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HYC-1280: Create intermediate ingest object (#738)
* Create object to store xml and parse jats xml Create intermediate object for parsing xml and translating to Hyrax objects - Move check for extra files in package - Do not map UNC affiliation until we can do so more reliably, put in "other affiliation" until then * Add and configure javascript driver for capybara, upgrade * Use ffaker for tests, do setup step once for feature, for faster run
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,224 @@ | ||
| # For information on the JATS metadata standard, see https://jats.nlm.nih.gov/ | ||
| # Currently used for Sage ingest | ||
| class JatsIngestWork | ||
| include ActiveModel | ||
| attr_reader :xml_path | ||
|
|
||
| def initialize(xml_path:) | ||
| @xml_path = xml_path | ||
| end | ||
|
|
||
| def jats_xml | ||
| @jats_xml ||= File.read(xml_path) | ||
| end | ||
|
|
||
| def document | ||
| @document ||= Nokogiri::XML(jats_xml) | ||
| end | ||
|
|
||
| def article_metadata | ||
| @article_metadata ||= document.xpath('.//article-meta') | ||
| end | ||
|
|
||
| def creators_metadata | ||
| @creators_metadata ||= document.xpath('.//contrib-group') | ||
| end | ||
|
|
||
| def journal_metadata | ||
| @journal_metadata ||= document.xpath('.//journal-meta') | ||
| end | ||
|
|
||
| def permissions | ||
| @permissions ||= article_metadata.xpath('.//permissions') | ||
| end | ||
|
|
||
| def abstract | ||
| article_metadata.xpath('.//abstract').map(&:inner_text) | ||
| end | ||
|
|
||
| def copyright_date | ||
| permissions.at('copyright-year').inner_text | ||
| end | ||
|
|
||
| def creators | ||
| @creators ||= begin | ||
| creators_metadata.xpath('.//contrib').map.with_index do |contributor, index| | ||
| [index, contributor_to_hash(contributor, index)] | ||
| end.to_h | ||
| end | ||
| end | ||
|
|
||
| # TODO: Map affiliation to UNC controlled vocabulary | ||
| def contributor_to_hash(contributor, index) | ||
| affiliation_ids = affiliation_ids(contributor) | ||
| first_affiliation = affiliation_map[affiliation_ids.first] | ||
| { | ||
| 'name' => "#{surname(contributor)}, #{given_names(contributor)}", | ||
| 'orcid' => orcid(contributor), | ||
| 'affiliation' => '', | ||
| # 'affiliation' => some_method, # Do not store affiliation until we can map it to the controlled vocabulary | ||
| 'other_affiliation' => first_affiliation, | ||
| 'index' => (index+1).to_s | ||
| } | ||
| end | ||
|
|
||
| def affiliation_map | ||
| @affiliation_map ||= begin | ||
| document.xpath('//aff').map do |affil| | ||
| [affil.attributes["id"].value, affiliation_to_s(affil)] | ||
| end.to_h | ||
| end | ||
| end | ||
|
|
||
| def affiliation_ids(elem) | ||
| references = elem.xpath('xref') | ||
| references.map do |ref| | ||
| reference_type = ref['ref-type'] | ||
| next unless reference_type=="aff" | ||
|
|
||
| ref["rid"] | ||
| end.compact | ||
| end | ||
|
|
||
| def affiliation_to_s(affil_elem) | ||
| affil_elem.children.map do |child| | ||
| # Don't include newlines or the order label | ||
| next if child.inner_text == "\n" || child.name == "label" | ||
|
|
||
| # Only include the institution name proper from the institution-wrap, don't include the institution-id | ||
| if child.xpath(".//institution").present? | ||
| child.xpath(".//institution").inner_text | ||
| else | ||
| child.inner_text | ||
| end | ||
| end.join | ||
| end | ||
|
|
||
| def date_of_publication | ||
| if publication_day && publication_month && publication_year | ||
| "#{publication_year}-#{publication_month}-#{publication_day}" | ||
| elsif publication_month && publication_year | ||
| "#{publication_year}-#{publication_month}" | ||
| else | ||
| publication_year | ||
| end | ||
| end | ||
|
|
||
| def funder | ||
| article_metadata.xpath('.//funding-source/institution-wrap/institution').map(&:inner_text) | ||
| end | ||
|
|
||
| # The Sage-assigned DOI | ||
| def identifier | ||
| article_metadata.xpath('.//article-id[@pub-id-type="doi"]').map(&:inner_text) | ||
| end | ||
|
|
||
| def issn | ||
| journal_metadata.xpath(".//issn").map(&:inner_text) | ||
| end | ||
|
|
||
| def journal_issue | ||
| article_metadata.at('issue')&.inner_text | ||
| end | ||
|
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||
| def journal_title | ||
| journal_metadata.xpath(".//journal-title-group/journal-title").inner_text | ||
| end | ||
|
|
||
| def journal_volume | ||
| article_metadata.at('volume')&.inner_text | ||
| end | ||
|
|
||
| def keyword | ||
| article_metadata.at('kwd-group').xpath("//kwd").map do |elem| | ||
| if elem.at('italic') | ||
| elem.at('italic').inner_text | ||
| else | ||
| elem.inner_text | ||
| end | ||
| end | ||
| end | ||
|
|
||
| def license | ||
| permissions.xpath(".//license/@xlink:href").map do |elem| | ||
| CdrLicenseService.authority.find(elem&.inner_text)[:id] | ||
| end | ||
| end | ||
|
|
||
| def license_label | ||
| license.map do |lic| | ||
| CdrLicenseService.label(lic) | ||
| end | ||
| end | ||
|
|
||
| def page_end | ||
| article_metadata.at('lpage')&.inner_text | ||
| end | ||
|
|
||
| def page_start | ||
| article_metadata.at('fpage')&.inner_text | ||
| end | ||
|
|
||
| def publisher | ||
| journal_metadata.xpath('.//publisher/publisher-name').map(&:inner_text) | ||
| end | ||
|
|
||
| def rights_holder | ||
| permissions.xpath('.//copyright-holder').map(&:inner_text) | ||
| end | ||
|
|
||
| def title | ||
| article_metadata.xpath('.//title-group/article-title').map(&:inner_text) | ||
| end | ||
|
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||
| private | ||
|
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||
| def publication_year | ||
| year = publication_date_node_set.at('year')&.inner_text&.to_i | ||
| format('%04d', year) if year | ||
| end | ||
|
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||
| def publication_month | ||
| month = publication_date_node_set.at('month')&.inner_text&.to_i | ||
| format('%02d', month) if month | ||
| end | ||
|
|
||
| def publication_day | ||
| day = publication_date_node_set.at('day')&.inner_text&.to_i | ||
| format('%02d', day) if day | ||
| end | ||
|
|
||
| def publication_date_node_set | ||
| if physical_publication_date.present? | ||
| physical_publication_date | ||
| elsif electronic_and_physical_publication_date.present? | ||
| electronic_and_physical_publication_date | ||
| elsif electronic_publication_date.present? | ||
| electronic_publication_date | ||
| end | ||
| end | ||
|
|
||
| def electronic_publication_date | ||
| article_metadata.xpath('.//pub-date[@pub-type="epub"]') | ||
| end | ||
|
|
||
| def electronic_and_physical_publication_date | ||
| article_metadata.xpath('.//pub-date[@pub-type="epub-ppub"]') | ||
| end | ||
|
|
||
| def physical_publication_date | ||
| article_metadata.xpath('.//pub-date[@pub-type="ppub"]') | ||
| end | ||
|
|
||
| def surname(contributor) | ||
| contributor.xpath('name/surname').inner_text | ||
| end | ||
|
|
||
| def given_names(contributor) | ||
| contributor.xpath('name/given-names').inner_text | ||
| end | ||
|
|
||
| def orcid(contributor) | ||
| contributor.xpath('contrib-id').inner_text | ||
| end | ||
| end |
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