toccatore 0.1

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Files changed (30) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +50 -0
  3. data/.travis.yml +19 -0
  4. data/CHANGELOG.md +5 -0
  5. data/Gemfile +3 -0
  6. data/Gemfile.lock +110 -0
  7. data/LICENSE.md +21 -0
  8. data/README.md +28 -0
  9. data/bin/toccatore +5 -0
  10. data/lib/toccatore.rb +1 -0
  11. data/lib/toccatore/base.rb +361 -0
  12. data/lib/toccatore/cli.rb +38 -0
  13. data/lib/toccatore/orcid_update.rb +56 -0
  14. data/lib/toccatore/version.rb +3 -0
  15. data/spec/cli_spec.rb +29 -0
  16. data/spec/fixtures/orcid_update.json +1015 -0
  17. data/spec/fixtures/orcid_update_nil.json +12 -0
  18. data/spec/fixtures/vcr_cassettes/Toccatore_CLI/orcid_update/should_fail.yml +149 -0
  19. data/spec/fixtures/vcr_cassettes/Toccatore_CLI/orcid_update/should_succeed.yml +3453 -0
  20. data/spec/fixtures/vcr_cassettes/Toccatore_OrcidUpdate/get_data/should_report_if_there_are_no_works_returned_by_the_Datacite_Metadata_Search_API.yml +38 -0
  21. data/spec/fixtures/vcr_cassettes/Toccatore_OrcidUpdate/get_data/should_report_if_there_are_works_returned_by_the_Datacite_Metadata_Search_API.yml +149 -0
  22. data/spec/fixtures/vcr_cassettes/Toccatore_OrcidUpdate/get_total/with_no_works.yml +38 -0
  23. data/spec/fixtures/vcr_cassettes/Toccatore_OrcidUpdate/get_total/with_works.yml +38 -0
  24. data/spec/fixtures/vcr_cassettes/Toccatore_OrcidUpdate/push_data/should_report_if_there_are_works_returned_by_the_Datacite_Metadata_Search_API.yml +3307 -0
  25. data/spec/fixtures/vcr_cassettes/Toccatore_OrcidUpdate/queue_jobs/should_report_if_there_are_no_works_returned_by_the_Datacite_Metadata_Search_API.yml +38 -0
  26. data/spec/fixtures/vcr_cassettes/Toccatore_OrcidUpdate/queue_jobs/should_report_if_there_are_works_returned_by_the_Datacite_Metadata_Search_API.yml +236 -0
  27. data/spec/orcid_update_spec.rb +120 -0
  28. data/spec/spec_helper.rb +91 -0
  29. data/toccatore.gemspec +37 -0
  30. metadata +314 -0
data/lib/toccatore/cli.rb ADDED
@@ -0,0 +1,38 @@
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+ # encoding: UTF-8
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+
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+ require "thor"
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+ require_relative 'orcid_update'
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+
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+ module Toccatore
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+ class CLI < Thor
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+ def self.exit_on_failure?
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+ true
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+ end
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+
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+ # from http://stackoverflow.com/questions/22809972/adding-a-version-option-to-a-ruby-thor-cli
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+ map %w[--version -v] => :__print_version
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+
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+ desc "--version, -v", "print the version"
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+ def __print_version
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+ puts Toccatore::VERSION
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+ end
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+
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+ desc "orcid_update", "push ORCID IDs from DataCite MDS to ORCID"
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+ method_option :access_token, type: :string, required: true
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+ method_option :from_date, type: :string
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+ method_option :until_date, type: :string
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+ method_option :push_url, type: :string
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+ def orcid_update
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+ orcid_update = Toccatore::OrcidUpdate.new
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+ orcid_update.process_data(options).each do |response|
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+ if response.body["data"].present?
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+ doi = response.body.fetch("data", {}).fetch("attributes", {}).fetch("doi", nil)
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+ orcid = response.body.fetch("data", {}).fetch("attributes", {}).fetch("orcid", nil)
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+ puts "DOI #{doi} for ORCID ID #{orcid} pushed to Profiles service."
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+ elsif response.body["errors"].present?
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+ puts "An error occured: #{response.body['errors'].first['title']}"
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+ end
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+ end
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+ end
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+ end
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+ end
data/lib/toccatore/orcid_update.rb ADDED
@@ -0,0 +1,56 @@
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+ require_relative 'base'
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+
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+ module Toccatore
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+ class OrcidUpdate < Base
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+ def source_id
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+ "orcid_update"
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+ end
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+
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+ def q
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+ "nameIdentifier:ORCID\\:*"
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+ end
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+
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+ def parse_data(result, options={})
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+ return result.body.fetch("errors") if result.body.fetch("errors", nil).present?
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+
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+ items = result.body.fetch("data", {}).fetch('response', {}).fetch('docs', nil)
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+
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+ Array(items).reduce([]) do |sum, item|
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+ doi = item.fetch("doi")
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+ name_identifiers = item.fetch("nameIdentifier", [])
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+
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+ if name_identifiers.blank?
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+ sum
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+ else
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+ name_identifiers.each do |name_identifier|
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+ orcid = name_identifier.split(':', 2).last
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+ orcid = validate_orcid(orcid)
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+
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+ next if orcid.blank?
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+
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+ sum << { "orcid" => orcid,
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+ "doi" => doi,
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+ "source_id" => source_id,
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+ "claim_action"=>"create" }
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+ end
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+ sum
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+ end
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+ end
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+ end
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+
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+ # push to Volpino API if no error and we have collected works
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+ def push_data(items, options={})
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+ push_url = (options[:push_url].presence || "https://profiles.datacite.org/api") + "/claims"
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+ access_token = options[:access_token]
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+
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+ return [] if items.empty?
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+ return [OpenStruct.new(body: { "errors" => [{ "title" => "Access token missing" }] })] if access_token.blank?
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+
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+ Array(items).map do |item|
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+ Maremma.post(push_url, data: { "claim" => item }.to_json,
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+ token: access_token,
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+ content_type: 'json')
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+ end
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+ end
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+ end
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+ end
data/lib/toccatore/version.rb ADDED
@@ -0,0 +1,3 @@
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+ module Toccatore
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+ VERSION = "0.1"
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+ end
data/spec/cli_spec.rb ADDED
@@ -0,0 +1,29 @@
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+ require 'spec_helper'
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+ require 'toccatore/cli'
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+
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+ describe Toccatore::CLI do
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+ let(:subject) do
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+ described_class.new
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+ end
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+
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+ let(:push_url) { ENV['VOLPINO_URL'] }
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+ let(:access_token) { ENV['VOLPINO_TOKEN'] }
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+ let(:from_date) { "2015-04-07" }
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+ let(:until_date) { "2015-04-08" }
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+ let(:cli_options) { { push_url: push_url,
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+ access_token: access_token,
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+ from_date: from_date,
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+ until_date: until_date } }
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+
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+ describe "orcid_update", vcr: true, :order => :defined do
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+ it 'should succeed' do
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+ subject.options = cli_options
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+ expect { subject.orcid_update }.to output(/DOI 10.6084\/M9.FIGSHARE.1041547 for ORCID ID 0000-0002-3546-1048 pushed to Profiles service.\n/).to_stdout
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+ end
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+
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+ it 'should fail' do
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+ subject.options = cli_options.except(:access_token)
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+ expect { subject.orcid_update }.to output("An error occured: Access token missing\n").to_stdout
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+ end
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+ end
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+ end
data/spec/fixtures/orcid_update.json ADDED
@@ -0,0 +1,1015 @@
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+ {
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+ "responseHeader": {
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+ "status": 0,
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+ "QTime": 1
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+ },
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+ "response": {
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+ "numFound": 55,
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+ "start": 0,
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+ "docs": [{
10
+ "minted": "2015-04-08T10:13:29Z",
11
+ "datacentre_symbol": "CDL.DIGSCI",
12
+ "xml": "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",
13
+ "updated": "2015-04-08T10:13:29Z",
14
+ "doi": "10.6084/M9.FIGSHARE.1226424",
15
+ "creator": [
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+ "Carlos Cotta",
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+ "Rafael Nogueras"
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+ ],
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+ "publisher": "Figshare",
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+ "title": [
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+ "Color mememaps of self-balancing strategies"
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+ ],
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+ "nameIdentifier": [
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+ "ORCID:0000-0001-8478-7549"
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+ ],
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+ "publicationYear": "2015",
27
+ "resourceTypeGeneral": "Image"
28
+ }, {
29
+ "minted": "2015-04-08T14:05:30Z",
30
+ "datacentre_symbol": "CDL.DIGSCI",
31
+ "xml": "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",
32
+ "updated": "2015-04-08T14:05:30Z",
33
+ "doi": "10.6084/M9.FIGSHARE.1371006",
34
+ "creator": [
35
+ "Ann Mayo"
36
+ ],
37
+ "publisher": "Figshare",
38
+ "title": [
39
+ "Comanche harvester ant colonies in GL site of FWNC"
40
+ ],
41
+ "nameIdentifier": [
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+ "ORCID:0000-0002-3546-1048"
43
+ ],
44
+ "publicationYear": "2015",
45
+ "resourceTypeGeneral": "Image"
46
+ }, {
47
+ "minted": "2015-04-08T14:12:36Z",
48
+ "datacentre_symbol": "CDL.DIGSCI",
49
+ "xml": "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",
50
+ "updated": "2015-04-08T14:12:36Z",
51
+ "doi": "10.6084/M9.FIGSHARE.1371005",
52
+ "creator": [
53
+ "Ann Mayo"
54
+ ],
55
+ "publisher": "Figshare",
56
+ "title": [
57
+ "Comanche harvester ant colonies at EP in the FWNC"
58
+ ],
59
+ "nameIdentifier": [
60
+ "ORCID:0000-0002-3546-1048"
61
+ ],
62
+ "publicationYear": "2015",
63
+ "resourceTypeGeneral": "Image"
64
+ }, {
65
+ "minted": "2015-04-07T03:09:59Z",
66
+ "datacentre_symbol": "CDL.DIGSCI",
67
+ "xml": "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",
68
+ "updated": "2015-04-07T03:09:59Z",
69
+ "doi": "10.6084/M9.FIGSHARE.1368269",
70
+ "creator": [
71
+ "Peter Arend"
72
+ ],
73
+ "publisher": "Figshare",
74
+ "title": [
75
+ "ABO phenotype and innate isoagglutinin specificities as they arise from glycosidic exclusion and relate to human reproduction. A hypothesis*"
76
+ ],
77
+ "nameIdentifier": [
78
+ "ORCID:0000-0002-4000-4167"
79
+ ],
80
+ "publicationYear": "2015",
81
+ "resourceTypeGeneral": "Dataset"
82
+ }, {
83
+ "minted": "2015-04-07T03:22:11Z",
84
+ "datacentre_symbol": "CDL.DIGSCI",
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