol: true)
  }
end

.remove_pk_prefix(p_key:) ⇒ Object

Strip off the PK prefix



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# File 'lib/uc3-dmp-id/helper.rb', line 51

def remove_pk_prefix(p_key:)
  p_key.is_a?(String) ? p_key.gsub(PK_DMP_PREFIX, '') : p_key
end

.remove_sk_prefix(s_key:) ⇒ Object

Strip off the SK prefix



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# File 'lib/uc3-dmp-id/helper.rb', line 63

def remove_sk_prefix(s_key:)
  s_key.is_a?(String) ? s_key.gsub(SK_DMP_PREFIX, '') : s_key
end